title: Non-productive exposure of PBMCs to SARS-CoV-2 induces cell-intrinsic innate immunity responses

abstract: Cell-intrinsic responses mounted in vivo in PBMCs during mild and severe COVID-19 differ quantitatively and qualitatively. Whether they are triggered by signals emitted by productively infected cells of the respiratory tract or are, at least partially, resulting from physical interaction with virus particles, remains unclear. Here, we analyzed susceptibility and expression profiles of PBMCs from healthy donors upon ex vivo exposure to SARS-CoV and SARS-CoV-2. In line with the absence of detectable ACE2 receptor expression, human PBMCs were refractory to productive infection. Bulk and single cell RNA-sequencing revealed JAK/STAT-dependent induction of interferon-stimulated genes, but not pro-inflammatory cytokines. This SARS-CoV-2-specific response was most pronounced in monocytes. SARS-CoV-2-RNA-positive monocytes displayed a lower ISG signature as compared to bystander cells of the identical culture. This suggests a preferential invasion of cells with a low ISG base-line profile or delivery of a SARS-CoV-2-specific sensing antagonist upon efficient particle internalization. Together, non-productive physical interaction of PBMCs with SARS-CoV-2-but not SARS-CoV particles stimulates JAK/STAT-dependent, monocyte-accentuated innate immune responses that resemble those detected in vivo in patients with mild COVID-19.


title: Comprehensive analysis of Arabidopsis thaliana DNA polymerase epsilon catalytic subunit A and B mutants - an insight into differentially expressed genes and protein-protein interactions

abstract: One of the main replicative enzymes in most eukaryotes, DNA polymerase {varepsilon} (POLE), is composed of four subunits, namely a single catalytic and three regulatory subunits. In Arabidopsis, the catalytic subunit of POLE is encoded by two genes: Arabidopsis thaliana DNA POLYMERASE EPSILON CATALYTIC SUBUNIT A (AtPOL2A) and B (AtPOL2B). Although studies have shown AtPOL2A to be involved in various biological processes, the role of AtPOL2B is unclear. Here, we investigated the transcriptomes of both atpol2a and atpol2b mutants, and the promoter sequences to provide a better insight into the targets of AtPOL2s at the molecular level. In the present study, leaf cDNA libraries of four AtPOL2 mutants (atpol2a-1 and atpol2b-1, -2 and - 3) were sequenced using the Illumina platform. Analysis of gene expression profiles identified a total of 198, 76, 141 and 67 differentially expressed genes in atpol2a-1, atpol2b-1, atpol2b-2 and atpol2b-3, respectively; the majority of pericentromeric transposable elements were transcriptionally active in atpol2a-1 as compared to atpol2b mutants and wild type. Protein-protein interaction network analysis and molecular docking identified three (CER1, RPA1E and AT5G60250) and two (PR1 and AT5G48490) proteins as potential interactors (cluster size > 60 and balanced score < -900) of AtPOL2A and AtPOL2B, respectively; Interestingly, these five proteins also showed a significant interaction between POLE catalytic subunit of Saccharomyces cerevisiae. Our in silico promoter analysis showed that the AtPOL2A promoter sequence is overrepresented with cis-acting regulatory elements (CREs) associate with cell cycle regulation, meristematic/reproductive tissue-specific pattern of expression and MYB protein recognition, whereas the AtPOL2B promoter sequence was mainly enriched with stress-responsive elements. The information provided here has led to the identification of targets of AtPOL2s at the molecular level and CREs putatively associated with the regulation of AtPOL2s. To our knowledge, this study provides the first comparative transcriptome profiling of single-gene mutants of AtPOL2s.

category: molecular biology


title: Lung evolution in vertebrates and the water-to-land transition

abstract: A crucial evolutionary change in vertebrate history was the Palaeozoic (Devonian ~400 million years ago) water-to-land transition, allowed by key morphological and physiological modifications including the acquisition of lungs. Nonetheless, the origin and early evolution of vertebrate lungs remain highly controversial, particularly whether the ancestral state was paired or unpaired. Due to the rarity of fossil soft tissue preservation, lung evolution can only be traced based on the extant phylogenetic bracket. Here we investigate, for the first time, lung morphology in extensive developmental series of key living lunged osteichthyans using synchrotron X-ray microtomography and histology. Our results shed light on the primitive state of vertebrate lungs as unpaired, evolving to be truly paired in the lineage towards the tetrapods. The water-to-land transition confronted profound physiological challenges and paired lungs were decisive for increasing the surface area and the pulmonary compliance and volume, especially during the air-breathing on land.

category: evolutionary biology


title: SARS-CoV-2 variants show a gradual declining pathogenicity and pro-inflammatory cytokine stimulation and an increasing antigenic and anti-inflammatory cytokine induction

abstract: Hyper-transmissibility with decreased disease severity are typical characteristics of Omicron variant. To understand this phenomenon, we used various bioinformatics approaches to analyze randomly selected genome sequences (one each) of the Gamma, Delta, and Omicron variants submitted to NCBI from 15 to 31 December 2021. We show that: (i) Pathogenicity of SARS-CoV-2 variants decreases in the order: Wuhan > Gamma > Delta > Omicron; however, the antigenic property follows the order: Omicron > Gamma > Wuhan > Delta. (ii) Omicron Spike RBD has lower pathogenicity but higher antigenicity than other variants. (iii) Decreased disease severity by Omicron variant may be due to its decreased pro-inflammatory and IL-6 stimulation and increased IFN-{gamma} and IL-4 induction efficacy. (iv) Mutations in N protein are associated with decreased IL-6 induction and human DDX21-mediated increased IL-4 production in Omicron. (v) Due to mutations, the stability of S, M, N, and E proteins decreases in the order: Omicron > Gamma > Delta > Wuhan. (vi) Stronger Spike RBD-hACE2 binding in Omicron is associated with increased transmissibility. However, the lowest stability of the Omicron Spike protein makes Spike RBD-hACE2 interaction weak for systemic infection and for causing severe disease. Finally (vii), the highest instability of Omicron E protein may also be associated with decreased viral maturation and low viral load leading to less severe disease and faster recovery. Our method may be used for other similar viruses, and these findings will contribute to the understanding of the dynamics of SARS-CoV-2 variants and the management of emerging variants.

category: bioinformatics


title: SARS-CoV-2 variants show a gradual declining pathogenicity and pro-inflammatory cytokine spur, an increasing antigenic and anti-inflammatory cytokine induction, and rising structural protein instability


title: SARS-CoV-2 Omicron BA.2 Variant Evades Neutralization by Therapeutic Monoclonal Antibodies

abstract: Monoclonal antibody therapy for the treatment of SARS-CoV-2 infection has been highly successful in decreasing disease severity; however, the recent emergence of the heavily mutated Omicron variant has posed a challenge to this treatment strategy. The Omicron variant BA.1 has been found to evade neutralization by several of the therapeutic monoclonal antibodies authorized for emergency use, while Vir-7831 and a cocktail consisting of monoclonal antibodies AZD8895+AZD1061 retain significant neutralizing activity. A newly emerged variant, Omicron BA.2, containing some of the BA.1 mutations plus an additional 6 mutations and 3 deletions, 3 of which lie in the receptor binding domain, has been found to be spreading with increased transmissibility. We report here, using spike protein-pseudotyped lentiviruses, decreased neutralization of BA.2 by several therapeutic monoclonal antibodies but that the mixture of AZD8895+AZD1061 retained substantial neutralizing activity against BA.2.

category: immunology


title: Neutralization of SARS-CoV-2 Omicron BA.2 by Therapeutic Monoclonal Antibodies


title: '4-Aminoquinazoline-6,7-diol' derivatives for enhanced EGFR binding (as inhibitor) against Lung cancer

abstract: The Epidermal growth factor receptor (EGFR) have been considered as potential targets for cancer therapy due to their role in regulating proliferation and survival of cancer cells. In the present study, the four  4-aminoquinazoline-6, 7-diol derivative molecules were selected to the theoretically investigate their inhibitory activity against EGFR protein. Molecules were evaluated on the basis of: (i) in-silico cytotoxic assay on human cancer cell lines expressing EGFR (A549 and A431), (ii) in-silico kinase assay, (iii) impact of molecular interaction on EGFR, (iv) molecular interaction stability, (v) inhibitory impact of molecules on combined expression of EGF-EGFR and (v) ADME observations. Studies were observed on the scale of two known EGFR inhibitors. In-silico cytotoxicity screening results demonstrated that the A431 lung cancer cell line was vulnerable to compound abc1-4. However, A549 cells were less sensitive to our designed molecules. From kinase inhibition assay results, compound abc1&2 were found to be an inhibitor against EGFR. According to the molecular interaction analysis, compounds abc1-4 performed in similar fashion of positive controls, acting at the catalytic site of EGFR. Altogether, these potent compounds, with compromised bioavailability, could likely be developed as a promising EGFR targeted drug(s) for cancer therapy.


title: Robust statistical evaluation of tumor incidences in long-term rodent carcinogenicity studies: the reformulated poly-k trend test

abstract: Mortality-adjusted tumor rates in long-term carcinogenicity rodent bioassays are commonly evaluated by means of the poly-k=3 Armitage trend test. However, this assumes exactly a linear dose-response curve and the Weibull parameter of k=3 for all tumor sites. These unrealistic assumptions can be circumvented by multiple testing across multiple possible dose-response shapes, multiple Weibull parameters, multiple effect sizes, multiple correlated tumors as well as pairwise and trend tests using the multiple marginal models approach. Based on data examples, different multiple tests are demonstrated using the CRAN R packages multcomp, tukeytrend, coin, MCPAN and multfisher.


title: A new pterosaur from Skye, Scotland and the early diversification of flying reptiles

abstract: The Middle Jurassic was a critical time in pterosaur evolution, witnessing the inception of major morphological innovations that underpinned successive radiations by rhamphorhynchids, basal monofenestratans and pterodactyloids. Frustratingly, this interval is particularly sparsely sampled, with a record consisting almost exclusively of isolated fragmentary remains. Here, we describe new material from the Bathonian-aged Kilmaluag Formation of Skye, Scotland, which helps to close this gap. REDACTED (gen. et sp. nov.) is based on a three-dimensionally preserved partial skeleton, which represents the first associated Middle Jurassic pterosaur. REDACTED is one of the first pterosaurs to be fully digitally prepared and CT scanning reveals multiple elements of the skeleton that remain fully embedded within the matrix, which are otherwise inaccessible. Novel anatomical features of this new Middle Jurassic pterosaur help to confirm the existence of the controversial clade Darwinoptera, greatly clarifying our understanding of Jurassic pterosaur evolution.

category: paleontology


title: Editing the CsDMR6 Gene in Citrus Results in Resistance to the Bacterial Disease Citrus Canker

abstract: Citrus is one of the most important fruit crops in the world. Citrus production worldwide faces challenges from devastating bacterial diseases, including citrus canker caused by Xanthomonas citri ssp. citri (Xcc). Improving citrus resistance to citrus canker and other major bacterial diseases has been a top priority in citrus biotechnology. Disabling disease susceptibility genes has emerged as a novel, promising approach to engineering disease resistance. The bottleneck for applying such an approach has been the identification of proper disease susceptibility-related genes in citrus. Here we show the first successful case of editing the CsDMR6 gene in citrus and obtaining strong resistance to citrus canker in six mutants in two citrus cultivars,  Duncan grapefruit and Carrizo citrange. Multiple types of deletions and insertions were induced in CsDMR6, resulting in frameshift of its coding region and presumably loss of gene function. The mutation frequency in most of the mutants reached 71.8% to 98.9%. The mutants showed 71.2% to 99.8% reduction in citrus canker lesion and greater than 99.7% or 2.45 to 4.95 Log10 unit reduction in Xcc bacterial cell population. Mutants also accumulated more salicylic acid and expressed much higher levels of the NPR1 gene than the wildtype with or without Xcc inoculation, which suggests potential resistance to other diseases in these mutants. The guide RNAs for targeting CsDMR6 were selected from highly conserved regions and have 100% nucleotide identity with DMR6 homologs in important citrus species; these guide RNAs are expected to work in other important citrus species and cultivars.

category: plant biology


title: Clonally heritable gene expression imparts a layer of diversity within cell types

abstract: Cell types can be classified based on shared patterns of transcription. Variability in gene expression between individual cells of the same type has been ascribed to stochastic transcriptional bursting and transient cell states. We asked whether long-term, heritable differences in transcription can impart diversity within a cell type. Studying clonal human lymphocytes and mouse brain cells, we uncover a vast diversity of heritable transcriptional states among different clones of cells of the same type in vivo. In lymphocytes we show that this diversity is coupled to clone specific chromatin accessibility, resulting in distinct expression of genes by different clones. Our findings identify a source of cellular diversity, which may have important implications for how cellular populations are shaped by selective processes in development, aging and disease.

category: systems biology


title: Utilising TMS-EEG to assess the response to cerebellar-brain inhibition

abstract:
BackgroundCerebellar-brain inhibition (CBI) is a transcranial magnetic stimulation (TMS) paradigm indexing excitability of cerebellar projections to motor cortex (M1). Stimulation involved with CBI is often considered to be uncomfortable, and alternative ways to index connectivity between cerebellum and the cortex would be valuable. Utilising electroencephalography in conjunction with TMS (combined TMS-EEG) to record the response to CBI has the potential to achieve this, but has not been attempted previously.

ObjectiveTo investigate the utility of TMS-EEG for characterising cerebellar-cortical interactions recruited by CBI.

MethodsA total of 33 volunteers (25.7 {+/-} 4.9 years, 20 females) participated across three experiments. These investigated EEG responses to CBI induced with a figure-of-eight (F8; experiment 1) or double cone (DC; experiment 2) conditioning coil over cerebellum, in addition to multisensory sham stimulation (experiment 3).

ResultsBoth F8 and DC coils suppressed early TMS-evoked EEG potentials (TEPs) produced by TMS to M1 (P < 0.05). Furthermore, the TEP produced by CBI stimulation was related to the motor inhibitory response to CBI recorded in a hand muscle (P < 0.05), but only when using the DC coil. Multisensory sham stimulation failed to modify the M1 TEP.

ConclusionsCerebellar conditioning produced changes in the M1 TEP that were not apparent following sham stimulation, and that were related to the motor inhibitory effects of CBI. Our findings therefore suggest it is possible to index the response to CBI using TMS-EEG. In addition, while both F8 and DC coils appear to recruit cerebellar projections, the nature of these may be different.

category: neuroscience


title: Behavioral signatures of Y-like neuronal responses in human vision

abstract:
Retinal ganglion cells (RGCs) initiating the magnocellular/Y-cell visual pathways are distinguished by responding nonlinearly to high spatial frequencies (SFs) and temporal frequencies (TFs). This nonlinearity is implicated in the processing of contrast modulation (CM) stimuli in cats and monkeys, but its contribution to human visual perception is not well understood. Here we formulated an approach to reveal the function of human Y-like RGCs by leveraging the Y-like carrier response properties of cortical neurons to CM stimuli consisting of a high SF contrast-reversing grating carrier whose contrast is modulated by a low SF drifting sinewave envelope. Subjects reported the direction of motion of CM envelopes or luminance modulation (LM) gratings, presented at different eccentricities. The dependence of task performance on SF (for LMs) or carrier SF (for CMs) was measured for different TFs (LMs) or carrier TFs (CMs). The best performance for LM stimuli was at lower TFs and SFs, which decreased systematically with eccentricity. However, performance with CM stimuli was bandpass with carrier SF, largely independent of carrier TF, and at the highest carrier TF (20 Hz) decreased minimally with eccentricity. Since the nonlinear subunits of Y -cells respond better at higher TFs compared to the linear response components, and respond best at higher SFs that are relatively independent of eccentricity, these results suggest that behavioral tasks employing CM stimuli with high spatiotemporal carrier frequencies can reveal the nonlinear contributions of retinal Y-like cells to human perception.

Significance StatementY-like retinal ganglion cells (RGCs), characterized by responding linearly at low spatial and temporal frequencies and nonlinearly at high spatiotemporal frequencies, have been well characterized neurophysiologically in cats and monkeys. However, a clear counterpart of Y-like RGCs has remained elusive in humans. Here, we leveraged these response properties to reveal a behavioral signature of Y-like cells in human observers. To drive linear or nonlinear response mechanisms, we presented drifting luminance modulation and contrast modulation stimuli respectively at multiple spatial and temporal frequencies and eccentricities. Our results suggest that humans exhibit behavioral response patterns to contrast modulation stimuli that are consistent with the nonlinear response properties of Y-like cells.


title: Gut Microbiome Contributes to Cold-climate Adaptation in Lizards

abstract:
The metabolic cold-climate adaption hypothesis predicts that animals from cold environments have relatively high metabolic rates compared with their warm-climate counterparts. However, studies testing this hypothesis are sparse. Here, we compared gut microbes between two cold-climate lizard species of the genus Phrynocephalus to test the hypothesis that gut microbiota can help lizards adapt to cold environments by promoting metabolism and absorption efficiency. We kept lizards at 24{degrees}C and 30{degrees}C for 25 d, and then collected their fecal samples to analyze and compare the microbiota based on 16S rRNA gene sequencing technology. The gut microbiota was mainly composed of Proteobacteria, Firmicutes, Bacteroidetes, and Verrucomicrobia at the phylum level in both species (Proteobacteria > Firmicutes > Verrucomicrobiota in P. erythrurus, and Bacteroidota > Proteobacteria > Firmicutes in P. przewalskii). Further analysis revealed that the gut microbiota contributed to the hosts cold adaptation, but with differences in the relative abundance of these contributory bacteria between the two species. KEGG analysis revealed that the gut microbiota primarily played roles in metabolism, genetic information processing, cellular processes, and environmental information processing in both species. Furthermore, genes related to metabolism were more abundant in P. erythrurus at 24 {degrees}C than in other species x temperature combinations, indicating the role of gut microbiota in long-term cold-climate adaptation. Our finding that gut microbiome contributes to cold-climate adaptation in both species but more evidently in P. erythrurus using colder habitats than P. przewalskii throughout a year confirms the gut microbiotas role in the cold-climate adaptation in lizards.

IMPORTANCEThis study proves that temperature affects the composition and relative abundance of the gut microbiota in two Phrynocephalus lizards in a species-specific manner. Both species harbor specific gut microbiota with significant roles in cold-climate adaptation. Specifically, P. erythrurus has a higher Proteobacteria ratio and relative abundance of metabolism-related microbial genes in the gut than P. przewalskii. Given that P. erythrurus uses colder habitats than P. przewalskii throughout a year, these results suggest that gut microbiota contributes to cold-climate adaptation in both species lizards but more evidently in P. erythrurus. This study provides evidence linking gut microbiome with cold adaptation. The co-evolution mechanism between gut microbiota and their hosts in extreme environments will provide new insights into animal adaptation.

category: ecology


title: Quantitatively defining species boundaries with moreefficiency and more biological realism

abstract: We introduce a widely applicable species delimitation method based on the multispecies coalescent model that is more efficient and more biologically realistic than existing methods. We extend the phylogenetic tree collapse model to the Yule-skyline model, allowing the ancestral speciation rate to vary through time as a smooth piecewise function. Furthermore, we introduce the cutting-edge proposal kernels of StarBeast3 to this model, thus enabling rapid species delimitation on large molecular datasets and allowing the use of relaxed molecular clock models. We validate these methods with genomic sequence data and SNP data, and show they are more efficient than existing methods at achieving parameter convergence during Bayesian MCMC. Lastly, we apply these methods to two datasets and find inconsistencies with the published literature. Our methods are powerful for rapid quantitative testing of species boundaries in large multilocus datasets and are implemented as an open source BEAST 2 package called SPEEDEMON.


title: Comparative sub-cellular proteome analyses reveals metabolic differentiation and production of effector-like molecules in the dieback phytopathogen Phytophthora cinnamomi.

abstract:
Phytopathogenic oomycetes pose a significant threat to global biodiversity and food security. The proteomes of these oomycetes likely contain important factors that contribute to their pathogenic success, making their discovery crucial for elucidating pathogenicity. Oomycetes secrete effector proteins that overcome or elicit a defence response in susceptible hosts. Phytophthora cinnamomi is a root pathogen that causes dieback in a wide variety of crops and a range of native vegetation world-wide. Virulence proteins produced by P. cinnamomi are not well defined and a large-scale approach to understand the biochemistry of this pathogen has not been documented. Here, soluble mycelial, zoospore and secreted proteomes were obtained and label-free quantitative proteomics was used to compare the composition of protein content of the three sub-proteomes by matching the MS/MS data to a sequenced P. cinnamomi genome. Mass spectra matched to a total of 4635 proteins, validating 17.7% of the predicted gene set of the P. cinnamomi genome. The mycelia were abundant in transporters for nutrient acquisition, metabolism and cellular proliferation. The zoospores had less metabolic related ontologies than the mycelia but were abundant in energy generating, motility and signalling associated proteins. Virulence-associated proteins were identified in the secretome such as candidate effector and effector-like proteins, which interfere with the host immune system. These include hydrolases, cell wall degrading enzymes, putative necrosis-inducing proteins and elicitins. The secretome elicited a hypersensitive response on the roots of a model host and thus suggests evidence of effector activity.

SignificancePhytophthora cinnamomi is a phytopathogenic oomycete that causes dieback disease in native vegetation and several horticultural crops such as avocado, pineapple and macadamia. Whilst this pathogen has significance world-wide, its pathogenicity and virulence have not been described in depth. We carried out comparative label-free proteomics of the mycelia, zoospores and secretome of P. cinnamomi. This study highlights the differential metabolism and cellular processes between the sub-proteomes. Proteins associated with metabolism, nutrient transport and cellular proliferation were over represented in the mycelia. The zoospores have a specialised proteome showing increased energy generation geared towards motility. Candidate effectors and effector-like secreted proteins were also identified, which can be exploited for genetic resistance. This demonstrates a better understanding of the biology and pathogenicity of P. cinnamomi infection that can subsequently be used to develop effective methods of disease management

category: biochemistry


title: Metabotropic purinergic receptor profiles and calcium signalling in primary mice myoblasts differ depending on their muscle origin and are altered in cells with mutated dystrophin gene (mdx mice)

abstract: Mortality of Duchenne Muscular Dystrophy (DMD) is a direct consequence of progressive wasting of muscle fibres leading to skeletal muscle deterioration and cardiomyopathy. However pathophysiological effects of mutations in the dystrophin encoding gene, which result in improper muscle maturation are detectable in muscle precursor cells which do not express dystrophin gene at the protein level because of early stage of differentiation thus irrespectively of changes in dystrophin-encoding gene. Among these abnormalities elevated activity of P2X7 receptors and increased store-operated calcium entry, have been identified in mdx mouse myoblasts. Moreover the increased response of immortalized mdx myoblasts to agonists activating metabotropic purinergic receptors was characterised. Experiments on immortalized myoblasts do not allow indicating potentially specific effects of mdx mutation on cells derived from particular muscles. Moreover an immortalization of cells itself may influence their metabolism in poorly defined way. Therefore here the metabotropic response of primary myoblasts derived from various muscles of normal and mdx mice to nucleotide stimulation has been investigated. Transcript and protein level of P2Y receptors, sensitivity to antagonist, and cellular localization clearly indicate P2RY2 as the most affected in mdx myoblasts. This meets our previous conclusion drawn from experiments with immortalized cells. However a pattern of expression and activity of P2Y receptors among myoblasts derived from four muscles differ. Also cellular levels of some other proteins belonging to the "calcium signalling toolkit" differ in myoblasts from various muscle and are differently changed due to mdx mutation. Finally, these results complement and strongly support previously formulated conclusion that phenotypic effects of DMD emerge as early as in undifferentiated muscle and therefore traditional understanding of DMD pathogenesis needs re-evaluation.


title: Chemophototherapy Overcomes Doxorubicin Resistance in Human Ovarian Cancer Cells

abstract: Porphyrin-phospholipid (PoP) liposomes loaded with Doxorubicin have been demonstrated to be an efficient vehicle for chemophototherapy (CPT). Multi-drug resistance (MDR) of cancer cells is a known resistance mechanism for cancer chemotherapies. We report a phototherapeutic measure to overcome Dox-resistance using Doxorubicin (Dox)-loaded PoP liposomes. In vitro studies using free Dox or Dox loaded into liposomes with 2 mol.% showed human ovarian carcinoma A2780 cells were more susceptible to these drugs compared to the corresponding Dox-resistant A2780-R cells. In contrast, when CPT was applied with LC-Dox-PoP liposomes, effective killing of both non-resistant and resistant A2780 cell lines was observed. An in vivo study to assess the efficiency of LC-Dox-PoP liposomes with phototreatment showed effective tumor shrinkage and prolonged survival of athymic nude mice bearing A2780-R tumor xenografts. Biodistribution analysis demonstrated enhanced tumoral drug uptake in Dox-resistant tumors with CPT, pointing to the likelihood that increased drug delivery overcame resistance mechanisms to provide for improved anti-cancer therapy.

category: bioengineering


title: Time-dependent Role of Bisphosphonates on Atherosclerotic Plaque Calcification

abstract: Atherosclerotic plaque calcification directly contributes to the leading cause of morbidity and mortality by affecting the plaque vulnerability and rupture risk. Small microcalcifications can increase plaque stress and promote rupture, whereas large calcifications can stabilize plaques. Drugs that target bone mineralization may lead to unintended consequences on ectopic plaque calcification and cardiovascular outcomes. Bisphosphonates, common anti-osteoporotic agents, elicited unexpected cardiovascular events in clinical trials. Here, we investigated the role of bisphosphonates treatment and timing on the disruption or promotion of vascular calcification and bone mineral in a mouse model of atherosclerosis. We started the bisphosphonate treatment either before plaque formation, at early plaque formation times associated with the onset of calcification, or at late stages of plaque development. Our data indicate that long term bisphosphonate treatment (beginning prior to plaque development) leads to higher levels of plaque calcification, with a narrower mineral size distribution. When given later in plaque development, we measured a wider distribution of mineral size. These morphological alterations may associate with higher risk of plaque rupture by creating stress foci. Yet, bone mineral density positively correlated with the duration of bisphosphonate treatment.


title: SciViewer- An interactive browser for visualizing single cell datasets

abstract: Single-cell sequencing improves our ability to understand biological systems at single-cell resolution and can be used to identify novel drug targets and optimal cell-types for target validation. However, tools that can interactively visualize and provide target-centric views of these large datasets are limited. We present SciViewer (Single-cell Interactive Viewer), a novel tool to interactively visualize, annotate and share single-cell datasets. SciViewer allows visualization of cluster, gene and pathway level information such as clustering annotation, differential expression, pathway enrichment, cell-type specificity, cellular composition, normalized gene expression and comparison across datasets. Further, we provide APIs for SciViewer to interact with publicly available pharmacogenomics databases for systematic evaluation of potential novel drug targets. We provide a module for non-programmatic upload of single-cell datasets. SciViewer will be a useful tool for data exploration and target discovery from single-cell datasets. It is available on GitHub (https://github.com/Dhawal-Jain/SciViewer).


title: Unbiased pangenome graphs

abstract:
MotivationPangenome variation graphs model the mutual alignment of collections of DNA sequences. A set of pairwise alignments implies a variation graph, but there are no scalable methods to generate such a graph from these alignments. Existing related approaches depend on a single reference, a specific ordering of genomes, or a de Bruijn model based on a fixed k-mer length. A scalable, self-contained method to build pangenome graphs without such limitations would be a key step in pangenome construction and manipulation pipelines.

ResultsWe design the seqwish algorithm, which builds a variation graph from a set of sequences and alignments between them. We first transform the alignment set into an implicit interval tree. To build up the variation graph, we query this tree-based representation of the alignments to reduce transitive matches into single DNA segments in a sequence graph. By recording the mapping from input sequence to output graph, we can trace the original paths through this graph, yielding a pangenome variation graph. We present an implementation that operates in external memory, using disk-backed data structures and lock-free parallel methods to drive the core graph induction step. We demonstrate that our method scales to very large graph induction problems by applying it to build pangenome graphs for several species.

Availabilityseqwish is published as free software under the MIT open source license. Source code and documentation are available at https://github.com/ekg/seqwish. seqwish can be installed via Bioconda https://bioconda.github.io/recipes/seqwish/README.html or GNU Guix https://github.com/ekg/guix-genomics/blob/master/seqwish.scm.

Contactegarris5@uthsc.edu


title: Microbiome Toolbox: Methodological approaches to derive and visualize microbiome trajectories

abstract:
SummaryThe gut microbiome changes rapidly under the influence of different factors such as age, dietary changes or medications to name just a few. To analyze and understand such changes we present a microbiome analysis toolbox. We implemented several methods for analysis and exploration to provide interactive visualizations for easy comprehension and reporting of longitudinal microbiome data. Based on abundance of microbiome features such as taxa as well as functional capacity modules, and with the corresponding metadata per sample, the toolbox includes methods for 1) data analysis and exploration, 2) data preparation including dataset-specific preprocessing and transformation, 3) best feature selection for log-ratio denominators, 4) two-group analysis, 5) microbiome trajectory prediction with feature importance over time, 6) spline and linear regression statistical analysis for testing universality across different groups and differentiation of two trajectories, 7) longitudinal anomaly detection on the microbiome trajectory, and 8) simulated intervention to return anomaly back to a reference trajectory.

Availability and implementationThe software tools are open source and implemented in Python. The link to the interactive dashboard is https://microbiome-toolbox.herokuapp.com/. For developers interested in additional functionality of the toolbox, the Python package can be downloaded from https://pypi.org/project/microbiome-toolbox/. The toolbox is modular allowing for further extension with custom methods and analysis. The code is available on Github https://github.com/JelenaBanjac/microbiome-toolbox.

ContactShaillayKumar.Dogra@rd.nestle.com

Supplementary InformationSupplementary data are available at Bioinformatics online.


title: GMMchi: Gene Expression Clustering Using Gaussian Mixture Modeling

abstract:
MotivationCancer evolution consists of a stepwise acquisition of genetic and epigenetic changes, which alter the gene expression profiles of cells in a particular tissue and result in phenotypic alterations acted upon by natural selection. The recurrent appearance of specific genetic lesions across individual cancers and cancer types suggests the existence of certain "driver mutations," which likely make up the major contribution to tumors selective advantages over surrounding normal tissue and as such are responsible for the most consequential aspects of the cancer cells gene expression patterns and phenotypes. We hypothesize that such mutations are likely to cluster with specific dichotomous shifts in the expression of the genes they most closely control, and propose GMMchi, a Python package that leverages Gaussian Mixture Modeling to detect and characterize bimodal gene expression patterns across cancer samples, as a tool to analyze such correlations using 2x2 contingency table statistics.

ResultsWe confirm that GMMchi robustly and reliably extracts bimodal patterns from both colorectal cancer (CRC) cell line-derived microarray and tumor-derived RNA-Seq data and verify previously reported gene expression correlates of some well-characterized CRC phenotypes. Using well-defined simulated data, we were able to confirm the robust performance of GMMchi, reaching 85% accuracy with a sample size of n = 90. We were also able to demonstrate a few examples of the application of GMMchi with respect to its capacity to characterize background florescent signal in microarray data, filter out uninformative background probe sets, as well as uncover novel genetic interrelationships and tumor characteristics. Our approach to analysing gene expression analysis in cancers provides an additional lens to supplement traditional continuous-valued statistical analysis by maximizing the information that can be gathered from bulk gene expression data.

AvailabilityThe Python package GMMchi and our cell line microarray data used in this paper is available for downloading on GitHub at https://github.com/jeffliu6068/GMMchi

Contactta-chun.liu@oncology.ox.ac.uk, peter.kalugin@hms.harvard.edu, walter.bodmer@hertford.ox.ac.uk


title: A possible way to relate the effects of SARS-CoV-2 induced changes in transferrin to severe COVID-19 associated diseases

abstract:
The potentially life-threatening Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) infection is responsible for the coronavirus pandemic in 2019 (COVID-19). The transferrin as an essential component of iron-metabolism was suggested to be a link between iron transport associated diseases and COVID-19 infection.

The effect of SARS-CoV-2 on human whole blood was studied by differential scanning calorimetry. The analysis and deconvolution of the thermal transition curves showed that the Tm of transferrin related second peak decreased by 5.16 {degrees}C (6.4%) in the presence of SARS-CoV-2 virus. The ratio of the under-curve area of the two main peaks was greatly affected while the total enthalpy of the heat denaturation was nearly unchanged in the presence of the virus.

Based on the results it is possible to conclude that SARS-CoV-2 through binding to transferrin can influence its Fe3+ uptake by inducing thermodynamic changes. Transferrin may stay in iron-free apo-conformational state, which probably depends on the SARS-CoV-2 concentration.

SARS-CoV-2 might induce disturbance in the erythropoiesis due to the free iron overload generated iron toxicity. As a late consequence iron toxicity related hepatocellular carcinoma can even develop.

Our work can support the basic role of transferrin in COVID-19 related severe diseases.

category: biophysics


title: Therapeutic resistance to FLT3 inhibition is driven by a novel ATM/mTOR pathway regulating oxidative phosphorylation

abstract: While leukemic cells are susceptible to various therapeutic insults, residence in the bone marrow microenvironment typically confers protection from a wide range of drugs. Thus, understanding the unique molecular changes elicited by the marrow is of critical importance towards improving therapeutic outcomes. In the present study, we demonstrate that aberrant activation of oxidative phosphorylation serves to induce therapeutic resistance in FLT3 mutant human AML cells challenged with FLT3 inhibitor drugs. Importantly, our findings show that AML cells are protected from apoptosis following FLT3 inhibition due to marrow-mediated activation of ATM, which in turn up-regulates oxidative phosphorylation via mTOR signaling. mTOR is required for the bone marrow stroma-dependent maintenance of protein translation, with selective polysome enrichment of oxidative phosphorylation transcripts, despite FLT3 inhibition. To investigate the therapeutic significance of this finding, we tested the mTOR inhibitor everolimus in combination with the FLT3 inhibitor quizartinib in primary human AML xenograft models. While marrow resident AML cells were highly resistant to quizartinib alone, the addition of everolimus induced profound reduction in tumor burden and prevented relapse. Taken together, these data provide a novel mechanistic understanding of marrow-based therapeutic resistance, and a promising strategy for improved treatment of FLT3 mutant AML patients.

category: cancer biology


title: Therapeutic resistance in acute myeloid leukemia cells is mediated by a novel ATM/mTOR pathway regulating oxidative phosphorylation


title: Tideglusib mitigates dystrophic pathology in skeletal muscle and restores diastolic function in young D2 mdx mice

abstract: Duchenne muscular dystrophy (DMD) is a severe muscle wasting disorder that leads to early mortality. We examined the pathogenic contribution of glycogen synthase kinase 3 (GSK3) to DMD using the mdx model. GSK3 is a serine/threonine kinase that has been implicated in other muscular dystrophies and our initial results showed that overactivation of GSK3 may contribute to increased disease severity found in DBA/2J (D2) mdx mice vs C57BL/10 mdx mice. In support of this, treating D2 mdx mice with the GSK3 inhibitor, tideglusib (10 mg/kg/day), increased muscle mass, strength, and fatigue resistance. We also found elevated proportions of oxidative fibers and increased utrophin mRNA, while muscle necrosis and oxidative stress were reduced. Finally, young D2 mdx mice displayed early diastolic dysfunction, and this was blunted with tideglusib treatment - an effect attributed to lowered oxidative stress and fibrosis. This study highlights the therapeutic potential of tideglusib and GSK3 inhibition for DMD.

category: physiology


title: Antigen-dependent inducible T cell reporter system for PET imaging of breast cancer and glioblastoma

abstract: For the past several decades, chimeric antigen receptor T cell (CAR T) therapies have shown promise in the treatment of cancers. These treatments would greatly benefit from companion imaging biomarkers to follow the trafficking and activation of T cells in vivo. Using synthetic biology, we engineered T cells with a chimeric receptor SyNthetic Intramembrane Proteolysis Receptor (SNIPR) that induces overexpression of an exogenous reporter gene cassette upon recognition of specific tumor markers. We then applied a SNIPR-based positron emission tomography (PET) reporter system to two cancer-relevant antigens, human epidermal growth factor receptor 2 (HER2) and epidermal growth factor receptor variant III (EGFRvIII), commonly expressed in breast and glial tumors respectively. Antigen-specific reporter induction of the SNIPR-PET T cells was confirmed in vitro using GFP fluorescence, luciferase luminescence, and the HSV-TK PET reporter with [18F]FHBG. Tumors were successfully imaged using PET in dual xenograft HER2+/HER2- and EGFRvIII+/EGFRvIII- animal models, with > 10-fold higher [18F]FHBG signals seen in antigen-expressing tumors versus the corresponding controls. The main innovation described is therefore PET detection of therapeutic T cells via specific antigen-induced signals, in contrast to reporter systems relying on constitutive gene expression.

category: synthetic biology


title: The development of receptive field tuning properties in mouse binocular primary visual cortex

abstract:
The mouse primary visual cortex is a model system for understanding the relationship between cortical structure, function, and behavior (Seabrook et al., 2017; Chaplin and Margrie, 2020; Hooks and Chen, 2020; Saleem, 2020; Flossmann and Rochefort, 2021). Binocular neurons in V1 are the cellular basis of binocular vision, which is required for predation (Scholl et al., 2013; Hoy et al., 2016; La Chioma et al., 2020; Berson, 2021; Johnson et al., 2021). The normal development of binocular responses, however, has not been systematically measured. Here, we measure tuning properties of neurons to either eye in awake mice of either sex from eye-opening to the closure of the critical period. At eye-opening, we find an adult-like fraction of neurons responding to the contralateral-eye stimulation, which are selective for orientation and spatial frequency; few neurons respond to ipsilateral eye and their tuning is immature. Fraction of ipsilateral-eye responses increases rapidly in the first few days after eye opening and more slowly thereafter, reaching adult levels by critical period closure. Tuning of these responses improves with a similar time course. The development and tuning of binocular responses parallels that of ipsilateral-eye responses. Four days after eye-opening, monocular neurons respond to a full range of orientations but become more biased to cardinal orientations. Binocular responses, by contrast, lose their cardinal bias with age. Together, these data provide an in-depth accounting of the development of monocular and binocular responses in the binocular region of mouse V1 using a consistent set of visual stimuli and measurements.

Significance statementIn this manuscript, we present a full accounting of the emergence and refinement of monocular and binocular receptive field tuning properties of thousands of pyramidal neurons in mouse primary visual cortex. Our data reveal new features of monocular and binocular development that revise current models on the emergence of cortical binocularity. Given the recent interest in visually guided behaviors in mice that require binocular vision, e.g. predation, our measures will provide the basis for studies on the emergence of the neural circuitry guiding these behaviors.


title: Functional and effective connectivity between dorsolateral prefrontal and subgenual anterior cingulate cortex depends on the timing of transcranial magnetic stimulation relative to the phase of prefrontal alpha EEG

abstract:
BACKGROUNDThe communication through coherence model posits that brain rhythms are synchronized across different frequency bands and that effective connectivity strength between interacting regions depends on their phase relation. Evidence to support the model comes mostly from electrophysiological recordings in animals while evidence from human data is limited.

METHODSHere, an fMRI-EEG-TMS (fET) instrument capable of acquiring simultaneous fMRI and EEG during noninvasive single pulse TMS applied to dorsolateral prefrontal cortex (DLPFC) was used to test whether prefrontal EEG alpha phase moderates TMS-evoked top-down influences on subgenual, rostral and dorsal anterior cingulate cortex (ACC). Results in healthy volunteers (n=11) were compared to those from patients with major depressive disorder (MDD) (n=17) collected as part of a ongoing clinical trial investigation.

RESULTSIn both groups, TMS-evoked functional connectivity between DLPFC and subgenual ACC (sgACC) depended on the EEG alpha phase. TMS-evoked DLPFC to sgACC effective connectivity (EC) was moderated by EEG alpha phase in healthy volunteers, but not in the MDD patients. Top-down EC was inhibitory for TMS onsets during the upward slope of the alpha wave relative to TMS timed to the downward slope of the alpha wave. Prefrontal EEG alpha phase dependent effects on TMS-evoked fMRI BOLD activation of the rostral anterior cingulate cortex were detected in the MDD patient group, but not in the healthy volunteer group.

DISCUSSIONResults demonstrate that TMS-evoked top-down influences vary as a function of the prefrontal alpha rhythm, and suggest clinical applications whereby TMS is synchronized to the brains internal rhythms in order to more efficiently engage deep therapeutic targets.


title: Improving functional recovery after severe spinal cord injury by a noninvasive dual functional approach of neuroprotection and neuromodulation

abstract: Despite tremendous unmet medical needs, there is no effective pharmacological treatment to promote functional recovery after spinal cord injury (SCI). Although multiple pathological events have been implicated in SCI, the development of a noninvasive pharmacological approach to simultaneously target the different mechanisms involved in SCI remains a formidable challenge. In this study, we report the development of a noninvasive nanodrug delivery system that consists of ROS-responsive amphiphilic copolymers and an encapsulated neurotransmitter-conjugated KCC2 agonist. We show that upon intravenous administration, the nanodrugs were able to enter the injured spinal cord due to blood spinal cord barrier disruption and ROS-responsive disassembly. Remarkably, once in the injured spinal cord, these nanodrugs exhibited dual functions: scavenging ROS accumulated in the lesion to protect spared connections and increasing neuronal excitability in the injured spinal cord through targeted delivery of the KCC2 agonist to inhibitory neurons. Thus, the noninvasive treatment led to significant functional recovery in the rats with contusive SCI. Together, these findings provide a much-needed translational pharmacological approach for treating severe SCI.


title: A simple self-decoding model for neural coding

abstract:
Neural coding is an important tool to discover the inner workings of mind. In this work, we propose and consider a simple but novel self-decoding model for neural coding based on the principle that the neuron body represents ongoing stimulus while dendrites are used to store that stimulus as a memory. In particular, suppose t spiking presynaptic neurons transmit any stimulus directly to a population of n postsynaptic neurons, a postsynaptic neuron spikes if it does not connect to an inhibitory presynaptic neuron, and every stimulus is represented by up to d spiking postsynaptic neurons.

Our hypothesis is that the brain is organized to functionally satisfy the following six criteria: (i) decoding objective, i.e., there are up to r-1 [≥] 0 additional spiking postsynaptic neurons in response to a stimulus along with the spiking postsynaptic neurons representing the stimulus, (ii) smoothness, i.e., similar stimuli are encoded similarly by the presynaptic neurons, (iii) optimal information transmission, i.e., t is minimized, (iv) optimal energetic cost, i.e., only the t presynaptic neurons and the postsynaptic neurons representing a stimulus spike, (v) low-dimensional representation, i.e., d = o(n), and (vi) sparse coding, i.e., t = o(n).

Our finding is that some criteria cause or correlate with others. Let the characteristic set of a postsynaptic neuron be the set of the presynaptic neurons it connects with. We prove that (i) holds if and only if the union of the r characteristic sets of any r postsynaptic neurons is not included in the union of the d characteristic sets of d other postsynaptic neurons. Consequently, (ii) is attained. More importantly, we suggest that the decoding objective (i) and optimal information transmission (iii) play a fundamental role in neural computation, while (v) and (vi) correlate to each other and correlate with (iii) and (iv). We examine our hypothesis by statistically testing functional connectivity network and the presynaptic-postsynaptic connectivity in layer 2 of the medial entorhinal cortex of a rat.


title: The impacts of anesthetic regimens on the middle cerebral artery occlusion outcomes in male rats

abstract:
ObjectivesThe middle cerebral artery occlusion (MCAO) model was introduced more than three decades ago to simulate human stroke. Till now, it is the most common platform to investigate stroke-induced pathological changes as well as discover new drugs and treatments. Induction of general anesthesia is mandatory to induce this model, and different laboratories are using various anesthetic drugs, which might affect MCAO results. Therefore, the present study was designed to compare the impacts of several widely used anesthetic regimens on the MCAO outcomes.

Materials and MethodsHere, adult male rats were anesthetized by isoflurane inhalation, intraperitoneal injection of chloral hydrate, intraperitoneal injection of ketamine-xylazine, or subcutaneous administration of ketamine-xylazine, then subjected to 30 min MCAO. Mortality rate, body weight change, infarct size, as well as cognitive and neurological performance were evaluated up to three days after the surgery.

ResultsOur findings revealed chloral hydrate caused the highest, while subcutaneous ketamine-xylazine led to the lowest mortality rate. Meanwhile, there were no significant differences in the body weight loss, infarct size, cognitive impairments, and neurological deficits among the experimental groups.

ConclusionsBased on the current results, we proposed that subcutaneous injection of ketamine-xylazine could be an effective anesthetic regimen in the rat model of MCAO with several advantages such as low mortality, cost-effectiveness, safety, ease of administration, and not requiring specialized equipment.


title: Neurovascular Uncoupling: Multimodal Imaging Delineates the Acute Effects of MDMA

abstract:
Psychedelic compounds have attracted increasing interest in recent years due to their therapeutic potential for psychiatric disorders. Methylenedioxymethamphetamine (MDMA) is currently being investigated in clinical trials to treat post-traumatic stress disorder. To understand the acute effects of psychedelic drugs in vivo, functional MR imaging (fMRI) has been widely used in recent years. Notably, fMRI studies have shown that MDMA leads to inhibition of brain activity, challenging earlier hypotheses indicating mainly excitatory effects. However, interpretation of hemodynamic changes induced by psychedelics is challenging because of the potent vascular effects associated with this class of substances. Therefore, this study aimed to investigate the acute effects of MDMA using simultaneous positron emission tomography (PET)/fMRI in rats. For this purpose, hemodynamic changes measured by BOLD-fMRI were related to alterations in glucose utilization and serotonin transporter (SERT) occupancy, investigated using [18F]FDG functional PET (fPET) and [11C]DASB PET.

We demonstrate that MDMA induces global hemodynamic decreases accompanied by localized metabolic increases. Elevated metabolism was found primarily in limbic projection areas involved in emotion processing. Concurrent BOLD-fMRI decreases, also found in extracerebral areas, indicate that the BOLD-fMRI reductions observed in the brain are of vascular, non-neuronal origin. We further show that higher SERT occupancy strongly correlates with regional BOLD-fMRI reductions. Therefore, increased serotonin levels induced by SERT blockage may cause a neurovascular uncoupling.

Correct understanding of the in vivo mechanism of MDMA not only supports ongoing research but also warrants a reassessment of previous studies on neuronal effects of psychedelics relying on neurovascular coupling.


title: Mathematical model of a cytokine storm

abstract: Cytokine storm is a life-threatening inflammatory response that is characterized by hyperactivation of the immune system, and which can be caused by various therapies, auto-immune conditions, or pathogens, such as respiratory syndrome coronavirus 2 (SARS-CoV-2), which causes coronavirus disease COVID-19. While initial causes of cytokine storms can vary, late-stage clinical manifestations of cytokine storm converge and often overlap, and therefore a better understanding of how normal immune response turns pathological is warranted. Here we propose a theoretical framework, where cytokine storm phenomenology is captured using a conceptual mathematical model, where cytokines can both activate and regulate the immune system. We simulate normal immune response to infection, and through variation of system parameters identify conditions where, within the frameworks of this model, cytokine storm can arise. We demonstrate that cytokine storm is a transitional regime, and identify three main factors that must converge to result in storm-like dynamics, two of which represent individual-specific characteristics, thereby providing a possible explanation for why some people develop CRS, while others may not. We also discuss possible ecological insights into cytokine-immune interactions and provide mathematical analysis for the underlying regimes. We conclude with a discussion of how results of this analysis can be used in future research.


title: Immune cell regulation in stem cell niche contacting glioblastomas.

abstract:
Glioblastomas (GBM) are tumors for which immune-targeted therapies have failed to show clinical benefit and for which few biomarkers provide context for meaningful therapeutic stratification. Radiographic contact of GBM tumors with the lateral ventricle stem cell niche correlates with worse patient prognosis; however, the extent to which proximity to the ventricle impacts antitumor immunity remains unknown. We demonstrate that T cell checkpoint receptor expression is elevated in ventricle-contacting GBM as is the abundance of a specific, suppressive CD32+CD44+HLADhigh myeloid population suggesting a distinct immunoregulatory influence on antitumor immunity in proximity to the lateral ventricle. Phospho-specific mass cytometric profiling revealed extensively impaired immune signaling in ventricle-contacting GBM in response to inflammatory cytokine stimulation, further supporting a suppressive milieu influencing immunity at the lateral ventricle. Collectively, we identify a regulatory impact of ventricle contact on antitumor immunity in the brain, and reveal novel clinically targetable mechanisms of immunomodulation in patients with glioblastoma.

Significance StatementWe demonstrate that the immune microenvironment of glioblastoma tumors contacting the lateral ventricle differs from non-contacting tumors. This work connects immune-biology to a radiographically detectable feature, the lateral ventricle, and highlights non-invasive imaging as a means to identify targetable immune features in glioblastoma tumors.


title: Lin28b specifies an innate-like lineage of CD8+ T cells in early life

abstract:
The immune system is stratified into layers of specialized cells with distinct functions. Recently, Lin28b was shown to serve as a master regulator of fetal lymphopoiesis, programming the development of more innate-like lymphocytes in early life. However, it remains unclear whether Lin28b specifies innate functions in more conventional adaptive lymphocytes. In this report, we discovered that Lin28b promotes the development of a more innate-like lineage of CD8+ T cells that is capable of protecting the host against a wide variety of pathogens in the absence of TCR stimulation. Using RNA-seq and ATAC-seq, we found that Lin28b transcriptionally and epigenetically programs CD8+ T cells to be highly responsive to innate cytokines. We also performed scRNAseq and found that the shift from innate-like CD8+ T cells in early life to adaptive CD8+ T cells in adulthood is mediated by changes in the abundance of distinct subsets of cells. Remarkably, the innate CD8+ T cell subset predominates in early life but is also present in adult mice and humans. Collectively, our findings demonstrate that neonatal CD8+ T cells are a distinct lineage of lymphocytes that provide the host with innate defense in early life.

One sentence SummaryHigh-dimensional analysis reveals how Lin28b programs neonatal CD8+ T cells for innate defense.


title: Bacterial community dynamics explain carbon mineralization and assimilation in soils of different land-use history

abstract:
Soil dwelling microorganisms are key players in the terrestrial carbon cycle, driving both the degradation and stabilization of soil organic matter. Bacterial community structure and function vary with respect to land-use, yet the ecological drivers of this variation remain poorly described and difficult to predict. We conducted a multi-substrate DNA-stable isotope probing experiment across cropland, old-field, and forest habitats to link carbon mineralization dynamics with the dynamics of bacterial growth and carbon assimilation. We tracked the movement of 13C derived from five distinct carbon sources as it was assimilated into bacterial DNA over time. We show that carbon mineralization, community composition, and carbon assimilation dynamics all differed with respect to land-use. We also show that microbial community dynamics affect carbon assimilation dynamics and are predictable from soil DNA content. Soil DNA yield is easy to measure and it predicts microbial community dynamics linked to soil carbon cycling.

Originality-Significance StatementSoil dwelling microorganisms are key players in the terrestrial carbon cycle, driving both the degradation and stabilization of soil organic matter. Microbial communities vary with respect to land-use, but we still have an incomplete understanding of how variation in community structure links to variation in community function. DNA stable isotope probing (DNA-SIP) is a high-resolution method that can identify specific microbial taxa that assimilate carbon in situ. We conducted a large-scale multi-substrate DNA-SIP experiment to explore differences in bacterial activity across land-use regimes. We show that microbial community dynamics vary with land-use, that these dynamics are linked to soil carbon cycling, and that they are predicted from easily measured soil properties.

category: microbiology


title: International spread of emerging multidrug-resistant Rhodococcus equi

abstract: The recently characterized multidrug-resistant clone of the animal and human zoonotic pathogen Rhodococcus equi, MDR-RE 2287, has been circulating among horse farms in the United States (US) since the early 2000s. Here, we report the first documented detection of the MDR-RE 2287 clone outside the US. The finding highlights the risk of MDR-RE spreading internationally with the movement of horses.


title: Experimental infection of mink with SARS-COV-2 Omicron (BA.1) variant leads to symptomatic disease with lung pathology and transmission

abstract: We report an experimental infection of American mink with SARS-CoV-2 Omicron variant and show that minks remain virus RNA positive for days, develop clinical signs and histopathological changes, and transmit the virus to uninfected recipients warranting further studies and preparedness.


title: Multi-state occupancy model estimates probability of detection of an aquatic parasite using environmental DNA: Pseudoloma neurophilia in zebrafish aquaria

abstract: Detecting the presence of important parasites within a host and its environment is critical to understanding the dynamics that influence a pathogens ability to persist, while accurate detection is also essential for implementation of effective control strategies. Pseudoloma neurophilia is the most common pathogen reported in zebrafish (Danio rerio) research facilities. The only assays currently available for P. neurophilia, are through lethal sampling, often requiring euthanasia of the entire population for accurate estimates of prevalence in small populations. We present a non-lethal screening method to detect Pseudoloma neurophilia in tank water based on detection of environmental DNA (eDNA) from this microsporidum, using a previously developed qPCR assay that was adapted to the digital PCR (dPCR) platform. Using the generated dPCR data, a multi-state occupancy model was also implemented to predict the probability of detection in tank water under different flow regimes and pathogen prevalence. The occupancy model revealed that samples collected in static conditions were more informative than samples collected from flow-through conditions, with a probability of detection at 80% and 47%, respectively. There was also a positive correlation with the prevalence of infection in water and prevalence in fish based on qPCR.


title: Mechanoregulation of biofilm architecture promotes Pseudomonas aeruginosa antibiotic tolerance.

abstract: In the wild, bacteria are most frequently found in the form of multicellular structures called biofilms1. Biofilms grow at the surface of abiotic and living materials with wide-ranging mechanical properties. Despite their co-occurrence during infection, we still lack a clear understanding of how mechanics regulate biofilm architecture and the physiology of resident bacteria. The opportunistic pathogen Pseudomonas aeruginosa forms biofilms on indwelling medical device2 and on soft tissues including burn wounds and the airway mucosa3. Here, we demonstrate that mechanical properties of hydrogel material substrates define P. aeruginosa biofilm architecture. We show that hydrogel mesh size regulates twitching motility, a surface exploration mechanism priming biofilms, ultimately controlling the arrangement of single cells in the multicellular community. The resulting architectural transitions increase P. aeruginosas tolerance to colistin, a last resort antibiotic. Our results thereby establish material properties as a regulator of biofilm architecture and antibiotic efficacy.


title: Target-enrichment sequencing yields valuable genomic data for difficult-to-culture bacteria of public health importance

abstract:
Genomic data contribute invaluable information to the epidemiological investigation of pathogens of public health importance. However, whole genome sequencing (WGS) of bacteria typically relies on culture, which represents a major hurdle for generating such data for a wide range of species for which culture is challenging. In this study, we assessed the use of culture-free target-enrichment sequencing as a method for generating genomic data for two bacterial species: 1) Bacillus anthracis, which causes anthrax in both people and animals and whose culture requires high level containment facilities; and 2) Mycoplasma amphoriforme, a fastidious emerging human respiratory pathogen. We obtained high quality genomic data for both species directly from clinical samples, with sufficient coverage (>15X) for confident variant calling over at least 80% of the baited genomes for over two thirds of the samples tested. Higher qPCR cycle threshold (Ct) values (indicative of lower pathogen concentrations in the samples), pooling libraries prior to capture, and lower captured library concentration were all statistically associated with lower capture efficiency. The Ct value had the highest predictive value, explaining 52% of the variation in capture efficiency. Samples with Ct values [≤] 30 were over 6 times more likely to achieve the threshold coverage than those with a Ct > 30. We conclude that target-enrichment sequencing provides a valuable alternative to standard WGS following bacterial culture and creates opportunities for an improved understanding of the epidemiology and evolution of many clinically important pathogens for which culture is challenging.

Data summaryThe authors confirm all supporting data, code and protocols have been provided within the article or through supplementary data files. Scripts used in this study can be accessed on GitHub at https://github.com/tristanpwdennis/bactocap. All sequence data generated during this study have been deposited in the European Nucleotide Archive (ENA) Sequence Read Archive (SRA) under project accession numbers PRJEB46822 (B. anthracis) and PRJEB50216 (M. amphoriforme). Accession numbers for individual samples, along with metadata, laboratory parameters and sequence quality metrics, are available at the University of Glasgows data repository, Enlighten, at http://dx.doi.org/10.5525/gla.researchdata.1249.


title: The Conserved CNOT1 Interaction Motif of Tristetraprolin Regulates ARE-mRNA Decay Independently of the p38 MAPK-MK2 Kinase Pathway

abstract: Regulation of the mRNA decay activator Tristetraprolin (TTP) by the p38 mitogen-activated protein kinase (MAPK) pathway during the mammalian inflammatory response represents a paradigm for the regulation of mRNA turnover by signaling. Phosphorylation of TTP by p38 MAPK-activated kinase 2 (MK2) inhibits the association of TTP with the CCR4-NOT deadenylase complex and represses TTP-mediated mRNA decay. Here we present evidence that TTP remains active in the presence of activated MK2 due to its highly conserved CNOT1 Interacting Motif (CIM), which remains unphosphorylated and capable of promoting deadenylation and decay. The CIM recruits the CCR4-NOT complex cooperatively with previously identified conserved tryptophan residues of TTP and deletion of the CIM strongly represses residual association with the deadenylase complex and activity of TTP in conditions of active MK2. A conserved serine in the CIM is not a target of MK2 but is instead phosphorylated by other kinases including the PKC pathway and regulates TTP activity independently of MK2. These results suggest that kinase pathways regulate TTP activity in a cooperative manner and that the p38 MAPK-MK2 pathway relies on the activation of additional kinase pathway(s) to fully control TTP function.


title: A single 2'-O-methylation of ribosomal RNA gates assembly of a functionalribosome

abstract: RNA modifications are widespread in biology, and particularly abundant in ribosomal RNA. However, the significance of these modifications is not well understood. We show that methylation of a single universally conserved nucleotide, in the catalytic center of the large subunit, gates ribosome assembly. Massively parallel mutational scanning of the essential nuclear GTPase Nog2 identified important interactions with ribosomal RNA helix 92, particularly with the methylated A-site base Gm2922. We found that 2-O-methylation of G2922 is needed for efficient nuclear export of the large subunit. Critically, we identified single amino acid changes in Nog2 that completely bypass its dependence on G2922 methylation. By solving the cryo-EM structure of the unmodified nascent subunit, we reveal how methylation flips Gm2922 into the active site channel of Nog2. This work demonstrates that a single RNA modification is a critical checkpoint in ribosome biogenesis, and suggests that RNA modifications can play an important role in regulation and assembly of macromolecular machines.


title: Structural basis for interaction between CLAMP and MSL2 proteins involved in the specific recruitment of the dosage compensation complex in Drosophila

abstract: Transcriptional regulators select their targets from a large pool of similar genomic sites. The binding of the Drosophila dosage compensation complex (DCC) exclusively to the male X chromosome provides insight into binding site selectivity rules. Previous studies showed that the male-specific organizer of the complex, MSL2, and ubiquitous DNA-binding protein CLAMP directly interact and play an important role in the specificity of X chromosome binding. Here we studied the highly specific interaction between the intrinsically disordered region of MSL2 and the N-terminal zinc-finger C2H2-type (C2H2) domain of CLAMP. We obtained the NMR structure of the CLAMP N-terminal C2H2 zinc finger, which has a classic C2H2 zinc-finger fold with a rather unusual distribution of residues typically used in DNA recognition. Substitutions of residues in this C2H2 domain had the same effect on the viability of males and females, suggesting that it plays a general role in CLAMP activity. The N-terminal C2H2 domain of CLAMP is highly conserved in insects. However, the MSL2 region involved in the interaction is conserved only within the Drosophila genus, suggesting that this interaction emerged during the evolution of a mechanism for the specific recruitment of the DCC on the male X chromosome in Drosophilidae.


title: Optimal resistance management for mixtures of high-risk fungicides: robustness to the initial frequency of resistance and pathogen sexual reproduction

abstract: There is a strong consensus that selection for fungicide resistant pathogen strains can be most effectively limited by using applications of mixtures of fungicides designed to balance disease control against selection. However, how to do this in practice is not entirely characterised. Previous work indicates optimal mixtures of pairs of fungicides which are both at a high risk of resistance can be constructed using pairs of doses which select equally for both single resistant strains in the first year of application. What has not been addressed thus far is the important real-world case in which the initial levels of resistance to each fungicide differ, for example because the chemicals have been available for different lengths of time. We show how recommendations based on equal selection in the first year can be sub-optimal in this case. We introduce a simple alternative approach, based on equalising the frequencies of single resistant strains in the year that achieving acceptable levels of control is predicted to become impossible. We show that this strategy is robust to changes in parameters controlling pathogen epidemiology and fungicide efficacy. We develop our recommendation using a pre-existing, parameterised model of Zymoseptoria tritici (the pathogen causing Septoria leaf blotch on wheat), which exemplifies the range of plant pathogens which predominantly spread clonally, but for which sexual reproduction forms an important component of the life cycle. We show that pathogen sexual reproduction can influence the rate at which fungicide resistance develops, but does not qualitatively affect our optimal resistance management recommendation.


title: Hoisted with his own petard: how sex-ratio meiotic drive in Drosophila affinis creates resistance alleles that limit its spread

abstract: Meiotic drivers are selfish genetic elements that tinker with gameto-genesis to bias their own transmission into the next generation of off-spring. Such tinkering can have significant consequences on gameto-genesis and end up hampering the spread of the driver. In Drosophila affrnis, sex-ratio meiotic drive is caused by an X-linked complex that, when in males with a susceptible Y chromosome, results in broods that are more than 95% female. Interestingly, D. affrnis males lacking a Y chromosome (XO) are fertile and males with the meiotic drive X and no Y produce only sons - effectively reversing the sex-ratio effect. Here, we show that meiotic drive dramatically increases the rate of nondisjunction of the Y chromosome (at least 50X), meaning that the driver is creating resistant alleles through the process of driving. We then model how the O might influence the spread, dynamics and equilibrium of the sex-ratio X chromosome. We find that the O can prevent the spread or reduce the equilibrium frequency of the sex-ratio X chromosome and it can even lead to oscillations in frequency. Finally, with reasonable parameters, the O is unlikely to lead to the loss of the Y chromosome, but we discuss how it might lead to sex-chromosome turnover indirectly.


title: A model of functionally buffered deleterious mutations can lead to signatures of positive selection distinguishable from an evolutionary conflict model

abstract: Selective pressures on DNA sequences often result in signatures of departures from neutral evolution that can be captured by the McDonald-Kreitman (MK) test. However, the nature of such selective forces mostly remains unknown to the experimentalists. Here we use the bag of marbles (bam) gene in Drosophila to investigate different types of driving forces behind positive selection. We examine two evolutionary models for bam. The Conflict model originates from a conflict of fitness between Drosophila and Wolbachia that causes reciprocal adaptations in each, resulting in diversifying selection on the bam protein. In the alternative Buffering model, Wolbachia protects bam from deleterious mutations during an infection and thereby allows such mutations to accumulate and even fix in the population. If Wolbachia is subsequently lost from the species, mutations that revert the gene back towards its original biological function become advantageous. We use simulations to show that both models produce signals of positive selection, though the levels of positive selection under the Conflict model are more easily detected by the MK test. By fitting the two models to the empirical divergence of D. melanogaster from an inferred ancestral sequence, we found that the Conflict model reproduced strong signals of positive selection like those observed empirically, while the Buffering model better recapitulated the physicochemical signatures of the amino acid sequence evolution at bam. Our demonstration that the Buffering model can lead to positive selection suggests a novel mechanism that needs to be considered behind observed signals of positive selection on protein coding genes.

category: genetics


title: Modeling exercise using optogenetically contractible Drosophila larvae

abstract: The pathophysiological effects of a number of metabolic and age-related disorders can be prevented to some extent by exercise and increased physical activity. However, the molecular mechanisms that contribute to the beneficial effects of muscle activity remain poorly explored. Availability of a fast, inexpensive, and genetically tractable model system for muscle activity and exercise will allow the rapid identification and characterization of molecular mechanisms that mediate the beneficial effects of exercise. Here, we report the development and characterization of an optogenetically-inducible muscle contraction (OMC) model in Drosophila larvae that we used to study acute exercise-like physiological responses. To characterize muscle-specific transcriptional responses to acute exercise, we performed bulk mRNA-sequencing, revealing striking similarities between acute exercise-induced genes in flies and those previously identified in humans. Our larval muscle contraction model opens a path for rapid identification and characterization of exercise-induced factors.

category: genomics


title: The Genetic and Evolutionary Basis of Gene Expression Variation in East Africans

abstract:
BackgroundMapping of quantitative trait loci (QTL) associated with molecular phenotypes is a powerful approach for identifying the genes and molecular mechanisms underlying human traits and diseases. How the genetic architecture of molecular traits varies across human populations, however, has been less explored. To better understand the genetics of gene regulation in East Africans, we perform expression and splicing QTL mapping in whole blood from a cohort of 162 diverse Africans from Ethiopia and Tanzania. We assess replication of these QTLs in cohorts of predominantly European ancestry and identify candidate genes under selection in human populations.

ResultsWe find the gene regulatory architecture of African and non-African populations is broadly shared, though there is a considerable amount of variation at individual loci across populations. Comparing our analyses to an equivalently sized cohort of European Americans, we find that QTL mapping in Africans improves the detection of expression QTLs and fine mapping of causal variation. Integrating our QTL scans with signatures of selection, we find several genes related to immunity and metabolism that are highly differentiated between Africans and non-Africans, as well as a gene associated with pigmentation, TMEM216, with evidence of population-specific selection in Nilo-Saharan speaking pastoralists.

ConclusionExtending QTL-mapping studies beyond groups of European ancestry, particularly to diverse indigenous populations, is vital for a complete understanding of the genetic architecture of human traits and can reveal novel functional variation underlying human traits and disease.


title: A small molecule probe elucidates the role of mitochondrial translocase TIMM44 in PINK1/Parkin regulated mitophagy

abstract: Neurodegenerative diseases have been linked to a dysfunctional mitochondrial quality control system that is partially maintained by proteins PINK1 and Parkin. Whereas mitophagy pathways are becoming well-characterized, less is known about the molecular mechanisms of PINK1 trafficking in mitochondria. Accordingly, we have used a small molecule probe (MitoBloCK-10/MB-10) that modulates the activity of TIMM44, an essential component of the protein associated motor (PAM) complex for the mitochondrial inner membrane (TIM23) translocase, to characterize PINK1 import. MB-10 did not inhibit the import or degradation of PINK1 in energized mitochondria. However, when mitophagy was induced by the addition of an uncoupler or respiratory inhibitor, MB-10 treatment altered PINK1 trafficking by inhibiting association with the TOM complex and impairing Parkin recruitment and subsequent mitophagy. MB-10 analogs that did not inhibit TIMM44 activity failed to impair mitophagy, thereby assigning specificity to MB-10. Because PINK1 undergoes lateral release from the TIM23 translocon to interact with inner membrane (IM) modulators, our studies support that TIMM44 may be a key regulator and that the PAM complex has a central role in regulating PINK1-dependent mitophagy. Our studies also provide a probe for dissecting PINK1/Parkin events for mitochondria as well as studying PINK1-dependent mitophagy in cell and animal models.


title: Substrate topology and cognate immunity modulate antibacterial toxicity of Tae cell wall hydrolases

abstract: Members of the bacterial T6SS amidase effector (Tae) superfamily of toxins are delivered between competing bacteria to degrade cell wall peptidoglycan. Although Taes share a common substrate, they exhibit distinct antimicrobial potency across different competitor species. To investigate the molecular basis governing these differences, we quantitatively defined the functional determinants of Tae1 from Pseudomonas aeruginosa PAO1 using a combination of nuclear magnetic resonance (NMR) and a high-throughput in vivo genetic approach called deep mutational scanning (DMS). As expected, combined analyses confirmed the role of critical residues near the Tae1 catalytic center. Unexpectedly, DMS revealed substantial contributions to enzymatic activity from a much larger, ring-like functional hot spot extending around the entire circumference of the enzyme. Comparative DMS across distinct growth conditions highlighted how functional contribution of different surfaces is highly context-dependent, varying alongside composition of targeted cell walls. These observations suggest that Tae1 engages with the intact cell wall network through a more distributed three-dimensional interaction interface than previously appreciated, providing an explanation for observed differences in antimicrobial potency across divergent Gram-negative competitors. Further binding studies of several Tae1 variants with their cognate immunity protein demonstrate that requirements to maintain protection from Tae activity may be a significant constraint on the mutational landscape of tae1 toxicity in the wild. In total, our work reveals that Tae diversification has likely been shaped by multiple independent pressures to maintain interactions with binding partners that vary across bacterial species and conditions.


title: Antibacterial potency of Type VI amidase effector toxins is dependent on substrate topology and cellular context


title: Monitoring the quality of eggs depending on the hens breeding systems by Raman spectroscopy.

abstract:
The aim of this study is show that Raman spectroscopy is a sensitive tool, which can be used for analyses eggs obtained in various hens housing system. This study provided a new and simple method for hens eggs breeding systems testing. Raman methods have potential to be applied by commercial inspections in food industry for verification indications placed on eggs. The development of functional technological methods to study the quality of eggs could be an interesting way to gain profitability for the food industry, in addition to improving the general conditions of public health. A label-free Raman method for detecting spectral changes in eggs from cage systems, barn systems, free range systems and ecological systems is presented. The most important advantage of Raman spectroscopy is the ability to identify biomarkers that help estimate the quality of eggs from various hens housing systems based on spectra typical for lipids, proteins and carotenoids. We have proved that ratios 1656/1004, 1656/1444, 1444/1520 and 1656/1156 can be used as universal biomarkers to distinguish eggs from various hens housing systems. Chemometric methods have shown that eggs from ecological systems and barn systems can be distinguished based on their vibrational properties.

Graphical Abstract

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title: Proteomic network analysis of bronchoalveolar lavage fluid in ex-smokers to discover implicated protein targets and novel drug treatments for chronic obstructive pulmonary disease

abstract:
RationaleBronchoalveolar lavage of the epithelial lining fluid can sample the profound changes in the airway lumen milieu prevalent in Chronic Obstructive Pulmonary Disease (COPD). Characterizing the proteins in bronchoalveolar lavage fluid in COPD with advanced proteomic methods will identify disease-related changes, provide insight into pathogenetic mechanisms and potential therapeutics that will aid in the discovery of more effective therapeutics for COPD.

ObjectivesWe compared epithelial lining fluid proteome of ex-smokers with moderate COPD who are not in exacerbation status COPD, to non-smoking healthy control subjects using advanced proteomics methods and applied proteome-scale translational bioinformatics approaches to identify potential therapeutic protein targets and drugs that modulate these proteins towards the treatment of COPD.

MethodsProteomic profiles of bronchalveolar lavage fluid were obtained from 1) never-smoker control subjects with normal lung function (n=10) or 2) individuals with stable moderate (GOLD stage 2, FEV1 50% - 80% predicted) COPD who were ex-smokers for at least one year (n=10). NIHs Database for Annotation, Visualization and Integrated Discovery (DAVID) and Ingenuitys Ingenuity Pathway Analysis (IPA) were the two bioinformatics tools employed for network analysis on the differentially expressed proteins to identify potential crucial hub proteins. The drug-proteome interaction signature comparison and ranking approach implemented in the Computational Analysis of Novel Drug Opportunities (CANDO) platform for multiscale therapeutic discovery was utilized to identify potential repurposable drugs for the treatment of COPD based on the BALF proteome. Subsequently, a literature-based knowledge graph was utilized to rank combinations of drugs that would most likely ameloriate inflammatory processes by inhibition or activation of their functions.

ResultsProteomic network analysis demonstrated that 233 of the >1800 proteins identified in the BALF were differentially expressed in COPD versus control, including proteins associated with inflammation, structural elements, and energy metabolism. Functional annotation of the differentially expressed proteins by their implicated biological processes, cellular localization, and transcription factor interactions was accomplished via DAVID. Canonical pathways containing the differential expressed proteins were detailed via the Ingenuity Pathway Analysis application. Topological network analysis demonstrated that four proteins act as central node proteins in the inflammatory pathways in COPD. The CANDO multiscale drug discovery platform was used to analyze the behavioral similarity between the interaction signatures of all FDA-approved drugs and the identified BALF proteins. The drugs with the signatures most similar interaction signatures to approved COPD drugs were extracted with the CANDO platform. The analysis revealed 189 drugs that putatively target the proteins implicated in COPD. The putative COPD drugs that were identified using CANDO were subsequently analyzed using a knowledge based technique to identify an optimal two drug combination that had the most appropriate effect on the central node proteins.

ConclusionAnalysis of the BALF proteome revealed novel differentially expressed proteins in the epithelial lining fluid that elucidate COPD pathogenesis. Network analyses identified critical targets that have critical roles in modulating COPD pathogenesis, for which we identified several drugs that could be repurposed to treat COPD using a multiscale shotgun drug discovery approach.


title: Clustered transposon insertion via formation of chromatin loops

abstract:
Transposons, which are DNA sequences that can move to new positions in the genome, make up a large fraction of eukaryotic genomes and occur in clusters. The insertion of transposons into the genome is hindered by compact folding of chromatin, supposedly preventing aberrant or even pathogenic insertion. Chromatin can, however, be decompacted as a consequence of transposon insertion, leading to increased accessibility and, in consequence, further insertions. While these observations suggest a positive feedback between chromatin unfolding and transposon insertion, how such a feedback might contribute to clustered transposon insertion remains poorly understood. In this study, we analyze polymer models of a self-interacting chromatin domain that unfolds as increasing numbers of transposons are inserted and block the self-interaction. On the one hand, we find that, if additional transposons are inserted adjacently to already inserted transposons, the unfolding of the chromatin domain changes from a sharp globule-coil transition to a more gradual extension of loops from a core that remains folded. On the other hand, we find that adjacent transposon insertion emerges either when transposases are excluded from densely packed chromatin, or when transposon insertion proceeds very quickly in relation to the thermal equilibration of polymer configurations. We thus derive from our model physical conditions for clustered transposon insertion and the resulting spatial compartmentalization of chromatin. An according role was recently suggested for LINE-1 and Alu repeats, which occur in clusters and drive the mesoscopic compartmentalization of the mammalian genome.

Significance StatementA large part of the genome is composed of repetitive sequences, so-called transposons. Transposons are involved in important processes, such as early embryonic development or control over which genes are used by the cell. Transposons frequently occur in clusters, where many similar sequence motifs are grouped together. Recent studies suggest that the insertion of transposons can result in local unfolding of the genome, favoring insertion of yet more transposons. Our work simulates a simplified region of the genome and transposases, which are the molecules that insert transposons into the genome. Surprisingly, large and fast-acting transposases favor the formation of distinct loops that contain most of the inserted transposons, providing a potential explanation for the clustered insertion of transposons.


title: Targeting OLIG2 increases therapeutic responses in SHH medulloblastoma mouse models and patient-derived medulloblastoma organoids

abstract: Recurrence after therapy is the primary life-threatening complication of medulloblastoma. In Sonic Hedgehog (SHH)-subgroup medulloblastoma, OLIG2-expressing tumour stem cells are crucial to recurrence. We investigated the potential of the small-molecule OLIG2 inhibitor CT-179 to decrease recurrence in patient-derived organoids, mice genetically-engineered to develop SHH-driven MB, and mice with MB patient-derived xenograft (PDX) tumours. We found that OLIG2 mRNA significantly correlated with poor survival in patients with SHH-MB, but not other subgroups. CT-179 rapidly downregulated OLIG2 protein in vitro and displayed nanomolar IC50 values. CT-179 arrested MB cells at G2/M, with degradation of cyclin B1 and phospho-CDK1 inducing apoptosis. In vivo CT-179 induced similar cell cycle changes in MBs in Smo-mutant mice and significantly increased mouse survival. In both MB organoids and mouse models, CT-179 combined with radiotherapy showed greater efficacy than either treatment alone. These data highlight the potential for OLIG2-targeted therapy to improve MB outcomes by targeting recurrent disease.


title: Ingestible capsule for detecting labile inflammatory biomarkers in situ

abstract: Transient molecules in the gastrointestinal (GI) tract, such as nitric oxide and hydrogen sulfide, are key signals and mediators of inflammatory bowel disease (IBD). Because these molecules are extremely short-lived in the body, they are difficult to detect. To track these reactive molecules in the GI tract, we have developed a miniaturized device that integrates genetically-engineered probiotic biosensors with a custom-designed photodetector and readout chip. Leveraging the molecular specificity of living sensors, we genetically encoded bacteria to respond to IBD-associated molecules by luminescing. Low-power electronic readout circuits (nanowatt power) integrated into the device convert the light from just 1 L of bacterial culture into a wireless signal. We demonstrate biosensor monitoring in the GI tract of small and large animal models and integration of all components into a sub-1.4 cm3 ingestible form factor capable of supporting wireless communication. The wireless detection of short-lived, disease-associated molecules could support earlier diagnosis of disease than is currently possible, more accurate tracking of disease progression, and more timely communication between patient and their care team supporting remote personalized care.


title: Creating De Novo Overlapped Genes

abstract: Future applications of synthetic biology will rely on deploying engineered cells outside of lab environments for long periods of time. Currently, a significant roadblock to this application is the potential for deactivating mutations in engineered genes. A recently developed method to protect engineered coding sequences from mutation is called Constraining Adaptive Mutations using Engineered Overlapping Sequences (CAMEOS). In this chapter we provide a workflow for utilising CAMEOS to create synthetic overlaps between two genes, one essential (infA) and one non-essential (aroB), to protect the non-essential gene from mutation and loss of protein function. In this workflow we detail the methods to collect large numbers of related protein sequences, produce multiple sequence alignments (MSAs), use the MSAs to generate Hidden Markov Models and Markov Random Field models, and finally generate a library of overlapping coding sequences through CAMEOS scripts. To assist practitioners with basic coding skills to try out the CAMEOS method, we have created a virtual machine containing all the required packages already installed, that can be downloaded and run locally.


title: The invasive land flatworm Obama nungara in La Reunion, a French island in the Indian Ocean, the first report of the species for Africa

abstract: The land flatworm Obama nungara, a species originating from South America and already invasive in many European countries, is recorded from La Reunion, a French island in the Indian Ocean. This is the first record of O. nungara from this locality and also the first record of the species for Africa. Two specimens were collected, one from Petite France (commune of Saint Paul) and one from La Plaine des Gregues (commune of Saint Joseph); the two localities are widely separated, one in the Western part and one in the South-eastern part of the island. This suggests that the species is already present in several locations in La Reunion. The sightings were communicated to us in 2021, but it is likely that the species is already present since 2020. A molecular analysis of the specimen from Petite France showed that it had the same cox1 haplotype as specimens previously recorded from several countries of Europe; it is hypothesized that the species was imported from Europe, probably from France. We mapped climatic suitability of the species in La Reunion and found that O. nungara could potentially invade a large part of the island. One record was apparently associated with the transport of plates of travertine, a construction material which has numerous cavities, suitable for the transport and survival of adult or cocoons of land flatworms.

category: zoology


title: Dissociable roles of theta and alpha in sub-second and supra-second time reproduction:An investigation of their links to depression and anxiety

abstract: The Striatal Beat Frequency model (Matell & Meck, 2004) suggests that multiple cortical oscillators contribute to human temporal cognition. Based on the theory, the current study examined the interactions between interval timing and neural oscillations, as predicted by timing deficits found in neuropsychiatric conditions. The interaction is predicted to manifest in frontal-midline theta and occipital alpha oscillations, which are two important cortical oscillatory sources engaged in working memory and time perception. Therefore, the main goal of the study is to examine how depression and anxiety modulate frontal-midline theta and occipital data during the encoding of sub- and supra-second intervals. In the current study, participants reproduced sub- (400, 600, 800ms) and supra-second (1600, 1800, 2000ms) intervals while they underwent scalp EEG recordings. Anxiety and depression levels were measured via self-report psychometrics. We found that higher levels of self-reported anxiety and depression were associated with shorter reproduction of lengths of durations. Further, time-frequency analysis of scalp EEG revealed a dissociation where state anxiety altered the links between frontal-midline theta power and sub-second interval reproduction, while depression and trait anxiety altered the association between occipital alpha power and supra-second interval reproduction. Our results suggest that anxiety and depression alter time perception, and this differentially relates to frontal-midline theta and occipital alpha as substrates for sub- and supra-second interval timing.