bluuebunny/crossref_metadata_2025 huggingface dataset:
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

The 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

The 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

Locomotion 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

Immune 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

The 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

Nematode-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.
Integration of transcriptomics and long-read genomics prioritizes structural variants in rare disease
Authors: Jensen Tanner D , Ni Bohan , Reuter Chloe , Gorzynski John E , Fazal Sarah , Bonner Devon E , Ungar Rachel Allison , Goddard Pagé C , Natarajan Raja Archana , Ashley Euan A , Bernstein Jonathan A , Zuchner Stephan ,   Undiagnosed Diseases Network, Greicius Michael D , Montgomery Stephen B , Schatz Michael C , Wheeler Matthew T , Battle Alexis
Published: March 2024

Rare structural variants (SVs) – insertions, deletions, and complex rearrangements – can cause Mendelian disease, yet they remain difficult to accurately detect and interpret. We sequenced and analyzed Oxford Nanopore long-read genomes of 68 individuals from the Undiagnosed Disease Network (UDN) with no previously identified diagnostic mutations from short-read sequencing. Using our optimized SV detection pipelines and 571 control long-read genomes, we detected 716 long-read rare (MAF < 0.01) SV alleles per genome on average, achieving a 2.4x increase from short-reads. To characterize the functional effects of rare SVs, we assessed their relationship with gene expression from blood or fibroblasts from the same individuals, and found that rare SVs overlapping enhancers were enriched (LOR = 0.46) near expression outliers. We also evaluated tandem repeat expansions (TREs) and found 14 rare TREs per genome; notably these TREs were also enriched near overexpression outliers. To prioritize candidate functional SVs, we developed Watershed-SV, a probabilistic model that integrates expression data with SV-specific genomic annotations, which significantly outperforms baseline models that do not incorporate expression data. Watershed-SV identified a median of eight high-confidence functional SVs per UDN genome. Notably, this included compound heterozygous deletions inFAM177A1shared by two siblings, which were likely causal for a rare neurodevelopmental disorder. Our observations demonstrate the promise of integrating long-read sequencing with gene expression towards improving the prioritization of functional SVs and TREs in rare disease patients.
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

Aims/hypothesis

For 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).

Methods

Individuals 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.

Results

In 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/interpretation

The 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

Purpose

To identify genetic etiologies and genotype/phenotype associations for unsolved ocular congenital cranial dysinnervation disorders (oCCDDs).

Methods

We 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.

Results

Analyses 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.

Conclusion

This 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.
Severus: accurate detection and characterization of somatic structural variation in tumor genomes using long reads
Authors: Keskus Ayse , Bryant Asher , Ahmad Tanveer , Yoo Byunggil , Aganezov Sergey , Goretsky Anton , Donmez Ataberk , Lansdon Lisa A. , Rodriguez Isabel , Park Jimin , Liu Yuelin , Cui Xiwen , Gardner Joshua , McNulty Brandy , Sacco Samuel , Shetty Jyoti , Zhao Yongmei , Tran Bao , Narzisi Giuseppe , Helland Adrienne , Cook Daniel E. , Chang Pi-Chuan , Kolesnikov Alexey , Carroll Andrew , Molloy Erin K. , Pushel Irina , Guest Erin , Pastinen Tomi , Shafin Kishwar , Miga Karen H. , Malikic Salem , Day Chi-Ping , Robine Nicolas , Sahinalp Cenk , Dean Michael , Farooqi Midhat S. , Paten Benedict , Kolmogorov Mikhail
Published: March 2024

Most current studies rely on short-read sequencing to detect somatic structural variation (SV) in cancer genomes. Long-read sequencing offers the advantage of better mappability and long-range phasing, which results in substantial improvements in germline SV detection. However, current long-read SV detection methods do not generalize well to the analysis of somatic SVs in tumor genomes with complex rearrangements, heterogeneity, and aneuploidy. Here, we present Severus: a method for the accurate detection of different types of somatic SVs using a phased breakpoint graph approach. To benchmark various short- and long-read SV detection methods, we sequenced five tumor/normal cell line pairs with Illumina, Nanopore, and PacBio sequencing platforms; on this benchmark Severus showed the highest F1 scores (harmonic mean of the precision and recall) as compared to long-read and short-read methods. We then applied Severus to three clinical cases of pediatric cancer, demonstrating concordance with known genetic findings as well as revealing clinically relevant cryptic rearrangements missed by standard genomic panels.
Screening and characterization of 133 physiologically-relevant environmental chemicals for reproductive toxicity
Authors: Ulaganathan Gurugowtham , Jiang Hui , Canio Noah , Oke Ashwini , Armstrong Sujit Silas , Abrahamsson Dimitri , Varshavsky Julia R. , Lam Juleen , Cooper Courtney , Robinson Joshua F. , Fung Jennifer C. , Woodruff Tracey J. , Allard Patrick
Published: March 2024

Reproduction is a functional outcome that relies on complex cellular, tissue, and organ interactions that span the developmental period to adulthood. Thus, the assessment of its disruption by environmental chemicals is remarkably painstaking in conventional toxicological animal models and does not scale up to the number of chemicals present in our environment and requiring testing.

We adapted a previously described low-throughputin vivochromosome segregation assay usingC. eleganspredictive of reproductive toxicity and leveraged available public data sources (ToxCast, ICE) to screen and characterize 133 physiologically-relevant chemicals in a high-throughput manner. The screening outcome was further validated in a second, independentin vivoassay assessing embryonic viability. In total, 13 chemicals were classified as reproductive toxicants with the two most active chemicals belonging to the large family of Quaternary Ammonium Compounds (QACs) commonly used as disinfectants but with limited available reproductive toxicity data. We compared the results from theC. elegansassay with ToxCastin vitrodata compiled from 700+ cell response assays and 300+ signaling pathways-based assays. We did not observe a difference in the bioactivity or in average potency (AC50) between the top and bottom chemicals. However, the intended target categories were significantly different between the classified chemicals with, in particular, an over-representation of steroid hormone targets for the high Z-score chemicals.

Taken together, these results point to the value ofin vivomodels that scale to high-throughput level for reproductive toxicity assessment and to the need to prioritize the assessment of QACs impacts on reproduction.
Characterizing the Binding Mechanism of Sparsentan to the Type-2 Angiotensin II Receptor Using AutoDock Vina
Authors: Geng Peter X.
Published: March 2024

The angiotensin II type-2 receptor (AT2R) is known to have a significant impact on cardiovascular physiology, and the elucidation of its drug interactions is crucial for advancing therapeutic interventions. Sparsentan is an antagonist of angiotensin II, which has received FDA approval due to its demonstrated efficacy in ameliorating proteinuria. While sparsentan exhibits a preferential affinity for angiotensin II type-1 receptor (AT1R) and may primarily target it, DrugBank identifies it as a drug that targets AT2R. Present databases lack detailed structural data on the interaction mechanism between sparsentan and AT2R, leaving no definitive evidence to confirm or refute an interaction with AT2R. This study aimed to explore the potential for an interaction between sparsentan and AT2R. Molecular docking simulations were conducted using AutoDock Vina to predict the binding conformation. The docking parameters were meticulously optimized to ensure the accuracy and reliability of the simulation results. Subsequently, the most stable sparsentan-AT2R complex was determined. We identified four primary types of interactions at the binding site containing hydrogen bonds, hydrophobic interactions, π-cation interactions, and π-stacking, that are likely to contribute to the affinity of sparsentan for AT2R. Our study indicates that sparsentan may potentially interact with AT2R, our results may serve as a valuable reference for elucidating the mechanism of sparsentan action and for guiding the design of AT2R-targeted drugs.
Microdissected tumor cuboids: a microscale cancer model for large-scale testing that retains a complex tumor microenvironment
Authors: Horowitz Lisa F , Rodriguez-Mias Ricard , Chan Marina , Zhu Songli , Gottshall Noah R , Stepanov Ivan , Stiles Casey , Yeung Marcus , Nguyen Tran NH , Lockhart Ethan J , Yeung Raymond S , Villen Judit , Gujral Taranjit S , Folch Albert
Published: March 2024

To bridge the gap between bench and bedside, there is a need for more faithful models of human cancers that can recapitulate key features of the human tumor microenvironment (TME) and simultaneously facilitate large-scale drug tests. Our recently developed microdissection method optimizes the yield of large numbers of cuboidal microtissues (“cuboids”, ∼(400 µm)3) from a tumor biopsy. Here we demonstrate that cuboids from syngeneic mouse tumor models and human tumors retain a complex TME, making them amenable for drug and immunotherapy evaluation. We characterize relevant TME parameters, such as cellular architecture, cytokine secretion, proteomics profiles, and response to drug panels in multi-well arrays. Despite the cutting procedure and the time spent in culture (up to 7 days), the cuboids display strong cytokine expression and drug responses, including to immunotherapy. Overall, our results suggest that cuboids could provide essential therapeutic information for personalized oncology applications and could help the development of TME-dependent therapeutics and cancer disease models, including for clinical trials.
Connectomic reconstruction of a cortical column
Authors: Sievers Meike , Motta Alessandro , Schmidt Martin , Yener Yagmur , Loomba Sahil , Song Kun , Bruett Johannes , Helmstaedter Moritz
Published: March 2024

The cerebral cortex of mammals has long been proposed to comprise unit-modules, so-called cortical columns. The detailed synaptic-level circuitry of such a neuronal network of about 104neurons is still unknown. Here, using 3-dimensional electron microscopy, AI-based image processing and automated proofreading, we report the connectomic reconstruction of a defined cortical column in mouse barrel cortex. The cortical column appears as a structural feature in the connectome, without need for geometrical or morphological landmarks. We then used the connectome for definition of neuronal cell types in the column, to determine intracolumnar circuit modules, analyze the logic of inhibitory circuits, investigate the circuits for combination of bottom-up and top-down signals in the column and the specificity of bottom-up and top-down cortical input, search for higher-order circuit structure within homogeneous neuronal populations, and estimate the degree and symmetry of Hebbian learning in the various connection types. With this, we provide a first column-level connectomic description of the cerebral cortex, the likely substrate for a synaptic-level mechanistic understanding of sensory-conceptual integration and learning.
Mass spectrometry-based top-down proteomics in nanomedicine: proteoform-specific measurement of protein corona
Authors: Sadeghi Seyed Amirhossein , Ashkarran Ali Akbar , Mahmoudi Morteza , Sun Liangliang
Published: March 2024

Conventional mass spectrometry (MS)-based bottom-up proteomics (BUP) analysis of protein corona [i.e., an evolving layer of biomolecules, mostly proteins, formed on the surface of nanoparticles (NPs) during their interactions with biomolecular fluids] enabled nanomedicine community to partly identify the biological identity of NPs. Such an approach, however, fails pinpoint the specific proteoforms—distinct molecular variants of proteins, which is essential for prediction of the biological fate and pharmacokinetics of nanomedicines. Recognizing this limitation, this study pioneers a robust and reproducible MS-based top-down proteomics (TDP) technique for precisely characterizing proteoforms in the protein corona. Our TDP approach has successfully identified hundreds of proteoforms in the protein corona of polystyrene NPs, ranging from 3-70 kDa, revealing over 20 protein biomarkers with combinations of post-translational modifications, signal peptide cleavages, and/or truncations—details that BUP could not fully discern. This advancement in MS-based TDP offers a more comprehensive and exact characterization of NP protein coronas, deepening our understanding of NPs’ biological identities and potentially revolutionizing the field of nanomedicine.
Single cell approaches define forebrain neural stem cell niches and identify microglial ligands that enhance precursor-mediated remyelination
Authors: Willis Ashleigh , Jeong Danielle , Liu Yunlong , Lithopoulos Marissa A. , Yuzwa Scott , Frankland Paul W. , Kaplan David R. , Miller Freda D.
Published: March 2024

Here we used single cell RNA-sequencing and single cell spatial transcriptomics to characterize the forebrain neural stem cell (NSC) niche under homeostatic and injury conditions. We define the dorsal and lateral ventricular-subventricular zones (V-SVZ) as two distinct neighborhoods, and show that following white matter injury, dorsal NSCs are locally activated to make oligodendrocytes for remyelination. This activation is coincident with a robust increase in transcriptionally-distinct microglia in the dorsal V-SVZ niche. We modeled ligand-receptor interactions within this changing niche and identified two remyelination-associated microglial ligands, IGF1 and OSM, that promote precursor proliferation and oligodendrogenesis in culture. Infusion of either ligand into the lateral ventricles also enhanced oligodendrogenesis, even in the lateral V-SVZ, where NSCs normally make neuroblasts. These data support a model where gliogenesis versus neurogenesis is determined by the local NSC neighborhood and where injury-induced niche alterations promote NSC activation, local oligodendrogenesis, and likely contribute to myelin repair.
Implantable Bioelectronics for Real-timein vivoRecordings of Enteric Neural Activity
Authors: Boys Alexander J. , Güemes Amparo , Gupta Rohit A. , Uhlig Friederike H. , Hyland Niall P. , Bulmer David C. , Malliaras George G. , Owens Róisín M.
Published: March 2024

The enteric nervous system represents a primary point of contact for a host of factors that influence bodily health and behavior. This division of the autonomic nervous system is unique in both its extensivity, with neurons distributed throughout the gastrointestinal tract from the esophagus to the rectum, and its capability for local information processing. Here, we show the construction and validation of a bioelectronic device to access neural information produced and processed in the gastrointestinal tract. We designed an implant and concurrent surgical procedure to place a neural recording device within the wall of the colon of rodents. We captured complex multi-frequency electrophysiological responses to neural stimulants and show that we can record activity in the context of mechanical activity mimicking gut motility. We also show the feasibility of utilizing this device for recording colonic activity in freely-moving animals. This work represents a step forward in devising functional bioelectronic devices for understanding the complex pathways of the gut-brain axis.

One-Sentence Summary

Bioelectronic device for real-time collection of neural information from the enteric nervous system.
PhosX: data-driven kinase activity inference from phosphoproteomics experiments
Authors: Lussana Alessandro , Petsalaki Evangelia
Published: March 2024

Motivation

The inference of kinase activity from phosphoproteomics data can point to causal mechanisms driving signalling processes and potential drug targets. Identifying the kinases whose change in activity explains the observed phosphorylation profiles, however, remains challenging, and constrained by the manually curated knowledge of kinase-substrate associations. Recently, experimentally determined substrate sequence specificities of human kinases have become available, but robust methods to exploit this new data for kinase activity inference are still missing.

Results

We present PhosX, a method to estimate differential kinase activity from phosphoproteomics data that combines stateof-the art statistics in enrichment analysis with kinases’ substrate sequence specificity information. Using a large phosphoproteomics dataset with known differentially regulated kinases we show that our method identifies upregulated and downregulated kinases by only relying on the input phosphopeptides’ sequences and intensity changes. We find that PhosX outperforms the currently available approach to perform the same task, and we therefore recommend its use for data-driven kinase activity inference.

Availability and implementation

PhosX is implemented in Python, open-source under the Apache-2.0 licence, and distributed on the Python Package Index. The code is available on GitHub (https://github.com/alussana/phosx).
CD4+T cells drive corneal nerve damage but not epitheliopathy in an acute aqueous-deficient dry eye model
Authors: Vereertbrugghen Alexia , Pizzano Manuela , Cernutto Agostina , Sabbione Florencia , Keitelman Irene A , Vera Aguilar Douglas , Podhorzer Ariel , Fuentes Federico , Corral-Vázquez Celia , Guzmán Mauricio , Giordano Mirta N , Trevani Analía , de Paiva Cintia S , Galletti Jeremías G
Published: March 2024

Dry eye disease (DED) is characterized by a dysfunctional tear film in which the cornea epithelium and its abundant nerves are affected by ocular desiccation and inflammation. Although adaptive immunity and specifically CD4+T cells play a role in DED pathogenesis, the exact contribution of these cells to corneal epithelial and neural damage remains undetermined. To address this, we explored the progression of a surgical DED model in wild-type (WT) and T cell-deficient mice. We observed that adaptive immune-deficient mice developed all aspects of DED comparably to WT mice except for the absence of functional and morphological corneal nerve changes, nerve damage-associated transcriptomic signature in the trigeminal ganglia, and sustained tear cytokine levels. Adoptive transfer of CD4+T cells from WT DED mice to T cell-deficient mice reproduced corneal nerve damage but not epitheliopathy. Conversely, T cell-deficient mice reconstituted solely with naive CD4+T cells developed corneal nerve impairment and epitheliopathy upon DED induction, thus replicating the WT DED phenotype. Collectively, our data show that while corneal neuropathy is driven by CD4+T cells in DED, corneal epithelia damage develops independently of the adaptive immune response. These findings have implications for T cell-targeting therapies currently in use for DED.

Graphical abstract

Significance Statement

Dry eye is a frequent ocular disorder in which damage to the corneal epithelium and nerves is triggered by inadequate lubrication. The local CD4+T cell-predominant immune response aggravates ocular surface impairment but the exact contribution of these cells to corneal epithelial and neural disease remains undetermined. Using adoptive transfer of T cells into T cell-deficient mice, trigeminal transcriptomics, and tear cytokine analysis, we delineate the pathogenic role of CD4+T cells, revealing that they drive corneal nerve damage but are dispensable for epithelial disease to develop in response to desiccation. CD4+T cells promote corneal neuropathy possibly by releasing proinflammatory cytokines onto the ocular surface. These findings have implications for T cell-targeting therapies currently used for dry eye.
Taxonize-gb: A tool for filtering GenBank non-redundant databases based on taxonomy
Authors: Sarhan Mohamed S. , Filosi Michele , Maixner Frank , Fuchsberger Christian
Published: March 2024

Analyzing taxonomic diversity and identification in diverse ecological samples has become a crucial routine in various research and industrial fields. While DNA barcoding marker-gene approaches were once prevalent, the decreasing costs of next-generation sequencing have made metagenomic shotgun sequencing more popular and feasible. In contrast to DNA-barcoding, metagenomic shotgun sequencing offers possibilities for in-depth characterization of structural and functional diversity. However, analysis of such data is still considered a hurdle due to absence of taxa-specific databases. Here we present taxonize-gb, a command-line software tool to extract GenBank non-redundant nucleotide and protein databases, related to one or more input taxonomy identifier. Our tool allows the creation of taxa-specific reference databases tailored to specific research questions, which reduces search times and therefore represents a practical solution for researchers analyzing large metagenomic data on regular basis. Taxonize-gb is an open-source command-line Python-based tool freely available for installation athttps://pypi.org/project/taxonize-gb/and on GitHubhttps://github.com/msabrysarhan/taxonize_genbank. It is released under Creative Commons Attribution-NonCommercial 4.0 International License (CC BY-NC 4.0).
Mutation of negative regulatory geneCEHC1encoding an FBXO3 protein results in normoxic expression ofHYDAgenes inChlamydomonas reinhardtii
Authors: Sun Xiaoqing , LaVoie Matthew , Lefebvre Paul A. , Gallaher Sean D. , Glaesener Anne G. , Strenkert Daniela , Mehta Radhika , Merchant Sabeeha S. , Silflow Carolyn D.
Published: March 2024

Oxygen is known to prevent hydrogen production in Chlamydomonas, both by inhibiting the hydrogenase enzyme and by preventing the accumulation of HYDA-encoding transcripts. We developed a screen for mutants showing constitutive accumulation ofHYDA1transcripts in the presence of oxygen. A reporter gene required for ciliary motility, placed under the control of theHYDA1promoter, conferred motility only in hypoxic conditions. By selecting for mutants able to swim even in the presence of oxygen we obtained strains that express the reporter gene constitutively. One mutant identified a gene encoding an F-box only protein 3 (FBXO3), known to participate in ubiquitylation and proteasomal degradation pathways in other eukaryotes. Transcriptome profiles revealed that the mutation, termedcehc1-1, leads to constitutive expression ofHYDA1and other genes regulated by hypoxia, and of many genes known to be targets of CRR1, a transcription factor in the nutritional copper signaling pathway.CRR1was required for the constitutive expression of theHYDA1reporter gene incehc1-1mutants. The CRR1 protein, which is normally degraded in Cu-supplemented cells, was stabilized incehc1-1cells, supporting the conclusion thatCEHC1acts to facilitate the degradation of CRR1. Our results reveal a novel negative regulator in theCRR1pathway and possibly other pathways leading to complex metabolic changes associated with response to hypoxia.
Autophagy at Crossroads: Modulating Responses to Combined Heat Stress and Bacterial Infection
Authors: Seybold Heike , Katz Ella , Soroka Yoram , Avin-Wittenberg Tamar
Published: March 2024

Plants face diverse stresses in natural environments, necessitating complex responses for survival. Abiotic and biotic stress responses are typically counteractive, posing challenges for breeding crops resilient to multiple stresses. Autophagy, a cellular transport process, plays a vital role in plant stress response, facilitating the degradation of cellular components and enabling nutrient recycling. Here, we asked what the role of autophagy is in combined abiotic (heat) and biotic (bacterial infection byXanthomonas campestrispv.vesicatoria) stress. We introduce a conceptual framework based on assays monitoring autophagy activation, bacterial infection, and metabolic profiling.

We observed that heat stress facilitates bacterial growth in an autophagy-dependent manner. Bacterial effectors facilitate this phenomenon. We also demonstrate the engagement of the autophagy-related 8 (ATG8) protein family members in stress-specific activation. Metabolic profiling highlights effector-dependent shifts in nutrient availability during stress, influencing bacterial performance. Our study challenges the assumption that combined stresses are simply the sum of individual responses as exemplified by activation of the autophagic pathway. Instead, it establishes autophagy as a link connecting environmental factors and plant-microbe interactions. Insights for our study can present a novel perspective for designing strategies to enhance crop resilience in the face of multifaceted challenges.
Assessment of thermochromic phantoms for characterizing microwave ablation devices
Authors: Zia Ghina , Lintz Amber , Hardin Clay , Bottiglieri Anna , Sebek Jan , Prakash Punit
Published: March 2024

Background and Purpose

Thermochromic gel phantoms provide a controlled medium for visual assessment of thermal ablation device performance. However, there are limited studies reporting on the comparative assessment of ablation profiles assessed in thermochromic gel phantoms against those inex vivotissue. The objective of this study was to compare microwave ablation zones in a thermochromic tissue mimicking gel phantom andex vivobovine liver, and to report on measurements of the temperature dependent dielectric and thermal properties of the phantom.

Methods

Thermochromic polyacrylamide phantoms were fabricated following a previously reported protocol. Phantom samples were heated to temperatures in the range of 20 – 90 °C in a temperature-controlled water bath, and colorimetric analysis of images of the phantom taken after heating were used to develop a calibration between color changes and temperature to which the phantom was heated. Using a custom, 2.45 GHz water-cooled microwave ablation antenna, ablations were performed in freshex vivoliver and phantoms using 65 W applied for 5 min or 10 min (n =3 samples in each medium for each power/time combination). Broadband (500 MHz – 6 GHz) temperature-dependent dielectric and thermal properties of the phantom were measured over the temperature range 22 – 100 °C.

Results

Colorimetric analysis showed that the sharp change in gel phantom color commences at a temperature of 57 °C. Short and long axes of the ablation zone in the phantom (as assessed by the 57 °C isotherm) for 65 W, 5 min ablations were aligned with extents of the ablation zone observed inex vivobovine liver. However, for the 65 W, 10 min setting, ablations in the phantom were on average 23.7% smaller in short axis and 7.4 % smaller in long axis than those observed inex vivoliver. Measurements of the temperature dependent relative permittivity, thermal conductivity, and volumetric heat capacity of the phantom largely followed similar trends to published values forex vivoliver tissue.

Conclusion

Thermochromic tissue mimicking phantoms provide a controlled, and reproducible medium for comparative assessment of microwave ablation devices and energy delivery settings, though ablation zone size and shapes may not accurately represent ablation sizes and shapes observed inex vivoliver tissue under similar conditions.
Effectiveness of fixation methods for wholemount immunohistochemistry across cellular compartments in chick embryos
Authors: Echeverria Camilo V. , Leathers Tess A. , Rogers Crystal D.
Published: March 2024

The choice of fixation method significantly impacts tissue morphology and protein visualization after immunohistochemistry (IHC). In this study, we compared the effects of paraformaldehyde (PFA) and trichloroacetic acid (TCA) fixation prior to IHC on chicken embryos. Our findings underscore the importance of validating fixation methods for accurate interpretation of IHC results, with implications for antibody validation and tissue-specific protein localization studies. We found that TCA fixation resulted in larger and more circular nuclei compared to PFA fixation. Additionally, TCA fixation altered the appearance of subcellular localization and fluorescence intensity of various proteins, including transcription factors and cytoskeletal proteins. Notably, TCA fixation revealed protein localization domains that may be inaccessible with PFA fixation. These results highlight the need for optimization of fixation protocols depending on the target epitope and model system, emphasizing the importance of methodological considerations in biological analyses.
A functional overlap between evidence accumulation, confidence, and changes of mind in the pre-supplementary motor area and insula
Authors: Goueytes Dorian , Stockart François , Robin Alexis , Gyger Lucien , Rouy Martin , Hoffmann Dominique , Minotti Lorella , Kahane Philippe , Pereira Michael , Faivre Nathan
Published: March 2024

Evidence accumulation models have proven to be powerful tools to explain the temporal dynamics of decisions, as well as their metacognitive components such as confidence judgments and changes of mind. However, it is still unclear how and where in the brain evidence accumulation leads to these two metacognitive components. To better understand the functional overlap between evidence accumulation, confidence, and changes of mind, we recorded intracranial high-gamma activity in patients with focal epilepsy while they reported the motion direction of a random dot kinetogram with a computer mouse, and estimated their confidence level. We found an anatomical overlap between the neural correlates of evidence accumulation, confidence, and changes of mind in the pre-supplementary motor area, as well as in the orbitofrontal, inferior frontal, and insular cortices. Both mouse-tracking behaviour and electrophysiological results were reproduced with a post-decisional evidence accumulation model. After characterising the temporal dynamics of decision-making with mouse-tracking and intracranial electrophysiology, we conclude that confidence and changes of mind result from evidence accumulation instantiated before the decision in the pre-supplementary motor area, and after the decision in the insula.
Retinal microglia exacerbate uveitis by functioning as local antigen-presenting cells
Authors: Shirahama Shintaro , Okunuki Yoko , Lee May Y. , Karg Margarete M. , Refaian Nasrin , Krasniqi Drenushe , Connor Kip M. , Gregory-Ksander Meredith S. , Ksander Bruce R.
Published: March 2024

Autoimmune uveitis is a major cause of blindness in the working-age population of developed countries. Experimental autoimmune uveitis (EAU) depends on activation of interphotoreceptor retinoid-binding protein (IRBP) specific CD4+effector T cells that migrate systemically and infiltrate into the retina. Following systemic induction of retinal antigen-specific T cells, the development of EAU can be broken down into three phases: early phase when inflammatory cells begin to infiltrate the retina, amplification phase, and peak phase. Although studied extensively, the function of local antigen-presenting cells (APCs) within the retina remains unclear. Two potential types of APCs are present during uveitis, resident microglia and infiltrating CD11c+dendritic cells (DCs). MHC class II (MHC II) is expressed within the retina on both CD11c+DCs and microglia during the amplification phase of EAU. Therefore, we used microglia specific (P2RY12 and TMEM119) and CD11c+DC specific MHC II knockout mice to study the function of APCs within the retina using the conventional and adoptive transfer methods of inducing EAU. Microglia were essential during all phases of EAU development: the early phase when microglia were MHC Il negative, and amplification and peak phases when microglia were MHC II positive. Unexpectedly, retinal infiltrating MHC Il+CD11c+DCs were present within the retina but their antigen-presenting function was not required for all phases of uveitis. Our data indicate microglia are the critical APCs within the retina and an important therapeutic target that can prevent and/or diminish uveitis even in the presence of circulating IRBP-specific CD4+effector T cells.