bluuebunny/crossref_metadata_2025 huggingface dataset:
Optogenetic Stimulation of Single Ganglion Cells in the Living Primate Fovea
Authors: Murphy Peter J. , McGregor Juliette E. , Xu Zhengyang , Yang Qiang , Merigan William , Williams David R.
Published: July 2023

Though the responses of the rich variety of retinal ganglion cells (RGCs) reflect the totality of visual processing in the retina and provide the sole conduit for those processed responses to the brain, we have much to learn about how the brain uses these signals to guide behavior. An impediment to developing a comprehensive understanding of the role of retinal circuits in behavior is the paucity of causal studies in the intact primate visual system. Here we demonstrate the ability to optogenetically activate individual RGCs with flashes of light focused on single RGC somasin vivo, without activation of neighboring cells. The ability to selectively activate specific cells is the first step toward causal experiments that directly link retinal circuits to visual experience and behavior.
Identification of a botulinum neurotoxin-like gene cluster inBacillus toyonensis
Authors: Wei Xin , Lobb Briallen , Wang Kang , Dong Min , Doxey Andrew C.
Published: July 2023

Clostridial neurotoxins, which include botulinum neurotoxins (BoNTs) and tetanus neurotoxin (TeNT) are the most potent toxins known, and are the causative agents of the neuroparalytic diseases, botulism and tetanus. Until recently, the clostridial neurotoxin family was restricted to the genusClostridium, but members of this protein family have been found in a growing number of non-Clostridiumspecies includingWeissella, Enterococcus, andParaclostridium. Here, we report the bioinformatic identification and analysis of a novel clostridial neurotoxin homolog in aBacillus toyonensisgenome recently deposited into the NCBI Genbank database. This putative toxin shares 26-29% identity with its closest BoNT relatives, suggesting that it is likely a novel BoNT-like toxin. It possesses key functional motifs (e.g., HExxH) indicative of toxin protease activity, contains the four characteristic BoNT domains, and is located in a BoNT-like genomic neighborhood containing the upstream non-toxic non-hemagglutinin (NTNH) gene as well as several P47-related genes. Phylogenetically, the toxin clusters as a divergent member of the recently discovered lineage of BoNT-like toxins that includes BoNT/X, BoNT/En, and the insecticidal PMP1. Genomic analysis of theB. toyonensisisolate CH177 revealed additional virulence factors and toxin genes indicative of potential pathogenicity targeting an unknown host species. TheBacillus toyonensisBoNT-like protein (BTNT) adds to a growing number of non-clostridial BoNT-like toxins, adding further information on the intriguing phylogenetic distribution and evolutionary history of the most potent toxins known.
Folding-upon-binding pathways of an intrinsically disordered protein from a deep Markov state model
Authors: Sisk Thomas , Robustelli Paul
Published: July 2023

A central challenge in the study of intrinsically disordered proteins is the characterization of the mechanisms by which they bind their physiological interaction partners. Here, we utilize a deep learning based Markov state modeling approach to characterize the folding-upon-binding pathways observed in a long-time scale molecular dynamics simulation of a disordered region of the measles virus nucleoprotein NTAILreversibly binding the X domain of the measles virus phosphoprotein complex. We find that folding-upon-binding predominantly occurs via two distinct encounter complexes that are differentiated by the binding orientation, helical content, and conformational heterogeneity of NTAIL. We do not, however, find evidence for the existence of canonical conformational selection or induced fit binding pathways. We observe four kinetically separated native-like bound states that interconvert on time scales of eighty to five hundred nanoseconds. These bound states share a core set of native intermolecular contacts and stable NTAILhelices and are differentiated by a sequential formation of native and non-native contacts and additional helical turns. Our analyses provide an atomic resolution structural description of intermediate states in a folding-upon-binding pathway and elucidate the nature of the kinetic barriers between metastable states in a dynamic and heterogenous, or “fuzzy”, protein complex.
Synthetic control removes spurious discoveries from double dipping in single-cell and spatial transcriptomics data analyses
Authors: Song Dongyuan , Chen Siqi , Lee Christy , Li Kexin , Ge Xinzhou , Li Jingyi Jessica
Published: July 2023

Double dipping is a well-known pitfall in single-cell and spatial transcriptomics data analysis: after a clustering algorithm finds clusters as putative cell types or spatial domains, statistical tests are applied to the same data to identify differentially expressed (DE) genes as potential cell-type or spatial-domain markers. Because the genes that contribute to clustering are inherently likely to be identified as DE genes, double dipping can result in false-positive cell-type or spatial-domain markers, especially when clusters are spurious, leading to ambiguously defined cell types or spatial domains. To address this challenge, we propose ClusterDE, a statistical method designed to identify post-clustering DE genes as reliable markers of cell types and spatial domains, while controlling the false discovery rate (FDR) regardless of clustering quality. The core of ClusterDE involves generating synthetic null data as anin siliconegative control that contains only one cell type or spatial domain, allowing for the detection and removal of spurious discoveries caused by double dipping. We demonstrate that ClusterDE controls the FDR and identifies canonical cell-type and spatial-domain markers as top DE genes, distinguishing them from housekeeping genes. ClusterDE’s ability to discover reliable markers, or the absence of such markers, can be used to determine whether two ambiguous clusters should be merged. Additionally, ClusterDE is compatible with state-of-the-art analysis pipelines like Seurat and Scanpy.
M1 recruitment during interleaved practice is important for encoding, not just consolidation, of novel skill memory
Authors: Kim Taewon , Kim Hakjoo , Philip Benjamin A. , Wright David L.
Published: July 2023

Primary motor cortex (M1) plays a major role in motor memory acquisition and retention in humans, but its role in interleaved practice (as opposed to repetitive practice) remains unknown. We anticipated that the improved retention typically associated with interleaved practice depends on M1, and thus cathodal transcranial direct current (ctDCS) stimulation to M1 during training would disrupt this improved retention. The benefits of interleaved practice have been reported to occur from more effective consolidation, manifested as rapid skill memory stabilization followed by more long-term enhancement. While we observed the expected decline in retention performance following interleaved practice paired with ctDCS, this reduced retention resulted from more modest encoding of novel skill memory during acquisition rather than from disruption of offline consolidation processes. These data highlight the broad role played by motor cortex for both encoding and retention of novel skill memory.
Three-dimensional single-cell transcriptome imaging of thick tissues
Authors: Fang Rongxin , Halpern Aaron R. , Rahman Mohammed Mostafizur , Huang Zhengkai , Lei Zhiyun , Hell Sebastian J. , Dulac Catherine , Zhuang Xiaowei
Published: July 2023

Multiplexed error-robust fluorescencein-situhybridization (MERFISH) allows genome-scale imaging of RNAs in individual cells in intact tissues. To date, MERFISH has been applied to image thin tissue samples of ∼10-µm thickness. Here, we present a thick-tissue three-dimensional (3D) MERFISH imaging method, which uses confocal microscopy for optical sectioning, deep learning for increasing imaging speed and quality, as well as sample preparation and imaging protocol optimized for image registration of thick samples. We demonstrated 3D MERFISH on mouse brain tissue sections of up to 200 µm thickness with high detection efficiency and accuracy. We anticipate that 3D thick-tissue MERFISH imaging will broaden the scope of questions that can be addressed by spatial genomics.
AlphaFold2 models of the active form of all 437 catalytically competent human protein kinase domains
Authors: Faezov Bulat , Dunbrack Roland L.
Published: July 2023

Abstract

Humans have 437 catalytically competent protein kinase domains with the typical kinase fold, similar to the structure of Protein Kinase A (PKA). Only 155 of these kinases are in the Protein Data Bank in their active form. The active form of a kinase must satisfy requirements for binding ATP, magnesium, and substrate. From structural bioinformatics analysis of 40 unique substrate-bound kinases, we derived several criteria for the active form of protein kinases. We include requirements on the DFG motif of the activation loop but also on the positions of the N-terminal and C-terminal segments of the activation loop that must be placed appropriately to bind substrate. Because the active form of catalytic kinases is needed for understanding substrate specificity and the effects of mutations on catalytic activity in cancer and other diseases, we used AlphaFold2 to produce models of all 437 human protein kinases in the active form. This was accomplished with templates in the active form from the PDB and shallow multiple sequence alignments of orthologs and close homologs of the query protein. We selected models for each kinase based on the pLDDT scores of the activation loop residues, demonstrating that the highest scoring models have the lowest or close to the lowest RMSD to 22 non-redundant substrate-bound structures in the PDB. A larger benchmark of all 130 active kinase structures with complete activation loops in the PDB shows that 80% of the highest-scoring AlphaFold2 models have RMSD < 1.0 Å and 90% have RMSD < 2.0 Å over the activation loop backbone atoms. Models for all 437 catalytic kinases are available athttp://dunbrack.fccc.edu/kincore/activemodels. We believe they may be useful for interpreting mutations leading to constitutive catalytic activity in cancer as well as for templates for modeling substrate and inhibitor binding for molecules which bind to the active state.
Mechanoreceptive Aβ primary afferents discriminate naturalistic social touch inputs at a functionally relevant time scale
Authors: Xu Shan , Hauser Steven C. , Nagi Saad S. , Jablonski James A. , Rezaei Merat , Jarocka Ewa , Marshall Andrew G. , Olausson Håkan , McIntyre Sarah , Gerling Gregory J.
Published: July 2023

Interpersonal touch is an important part of our social and emotional interactions. How these physical, skin-to-skin touch expressions are processed in the peripheral nervous system is not well understood. From single-unit microneurography recordings in humans, we evaluated the capacity of six subtypes of cutaneous afferents to differentiate perceptually distinct social touch expressions. By leveraging conventional statistical analyses and classification analyses using convolutional neural networks and support vector machines, we found that single units of multiple Aβ subtypes, especially slowly adapting type II (SA-II) and fast adapting hair follicle afferents (HFA), can reliably differentiate the skin contact of those expressions at accuracies similar to those perceptually. Rapidly adapting field (Field) afferents exhibit lower accuracies, whereas C-tactile (CT), fast adapting Pacinian corpuscles (FA-II), and muscle spindle (MS) afferents can barely differentiate the expressions, despite responding to the stimuli. We then identified the most informative firing patterns of SA-II and HFA afferents’ spike trains, which indicate that an average duration of 3-4 s of firing provides sufficient discriminative information. Those two subtypes also exhibit robust tolerance to shifts in spike-timing of up to 10 ms. A greater shift in spike-timing, however, drastically compromises an afferent’s discrimination capacity, and can change a firing pattern’s envelope to resemble that of another expression. Altogether, the findings indicate that SA-II and HFA afferents differentiate the skin contact of social touch at time scales relevant for such interactions, which is 1-2 orders of magnitude longer than those relevant for discriminating non-social touch inputs.
Growth directions and stiffness across cell layers determine whether tissues stay smooth or buckle
Authors: Yadav Avilash S. , Hong Lilan , Klees Patrick M. , Kiss Annamaria , Petit Manuel , He Xi , Barrios Iselle M. , Heeney Michelle , Galang Anabella Maria D. , Smith Richard S. , Boudaoud Arezki , Roeder Adrienne H.K.
Published: July 2023

From smooth to buckled, nature exhibits organs of various shapes and forms. How cellular growth patterns produce smooth organ shapes such as leaves and sepals remains unclear. Here we show that unidirectional growth and comparable stiffness across both epidermal layers of Arabidopsis sepals are essential for smoothness. We identified a mutant with ectopicASYMMETRIC LEAVES 2(AS2) expression on the outer epidermis. Our analysis reveals that ectopicAS2expression causes outer epidermal buckling at early stages of sepal development, due to conflicting growth directions and unequal epidermal stiffnesses. Aligning growth direction and increasing stiffness of the outer epidermis restores smoothness. Furthermore, buckling influences auxin efflux transporter protein PIN-FORMED 1 polarity to generate outgrowth in the later stages, suggesting that buckling is sufficient to initiate outgrowths. Our findings suggest that in addition to molecular cues influencing tissue mechanics, tissue mechanics can also modulate molecular signals, giving rise to well-defined shapes.

One-Sentence Summary

Theasymmetric leaves 2-7Dmutant sepals buckle due to discoordination of growth between the two epidermal layers.
Ocular dominance columns in mouse visual cortex
Authors: Goltstein Pieter M. , Laubender David , Bonhoeffer Tobias , Hübener Mark
Published: July 2023

The columnar organization of response properties is a fundamental feature of the mammalian visual cortex. However, columns have not been observed universally across all mammalian species. Here, we report the discovery of ocular dominance columns in mouse visual cortex. Our observation in this minute cortical area sets a new boundary condition for models explaining the emergence of columnar organizations in the neocortex.
Landing the ‘Tiger of Rivers’: Understanding Recreational Angling of Mahseers in India using YouTube Videos
Authors: Das Prantik , Binoy V.V.
Published: July 2023

Megafish mahseers popularly known as the ‘tiger of rivers’, are the dream catch of recreational anglers in India. The present study explored the Recreational Angling (RA) videos of five mahseer speciesTor khudree(deccan mahseer),T. putitora(golden mahseer),T. remadevii(humpback mahseer),T. mosal(mosal mahseer) andNeolissochilus hexagonolepis(chocolate mahseer) recorded from India and uploaded on the social media platform YouTube from January 2010 to October 2022. We did not come across any RA videos ofT. mosalandT. remadeviion YouTube hence further analyses were carried out on the remaining three focal species. No seasonality was observed in the frequency of RA videos uploaded on YouTube andT. khudreeattracted the highest number of views per video. Catch and Release (C&R), an ethical RA practice was noticeably low in the case ofN. hexagonolepis. The size of the catch was found to be positively associated with the social engagement received by the RA videos of all the three mahseer species focused. Angler and angling-related remarks and words associated with the emotion ‘trust’ dominated the comments received by the videos. The results are discussed in light of the trending discourses on developing social media data as a complementary tool for monitoring and managing RA and conserving fish.
Transcriptomic signatures of progressive and regressive liver fibrosis and portal hypertension
Authors: Petrenko Oleksandr , Königshofer Philipp , Brusilovskaya Ksenia , Hofer Benedikt S , Bareiner Katharina , Simbrunner Benedikt , Trauner Michael , Kauschke Stefan G , Pfisterer Larissa , Simon Eric , Rendeiro André F , de Rooij Laura P M H , Schwabl Philipp , Reiberger Thomas
Published: July 2023

Persistent liver injury triggers a fibrogenic program that causes pathologic remodelling of the hepatic microenvironment (i.e., liver fibrosis) and portal hypertension. The dynamics of gene regulation during liver disease progression and regression remain understudied. Here, we generated hepatic transcriptome profiles in two well-established liver disease models at peak fibrosis and during spontaneous regression after the removal of the inducing agents. We linked the dynamics of key liver disease readouts, such as portal pressure, collagen proportionate area, and transaminase serum levels, to most differentially expressed genes, enabling the identification of transcriptomic signatures of progressive vs. regressive liver fibrosis and portal hypertension. These candidate biomarkers (e.g.,Scube1,Tcf4,Src,Hmga1,Trem2,Mafk,Mmp7) were also validated in RNA-seq datasets of patients with cirrhosis and portal hypertension. Finally, deconvolution analysis identified major cell types and suggested an association of macrophage and portal hepatocyte signatures with portal hypertension and fibrosis area in both models.
Collaborative network analysis for the interpretation of transcriptomics data in rare diseases, an application to Huntington’s disease
Authors: Ozisik Ozan , Kara Nazli Sila , Abbassi-Daloii Tooba , Térézol Morgane , Queralt-Rosinach Núria , Jacobsen Annika , Sezerman Osman Ugur , Roos Marco , Evelo Chris T. , Baudot Anaïs , Ehrhart Friederike , Mina Eleni
Published: July 2023

Background

Rare diseases may affect the quality of life of patients and in some cases be life-threatening. Therapeutic opportunities are often limited, in part because of the lack of understanding of the molecular mechanisms that can cause disease. This can be ascribed to the low prevalence of rare diseases and therefore the lower sample sizes available for research. A way to overcome this is to integrate experimental rare disease data with prior knowledge using network-based methods. Taking this one step further, we hypothesized that combining and analyzing the results from multiple network-based methods could provide data-driven hypotheses of pathogenicity mechanisms from multiple perspectives.

Results

We analyzed a Huntington’s disease (HD) transcriptomics dataset using six network-based methods in a collaborative way. These methods either inherently reported enriched annotation terms or their results were fed into enrichment analyses. The resulting significantly enriched Reactome pathways were then summarized using the ontological hierarchy which allowed the integration and interpretation of outputs from multiple methods. Among the resulting enriched pathways, there are pathways that have been shown previously to be involved in HD and pathways whose direct contribution to disease pathogenesis remains unclear and requires further investigation.

Conclusions

In summary, our study shows that collaborative network analysis approaches are well-suited to study rare diseases, as they provide hypotheses for pathogenic mechanisms from multiple perspectives. Applying different methods to the same case study can uncover different disease mechanisms that would not be apparent with the application of a single method.
The spatial extent of anatomical connections within the thalamus varies across the cortical hierarchy in humans and macaques
Authors: Howell Amber M. , Warrington Shaun , Fonteneau Clara , Cho Youngsun T. , Sotiropoulos Stamatios N. , Murray John D. , Anticevic Alan
Published: July 2023

Each cortical area has a distinct pattern of anatomical connections within the thalamus, a central subcortical structure composed of functionally and structurally distinct nuclei. Previous studies have suggested that certain cortical areas may have more extensive anatomical connections that target multiple thalamic nuclei, which potentially allows them to modulate distributed information flow. However, there is a lack of quantitative investigations into anatomical connectivity patterns within the thalamus. Consequently, it remains unknown if cortical areas exhibit systematic differences in the extent of their anatomical connections within the thalamus. To address this knowledge gap, we used diffusion magnetic resonance imaging (dMRI) to perform brain-wide probabilistic tractography for 828 healthy adults from the Human Connectome Project. We then developed a framework to quantify the spatial extent of each cortical area’s anatomical connections within the thalamus. Additionally, we leveraged resting-state functional MRI, cortical myelin, and human neural gene expression data to test if the extent of anatomical connections within the thalamus varied along the cortical hierarchy. Our results revealed two distinct cortico-thalamic tractography motifs: 1) a sensorimotor cortical motif characterized by focal thalamic connections targeting posterolateral thalamus, associated with fast, feed-forward information flow; and 2) an associative cortical motif characterized by diffuse thalamic connections targeting anteromedial thalamus, associated with slow, feed-back information flow. These findings were consistent across human subjects and were also observed in macaques, indicating cross-species generalizability. Overall, our study demonstrates that sensorimotor and association cortical areas exhibit differences in the spatial extent of their anatomical connections within the thalamus, which may support functionally-distinct cortico-thalamic information flow.
Dendritic Cells Overcome Cre/Lox Induced Gene Deficiency by Siphoning Material From Neighboring Cells Using Intracellular Monitoring—a Novel Mechanism of Antigen Acquisition
Authors: Herbst Christopher H. , Bouteau Aurélie , Menykő Evelin J. , Qin Zhen , Su Qingtai , Buelvas Dunia M. , Gyenge Ervin , Mabbott Neil A. , Igyártó Botond Z.
Published: July 2023

Macrophages and dendritic cells (DCs) in peripheral tissue interact closely with their local microenvironment by scavenging protein and nucleic acids released by neighboring cells. Material transfer between cell types is necessary for pathogen detection and antigen presentation, but thought to be relatively limited in scale. Recent reports, however, demonstrate that the quantity of transferred material can be quite large when DCs are in direct contact with live cells. This observation may be problematic for conditional gene deletion models that assume gene products will remain in the cell they are produced in. Here, we investigate whether conditional gene deletions induced by the widely used Cre/Lox system can be overcome at the protein level in DCs. Of concern, using the human Langerin Cre mouse model, we find that epidermal Langerhans cells and CD11b+CD103+ mesenteric DCs can overcome gene deletion if the deleted gene is expressed by neighboring cells. Surprisingly, we also find that the mechanism of material transfer does not resemble known mechanisms of antigen uptake, is dependent on extra- and intracellular calcium, PI3K, and scavenger receptors, and mediates a majority of material transfer to DCs. We term this novel processintracellular monitoring,and find that it is specific to DCs, but occurs in all murine DC subsets tested, as well as in human DCs. Transferred material is successfully presented and cross presented on MHC-II and MHC-I, and occurs between allogeneic donor and acceptors cells—implicating this widespread and unique process in immunosurveillance and organ transplantation.

ONE SENTENCE SUMMARY

Dendritic cells maintain RNA and protein levels for conditionally deleted genes by siphoning material from neighboring cells using a novel mechanism.
Matrix confinement modulates 3D spheroid sorting and burst-like collective migration
Authors: Cai Grace , Li Xinzhi , Lin Shan-Shan , Chen Samuel J. , Rodgers Nicole C. , Koning Katherine M. , Bi Dapeng , Liu Allen P.
Published: July 2023

While it is known that cells with differential adhesion tend to segregate and preferentially sort, the physical forces governing sorting and invasion in heterogeneous tumors remain poorly understood. To investigate this, we tune matrix confinement, mimicking changes in the stiffness and confinement of the tumor microenvironment, to explore how physical confinement influences individual and collective cell migration in 3D spheroids. High levels of confinement lead to cell sorting while reducing matrix confinement triggers the collective fluidization of cell motion. Cell sorting, which depends on cell-cell adhesion, is crucial to this phenomenon. Burst-like migration does not occur for spheroids that have not undergone sorting, regardless of the degree of matrix confinement. Using computational Self-Propelled Voronoi modeling, we show that spheroid sorting and invasion into the matrix depend on the balance between cell-generated forces and matrix resistance. The findings support a model where matrix confinement modulates 3D spheroid sorting and unjamming in an adhesion-dependent manner, providing insights into the mechanisms of cell sorting and migration in the primary tumor and toward distant metastatic sites.
Bilingual Language Model for Protein Sequence and Structure
Authors: Heinzinger Michael , Weissenow Konstantin , Sanchez Joaquin Gomez , Henkel Adrian , Mirdita Milot , Steinegger Martin , Rost Burkhard
Published: July 2023

Adapting large language models (LLMs) to protein sequences spawned the development of powerful protein language models (pLMs). Concurrently, AlphaFold2 broke through in protein structure prediction. Now we can systematically and comprehensively explore the dual nature of proteins that act and exist as three-dimensional (3D) machines and evolve as linear strings of one-dimensional (1D) sequences. Here, we leverage pLMs to simultaneously model both modalities by combining 1D sequences with 3D structure in a single model. We encode protein structures as token sequences using the 3Di-alphabet introduced by the 3D-alignment methodFoldseek. This new foundation pLM extracts the features and patterns of the resulting “structure-sequence” representation. Toward this end, we built a non-redundant dataset from AlphaFoldDB and fine-tuned an existing pLM (ProtT5) to translate between 3Di and amino acid sequences. As a proof-of-concept for our novel approach, dubbed Protein structure-sequence T5 (ProstT5), we showed improved performance for subsequent prediction tasks, and for “inverse folding”, namely the generation of novel protein sequences adopting a given structural scaffold (“fold”). Our work showcased the potential of pLMs to tap into the information-rich protein structure revolution fueled by AlphaFold2.ProstT5paves the way to develop new tools integrating the vast resource of 3D predictions, and opens new research avenues in the post-AlphaFold2 era. Our model is freely available for all athttps://github.com/mheinzinger/ProstT5.
Deep learning-based cell profiling based on neuronal morphology
Authors: Liu Qiang , Nicholls Francesca , Rowland Helen A. , Dangla-Valls Adrià , Li Shuhan , Zhang Yi , Kalinowski Piotr , Ribe Elena , Ifkovits Jamie L. , Kumar Sanjay , Nguyen Cuong Q. , Nevado-Holgado Alejo , Buckley Noel J. , Kormilitzin Andrey
Published: July 2023

Treatment of neurons with β-amyloid peptide (Aβ1-42) has been widely used as a model to interrogate the cellular and molecular mechanisms underlying Alzheimer’s disease, and as an assay system to identify drugs that reverse or block disease phenotype. Prior studies have largely relied on high content imaging (HCI) to extract cellular features such as neurite length or branching, but these have not offered a robust/comprehensive means of relating readout to Aβ1-42concentrations. Here, we use a deep learning-based cell profiling technique to directly measure the impact of Aβ1-42on primary murine cortical neurons. The deep learning model achieved approximately 80% accuracy, compared to 54% for the cell phenotypic feature-based approach. The deep learning model could distinguish subtle neuronal morphological changes induced by a range of Aβ1-42concentration. When tested on a separate dataset, the accuracy remained comparable and dropped by only 2%. Our study demonstrates that deep learning-based cell profiling is superior to HCI-based feature extraction on neuronal morphology and it provides an alternative to a dose/response curve, where the modality of the response does not have to be pre-determined. Moreover, this approach could form the basis of a screening tool that can be applied to any cellular model where appropriate phenotypic markers based on genotypes and/or pathological insults are available.
Natural Product Screen Identifies Asiatic Acid Targeting Mutant p53
Authors: Swargiary Geeta , Jamal Qazi S , Ojha Shreesh , Jha Niraj Kumar , Singh Keshav K , Mani Shalini
Published: July 2023

Mutations in p53 are common in different cancer types and are reported to protect cancer via different mechanisms. R175H, R248Q, and R273H are the hotspot mutations of p53 and are suggested to increase aerobic glycolysis in cancer cells. Cancer cells rely mostly upon aerobic glycolysis, so it will be interesting to target these three p53 mutants for designing alternative cancer therapy. The class of compounds studied for their potential to target energy metabolism of cancer cells is called mitocans. The current study is an approach to explore if these selected 3 mutants of p53 may act as suitable target(s) for natural mitocans. Hereby, we selected 60 phytocompounds altogether fromAndrographis paniculataandCentella asiaticaand docked against all three p53 mutants, using Autodock vina. 11 compounds were sorted based on their binding energies and drug-like properties, and toxicity levels prediction showed asiatic acid to be the most significant. As asiatic acid was observed to significantly bind with R248Q only, R248Q-Asiatic acid was identified for molecular dynamics simulation using GROMACS which showed significant interactions. In conclusion, mutant R248Q was observed to be the best target for asiatic acid, though additionalin-vitroexperiments are important to validate the findings of this study.
The Role of Rivers as Geographical Barriers in Shaping Genetic Differentiation and Diversity of Neotropical Primates
Authors: Helenbrook William D. , Valdez Jose
Published: July 2023

We quantitatively tested the riverine barrier hypothesis and its influence on biogeographical distributions and molecular variation in New World monkeys (Parvorder: Platyrrhini). Using mitochondrial markers (cytochrome oxidase subunit II and cytochrome b), we analyzed taxonomic differences and the effects of geographical barriers on molecular patterns across Central and South America. Nearly 80% of described species are separated by geographical barriers. River width exhibited a positive correlation with molecular dissimilarity in adjacent taxa for both molecular markers. Streamflow also showed a positive association, although not statistically significant, likely due to limited sample size. Several presently described taxa were not supported based solely on these molecular phylogenetic markers, includingSaimiri,Mico,Cebus,Sapajus, andCherecebus. These taxonomic issues are far more common where river barriers do not exist. In conclusion, we found a significant correlation between river width and molecular divergence in adjacent taxa, indicating that wider rivers were associated with greater molecular dissimilarity for two commonly used mitochondrial genes. Species boundaries were predominantly found at river interfaces, and in the absence of discernable geological barriers, adjoining species were more likely to exhibit molecular similarity. Our findings suggest that both river and mountain barriers significantly restrict gene flow for the majority of neotropical taxa, with geological formation of river barriers coinciding with estimated speciation events. Additionally, river width proves to be a valuable tool for estimating molecular divergence in adjacent taxa, particularly in regions with limited sampling.
Allostery in Protein Tyrosine Phosphatases is Enabled by Divergent Dynamics
Authors: Welsh Colin L. , Madan Lalima K.
Published: July 2023

Dynamics-driven allostery provides important insights into the working mechanics of proteins, especially enzymes. In this study we employ this paradigm to answer a basic question: in enzyme superfamilies where the catalytic mechanism, active sites and protein fold are conserved, what accounts for the difference in the catalytic prowess of the individual members? We show that when subtle changes in sequence do not translate to changes in structure, they do translate to changes in dynamics. We use sequentially diverse PTP1B, TbPTP1, and YopH as the representatives of the conserved Protein Tyrosine Phosphatase (PTP) superfamily. Using amino acid network analysis of group behavior (community analysis) and influential node dominance on networks (eigenvector centrality), we explain the dynamic basis of catalytic variations seen between the three proteins. Importantly, we explain how a dynamics-based blueprint makes PTP1B amenable to allosteric control and how the same is abstracted in TbPTP1 and YopH.
Establishment of Tuberculosis Meningitis Mouse Model Using Aerosol Route ofW. BeijingHN878 strain
Authors: Khatri Bhagwati , Goulding Sara , Rannow Vicky , Dagg Belinda , Ho Mei Mei
Published: July 2023

In this study, we report the development of a tuberculosis meningitis (TBM) mouse model using the HN878 strain via the aerosol route. Three genetically different strains of mice, CB6F1, C57BL/6 and BALB/c mice, were used to determine the dissemination of HN878 in the brain. The 8 x 108CFU/ml of HN878 dose was used to infect CB6F1 mice and deposited approximately 3.8 (0.07, SD) log10CFU in the lungs. The burden of HN878 in the brain of the control group (administered saline) after approximately 16/17 days post-infection for CB6F1, C57BL/6 and BALB/c were 4.00 (0.47 SD), 3.79 (0.27, SD) and 2.12 (0.41, SD) log10CFU/brain, respectively. The log10CFU/brain in the BCG vaccinated CB6F1, C57BL/6 and BALB/c mice were 1.05 (0.61, SD), 2.13 (0.33, SD) and 1.42 (0.38, SD) respectively, which, if compared to the control groups, BCG vaccinated mice inhibited dissemination of HN878 in the brain by an impressive 2.94 (CB6F1), 1.66 (C57BL/6) and 0.69 (BALB/c) log10CFU/brain reduction. In conclusion, we have established a relatively inexpensive TBM mouse model using an aerosol, a natural route of infection, which will advance research in understanding TBM dissemination to the brain, and preclinical tuberculosis vaccine/drug discovery/drug regimens against TBM.
Quantification of Covid-19 Vaccine Coercion in India: A Survey Study
Authors: Raman Bhaskaran , Banerjee Amitav , Vajjala Sai Mahesh
Published: July 2023

Introduction

Informed consent is the cornerstone of medical ethics, enshrined in the constitution of most countries, as well as in international documents. However, mandates for Covid-19 vaccination as well as coercion was prevalent in many places in the world, including in India. Against this background, we did a cross sectional study to assess and quantify the extent of Covid-19 vaccine coercion in India.

Methods

A cross sectional study was conducted after obtaining ethical clearance from IIT Bombay. This survey was conducted using a pretested questionnaire anonymously amongst the college students and adults in Mumbai from October 2022 to December 2022. The questionnaire contained details of why the vaccine was taken, and if the participant was a student. Descriptive analysis was conducted and frequencies, percentages along with 95% confidence intervals were used to summarize the findings.

Results

A total of 483 participants responded, which included both students and non-students, of which 470 participants reported having taken the vaccine. A total of 106 (21.95%, 95% C.I. 18.48%-25.85%) reported to have pressured into taking the vaccine. The level of coercion was similar among college students 78 (21.61%, 95% C.I. 17.67%-26.14%) and non-student adults 28 (22.95%, 95% C.I. 15.82% – 31.43%).

Conclusion

A significant proportion was coerced into taking the vaccines, violating the requirement for informed consent. These results are of paramount importance for future policies as well as for posterity.
Cuprizone drives divergent neuropathological changes in different mouse models of Alzheimer’s disease
Authors: Cheng Gerald Wai-Yeung , Ma Iris Wai-Ting , Huang Jianpan , Yeung Sunny Hoi-Sang , Ho Paolo , Chen Zilin , Mak Henry Ka Fung , Herrup Karl , Chan Kannie Wai Yan , Tse Kai-Hei
Published: July 2023

Myelin degradation is a normal feature of brain aging that accelerates in Alzheimer’s disease (AD). To date, however, the underlying biological basis of this correlation remains elusive. The amyloid cascade hypothesis predicts that demyelination is caused by increased levels of the β-amyloid (Aβ) peptide. Here we report on work supporting the alternative hypothesis that early demyelination is upstream of amyloid. We challenged two different mouse models of AD (R1.40 and APP/PS1) using cuprizone-induced demyelination and tracked the responses with both neuroimaging and neuropathology. In oppose to amyloid cascade hypothesis, R1.40 mice, carrying only a single human mutant APP (Swedish; APPSWE) transgene, showed a more abnormal changes of magnetization transfer ratio and diffusivity than in APP/PS1 mice, which carry both APPSWEand a second PSEN1 transgene (delta exon 9; PSEN1dE9). Although cuprizone targets oligodendrocytes (OL), magnetic resonance spectroscopy and targeted RNA-seq data in R1.40 mice suggested a possible metabolic alternation in axons. In support of alternative hypotheses, cuprizone induced significant intraneuronal amyloid deposition in young APP/PS1, but not in R1.40 mice, and it suggested the presence of PSEN deficiencies, may accelerate Aβ deposition upon demyelination. In APP/PS1, mature OL is highly vulnerable to cuprizone with significant DNA double strand breaks (53BP1+) formation. Despite these major changes in myelin, OLs, and Aβ immunoreactivity, no cognitive impairment or hippocampal pathology was detected in APP/PS1 mice after cuprizone treatment. Together, our data supports the hypothesis that myelin loss can be the cause, but not the consequence, of AD pathology.

SIGNIFICANCE STATEMENT

The causal relationship between early myelin loss and the progression of Alzheimer’s disease remains unclear. Using two different AD mouse models, R1.40 and APP/PS1, our study supports the hypothesis that myelin abnormalities are upstream of amyloid production and deposition. We find that acute demyelination initiates intraneuronal amyloid deposition in the frontal cortex. Further, the loss of oligodendrocytes, coupled with the accelerated intraneuronal amyloid deposition, interferes with myelin tract diffusivity at a stage before any hippocampus pathology or cognitive impairments occur. We propose that myelin loss could be the cause, not the consequence, of amyloid pathology during the early stages of Alzheimer’s disease.
ScopeViewer: A Browser-Based Solution for Visualizing Spatial Transcriptomics Data
Authors: Luo Danni , Robertson Sophie , Zhan Yuanchun , Rong Ruichen , Wang Shidan , Jiang Xi , Yang Sen , Palmer Suzette , Jia Liwei , Li Qiwei , Xiao Guanghua , Zhan Xiaowei
Published: July 2023

Motivation

Spatial transcriptomics (ST) enables a high-resolution interrogation of molecular characteristics within specific spatial contexts and tissue morphology. Despite its potential, visualization of ST data is a challenging task due to the complexities in handling, sharing and visualizing large image datasets together with molecular information.

Results

We introduce ScopeViewer, a browser-based software designed to overcome these challenges. ScopeViewer offers the following functionalities: (1) It visualizes large image data and associated annotations at various zoom levels, allowing for intricate exploration of the data; (2) It enables dual interactive viewing of the original images along with their annotations, providing a comprehensive understanding of the context; (3) It displays spatial molecular features with optimized bandwidth, ensuring a smooth user experience; and (4) It bolsters data security by circumventing data transfers.

Availability

ScopeViewer is available at:https://datacommons.swmed.edu/scopeviewer

Contact

Xiaowei.Zhan@UTSouthwestern.edu,Guanghua.Xiao@UTSouthwestern.edu

Supplementary information

Supplementary data are available at Bioinformatics online.
A Strategy for Differential Abundance Analysis of Sparse Microbiome Data with Group-wise Structured Zeros
Authors: Abegaz Fentaw , Abedini Davar , White Fred , Guerrieri Alessandra , Zancarini Anouk , Dong Lemeng , Westerhuis Johan A. , van Eeuwijk Fred , Bouwmeester Harro , Smilde Age K.
Published: July 2023

Comparing the abundance of microbial communities between different groups or obtained under different experimental conditions using count sequence data is a challenging task due to various issues such as inflated zero counts, overdispersion, and non-normality. Several methods and procedures based on counts, their transformation and compositionality have been proposed in the literature to detect differentially abundant species in datasets containing hundreds to thousands of microbial species. Despite efforts to address the the large numbers of zeros present in microbiome datasets, even after careful data preprocessing, the performance of existing methods is impaired by the presence of inflated zero counts and group-wise structured zeros (i.e., all zero counts in a group). We propose and validate using extensive simulations an approach combining two differential abundance testing methods, namely DESeq2-ZINBWaVE and DESeq2, to address the issues of zero-inflation and group-wise structured zeros, respectively. This combined approach was subsequently successfully applied to two plant microbiome datasets that revealed a number of taxa as interesting candidates for further experimental validation.
Mechanisms of extracellular electron transfer in anaerobic methanotrophic archaea
Authors: Ouboter Heleen T , Mesman Rob , Sleutels Tom , Postma Jelle , Wissink Martijn , Jetten Mike S M , Heijne Annemiek ter , Berben Tom , Welte Cornelia U
Published: July 2023

Anaerobic methanotrophic (ANME) archaea are environmentally important uncultivated microorganisms mitigating the release of the potent greenhouse gas methane. During methane oxidation ANME archaea engage in extracellular electron transfer (EET) with other microorganisms, metal oxides, and electrodes, through a currently unknown mechanism. To shed light on this mechanism, we cultivated ANME-2d archaea (’Ca. Methanoperedens’) in bioelectrochemical systems and observed strong methane-dependent current (91-93% of total current) associated with high enrichment of ‘Ca. Methanoperedens’ on the anode (up to 82% of the community) determined by metagenomics and transmission electron microscopy. Electrochemistry and metatranscriptomics indicated that the EET mechanism was similar at various electrode potentials pointing to the involvement of an so far uncharacterized short-range electron transport protein complex and OmcZ nanowires, suggesting a unique EET pathway in all ANME-2 archaea. Our findings furthermore indicate that bioelectrochemical cells might be powerful tools for the cultivation, and possibly isolation, of uncultured electroactive microorganisms.
Revealing and evaluation of antivirals targeting multiple druggable sites of RdRp complex in SARS-CoV-2
Authors: Rani Ruchi , Nehul Sanketkumar , Choudhary Shweta , Upadhyay Anushka , Sharma Gaurav Kumar , Kumar Pravindra , Tomar Shailly
Published: July 2023

SARS-CoV-2 RNA-dependent RNA polymerase (RdRp) complex consisting of nsp12, nsp7, and nsp8 as the key enzyme for viral genome replication and is a proven antiviral drug target. In this study, molecular interactions of nsp7 and nsp8 with nsp12 and the active site of nsp12 were coterminously targeted usingin-silicoscreening of small molecule libraries to identify potential antivirals. Surface plasmon resonance (SPR) based assay using purified nsp7 and nsp8 proteins was developed, and the binding of identified molecules to targets was validated. The antiviral efficacy of identified small molecules was evaluated using cell-based assays, and potent antiviral effect with EC50values of 0.56 μM, 0.73 μM, and 2.8 μM was demonstrated by fangchinoline, cepharanthine, and sennoside B, respectively. Furtherin vivo,investigation usinghACE2mice is being conducted. This is the first study that targets multiple sites in the RdRp complex of SARS-CoV-2 using a structure-based molecular repurposing approach and suggests potential therapeutic options for emerging variants of SARS-CoV-2.
tUbe net: a generalisable deep learning tool for 3D vessel segmentation
Authors: Holroyd Natalie , Li Zhongwang , Walsh Claire , Brown Emmeline , Shipley Rebecca , Walker-Samuel Simon
Published: July 2023

Deep learning has become an invaluable tool for bioimage analysis but, while open-source cell annotation software such as cellpose are widely used, an equivalent tool for three-dimensional (3D) vascular annotation does not exist. With the vascular system being directly impacted by a broad range of diseases, there is significant medical interest in quantitative analysis for vascular imaging. However, existing deep learning approaches for this task are specialised to particular tissue types or imaging modalities. We present a new deep learning model for segmentation of vasculature that is generalisable across tissues, modalities, scales and pathologies. To create a generalisable model, a 3D convolutional neural network was trained using data from multiple modalities including optical imaging, computational tomography and photoacoustic imaging. Through this varied training set, the model was forced to learn common features of vessels cross-modality and scale. Following this, the general model was fine-tuned to different applications with a minimal amount of manually labelled ground truth data. It was found that the general model could be specialised to segment new datasets, with a high degree of accuracy, using as little as 0.3% of the volume of that dataset for fine-tuning. As such, this model enables users to produce accurate segmentations of 3D vascular networks without the need to label large amounts of training data.