bluuebunny/crossref_metadata_2025 huggingface dataset:
Bile acids mediate liver-bone marrow crosstalk
Authors: Vitale Daniele , Azardaryany Mahmoud Karimi , Talesh Ghazal Alipour , Shahidi Mahsa , Ho Vikki , Dervish Suat , Haryanto Jong FX Himawan , Suo Maito , George Jacob , Esmaili Saeed
Published: July 2023

The modern dietary exposome is calorie dense and poor in nutritional quality resulting in high prevalence of fatty liver disease and an increasing incidence of cardiometabolic disease and cancer. We investigated the impact of dietary composition on the interaction between the liver and haematopoietic systems in mice. Using xenograft and chemical-induced liver cancer models, we find that liver tumoursper sehave a minimal impact on haematopoietic stem and progenitor cell (HSPC) responses. In contrast, alterations in dietary composition have profound effects on the liver-bone marrow axis. Specifically, exposure to sucrose with or without dietary cholesterol has minimal impact on the HSPC response, while perturbations in bile acid biosynthesis synergises with excess dietary cholesterol to enhance HSPC responses. Pharmacological restoration of bile acid biosynthesis partially reversed these effects. We conclude that the crosstalk between liver and bone marrow, and subsequent HSPC responses is regulated by bile acid biosynthesis.
Acetylcholine release from basal forebrain promotes cortical synaptic plasticity via somatostatin interneurons
Authors: Zhao Xueyang , Zhang Yu E. , Yang Lu , Yang Yang
Published: July 2023

Basal forebrain (BF) cholinergic projections densely innervate the neocortex, releasing acetylcholine (ACh) to modulate neuronal excitability, thereby influencing sensory processing and cognitive functions. However, the synaptic basis of such ACh-induced effectsin vivoremains elusive. To investigate how ACh release from BF regulates synaptic dynamics in the neocortex, we selectively stimulated BF cholinergic neurons in mice, and used two-photon microscopy to track structural changes of dendritic spines on cortical pyramidal neurons. We found that optogenetic and chemogenetic stimulation of BF cholinergic neurons rapidly induced spine formation in layer 5 pyramidal neurons in the auditory cortex and the posterior parietal cortex. Selective blockage of ACh receptors (AChRs) demonstrated that nicotinic AChRs are required for the ACh-induced spine formation. We also found that Ach-induced spine formation of pyramidal neurons requires the activity of cortical somatostatin-expressing inhibitory interneurons. Together, our study revealed ACh-induced synaptic plasticity in the cortical microcircuitin vivo, providing a synaptic mechanism for cortical neuronal plasticity and functional changes associated with BF ACh release.
RamanSPy: An open-source Python package for integrative Raman spectroscopy data analysis
Authors: Georgiev Dimitar , Pedersen Simon Vilms , Xie Ruoxiao , Fernández-Galiana Álvaro , Stevens Molly M. , Barahona Mauricio
Published: July 2023

Raman spectroscopy is a non-destructive and label-free chemical analysis technique, which plays a key role in the analysis and discovery cycle of various branches of science. Nonetheless, progress in Raman spectroscopic analysis is still impeded by the lack of software, methodological and data standardisation, and the ensuing fragmentation and lack of reproducibility of analysis workflows thereof. To address these issues, we introduceRamanSPy, an open-source Python package for Raman spectroscopic research and analysis.RamanSPyprovides a comprehensive library of ready-to-use tools for spectroscopic analysis, which streamlines day-to-day tasks, integrative analyses, as well as novel research and algorithmic development.RamanSPyis modular and open source, not tied to a particular technology or data format, and can be readily interfaced with the burgeoning ecosystem for data science, statistical analysis and machine learning in Python.
Trace_y: Software algorithms for structural analysis of individual helical filaments by three-dimensional contact point reconstruction atomic force microscopy
Authors: Xue Wei-Feng
Published: July 2023

Atomic force microscopy (AFM) is a powerful and increasingly accessible technology that has a wide range of imaging applications. AFM is capable of producing detailed three-dimensional topographical height images with a high signal-to-noise ratio. This is a key capability of AFM, which enables the structural features of individual molecules to be studied without the need for ensemble averaging, and could offer structural analysis applications where heterogeneity of molecular populations, structural variations between individual molecules, or population distribution properties in general, hold important information. Here, a software tool called Trace_y designed to reconstruct the three-dimensional (3D) surface envelopes of individual helical filament structures from topographical AFM height images is presented. Workflow using Trace_y is demonstrated on the structural analysis of individual helical amyloid protein fibrils where the assembly mechanism of heterogeneous, complex and diverse fibril populations from a single amino-acid sequence due to structural polymorphism is not fully understood. The software and the workflow presented here allows the structural information encoded in topographical AFM height images to be extracted and understood as 3D contact point clouds. This approach will facilitate the use of AFM in structural biology, in integrated methodologies together with other structural analysis tools to understand the structures and behaviours at individual molecule level.
Multiple Pleistocene refugia for Arctic White Heather (Cassiope tetragona) supported by population genomics analyses of contemporary and Little-Ice-Age samples
Authors: Elphinstone Cassandra , Hernandez Fernando , Todesco Marco , Légaré Jean-Sébastien , Cheung Winnie , Sokoloff Paul C. , Hofgaard Annika , Christiansen Casper T. , Frei Esther R. , Lévesque Esther , Daskalova Gergana N. , Thomas Haydn J. D. , Myers-Smith Isla H. , Harris Jacob A. , Saarela Jeffery M. , May Jeremy L. , Obst Joachim , Boike Julia , Clark Karin , MacIntosh Katie , Betway-May Katlyn R. , Björkman Mats P. , Moody Michael L. , Schmidt Niels Martin , Molgaard Per , Björk Robert G. , Hollister Robert D. , Bull Roger D. , Agger Sofie , Maire Vincent , Case Liam , Henry Greg H.R. , Rieseberg Loren H.
Published: July 2023

Aim

Arctic plants survived the Pleistocene glaciations in unglaciated refugia, but the number of these refugia is often unclear. We use high-resolution genomic data from present-day and Little-Ice-Age populations of Arctic White Heather (Cassiope tetragona) to re-evaluate the biogeography of this species and determine whether it had multiple independent refugia or a single refugium in Beringia.

Location

Circumpolar Arctic and Coastal British Columbia (BC) alpine

Taxon

Cassiope tetragonaL., subspeciessaximontanaandtetragona,outgroupC. mertensiana(Ericaceae)

Methods

We built genotyping-by-sequencing (GBS) libraries usingCassiope tetragonatissue from 36 Arctic locations, including two ∼250-500-year-old populations collected under glacial ice on Ellesmere Island, Canada. We assembled ade novoGBS reference and called variants in dDocent. Population structure, genetic diversity, and demography were inferred from PCA, ADMIXTURE, fastsimcoal2, SplitsTree, and several population genomics statistics.

Results

Population structure analyses identified 4-5 clusters that align with geographic locations. Nucleotide diversity was highest in Beringia and decreased eastwards across Canada. Demographic coalescent analysis of the site-frequency-spectrum dated the following splits from Alaska: BC subspeciessaximontana(6 mya), Russia (1.5 mya), Europe (>300-600 kya), Greenland (100 kya). Northern Canada populations appear to be from the current interglacial (7-9 kya). Genetic variants from Alaska appeared more frequently in present-day than historic plants on Ellesmere Island.

Conclusions

Demographic analyses show BC, Alaska, Russia, Europe, and Greenland all had separate refugia during the last major glaciations. Northern Canadian populations appear to be founded during the current interglacial with genetic contributions from Alaska, Europe, and Greenland. On Ellesmere Island, there is evidence for continued, recent gene flow with foreign variants introduced in the last 250-500 years. These results suggest that a re-analysis of other Arctic species with shallow population structure using higher resolution genomic markers and demographic analyses may help reveal deeper structure and other circumpolar glacial refugia.
Mapping general anesthesia states based on electro-encephalogram transition phases
Authors: Loison V. , Voskobiynyk Y. , Lindquist B. , Necula D. , Longrois D. , Paz J. , Holcman D.
Published: July 2023

Cortical electro-encephalography (EEG) has become the clinical reference for monitoring unconsciousness during general anesthesia. The current EEG-based monitors classify general anesthesia states simply as underdosed, adequate, or overdosed, with no transition phases among these states, and therefore no predictive power. To address the issue of transition phases, we analyzed EEG signal of isoflurane-induced general anesthesia in mice. We adopted a data-driven approach and utilized signal processing to trackθ- andδ- band dynamics as well as iso-electric suppressions. By combining this approach with machine learning, we developed a fully-automated algorithm. We found that the dampening of theδ-band occurred several minutes before significant iso-electric suppression episodes. Additionally, we observed a distinctγ-frequency oscillation that persisted for several minutes during the recovery phase following isoflurane-induced overdose. Finally, we constructed a map summarizing multiple states and their transitions which can be utilized to predict and prevent overdose during general anesthesia. The transition phases we identified and algorithm we developed may allow clinicians to prevent inadequate anesthesia, and thus individually tailor anesthetic regimens.

1

Significance statement

In human patients, overdosing during general anesthesia can lead to cognitive impairment. Cortical electro-encephalograms are used to measure the depth of anesthesia. They allow for correction, but not prevention, of overdose. However, data-driven approaches open new possibilities to predict the depth of anesthesia. We established an electro-encephalogram signalprocessing pipeline, and constructed a predictive map representing an ensemble of gradual sedation states during general anesthesia in mice. In particular, we identified key electroencephalogram patterns which anticipate signs of overdose several minutes before they occur. Our results bring a novel paradigm to the medical community, allowing for the development of individually tailored and predictive anesthetic regimens.
Social influence in adolescence: behavioral and neural responses to peer and expert opinion
Authors: Irani Fatemeh , Muotka Joona , Lyyra Pessi , Parviainen Tiina , Monto Simo
Published: July 2023

Social influence plays a crucial role during the teen years, with adolescents supposedly exhibiting heightened sensitivity to their peers. In this study, we examine how social influence from different sources, particularly those with varying normative and informational significance, affect adolescents’ opinion change. Furthermore, we investigate underlying neural dynamics to determine whether these two behaviorally similar influences share their neural mechanisms. Twenty-three participants (14-17 years old) gave their opinions about facial stimuli and received feedback from either a peer group or an expert group, while brain responses were recorded using concurrent magnetoencephalography. In a second rating session, we found that participants’ opinions changed in line with conflicting feedback, but only when the feedback was lower than their initial evaluation. On the neural level, conflict with the peer group evoked stronger neural responses than conflict with experts in the 230-400 ms time window. Nevertheless, there was no greater conformity toward peers. Moreover, conflict compared to no conflict decreased neural oscillations in the beta frequency range (20–27 Hz) at the right frontal and parietal channels. Taken together, our findings do not support the general assumption that adolescent behavior is excessively vulnerable to peer norms, although we found heightened neural sensitivity to peer feedback.
A novel tamanavirus (Flaviviridae) of the European common frog (Rana temporaria) encodes a divergent class 1b XRN1-resistant RNA element
Authors: Parry Rhys , Slonchak Andrii , Campbell Lewis J. , Newton Natalee D. , Debat Humberto J. , Gifford Robert J. , Khromykh Alexander A
Published: July 2023

Flavivirids are small, enveloped, positive-sense RNA viruses from theFlaviviridaefamily with genomes between ∼9-13kb. Metatranscriptomic analyses of metazoan organisms have revealed a diversity of flavivirus-like or flavivirid viral sequences in fish and marine invertebrate groups. To date, however, no flavivirus-like or flavivirid has been identified in amphibians. To remedy this, we investigated the virome of the European common frog (Rana temporaria) in the United Kingdom, utilising high-throughput sequencing at six catch locations. De novo assembly revealed a coding-complete virus contig of a novel flavivirid ∼11.2kb in length. The virus encodes a single open reading frame of 3456 amino acids and 5’ and 3’ untranslated regions (UTRs) of 227 and 666nt, respectively. We named this virus Rana tamanavirus (RaTV), as BLASTp analysis of the polyprotein showed the closest relationships to Tamana bat virus (TABV) and Cyclopterus lumpus virus fromPteronotus parnelliiandCyclopterus lumpus, respectively. Phylogenetic analysis of the RaTV polyprotein compared toFlavivirusand Flavivirus-like members indicated that RaTV was sufficiently divergent and basal to the vertebrate Tamanavirus clade. In addition to the Mitcham strain, partial but divergent RaTV, 95.64-97.39% pairwise nucleotide identity, were also obtained from the Poole and Deal samples, indicating that RaTV is widespread in UK frog samples. Bioinformatic analyses of putative secondary structures in the 3′-UTR of RaTV indicated a potential exoribonuclease-resistant RNA (xrRNA) structure identified in flaviviruses and TABV. To examine this biochemically, we conducted an in vitro XRN1 digestion assay showing that RaTV likely forms a divergent but functionally homologous XRN1-resistant xrRNA.
Epigenetic and neural correlates of selective social attention across adulthood
Authors: Puglia Meghan H. , Lynch Morgan E. , Nance Madelyn G. , Connelly Jessica J. , Morris James P.
Published: July 2023

Social isolation is one of the strongest predictors of increased risk of mortality in older adulthood. The ability to form and maintain the social relationships that mitigate this risk is partially regulated by the oxytocinergic system and one’s ability to attend to and process social information. We have previously shown that an epigenetic change to the DNA of the oxytocin receptor gene (OXTRmethylation) affects the salience of social information in young adults. Little is known about how the oxytocinergic system ages and what effect this aging system has on social cognitive abilities throughout the lifespan. Here we explore age-related differences in the association between neural response during selective social attention andOXTRDNA methylation in young and older adults. We find that older adults activate diffuse areas of visual cortex and dorsolateral prefrontal cortex during selective social attention, consistent with the dedifferentiation and compensatory neural activation commonly reported in aging. We find a significant age-by-OXTRmethylation interaction on neural response when attending to social stimuli in a complex display; young adults display a positive association betweenOXTRmethylation and neural activation, replicating our prior finding that young adults with presumed diminished endogenous access to oxytocin recruit regions of the attentional cortex to a greater extent. This association does not hold for older adults. Instead, perceived social support interacts withOXTRmethylation to influence neural response during selective social attention. These data suggest that environmental factors like social support moderate biological processes in aging and highlight the importance of a lifespan perspective for understanding associations between individual differences in the oxytocinergic system, neural function, and social behavior.
Cellular traits regulate fluorescence-based bio-optical phenotypes of coral photosymbionts livingin-hospite
Authors: McQuagge Audrey , Pahl K. Blue , Wong Sophie , Melman Todd , Linn Laura , Lowry Sean , Hoadley Kenneth D.
Published: July 2023

Abstract

Diversity across algal familySymbiodiniaceaecontributes to the environmental resilience of certain coral species. Chlorophyll-afluorescence measurements are frequently used to determine symbiont health and resilience, but more work is needed to refine these tools and establish how they relate to underlying cellular traits. We examined trait diversity in symbionts from the generasCladocopiumandDurusdinium,collected from 12 aquacultured coral species. Photophysiological metrics (ΦPSII, σPSII, ρ, τ1, τ2, ABQ, NPQ, and qP) were assessed using a prototype multi-spectral fluorometer over a variable light protocol which yielded a total of 1360 individual metrics. Photophysiological metrics were then used to establish four unique phenotypic variants. Corals harboring C15 were predominantly found within a single phenotype which clustered separately from all other coral fragments. The majority ofDurusdiniumdominated colonies also formed a separate phenotype which it shared with a few C1 dominated corals. C15 and D1 symbionts appear to differ in which mechanisms they employ to dissipate excess light energy. Spectrally dependent variability is also observed across phenotypes that may relate to differences in photopigment utilization. Cell physiology (atomic C:N:P, cell size, chlorophyll-a, neutral lipid content) was also assessed within each sample and differ across phenotypes, linking photophysiological metrics with underlying primary cellular traits. Strong correlations between first– and second-order traits, such as Quantum Yield and cellular N:P content, or light dissipation pathways (qP and NPQ) and C:P underline differences across symbiont types and may also provide a means for using fluorescence-based metrics as biomarkers for certain primary-cellular traits.
Myeloid cell activation during Zika virus encephalitis predicts recovery of functional cortical connectivity
Authors: Agner Shannon C. , Brier Lindsey M. , Hill Jeremy , Liu Ethan , Bice Annie , Rahn Rachel M. , Culver Joseph P. , Klein Robyn S.
Published: July 2023

Neurologic complications of Zika virus (ZIKV) infection across the lifespan have been described during outbreaks in Southeast Asia, South America, and Central America since 2016. In the adult CNS ZIKV tropism for neurons is tightly linked to its effects, with neuronal loss within the hippocampus during acute infection and protracted synapse loss during recovery, which is associated with cognitive deficits. The effects of ZIKV on cortical networks have not been evaluated. Although animal behavior assays have been used previously to model cognitive impairment, in vivo brain imaging can provide orthogonal information regarding the health of brain networks in real time, providing a tool to translate findings in animal models to humans. In this study, we use widefield optical imaging to measure cortical functional connectivity (FC) in mice during acute infection with, and recovery from, intracranial infection with a mouse-adapted strain of ZIKV. Acute ZIKV infection leads to high levels of myeloid cell activation, with loss of neurons and presynaptic termini in the cerebral cortex and associated loss of FC primarily within the somatosensory cortex. During recovery, neuron numbers, synapses and FC recover to levels near those of healthy mice. However, hippocampal injury and impaired spatial cognition persist. The magnitude of activated myeloid cells during acute infection predicted both recovery of synapses and the degree of FC recovery after recovery from ZIKV infection. These findings suggest that a robust inflammatory response may contribute to the health of functional brain networks after recovery from infection.

Significance Statement

Determining the long-term cognitive impact of infections is clinically challenging. We found that the degree of myeloid cell activation correlated with the degree of recovery of functional connectivity after recovery from ZIKV encephalitis. Using functional cortical connectivity, we demonstrate that interhemispheric cortical connectivity is decreased in individuals with acute ZIKV encephalitis. This correlates with decreased presynaptic terminals in the somatosensory cortex. During recovery from ZIKV infection, presynaptic terminals recover, which is associated with recovered interhemispheric connectivity. This suggests a role for activated myeloid cells in maintenance of cognition and further supports the contribution of synapses in the cortex to functional networks in the brain, which can be detected by widefield optical imaging. These findings also suggest neuroinflammation may play a neuroprotective role in addition to aiding in local virologic control.
This microtubule does not exist: Super-resolution microscopy image generation by a diffusion model
Authors: Saguy Alon , Nahimov Tav , Lehrman Maia , Gómez-de-Mariscal Estibaliz , Hidalgo-Cenalmor Iván , Alalouf Onit , Henriques Ricardo , Shechtman Yoav
Published: July 2023

Generative models, such as diffusion models, have made significant advancements in recent years, enabling the synthesis of high-quality realistic data across various domains. Here, we explore the adaptation and training of a diffusion model on super-resolution microscopy images from publicly available databases. We show that the generated images resemble experimental images, and that the generation process does not memorize existing images from the training set. Additionally, we compare the performance of a deep learning-based deconvolution method trained using our generated high-resolution data versus training using high-resolution data acquired by mathematical modeling of the sample. We obtain superior reconstruction quality in terms of spatial resolution using a small real training dataset, showing the potential of accurate virtual image generation to overcome the limitations of collecting and annotating image data for training. Finally, we make our pipeline publicly available, runnable online, and user-friendly to enable researchers to generate their own synthetic microscopy data. This work demonstrates the potential contribution of generative diffusion models for microscopy tasks and paves the way for their future application in this field.
A Novel Drosophila Model to Investigate Adipose Tissue Macrophage Infiltration (ATM) and Obesity highlights the Therapeutic Potential of Attenuating Eiger/TNFα Signaling to Ameliorate Insulin Resistance and ATM
Authors: Mirzoyan Zhasmine , Valenza Alice , Zola Sheri , Bonfanti Carola , Arnaboldi Lorenzo , Ferrari Nicholas , Pollard John , Lupi Valeria , Cassinelli Matteo , Frattaroli Matteo , Sahin Mehtap , Pasini Maria Enrica , Bellosta Paola
Published: July 2023

Obesity is a global health concern associated with various metabolic disorders including insulin resistance and adipose tissue inflammation characterized by adipose tissue macrophage (ATM) infiltration. In this study, we present a novelDrosophilamodel to investigate the mechanisms underlying ATM infiltration and its association with obesity-related pathologies. Furthermore, we demonstrate the therapeutic potential of attenuating Eiger/TNFα signaling to ameliorate insulin resistance and ATM. To study ATM infiltration and its consequences, we established a novelDrosophilamodel (OBL) that mimics key aspects of human adipose tissue and allows for investigating ATM infiltration and other related metabolic disorders in a controlled experimental system. We employed genetic manipulation to reduce ecdysone levels to prolong the larval stage. These animals are hyperphagic, and exhibit features resembling obesity in mammals, including increased lipid storage, adipocyte hypertrophy, and high levels of circulating glucose. Moreover, we observed a significant infiltration of immune cells (hemocytes) in the fat bodies accompanied by insulin resistance and systemic metabolic dysregulation. Furthermore, we found that attenuation of Eiger/TNFα signaling and using metformin and anti-oxidant bio-products like anthocyanins led to a reduction in ATM infiltration and improved insulin sensitivity.

Our data suggest that the key mechanisms that trigger immune cell infiltration into adipose tissue are evolutionarily conserved and may provide the opportunity to developDrosophilamodels to better understand pathways critical for immune cell recruitment into adipose tissue, in relation to the development of insulin resistance in metabolic diseases such as obesity and type 2 diabetes, and non-alcoholic fatty liver disease (NAFLD). We believe that our OBL model can also be a valuable tool and provide a platform either to perform genetic screens or to test the efficacy and safety of novel therapeutic interventions for these diseases.
Exogenous butyrate inhibits butyrogenic metabolism and alters expression of virulence genes inClostridioides difficile
Authors: Pensinger Daniel A. , Dobrila Horia A. , Stevenson David M. , Davis Nicole M. , Amador-Noguez Daniel , Hryckowian Andrew J.
Published: July 2023

The gut microbiome engenders colonization resistance against the diarrheal pathogenClostridioides difficilebut the molecular basis of this colonization resistance is incompletely understood. A prominent class of gut microbiome-produced metabolites important for colonization resistance againstC. difficileis short chain fatty acids (SCFAs). In particular, one SCFA (butyrate) decreases the fitness ofC. difficilein vitro and is correlated withC. difficile- inhospitable gut environments, both in mice and in humans. Here, we demonstrate that butyrate-dependent growth inhibition inC. difficileoccurs under conditions whereC. difficilealso produces butyrate as a metabolic end product. Furthermore, we show that exogenous butyrate is internalized intoC. difficilecells, is incorporated into intracellular CoA pools where it is metabolized in a reverse (energetically unfavorable) direction to crotonyl-CoA and (S)-3-hydroxybutyryl-CoA and/or 4-hydroxybutyryl-CoA. This internalization of butyrate and reverse metabolic flow of butyrogenic pathway(s) inC. difficilecoincides with alterations in toxin production and sporulation. Together, this work highlights butyrate as a signal of aC. difficileinhospitable environment to whichC. difficileresponds by producing its diarrheagenic toxins and producing environmentally-resistant spores necessary for transmission between hosts. These findings provide foundational data for understanding the molecular and genetic basis of howC. difficilegrowth is inhibited by butyrate and how butyrate serves as a signal to alterC. difficilevirulence in the face of a highly competitive and dynamic gut environment.

IMPORTANCE

The gut microbiome engenders colonization resistance against the diarrheal pathogenClostridioides difficilebut the molecular basis of this colonization resistance is incompletely understood, which hinders the development of novel therapeutic interventions forC. difficileinfection (CDI). We investigated howC. difficileresponds to butyrate, an end-product of gut microbiome community metabolism which inhibitsC. difficilegrowth. We show that exogenously-produced butyrate is internalized intoC. difficile, which inhibitsC. difficilegrowth by interfering with its own butyrate production. This growth inhibition coincides with the expression of virulence-related genes. Future work to disentangle the molecular mechanisms underlying these growth and virulence phenotypes will likely lead to new strategies to restrictC. difficilegrowth in the gut and minimize its pathogenesis during CDI.
Cellular underpinnings of the selective vulnerability to tauopathic insults in Alzheimer’s disease
Authors: Torok Justin , Maia Pedro D. , Anand Chaitali , Raj Ashish
Published: July 2023

Neurodegenerative diseases such as Alzheimer’s disease (AD) exhibit pathological changes in the brain that proceed in a stereotyped and regionally specific fashion, but the cellular and molecular underpinnings of regional vulnerability are currently poorly understood. Recent work has identified certain subpopulations of neurons in a few focal regions of interest, such as the entorhinal cortex, that are selectively vulnerable to tau pathology in AD. However, the cellular underpinnings of regional susceptibility to tau pathology are currently unknown, primarily because whole-brain maps of a comprehensive collection of cell types have been inaccessible. Here, we deployed a recent cell-type mapping pipeline, Matrix Inversion and Subset Selection (MISS), to determine the brain-wide distributions of pan-hippocampal and neocortical neuronal and non-neuronal cells in the mouse using recently available single-cell RNA sequencing (scRNAseq) data. We then performed a robust set of analyses to identify general principles of cell-type-based selective vulnerability using these cell-type distributions, utilizing 5 transgenic mouse studies that quantified regional tau in 12 distinct PS19 mouse models. Using our approach, which constitutes the broadest exploration of whole-brain selective vulnerability to date, we were able to discover cell types and cell-type classes that conferred vulnerability and resilience to tau pathology. Hippocampal glutamatergic neurons as a whole were strongly positively associated with regional tau deposition, suggesting vulnerability, while cortical glutamatergic and GABAergic neurons were negatively associated. Among glia, we identified oligodendrocytes as the single-most strongly negatively associated cell type, whereas microglia were consistently positively correlated. Strikingly, we found that there was no association between the gene expression relationships between cell types and their vulnerability or resilience to tau pathology. When we looked at the explanatory power of cell types versus GWAS-identified AD risk genes, cell type distributions were consistently more predictive of end-timepoint tau pathology than regional gene expression. To understand the functional enrichment patterns of the genes that were markers of the identified vulnerable or resilient cell types, we performed gene ontology analysis. We found that the genes that are directly correlated to tau pathology are functionally distinct from those that constitutively embody the vulnerable cells. In short, we have demonstrated that regional cell-type composition is a compelling explanation for the selective vulnerability observed in tauopathic diseases at a whole-brain level and is distinct from that conferred by risk genes. These findings may have implications in identifying cell-type-based therapeutic targets.
Protein Binding Leads to Reduced Stability and Solvated Disorder in the Polystyrene Nanoparticle Corona
Authors: Somarathne Radha P. , Amarasekara Dhanush L. , Kariyawasam Chathuri S. , Robertson Harley A. , Mayatt Railey , Fitzkee Nicholas C.
Published: July 2023

Understanding the conformation of proteins in the nanoparticle corona has important implications in how organisms respond to nanoparticle-based drugs. These proteins coat the nanoparticle surface, and their properties will influence the nanoparticle’s interaction with cell targets and the immune system. While some coronas are thought to be disordered, two key unanswered questions are the degree of disorder and solvent accessibility. Here, using a comprehensive thermodynamic approach, along with supporting spectroscopic experiments, we develop a model for protein corona disorder in polystyrene nanoparticles of varying size. For two different proteins, we find that binding affinity decreases as nanoparticle size increases. The stoichiometry of binding, along with changes in the hydrodynamic size, support a highly solvated, disordered protein corona anchored at a small number of enthalpically-driven attachment sites. The scaling of the stoichiometry vs. nanoparticle size is consistent disordered polymer dimensions. Moreover, we find that proteins are destabilized less severely in the presence of larger nanoparticles, and this is supported by measurements of hydrophobic exposure, which becomes less pronounced at lower curvatures. Our observations hold for flat polystyrene surfaces, which, when controlled for total surface area, have the lowest hydrophobic exposure of all systems. Our model provides an explanation for previous observations of increased amyloid fibrillation rates in the presence of larger nanoparticles, and it may rationalize how cell receptors can recognize protein disorder in therapeutic nanoparticles.

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Prospects for a sequence-based taxonomy of influenza A virus subtypes
Authors: Poon Art F. Y.
Published: July 2023

The hemagglutinin (HA) and neuraminidase (NA) proteins are the primary antigenic targets of influenza A virus (IAV) infections. IAV infections are generally classified into subtypes of HA and NA proteins,e.g., H3N2. Most of the known subtypes were originally defined by a lack of antibody cross-reactivity. However, genetic sequencing has played an increasingly important role in characterizing the evolving diversity of IAV. Novel subtypes have recently been described solely by their genetic sequences, and IAV infections are routinely subtyped by molecular assays,e.g., real-time PCR, or the comparison of sequences to references. In this study, I carry out a phylogenetic analysis of all available IAV protein sequences in the Genbank database (over 1.1 million records) to determine whether the serologically-defined subtypes can be reproduced with sequence-based criteria. I show that a robust genetic taxonomy of HA and NA subtypes can be obtained with a simple clustering method, namely by progressively partitioning the phylogeny on its longest internal branches. However, this taxonomy also requires some amendments to the current nomenclature. For example, two IAV isolates from bats previously characterized as a divergent lineage of H9N2 should be separated into their own subtype. With the exception of these small and highly divergent lineages, the phylogenies relating each of the other six genomic segments do not support partitions into major subtypes.
Massive contractions of Myotonic Dystrophy Type 2-associated CCTG tetranucleotide repeats occur via double strand break repair with distinct requirements for helicases
Authors: Papp David , Hernandez Luis A. , Mai Theresa A. , Haanen Terrance J. , O’Donnell Meghan A. , Duran Ariel T. , Hernandez Sophia M. , Narvanto Jenni E. , Arguello Berenice , Onwukwe Marvin O. , Kolar Kara , Mirkin Sergei M. , Kim Jane C.
Published: July 2023

Myotonic Dystrophy Type 2 (DM2) is a genetic disease caused by expanded CCTG DNA repeats in the first intron ofCNBP. The number of CCTG repeats in DM2 patients ranges from 75-11,000, yet little is known about the molecular mechanisms responsible for repeat expansions or contractions. We developed an experimental system inSaccharomyces cerevisiaethat enables selection of large-scale contractions of (CCTG)100within the intron of a reporter gene and subsequent genetic analysis. Contractions exceeded 80 repeat units, causing the final repetitive tract to be well below the threshold for disease. We found that Rad51 and Rad52 are required for these massive contractions, indicating a mechanism that involves homologous recombination. Srs2 helicase was shown previously to stabilize CTG, CAG, and CGG repeats. Loss of Srs2 did not significantly affect CCTG contraction rates in unperturbed conditions. In contrast, loss of the RecQ helicase Sgs1 resulted in a 6-fold decrease in contraction rate with specific evidence that helicase activity is required for large-scale contractions. Using a genetic assay to evaluate chromosome arm loss, we determined that CCTG and reverse complementary CAGG repeats elevate the rate of chromosomal fragility compared to a low-repeat control. Overall, our results demonstrate that the genetic control of CCTG repeat contractions is notably distinct among disease-causing microsatellite repeat sequences.
Using Published Pathway Figures in Enrichment Analysis and Machine Learning
Authors: Shin Min-Gyoung , Pico Alexander R.
Published: July 2023

Abstract

Pathway Figure OCR (PFOCR) is a novel kind of pathway database approaching the breadth and depth of Gene Ontology while providing rich, mechanistic diagrams and direct literature support. PFOCR content is extracted from published pathway figures currently emerging at a rate of 1000 new pathways each month. Here, we compare the pathway information contained in PFOCR against popular pathway databases with respect to overall and disease-specific coverage. In addition to common pathways analysis use cases, we present two advanced case studies demonstrating unique advantages of PFOCR in terms of cancer subtype and grade prediction analyses.
Neuromorphic Cytometry: Implementation on cell counting and size estimation
Authors: Zhang Ziyao , Xu Zhangyu , McGuire Helen M. , Essam Chip , Nicholson Andrew , Hamilton Tara J. , Li Jiayin , Eshraghian Jason K. , Yong Ken-Tye , Vigolo Daniele , Kavehei Omid
Published: July 2023

Flow cytometry is a widespread and high-throughput technology that can measure the features of cells and can be combined with fluorescence analysis for additional phenotypical characterisations but only provide low-dimensional output and spatial resolution. Imaging flow cytometry is another technology that offers rich spatial information, allowing more profound insight into single-cell analysis. However, offering such high-resolution, full-frame feedback can compromise speed and has become a significant trade-off challenge to tackle during development. In addition, the current dynamic range offered by conventional photosensors can only capture limited fluorescence signals, exacerbating the difficulties in elevating performance speed. Neuromorphic photo-sensing architecture focuses on the events of interest via individual-firing pixels to reduce data redundancy and provide low latency in data processing. With the inherent high dynamic range, this architecture has the potential to drastically elevate the performance in throughput by incorporating motion-activated spatial resolution. Herein, we presented an early demonstration of neuromorphic cytometry with the implementation of object counting and size estimation to measure 8μm and 15μm polystyrene-based microparticles and human monocytic cell line (THP-1). In this work, our platform has achieved highly consistent outputs with a widely adopted flow cytometer (CytoFLEX) in detecting the total number and size of the microparticles. Although the current platform cannot deliver multiparametric measurements on cells, future endeavours will include further functionalities and increase the measurement parameters (granularity, cell condition, fluorescence analysis) to enrich cell interpretation.
The canonical single-stranded DNA binding protein SSB is not an essential replication protein but an RNA chaperon in the hyperthermophilic archaeonSaccharolobus islandicusREY15A
Authors: Xiao Yuanxi , Jiang Zhichao , Zhang Mengqi , Zhang Xuemei , Gan Qi , Yang Yunfeng , Wu Pengju , Feng Xu , Ni Jinfeng , Dong Xiuzhu , She Qunxin , Huang Qihong , Shen Yulong
Published: July 2023

Single-stranded DNA binding proteins (SSBs) have been regarded as indispensable factors in all three domains of life since they play vital roles in DNA replication. Herein, we report that genes coding for the canonical SSB (SisSSB) and the non-canonical SSB (SisDBP) in the hyperthermophilic archaeonSaccharolobus islandicusREY15A can both be deleted. The growth is not affected, and the cell cycle progression and genome stability of the deletion strains is not impaired, suggesting that SisSSB and SisDBP are not essential for cell viability. Interestingly, at a lower temperature (55°C), the protein level of SisSSB increases ∼1.8 fold in the wild type and the growth of ΔSisssband ΔSisssbΔSisdbpis retarded. SisSSB exhibits melting activity on dsRNA and DNA/RNA hybridin vitroand unwinding RNA hairpin inEscherichia coli. Furthermore, the core SisSSB domain is able to complement the absence of the cold shock proteins CspABGE inE. coli, suggesting that SisSSB functions as RNA chaperon. We show that a two-fold overexpression of SisSSB is beneficial to the cell growth at lower temperature, but it has detrimental effect on the cell growth and cell cycle progression at normal growth temperature, which differs from bacterial Csp proteins. Importantly, thesein vitroandin vivoactivities are conserved in SSB subtype SSB-1 in Crenarchaeota species that lack bacterial Csp homologs. Overall, we have clarified the function of the archaeal canonical SSB which does not function as a DNA processing factor, but plays a role in processes requiring dsRNA or DNA/RNA hybrid unwinding.
Genetic mixing and demixing on expanding spherical frontiers
Authors: Vázquez Alba García , Mitarai Namiko , Jauffred Liselotte
Published: July 2023

Genetic fluctuation during range expansion is a key process driving evolution. When a bacterial population is expanding on a 2D surface, random fluctuations in the growth of the pioneers at the front line cause a strong de-mixing of genotypes. Even when there is no selective advantage, sectors of low genetic diversity are formed. Experimental studies of range expansions in surface-attached colonies of fluorescently-labeled microorganisms have contributed significantly to our understanding of fundamental evolutionary dynamics. However, experimental studies on genetic fluctuations in 3D range expansions have been sparse, despite their importance for tumour or biofilm development. We encapsulated populations of two fluorescentEscherichia colistrains in inoculation droplets (volumes ∼0.1 nl). The confined ensemble of cells grew when embedded in a hydrogel – with nutrients – and developed 3D colonies with well-defined, sector-like regions. Using a confocal laser scanning microscope (CLSM), we imaged the development of 3D colonies and the emergence of sectors. We characterised how cell concentration in the inoculation droplet controls sectors, growth rate, and the transition from branched colonies to quasi-spherical colonies. We further analysed how sectors on the surface change over time. We complement these experimental results with a modified 3D Eden growth model. The model in 3D spherical growth predicts a phase, where sectors are merging, followed by a steady increase (constant rate), and the experimentally analysed sectors were consistent with this prediction. Ergo, our results demonstrate qualitative differences between radial (2D) and spherical (3D) range expansions and their importance in gene fixation processes.
Outer membrane vesicles as realistic models of bacterial membranes in interaction studies by Surface Plasmon Resonance
Authors: Bril’kov Maxim S. , Stenbakk Victoria , Jakubec Martin , Vasskog Terje , Kristoffersen Tone , Cavanagh Jorunn Pauline , Ericson Johanna U. , Isaksson Johan , Flaten Gøril Eide
Published: July 2023

One way to mitigate the ongoing antimicrobial resistance crisis is to discover and develop new classes of antibiotics. As all antibiotics at some point needs to either cross or interact with the bacterial membrane, there is a need for representative models of bacterial membranes and efficient methods to characterize the interactions to novel antimicrobials – both to generate new knowledge and to screen compound libraries. Since the bacterial cell envelope is a complex assembly of lipids, lipopolysaccharides, membrane proteins and other components, constructing realistic synthetic liposome-based models of the membrane is both difficult and expensive.

We here propose to let the bacteria do the hard work for us. Outer membrane vesicles (OMVs) are naturally secreted by Gram-negative bacteria, playing a role in communication between bacteria, as virulence factors, molecular transport or being a part of the antimicrobial resistance mechanism. OMVs consist of the bacterial outer membrane and thus inherit many components and properties of the native outer cell envelope. In this work we have isolated and characterized OMVs fromE. colimutant strains and clinical isolates of the ESKAPE membersKlebsiella pneumoniae, Acinetobacter baumanniiandPseudomonas aeruginosa. The OMVs were shown to be representative models for the bacterial membrane in terms of lipid composition with strain specific variations. The OMVs were further used to probe the interactions between OMV and antimicrobial peptides (AMPs) as model compounds by Surface Plasmon Resonance (SPR) and provide proof-of-principle that OMVs can be used as an easily accessible and highly realistic model for the bacterial surface in interaction studies. This further enables direct monitoring of the effect of induction by antibiotics, or the response to host-pathogen interactions.
Characterization of Novel Peptides with Antimicrobial and Immunomodulatory Potential
Authors: Kakkerla Swetha , Kavela Sridhar , Kadivella Mohammad , Thupurani Murali Krishna , Chintalpani Sathvika
Published: July 2023

In this study, we designed six peptides based on the characteristics of natural antimicrobial peptides (AMPs), including small size, cationicity, amphipathicity, andα-helix structure. The peptides were evaluated for their antimicrobial activity, hemolytic potential, binding affinity to TLR4/MD-2 receptors, and immunomodulatory effects. Five out of the six designed peptides were classified as AMPs, while one peptide was predicted to be a non-antimicrobial peptide (NAMP) by the AxPEP server. The designed peptides exhibited varying degrees of antimicrobial activity against Escherichia coli, Staphylococcus aureus, Klebsiella pneumoniae, and Pseudomonas aeruginosa, with SK1217 and SK1260 demonstrating stronger antimicrobial potential. Hemolytic assays revealed minimal hemolytic activity for SK1203, SK1217, SK1260, and SK1281, indicating a low propensity to cause red blood cell (RBC) lysis. However, SK1286 and SK1283 exhibited significant hemolytic effects at higher concentrations, with SK1286 causing complete hemolysis at 100 μg/mL. Molecular docking analysis showed favourable binding affinities of SK1260, SK1217, and SK1286 with TLR4/MD-2 receptors. Furthermore, SK1260 displayed potent immunomodulatory activity, reducing the release of pro-inflammatory cytokines IL-6 and TNF-α in LPS-stimulated macrophage cells. Cell viability assays demonstrated minimal cytotoxicity of SK1260. In vivo studies on infected mice showed that SK1260 treatment increased leukocyte recruitment and cytokine levels (GM-CSF, INF-g, and MCP-1) in the peritoneal lavage fluid. Overall, these findings highlight the promising potential of these cationic AMPs as antimicrobial and immunomodulatory agents for further therapeutic exploration.
Deep FASTQ and BAM co-compression in Genozip 15
Authors: Lan Divon Mordechai , Hughes Daniel S.T. , Llamas Bastien
Published: July 2023

We introduce Genozip Deep, a method for losslessly co-compressing FASTQ and BAM files. Benchmarking demonstrates improvements of 75% to 96% versus the already-compressed source files, translating to 2.3X to 6.8X better compression than current state-of-the-art algorithms that compress FASTQ and BAM separately. The Deep method is independent of the underlying FASTQ and BAM compressors, and here we present its implementation in Genozip, an established genomic data compression software.