bluuebunny/crossref_metadata_2025 huggingface dataset:
Topological Structure of Population Activity in Mouse Visual Cortex Encodes Visual Scene Rotations
Authors: Beshkov Kosio , Einevoll Gaute T.
Published: February 2023

The primary visual cortex is one of the most well understood regions supporting the processing involved in sensory computation. Historically, our understanding of this part of the brain has been driven by describing the features to which individual neurons respond. An alternative approach, which is rapidly becoming a staple in neuroscience, is to study and analyze the geometry and topology of the manifold generated by the neural activity of large populations of neurons.

In this work, we introduce a rigorous quantification of the structure of such neural manifolds and address some of the problems the community has to face when conducting topological data analysis on neural data. We do this by analyzing publicly available two-photon optical recordings of primary mouse visual cortex in response to visual stimuli with a densely sampled rotation angle. Since the set of twodimensional rotations lives on a circle, one would hypothesize that they induce a circle-like manifold in neural activity. We confirm this hypothesis by discovering a circle-like neural manifold in the population activity of primary visual cortex. To achieve this, we applied a shortest-path (geodesic) approximation algorithm for computing the persistent homology groups of neural activity in response to visual stimuli. It is important to note that the manifold is highly curved and standard Euclidean approaches failed to recover the correct topology.

Furthermore, we identify subpopulations of neurons which generate both circular and non-circular representations of the rotated stimuli, with the circular representations being better for angle decoding. We found that some of these subpopulations, made up of orientationally selective neurons, wrap the original set of rotations on itself which implies that the visual cortex also represents rotations up to 180 degrees.

Given these results we propose that population activity can represent the angle of rotation of a visual scene, in analogy with how individual direction-selective neurons represent the angle of direction in local patches of the visual field. Finally, we discuss some of the obstacles to reliably retrieving the truthful topology generated by a neural population.
rtPA Directly Protects Neurons After Intracerebral Hemorrhage through PI3K/AKT/mTOR Pathway
Authors: Jing Jie , Chen Shiling , Wu Xuan , Yang Jingfei , Liu Xia , Wang Jiahui , Wang Jingyi , Li Yunjie , Zhang Ping , Tang Zhouping
Published: February 2023

Intracerebral hemorrhage (ICH) is an acute cerebrovascular disease with high disability and mortality rates. Recombinant tissue plasminogen activator (rtPA) is commonly applied for hematoma evacuation in minimally invasive surgery (MIS) after ICH. However, rtPA may contact directly with brain tissue during MIS procedure, which makes it necessary to discuss the safety of rtPA. We found that, in the in vivo ICH model induced by VII-type collagenase, rtPA treatment improved the neurological function of ICH mice, alleviated the pathological damage and decreased the apoptosis and autophagy level of the peri-hematoma tissue. In the in-vitro model of ICH induced by hemin, the administration of rtPA down-regulated neuronal apoptosis, autophagy, and endoplasmic reticulum stress of neurons. Transcriptome sequencing analysis showed that rtPA treatment upregulated the PI3K/AKT/mTOR pathway in neurons, and PI3K inhibitor (LY294002) can reverse the protective effects of rtPA in inhibiting excessive apoptosis, autophagy and ER-stress. Epidermal growth factor receptor inhibitor (AG-1487) reversed the effect of rtPA on PI3K/AKT/mTOR pathway, which might indicate that the EGF domain played an important role in the activation of PI3K/AKT/mTOR pathway.
Distinct regulatory networks control toxin gene expression in elapid and viperid snakes
Authors: Modahl Cassandra M. , Han Summer Xia , van Thiel Jory , Vaz Candida , Dunstan Nathan L. , Frietze Seth , Jackson Timothy N. W. , Mackessy Stephen P. , Kini R. Manjunatha
Published: February 2023

Venom systems are ideal models to study genetic regulatory mechanisms that underpin evolutionary novelty. Snake venom glands are thought to share a common origin, but there are major distinctions between venom toxins from the medically significant snake families Elapidae and Viperidae, and toxin gene regulation in elapids is largely unexplored. Here, we used high-throughput RNA-sequencing to profile gene expression and microRNAs between active (milked) and resting (unmilked) venom glands in an elapid (Eastern Brown Snake,Pseudonaja textilis), in addition to comparative genomics, to identifycis- andtrans- acting regulation of venom production in an elapid in comparison to viperids (Crotalus viridisandC. tigris). Although there is conservation in high-level mechanistic pathways regulating venom production, there are histone methylation, transcription factor, and microRNA regulatory differences between these two snake families. Histone methyltransferases (KMT2A, KMT2C and KMT2D) and transcription factor (TF) specificity protein 1 (Sp1) were highly upregulated in the milked elapid venom gland, whereas nuclear factor I (NFI) TFs were upregulated after viperid venom milking. Sp1 and NFIcis-regulatory elements were common to toxin gene promoter regions, but many unique elements were also present between elapid and viperid toxins. microRNA profiles were distinctive between milked and unmilked venom glands for both snake families, and microRNAs were predicted to target different toxin transcripts. Our comparative transcriptomic and genomic analyses between toxin genes and isoforms in elapid and viperid snakes suggests independent toxin evolution between these two snake families, demonstrating multiple toxin genes and regulatory mechanisms converged to underpin a highly venomous phenotype.
Fgf signalling triggers an intrinsic mesodermal timer that determines the duration of limb patterning
Authors: Perez Sofia Sedas , McQueen Caitlin , Pickering Joseph , Chinnaiya Kavitha , Saiz-Lopez Patricia , Ros Maria A. , Towers Matthew
Published: February 2023

Complex signalling between the apical ectodermal ridge (AER - a thickening of the distal epithelium) and the mesoderm controls limb patterning along the proximo-distal axis (humerus to digits). However, the essential requirement for AER-Fgf signalling duringin vivodevelopment makes it difficult to understand the exact roles that it fulfils. To overcome this barrier, we developed an amenableex vivochick wing tissue explant system that faithfully replicatesin vivoparameters. Using inhibition experiments and RNA-sequencing, we identify a transient role for Fgfs in triggering the distal patterning phase. Fgfs are then dispensable for the maintenance of an intrinsic mesodermal transcriptome, which controls proliferation/differentiation timing and the duration of patterning. We also uncover additional roles for Fgf signalling in maintaining AER-related gene expression and in suppressing myogenesis. We describe a simple logic for limb patterning duration, which is potentially applicable to other systems, including the main body axis.
Protein-protein interfaces as druggable targets: A common motif of the pyridoxal-5’-phosphate-dependent enzymes to receive the coenzyme from its producers
Authors: Aleshin Vasily A. , Bunik Victoria I.
Published: February 2023

Pyridoxal-5’-phosphate (PLP), a phosphorylated form of vitamin B6, acts as a coenzyme for numerous reactions, including those changed in cancer and/or associated with the disease prognosis. Since highly reactive PLP may modify cellular proteins, it is hypothesized to be directly transferred from its donors to acceptors. Our goal is to validate the hypothesis by finding common motif(s) in a multitude of the PLP-dependent enzymes for binding the limited number of the PLP donors, namely pyridoxal kinase (PdxK), pyridox(am)in-5’-phosphate oxidase (PNPO) and the PLP-binding protein (PLPBP). Experimentally confirmed interactions between the PLP donors and acceptors reveal that PdxK and PNPO interact with the PLP acceptors of folds I and II, while PLPBP – with those of folds III and V. Aligning the sequences and 3D structures of the identified interactors of PdxK and PNPO, we have found a common motif in the PLP-dependent enzymes of folds I and II. The motif extends from the enzyme surface to the neighborhood of the PLP binding site, represented by an exposed alfa-helix, a partially buried beta-strand and residual loops. Pathogenicity of mutations in human PLP-dependent enzymes within or in the vicinity of the motif, but outside of the active sites, supports functional significance of the motif that may provide an interface for the direct transfer of PLP from the sites of its synthesis to those of the coenzyme binding. The enzyme-specific amino acid residues of the common motif may be useful to develop selective inhibitors blocking PLP delivery to the PLP-dependent enzymes critical for proliferation of malignant cells.
Floral volatiles evoke partially similar responses in both florivores and pollinators and are correlated with non-volatile reward chemicals
Authors: Sasidharan Rohit , Junker Robert R. , Eilers Elisabeth J. , Müller Caroline
Published: February 2023

Background

Plants use floral displays to attract mutualists, but simultaneously need to prevent attacks by antagonists. Chemical displays detectable from a distance include attractive or repellent floral volatile organic compounds (FVOCs). Post-landing, visitors perceive contact chemicals including nutrients, but also deterrent or toxic constituents in pollen and nectar, protecting flowers from overexploitation. The composition of FVOCs and pollen chemistry is well known to vary among and within species. However, we lack knowledge about differences and similarities in the detectability of and behavioural responses towards these compounds for insect flower visitor groups of key importance, i.e., mutualistic pollinators versus antagonistic florivores, as well as the correlation between FVOCs and pollen chemodiversity.

Scope

We reviewed how FVOCs and non-volatile floral chemical displays, i.e., nutrients and toxins of pollen, vary in composition and how they affect the detection and behaviour of insect flower visitors. Moreover, we used a meta-analytic approach to evaluate the detection of and responses towards FVOCs by pollinators vs. florivores within the same plant genera. Furthermore, we tested whether the chemodiversity of FVOCs as well as nutrients and toxins stored in pollen are correlated and hence informative about each other.

Key Results

According to the available data, florivores are more likely to detect FVOCs than pollinators. Common FVOCs such as linalool and methyl salicylate were often reported as attractive to pollinators and repellent towards florivores. A higher number of FVOCs was found to be attractive to both mutualists and antagonists compared to shared repellent compounds. Furthermore, a negative correlation between FVOC richness and the number of pollen toxin classes was revealed, besides a trend towards a positive correlation between pollen protein amount and the number of pollen toxins.

Conclusions

Plants face critical trade-offs when producing floral chemicals, as these partly mediate the same information, particularly attraction but also repellence or toxicity, to both mutualists and antagonists. Moreover, chemodiversity of different floral parts is partly correlated and thus highly relevant for investigations of flower-insect interactions. Further research is needed on more different wild and cultivated plant species and mutualistic and antagonistic interaction partners to test for generalisation of these patterns.
From Cell-Lines to Cancer Patients: Personalized Drug Synergy Prediction
Authors: Kuru Halil Ibrahim , Cicek A. Ercument , Tastan Oznur
Published: February 2023

Combination drug therapies are effective treatments for cancer. However, the genetic heterogeneity of the patients and exponentially large space of drug pairings pose significant challenges for finding the right combination for a specific patient. Currentin silicoprediction methods can be instrumental in reducing the vast number of candidate drug combinations. However, existing powerful methods are trained with cancer cell line gene expression data, which limits their applicability in clinical settings. While synergy measurements on cell lines models are available at large scale, patient-derived samples are too few to train a complex model. On the other hand, patient-specific single-drug response data are relatively more available. In this work, we propose a deep learning framework,PersonalizedDeepSynergyPredictor (PDSP), that enables us to use the patient-specific single drug response data for customizing patient drug synergy predictions. PDSP is first trained to learn synergy scores of drug pairs and their single drug presonses for a given cell line using drug structures and large scale cell line gene expression data. Then, the model is fine-tuned for patients with their patient gene expression data and associated single drug response measured on the patientex vivosamples. In this study, we evaluate PDSP on data from three leukemia patients and observe that it improves the prediction accuracy by 27% compared to models trained on cancer cell line data. PDSP is built and available athttps://github.com/hikuru/PDSP
Delaying the GABA shift indirectly affects membrane properties in the developing hippocampus
Authors: Peerboom C. , De Kater S. , Jonker N. , Rieter M. , Wijne T. , Wierenga C.J.
Published: February 2023

During the first two postnatal weeks intraneuronal chloride concentrations in rodents gradually decrease, causing a shift from depolarizing to hyperpolarizing γ-aminobutyric acid (GABA) responses. The postnatal GABA shift is delayed in rodent models for neurodevelopmental disorders and in human patients, but the impact of a delayed GABA shift on the developing brain remain obscure. Here we examine the direct and indirect consequences of a delayed postnatal GABA shift on network development in organotypic hippocampal cultures made from 6 to 7-day old mice by treating the cultures for one week with VU0463271, a specific inhibitor of the chloride exporter KCC2. We verified that VU treatment delayed the GABA shift and kept GABA signaling depolarizing until day in vitro (DIV) 9. We found that the structural and functional development of excitatory and inhibitory synapses at DIV9 was not affected after VU treatment. In line with previous studies, we observed that GABA signaling was already inhibitory in control and VU-treated postnatal slices. Surprisingly, fourteen days after the VU treatment had ended (DIV21), we observed an increased frequency of spontaneous inhibitory post-synaptic currents in CA1 pyramidal cells, while excitatory currents were not changed. Synapse numbers and release probability were unaffected. We found that dendrite-targeting interneurons in thestratum Radiatumhad an elevated resting membrane potential, while pyramidal cells were less excitable compared to control slices. Our results show that depolarizing GABA signaling does not promote synapse formation after P7, and suggest that postnatal intracellular chloride levels indirectly affect membrane properties in a cell-specific manner.

Significance Statement

During brain development the action of neurotransmitter GABA shifts from depolarizing to hyperpolarizing. This shift is a thought to play a critical role in synapse formation. A delayed shift is common in rodent models for neurodevelopmental disorders and in human patients, but its consequences for synaptic development remain obscure. Here, we delayed the GABA shift by one week in organotypic hippocampal cultures and carefully examined the consequences for circuit development. We find that delaying the shift has no direct effects on synaptic development, but instead leads to indirect, cell type-specific changes in membrane properties. Our data call for careful assessment of alterations in cellular excitability in neurodevelopmental disorders.
Tuning plant promoters using a simple split luciferase method for quantifying transcription factor binding affinity
Authors: Cai Y-M , Witham S , Patron NJ
Published: February 2023

Sequence features, including the binding affinity of binding motifs for their cognate transcription factors, are important contributors to promoter behavior. The ability to predictably recode affinity enables the development of synthetic promoters with varying levels of response to known cellular signals. Here we describe a luminescence-based microplate assay for comparing the interactions of transcription factors with short DNA probes. We then demonstrate how this data can be used to design synthetic plant promoters of varying strengths that respond to the same transcription.
Cementochronology using synchrotron radiation tomography to determine age at death and developmental rate in the holotype ofHomo luzonensis
Authors: van Heteren Anneke H. , King Andrew , Berenguer Felisa , Mijares Armand Salvador , Détroit Florent
Published: February 2023

Homo luzonensis, a fossil hominin from the Philippines, is smaller than modern humans. At present, very little is known about the life history of this species. Cementochronology can answer life history questions, but usually involves destructive sampling. Here, we use synchrotron radiation to count the yearly cement lines of teeth belonging to a single individual. This approach allows us to determine that this individual was likely 31 years old at time of death and apparently had a developmental pattern comparable to chimpanzees. To our knowledge, this is the first time that cementochronology using synchrotron radiation tomography is used for life history and age-at-death estimation.
Utilizing high resolution ribosome profiling for the global investigation of gene expression inChlamydomonas
Authors: Gotsmann Vincent Leon , Ting Michael Kien Yin , Haase Nadin , Rudorf Sophia , Zoschke Reimo , Willmund Felix
Published: February 2023

Ribosome profiling (Ribo-seq) is a powerful method for the deep analysis of translation mechanisms and regulatory circuits during gene expression. Here, we established an optimized and high resolution Ribo-seq protocol for the unicellular model algaChlamydomonas reinhardtii(Chlamydomonas). Comparing different nuclease treatments for the extraction and sequencing of ribosome-protected fragments (RPFs) and parallel RNA-seq, provided deep insight into translational dynamics and post-transcriptional control of gene expression, thoroughly covering more than 10,000 different transcripts. Our high quality Ribo-seq protocol captures the 3-nucleotide movement of elongating ribosomes along nuclear and chloroplast transcripts. Detailed analysis of the ribosomal offsets on transcripts uncovers presumable transition states during translocation of elongating ribosomes within the 5’- and 3’-sections of transcripts and features of eukaryotic translation termination. These offsets reveal drastic differences between the nature of cytosolic and chloroplast translation mechanisms. Chloroplast translation is further characterized by heterogenous RPF size distribution. We found that local accumulation of small RPFs correlates with local slowdown ofpsbAtranslation, possibly revealing an uncharacterized regulator step during PsbA/D1 synthesis. Further analyses of RPF distribution along specific cytosolic transcripts revealed characteristic patterns of translation elongation exemplified for the major light harvesting complex proteins, LHCs. Moreover, our Ribo-seq data can be utilized to survey coding sequence annotations and the expression preference of alternatively spliced transcripts in Chlamydomonas. We made these features easily accessible for the research community by attaching our Ribo-seq data to the most recent Chlamydomonas reference genome.
Cell type-specific Interaction Analysis using Doublets in scRNA-seq (CIcADA)
Authors: Schiebout Courtney , Lust Hannah E. , Huang Yina H. , Frost H. Robert
Published: February 2023

Motivation

Doublets are usually considered an unwanted artifact of single-cell RNA-sequencing (scRNA-seq) and are only identified in datasets for the sake of removal. However, if cells have a juxtacrine attachment to one another in situ and maintain this association through an scRNA-seq processing pipeline that only partially dissociates the tissue, these doublets can provide meaningful biological information regarding the interactions and cell processes occurring in the analyzed tissue. This is especially true for cases such as the immune compartment of the tumor microenvironment, where the frequency and type of immune cell juxtacrine interactions can be a prognostic indicator.

Results

We developed Cell type-specific Interaction Analysis using Doublets in scRNA-seq (CIcADA) as a pipeline for identifying and analyzing biological doublets in scRNA-seq data. CIcADA identifies putative doublets using multi-label cell type scores and characterizes interaction dynamics through a comparison against synthetic doublets of the same cell type composition. In performing CIcADA on several scRNA-seq tumor datasets, we found that the identified doublets were consistently upregulating expression of immune response genes.

Contact

Courtney.T.Schiebout.GR@Dartmouth.edu,Hildreth.R.Frost@Dartmouth.edu
Explainable Fuzzy Clustering Framework Reveals Divergent Default Mode Network Connectivity Dynamics in Schizophrenia
Authors: Ellis Charles A. , Miller Robyn L. , Calhoun Vince D.
Published: February 2023

Dynamic functional network connectivity (dFNC) analysis of resting state functional magnetic resonance imaging data has yielded insights into many neurological and neuropsychiatric disorders. A common dFNC analysis approach uses hard clustering methods like k-means clustering to assign samples to states that summarize network dynamics. However, hard clustering methods obscure network dynamics by assuming (1) that all samples within a cluster are equally like their assigned centroids and (2) that samples closer to one another in the data space than to their centroids are well-represented by their centroids. In addition, it can be hard to compare subjects, as in some cases an individual may not manifest a state strongly enough to enter a hard cluster. Approaches that allow a dimensional approach to connectivity patterns (e.g., fuzzy clustering) can mitigate these issues. In this study, we present an explainable fuzzy clustering framework by combining fuzzy c-means clustering with several explainability metrics. We apply our framework for schizophrenia (SZ) default mode network analysis, identifying 5 states and characterizing those states with a new explainability approach. While also showing that features typically used in hard clustering can be extracted in our framework, we present a variety of unique features to quantify state dynamics and identify effects of SZ upon network dynamics. We further uncover relationships between symptom severity and interactions of the precuneus with the anterior and posterior cingulate cortex. Given the ease of implementing our framework and its enhanced insight into network dynamics, it has great potential for use in future dFNC studies.
Quantification and modeling of turnover dynamics ofde novotranscripts inDrosophila melanogaster
Authors: Grandchamp Anna , Czuppon Peter , Bornberg-Bauer Erich
Published: February 2023

Most of the transcribed eukaryotic genomes are composed of non-coding transcripts. Among these transcripts, some are newly transcribed when compared to outgroups and are referred to asde novotranscripts.De novotranscripts have been shown to play a major role inde novogene emergence. However, little is known about the rates at whichde novotranscripts are gained and lost in individuals of the same species. Here, we address this gap and estimate for the first time thede novotranscript turnover rate. We use DNA long reads and RNA short reads from seven samples of inbred individuals ofDrosophila melanogasterto detectde novotranscripts that are (transiently) gained on a short evolutionary time scale. Overall, each sampled individual contains between 2,320 and 2,809 unsplicedde novotranscripts with most of them being sample specific. We estimate that around 0.15 transcripts are gained per year, and that each gained transcript is lost at a rate around 5×10−5per year. This high turnover of transcripts suggests frequent exploration of new genomic sequences within species. These rates provide first empirical estimates to better predict and comprehend the process ofde novogene birth.
Unraveling Spatial Gene Associations with SEAGAL: a Python Package for Spatial Transcriptomics Data Analysis and Visualization
Authors: Wang Linhua , Liu Chaozhong , Liu Zhandong
Published: February 2023

In the era where transcriptome profiling moves towards single-cell and spatial resolutions, the traditional co-expression analysis lacks the power to fully utilize such rich information to unravel spatial gene associations. Here we present a Python package called Spatial Enrichment Analysis of Gene Associations using L-index (SEAGAL) to detect and visualize spatial gene correlations at both single-gene and gene-set levels. Our package takes spatial transcriptomics data sets with gene expression and the aligned spatial coordinates as input. It allows for analyzing and visualizing spatial correlations at both single-gene and gene-set levels. The output could be visualized as volcano plots and heatmaps with a few lines of code, thus providing an easy-yet-comprehensive tool for mining spatial gene associations.

Availability and Implementation

The Python package SEAGAL can be installed using pip:https://pypi.org/project/seagal/. The source code and step-by-step tutorials are available at:https://github.com/linhuawang/SEAGAL.

Contact

linhuaw@bcm.edu
Quantification of ligand and mutation-induced bias in EGFR phosphorylation in direct response to ligand binding
Authors: Wirth Daniel , Özdemir Ece , Hristova Kalina
Published: February 2023

The 58 receptor tyrosine kinases (RTKs) are critically important for human development, and are implicated in many growth disorders and cancers. Here we introduce a methodology to identify and quantify bias in RTK signal transduction across the plasma membrane, and to quantify phosphorylation efficiencies, without contributions from feedback loops and system bias. We show that RTK biased signaling can occur in the first step of signal transduction not only in response to different ligands, but as a consequence of RTK pathogenic mutations as well. Ligand bias and mutation-induced bias are uncoupled here based on a comprehensive data set of dose response curves acquired for three ligands, EGF, TGFα and epiregulin, for wild-type EGFR and for the oncogenic L834R EGFR mutant found in patients with non-small-cell lung cancer (NSCLC). Ligand bias has been extensively studied for GPCRs, and has revolutionized the GPCR field. The demonstration of pathogenic mutation-induced bias in RTK signal transduction across the plasma membrane will open new avenues for the exploration of RTK biased inhibitors as highly specific anti-cancer therapies.
SARS-CoV-2 Neutralizing Antibodies After Bivalent vs. Monovalent Booster
Authors: Wang Qian , Bowen Anthony , Tam Anthony R. , Valdez Riccardo , Stoneman Emily , Mellis Ian A. , Gordon Aubree , Liu Lihong , Ho David D.
Published: February 2023

Bivalent mRNA vaccine boosters expressing Omicron BA.5 spike and ancestral D614G spike were introduced to attempt to boost waning antibody titers and broaden coverage against emerging SARS-CoV-2 lineages. Previous reports showed that peak serum neutralizing antibody (NAb) titers against SARS-CoV-2 variants following bivalent booster were similar to peak titers following monovalent booster. It remains unknown whether these antibody responses would diverge over time. We assessed serum virus-neutralizing titers in 41 participants who received three monovalent mRNA vaccine doses followed by bivalent booster, monovalent booster, or BA.5 breakthrough infection at one month and three months after the last vaccine dose or breakthrough infection using pseudovirus neutralization assays against D614G and Omicron subvariants (BA.2, BA.5, BQ.1.1, and XBB.1.5). There was no significant difference at one month and three months post-booster for the two booster cohorts. BA.5 breakthrough patients exhibited significantly higher NAb titers at three months against all Omicron subvariants tested compared against monovalent and bivalent booster cohorts. There was a 2-fold drop in mean NAb titers in the booster cohorts between one and three month time points, but no discernible waning of titers in the BA.5 breakthrough cohort over the same period. Our results suggest that NAb titers after boosting with one dose of bivalent mRNA vaccine are not higher than boosting with monovalent vaccine. Perhaps inclusion of D614G spike in the bivalent booster exacerbates the challenge posed by immunological imprinting. Hope remains that a second bivalent booster could induce superior NAb responses against emerging variants.
Reproducible evaluation of transposable element detectors with McClintock 2 guides accurate inference of Ty insertion patterns in yeast
Authors: Chen Jingxuan , Basting Preston J. , Han Shunhua , Garfinkel David J. , Bergman Casey M.
Published: February 2023

Background

Many computational methods have been developed to detect non-reference transposable element (TE) insertions using short-read whole genome sequencing data. The diversity and complexity of such methods often present challenges to new users seeking to reproducibly install, execute or evaluate multiple TE insertion detectors.

Results

We previously developed the McClintock meta-pipeline to facilitate the installation, execution, and evaluation of six first-generation short-read TE detectors. Here, we report a completely re-implemented version of McClintock written in Python using Snakemake and Conda that improves its installation, error handling, speed, stability, and extensibility. McClintock 2 now includes 12 short-read TE detectors, auxiliary pre-processing and analysis modules, interactive HTML reports, and a simulation framework to reproducibly evaluate the accuracy of component TE detectors. When applied to the model microbial eukaryoteSaccharomyces cerevisiae, we find substantial variation in the ability of McClintock 2 components to identify the precise locations of non-reference TE insertions, with RelocaTE2 showing the highest recall and precision in simulated data. We find that RelocaTE2, TEMP, TEMP2 and TEBreak provide a consistent and biologically meaningful view of non-reference TE insertions in a species-wide panel of ~1000 yeast genomes, as evaluated by coverage-based abundance estimates and expected patterns of tRNA promoter targeting. Finally, we show that best-in-class predictors for yeast have sufficient resolution to reveal a dyad pattern of integration in nucleosome-bound regions upstream of yeast tRNA genes for Ty1, Ty2, and Ty4, allowing us to extend knowledge about fine-scale target preferences first revealed experimentally for Ty1 to natural insertions and related copia-superfamily retrotransposons in yeast.

Conclusion

McClintock (https://github.com/bergmanlab/mcclintock/) provides a user-friendly pipeline for the identification of TEs in short-read WGS data using multiple TE detectors, which should benefit researchers studying TE insertion variation in a wide range of different organisms. Application of the improved McClintock system to simulated and empirical yeast genome data reveals best-in-class methods and novel biological insights for one of the most widely-studied model eukaryotes and provides a paradigm for evaluating and selecting non-reference TE detectors for other species.
Polyether ionophore antibiotics target drug-resistant clinical isolates, persister cells, and biofilms
Authors: Wollesen Malene , Mikkelsen Kasper , Tvilum Marie Selch , Vestergaard Martin , Wang Mikala , Meyer Rikke L. , Ingmer Hanne , Poulsen Thomas B. , Tørring Thomas
Published: February 2023

Polyether ionophores are complex natural products known to transport various cations across biological membranes. While several members of this family are used in agriculture, e.g. as anti-coccidiostats, and have potent antibacterial activity, they are not currently pursued as antibiotics for human use. Polyether ionophores are typically grouped as having similar functions, despite the fact that they differ significantly in structure, and for this reason, it remains unclear how structure and activity are related. To triage whether certain members of the family constitute particularly interesting springboards for in-depth investigations, and future synthetic optimization, we here conduct a systematic comparative study of nine different polyether ionophores for their potential as antibiotics. This includes clinical isolates from bloodstream infections and studies of the compounds’ effects on bacterial biofilms and persister cells. We uncover distinct differences within the compound class and identify the compounds lasalocid, calcimycin, and nanchangmycin as having particularly interesting activity profiles for further development.
Propylene glycol inactivates respiratory viruses and prevents airborne transmission
Authors: Styles Christine T. , Zhou Jie , Flight Katie E. , Brown Jonathan C. , Vanden Oever Michael , Peacock Thomas P. , Wang Ziyin , Millns Rosie , O’Neill John S. , Barclay Wendy S. , Tregoning John S. , Edgar Rachel S.
Published: February 2023

Viruses are vulnerable as they transmit between hosts and we aimed to exploit this critical window. We found that the ubiquitous, safe, inexpensive and biodegradable small molecule propylene glycol (PG) has robust virucidal activity. Propylene glycol rapidly inactivates influenza, SARS-CoV-2 and a broad range of other enveloped viruses, and reduces disease burden in mice when administered intranasally at concentrations commonly found in nasal sprays. Most critically, aerosolized PG efficiently abolishes influenza and SARS-CoV-2 infectivity within airborne droplets, potently preventing infection at levels significantly below those well-tolerated by mammals. We present PG vapor as a first-in-class non-toxic airborne virucide, to prevent transmission of existing and emergent viral pathogens, with clear and immediate implications for public health.

One-sentence summary

Propylene glycol is a potent and safe virucidal compound that could be used to limit and control infections.
HIV Pharmacology Data Repository (PDR): Setting the New Information Sharing Standard for Pharmacokinetic Studies
Authors: Tompkins Lauren A.R. , Kapeljushnik Oleg , Hubal Robert , Khoei Adrian , Dumond Julie , Kashuba Angela D.M. , Tropsha Alexander , Cottrell Mackenzie L.
Published: February 2023

Clinical therapeutics are becoming increasingly reliant on data science and computational data analytical tools to predict drug behavior in unobserved conditions or populations. Thesein silicoapproaches, collectively termed “pharmacometrics”, derive biological meaning from the analysis of pooled drug concentration vs. time (CvT) datasets. However, the field lacks standardization for pharmacokinetic (PK) data description and sharing, instead requiring deep dives into the literature and expert data annotation for aggregate data mining. Here we introduce a minimum information sharing standard for PK studies composed of three categories (Intervention, System, and Effects) and implement this standard in the development of a web-based PK database: the HIV Pharmacology Data Repository (PDR). We demonstrate the utility of the HIV PDR by computational modeling of aggregated and curated CvT data extracted from the HIV PDR.
Hyperpolarization-activated cation channels shape the spiking frequency preference of human cortical layer 5 pyramidal neurons
Authors: Inibhunu Happy , Chameh Homeira Moradi , Skinner Frances K , Rich Scott , Valiante Taufik A
Published: February 2023

Discerning the contribution of specific ionic currents to complex neuronal dynamics is a difficult, but important, task. This challenge is exacerbated in the human setting, although the widely-characterized uniqueness of the human brain as compared to preclinical models necessitates the direct study of human neurons. Neuronal spiking frequency preference is of particular interest given its role in rhythm generation and signal transmission in cortical circuits. Here, we combine the frequency-dependent gain (FDG), a measure of spiking frequency preference, and novelin silicoanalyses to dissect the contributions of individual ionic currents to key FDG features of human L5 neurons. We confirm that a contemporary model of such a neuron, primarily constrained to capture subthreshold activity driven by the hyperpolarization-activated cyclic nucleotide gated (h-) current, replicates key features of thein vitroFDG both with and without h-current activity. With the model confirmed as a viable approximation of the biophysical features of interest, we applied new analysis techniques to quantify the activity of each modeled ionic current in the moments prior to spiking, revealing unique dynamics of the h-current. These findings motivated patch-clamp recordings in analogous rodent neurons to characterize their FDG, which confirmed that a biophysically-detailed model of these neurons captures key inter-species differences in the FDG. These differences are correlated with distinct contributions of the h-current to neuronal activity. Together, this interdisciplinary and multi-species study provides new insights directly relating the dynamics of the h-current to neuronal spiking frequency preference in human L5 neurons.

Significance Statement

Understanding the contributions of individual ionic currents to neuronal activity is vital, considering the established role of ion channel modifications in neuropsychiatric conditions. We combinein vitrocharacterization of the spiking frequency preference of human L5 cortical pyramidal neurons via the frequency-dependent gain (FDG) with new analyses of a biophysically-detailed computational model of such a neuron to delineate the connection between the dynamics of the hyperpolarization-activated cyclic nucleotide gated (h-) current prior to spiking and key properties of the FDG. By further determining that both these FDG properties and h-current dynamics are distinct in analogous rodent neurons, we provide convincing evidence for the key role of the h-current in the frequency preference of human L5 cortical neurons.
Unraveling Chamber-specific Differences in Intercalated Disc Ultrastructure and Molecular Organization and Their Impact on Cardiac Conduction
Authors: Struckman Heather L. , Moise Nicolae , King D. Ryan , Soltisz Andrew , Buxton Andrew , Dunlap Izabella , Chen Zhenhui , Radwański Przemysław B. , Weinberg Seth H. , Veeraraghavan Rengasayee
Published: February 2023

During each heartbeat, the propagation of action potentials through the heart coordinates the contraction of billions of individual cardiomyocytes and is thus, a critical life process. Unsurprisingly, intercalated discs, which are cell-cell contact sites specialized to provide electrical and mechanical coupling between adjacent cardiomyocytes, have been the focus of much investigation. Slowed or disrupted propagation leads to potentially life-threatening arrhythmias in a wide range of pathologies, where intercalated disc remodeling is a common finding. Hence, the importance and urgency of understanding intercalated disc structure and its influence on action potential propagation. Surprisingly, however, conventional modeling approaches cannot predict changes in propagation elicited by perturbations that alter intercalated disc ultrastructure or molecular organization, owing to lack of quantitative structural data at subcellular through nano scales. In order to address this critical gap in knowledge, we sought to quantify intercalated disc structure at these finer spatial scales in the healthy adult mouse heart and relate them to function in a chamber-specific manner as a precursor to understanding the impacts of pathological intercalated disc remodeling. Using super-resolution light microscopy, electron microscopy, and computational image analysis, we provide here the first ever systematic, multiscale quantification of intercalated disc ultrastructure and molecular organization. By incorporating these data into a rule-based model of cardiac tissue with realistic intercalated disc structure, and comparing model predictions of electrical propagation with experimental measures of conduction velocity, we reveal that atrial intercalated discs can support faster conduction than their ventricular counterparts, which is normally masked by inter-chamber differences in myocyte geometry. Further, we identify key ultrastructural and molecular organization features underpinning the ability of atrial intercalated discs to support faster conduction. These data provide the first stepping stone to elucidating chamber-specific impacts of pathological intercalated disc remodeling, as occurs in many arrhythmic diseases.
BHLHE40/41 regulate macrophage/microglia responses associated with Alzheimer’s disease and other disorders of lipid-rich tissues
Authors: Podlesny-Drabiniok Anna , Novikova Gloriia , Liu Yiyuan , Dunst Josefine , Temizer Rose , Giannarelli Chiara , Marro Samuele , Kreslavsky Taras , Marcora Edoardo , Goate Alison Mary
Published: February 2023

Background

Genetic and experimental evidence strongly implicates myeloid cells in the etiology of AD and suggests that AD-associated alleles and genes may modulate disease risk by altering the transcriptional and cellular responses of macrophages (like microglia) to damage of lipid-rich tissues (like the brain). Specifically, recent single-cell/nucleus RNA sequencing (sc/nRNA-seq) studies identified a transcriptionally distinct state of subsets of macrophages in aging or degenerating brains (usually referred to as disease- associated microglia or DAM) and in other diseased lipid-rich tissues (e.g., obese adipose tissue, fatty liver, and atherosclerotic plaques). We collectively refer to these subpopulations as lipid-associated macrophages or LAMs. Importantly, this particular activation state is characterized by increased expression of genes involved in the phagocytic clearance of lipid-rich cellular debris (efferocytosis), including several AD risk genes.

Methods

We used sc/nRNA-seq data from human and mouse microglia from healthy and diseased brains and macrophages from other lipid-rich tissues to reconstruct gene regulatory networks and identify transcriptional regulators whose regulons are enriched for LAM response genes (LAM TFs) across species. We then used gene knock- down/knock-out strategies to validate some of these LAM TFs in human THP-1 macrophages and iPSC-derived microgliain vitro, as well as mouse microgliain vivo.

Results

We nominate 11 strong candidate LAM TFs shared across human and mouse networks (BHLHE41,HIF1A,ID2,JUNB,MAF,MAFB,MEF2A,MEF2C,NACA, POU2F2andSPI1). We also demonstrate a strong enrichment of AD risk alleles in the cistrome ofBHLHE41(and its close homologBHLHE40), thus implicating its regulon in the modulation of disease susceptibility. Loss or reduction ofBHLHE40/41expression in human THP-1 macrophages and iPSC-derived microglia, as well as loss ofBhlhe40/41in mouse microglia led to increased expression of LAM response genes, specifically those involved in cholesterol clearance and lysosomal processing, with a concomitant increase in cholesterol efflux and storage, as well as lysosomal mass and degradative capacity.

Conclusions

Taken together, this study nominates transcriptional regulators of the LAM response, experimentally validates BHLHE40/41 in human and mouse macrophages/microglia, and provides novel targets for therapeutic modulation of macrophage/microglia function in AD and other disorders of lipid-rich tissues.

Graphical abstract
Microcircuit failure inSTXBP1encephalopathy leads to hyperexcitability
Authors: dos Santos Altair Brito , Larsen Silas Dalum , Guo Liangchen , Montalant Alexia , Verhage Matthijs , Sørensen Jakob Balslev , Perrier Jean-François
Published: February 2023

De novomutations inStxbp1are among the most prevalent causes of neurodevelopmental disorders, and lead to haploinsufficiency, cortical hyperexcitability, epilepsy and other symptoms. Given that Munc18-1, the protein encoded byStxbp1, is essential for both excitatory and inhibitory synaptic transmission, it is currently not understood why mutations cause hyperexcitability. We discovered that overall inhibition in canonical feedforward microcircuits is defective in a validated mouse model forStxbp1haploinsufficiency. However, unexpectedly, we found that inhibitory synapses were largely unaffected. Instead, excitatory synapses failed to recruit inhibitory interneurons. Modelling experiments confirmed that defects in the recruitment of inhibitory neurons in microcircuits cause hyperexcitation. Ampakines, compounds that enhance excitatory synapses, restored interneuron recruitment and prevented hyperexcitability. These findings identify deficits in excitatory synapses in microcircuits as a key underlying mechanism for cortical hyperexcitability inStxbp1disorder and identify compounds enhancing excitation as a direction for therapy design.

Highlights

- Neocortical microcircuits fail inStxbp1haploinsufficiency mouse models (Stxbp1hap)

- Microcircuit impairments leads to cortical hyperexcitability due to a lack of inhibition.

- Inhibitory synapses are not severely affected inStxbp1hap, instead, excitatory synapses fail to recruit interneurons.

- AMPAkines rescue microcircuit failure inStxbp1hap
The influence of transformational and learning through R&D capabilities on the competitive advantage of firms
Authors: Aldabbas Hazem , Oberholzer Niël
Published: February 2023

Purpose

This study provides theoretical and empirical insights into how firms can enhance their performance strategically and financially by integrating learning and transformational capabilities into research and development (R&D) activities based on the dynamic capabilities approach. To achieve this, the authors propose that transformational capabilities in R&D mediate the relationship between learning capabilities in R&D and competitive advantage.

Design/methodology/approach

Using a purposive sampling technique and standardized questionnaires, data were collected from 118 R&D and senior managers. To analyze the data, multiple regression analysis, along with SPSS PROCESS macro (Model 4), was used.

Findings

The results support the theoretical assumption that there are direct and indirect positive and significant effects between learning capabilities in R&D and competitive advantage as mediated by transformational R&D capabilities.

Originality/value

This study explores R&D from a dynamic capabilities perspective and suggests that learning capabilities should come first to enhance businesses’ competitive advantage. Furthermore, transformational R&D capabilities can explain the relationship between learning capabilities in R&D and competitive advantage. The authors recommend that researchers should investigate the contributions of R&D to promote competitive advantage.