bluuebunny/crossref_metadata_2025 huggingface dataset:
Oblique Line Scan Illumination Enables Expansive, Accurate and Sensitive Single Protein Measurements in Solution and in Living Cells
Authors: Driouchi Amine , Bretan Mason , Davis Brynmor J. , Heckert Alec , Seeger Markus , Bradley Silva Maité , Forrest William SR. , Hsiung Jessica , Tan Jiongyi , Yang Hongli , McSwiggen David T. , Song Linda , Sule Askhay , Abaie Behnam , Conroy Brianna , Elliott Liam A. , Gonzalez Eric , Ilkov Fedor , Isaacs Joshua , Labaria George , Lagana Michelle , Larsen Delaine D. , Margolin Brian , Nguyen Mai K. , Rine Jeremy , Tang Yangzhong , Vana Martin , Wilkey Andrew , Zhang Zhengjian , Basham Stephen , Ho Jaclyn J. , Johnson Stephanie , Klammer Aaron A. , Lin Kevin , Darzacq Xavier , Betzig Eric , Berman Russell T. , Anderson Daniel J.
Published: December 2023

Single-molecule localization microscopy (SMLM) techniques, such as single-molecule tracking (SMT), enablein situmeasurements in cells from which data-rich metrics can be extracted. SMT has been successfully applied to a variety of biological questions and model systems, aiming to unravel the spatiotemporal regulation of molecular mechanisms that govern protein function, downstream pathway effects, and cellular function. While powerful, SMLM often suffers from low throughput and illumination inhomogeneity, along with microscope and user-induced technical biases. Due to technical limitations in scaling SMLM techniques, a tradeoff between spatiotemporal resolution and throughput has been made historically, restricting broad application of these technologies. Here we address these limitations using Oblique Line Scan (OLS), a robust single-objective light-sheet based illumination and detection modality that achieves nanoscale spatial resolution and sub-millisecond temporal resolution across a 250 × 190 μm field of view. We demonstrate OLS-enabled SMT on Halo-Tagged proteins in living cells capturing protein motion up to 14 μm2/s. By exploiting the adaptability of the acquisition frame rate and the improved rejection of out of focus light, we extend the utility of OLS beyond cellular compartments with in-solution SMT (isSMT) for single-molecule measurement of ligand-protein interactions and disruption of protein-protein interactions (PPI). We illustrate the versatility of OLS by showcasing two-color SMT, STORM, and single molecule fluorescence recovery after photobleaching (FRAP). OLS expands the range of SMLM applications and paves the way for robust, high-throughput single-molecule investigations of protein dynamics required for drug screening and systems biology studies, both in cells and in solution.
Cytosolic acetyl-CoA synthetase (ACSS2) does not generate butyryl- and crotonyl-CoA
Authors: Zeaiter Nour , Belot Laura , Cunin Valérie , Nahed Roland Abi , Tokarska-Schlattner Malgorzata , Le Gouellec Audrey , Petosa Carlo , Khochbin Saadi , Schlattner Uwe
Published: December 2023

Acetyl and other acyl groups from different short-chain fatty acids (SCFA) competitively modify histones at various lysine sites. To fully understand the functional significance of such histone acylation, a key epigenetic mechanism, it is crucial to characterize the cellular sources of the corresponding acyl-CoA molecules required for the lysine modification. Like acetate, SCFAs such as propionate, butyrate and crotonate are thought to be the substrates used to generate the corresponding acyl-CoAs by enzymes known as acyl-CoA synthetases. The acetyl-CoA synthetase, ACSS2, which produces acetyl-CoA from acetate in the nucleocytoplasmic compartment, has been proposed to also mediate the synthesis of acyl-CoAs such as butyryl- and crotonyl-CoA from the corresponding SCFAs. This idea is now widely accepted and is sparking new research projects. However, based on our directin vitroexperiments with purified or recombinant enzymes and structural considerations, we demonstrate that ACSS2 is unable to mediate the generation of non-acetyl acyl-CoAs like butyryl- and crotonyl-CoA. It is therefore essential to re-examine published data and corresponding discussions in the light of this new finding.
Anhedonia severity mediates the relationship between attentional networks recruitment and emotional blunting during music listening
Authors: Cahart Marie-Stephanie , Giampietro Vincent , Naysmith Laura , Zelaya Fernando , Williams Steven , O’Daly Owen
Published: December 2023

Recent studies have reported atypical emotional processing in individuals with greater levels of anhedonic depressive symptoms. However, the relationship between brain networks dynamics and moment-to-moment affective responses to naturalistic paradigms, as emotions are unfolding, remains unclear. In this study, we used the unique temporal characteristics of music to investigate behavioural and brain network dynamics as a function of anhedonic depressive symptoms severity in healthy adults during an emotionally provocative music listening task. Thirty-one neurotypical participants aged 18-30 years were required to continuously rate happy, neutral and sad pieces of music whilst undergoing MRI scanning. They were also asked to fill in questionnaires assessing their levels of anhedonic depressive symptoms. Using a novel fMRI analysis method called Leading Eigenvector Dynamics Analysis (LEiDA), we found an increased probability of occurrence of attentional networks and a blunted emotional response to both happy and sad pieces of music in participants with greater levels of anhedonic depressive symptoms. More specifically, anhedonic depressive symptoms mediated the relationship between attentional networks recruitment and emotional blunting. Furthermore, the elevated recruitment of attentional networks during emotional pieces of music carried over into subsequent neutral music. Future studies are needed to investigate whether these findings could be generalised to a clinical population (i.e., Major Depressive Disorder).
Rab3 mediates cyclic AMP-dependent presynaptic plasticity and olfactory learning
Authors: Sachidanandan Divya , Aravamudhan Aishwarya , Mrestani Achmed , Nerlich Jana , Lamberty Marius , Hasenauer Natalie , Ehmann Nadine , Pauls Dennis , Seubert Teresa , Maiellaro Isabella , Selcho Mareike , Heckmann Manfred , Hallermann Stefan , Kittel Robert J.
Published: December 2023

Presynaptic forms of plasticity occur throughout the nervous system and play an important role in learning and memory but the underlying molecular mechanisms are insufficiently understood. Here we show that the small GTPase Rab3 is a key mediator of cyclic AMP (cAMP)-induced presynaptic plasticity inDrosophila. Pharmacological and optogenetic cAMP production triggered concentration-dependent alterations of synaptic transmission, including potentiation and depression of evoked neurotransmitter release, as well as strongly facilitated spontaneous release. These changes correlated with a nanoscopic rearrangement of the active zone protein Unc13A and required Rab3. To link these results to animal behaviour, we turned to the established role of cAMP signalling in memory formation and demonstrate that Rab3 is necessary for olfactory learning. As Rab3 is dispensable for basal synaptic transmission, these findings highlight a molecular pathway specifically dedicated to tuning neuronal communication and adaptive behaviour.
ChimericFragments: Computation, analysis, and visualization of global RNA networks
Authors: Siemers Malte , Lippegaus Anne , Papenfort Kai
Published: December 2023

RNA-RNA interactions are key for post-transcriptional gene regulation in all domains of life. While ever more experimental protocols are being developed to study RNA-RNA interactions on a genome-wide scale, computational methods to analyze the underlying data are lagging behind. Here, we present ChimericFragments, an analysis and visualization framework for RNA-seq experiments producing chimeric RNA molecules. ChimericFragments implements a novel statistical method based on the complementarity of the base-pairing RNAs around their ligation site and is compatible with several widely used experimental procedures. We demonstrate that ChimericFragments enables the systematic identification of RNA regulators and RNA-RNA pairs and outperforms existing approaches.
SOAPy: a Python package to dissect spatial architecture, dynamics and communication
Authors: Wang Heqi , Li Jiarong , Jing Siyu , Lin Ping , Li Yu , Zhang Haibing , Chen Yujie , Wang Zhen , Li Hong
Published: December 2023

Advances in spatial omics technologies have brought opportunities to dissect tissue microenvironment, while also posing more requirements and challenges for computational methods. Here we developed a package SOAPy to systematically dissect spatial architecture, dynamics and communication from spatial omics data. Specifically, it provides analysis methods for multiple spatial-related tasks, including spatial domain, spatial expression tendency, spatiotemporal expression pattern, cellular co-localization, multi-cellular niches, and ligand-receptor-mediated and spatial-constrained cell communication. Applying SOAPy on different spatial omics technologies and diverse biological fields has demonstrated its power on elucidation of biological questions about tumors, embryonic development, and normal physiological structures. Overall, SOAPy is a universal tool for spatial omics analysis, providing a foundation for continued investigation of the microenvironment.
An integrated analysis of the structural changes and gene expression of spleen in human visceral leishmaniasis with and without HIV coinfection
Authors: Fontes Jonathan L. M. , Khouri Ricardo , Reinaldo Luis Gustavo C. , Hassegawa Erina M. A. , Filho Antônio José Meneses , de Melo Caroline V. B. , Ramos Pablo Ivan P. , de Deus Moura Rafael , Pagliari Carla , Santos Marta , Araújo Raimundo José C. , Van Weyenbergh Johan , de Freitas Luiz A. R. , Costa Carlos Henrique N. , dos-Santos Washington L. C.
Published: December 2023

The spleen plays a pivotal role in the pathogenesis of visceral leishmaniasis. In severe forms of the disease, the spleen undergoes changes that can compromise its function in surveilling blood-circulating pathogens. In this study, we present an integrated analysis of the structural and gene expression alterations in the spleens of three patients with relapsing visceral leishmaniasis, two of whom were coinfected with HIV. Our findings reveal that the IL6 signaling pathway plays a significant role in the disorganization of the white pulp, whileBCL10andICOSLGare associated with spleen organization. Patients coinfected with HIV and visceral leishmaniasis exhibited lower splenic CD4+ cell density and reduced expression of genes such asIL15. These effects may contribute to a compromised immune response againstL. infantumin coinfected individuals, further impacting the structural organization of the spleen.
CSF plasma cell expansion in LGI1-/CASPR2-autoimmune encephalitis is associated with loss of regulatory MAIT cells
Authors: Esser Daniela , Müller-Miny Louisa , Heming Michael , Paunovic Manuela , van Duijn Martijn , Cabrera Ligia Abrante , Mair Katharina , Strippel Christine , Räuber Saskia , Bindels Eric , Dargvainiene Justina , Wiendl Heinz , Meuth Sven G. , Bauer Jan , Melzer Nico , Titulaer Maarten J. , Leypoldt Frank , Meyer zu Hörste Gerd ,   EMC-AIE Study group
Published: December 2023

Anti-Leucine-rich glioma inactivated-1 (LGI1) and anti-contactin-associated-protein-2 (CASPR2) associated autoimmune encephalitis (AIE) variants are characterized by directly pathogenic autoantibodies present in serum and CSF. The dynamics and drivers of intrathecal and systemic autoantibody production are incompletely understood. We aimed to elucidate the immunologic basis of the LGI1-/CASPR2-associated AIE variants by performing multi-omic profiling of CSF/blood in untreated patients. We validated findings by flow cytometry in independent cohorts and confirmed functionality using rodent immunization.

We identified clonal IgG2 and IgG4 plasma cell expansion and affinity maturation in the CSF together with clonally restricted, activated, antigen-experienced CD8 and CD4 T cells as a hallmark of these encephalitis variants. Using recombinant cloning, we confirmed that expanded CSF plasma cell clones almost exclusively bound the respective neuronal autoantigen. In addition, we found a loss of regulatory mucosa-associated invariant T (MAIT) cells and gamma delta T cells in the CSF and – to a lesser degree – in blood. We validated the functional role of these invariant T cells using a novel murine active immunization paradigm using both autoantigens: MAIT cells suppressed systemic formation of LGI1 and CASPR2-specific anti-neuronal antibodies.

We propose that loss of systemic and intrathecal regulatory mechanisms mediated by innate-like T cells promote plasma cell expansion and autoantibody production as a shared mechanism in AIE.

One sentence summary

Cerebrospinal fluid (CSF) and peripheral blood (PB) single cell transcriptomics of patients with untreated anti-LGI1 and anti-CASPR2 autoimmune encephalitis demonstrated CSF specific expansion of autoantigen-specific plasma cell clones and systemic loss of invariant mucosa-associated T-cells (MAIT).
Impaired Myofibroblast Proliferation is a Central Feature of Pathologic Post-Natal Alveolar Simplification
Authors: Khan Imran S. , Molina Christopher , Ren Xin , Auyeung Vincent C. , Cohen Max , Tsukui Tatsuya , Atakilit Amha , Sheppard Dean
Published: December 2023

Premature infants with bronchopulmonary dysplasia (BPD) have impaired alveolar gas exchange due to alveolar simplification and dysmorphic pulmonary vasculature. Advances in clinical care have improved survival for infants with BPD, but the overall incidence of BPD remains unchanged because we lack specific therapies to prevent this disease. Recent work has suggested a role for increased transforming growth factor-beta (TGFβ) signaling and myofibroblast populations in BPD pathogenesis, but the functional significance of each remains unclear. Here, we utilize multiple murine models of alveolar simplification and comparative single-cell RNA sequencing to identify shared mechanisms that could contribute to BPD pathogenesis. Single-cell RNA sequencing reveals a profound loss of myofibroblasts in two models of BPD and identifies gene expression signatures of increased TGFβ signaling, cell cycle arrest, and impaired proliferation in myofibroblasts. Using pharmacologic and genetic approaches, we find no evidence that increased TGFβ signaling in the lung mesenchyme contributes to alveolar simplification. In contrast, this is likely a failed compensatory response, since none of our approaches to inhibit TGFb signaling protect mice from alveolar simplification due to hyperoxia while several make simplification worse. In contrast, we find that impaired myofibroblast proliferation is a central feature in several murine models of BPD, and we show that inhibiting myofibroblast proliferation is sufficient to cause pathologic alveolar simplification. Our results underscore the importance of impaired myofibroblast proliferation as a central feature of alveolar simplification and suggest that efforts to reverse this process could have therapeutic value in BPD.
Neutrophil extracellular traps formation is associated with postoperative complications in neonates and infants undergoing congenital cardiac surgery
Authors: Maisat Wiriya , Hou Lifei , Sandhu Sumiti , Sin Yi-Cheng , Kim Samuel , Pelt Hanna Van , Chen Yue , Emani Sirisha , Kong Sek Won , Emani Sitram , Ibla Juan , Yuki Koichi
Published: December 2023

Pediatric patients with congenital heart diseases (CHD) often undergo surgical repair on cardiopulmonary bypass (CPB). Despite a significant medical and surgical improvement, the mortality of neonates and infants remains high. Damage-associated molecular patterns (DAMPs) are endogenous molecules released from injured/damaged tissues as danger signals. We examined 101 pediatric patients who underwent congenital cardiac surgery on CPB. The mortality rate was 4.0%, and the complication rate was 31.6%. We found that neonates/infants experienced multiple complications most, consistent with the previous knowledge. Neonates and infants in the complication group had received more transfusion intraoperatively than the non-complication arm with lower maximum amplitude (MA) on rewarming CPB thromboelastography (TEG). Despite TEG profiles were comparable at ICU admission between the two groups, the complication arm had higher postoperative chest tube output, requiring more blood transfusion. The complication group showed greater neutrophil extracellular traps (NETs) formation at the end of CPB and postoperatively. Plasma histones and high mobility group box 1 (HMGB1) levels were significantly higher in the complication arm. Both induced NETsin vitroandin vivo. As histones and HMGB1 target Toll-like receptor (TLR)2 and TLR4, their mRNA expression in neutrophils was upregulated in the complication arm. Taken together, NETs play a major role in postoperative complication in pediatric cardiac surgery and would be considered a target for intervention.

Key points

Neonates and infants showed highest postoperative complications with more upregulation of inflammatory transcriptomes of neutrophils.

Neonates and infants with organ dysfunction had more NETs formation with higher plasma histones and HMGB1 levels.
Pre-training with pseudo-labeling compares favorably with large language models for regulatory sequence prediction
Authors: Mourad Raphaël
Published: December 2023

Predicting molecular processes using deep learning is a promising approach to provide biological insights for non-coding SNPs identified in genome-wide association studies. However, most deep learning methods rely on supervised learning, which requires DNA sequences associated with functional data, and whose amount is severely limited by the finite size of the human genome. Conversely, the amount of mammalian DNA sequences is growing exponentially due to ongoing large-scale sequencing projects, but in most cases without functional data. To alleviate the limitations of supervised learning, we propose a novel semi-supervised learning based on pseudo-labeling, which allows to exploit unlabeled DNA sequences from numerous genomes during model pre-training. The approach is very flexible and can be used to train any neural architecture including state-of-the-art models, and shows in certain situations strong predictive performance improvements compared to standard supervised learning in most cases. Moreover, small models trained by SSL showed similar or better performance than large language model DNABERT2.
Structural dynamics and functional cooperativity of human NQO1 by ambient temperature serial crystallography and simulations
Authors: Grieco Alice , Boneta Sergio , Gavira José A. , Pey Angel L. , Basu Shibom , Orlans Julien , de Sanctis Daniele , Medina Milagros , Martin-Garcia Jose Manuel
Published: December 2023

The human NQO1 (hNQO1) is a FAD-dependent oxidoreductase that catalyzes the two-electron reduction of quinones to hydroquinones, being essential for the antioxidant defense system, stabilization of tumor suppressors, and activation of quinone-based chemotherapeutics, and it is over-expressed in several tumors, which makes it an attractive cancer drug target. To decipher new structural insights into the flavin reductive half-reaction of the catalytic mechanism of hNQO1, we have carried serial crystallography experiments at new ID29 beamline of the ESRF to determine, to the best of our knowledge, the first structure of the hNQO1 in complex with NADH. The use of room temperature serial crystallography with microcrystals has been key to study this mechanism. We have also performed molecular dynamics simulations of free hNQO1 and in complex with NADH. Both structural results and MD simulations have supported that the binding of NADH significantly decreases protein dynamics and stabilizes hNQO1 especially at the dimer core and interface. This is the first structural evidence that the hNQO1 functional cooperativity is driven by structural communication between the active sites through long-range propagation of cooperative effects across the hNQO1 structure. Altogether, these results pave the way for future time-resolved studies, both at XFELs and synchrotrons, of the dynamics of hNQO1 upon binding to NADH as well as during the FAD cofactor reductive half-reaction. This knowledge will allow us to reveal unprecedented structural information of the relevance of the dynamics during the catalytic function of hNQO1.
Assessing cross-contamination in spike-sorted electrophysiology data
Authors: Vincent Jack P. , Economo Michael N.
Published: December 2023

Recent advances in extracellular electrophysiology now facilitate the recording of spikes from hundreds or thousands of neurons simultaneously. This has necessitated both the development of new computational methods for spike sorting and better methods to determine spike sorting accuracy. One longstanding method of assessing the false discovery rate (FDR) of spike sorting – the rate at which spikes are misassigned to the wrong cluster – has been the rate of inter-spike-interval (ISI) violations. Despite their near ubiquitous usage in spike sorting, our understanding of how exactly ISI violations relate to FDR, as well as best practices for using ISI violations as a quality metric, remain limited. Here, we describe an analytical solution that can be used to predict FDR from ISI violation rate. We test this model in silico through Monte Carlo simulation, and apply it to publicly available spike-sorted electrophysiology datasets. We find that the relationship between ISI violation rate and FDR is highly nonlinear, with additional dependencies on firing rate, the correlation in activity between neurons, and contaminant neuron count. Predicted median FDRs in public datasets were found to range from 3.1% to 50.0%. We find that stochasticity in the occurrence of ISI violations as well as uncertainty in cluster-specific parameters make it difficult to predict FDR for single clusters with high confidence, but that FDR can be estimated accurately across a population of clusters. Our findings will help the growing community of researchers using extracellular electrophysiology assess spike sorting accuracy in a principled manner.

SIGNIFICANCE STATEMENT

High-density silicon probes are widely used to record the activity of large populations of neurons while animals are engaged in complex behavior. In this approach, each electrode records spikes from many neurons, and “spike sorting” algorithms are used to group the spikes originating from each neuron together. This process is error-prone, however, and so the ability to assess spike sorting accuracy is essential for properly interpreting neural activity. The rate of inter-spike-interval (ISI) violations is commonly used to assess spike sorting accuracy, but the relationship between ISI violation rate and sorting accuracy is complex and poorly understood. Here, we describe this relationship in detail and provide guidelines for how to properly use ISI violation rate to assess spike sorting accuracy.
The Treatment of diarrheal mice with Tenebrio Molitor meal
Authors: Liu Tingting , Wang Qiaoli , Wang Zhengli , Yan Jiaxu , Zhu Jianjun , Shen Hong , Wang Jungang
Published: December 2023

Feeding Tenebrio Molitor meal has an important effect on promoting the growth, absorption, reproduction, and disease resistance of animals. In this study, 3×108cfu/ml Escherichia coli was used to establish a mouse diarrhea model. Different doses (8%, 5%, 2.5%) of tenebrio molitor meal were added to the basic diet, respectively. The feed intake, water intake, body weight, loose stool rate, diarrhea rate, intestinal flora number, immune organ index, intestinal enzyme, and serum enzyme activities of the diarrhea mice were detected. The results showed that compared with the model group, the feed intake, water intake, and body weight of mice with diarrhea were improved by adding tenebrio molitor meal, and the dosage was proportional to that of tenebrio molitor meal. The rate of loose stool and diarrhea decreased with the increase of tenebrio molitor meal. The total bacterial count and Escherichia coli count in the intestinal tract of mice with diarrhea were negatively correlated with the dosage of tenebrio molitor meal. The immune organ index of the diarrhea mice in the three tenebrio molitor meal supplementation groups was higher than that in the model group and was proportional to the dosage. The liver index of the 8% tenebrio molitor meal supplementation group was 11.79mg/g higher than that in the blank group. Compared with the blank group, diarrhea significantly decreased the activities of various enzymes in the intestinal tract and serum of mice (P<0.05). Compared with the model group, the activities of intestinal and serum protective enzymes (superoxide dismutase, peroxidase, catalase), detoxification enzymes (glutathione-S transferase, acetylcholinesterase, acid phosphatase) and digestive enzymes (serum amylase, serum lipase, lactate dehydrogenase) in diarrhea mice were increased by adding tenebrio molitor meal (P<0.05). The results showed that tenebrio molitor meal had a positive effect on the treatment of diarrhea in mice.
The Effects of Multi-Colour Light Filtering Glasses on Human Brain Wave Activity
Authors: Boere Katherine , Krigolson Olave E.
Published: December 2023

The prevalence of electronic screens in modern society has significantly increased our exposure to high-energy blue and violet light wavelengths. Accumulating evidence links this exposure to adverse visual and cognitive effects and sleep disturbances. To mitigate these effects, the optical industry has introduced a variety of filtering glasses. However, the scientific validation of these glasses has often been based on subjective reports and a narrow range of objective measures, casting doubt on their true efficacy. In this study, we used electroencephalography (EEG) to record brain wave activity to evaluate the effects of glasses that filter multiple wavelengths (blue, violet, indigo, and green) on human brain function. Our results demonstrate that wearing these multi-colour light filtering glasses significantly reduces beta wave power (13-30 Hz) compared to control or no glasses. Prior research has associated a reduction in beta power with the calming of heightened mental states, such as anxiety. As such, our results suggest that wearing glasses such as the ones used in this study may also positively change mental states, for instance, by promoting relaxation. This investigation is innovative in applying neuroimaging techniques to confirm that light-filtering glasses can induce measurable changes in brain activity.
RELEVANCE OF SHAM CONTROL GROUP IN PRECLINICAL ANIMAL STUDIES OF CEREBRAL ISCHEMIA
Authors: Candamo-Lourido María , López-Arias Esteban , López-Amoedo Sonia , Correa-Paz Clara , Bravo Susana B. , Bugallo-Casal Ana , del Pozo-Filíu Lucía , Pérez-Gayol Lara , Palomar-Alonso Nuria , Chantada-Vázquez María Pilar , Campos Francisco , Pérez-Mato María
Published: December 2023

Background

In experimental animal studies, control sham groups are essential to reduce the influence of the surgical intervention on the analysis. The intraluminal filament procedure is one of the most common models of middle cerebral artery occlusion (MCAO) used in the study of cerebral ischemia. However, in these studies, the sham group has not usually been included in the experimental design because of the assumption that the surgical procedure required to access the middle cerebral artery does not affect brain tissue, or that the results obtained from this group are not relevant.

Objectives

In this study, we aimed to evaluate the relevance of the sham group by analyzing and comparing the brain protein profile of a sham and an ischemic group subjected to the surgical intraluminal filament occlusion of the middle cerebral artery.

Material and Methods

Three randomized experimental groups were tested: control group (healthy animals), sham group, and ischemic group. Twenty-four hours after the interventional procedure, the brain tissue was evaluated by magnetic resonance imaging (MRI). After animal perfusion, the brain is removed for proteomic analysis by liquid chromatography-mass spectrometry (LC-MS/MS) using both a qualitative analysis by data-dependent acquisition (DDA) mode and a quantitative analysis, using a sequential window acquisition of all theoretical mass spectra (SWATH-MS) method on a hybrid quadrupole time-of-flight mass spectrometer.

Results

MRI results showed that only animals subjected to cerebral ischemia had ischemic injury. In the sham group 137 dysregulated proteins were detected compared to the 65 in the ischemic group. Moreover, a comparative study of both protein profiles showed the existence of a pool of 17 that appeared dysregulated in both sham and ischemic animals. These results indicate that the surgical procedure required for intraluminal occlusion of the MCA induce changes on brain protein expression that are not associated with the ischemic lesion.

Conclusion

This study highlights the importance of including a sham group in the experimental model design to guarantee that the therapeutic target under study is not affected by the surgical intervention.
Dynamics of single-cell protein covariation during epithelial–mesenchymal transition
Authors: Khan Saad , Conover Rachel , Asthagiri Anand R. , Slavov Nikolai
Published: December 2023

Physiological processes, such as epithelial–mesenchymal transition (EMT), are mediated by changes in protein interactions. These changes may be better reflected in protein covariation within cellular cluster than in the temporal dynamics of cluster-average protein abundance. To explore this possibility, we quantified proteins in single human cells undergoing EMT. Covariation analysis of the data revealed that functionally coherent protein clusters dynamically changed their protein-protein correlations without concomitant changes in cluster-average protein abundance. These dynamics of protein-protein correlations were monotonic in time and delineated protein modules functioning in actin cytoskeleton organization, energy metabolism and protein transport. These protein modules are defined by protein covariation within the same time point and cluster and thus reflect biological regulation masked by the cluster-average protein dynamics. Thus, protein correlation dynamics across single cells offer a window into protein regulation during physiological transitions.
Molecular dynamics of outer membrane-embedded polysaccharide secretion porins reveals closed resting-state surface gates targetable by virtual fragment screening for drug hotspot identification
Authors: França Tanos C. C. , Saïdi Fares , Ajamian Alain , Islam Salim T. , LaPlante Steven R.
Published: December 2023

Recent advances in iterative neural-network analyses (e.g. AlphaFold2 and RoseTTA fold) have been revolutionary for protein 3D-structure prediction, especially for difficult-to-manipulate α-helical/β-barrel integral membrane proteins. These model structures are calculated based on the co-evolution of amino acids within the protein of interest and similarities to existing protein structures; local effects of the membrane on folding and stability of the calculated model structures are not considered. We recently reported the discovery, 3D modelling, and characterization of 18-β-stranded outer-membrane (OM) WzpX, WzpS, and WzpB β-barrel secretion porins for the exopolysaccharide (EPS), major spore coat polysaccharide (MASC), and biosurfactant polysaccharide (BPS) pathways (respectively) in the Gram-negative social predatory bacteriumMyxococcus xanthusDZ2. However, information was not obtained regarding the dynamic behavior of surface-gating WzpX/S/B loop domains, nor on potential treatments to inactivate these porins. Herein, we developed a molecular dynamics (MD) protocol to study the core stability and loop dynamism of neural network-based integral membrane protein structure models embedded in an asymmetric OM bilayer, using theM. xanthusWzpX, WzpS, and WzpB proteins as test candidates. This was accomplished through integration of the CHARMM-graphical user interface (GUI) and Molecular Operating Environment (MOE) workflows to allow for rapid simulation system setup and facilitate data analysis. In addition to serving as a method of model-structure validation, our molecular dynamics simulations revealed minimal movement of extracellular WzpX/S/B loops in the absence of an external stimulus, as well as druggable cavities between the loops. Virtual screening of a commercial fragment library against these cavities revealed putative fragment-binding hotspots on the cell-surface face of each β-barrel, along with key interacting residues, and identified promising hits for the design of potential binders capable of plugging the β-barrels and inhibiting polysaccharide secretion.
Integrated data models on Receptor-Like Kinases for novel domain discovery and functional inference in the plant kingdom
Authors: Liu Qian , Fu Qiong , Yan Yujie , Jiang Qian , Mao Longfei , Wang Long , Yu Feng , Zheng Heping
Published: December 2023

Receptor-like kinases (RLKs) are the largest signal transduction component in plants, determining how different plants adapt to their ecological environment, resulting in plant-specific ecological niches. Current research on RLKs has focused mainly on a small number of typical RLK members of a few model plants. There is an urgent need to study the composition, distribution, and evolution of RLKs at the holistic level to accelerate the understanding of how RLK assists in the ecological adaptation of different plants. In this study, we have collected 528 plant genomes and established an RLK data model, resulting in the discovery and characterization of 524,948 RLK members. Each member is subject to systematic topology classification and coherent gene ID assignment. Using this data model, we discovered two novel families (Xiao and Xiang) of RLKs. Evolutionary analysis of the RLK families indicates that RLCK-XVII and RLCK-XII-2 exist exclusively in dicots, suggesting that the diversification in RLKs between monocots and dicots could cause differences in downstream cytoplasmic responses. We also use interaction proteome to help empower the data mining of inferring new functions of RLK from a global perspective, with the ultimate goal of understanding how RLKs shape the adaptation of different plants to the environment/ecology. The RLK data model compiled herein, together with the annotations and analytic tools, form an integrated data foundation involving multi-omics data and is publicly accessible via the web portal (http://metaRLK.biocloud.top).
Predicting the Structural Impact of Human Alternative Splicing
Authors: Song Yuxuan , Zhang Chengxin , Omenn Gilbert S. , O’Meara Matthew J. , Welch Joshua D.
Published: December 2023

Protein structure prediction with neural networks is a powerful new method for linking protein sequence, structure, and function, but structures have generally been predicted for only a single isoform of each gene, neglecting splice variants. To investigate the structural implications of alternative splicing, we used AlphaFold2 to predict the structures of more than 11,000 human isoforms. We employed multiple metrics to identify splicing-induced structural alterations, including template matching score, secondary structure composition, surface charge distribution, radius of gyration, accessibility of post-translational modification sites, and structure-based function prediction. We identified examples of how alternative splicing induced clear changes in each of these properties. Structural similarity between isoforms largely correlated with degree of sequence identity, but we identified a subset of isoforms with low structural similarity despite high sequence similarity. Exon skipping and alternative last exons tended to increase the surface charge and radius of gyration. Splicing also buried or exposed numerous post-translational modification sites, most notably among the isoforms ofBAX. Functional prediction nominated numerous functional differences among isoforms of the same gene, with loss of function compared to the reference predominating. Finally, we used single-cell RNA-seq data from the Tabula Sapiens to determine the cell types in which each structure is expressed. Our work represents an important resource for studying the structure and function of splice isoforms across the cell types of the human body.
Relationship between alcohol consumption and dementia with Mendelian randomization approaches among older adults in the United States
Authors: Campbell Kyle A. , Fu Mingzhou , MacDonald Elizabeth , Zawistowski Matthew , Bakulski Kelly M. , Ware Erin B.
Published: December 2023

Background

In observational studies, the association between alcohol consumption and dementia is mixed.

Methods

We performed two-sample Mendelian randomization (MR) using summary statistics from genome-wide association studies of weekly alcohol consumption and late-onset Alzheimer’s disease and one-sample MR in the Health and Retirement Study (HRS), wave 2012. Inverse variance weighted two-stage regression provided odds ratios of association between alcohol exposure and dementia or cognitively impaired, non-dementia relative to cognitively normal.

Results

Alcohol consumption was not associated with late-onset Alzheimer’s disease using two-sample MR (OR=1.15, 95% confidence interval (CI):[0.78, 1.72]). In HRS, doubling weekly alcohol consumption was not associated with dementia (African ancestries, n=1,322, OR=1.00, 95% CI [0.45, 2.25]; European ancestries, n=7,160, OR=1.37, 95% CI [0.53, 3.51]) or cognitively impaired, non-dementia (African ancestries, n=1,322, OR=1.17, 95% CI [0.69, 1.98]; European ancestries, n=7,160, OR=0.75, 95% CI [0.47, 1.22]).

Conclusion

Alcohol consumption was not associated with cognitively impaired, non-dementia or dementia status.
Artemisinin resistance mutations inPfcoroninimpede hemoglobin uptake
Authors: Ullah Imran , Farringer Madeline A. , Burkhard Anna Y. , Hathaway Erica , Khushu Malhar , Willett Bailey C. , Shin Sara H. , Sharma Aabha I. , Martin Morgan C. , Shao Kairon L. , Dvorin Jeffrey D. , Hartl Daniel L. , Volkman Sarah K. , Bopp Selina , Absalon Sabrina , Wirth Dyann F.
Published: December 2023

Artemisinin (ART) combination therapies have been critical in reducing malaria morbidity and mortality, but these important drugs are threatened by growing resistance associated with mutations inPfcoroninandPfkelch13. Here, we describe the mechanism ofPfcoronin-mediated ART resistance.PfCoronin interacts withPfActin and localizes to the parasite plasma membrane (PPM), the digestive vacuole (DV) membrane, and membrane of a newly identified preDV compartment—all structures involved in the trafficking of hemoglobin from the RBC for degradation in the DV.Pfcoroninmutations alterPfActin homeostasis and impair the development and morphology of the preDV. Ultimately, these changes are associated with decreased uptake of red blood cell cytosolic contents by ring-stagePlasmodium falciparum. Previous work has identified decreased hemoglobin uptake as the mechanism ofPfkelch13-mediated ART resistance. This work demonstrates thatPfCoronin appears to act via a parallel pathway. For bothPfkelch13-mediated andPfcoronin-mediated ART resistance, we hypothesize that the decreased hemoglobin uptake in ring stage parasites results in less heme-based activation of the artemisinin endoperoxide ring and reduced cytocidal activity. This study deepens our understanding of ART resistance, as well as hemoglobin uptake and development of the DV in early-stage parasites.
Development and patterning of a highly versatile visual system in spiders
Authors: Gonzalez Luis Baudouin , Schönauer Anna , Harper Amber , Arif Saad , Leite Daniel J. , Steinhoff Philip O. M. , Pechmann Matthias , Telizhenko Valeriia , Pande Atal , Kosiol Carolin , McGregor Alistair P. , Sumner-Rooney Lauren
Published: December 2023

Visual systems provide a key interface between organisms and their surroundings, and have evolved in many forms to perform diverse functions across the animal kingdom. Spiders exhibit a range of visual abilities and ecologies, the diversity of which is underpinned by a highly versatile, modular visual system architecture. This typically includes eight eyes of two developmentally distinct types, but the number, size, location, and function of the eyes can vary dramatically between lineages. Previous studies of visual system development in spiders have confirmed that many components of the retinal determination gene (RDG) network are conserved with other arthropods, but so far, comparative studies among spiders are lacking. We characterised visual system development in eight species of spiders representing a range of morphologies, visual ecologies, and phylogenetic positions, to determine how these diverse configurations are formed, and how they might evolve. Combining synchrotron radiation tomography, transcriptomics, in situ hybridisation, and selection analyses, we characterise the repertoires and expression of key RDGs in relation to adult morphology. We identify key molecular players, timepoints, and developmental events that may contribute to adult diversity, in particular the molecular and developmental underpinnings of eye size, number, position, and identity across spiders.
The RNA-binding protein RbpB is a central regulator of polysaccharide utilization in gutBacteroides
Authors: Rüttiger Ann-Sophie , Ryan Daniel , Spiga Luisella , Lamm-Schmidt Vanessa , Prezza Gianluca , Reichardt Sarah , Barquist Lars , Faber Franziska , Zhu Wenhan , Westermann Alexander J.
Published: December 2023

Paramount to human health, symbiotic bacteria in the gastrointestinal tract rely on the breakdown of complex polysaccharides to thrive in this sugar-deprived environment. GutBacteroidesare metabolic generalists and deploy dozens of polysaccharide utilization loci (PULs) to forage diverse dietary and host-derived glycans. The expression of the multi-protein PUL complexes is tightly regulated at the transcriptional level. However, how PULs are orchestrated at translational level in response to the fluctuating levels of their cognate substrates is unknown. Here, we identify the RNA-binding protein RbpB and a family of noncoding RNAs as key players in post-transcriptional PUL regulation. Ablation of RbpB inBacteroides thetaiotaomicrondisplays compromised colonization in the mouse gut in a host diet-dependent manner. Current dogma holds that individual PULs are regulated by dedicated transcriptional regulators. We demonstrate that RbpB acts as a global RNA binder that directly interacts with several hundred cellular transcripts. This includes a paralogous noncoding RNA family comprised of 14 members, the FopS (familyofparalogoussRNAs) cluster. Through a series ofin-vitroandin-vivoassays, we reveal that FopS sRNAs repress the translation of a SusC-like glycan transporter when substrates are limited—an effect antagonized by RbpB. Together, this study implicates RNA-coordinated metabolic control as an important, yet previously overlooked, factor contributing to thein-vivofitness of predominant microbiota species in dynamic nutrient landscapes.
FGF8-mediated gene regulation affects regional identity in human cerebral organoids
Authors: Bertacchi Michele , Maharaux Gwendoline , Loubat Agnès , Jung Mathieu , Studer Michèle
Published: December 2023

The morphogen FGF8 establishes graded positional cues imparting regional cellular responsesviamodulation of early target genes. The roles of FGF signaling and its effector genes remain poorly characterized in human experimental models mimicking early fetal telencephalic development. We used hiPSC-derived cerebral organoids as an in vitro platform to challenge the effect of FGF8 signaling on neural identity and differentiation. We found that FGF8 treatment increases cellular heterogeneity leading to distinct telencephalic and mesencephalic-like domains that co-develop in multi-regional organoids. Within telencephalic domains, FGF8 affects the anteroposterior and dorsoventral identity of neural progenitors, the balance between GABAergic and glutamatergic neurons, thus impacting spontaneous neuronal network activity. Moreover, FGF8 efficiently modulates key regulators responsible for several human neurodevelopmental disorders. Overall, our results show that FGF8 signaling is directly involved in both regional patterning and cellular diversity in human cerebral organoids and in modulating genes associated with normal and pathological neural development.
Mefloquine-induced conformational shift in Cx36 N-terminal helix leading to channel closure mediated by lipid bilayer
Authors: Cho Hwa-Jin , Lee Hyung Ho
Published: December 2023

Connexin 36 (Cx36) forms interneuronal gap junctions, establishing electrical synapses for rapid synaptic transmission. In disease conditions, inhibiting Cx36 gap junction channels (GJCs) is beneficial, as it prevents abnormal synchronous neuronal firing and apoptotic signal propagation, mitigating seizures and progressive cell death. Here, we present cryo-electron microscopy structures of human Cx36 GJC in complex with known channel inhibitors, such as mefloquine, arachidonic acid, and 1-hexanol. Notably, these inhibitors competitively bind to the binding pocket of the N-terminal helices (NTH), inducing a conformational shift from the pore-lining NTH (PLN) state to the flexible NTH (FN) state. This leads to the obstruction of the channel pore by flat double-layer densities of lipids. These studies elucidate the molecular mechanisms of how Cx36 GJC can be modulated by inhibitors, providing valuable insights into potential therapeutic applications.