bluuebunny/crossref_metadata_2025 huggingface dataset:
Progressive circuit hyperexcitability in mouse neocortical slice cultures with increasing duration of activity silencing
Authors: Wise Derek L. , Greene Samuel B. , Escobedo-Lozoya Yasmin , Van Hooser Stephen D. , Nelson Sacha B.
Published: July 2023

Forebrain neurons deprived of activity become hyperactive when activity is restored. Rebound activity has been linked to spontaneous seizuresin vivofollowing prolonged activity blockade. Here we measured the time course of rebound activity and the contributing circuit mechanisms using calcium imaging, synaptic staining and whole cell patch clamp in organotypic slice cultures of mouse neocortex. Calcium imaging revealed hypersynchronous activity increasing in intensity with longer periods of deprivation. While activity partially recovered three days after slices were released from five days of deprivation, they were less able to recover after ten days of deprivation. However, even after the longer period of deprivation, activity patterns eventually returned to baseline levels. The degree of deprivation-induced rebound was age-dependent, with the greatest effects occurring when silencing began in the second week. Pharmacological blockade of NMDA receptors indicated that hypersynchronous rebound activity did not require Hebbian plasticity evoked. In single neuron recordings, input resistance roughly doubled with a concomitant increase in intrinsic excitability. Synaptic imaging of pre- and postsynaptic proteins revealed dramatic reductions in the number of presumptive synapses with a larger effect on inhibitory than seen in excitatory synapses. Putative excitatory synapses colocalizing PSD-95 and Bassoon declined by 39% and 56% following five and ten days of deprivation, but presumptive inhibitory synapses colocalizing gephyrin and VGAT declined by 55% and 73% respectively. The results suggest that with prolonged deprivation, a progressive reduction in synapse number is accompanied by a shift in the balance between excitation and inhibition and increased cellular excitability.

SIGNIFICANCE STATEMENT

When cortical activity is silenced during development, lifelong seizures often result. Here we explored whether these seizures result from overcompensation of homeostatic recovery mechanisms. Prior work showed that neurons briefly deprived of the ability to fire action potentials compensate by becoming more excitable, increasing synaptic drive and intrinsic excitability. We found that prolonged silencing of cortex produced a profound loss of synapse density, especially for inhibitory synapses, pointing to a circuit unable to maintain excitatory/inhibitory balance. These results show that homeostatic responses, which are normally restorative, can result in maladaptive circuit configurations when brought to extremes.
Spared nerve injury causes motor phenotypes unrelated to pain in mice
Authors: Norris Makenzie R. , Dunn Samantha S. , Aravamuthan Bhooma R. , McCall Jordan G.
Published: July 2023

Most animal models of neuropathic pain use targeted nerve injuries quantified with motor reflexive measures in response to an applied noxious stimulus. These motor reflexive measures can only accurately represent a pain response if motor function in also intact. The commonly used spared nerve injury (SNI) model, however, damages the tibial and common peroneal nerves that should result in motor phenotypes (i.e., an immobile or “flail” foot) not typically captured in sensory assays. To test the extent of these issues, we used DeepLabCut, a deep learning-based markerless pose estimation tool to quantify spontaneous limb position in C57BL/6J mice during tail suspension following either SNI or sham surgery. Using this granular detail, we identified the expected flail foot-like impairment, but we also found SNI mice hold their injured limb closer to the body midline compared to shams. These phenotypes were not present in the Complete Freunds Adjuvant model of inflammatory pain and were not reversed by multiple analgesics with different mechanisms of action, suggesting these SNI-specific phenotypes are not directly related to pain. Together these results suggest SNI causes previously undescribed phenotypes unrelated to altered sensation that are likely underappreciated while interpreting preclinical pain research outcomes.
Cell Lineage-Guided Microanalytical Mass Spectrometry Reveals Increased Energy Metabolism and Reactive Oxygen Species in the Vertebrate Organizer
Authors: Baxi Aparna B. , Li Jie , Quach Vi M. , Nemes Peter
Published: July 2023

Molecular understanding of the vertebrate Organizer, a tissue center critical for inductive signaling during gastrulation, has so far been limited to transcripts and some proteins due to limitations in detection and sensitivity. The Spemann-Mangold Organizer (SMO) in the South African Clawed Frog (X. laevis), a popular model of development, has long been discovered to induce the patterning of the central nervous system. Molecular screens on the tissue have identified several genes, such as goosecoid, chordin, and noggin, with independent ability to establish a body axis. A comprehensive study of proteins and metabolites produced in the SMO and their functional roles has been lacking. Here, we pioneer a deep discovery proteomic and targeted metabolomic screen of the SMO in comparison to the rest of the embryo using liquid chromatography high-resolution mass spectrometry (HRMS). Quantification of ∼4,600 proteins and a panel of metabolites documented differential expression for ∼450 proteins and multiple intermediates of energy metabolism in the SMO. Upregulation of oxidative phosphorylation (OXPHOS) and redox regulatory proteins gave rise to elevated oxidative stress and an accumulation of reactive oxygen species in the Organizer. Imaging experiments corroborated these findings, discovering enrichment of hydrogen peroxide in the SMO tissue. Chemical perturbation of the redox gradient affected mesoderm involution during early tissue movements of gastrulation. HRMS expands the bioanalytical toolbox of cell and developmental biology, providing previously unavailable information on molecular classes to challenge and refine our classical understanding of the Organizer and its function during early patterning of the embryo.
Mitochondrial-Derived Compartments Remove Surplus Proteins from the Outer Mitochondrial Membrane
Authors: Wilson Zachary N. , Balasubramaniam Sai Sangeetha , Wopat Mitchell , Hughes Adam L.
Published: July 2023

The outer mitochondrial membrane (OMM) creates a boundary that imports most of the mitochondrial proteome while removing extraneous or damaged proteins. How the OMM senses aberrant proteins and remodels to maintain OMM integrity remains unresolved. Previously, we identified a piecemeal autophagic mechanism called themitochondrial-derivedcompartment (MDC) that removes a subset of the mitochondrial proteome. Here we show that MDCs specifically sequester proteins localized only at the OMM, providing an explanation for how select mitochondrial proteins are removed by MDCs. Remarkably, selective sorting into MDCs also occurs within the OMM, as subunits of the translocase of the outer membrane (TOM) complex are excluded from MDCs unless assembly of the TOM complex is impaired. Considering that overloading the OMM with mitochondrial membrane proteins or mistargeted tail-anchored membrane proteins induces MDCs to form and sequester these proteins, we propose that one functional role of MDCs is to create an OMM-enriched trap that segregates and sequesters excess proteins from the mitochondrial surface.

Wilson and colleagues observe that mitochondrial-derived compartments (MDCs) selectively incorporate proteins from only the outer mitochondrial membrane (OMM), and robustly sequester both excess and mistargeted proteins into this OMM-enriched domain, suggesting MDCs act to remove surplus hydrophobic cargo from mitochondria.
Reprogramming method does not impact the neuronal differentiation potential of 16p11.2 deletion patient iPSCs
Authors: Wells Michael F. , Guss Ellen J. , Zhou Hongyan , Sun Bruce , Martinez Hector ,   The NYSCF Global Stem Cell Array Team, Akopian Veronika , Noggle Scott , Paull Daniel , Moore Jennifer , Sheldon Michael , Sommer Julia E. , Benedetti Marta , Meissner Alexander , Eggan Kevin
Published: July 2023

A major impediment to the actualization of the induced pluripotent stem cell (iPSC)-based personalized medicine revolution is the lack of widely accepted standard operating procedures (SOPs) across different groups and institutions. The various methods employed can include choice of starting materials, reprogramming agents, and culture conditions, with each of these factors hypothesized to influence the reprogramming efficiency and transcriptional identity of iPSCs. As such, we systematically compared iPSC reprogramming procedures using cells derived from the somatic cells of three patients with 16p11.2 deletion syndrome (16p11.2del) and found remarkable similarity among the different methods. FACS analysis revealed that regardless of somatic cell type (fibroblast, lymphocyte, erythroblast), route of reprogramming factor introduction (mRNA, Sendai virus, episome), donor sex, or facility (Rutgers, NYSCF), 16p11.2del patient iPSCs were viable as high purity cultures expressing pluripotency marker proteins. This observation was supported at the transcript level by qPCR analysis, which demonstrated the ability for the iPSCs to differentiate into all three embryonic germ cell lineages after 12 days in culture as embryoid bodies. NGN2-mediated differentiation of these iPSCs produced functional neurons that formed active synaptic networks as revealed by multi-electrode array (MEA) recordings. Importantly, no group-wise comparisons among the reprogramming methods yielded consistent statistically significant differences, indicating that these procedures are equally capable of producing pluripotent stem cells that can efficiently differentiate into mature, functional neurons. This work highlights the utility of these reprogramming methods and supports the use of differentially reprogrammed iPSCs for direct comparative studies of human neurodevelopment.
Antimicrobial peptides and other potential biomarkers of critical illness in Sars-CoV-2 patients with acute kidney injury
Authors: dos Santos Lucas Ferreira Theotonio , Barbeiro Hermes Vieira , Barbeiro Denise Frediani , de Souza Heraldo Possolo , Pinheiro da Silva Fabiano
Published: July 2023

Antimicrobial peptides (AMPs) are a complex network of 10-100 amino acid sequence molecules, widely distributed in Nature. Even though more than 300 AMPs have been described in mammals, cathelicidins and defensins remain the most investigated to date.

Some publications examined the role of AMPs in COVID-19, but the findings are preliminary andin vivostudies are still lacking. Here, we report the plasma levels of five AMPs (LL-37, α-defensin 1, α-defensin 3, β-defensin 1 and β-defensin 3) and five cytokines (tumor necrosis factor-α, interleukin-1β, interleukin-6, interleukin-10, interferon-γ and monocyte chemoattractant protein-1), in 15 healthy volunteers, 36 COVID-19 patients without Acute Kidney Injury (AKI) and 17 COVID-19 patients with AKI, since AKI is a well-known marker of worse prognosis in Sars-CoV-2 infections.

We found increased levels of α-defensin 1, α-defensin 3 and β-defensin 3, but not LL-37 or β-defensin 3, in our COVID-19 population, when compared with the healthy controls, in conjunction with higher levels of interleukin-6, interleukin-10, interferon-γ and monocyte chemoattractant protein-1, putting in evidence that these AMPs and cytokines may have an important role in the systemic inflammatory response and tissue damage that characterizes severe COVID-19.

Graphic Abstract
Fronto-parietal network dynamics to understand deficits in attention performance in multiple sclerosis
Authors: Welton Thomas , Meng Dewen , das Nair Roshan , Constantinescu Cris S , Auer Dorothee P , Dineen Rob A
Published: July 2023

Introduction

Impaired attention performance is a significant burden to people with multiple sclerosis (MS). Brain connectivity fluctuates with transitions between cognitive states, so measurement of network dynamics during these conditions may help to understand MS-related attention impairment.

Methods

In people with MS and healthy controls, attention was measured using the Attention Network Test. 3T MRI was used to measure structural connectivity and both static and dynamic functional connectivity in the attention-related fronto-parietal network (FPN) at rest and during an attentionally-demanding task. Groups were compared on connectivity of the FPN during rest and task performance. Relationships between network connectivity and attention performance were tested using linear regression.

Results

The sample comprised 37 people with MS and 23 matched controls. At rest, people with MS had significantly lower structural connectivity (R2=0.13, p=0.004), lower static functional connectivity (R2=0.07, p=0.032) and higher dynamic functional connectivity (R2=0.08, p=0.026) of the FPN. Higher dynamic connectivity was significantly associated with poorer attention performance in people with MS (R2=0.20, p=0.008). During attention-task performance, static functional connectivity was greater in people with MS than controls (R2=0.10, p=0.008). The task-induced reduction in static connectivity (relative to rest) was directly related to attention performance (R2=0.23, p<0.001).

Conclusion

Increased dynamic functional connectivity of the FPN at rest may be a useful indicator of deficits in sustained attention in people with MS. The transition from rest to active-attentive state is accompanied by an increase in dynamic connectivity, and decrease in static connectivity which may be helpful in understanding aetiology and treatment of attention impairment.
Performance of BD Onclarity HPV assay on FLOQSwabs vaginal self-samples
Authors: Martinelli Marianna , Latsuzbaia Ardashel , Bonde Jesper , Pedersen Helle , Iacobone Anna D. , Bottari Fabio , Piana Andrea F. , Pietri Roberto , Cocuzza Clementina E. , Arbyn Marc ,   Extended Valhudes Study Group
Published: July 2023

This study assessed the accuracy of hrHPV testing of BD Onclarity™ HPV (Onclarity) assay on vaginal self-collected FLOQSwab® versus cervical samples to ensure similar accuracy to detect cervical intraepithelial neoplasia. Testing was performed on two automated platforms, BD Viper™ and BD COR™, to evaluate the effect of machine and using two vaginal self-samples to analyse the influence of collection, transport, and freezing-unfreezing on the results.

A cervical sample and two self-samples were collected from 300 women. The first collected vaginal and the cervical sample were tested on BD Viper™ and the second swab was frozen and subsequently tested on both automated systems. Test results on vaginal and cervical specimens were considered the index and comparator, respectively; colposcopy and histology were reference standards.

Relative sensitivity for ≥CIN2 on vaginal samples analysed using the three different workflows vs the cervical sample was 1.01 (0.97-1.06), 1.01 (0.97-1.06), and 1.00 (0.95-1.05), respectively.

Relative specificity resulted 0.83 (0.73-0.94), 0.76 (0.67-0.87) and 0.82 (0.73-0.92) for the 1st, 2nd self-collected sample tested on BD VIPER™ and 2nd self-collected sample tested on BD COR™.

Cut-off optimization for HPV positivity defined at Ct ≤38.3 for HPV16, ≤34.2 for HPV18 and ≤31.5 for all other types showed an increased relative specificity with similar sensitivity. No significant difference was observed between self-samples tested with the two platforms and between first and second-collected swabs.

Onclarity assay on FLOQSwab®using both platforms showed similar sensitivity but lower specificity to detect ≥CIN2 compared to cervical samples. By cut-off optimization, non-inferior specificity could be reached.
A systems-level analysis of the mutually antagonistic roles of RKIP and BACH1 in dynamics of cancer cell plasticity
Authors: Shyam Sai , Soundharya R , Sehgal Manas , Jolly Mohit Kumar
Published: July 2023

Phenotypic plasticity is a hallmark of cancer metastasis. Epithelial-mesenchymal transition (EMT) is an important axis of phenotypic plasticity. Raf kinase-B inhibitor protein (RKIP) and BTB and CNC homology 1 (BACH1) are two proteins reported to influence EMT. In breast cancer, they act antagonistically, but the exact nature of their roles in mediating EMT and associated other axes of plasticity remains unclear. Here, analysing transcriptomic data, we reveal their antagonistic trends in a pan-cancer manner, in terms of association with EMT, metabolic reprogramming and immune evasion via PD-L1. Next, we developed and simulated a mechanism-based gene regulatory network that captures how RKIP and BACH1 engage in feedback loops with drivers of EMT and stemness. We found that RKIP and BACH1 belong to two separate “teams” of players – while BACH1 belonged to the one that drove pro-EMT, stem-like and therapy-resistant cell-states, RKIP is a member of a team that enables pro-epithelial, less stem-like and therapy-sensitive phenotypes. Finally, we observed that low RKIP levels and concomitant upregulated BACH1 levels associated with worse clinical outcomes in many cancer types. Together, our systems-level analysis indicates that the emergent dynamics of underlying regulatory network underlie the antagonistic patterns of RKIP and BACH1 with various axes of cancer cell plasticity, as well as with patient survival data.
The Use of Fluid-phase 3D Printing to Pattern Alginate-gelatin Hydrogel Properties to Guide Cell Growth and BehaviourIn Vitro
Authors: Andrea Souza , Kevin McCarthy , Brian J. Rodriguez , Emmanuel G Reynaud
Published: July 2023

3D (bio)printing technology has boosted the advancement of the biomedical field. However, tissue engineering is in its infancy and (bio)printing biomimetic constructions for tissue formationin vitrois still a default. As a new methodology to improvein vitrostudies, we suggest the use of a cross-linkable aqueous support bath to pattern the characteristics of the scaffolds during the 3D printing process. Using fluid-phase, different molecules can be added to specific locations of the substrate promoting cell behaviour guidance and compartmentalization. Moreover, mechanical aspects can be customized by changing the type or concentration of the solution in which the (bio)printing is acquired. In this study, we first assessed different formulations of alginate/gelatin to improve cell colonization in our printings. On formulations with lower gelatin content, the U2OS cells increased 2.83 times the cell growth. In addition, the alginate-gelatin hydrogel presented a good printability in both air and fluid-phase, however the fluid-phase printings showed better printing fidelity as it diminished the collapsing and the spreading of the hydrogel strand. Next, the fluid-phase methodology was used to guide cell colonization in our printings. First, different stiffness were created by crosslinking the hydrogel with different concentrations of CaCl2during the printing process. As a result, the U2OS cells were compartmentalized on the stiffer parts of the printings. In addition, using fluid-phase to add RGD molecules to specific parts of the hydrogel has also promoted guidance on cell growth. Finally, our results showed that by combining stiffer alginate-gelatin hydrogel with RGD increasing concentrations we can create a synergetic effect and boost cell growth by up to 3.17-fold. This work presents a new printing process for tailoring multiple parameters in hydrogel substrates by using fluid-phase to generate a more faithful replication of thein vivoenvironment.
Drosophila Amus and Bin3 methylases functionally replace mammalian MePCE for capping and the stabilization of U6 and 7SK snRNAs
Authors: Peng Qiu , Wang Yiqing , Xiao Ying , Chang Hua , Luo Shishi , Wang Danling , Rong Yikang S.
Published: July 2023

U6 and 7SK snRNAs process a 5’ cap, believed to be essential for their stability and maintained by mammalian MePCE or Drosophila Bin3 enzymes. Although loss of either protein results in 7SK instability, loss of neither is associated with U6 reduction. Their yeast homolog is also not required for U6 stability, casting further doubts on the function of capping U6. Here we show that the Drosophila Amus protein, homologous to both Bin3 and MePCE, is essential for U6 but not 7SK stability. A full function of Amus is required for Drosophila development, and that rests primarily on Amus’s methylase activity. Remarkably, the loss of U6 is rescued by the expression of an Amus-MePCE hybrid protein harboring the methyltransferase domain from MePCE, highlighting the conserved function of the two proteins as the U6 capping enzyme. Our new investigations in human cells establish a dependence of both U6 and 7SK stability on MePCE, resolving a long-standing uncertainty. While uncovering an interesting division of labor of Bin3/MePCE/Amus proteins, we discovered a “Bin3-Box” domain present only in enzymes associated with 7SK regulation. Targeted mutagenesis in Drosophila confirmed its importance for Bin3 function, revealing a possible conserved element in 7SK but not U6 biology.
Multivalent dynamic colocalization of avian influenza polymerase and nucleoprotein by intrinsically disordered ANP32A reveals the molecular basis of human adaptation
Authors: Camacho-Zarco Aldo R. , Yu Lefan , Krischuns Tim , Dedeoglu Selin , Maurin Damien , Bouvignies Guillaume , Crépin Thibaut , Ruigrok Rob W.H. , Cusack Stephan , Naffakh Nadia , Blackledge Martin
Published: July 2023

Adaptation of avian influenza RNA polymerase (FluPol) to human cells requires mutations on the 627-NLS domains of the PB2 subunit. The E627K adaptive mutation compensates a 33-amino-acid deletion in the acidic intrinsically disordered domain of the host transcription regulator ANP32A, a deletion that restricts FluPol activity in mammalian cells. The function of ANP32A in the replication transcription complex and in particular its role in host restriction remain poorly understood. Here we characterise ternary complexes formed between ANP32A, FluPol and the viral nucleoprotein, NP, supporting the putative role of ANP32A in shuttling NP to the replicase complex. We demonstrate that while FluPol and NP can simultaneously bind distinct linear motifs on avian ANP32A, the deletion in the shorter human ANP32A blocks this mode of colocalization. NMR reveals that NP and human-adapted Pol, containing the E627K mutation, simultaneously bind the identical extended linear motif on human ANP32A, in an electrostatically driven, highly dynamic and multivalent ternary complex. This study reveals a probable molecular mechanism underlying host adaptation, whereby E627K, which enhances the basic surface of the 627 domain, is selected to confer the necessary multivalent properties to allow ANP32A to colocalize NP and FluPol in human cells.
Grand Biological Universe: Genome space geometry unravels looking for a single metric is likely to be futile in evolution
Authors: Sun Nan , Yu Hongyu , Ren Ruohan , Zhou Tao , Guan Mengcen , Zhao Leqi , Yau Stephen S.-T.
Published: July 2023

Understanding the differences between genomic sequences of different lives is crucial for biological classification and phylogeny. Here, we downloaded all the reliable sequences of the seven kingdoms and determined the dimensions of the genome space embedded in the Euclidean space, along with the corresponding Natural Metrics. The concept of the Grand Biological Universe is further proposed. In the grand universe, the convex hulls formed by the universes of seven kingdoms are mutually disjoint, and the convex hulls formed by different biological groups within each kingdom are mutually disjoint. This study provides a novel geometric perspective for studying molecular biology and also offers an accurate way for large-scale sequence comparison in a real-time manner. Most importantly, this study shows that, due to the space-time distortion in the biological genome space similar to Einstein’s theory, it is futile to look for a single metric to measure different biological universes, as previous studies have done.
ZEB1 shapes AML immunological niches suppressing CD8 T-cell activity while fostering Th17 cell expansion
Authors: Bassani Barbara , Simonetti Giorgia , Cancila Valeria , Ciciarello Marilena , Piva Annamaria , Chiodoni Claudia , Lecis Daniele , Gulino Alessandro , Fonzi Eugenio , Botti Laura , Portararo Paola , Costanza Massimo , Schwaller Juerg , Tzankov Alexandar , Ponzoni Maurilio , Ciceri Fabio , Bolli Niccolò , Curti Antonio , Tripodo Claudio , Colombo Mario P. , Sangaletti Sabina
Published: July 2023

Acute myeloid leukemia (AML) development and progression is favored by immune suppression directly triggered by leukemia cells. ZEB1 is a key transcription factor in epithelial-to-mesenchymal transition which, we show here, is capable immune regulation in AML. Leukemic cells which had ZEB1 knocked down have reduced engraftment and extramedullary disease when transplanted into immune competent mice due to concomitant activation of CD8 T lymphocytes and reduced expansion of Th17 cells. Differently, in ZEB1 competent AML, IL-17 sustains the development of a pro-invasive and self-maintaining loop inducingMMPsandSOCS2.In humans, AML patients show,in situon bone marrow biopsies, a direct correlation between ZEB1 and Th17 and, in gene expression profile when divided according to the median value ofZEB1expression, a different overall survival and relapse along with the expression of MMPs, SOCS2 and Th17 cells enrichment. Overall, our data shed new light into the role of ZEB1 in AML that entwines both pro-tumoral and immune regulatory capacity in AML blasts.
Epigenetic variation causes heritable variation in complex traits in the molluskBiomphalaria glabrata, vector of the human parasiteSchistosoma mansoni
Authors: Luviano Nelia , Lopez Marie , Gawehns Fleur , Haegeman Bart , Mouginot Pierick , Chaparro Cristian , Arimondo Paola B. , Pujol Benoit , Pouzol Damien , Cosseau Céline , Grunau Christoph
Published: July 2023

DNA methylation variation may play a role in phenotypic variation as it can be directly affected by the environment and be inherited. DNA methylation variations were introduced into the parasite vector snailBiomphalaria glabratawith low genetic diversity by chemical treatment in F0 and followed over 3 generations using epigenetic recombinant inbred lines (epiRILs). We observed phenotypic variation in complex traits such as fecundity and susceptibility to infestation bySchistosoma mansoniand DNA methylation differences in F3. Both, increase and decrease of infestation success (up to 100% and down to 20% prevalence in epiRILs and from 86% to 94% in control RILs) indicated variation in complex resistance/compatibility trait. Average prevalence in control RILs was 84±5% but only 68±21 % in epiRILs. Fecundity also changed and was in average 47±7% in control RILs and 59±18% in epiRILs, being 12% higher in epiRILs. We found that the heritabilityh2of the fecundity in the epiRILs was between 0.5 and 0.6 depending on the method used to estimate it. We developed a model for introducing epimutant offspring snails into resident susceptible populations. If genetic assimilation of the resistant phenotype occured in a small fraction of the introduced epimutant snails, we predict that the susceptible phenotype is replaced by the resistant phenotype after 50-70 generations.
Single-cell T cell receptor sequencing of paired tissue and blood samples reveals clonal expansion of CD8+ effector T cells in patients with calcific aortic valve disease
Authors: Bartoli-Leonard Francesca , Chelvanambi Sarvesh , Pham Tan , Turner Mandy E , Blaser Mark C , Caputo Massimo , Aikawa Masanori , Pang Amanda , Muehlschlegel Jochen , Aikawa Elena
Published: July 2023

Calcific aortic valve disease (CAVD) is a complex cardiovascular pathology, culminating in aortic stenosis, heart failure and premature mortality, with no comprehensive treatment strategy, except valve replacement. While T cells have been identified within the valve, their contribution to pathogenesis remains unclear. To elucidate the heterogenous phenotype of the immune populations present within patients with CAVD, deep phenotypic screens of paired valve and peripheral blood cells were conducted via flow cytometry (n=20) and immunohistochemistry (n=10). Following identification of a significant population of memory T cells; specifically, CD8+ T cells within the valve, single cell RNA sequencing and paired single T cell receptor sequencing was conducted on a further 4 patients on CD45+ CD3+, CD4+ or CD8+ T cells. Through unsupervised clustering, 7 T cell populations were identified within the blood and 10 identified within the valve. Tissue resident memory (TRM) T cells were detected for the first time within the valve, exhibiting a highly cytotoxic, activated, and terminally differentiated phenotype. This pan-pro-inflammatory signal was differentially identified in T cells originating from the valve, and not observed in the blood, indicative of an adaptive, local not-systemic inflammatory signature in CAVD patients. T cell receptor analysis identified hyperexpanded clones within the CD8+ T cell central memory (TCM) population, with TRMcells comprising the majority of large and medium clonal expansion within the entire T cell population. Clonal interaction network analysis demonstrated the greatest proportion of clones originating from CD8+ T cell effector memory (TEM) and CD4+ naïve / TCMpopulations and ending in the CD8+ TRMand CD8+ TCMclusters, suggesting a clonal expansion and predicted trajectory of T cells towards a tissue resident, cytotoxic environment within the valve. CDR3 epitope predictive analysis identified 7 potential epitope targets, of whichGALNT4andCR1Lhave previously been implicated in a cardiovascular context as mediators of inflammation. Taken together, the data identified T cell sub-populations within the context of CAVD and further predicted possible epitopes responsible for the clonal expansion of the valvular T cells, which may be important for propagating inflammation in CAVD.
From enhancers to genome conformation: complex transcriptional control underlies expression of a single herpesviral gene
Authors: Morgens David W , Gulyas Leah , Rivera-Madera Alejandro , Souza Annabelle S , Glaunsinger Britt A
Published: July 2023

Complex transcriptional control is a conserved feature of both eukaryotes and the viruses that infect them. Here, we illustrate this by combining high-density functional genomics, expression profiling, and viral-specific chromosome conformation capture to define with unprecedented detail the transcriptional regulation of a single gene, ORF68, from Kaposi’s sarcoma-associated herpesvirus (KSHV). We first identified seven cis-regulatory regions by densely tiling the ∼154 kb KSHV genome with CRISPRi. A parallel Cas9 nuclease screen indicated that three of these regions act as promoters of genes that regulate ORF68. RNA expression profiling demonstrated that three more of these regions act by either repressing or enhancing other distal viral genes involved in ORF68 transcriptional regulation. Finally, we tracked how the 3D structure of the viral genome changes during its lifecycle, revealing that these enhancing regulatory elements are physically closer to their targets when active, and that disrupting some elements caused large- scale changes to the 3D genome. These data enable us to construct a complete model revealing that the mechanistic diversity of this essential regulatory circuit matches that of human genes.
The Role of Phylogenetic Structure on Canidae Lineage Distribution and Trait Variation across the Globe
Authors:   Geographical patterns of Canidae phylogenetic information, Porto Lucas Marafina Vieira , Machado Arielli Fabricio
Published: July 2023

Aim

Understanding the spatial structuring of ecological communities requires us to consider the interplay between evolutionary history and environmental factors. In this study, we investigated the influence of Canidae phylogenetic structure on the distribution and trait patterns of lineages across the planet.

Location

Americas, Africa, Eurasia.

Time period

12 million years ago – present.

Major taxa studied

Canidae.

Methods

Using distribution data and phylogenetic information for 37 Canidae species, we employed phylogenetic fuzzy-weighting to compare assemblages based on their phylogenetic similarity.

Results

Our results revealed distinct global patterns of body size, body mass, range size, habitat type, and evolutionary distinctiveness among lineages. We also identified the shared contributions of phylogenetic structure and temperature to trait variation using variance partitioning analysis. The PCPS axes highlighted the influence of phylogenetic relationships on Canidae assemblages, particularly in South America.

Main conclusions

Notably, the study challenges the applicability of Bergmann’s and Rapoport’s rules in explaining canids’ sizes and range sizes geographic variation across continents, emphasizing the importance of phylogenetic information. The unique diversification history of Canidae in South America and Africa and their diverse environmental conditions likely contribute to the observed trait patterns that make both continents so distinguished when compared to N. America and Eurasia. Our findings underscore the need to incorporate phylogenetic information in models assessing trait variation across geographic scales for unbiased estimations.
Conserved and repetitive motifs in an intrinsically disordered protein drive α-carboxysome assembly
Authors: Turnšek Julia B. , Oltrogge Luke M. , Savage David F.
Published: July 2023

All photosynthetic bacteria and some chemoautotrophic bacteria fix CO2into sugars in specialized proteinaceous compartments called carboxysomes. Carboxysomes enclose the enzymes Rubisco and carbonic anhydrase inside a layer of shell proteins to increase the CO2concentration for efficient carbon fixation by Rubisco. In the α-carboxysome lineage, a disordered and highly repetitive protein named CsoS2 is essential for carboxysome formation and function. Without it, the bacteria are unable to fix enough carbon to grow in air. How a protein lacking structure serves as the architectural scaffold for such a vital cellular compartment remains unknown. In this study, we identify key residues in CsoS2 that are necessary for building functional α-carboxysomesin vivo. These highly conserved and repetitive residues, VTG and Y, contribute to the interaction between CsoS2 and shell proteins. We also demonstratein vitroreconstitution of the α-carboxysome into spherical condensates with CsoS2, Rubisco, and shell proteins, and show the utility of reconstitution as a biochemical tool to study carboxysome biogenesis. The precise self-assembly of thousands of proteins is crucial for carboxysome formation, and understanding this process could enable their use in alternative biological hosts or industrial processes as effective tools to fix carbon.
The Fraser complex interconnects tissue layers to support basal epidermis and osteoblast integrated morphogenesis underlying fin skeletal patterning
Authors: Robbins Amy E. , Horst Samuel G. , Lewis Victor M. , Stewart Scott , Stankunas Kryn
Published: July 2023

Fraser Syndrome is a rare, multisystemic autosomal recessive disorder characterized by disrupted epithelial-mesenchymal associations upon loss of Fraser Complex genes. Disease manifestation and affected organs are highly variable. Digit malformations such as syndactyly are common but of unclear developmental origins. We explored if zebrafishfraser extracellular matrix complex subunit 1 (fras1)mutants model Fraser Syndrome-associated appendicular skeleton patterning defects. Approximately 10% offras1mutants survive to adulthood, displaying striking and varied fin abnormalities, including endochondral bone fusions, ectopic cartilage, and disrupted caudal fin symmetry. The fins of survivingfras1mutants frequently have fewer and unbranched bony rays.fras1mutant fins regenerate to their original size but with exacerbated ray branching and fin symmetry defects. Single cell RNA-Seq analysis,in situhybridizations, and antibody staining show specific Fraser complex expression in the basal epidermis during regenerative outgrowth. Fras1 and Fraser Complex component Frem2 accumulate along the basal side of distal-most basal epidermal cells. Greatly reduced and mislocalized Frem2 accompanies loss of Fras1 infras1mutants. The Sonic hedgehog signaling between distal basal epidermis and adjacent mesenchymal pre-osteoblasts that promotes ray branching persists upon Fraser Complex loss. However,fras1mutant regenerating fins exhibit extensive sub-epidermal blistering associated with a disorganized basal epidermis and adjacent pre-osteoblasts. We propose Fraser Complex-supported tissue layer adhesion enables robust integrated tissue morphogenesis involving the basal epidermis and osteoblasts. Further, we establish zebrafish fin development and regeneration as an accessible model to explore mechanisms of Fraser Syndrome-associated digit defects and Fraser Complex function at epithelial-mesenchymal interfaces.
Multi-Omic Graph Diagnosis (MOGDx) : A data integration tool to perform classification tasks for heterogeneous diseases
Authors: Ryan Barry , Marioni Riccardo E. , Simpson T. Ian
Published: July 2023

Heterogeneity in human diseases presents challenges in diagnosis and treatments due to the broad range of manifestations and symptoms. With the rapid development of labelled multi-omic data, integrative machine learning methods have achieved breakthroughs in treatments by redefining these diseases at a more granular level. These approaches often have limitations in scalability, oversimplification, and handling of missing data. In this study, we introduce Multi-Omic Graph Diagnosis (MOGDx), a flexible command line tool for the integration of multi-omic data to perform classification tasks for heterogeneous diseases. MOGDx is a network integrative method that combines patient similarity networks with a reduced vector representation of genomic data. The reduced vector is derived from the shared latent embedding of a multi-modal encoder and the combined network is fed into a graph convolutional network for classification. The multi-modal encoder and graph convolutional network are trained simultaneously making a fully supervised pipeline. MOGDx was evaluated on three datasets from the cancer genome atlas for breast invasive carcinoma, kidney cancer, and low grade glioma. MOGDx demonstrated state-of-the-art performance and an ability to identify relevant multi-omic markers in each task. It did so while integrating more genomic measures with greater patient coverage compared to other network integrative methods. MOGDx is available to download fromhttps://github.com/biomedicalinformaticsgroup/MOGDx. Overall, MOGDx is a promising tool for integrating multi-omic data, classifying heterogeneous diseases, and interpreting genomic markers.
Performance of ChatGPT on Chinese National Medical Licensing Examinations: A Five-Year Examination Evaluation Study for Physicians, Pharmacists and Nurses
Authors: Zong Hui , Li Jiakun , Wu Erman , Wu Rongrong , Lu Junyu , Shen Bairong
Published: July 2023

Background

Large language models like ChatGPT have revolutionized the field of natural language processing with their capability to comprehend and generate textual content, showing great potential to play a role in medical education.

Objective

This study aimed to quantitatively evaluate and comprehensively analysis the performance of ChatGPT on three types of national medical examinations in China, including National Medical Licensing Examination (NMLE), National Pharmacist Licensing Examination (NPLE), and National Nurse Licensing Examination (NNLE).

Methods

We collected questions from Chinese NLMLE, NPLE and NNLE from year 2017 to 2021. In NMLE and NPLE, each exam consists of 4 units, while in NNLE, each exam consists of 2 units. The questions with figures, tables or chemical structure were manually identified and excluded by clinician. We applied direct instruction strategy via multiple prompts to force ChatGPT to generate the clear answer with the capability to distinguish between single-choice and multiple-choice questions.

Results

ChatGPT failed to pass the threshold score (0.6) in any of the three types of examinations over the five years. Specifically, in the NMLE, the highest recorded score was 0.5467, which was attained in both 2018 and 2021. In the NPLE, the highest score was 0.5599 in 2017. In the NNLE, the most impressive result was shown in 2017, with a score of 0.5897, which is also the highest score in our entire evaluation. ChatGPT’s performance showed no significant difference in different units, but significant difference in different question types. ChatGPT performed well in a range of subject areas, including clinical epidemiology, human parasitology, and dermatology, as well as in various medical topics such as molecules, health management and prevention, diagnosis and screening.

Conclusions

These results indicate ChatGPT failed the NMLE, NPLE and NNLE in China, spanning from year 2017 to 2021. but show great potential of large language models in medical education. In the future high-quality medical data will be required to improve the performance.
Calcium and Integrin-binding protein 2 (CIB2) controls force sensitivity of the mechanotransducer channels in cochlear outer hair cells
Authors: Aristizábal-Ramírez Isabel , Dragich Abigail K. , Giese Arnaud P.J. , Sofia Zuluaga-Osorio K. , Watkins Julie , Davies Garett K. , Hadi Shadan E. , Riazuddin Saima , Vander Kooi Craig W. , Ahmed Zubair M. , Frolenkov Gregory I.
Published: July 2023

Calcium and Integrin-Binding Protein 2 (CIB2) is an essential subunit of the mechano-electrical transduction (MET) complex in mammalian auditory hair cells. CIB2 binds to pore-forming subunits of the MET channel, TMC1/2 and is required for their transport and/or retention at the tips of mechanosensory stereocilia. Since genetic ablation of CIB2 results in complete loss of MET currents, the exact role of CIB2 in the MET complex remains elusive. Here, we generated a new mouse strain with deafness-causing p.R186W mutation inCib2and recorded small but still measurable MET currents in the cochlear outer hair cells. We found that R186W variant causes increase of the resting open probability of MET channels, steeper MET current dependence on hair bundle deflection (I-X curve), loss of fast adaptation, and increased leftward shifts of I-X curves upon hair cell depolarization. Combined with AlphaFold2 prediction that R186W disrupts one of the multiple interacting sites between CIB2 and TMC1/2, our data suggest that CIB2 mechanically constraints TMC1/2 conformations to ensure proper force sensitivity and dynamic range of the MET channels. Using a custom piezo-driven stiff probe deflecting the hair bundles in less than 10 µs, we also found that R186W variant slows down the activation of MET channels. This phenomenon, however, is unlikely to be due to direct effect on MET channels, since we also observed R186W-evoked disruption of the electron-dense material at the tips of mechanotransducing stereocilia and the loss of membrane-shaping BAIAP2L2 protein from the same location. We concluded that R186W variant of CIB2 disrupts force sensitivity of the MET channels and force transmission to these channels.
Spatial organization and function of RNA molecules within phase-separated condensates are controlled by Dnd1
Authors: Westerich Kim Joana , Tarbashevich Katsiaryna , Schick Jan , Gupta Antra , Zhu Mingzhao , Hull Kenneth , Romo Daniel , Zeuschner Dagmar , Goudarzi Mohammad , Gross-Thebing Theresa , Raz Erez
Published: July 2023

Germ granules, condensates of phase-separated RNA and protein, are organelles essential for germline development in different organisms The patterning of the granules and its relevance for germ cell fate are not fully understood. Combining three-dimensionalin vivostructural and functional analyses, we study the dynamic spatial organization of molecules within zebrafish germ granules. We find that localization of RNA molecules to the periphery of the granules, where ribosomes are localized depends on translational activity at this location. In addition, we find that the vertebrate-specific Dead end (Dnd1) protein is essential fornanos3RNA localization at the condensates’ periphery. Accordingly, in the absence of Dnd1, or when translation is inhibited,nanos3RNA translocates into the granule interior, away from the ribosomes, a process that is correlated with loss of germ cell fate. These findings highlight the relevance of sub-granule compartmentalization for posttranscriptional control, and its importance for preserving germ cell totipotency.
Introduction to Python Dynamic Diffraction Toolkit (PyDDT): structural refinement of single crystals via X-ray phase measurements
Authors: Penacchio Rafaela F. S. , Estradiote Maurício B. , Remédios Cláudio M. R. , Calligaris Guilherme A. , Torikachvili Milton S. , Kycia Stefan W. , Morelhão Sérgio L.
Published: July 2023

PyDDT is a free Python package of computer codes for exploiting X-ray dynamic multiple diffraction in single crystals. A wide range of tools are available for evaluating the usefulness of the method, planning feasible experiments, extracting phase information from experimental data and further improving model structures of known materials. Graphical tools are also useful in analytical methodologies related to the three-dimensional aspect of multiple diffraction. For general X-ray users, the PyDDT tutorials provide the insight needed to understand the principles of phase measurements and other related methodologies. Key points behind structure refinement using the current approach are presented, and the main features of PyDDT are illustrated for amino acid and filled skutterudite single crystals.
Low-dimensional compounds containing bioactive ligands. XXII. First crystal structure, cytotoxic activity and DNA and HSA binding of a zirconium(IV) complex with 8-hydroxyquinoline-2-carboxylic acid
Authors: Harmošová Michaela , Vilková Mária , Kello Martin , Smolko Lukáš , Samol'ová Erika , Šebová Dominika , Potočňák Ivan
Published: July 2023

A new zirconium(IV) complex, diaquabis(8-hydroxyquinoline-2-carboxylato-κ3
N,O
2,O
8)zirconium(IV) dimethylformamide disolvate, [Zr(C10H5NO3)2(H2O)2]·2C3H7NO or [Zr(QCa)2(H2O)2]·2DMF (1) (HQCaH is 8-hydroxyquinoline-2-carboxylic acid and DMF is dimethylformamide), was prepared and characterized by elemental analysis, IR spectroscopy and single-crystal X-ray structure analysis. Complex 1 is a mononuclear complex in which the ZrIV atoms sit on the twofold axis and they are octacoordinated by two N and six O atoms of two tridentate anionic QCa2− ligands, and two aqua ligands. Outside the coordination sphere are two DMF molecules bound to the complex unit by hydrogen bonds. The structure and stability of complex 1 in dimethyl sulfoxide were verified by NMR spectroscopy. The cytotoxic properties of 1 and HQCaH were studied in vitro against eight cancer cell lines, and their selectivity was tested on the BJ-5ta noncancerous cell line. Both the complex and HQCaH exhibited low activity, with IC50 > 200 µM. DNA and human serum albumin (HSA) binding studies showed that 1 binds to calf thymus (CT) DNA via intercalation and is able to bind to the tryptophan binding site of HSA (Trp-214).
Crystal structure and luminescence spectrum of a one-dimensional nickel(II) coordination polymer incorporating 1,4-bis[(2-methylimidazol-1-yl)methyl]benzene and adamantane-1,3-dicarboxylate co-ligands
Authors: Zhang Yong , Qin Hongni , Wu Bing
Published: July 2023

An NiII coordination polymer, namely, poly[(μ2-adamantane-1,3-dicarboxylato-κ4
O
1,O
1′:O
3,O
3′)[μ2-1,4-bis(2-methyl-imidazol-1-ylmethyl)benzene-κ2
N
3:N
3′]nickel(II)], [Ni(C12H14O4)(C16H18N4)]
n
or [Ni(adc)(bmib)]
n
, (I) [adc = adamantane-1,3-dicarboxylate, C12H14O4
2– and bmib = 1,4-bis(2-methyl-imidazol-1-ylmethyl)benzene, C16H18N4] was synthesized and characterized. It exhibits a one-dimensional extended structure built up from alternating [Ni2(bmib)2] 26-membered rings and [Ni2(adc)2] 16-membered rings. The nickel atom lies on a crystallographic twofold axis and both ligands are completed by mirror symmetry. The solid-state luminescence spectra of (I) and the bmib ligand show strong emissions at 442 and 410 nm, respectively.