bluuebunny/crossref_metadata_2025 huggingface dataset:
Residual force depression is not related to positive muscle fascicle work during submaximal voluntary dorsiflexion contractions in humans
Authors: Raiteri Brent James , Lauret Leon , Hahn Daniel
Published: September 2023

Residual force depression (rFD) following active muscle shortening is commonly assumed to strongly and linearly increase with increasing muscle work, but this has not been systematically tested during voluntary contractions in humans. Using dynamometry, we compared steady-state ankle joint torques (N=16) following tibialis anterior (TA) muscle-tendon unit (MTU) lengthening and shortening to the torque during submaximal voluntary fixed-end dorsiflexion reference contractions (REF) at a matched MTU length and EMG amplitude. B-mode ultrasound revealed that TA fascicle shortening amplitudes were significantly reduced (p<0.001) during MTU lengthening with no preload over small (LENsmall) and medium (LENmedium) amplitudes, respectively, relative to REF. MTU lengthening with a preload over a large (LENlargeP) amplitude significantly (p<0.001) increased fascicle shortening relative to REF, as well as stretch amplitudes relative to LENsmalland LENmedium(p≤0.001), but the significant (p≤0.028) steady-state fascicle force enhancement relative to REF was similar to LENsmalland LENmedium(3-5%). MTU shortening with and without a preload over small (SHOsmallP/SHOsmall) and large (SHOlargeP/SHOlarge) amplitudes significantly (p<0.001) increased positive fascicle and MTU work relative to REF, but significant (p≤0.006) rFD was observed in SHOsmallPand SHOlargeP(7-10%) only. rFD was linearly related to positive MTU work (rrm(47)=0.48,p<0.001), but not positive fascicle work (rrm(47)=0.16,p=0.277). Our findings indicate that MTU lengthening without substantial fascicle stretch enhances steady-state force output, which might be due to less shortening-induced rFD. Our findings also indicate that different amounts of positive fascicle and MTU work induce similar rFD, which cautions against using work to predict rFD during submaximal voluntary contractions.
Hound: A novel tool for automated mapping of genotype to phenotype in bacterial genomes assembled de novo
Authors: Reding Carlos , Satapoomin Naphat , Avison Matthew B.
Published: September 2023

Increasing evidence suggests that microbial species have a strong within species genetic heterogeneity. This can be problematic for the analysis of prokaryote genomes, which commonly relies on a reference genome to guide the assembly process. Any difference between reference and sample genomes can introduce errors in the detection of small insertions, deletions, structural variations and even point mutations. This phenomenon jeopardises the genomic surveillance of antibiotic-resistant bacteria, with predictions of resistance varying between laboratories. Here we present Hound, an analysis pipeline that integrates publicly available tools to locally assemble prokaryote genomesde novo, detect genes by similarity using the proteins they encode as query, and report the mutations found. Three features are exclusive to Hound: it reports relative gene copy number, retrieves sequences upstream the start codon to detect mutations in promoter regions—which allow gene expression signals to be integrated—and, importantly, can merge contigs based on a user-given query sequence to reconstruct genes that are fragmented by the assembler. To demonstrate Hound, we screened through 5,032 bacterial whole-genome sequences isolated from farmed animals and human infections, using the amino acid sequence encoded byblaTEM-1, to predict resistance to amoxicillin/clavulanate which is driven by over-expression of this gene. We believe this tool can facilitate the analysis of prokaryote species that currently lack a reference genome, and can be scaled up to build automated systems for antibiotic susceptibility prediction.
Molecular and phenotypic blueprint of the hematopoietic compartment reveals proliferation stress as a driver of age-associated human stem cell dysfunctions
Authors: Lettera Emanuele , Scala Serena , Basso-Ricci Luca , Tavella Teresa , Volpe Lucrezia della , Furno Elena Lo , Kaufmann Kerstin B. , Garcia-Prat Laura , Quaranta Pamela , Hernandez Raisa Jofra , Murison Alex , Giannetti Kety , Aguilar-Navarro Alicia G. , Beretta Stefano , Conti Anastasia , Farina Giacomo , Flores-Figueroa Eugenia , Conte Pietro , Ometti Marco , Merelli Ivan , Xie Stephanie Z. , Aiuti Alessandro , Micco Raffaella Di
Published: September 2023

Hematopoietic stem/progenitor cell (HSPC) aging studies have been associated with myeloid skewing, reduced clonal output, and impaired regenerative capacity, but quantitative immunophenotypic and functional analysis across human aging is lacking. Here, we provide a comprehensive phenotypic, transcriptional, and functional dissection of human hematopoiesis across the lifespan. Although primitive HSPC numbers were stable during aging, overall cellularity was reduced, especially for erythroid and lymphoid lineages. Notably, HSPC from aged individuals had superior repopulating frequency than younger counterparts in xenografts; yet aged HSPC displayed epigenetic dysregulation of cell cycle, inflammatory signatures, and a reduced capacity to counteract activation-induced proliferative stress with concomitant accumulation of DNA damage and senescence-like features upon xenotransplantation. This phenotype was recapitulated by enforcing proliferative stressin vivoon cord blood (CB) HSPC. Overall, our work sheds light on dysregulated responses to activation-induced proliferation underlying HSPC aging and establishes CB xenotransplantation-based models as suitable for studying age-associated hematopoietic defects.
Trogocytosis of cancer-associated fibroblasts promotes pancreatic cancer growth and immune suppression via phospholipid scramblase anoctamin 6 (ANO6)
Authors: Ogier Charline , Solomon Akino Mercy Charles , Lu Zhen , Recoules Ludmila , Klochkova Alena , Gabitova-Cornell Linara , Bayarmagnai Battuya , Restifo Diana , Surumbayeva Aizhan , Vendramini-Costa Débora B. , Deneka Alexander Y. , Francescone Ralph , Lilly Anna C. , Sipman Alyssa , Gardiner Jaye C. , Luong Tiffany , Franco-Barraza Janusz , Ibeme Nina , Cai Kathy Q. , Einarson Margret B. , Nicolas Emmanuelle , Efimov Andrei , Megill Emily , Snyder Nathaniel W. , Bousquet Corinne , Cros Jerome , Zhou Yunyun , Golemis Erica A. , Gligorijevic Bojana , Soboloff Jonathan , Fuchs Serge Y. , Cukierman Edna , Astsaturov Igor
Published: September 2023

In pancreatic ductal adenocarcinoma (PDAC), the fibroblastic stroma constitutes most of the tumor mass and is remarkably devoid of functional blood vessels. This raises an unresolved question of how PDAC cells obtain essential metabolites and water-insoluble lipids. We have found a critical role for cancer-associated fibroblasts (CAFs) in obtaining and transferring lipids from blood-borne particles to PDAC cells via trogocytosis of CAF plasma membranes. We have also determined that CAF-expressed phospholipid scramblase anoctamin 6 (ANO6) is an essential CAF trogocytosis regulator required to promote PDAC cell survival. During trogocytosis, cancer cells and CAFs form synapse-like plasma membranes contacts that induce cytosolic calcium influx in CAFs via Orai channels. This influx activates ANO6 and results in phosphatidylserine exposure on CAF plasma membrane initiating trogocytosis and transfer of membrane lipids, including cholesterol, to PDAC cells. Importantly, ANO6-dependent trogocytosis also supports the immunosuppressive function of pancreatic CAFs towards cytotoxic T cells by promoting transfer of excessive amounts of cholesterol. Further, blockade of ANO6 antagonizes tumor growth via disruption of delivery of exogenous cholesterol to cancer cells and reverses immune suppression suggesting a potential new strategy for PDAC therapy.
Driver lines for studying associative learning in Drosophila
Authors: Shuai Yichun , Sammons Megan , Sterne Gabriella R , Hibbard Karen , Yang He , Yang Ching-Po , Managan Claire , Siwanowicz Igor , Lee Tzumin , Rubin Gerald M. , Turner Glenn C , Aso Yoshinori
Published: September 2023

The mushroom body (MB) is the center for associative learning in insects. In Drosophila, intersectional split-GAL4 drivers and electron microscopy (EM) connectomes have laid the foundation for precise interrogation of the MB neural circuits. However, investigation of many cell types upstream and downstream of the MB has been hindered due to lack of specific driver lines. Here we describe a new collection of over 800 split-GAL4 and split-LexA drivers that cover approximately 300 cell types, including sugar sensory neurons, putative nociceptive ascending neurons, olfactory and thermo-/hygro-sensory projection neurons, interneurons connected with the MB-extrinsic neurons, and various other cell types. We characterized activation phenotypes for a subset of these lines and identified the sugar sensory neuron line most suitable for reward substitution. Leveraging the thousands of confocal microscopy images associated with the collection, we analyzed neuronal morphological stereotypy and discovered that one set of mushroom body output neurons, MBON08/MBON09, exhibits striking individuality and asymmetry across animals. In conjunction with the EM connectome maps, the driver lines reported here offer a powerful resource for functional dissection of neural circuits for associative learning in adult Drosophila.
Solution State Methyl NMR Spectroscopy of Large Non-Deuterated Proteins Enabled by Deep Neural Networks
Authors: Karunanithy Gogulan , Shukla Vaibhav Kumar , Hansen D. Flemming
Published: September 2023

Methyl-TROSY nuclear magnetic resonance (NMR) spectroscopy is a powerful technique for characterising large biomolecules in solution. However, preparing samples for these experiments is arduous and entails deuteration, limiting its use. Here we demonstrate that NMR spectra recorded on protonated, uniformly13C labelled, samples can be processed using deep neural networks to yield spectra that are of similar quality to typical deuterated methyl-TROSY spectra, potentially providing more information at a fraction of the cost. We validated the new methodology experimentally on three proteins with molecular weights in the range 42-360 kDa and further by analysing deep learning-processed NOESY spectra of Escherichia coli Malate Synthase G (81 kDa), where observed NOE cross-peaks were in good agreement with the available structure. The new method represents a substantial advance in the field of using deep learning to analyse complex magnetic resonance data and could have a major impact on the study of large biomolecules in the years to come.
Improved Protein Model in SPICA Force Field
Authors: Yamada Teppei , Miyazaki Yusuke , Harada Shogo , Kumar Ashutosh , Vanni Stefano , Shinoda Wataru
Published: September 2023

The previous version of the SPICA coarse-grained (CG) force field (FF) protein model focused primarily on membrane proteins and successfully reproduced the dimerization free energies of several transmembrane helices and stable structures of various membrane protein assemblies. However, that model had limited accuracy when applied to other proteins, such as intrinsically disordered proteins (IDPs) and peripheral proteins, because the dimensions of the IDPs in an aqueous solution were too compact, and protein binding on the lipid membrane surface was over-stabilized. To improve the accuracy of the SPICA FF model for the simulation of such systems, in this study we introduce protein secondary structure-dependent nonbonded interaction parameters to the backbone segments and re-optimize almost all nonbonded parameters for amino acids. The improved FF proposed here successfully reproduces the radius of gyration of various IDPs, the binding sensitivity of several peripheral membrane proteins, and the dimerization free energies of several transmembrane helices. The new model also shows improved agreement with experiments on the free energy of peptide association in water. In addition, an extensive library of nonbonded interactions between proteins and lipids, including various glycerophospholipids, sphingolipids, and cholesterol, allows the study of specific interactions between lipids and peripheral and transmembrane proteins. Hence, the new SPICA FF (version 2) proposed herein is applicable with high accuracy for simulating a wide range of protein systems.

Graphical abstract
Warnings/Cautions when collecting Brassica diversity along a large climatic gradient
Authors: Falentin Cyril , Hadj-Arab Houria , Aissiou Fella , Bartoli Claudia , Bazan Giuseppe , Boudet Matéo , Bousset-Vaslin Lydia , Chwikhi Marwa , Coriton Olivier , Deniot Gwenaëlle , de Carvalho Julie Ferreira , Gay Laurène , Geraci Anna , Glory Pascal , Huteau Virginie , Ilahy Riadh , Ilardi Vincenzo , Jarillo José A. , Meglič Vladimir , Oddo Elisabetta , Pernas Mónica , Piñeiro Manuel , Pipan Barbara , Rhim Thouraya , Richer Vincent , Rizza Fulvia , Ronfort Joëlle , Rousseau-Gueutin Mathieu , Schicchi Rosario , Sinkovič Lovro , Taburel Maryse , Terzi Valeria , Théréné Sylvain , Tiret Mathieu , Tlili Imen , Badeck Franz Werner , Chèvre Anne-Marie
Published: September 2023

Agriculture faces great challenges to overcome global warming and to improve system sustainability, requiring access to novel genetic diversity. So far, wild populations and local landraces remain poorly explored. This is notably the case for the two diploid species,Brassica oleraceaL. (CC, 2n=2x=18) andB. rapaL. (AA, 2n=2x=20). In order to explore genetic diversity in both species, we have collected numerous populations in their center of origin, the Mediterranean basin, on a large contrasting climatic and soil gradient from northern Europe to southern sub-Saharan regions. In these areas, we also collected 14 populations belonging to fiveB. oleraceaclosely related species. Before further genetic and agronomic investigations, we controlled the absence of species misidentification using flow cytometry, sequencing of species specific chloroplast genomic region, as well as cytogenetic analyses in case of unexpected results. Looking at the 102B. oleraceaand 146B. rapapopulations showing a good germination among the 112 and 154 populations collected, seventeen populations were misidentified. The most frequent mistake was a confusion of these diploid species withB. napus. Additionally forB. rapa, 2 autotetraploid populations were observed. Habitats of the collected wild populations and landraces are described in our work. This provides a unique plant material characterization that will pave the way for further analyses investigating the genomic regions involved in climatic and microbiota adaptation. This research is supported by the H2020 Prima project ‘BrasExplor’.
Tip Growth Defective1 interacts with the cellulose synthase complex to regulate cellulose synthesis in Arabidopsis thaliana
Authors: Lampugnani Edwin R , Persson Staffan , Khan Ghazanfar Abbas
Published: September 2023

Plant cells possess robust and flexible cell walls composed primarily of cellulose, a polysaccharide that provides structural support and enables cell expansion. Cellulose is synthesised by the Cellulose Synthase A (CESA) catalytic subunits, which form cellulose synthase complexes (CSCs). While significant progress has been made in unravelling CSC function, the trafficking of CSCs and the involvement of post-translational modifications in cellulose synthesis remain poorly understood. In order to deepen our understanding of cellulose biosynthesis, this study utilised immunoprecipitation techniques with CESA6 as the bait protein to explore the CSC and its interactors. We successfully identified the core proteins of the CSC complex and discovered new potential interactors involved in CSC trafficking and the coordination of cell wall synthesis. Moreover, we identified TIP GROWTH DEFECTIVE 1 (TIP1) protein S-acyl transferases (PATs) as an interactor of the CSC complex. We confirmed the interaction between TIP1 and the CSC complex through multiple independent approaches. Further analysis revealed thattip1mutants exhibited stunted growth and reduced levels of crystalline cellulose in leaves. These findings suggest that TIP1 positively influences cellulose biosynthesis, potentially mediated by its role in the S-acylation of the CSC complex.
Interferon-α promotes neo-antigen formation and preferential HLA-B-restricted antigen presentation in pancreatic β-cells
Authors: Carré Alexia , Zhou Zhicheng , Perez-Hernandez Javier , Samassa Fatoumata , Lekka Christiana , Manganaro Anthony , Oshima Masaya , Liao Hanqing , Parker Robert , Nicastri Annalisa , Brandao Barbara , Colli Maikel L. , Eizirik Decio L. , Göransson Marcus , Burgos Morales Orlando , Anderson Amanda , Landry Laurie , Kobaisi Farah , Scharfmann Raphael , Marselli Lorella , Marchetti Piero , You Sylvaine , Nakayama Maki , Hadrup Sine R. , Kent Sally C. , Richardson Sarah J. , Ternette Nicola , Mallone Roberto
Published: September 2023

Interferon (IFN)-α is the earliest cytokine signature observed in individuals at risk for type 1 diabetes (T1D), but its effect on the repertoire of HLA Class I (HLA-I)-bound peptides presented by pancreatic β-cells is unknown. Using immunopeptidomics, we characterized the peptide/HLA-I presentation inin-vitroresting and IFN-α-exposed β-cells. IFN-α increased HLA-I expression and peptide presentation, including neo-sequences derived from alternative mRNA splicing, post-translational modifications - notably glutathionylation - and proteincis-splicing. This antigenic landscape relied on processing by both the constitutive and immune proteasome. The resting β-cell immunopeptidome was dominated by HLA-A-restricted ligands. However, IFN-α only marginally upregulated HLA-A and largely favored HLA-B, translating into a major increase in HLA-B-restricted peptides and into an increased activation of HLA-B-restricted vs. HLA-A-restricted CD8+T-cells. A preferential HLA-B hyper-expression was also observed in the islets of T1D vs. non-diabetic donors, and we identified islet-infiltrating CD8+T-cells from T1D donors reactive to HLA-B-restricted granule peptides. Thus, the inflammatory milieu of insulitis may skew the autoimmune response toward epitopes presented by HLA-B, hence recruiting a distinct T-cell repertoire that may be relevant to T1D pathogenesis.
Sperm Cell Painting: A Mechanism Driven Approach for Drug Discovery in Human Spermatozoa
Authors: Johnston Zoe C , Gruber Franz S , Myles Rachel , Kane Shruti V. , Richardson Anthony , Day David P. , Wilson Caroline , Read Kevin D. , Gilbert Ian H. , Martins da Silva Sarah , Barratt Christopher LR , Swedlow Jason R.
Published: September 2023

We have adapted the cell painting assay developed by Carpenter and colleagues on cultured U2OS cells to human spermatozoa. In Sperm Cell Painting (SCP) we assemble an image-based quantitative fingerprint of the functional state of sperm. We use this assay to gain insight into the mechanism of action of compounds that modify sperm function and as a platform for contraceptive discovery.
Thermo- and photoreceptors of eyes as regulators of circadian rhythm and glymphatic system
Authors: Kholmanskiy Alexander
Published: September 2023

The dynamics of hydrogen bonds in bulk and hydrated water affected the activation energies of temperature dependence of ion currents of voltage-dependent channels that regulate communication and trophic bonds in the neuropil of the cortical parenchyma. The physics of minimizing of isobaric heat capacity of water made it possible to explain stabilization and functional optimization of thermodynamics of eyeball fluids at 34.5 °C and human brain during sleep at 36.5 °C. At these temperatures, thermoreceptors of cornea and cells of ganglionic layer of the retina, through connections with suprachiasmatic nucleus and pineal gland, switch brain metabolism from daytime to nighttime modes. The phylogenesis of circadian rhythm was reflected in dependence of duration of nighttime sleep of mammals on diameter of eyeball, mass of pineal gland, and density of neurons in parenchyma of cortex. The activity of all nerves of eyeball led to division of nocturnal sleep into slow and fast phases. These phases correspond to two modes of glymphatic system - electrochemical and dynamic. The first is responsible for relaxation processes of synaptic plasticity and chemical neutralization of toxins with participation of water and melatonin. Rapid eye movement and an increase in cerebral blood flow in second mode increase water exchange in parenchyma and flush out toxins into venous system.
PD-1 Mediated Regulation of Unique Activated CD8+T Cells by NK Cells in the Submandibular Gland
Authors: Borys Samantha M. , Reilly Shanelle P. , Magill Ian , Zemmour David , Brossay Laurent
Published: September 2023

The increasing utilization of anti-PD-1 immune checkpoint blockade (ICB) has led to the emergence of immune-related adverse events (irAEs), including sicca syndrome. Interestingly, we found that the submandibular gland (SMG) of PD-1 deficient mice harbors a large population of CD8+T cells, reminiscing ICB induced sicca. This phenotype was also observed in the SMG of both NK cell-depleted C57BL/6 animals and NK cell-deficient animals. Mechanistically, using mice conditionally deficient for PD-L1 in the NK cell lineage, we discovered that NK cells regulate CD8+T cell homeostasis via the PD-1/PD-L1 axis in this organ. Importantly, single-cell RNA sequencing of PD-1 deficient SMG CD8+T cells reveals a unique transcriptional profile consistent with TCR activation. These cells have limited TCR diversity and phenotypically overlap with GzmK+CD8+T autoimmune cells identified in primary Sjögren’s syndrome patients. These insights into NK cell immunoregulation in the SMG, and the consequences of disrupted CD8+T cell homeostasis, provide opportunities for preventing the development of irAEs.

Highlights

Elevated CD8+T cells in the submandibular gland (SMG) of PD-1 deficient mice parallel sicca-like irAEs seen in ICB patients.

In addition to their previously described hyporesponsive phenotype, NK cells in the SMG regulate CD8+T cell homeostasis through the PD-L1/PD-1 axis.

PD-1 deficient SMG CD8+T cells display unique transcriptional profiles associated with proinflammatory functions, TCR activation, interferon stimulation, and exhaustion.

Oligoclonal expansion and similarities in TCR sequences indicate T cell activation and a preference for recognizing specific antigens.
Adenine methylation is very scarce in the drosophila genome and not erased by the Ten Eleven Translocation dioxygenase
Authors: Boulet Manon , Gilbert Guerric , Renaud Yoan , Schmidt-Dengler Martina , Plantié Emilie , Bertrand Romane , Nan Xinsheng , Jurkowski Tomasz , Helm Mark , Vandel Laurence , Waltzer Lucas
Published: September 2023

N6-methyladenine (6mA) DNA modification has recently been described in metazoans, including in drosophila, for which the erasure of this epigenetic mark has been ascribed to the Ten Eleven Translocation (TET) enzyme. Here, we re-evaluated 6mA presence and TET impact on drosophila genome. Using axenic or conventional breeding conditions, we found traces of 6mA by LC-MS/MS and no significant increase in 6mA levels in the absence of TET, suggesting that this modification is present at very low levels in the drosophila genome but not regulated by TET. Consistent with this latter hypothesis, further molecular and genetic analyses showed that TET does not demethylate 6mA but acts essentially in an enzymatic-independent manner. Our results call for further caution concerning the role and regulation of 6mA DNA modification in metazoans and underline the importance of TET non-enzymatic activity for fly development.
Sulfatase 2 Inhibition Sensitizes Triple-Negative Breast Cancer Cells to Chemotherapy Through Augmentation of Extracellular ATP
Authors: Manouchehri Jasmine M , Marcho Lynn , Cherian Mathew A
Published: September 2023

Background

Breast cancer is the leading cause of cancer-related death among women worldwide. Patients diagnosed with triple-negative breast cancer (TNBC) have limited therapeutic options that produce durable responses. Hence, a diagnosis of TNBC is associated with a poor prognosis compared to other types of breast cancer. As a result, there is a critical need for novel therapies that can deepen and prolong responses.

We previously found that chemotherapy causes the release of extracellular adenosine triphosphate (eATP). Augmenting eATP release can boost the response of TNBC cells to chemotherapy and cause increased cell death. However, eATP concentrations are limited by several families of extracellular ATPases, which complicates the design of compounds that attenuate eATP degradation.

In this study, we hypothesized that heparan sulfate (HS) would inhibit extracellular ATPases and accentuate chemotherapy-induced cytotoxicity in TNBC by augmenting eATP. HS can be desulfated by sulfatase 1 and 2; sulfatase 2 is consistently highly expressed in a variety of cancers including breast cancer, whereas sulfatase 1 is not. We hypothesized that the sulfatase 2 inhibitor OKN-007 would exacerbate chemotherapy-induced eATP release and TNBC cell death.

Methods

TNBC cell lines and nontumorigenic immortal mammary epithelial cells were treated with paclitaxel in the presence of heparan sodium sulfate and/or OKN-007; eATP content and cell viability were evaluated. In addition, protein and cell surface expression of sulfatases 1 and 2 were determined in all examined cell lines via ELISA, Western blot, and flow cytometry analyses.

Results

Sulfatase 2 was highly expressed in TNBC cell lines and human breast cancer samples but not in immortal mammary epithelial cells and much less so in normal human breast tissue and ductal carcinoma in situ samples. OKN-007 exacerbated chemotherapy-induced eATP release and chemotherapy-induced TNBC cell death. When combined with chemotherapy, OKN-007 attenuated cells with a cancer-initiating cell phenotype.

Conclusions

These results suggest that sulfatase 2 inhibitors in combination with chemotherapy attenuate the viability of TNBC cells more than chemotherapy alone by exacerbating eATP release. These effects, as well as their capacity to attenuate the cancer-initiating cell fraction, may translate into combination therapies for TNBC that induce deeper and more durable responses.
Unravelling Paralog-Specific Notch Signaling through Ternary Complex Stability and Transcriptional Activation Measurements Using Chimeric Receptors
Authors: Ramsey Kristen M. , Barrick Doug
Published: September 2023

Notch signaling is mediated by four paralogous receptors with conserved architectures and overlapping yet non-redundant functions. Notch signaling generates a transcriptional activation complex (NTC) wherein the N-terminal RAM and ankyrin repeat (ANK) regions of the Notch intracellular domain (NICD) bind transcription factor CSL and recruit co-activator Mastermind-like (MAML). To better understand paralog-specific differences in Notch signaling, we analyzed the thermodynamics of binary and ternary NTCs for all four Notch paralogues and chimeric constructs. We find that RAMANK:CSL stability (ΔGRA) is primarily determined by the RAM region while MAML binding to preformed RAMANK:CSL complexes (ΔGMAML) is largely determined by the ANK region. We determined transcriptional activation data for the paralogous and chimeric NICDs and analyzed the data with an independent multiplicative model. This analysis shows ternary complex stability (ΔGTC, where ΔGTC= ΔGRA+ΔGMAML) correlates well with transcriptional activations and provides insights into contributions of RAM, ANK and the C-terminal regions to Notch signaling.
Mapping the Changing Neural Architecture of Narrative Processing Using Naturalistic Stimuli: an fMRI Study
Authors: Haines Christina , Sullivan KiAnna , Klamer Keva , Craig Joshua , Ekstrand Chelsea
Published: September 2023

A narrative is a coherent representation of actual or fictional events designed to connect experiences. Narratives provide a unique opportunity to investigate brain functions in scenarios more closely resembling real-world experiences. However, most neuroimaging studies examining narrative formation have utilized static stimuli that fail to capture the intricacies of narrative construction in everyday life, particularly how cognitive demands change over the course of narrative processing. The current research uses functional magnetic resonance imaging (fMRI) to examine dynamic narrative processing over the course of a full-length audiovisual narrative. We examined changes in neural synchrony (as quantified by intersubject correlations) in areas related to semantic memory, episodic memory, and visuospatial attention between the beginning, middle, and end of the narrative. Results from two experiments identified two core narrative processing networks responsible for constructing coherent representations across extended timescales. The first network is associated with the early narrative construction, and includes the right intraparietal sulcus/superior parietal lobule, bilateral angular gyrus, bilateral precuneus, and left fusiform gyrus. The second network consists of the right ventral frontal cortex and bilateral parahippocampal cortices, and is associated with longer term narrative integration. Together, these regions provide the framework for successful narrative processing during naturalistic stimuli.
The impact of Parkinson’s disease on striatal network connectivity and cortico-striatal drive: an in-silico study
Authors: Carannante Ilaria , Scolamiero Martina , Hjorth J. J. Johannes , Kozlov Alexander , Bekkouche Bo , Guo Lihao , Kumar Arvind , Chachólski Wojciech , Hellgren Kotaleski Jeanette
Published: September 2023

Striatum, the input stage of the basal ganglia, is important for sensory-motor integration, initiation and selection of behaviour, as well as reward learning. Striatum receives glutamatergic inputs from mainly cortex and thalamus. In rodents, the striatal projection neurons (SPNs), giving rise to the direct and the indirect pathway (dSPNs and iSPNs, respectively), account for 95% of the neurons and the remaining 5% are GABAergic and cholinergic interneurons. Interneuron axon terminals as well as local dSPN and iSPN axon collaterals form an intricate striatal network. Following chronic dopamine depletion as in Parkinson’s disease (PD), both morphological and electrophysiological striatal neuronal features have been shown to be altered in rodent models. Our goal with thisin-silicostudy is twofold: a) to predict and quantify how the intrastriatal network connectivity structure becomes altered as a consequence of the morphological changes reported at the single neuron level, and b) to investigate how the effective glutamatergic drive to the SPNs would need to be altered to account for the activity level seen in SPNs during PD. In summary we predict that the richness of the connectivity motifs in the striatal network is significantly decreased during PD, while at the same time a substantial enhancement of the effective glutamatergic drive to striatum is present.

AUTHOR SUMMARY

Thisin-silicostudy predicts the impact that the single cell neuronal morphological alterations will have on the striatal microcircuit connectivity. We find that the richness in the topological striatal motifs is significantly reduced in Parkinson’s disease, highlighting that just measuring the pairwise connectivity between neurons gives an incomplete description of network connectivity. Moreover, we predict how the resulting electrophysiological changes of SPN excitability together with their reduced number of dendritic branches affect their response to the glutamatergic drive from cortex and thalamus. We find that the effective glutamatergic drive is likely significantly increased in PD, in accordance with the hyperglutamatergic hypothesis.
Effects of dim light at night in C57BL/6J mice on recovery after spinal cord injury
Authors: Aldrich John C. , Scheinfeld Ashley R. , Lee Sydney E. , Dusenbery Kalina J. , Mahach Kathryn M. , Van de Veire Brigid C. , Fonken Laura K. , Gaudet Andrew D.
Published: September 2023

Spinal cord injury (SCI) can cause long-lasting locomotor deficits, pain, and mood disorders. Anatomical and functional outcomes are exacerbated by inflammation after SCI, which causes secondary damage. One promising target after SCI is manipulating the circadian system, which optimizes biology and behavior for time of day – including neuroimmune responses and mood- related behaviors. Circadian disruption after SCI is likely worsened by a disruptive hospital environment, which typically includes dim light-at-night (dLAN). Here, we hypothesized that mice subjected to SCI, then placed in dLAN, would exhibit worsened locomotor deficits, pain- like behavior, and anxiety-depressive-like symptoms compared to mice maintained in light days with dark nights (LD). C57BL/6J mice received sham surgery or moderate T9 contusion SCI, then were placed permanently in LD or dLAN. dLAN after SCI did not worsen locomotor deficits; rather, SCI-dLAN mice showed slight improvement in open-field locomotion at the final timepoint. Although dLAN did not alter SCI-induced heat hyperalgesia, SCI-dLAN mice exhibited an increase in mechanical allodynia at 13 days post-SCI compared to SCI-LD mice. SCI-LD and SCI-dLAN mice had similar outcomes using sucrose preference (depressive-like) and open-field (anxiety-like) tests. At 21 dpo, SCI-dLAN mice had reduced preference for a novel juvenile compared to SCI-LD, implying that dLAN combined with SCI may worsen this mood-related behavior. Finally, lesion size was similar between SCI-LD and SCI-dLAN mice. Therefore, newly placing C57BL/6J mice in dLAN after SCI had modest effects on locomotor, pain-like, and mood-related behaviors. Future studies should consider whether clinically-relevant circadian disruptors, alone or in combination, could be ameliorated to enhance outcomes after SCI.
Unveiling the phenology and associated floral regulatory pathways ofHumulus lupulusL. in subtropical conditions
Authors: Gutiérrez Robert Márquez , de Oliveira Raphael Ricon , Ribeiro Thales Henrique Cherubino , de Oliveira Kellen Kauanne Pimenta , Silva João Victor Nunes , Alves Tamires Caixeta , do Amaral Laurence Rodrigues , Gomes Marcos de Souza , Gomes Matheus de Souza , Chalfun-Junior Antonio
Published: September 2023

TheHumulus lupulusL. (hops) is traditionally produced in temperate regions, historically attributed to the belief that vernalization was necessary for reproductive transition. Nevertheless, recent studies have revealed the potential for hop plants to flower in tropical and subtropical climates, thereby reshaping cultivation prospects once the developmental disparities are understood and adapted for optimized production. Here, we delved into the hop phenological cycle and the underlying floral regulatory pathways ultimately, seeking to devise strategies to modulate development and enhance production in regions with low latitudes. In contrast to cultivation in temperate regions, hops grown in the subtropical climate of Minas Gerais, Brazil, flower multiple times throughout the year, independently of the season. Hop is a short-day plant, and in Brazil, the photoperiod is consistently inductive due to daylight hours always being below the described threshold (16,5 h of light critical point). We observed that the reproductive transition of hop initiates after a specific number of nodes, 25 to 28, leading us to hypothesize that this process is primarily controlled by endogenous factors. To explore this issue, we first identified in the hop genome families of miRNAs related to reproductive transition, such as the families MIR156 and MIR172, and the PEBP family which includes the FLOWERING LOCUS T (FT). The expression of miR156 decreased along development inversely to miR172 and in synchrony with the upregulation of HlFT3 and HlFT5. These findings strongly support that the reproductive transition in hops under inductive photoperiodic conditions is primarily regulated by endogenous factors related to development and aging throughout the miRNA and FT-associated pathways. Thus, our study shedded light on the intricate molecular mechanisms that underlie hop floral development paving the way for potential advancements in hop production on a global scale.
Robust and scalable single-molecule protein sequencing with fluorosequencing
Authors: Mapes James H. , Stover Julia , Stout Heather D. , Folsom Tucker M. , Babcock Emily , Loudwig Sandra , Martin Christopher , Austin Mariah J. , Tu Fan , Howdieshell Casey J. , Simpson Zachary B. , Blom Thomas , Weaver Daniel , Winkler Daniel , Velden Kent Vander , Ossareh Parham M. , Beierle John M , Somekh Talli , Bardo Angela M. , Anslyn Eric V. , Marcotte Edward M. , Swaminathan Jagannath
Published: September 2023

The need to accurately survey proteins and their modifications with ever higher sensitivities, particularly in clinical settings with limited samples, is spurring development of new single molecule proteomics technologies. Fluorosequencing is one such highly parallelized single molecule peptide sequencing platform, based on determining the sequence positions of select amino acid types within peptides to enable their identification and quantification from a reference database. Here, we describe substantial improvements to fluorosequencing, including identifying fluorophores compatible with the sequencing chemistry, mitigating dye-dye interactions through the use of extended polyproline linkers, and developing an end-to-end workflow for sample preparation and sequencing. We demonstrate by fluorosequencing peptides in mixtures and identifying a target neoantigen from a database of decoy MHC peptides, highlighting the potential of the technology for high sensitivity clinical applications.
Exponentially decreasing exposure of antigen generates anti-inflammatory T-cell responses
Authors: Esrafili Arezoo , Kupfer Joshua , Thumsi Abhirami , Sekhar Jaggarapu Madhan Mohan Chandra , Suresh Abhirami P. , Talitckii Aleksandr , Khodaei Taravat , Swaminathan Srivatsan J. , Mantri Shivani , Peet Matthew M , Acharya Abhinav P.
Published: September 2023

Rheumatoid Arthritis (RA) is a chronic debilitating disease characterized by auto-immune reaction towards self-antigen such as collagen type II. In this study, we investigated the impact of exponentially decreasing levels of antigen exposure on pro-inflammatory T cell responses in the collagen-induced arthritis (CIA) mouse model. Using a controlled delivery experimental approach, we manipulated the collagen type II (CII) antigen concentration presented to the immune system. We observed that exponentially decreasing levels of antigen generated reduced pro-inflammatory T cell responses in secondary lymphoid organs in mice suffering from RA. Specifically, untreated mice exhibited robust pro-inflammatory T cell activation and increased paw inflammation, whereas, mice exposed to exponentially decreasing concentrations of CII demonstrated significantly reduced pro-inflammatory T cell responses, exhibited lower levels of paw inflammation, and decreased arthritis scores in right rear paw. The data also demonstrate that the decreasing antigen levels promoted the induction of regulatory T cells (Tregs), which play a crucial role in maintaining immune tolerance and suppressing excessive inflammatory responses. Our findings highlight the importance of antigen concentration in modulating pro-inflammatory T cell responses in the CIA model. These results provide valuable insights into the potential therapeutic strategies that target antigen presentation to regulate immune responses and mitigate inflammation in rheumatoid arthritis and other autoimmune diseases. Further investigations are warranted to elucidate the specific mechanisms underlying the antigen concentration-dependent modulation of T cell responses and to explore the translational potential of this approach for the development of novel therapeutic interventions in autoimmune disorders.
Humanin vivomidtarsal and subtalar joint kinematics during walking, running, and hopping
Authors: Behling Anja-Verena , Welte Lauren , Kelly Luke , Rainbow Michael J
Published: September 2023

The interaction among joints of the midtarsal complex and subtalar joint is essential role for locomotor function; however, its complexity poses substantial challenges in quantifying their motions. We determine the mobility of these joints across locomotion tasks and investigate their alignment with individual talus morphology.

Utilizing highly accurate biplanar videoradiography, three-dimensional bone kinematics were captured during walking, running, and hopping. We calculated the axis of rotation of each midtarsal and subtalar joint for the landing and push-off phases, respectively. A comparison was made between these rotation axes and the morphological subtalar axis. Measurement included total rotation about, the orientation of the rotation axes in the direction of the subtalar joint and its deviation via spatial angles for both phases.

The rotation axes of all three bones relative to the talus closely align with the morphological subtalar axis. This suggests that the midtarsal and subtalar joints’ motions might be described by one commonly oriented axis. Despite having such axis, the location of axes and ranges of motion differed among the bones.

Our results provide a novel perspective of healthy foot function across different sagittal plane-dominant locomotion tasks underscoring the importance of midtarsal and subtalar motion with respect to subject-specific talus morphology.
WCRC-25: A novel luminal Invasive Lobular Carcinoma cell line model
Authors: Elangovan Ashuvinee , Bossart Emily A. , Basudan Ahmed , Tasdemir Nilgun , Shah Osama Shiraz , Ding Kai , Meier Carolin , Heim Tanya , Neumann Carola , Attaran Shireen , Brown Lauren , Hooda Jagmohan , Miller Lori , Liu Tiantong , Puhalla Shannon L. , Gurda Grzegorz , Lucas Peter C. , McAuliffe Priscilla F. , Atkinson Jennifer M. , Lee Adrian V. , Oesterreich Steffi
Published: September 2023

Breast cancer is categorized by the molecular and histologic presentation of the tumor, with the major histologic subtypes being No Special Type (NST) and Invasive Lobular Carcinoma (ILC). ILC are characterized by growth in a single file discohesive manner with stromal infiltration attributed to their hallmark pathognomonic loss of E-cadherin (CDH1). Few ILC cell line models are available to researchers. Here we report the successful establishment and characterization of a novel ILC cell line, WCRC-25, from a metastatic pleural effusion from a postmenopausal Caucasian woman with metastatic ILC. WCRC-25 is an ER-negative luminal epithelial ILC cell line with both luminal and Her2-like features. It exhibits anchorage independent growth and haptotactic migration towards Collagen I. Sequencing revealed aCDH1Q706* truncating mutation, together with mutations inFOXA1, CTCF, BRCA2andTP53, which were also seen in a series of metastatic lesions from the patient. Copy number analyses revealed amplification and deletion of genes frequently altered in ILC while optical genome mapping revealed novel structural rearrangements. RNA-seq analysis comparing the primary tumor, metastases and the cell line revealed signatures for cell cycle progression and receptor tyrosine kinase signaling. To assess targetability, we treated WCRC-25 with AZD5363 and Alpelisib confirming WCRC-25 as susceptible to PI3K/AKT signaling inhibition as predicted by our RNA sequencing analysis. In conclusion, we report WCRC-25 as a novel ILC cell line with promise as a valuable research tool to advance our understanding of ILC and its therapeutic vulnerabilities.

Financial support

The work was in part supported by a Susan G Komen Leadership Grant to SO (SAC160073) and NCI R01 CA252378 (SO/AVL). AVL and SO are Komen Scholars, Hillman Foundation Fellows and supported by BCRF. This project used the UPMC Hillman Cancer Center and Tissue and Research Pathology/Pitt Biospecimen Core shared resource which is supported in part by award P30CA047904. This research was also supported in part by the University of Pittsburgh Center for Research Computing, RRID:SCR_022735, through the resources provided. Specifically, this work used the HTC cluster, which is supported by NIH award number S10OD028483. Finally, partial support was provided by the Magee-Womens Research Institute and Foundation, The Shear Family Foundation, and The Metastatic Breast Cancer Network.
Tap Dancing Frogs: Posterior Toe Tapping and Feeding inDendrobates tinctorius
Authors: Parrish Thomas Q , Fischer Eva K
Published: September 2023

Animals have myriad adaptations to help them hunt and feed in the most efficient and effective manner. One mysterious behavior related to hunting and feeding is the posterior toe tapping behavior of some frogs. Biologists and hobbyists alike have long noticed this behavior, but there is little empirical data to explain its causes and consequences. To test the hypothesis that tapping is related to feeding and modulated by environmental context, we conducted a series of related experiments in the Dyeing poison frog,Dendrobates tinctorius. We first confirmed that tap rate was higher during feeding as has been observed in other species. Interestingly, this effect was heightened in the presence of a conspecific. We next asked whether frogs tapped less under conditions when prey were visible, but inaccessible. Finally, we asked whetherD. tinctoriusadjusted tap rate based on substrate characteristics and whether prey capture success was higher when tapping. In addition to confirming an association between tapping and feeding, our work demonstrates modulation of toe tapping based on social context, prey accessibility, and substrate characteristics. Based on our findings, we suggest that tapping could act to induce prey movement and thereby facilitate prey detection and capture by frogs.

Significance Statement

The toe tapping of some amphibians is an intriguing behavior that has attracted attention from researchers and hobbyists, yet the functional role of toe tapping remains poorly understood. Previous studies have noted an association between toe tapping and feeding in other species, and our work does so quantitatively and experimentally in Dyeing poison frogs,Dendrobates tinctorius. We demonstrate that frogs modulate tap rate based on the presence of conspecifics, prey accessibility, and substrate type. We speculate that – alongside other potential functions – toe tapping may act as a vibrational stimulus to facilitate prey detection and capture.