bluuebunny/crossref_metadata_2025 huggingface dataset:
TooManyCellsInteractive: a visualization tool for dynamic exploration of single-cell data
Authors: Klamann Conor , Lau Christie , Schwartz Gregory W.
Published: June 2023

As single-cell sequencing data sets grow in size, visualizations of large cellular populations become difficult to parse and require extensive processing to identify subpopulations of cells. Managing many of these charts is laborious for technical users and unintuitive for non-technical users. To address this issue, we developed TooManyCellsInteractive (TMCI), a browser-based JavaScript application for visualizing hierarchical cellular populations as an interactive radial tree. TMCI allows users to explore, filter, and manipulate hierarchical data structures through an intuitive interface while also enabling batch export of high-quality custom graphics. Here we describe the software architecture and illustrate how TMCI has identified unique survival pathways among drug-tolerant persister cells in a pan-cancer analysis. TMCI will help guide increasingly large data visualizations and facilitate multi-resolution data exploration in a user-friendly way.
Collective pooling of foraging information in animal fission-fusion dynamics
Authors: Ramos-Fernandez Gabriel , Smith Aguilar Sandra E.
Published: June 2023

1

In animal species with fission-fusion dynamics, individuals can split from or follow others during collective movements. In spider monkeys (Ateles geoffroyi) this decision depends in part on the information they have about the location of available feeding trees. Foraging widely and continuously splitting and joining from others, individuals could be pooling their partial information such that the group as a whole has a more complete picture of a heterogeneous foraging environment. Here we use individual utilization areas over a realistic foraging landscape to infer the sets of potentially known trees by each individual. Then we measure the spatial entropy of these areas, considering tree species diversity and spatial distribution. We measure how complementary pairs of areas are, by decomposing the spatial entropy into redundant and unique components. We find that the areas uniquely known by each pair member still contain considerable amounts of information, but there is also a high redundancy in the information that a pair has about the foraging landscape. The networks joining individuals based on the unique information components seem to be structured efficiently for information transmission. Distributed foraging in fission-fusion dynamics would be an example of adaptive pooling of information and thus, collective intelligence.
The AusTraits Plant Dictionary
Authors: Wenk Elizabeth H. , Sauquet Hervé , Gallagher Rachael V. , Brownlee Rowan , Boettiger Carl , Coleman David , Yang Sophie , Auld Tony , Barrett Russell , Brodribb Timothy , Choat Brendan , Dun Lily , Ellsworth David , Gosper Carl , Guja Lydia , Jordan Gregory J. , Breton Tom Le , Leigh Andrea , Lu-Irving Patricia , Medlyn Belinda , Nolan Rachael , Ooi Mark , Sommerville Karen D. , Vesk Peter , White Mathew , Wright Ian J. , Falster Daniel S.
Published: June 2023

Traits with intuitive names, a clear scope and explicit description are essential for all trait databases. Reanalysis of data from a single database, or analyses that integrate data across multiple databases, can only occur if researchers are confident the trait concepts are consistent within and across sources. The lack of a unified, comprehensive resource for plant trait definitions has previously limited the utility of trait databases. Here we describe the AusTraits Plant Dictionary (APD), which extends the trait definitions included in the new trait database AusTraits. The development process of the APD included three steps: review and formalisation of the scope of each trait and the accompanying trait description; addition of trait meta-data; and publication in both human and machine-readable forms. Trait definitions include keywords, references and links to related trait concepts in other databases, and the traits are grouped into a hierarchy for easy searching. As well as improving the usability of AusTraits, the Dictionary will foster the integration of trait data across global and regional plant trait databases.
Transcriptome data from silica-preserved leaf tissue reveals gene flow patterns in a Caribbean bromeliad
Authors: Ruiz-Vargas Natalia , Ramanauskas Karolis , Tyszka Alexa S. , Mason-Gamer Roberta J. , Walker Joseph F.
Published: June 2023

Transcriptome sequencing is a cost-effective approach that allows researchers to study a broad range of questions. However, to preserve RNA for transcriptome sequencing, tissue is often kept under special conditions, such as immediate ultracold freezing. Here, we demonstrate that RNA can be obtained from six-month-old, field collected samples stored in silica gel at room temperature. Using these transcriptomes, we explore the evolutionary relationships of the genusPitcairnia(Bromeliaceae) in the Dominican Republic and infer barriers to gene flow.

We extracted RNA from silica-dried leaf tissue from 19Pitcairniaindividuals collected across the Dominican Republic. We used a series of macro-and micro-evolutionary approaches to examine the relationships and patterns of gene flow among individuals.

We produced high-quality transcriptomes from silica-dried material and demonstrated that evolutionary relationships on the island match geography more closely than species delimitation methods. A population genetic examination indicates that a combination of ecological and geographic features are barriers to gene flow inPitcairnia.

High-quality transcriptomes can be obtained from silica-preserved tissue. The genetic diversity amongPitcairniapopulations does not warrant classification as separate species, but the Dominican Republic contains several barriers to gene flow, notably the Cordillera Central mountain range.
Proteins containing 6-crossing knot types and their folding pathways
Authors: Sikora Maciej , Flapan Erica , Wong Helen , Rubach Pawel , Garstka Wojciech , Niewieczerzal Szymon , Rawdon Eric J , Sulkowska Joanna I.
Published: June 2023

Studying complex protein knots can provide new insights into potential knot folding mechanisms and other fundamental aspects of why and how proteins knot. This paper presents results of a systematic analysis of the 3D structure of proteins with 6-crossings knots predicted by the artificial intelligence program AlphaFold 2. Furthermore, using a coarse-grained native based model, we found that three representative proteins can self tie to a 63knot, the most complex knot found in a protein thus far. Because it is not a twist knot, the 63knot cannot be folded via a simple mechanism involving the threading of a single loop. Based on successful trajectories for each protein, we determined that the 63knot is formed after folding a significant part of the protein backbone to the native conformation. Moreover, we found that there are two distinct knotting mechanisms, which are described here. Also, building on aloop flipping theorydeveloped earlier, we present two new theories of protein folding involving the creation and threading of two loops, and explain how our theories can describe the successful folding trajectories for each of the three representative 63-knotted proteins.
Simultaneous assessment of human genome and methylome data in a single experiment using limited deamination of methylated cytosine
Authors: Yan Bo , Wang Duan , Ettwiller Laurence
Published: June 2023

Multi-omics requires concerted recording of independent information, ideally from a single experiment. In this study, we introduce RIMS-seq2, a high-throughput technique to simultaneously sequence genomes and overlay methylation information while requiring only a small modification of the experimental protocol for high throughput DNA sequencing to include a controlled deamination step. Importantly, the rate of deamination of 5mC is negligible and thus, do not interfere with standard DNA sequencing and data processing. Thus, RIMS-seq2 libraries from whole or targeted genome sequencing show the same germline variation calling accuracy and sensitivity as compared to standard DNA-seq. Additionally, regional methylation levels provide an accurate map of the human methylome.
Forecasting histone methylation by Polycomb complexes with minute-scale precision
Authors: Lundkvist Moa J. , Lizana Ludvig , Schwartz Yuri B.
Published: June 2023

All animals use the Polycomb system to epigenetically repress developmental genes. The repression requires tri-methylation of Lysine 27 of histone H3 (H3K27me3) by Polycomb Repressive Complex 2 (PRC2), but the dynamics of this process is poorly understood. To bridge the gap, we developed a computational model that forecasts H3K27 methylation inDrosophilawith high temporal resolution and spatial accuracy of contemporary experimental techniques. Using this model, we show that pools of methylated H3K27 in dividing cells are defined by the effective concentration of PRC2 and the replication frequency. We find that the allosteric stimulation by pre-existing H3K27me3 makes PRC2 better in methylating developmental genes as opposed to indiscriminate methylation throughout the genome. Applied toDrosophiladevelopment, our model argues that, in this organism, the intergenerationally inherited H3K27me3 does not “survive” rapid cycles of embryonic chromatin replication and is unlikely to transmit the memory of epigenetic repression to the offspring. We foresee that our model is adaptable to other organisms, including mice and humans.
Context-specific GITR agonism potentiates anti-PD-L1 and CD40-based immuno-chemotherapy combination in heterogeneous pancreatic tumors
Authors: Ragulan Chanthirika , Desai Krisha , Lawrence Patrick Varun , Ikami Yuta , Aalam Mohammed Musheer , Ps Hari , Kannan Nagarajan , Cunningham David , Starling Naureen , Sadanandam Anguraj
Published: June 2023

Immunotherapy has shown limited success in pancreatic adenocarcinoma (PDAC) patients. To improve clinical management of cancer, it is crucial to identify alternative immunostimulatory targets associated with mechanisms of tumor evolution to facilitate the development of novel combination immunotherapies. Here we categorized PDACs and other cancers (n>7,500) into subgroups based on immunostimulatory glucocorticoid-induced tumor necrosis factor receptor (TNFR)-related ligand (GITRL) and receptor (GITR) expression:GITRLhigh+GITRhighandGITRLhigh/low+GITRlow. We characterized immune evasion mechanisms using immunotherapy preclinical trials in four representative immunocompetent mouse models, finding that the GITR agonist, DTA-1 significantly improved responses in GITRLhigh(+GITRhigh) tumors (n=2). Further characterization revealed increased activation of CD8+T-cells (but not T-regulatory; Tregs cells) and enhanced interferon-γ, immunoproteosome, antigen presentation, and T-cell receptor (TCR) gene expression in DTA-1 responders.In vivoclonal tracking using DNA barcoding showed that GITR agonist therapy significantly reduced tumor burden by targeting expansion of heterogeneous PDAC clones and not clone-initiating cells (representing potential resistance). However, emerging GITRLhigh+GITRhighepithelial-like oligoclones from the responder model escaped immune surveillance to GITR agonist treatment via increased PD-L1, offering a combined anti-PD-L1, CD40 agonist and DTA-1 immunotherapy regimens (with/without chemotherapy) that further improved responses by decreasing PD-L1+myeloid cells. Conversely, mesenchymal-enriched GITRLlowmodels exhibited primary (intrinsic) resistance to GITR agonist treatment due to reduced T-cells and increased myeloid and/or PD-L1+non-immune cells. These results provide pre-clinical context for GITR+PD-L1+CD40- based personalized immuno-chemotherapy combinations for PDAC.
Effects of dopamine and opioid receptor antagonism on the neural processing of social and non-social rewards
Authors: Massaccesi Claudia , Korb Sebastian , Götzendorfer Sebastian , Chiappini Emilio , Willeit Matthaeus , Lundström Johan N. , Windischberger Christian , Eisenegger Christoph , Silani Giorgia
Published: June 2023

Rewards are a broad category of stimuli inducing approach behavior to aid survival. Extensive evidence from animal research has shown that wanting (the motivation to pursue a reward) and liking (the pleasure associated with its consumption) are mostly regulated by dopaminergic and opioidergic activity in dedicated brain areas. However, less is known about the neuroanatomy of dopaminergic and opioidergic regulation of reward processing in humans, especially when considering different types of rewards (i.e., social and non-social). To fill this gap of knowledge, we combined dopaminergic and opioidergic antagonism (via amisulpride and naltrexone administration) with functional neuroimaging to investigate the neurochemical and neuroanatomical bases of wanting and liking of matched non-social (food) and social (interpersonal touch) rewards, using a randomized, between-subject, placebo-controlled, double-blind design. While at the behavioral level no drug effect was observed, brain activity was modulated by the administered compounds. In particular, opioid antagonism, compared to placebo, was associated with reduced activity in the medial orbitofrontal cortex during consumption of the most valued social and non-social rewards. Dopamine antagonism, however, had no clear effects on brain activity in response to rewards anticipation. These findings provide insights into the neurobiology of human reward processing and suggest a similar opioidergic regulation of the neural responses to social and non-social reward consumption.
Design of four component T=4 tetrahedral, octahedral, and icosahedral protein nanocages through programmed symmetry breaking
Authors: Lee Sangmin , Kibler Ryan D. , Hsia Yang , Borst Andrew J. , Philomin Annika , Kennedy Madison A. , Stoddard Barry , Baker David
Published: June 2023

Four, eight or twenty C3 symmetric protein trimers can be arranged with tetrahedral (T-sym), octahedral (O-sym) or icosahedral (I-sym) point group symmetry to generate closed cage-like structures1,2. Generating more complex closed structures requires breaking perfect point group symmetry. Viruses do this in the icosahedral case using quasi-symmetry or pseudo-symmetry to access higher triangulation number architectures3–9, but nature appears not to have explored higher triangulation number tetrahedral or octahedral symmetries. Here, we describe a general design strategy for building T = 4 architectures starting from simpler T = 1 structures through pseudo-symmetrization of trimeric building blocks. Electron microscopy confirms the structures of T = 4 cages with 48 (T-sym), 96 (O-sym), and 240 (I-sym) subunits, each with four distinct chains and six different protein-protein interfaces, and diameters of 33nm, 43nm, and 75nm, respectively. Higher triangulation number viruses possess very sophisticated functionalities; our general route to higher triangulation number nanocages should similarly enable a next generation of multiple antigen displaying vaccine candidates10,11and targeted delivery vehicles12,13.
PARP12 is required to repress the replication of a Mac1 mutant coronavirus in a cell and tissue specific manner
Authors: Kerr Catherine M. , Parthasarathy Srivatsan , Schwarting Nancy , O’Connor Joseph J. , Giri Emily , More Sunil , Orozco Robin C. , Fehr Anthony R.
Published: June 2023

ADP-ribosyltransferases (ARTs) mediate the transfer of ADP-ribose from NAD+to protein or nucleic acid substrates. This modification can be removed by several different types of proteins, including macrodomains. Several ARTs, also known as PARPs, are stimulated by interferon, indicating ADP-ribosylation is an important aspect of the innate immune response. All coronaviruses (CoVs) encode for a highly conserved macrodomain (Mac1) that is critical for CoVs to replicate and cause disease, indicating that ADP-ribosylation can effectively control coronavirus infection. Our siRNA screen indicated that PARP12 might inhibit the replication of a MHV Mac1 mutant virus in bone-marrow derived macrophages (BMDMs). To conclusively demonstrate that PARP12 is a key mediator of the antiviral response to CoVs both in cell culture andin vivo, we produced PARP12−/−mice and tested the ability of MHV A59 (hepatotropic/neurotropic) and JHM (neurotropic) Mac1 mutant viruses to replicate and cause disease in these mice. Notably, in the absence of PARP12, Mac1 mutant replication was increased in BMDMs and in mice. In addition, liver pathology was also increased in A59 infected mice. However, the PARP12 knockout did not restore Mac1 mutant virus replication to WT virus levels in all cell or tissue types and did not significantly increase the lethality of Mac1 mutant viruses. These results demonstrate that while PARP12 inhibits MHV Mac1 mutant virus infection, additional PARPs or innate immune factors must contribute to the extreme attenuation of this virus in mice.

IMPORTANCE

Over the last decade, the importance of ADP-ribosyltransferases (ARTs), also known as PARPs, in the antiviral response has gained increased significance as several were shown to either restrict virus replication or impact innate immune responses. However, there are few studies showing ART-mediated inhibition of virus replication or pathogenesis in animal models. We found that the CoV macrodomain (Mac1) was required to prevent ART-mediated inhibition of virus replication in cell culture. Here, using knockout mice, we found that PARP12, an interferon-stimulated ART, was required to repress the replication of a Mac1 mutant CoV both in cell culture and in mice, demonstrating that PARP12 represses coronavirus replication. However, the deletion of PARP12 did not fully rescue Mac1 mutant virus replication or pathogenesis, indicating that multiple PARPs function to counter coronavirus infection.
Characterization of human lightness discrimination thresholds for independent spectral variations
Authors: Reynolds Devin , Singh Vijay
Published: June 2023

The lightness of an object is an intrinsic property that depends on its surface reflectance spectrum. The visual system estimates an object’s lightness from the light reflected off its surface. The light reflected also depends on object extrinsic properties of the scene. For stable perception, the visual system needs to discount variations due to extrinsic properties. We characterize this perceptual stability for variation in two spectral properties of the scene: the reflectance spectra of background objects and the intensity of light sources. We use a two-alternative forced-choice task to measure human observers’ thresholds of discriminating computer-generated images of 3D scenes based on the lightness of a spherical target object in the scene. We measured how the discrimination thresholds changed as we varied the reflectance spectra of the objects and the intensity of the light sources in the scene, both individually and simultaneously. For small amounts of extrinsic variations, the thresholds of discrimination remained constant indicating that the thresholds were dominated by observers’ intrinsic representation of lightness. As extrinsic variation increased, it started affecting observers’ lightness judgment and the thresholds increased. We estimated that the effects of extrinsic variations were comparable to observers’ intrinsic variation in the representation of object lightness. Moreover, for simultaneous variation of these spectral properties, the increase in threshold square compared to no variation condition was a linear sum of the corresponding increase in threshold squares for the individual properties, indicating that the variation from these independent sources combines linearly.
Development and deployment of improvedAnopheles gambiaes.l. field surveillance by adaptive spatial sampling design
Authors: Monteiro Gabriel M. , Djogbénou Luc S. , Donnelly Martin J. , Sedda Luigi
Published: June 2023

Accurate assessments of vector occurrence and abundance, particularly in widespread vector-borne diseases such as malaria, is essential for efficient deployment of disease surveillance and control interventions. This study emphasizes the need for flexible spatial sampling designs that can capture the dynamic relationships between disease vector species and the environment. Although previous studies have examined the benefits of adaptive sampling for disease hotspot identification (mostly by simulations), limited research has been conducted on field surveillance of malaria vectors. Here, an adaptive spatial sampling design targeting potential and uncertainAn. gambiaehotspots, a major malaria vector in sub-Saharan Africa, is presented. The first phase of the proposed design involved ecological zone delineation and a proportional lattice with close pairs sampling design to maximise spatial coverage, representativeness of ecological zones and vector spatial autocorrelation (by the employment of close pairs). In the second phase, a spatial adaptive sampling design targeted high-risk areas with the largest uncertainty. For the second phase, the sample size was reduced compared to the first phase, but predictions improved for out-of-sample and training data. However, the overall model uncertainty increased, highlighting the trade-off in multi-criteria adaptive sampling designs. It is important that future research focuses on these trade-offs to reduce the timescale for effective malaria control and elimination efforts.
Formalin fixation and paraffin embedding interfere with preservation of optical metabolic assessments based on endogenous NAD(P)H and FAD two photon excited fluorescence
Authors: Sánchez-Hernández Adriana , Polleys Christopher M. , Georgakoudi Irene
Published: June 2023

Endogenous NAD(P)H and FAD two-photon excited fluorescence (TPEF) images provide functional metabolic information with high spatial resolution for a wide range of living specimens. Preservation of metabolic function optical metrics upon fixation would facilitate studies which assess the impact of metabolic changes in the context of numerous diseases. However, robust assessments of the impact of formalin fixation, paraffin embedding, and sectioning on the preservation of optical metabolic readouts are lacking. Here, we evaluate intensity and lifetime images at excitation/emission settings optimized for NAD(P)H and FAD TPEF detection from freshly excised murine oral epithelia and corresponding bulk and sectioned fixed tissues. We find that fixation impacts the overall intensity as well as the intensity fluctuations of the images acquired. Accordingly, the depth-dependent variations of the optical redox ratio (defined as FAD/(NAD(P)H + FAD)) across squamous epithelia are not preserved following fixation. This is consistent with significant changes in the 755 nm excited spectra, which reveal broadening upon fixation and additional distortions upon paraffin embedding and sectioning. Analysis of fluorescence lifetime images acquired for excitation/emission settings optimized for NAD(P)H TPEF detection indicate that fixation alters the long lifetime of the observed fluorescence and the long lifetime intensity fraction. These parameters as well as the short TPEF lifetime are significantly modified upon embedding and sectioning. Thus, our studies highlight that the autofluorescence products formed during formalin fixation, paraffin embedding and sectioning overlap highly with NAD(P)H and FAD emission and limit the potential to utilize such tissues to assess metabolic activity.
Dual effects of the small-conductance Ca2+-activated K+current on human atrial electrophysiology and Ca2+-driven arrhythmogenesis: anin silicostudy
Authors: Herrera Nathaniel T. , Zhang Xianwei , Ni Haibo , Maleckar Mary M. , Heijman Jordi , Dobrev Dobromir , Grandi Eleonora , Morotti Stefano
Published: June 2023

By sensing changes in intracellular Ca2+, small-conductance Ca2+-activated K+(SK) channels dynamically regulate the dynamics of the cardiac action potential (AP) on a beat-to-beat basis. Given their predominance in atria vs. ventricles, SK channels are considered a promising atrial-selective pharmacological target against atrial fibrillation (AF), the most common cardiac arrhythmia. However, the precise contribution of SK current (ISK) to atrial arrhythmogenesis is poorly understood, and may potentially involve different mechanisms that depend on species, heart rates, and degree of AF-induced atrial remodeling. Both reduced and enhanced ISKhave been linked to AF. Similarly, both SK channel up- and downregulation have been reported in chronic AF (cAF) vs. normal sinus rhythm (nSR) patient samples. Here, we use our multi-scale modeling framework to obtain mechanistic insights into the contribution of ISKin human atrial myocyte electrophysiology. We simulate several protocols to quantify how ISKmodulation affects the regulation of AP duration (APD), Ca2+transient, refractoriness, and occurrence of alternans and delayed afterdepolarizations (DADs). Our simulations show that ISKactivation shortens the APD and atrial effective refractory period, limits Ca2+cycling, and slightly increases the propensity for alternans in both nSR and cAF conditions. We also show that increasing ISKcounteracts DAD development by reducing the coupling between transmembrane potential and intracellular Ca2+. Taken together, our results suggest that increasing ISKin human atrial myocytes could promote reentry, while protecting against triggered activity. Depending on the leading arrhythmogenic mechanism, ISKinhibition may thus be a beneficial or detrimental anti-AF strategy.
Demographic Reconstruction of the Western Sheep Expansion from Whole-Genome sequences
Authors: Miranda Pedro Morell , Soares André ER , Günther Torsten
Published: June 2023

As one of the earliest livestock, Sheep (Ovis aries) were domesticated in the Fertile Crescent about 12000−10000 years ago and have a nearly worldwide distribution today. Most of our knowledge about the timing of their expansions stems from archaeological data but it is unclear how the genetic diversity of modern sheep fits with these dates. We used whole-genome sequencing data of 63 domestic breeds and their wild relatives, the Asiatic mouflon (O. gmelini), to explore the demographic history of sheep. On the global scale, our analysis revealed geographic structuring among breeds with unidirectional recent gene flow from domestics into Asiatic mouflons. We then selected four representative breeds from Spain, Morocco, the UK and Iran to build a comprehensive demographic model of the Western sheep expansion. We inferred a single domestication event around 9000 years ago, slightly later than archaeological evidence suggests which might reflect uncertainties in the generation time used for these estimates. The westward expansion is dated to approximately 5000 years ago, later than the original Neolithic expansion of sheep and approximately matching the Secondary Product Revolution associated with woolly sheep. We see some signals of recent gene flow from an ancestral population into Southern European breeds which could reflect admixture with feral European mouflon. Furthermore, our results indicate that many breeds experienced a reduction of their effective population size during the last centuries, probably associated with modern breed development. Our study provides insights into the complex demographic history of Western Eurasian sheep, highlighting interactions between breeds and their wild counterparts.
NMFClustering: Accessible NMF-based clustering utilizing GPU acceleration
Authors: Liefeld Ted , Huang Edwin , Wenzel Alexander T. , Yoshimoto Kenneth , Sharma Ashwyn K , Sicklick Jason K , Mesirov Jill P , Reich Michael
Published: June 2023

Non-negative Matrix Factorization (NMF) is an algorithm that can reduce high dimensional datasets of tens of thousands of genes to a handful of metagenes which are biologically easier to interpret. Application of NMF on gene expression data has been limited by its computationally intensive nature, which hinders its use on large datasets such as single-cell RNA sequencing (scRNA-seq) count matrices. We have implemented NMF based clustering to run on high performance GPU compute nodes using CuPy, a GPU backed python library, and the Message Passing Interface (MPI). This reduces the computation time by up to three orders of magnitude and makes the NMF Clustering analysis of large RNA-Seq and scRNA-seq datasets practical. We have made the method freely available through the GenePattern gateway, which provides free public access to hundreds of tools for the analysis and visualization of multiple ‘omic data types. Its web-based interface gives easy access to these tools and allows the creation of multi-step analysis pipelines on high performance computing (HPC) clusters that enable reproduciblein silicoresearch for non-programmers.

Availability and Implementation

NMFClustering is freely available on the public GenePattern server athttps://genepattern.ucsd.edu. Code for the NMFClustering is available under a BSD style license on github athttps://github.com/genepattern/nmf-gpu.

Contact

Ted Liefeld,jliefeld@cloud.ucsd.edu

Supplementary Information

Supplementary data are available at Bioinformatics online and athttps://datasets.genepattern.org/?prefix=data/test_data/NMFClustering/.
Neuronal modeling of magnetoencephalography responses in auditory cortex to auditory and visual stimuli
Authors: Lankinen Kaisu , Ahveninen Jyrki , Jas Mainak , Raij Tommi , Ahlfors Seppo P.
Published: June 2023

Previous studies have demonstrated that auditory cortex activity can be influenced by crosssensory visual inputs. Intracortical recordings in non-human primates (NHP) have suggested a bottom-up feedforward (FF) type laminar profile for auditory evoked but top-down feedback (FB) type for cross-sensory visual evoked activity in the auditory cortex. To test whether this principle applies also to humans, we analyzed magnetoencephalography (MEG) responses from eight human subjects (six females) evoked by simple auditory or visual stimuli. In the estimated MEG source waveforms for auditory cortex region of interest, auditory evoked responses showed peaks at 37 and 90 ms and cross-sensory visual responses at 125 ms. The inputs to the auditory cortex were then modeled through FF and FB type connections targeting different cortical layers using the Human Neocortical Neurosolver (HNN), which consists of a neocortical circuit model linking the cellular– and circuit-level mechanisms to MEG. The HNN models suggested that the measured auditory response could be explained by an FF input followed by an FB input, and the crosssensory visual response by an FB input. Thus, the combined MEG and HNN results support the hypothesis that cross-sensory visual input in the auditory cortex is of FB type. The results also illustrate how the dynamic patterns of the estimated MEG/EEG source activity can provide information about the characteristics of the input into a cortical area in terms of the hierarchical organization among areas.

Significance statement

Laminar intracortical profiles of activity characterize feedforward– and feedback-type influences in the inputs to a cortical area. By combining magnetoencephalography (MEG) and biophysical computational neural modeling, we obtained evidence of cross-sensory visual evoked activity in human auditory cortex being of feedback type. The finding is consistent with previous intracortical recordings in non-human primates. The results illustrate how patterns of MEG source activity can be interpreted in the context of the hierarchical organization among cortical areas.
Cortical Surface Area Relates to Distinct Computational Properties in Human Visual Perception
Authors: Murray Scott O. , Kolodny Tamar , Webb Sara Jane
Published: June 2023

Understanding the relationship between cortical structure and function is essential for elucidating the neural basis of human behavior. However, the impact of cortical structural features on the computational properties of neural circuits remains poorly understood. In this study, we demonstrate that a simple structural feature – cortical surface area (SA) – relates to specific computational properties underlying human visual perception. By combining psychophysical, neuroimaging, and computational modeling approaches, we show that differences in SA in the parietal and frontal cortices are associated with distinct patterns of behavior in a motion perception task. These behavioral differences can be accounted for by specific parameters of a divisive normalization model, suggesting that SA in these regions contributes uniquely to the spatial organization of cortical circuitry. Our findings provide novel evidence linking cortical structure to distinct computational properties and offer a framework for understanding how cortical architecture can impact human behavior.
Expanding the toolkit for genetic manipulation and discovery inCandidaspecies using a CRISPR ribonucleoprotein-based approach
Authors: Gregor Justin B. , Gutierrez-Schultz Victor A. , Hoda Smriti , Baker Kortany M. , Saha Debasmita , Burghaze Madeline G. , Briggs Scott D.
Published: June 2023

The World Health Organization recently published the first list of priority fungal pathogens highlighting multipleCandidaspecies includingC. glabrata,C. albicans, andC. auris. The use of CRISPR-Cas9 and auxotrophicC. glabrataandC. albicansstrains have been instrumental in the study of these fungal pathogens. Dominant drug resistance cassettes are also critical for genetic manipulation and eliminate the concern of altered virulence when using auxotrophic strains. However, genetic manipulation has been mainly limited to the use of two drug resistance cassettes,NatMXandHphMX. Using anin vitroassembled CRISPR-Cas9 ribonucleoprotein (RNP)-based system and 130-150 bp homology regions for directed repair, we expand the drug resistance cassettes forCandidato includeKanMXandBleMX, commonly used inS. cerevisiae. As a proof of principle, we demonstrated efficient deletion ofERGgenes usingKanMXandBleMX. We also showed the utility of the CRISPR-Cas9 RNP system for generating double deletions of genes in the ergosterol pathway and endogenous epitope tagging ofERGgenes using an existingKanMXcassette. This indicates that CRISPR-Cas9 RNP can be used to repurpose theS. cerevisiaetoolkit. Furthermore, we demonstrated that this method is effective at deletingERG3inC. aurisusing a codon optimizedBleMXcassette and effective at deleting the epigenetic factor,SET1, inC. albicansusing a recyclableSAT1.Using this expanded toolkit, we discovered new insights into fungal biology and drug resistance.

IMPORTANCE

The increasing problem of drug resistance and emerging pathogens is an urgent global health problem that necessitates the development and expansion of tools for studying fungal drug resistance and pathogenesis. We have demonstrated the effectiveness of an expression-free CRISPR-Cas9 RNP-based approach employing 130-150 bp homology regions for directed repair. Our approach is robust and efficient for making gene deletions inC. glabrata,C. aurisandC. albicansas well as epitope tagging inC. glabrata. Furthermore, we demonstrated thatKanMXandBleMXdrug resistance cassettes can be repurposed inC. glabrataandBleMXinC. auris. Overall, we have expanded the toolkit for genetic manipulation and discovery in fungal pathogens.
The phoretic mite (Arachnida: Acari) assemblage of the Douglas-fir beetle,Dendroctonus pseudotsugaeHopkins (Coleoptera: Curculionidae)
Authors: Browning Laura-Anne , Huber Dezene P.W.
Published: June 2023

The phoretic mite assemblage of the Douglas-fir beetle,Dendroctonus pseudotsugaeHopkins (Coleoptera: Curculionidae) has not been as thoroughly documented as that of some other ecologically and economically important bark beetle species. Phoretic mites can impact individual fitness and population dynamics of their hosts and documenting the mite assemblage associated with a bark beetle may provide information on their ecological and interactive roles. We caught Douglas-fir beetles over two summers in central British Columbia, Canada and sorted the associated mites into morphospecies. Representatives of the morphospecies were DNA barcoded (cytochrome oxidate I barcode region) which indicated at least nine distinct Operational Taxonomic Units (OTUs). There was a mean of 50.5 ± 4.7 mites per beetle with both females and males carrying similar numbers of most mite species. However one OTU (Sarcoptiformes: Hemisarcoptidae) was found in substantially higher numbers than all other OTUs, and was always clustered in large aggregations in an anterior pocket on the sub-elytral surface. When B1 was removed from the mean, there were only 1.3 ± 0.2 mites per beetle. The consistent high numbers of that OTU in conjunction with its consistent anatomical aggregation suggests an important interaction between that mite species and the Douglas-fir beetle.
Changes in ADAR RNA Editing Patterns in CMV and ZIKV Congenital Infections
Authors: Wales-McGrath Benjamin , Mercer Heather , Piontkivska Helen
Published: June 2023

Background

RNA editing is a process that increases transcriptome diversity, often through Adenosine Deaminases Acting on RNA (ADARs) that catalyze the deamination of adenosine to inosine. ADAR editing plays an important role in regulating brain function and immune activation, and is dynamically regulated during brain development. Additionally, the ADAR1 p150 isoform is induced by interferons in viral infection and plays a role in antiviral immune response. However, the question of how virus-induced ADAR expression affects host transcriptome editing remains largely unanswered. This question is particularly relevant in the context of congenital infections, given the dynamic regulation of ADAR editing during brain development, the importance of this editing for brain function, and subsequent neurological symptoms of such infections, including microcephaly, sensory issues, and other neurodevelopmental abnormalities. Here, we begin to address this question, examining ADAR expression in publicly available datasets of congenital infections of human cytomegalovirus (HCMV) microarray expression data, as well as mouse cytomegalovirus (MCMV) and mouse/ human induced pluripotent neuroprogenitor stem cell (hiNPC) Zika virus (ZIKV) RNA-seq data.

Results

We found that in all three datasets, ADAR1 was overexpressed in infected samples compared to uninfected samples. In the RNA-seq datasets, editing rates were also analyzed. In all mouse infections cases, the number of editing sites was significantly increased in infected samples, albeit this was not the case for hiNPC ZIKV samples. Mouse ZIKV samples showed altered editing of well-established protein-recoding sites such as Gria3, Grik5, and Nova1, as well as editing sites that may impact miRNA binding.

Conclusions

Our findings provide evidence for changes in ADAR expression and subsequent dysregulation of ADAR editing of host transcriptomes in congenital infections. These changes in editing patterns of key neural genes have potential significance in the development of neurological symptoms, thus contributing to neurodevelopmental abnormalities. Further experiments should be performed to explore the full range of editing changes that occur in different congenital infections, and to confirm the specific functional consequences of these editing changes.
Systems engineering ofSaccharomyces cerevisiaefor synthesis and accumulation of vanillin
Authors: Mo Qiwen , Yuan Jifeng
Published: June 2023

Vanillin represents one of the most widely used flavoring agents in the world. However, microbial synthesis of vanillin is hindered by the host native metabolism that could rapidly degrade vanillin to the byproducts. Here, we report that the industrial workhorseSaccharomyces cerevisiaewas engineered by systematic deletion of oxidoreductases to improve the vanillin accumulation. Subsequently, we harnessed thereduced aromaticaldehydereduction (RARE) yeast platform forde novosynthesis of vanillin from glucose. We investigated multiple coenzyme-A free pathways to improve vanillin production in yeast. The vanillin productivity in yeast was further enhanced by systems engineering to optimize the supply of cofactors (NADPH andS-adenosylmethionine) together with metabolic reconfiguration of yeast central metabolism. The final yeast strain with overall 24 genetic modifications produced 365.55 ± 7.42 mg L−1under shake-flasks, which represents the highest vanillin titer from glucose achieved to date. Taken together, our work lays a foundation for the future implementation of vanillin production from glucose in budding yeast.

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A Two-Filter Adaptation to Achieve Hemodiafiltration with Enhanced Performance
Authors: Chu Kyle , Li Pei , Ausri Irfani , Vasconez Cesar , Tang Xiaowu (Shirley)
Published: June 2023

Introduction

Advancements in hemodialysis (HD) instrumentation have resulted in numerous breakthroughs in technology and significantly enhanced patient outcomes. Today, hemodiafiltration (HDF) which combines HD and hemofiltration has been widely used as an alternative to conventional HD in many countries. HDF is known to outperform conventional HD, offering more effective waste clearance and better fluid balance to patients. However, HDF requires newer-generation machines that are not accessible in many under-resourced geographical regions and societies. This study investigates a facile adaptation of conventional HD machines to achieve HDF. The objectives are to address the premature obsolescence of older but fully functional machines and to advocate for equal access to improved medical care and treatment.

Methods

A bench-top experimental setup was established to evaluate the performance of HDF using a two-filter adaptation in comparison to that of standard HD. Urea clearance, human serum album loss, and hemolysis were assessed under identical operational conditions for both configurations.

Findings

Our results show that the HDF configuration outperformed the HD configuration, with significantly higher urea clearance (268.31±44.17 mL/min via HDF vs. 53.33±13.20 mL/min via HD), but comparable human serum albumin loss and hemolysis levels.

Discussion

The explored two-filter adaptation presents a cost-effective method to achieve HDF with improved performance using conventional HD machines, with no added risk to patients. Further validation on patients in a hospital setting is necessary.
Nyctinastic leaf folding mimic reduces herbivory byChromacris trogongrasshoppers (Orthoptera:Romaleidae)
Authors: Bell Aidan B.
Published: June 2023

Arachis pintoi(Fabaceae) is a common relative of the cultivated peanut, and folds its four leaflets up to look like one at night. The adaptive significance of this behavior (foliar nyctinasty) is unknown. To test the hypothesis that leaflet folding alone can deter herbivores, a leaf preference experiment was performed onChromacris trogongrasshoppers. Small oval cutouts were made from leaves of the grasshopper’s preferred food source,Iochroma arborescens(Solanaceae), and were combined with small pieces of tape and dry grass to construct artificial leaves resembling the day and night form ofA. pintoi. In the experiment, groups of three grasshoppers were starved for 24 hours and then placed in petri dishes containing one closed and one open artificial leaf. After 30 six-hour trials, the average herbivory of open leaves was 12.3%, while closed leaves was 5.2% (p = 0.00145), indicating a significant preference for open leaves. This suggests that the folded configuration ofA. pintoileaves can be a defense against herbivory.
Hierarchical design of pseudosymmetric protein nanoparticles
Authors: Dowling Quinton M. , Park Young-Jun , Gerstenmaier Neil , Yang Erin C. , Wargacki Adam , Hsia Yang , Fries Chelsea N. , Ravichandran Rashmi , Walkey Carl , Burrell Anika , Veesler David , Baker David , King Neil P.
Published: June 2023

Discrete protein assemblies ranging from hundreds of kilodaltons to hundreds of megadaltons in size are a ubiquitous feature of biological systems and perform highly specialized functions1–3. Despite remarkable recent progress in accurately designing new self-assembling proteins, the size and complexity of these assemblies has been limited by a reliance on strict symmetry4,5. Inspired by the pseudosymmetry observed in bacterial microcompartments and viral capsids, we developed a hierarchical computational method for designing large pseudosymmetric self-assembling protein nanomaterials. We computationally designed pseudosymmetric heterooligomeric components and used them to create discrete, cage-like protein assemblies with icosahedral symmetry containing 240, 540, and 960 subunits. At 49, 71, and 96 nm diameter, these nanoparticles are the largest bounded computationally designed protein assemblies generated to date. More broadly, by moving beyond strict symmetry, our work represents an important step towards the accurate design of arbitrary self-assembling nanoscale protein objects.
Genome-wide, Organ-delimited gene regulatory networks (OD-GRNs) provide high accuracy in candidate TF selection across diverse processes
Authors: Ranjan Rajeev , Srijan Sonali , Balekuttira Somaiah , Agarwal Tina , Ramey Melissa , Dobbins Madison , Wang Xiaojin , Hudson Karen , Li Ying , Varala Kranthi
Published: June 2023

Construction of organ-specific gene expression datasets that include hundreds to thousands of experiments would greatly aid reconstruction of gene regulatory networks with organ-level spatial resolution. However, creating such datasets is greatly hampered by the requirements of extensive and tedious manual curation. Here we trained a supervised classification model that can accurately classify the organ-of-origin for a plant transcriptome. This K-Nearest Neighbor-based multiclass classifier was used to create organ-specific gene expression datasets for the leaf, root, shoot, flower, seed, seedling, silique, and stem in the model plantArabidopsis thaliana. In the leaf, root, flower, seed and, a gene regulatory network (GRN) inference approach was used to determine:i. influential transcription factors (TFs) in that organ and,ii. the most influential TFs for specific biological processes in the organ. These genome-wide, organ-delimited GRNs (OD-GRNs), identifiedde novomany known regulators of organ development and processes operating in those organs. Moreover, many previously unknown TF regulators were highly ranked as potential master regulators of organ development or organ-specific processes. As a proof-of-concept, we focused on experimentally validating the predicted TF regulators of lipid biosynthesis in seeds, with relevance to food and biofuel production. Of the top twenty candidate TFs, eight (e.g., WRI1, LEC1, and FUS3) are known regulators of seed oil content. Importantly, we validated that seven more candidate TFs, whose role was previously unknown in seed lipid biosynthesis, indeed affect this process by genetics and physiological approaches, thus yielding a net accuracy rate of >75% for thede novoTF predictions. The general approach developed here could be extended to any species with sufficiently large gene expression datasets to speed up hypothesis generation and testing for constructing gene regulatory networks at a high spatial resolution.

Significance Statement

Our study develops a machine-learning framework for building extremely large gene expression datasets for each organ, and to infer organ-delimited gene regulatory networks. We show that this approach is very successful at predicting which transcription factors are going to regulate processes at an organ level. We validated the accuracy of the predictions for transcription factor regulators using the seed lipid synthesis pathway as a case study. We demonstrated a very high success rate for uncovering both known and novel transcription factor regulators for the seed lipid biosynthesis pathway. The approach described in this study is broadly applicable across any organism (plant or animal) that has a large body of public gene expression data.