title: AtPQT11, a P450 enzyme, detoxifies paraquat via N-demethylation

abstract: Paraquat is one of the most widely used nonselective herbicides in agriculture. Due to its wide use, paraquat resistant weeds have emerged and is becoming a potential threat to agriculture. The molecular mechanisms of paraquat resistance in weeds remain largely unknown. Physiological studies indicated that the impaired translocation of paraquat and enhanced antioxidation could improve paraquat resistance in plants. However, the detoxification of paraquat via active metabolism by plants has not been reported to date. Here we report that an activated expression of At1g01600 encoding the P450 protein CYP86A4 confers paraquat resistance as revealed by the gain-of-function mutant paraquat tolerance 11D (pqt11D), in which a T-DNA with four 35S enhancers was inserted at 1646 bp upstream the ATG of At1g01600. The paraquat resistance can be recapitulated in Arabidopsis wild type by overexpressing AtPQT11 (At1g01600), while its knockout mutant is hypersensitive to paraquat. Moreover, AtPQT11 also confers paraquat resistance in E. coli when overexpressed. We further demonstrate that AtPQT11 has P450 enzyme activity that converts paraquat to N-demethyl paraquat nontoxic to Arabidopsis, therefore detoxifying paraquat in plants. Taken together, our results unequivocally demonstrate that AtPQT11/ CYP86A4 detoxifies paraquat via active metabolism, thus revealing a novel molecular mechanism of paraquat resistance in plants and providing a means potentially enabling crops to resist paraquat.


title: A Multi-omics Strategy Enabled by Sequential Metabolomics and Proteomics for Human Pluripotent Stem Cell-derived Cardiomyocytes

abstract: Human pluripotent stem cell-derived cardiomyocytes (hPSC-CMs) show immense promise for patient-specific disease modeling, cardiotoxicity screening, and regenerative therapy development. However, hPSC-CMs in culture have not recapitulated the structural or functional properties of adult CMs in vivo thus far. To gain global insight into hPSC-CM biology, we established a multi-omics method for analyzing the hPSC-CM metabolome and proteome from the same cell culture, creating multi-dimensional profiles of hPSC-CMs. Specifically, we developed a sequential extraction to capture metabolites and proteins from the same hPSC-CM monolayer cultures, and analyzed these extracts using high-resolution mass spectrometry (MS). Using this method, we annotated 205 metabolites/lipids and 4,008 proteins from 106 cells with high reproducibility. We further integrated the proteome and metabolome measurements to create network profiles of molecular phenotypes for hPSC-CMs. Out of 310 pathways identified using metabolomics and proteomics, 40 pathways were considered significantly overrepresented (FDR-corrected p [≤] 0.05). Highly populated pathways included those involved in protein synthesis (ribosome, spliceosome), ATP generation (oxidative phosphorylation), and cardiac muscle contraction. This multi-omics method achieves deep coverage of metabolites and proteins, creating a multidimensional view of the hPSC-CM phenotype, which provides a strong technological foundation to advance the understanding of hPSC-CM biology.

category: systems biology


title: A Multi-omics Method Enabled by Sequential Metabolomics and Proteomics for Human Pluripotent Stem Cell-derived Cardiomyocytes


title: The neural basis of temperature-driven host seeking in the human threadworm Strongyloides stercoralis

abstract: Soil-transmitted parasitic nematodes infect approximately one billion people and are a major cause of morbidity worldwide1-8. The infective larvae (iL3s) of these parasites actively search for hosts in a poorly understood, sensory-driven process that requires thermal cues9,10. Here, we describe the neural basis of temperature-driven host seeking in parasitic nematodes using the human threadworm Strongyloides stercoralis. We show that S. stercoralis thermosensation is mediated by the AFD neurons, a thermosensory neuron class that is conserved between parasitic and free-living nematodes11. We demonstrate that S. stercoralis AFD displays parasite-specific adaptations that enable both nonlinear and linear encoding of temperatures up to human body temperature. Furthermore, we describe a novel thermosensory behavior in which S. stercoralis iL3s generate spontaneous reversals of temperature preference at below-body temperatures. Finally, we identify three thermoreceptors selectively expressed in S. stercoralis AFD that display parasite-specific sensitivities to human body temperatures and likely enable temperature-driven host seeking by iL3s. Our results are the first direct evidence that the sensory neurons of soil-transmitted parasitic nematodes exhibit parasite-specific neural adaptations and sensory coding strategies that allow them to target human hosts, a finding with important implications for efforts to develop new therapeutic strategies for nematode control.

category: neuroscience


title: Mapping the corticoreticular pathway from cortex-wide anterograde axonal tracing in the mouse

abstract:
The corticoreticular pathway (CRP) has been implicated as an important mediator of motor recovery and rehabilitation after central nervous system damage. However, its origins, trajectory and laterality are not well understood. This study mapped the mouse CRP in comparison with the corticospinal tract (CST). We systematically searched the Allen Mouse Brain Connectivity Atlas ((C) 2011 Allen Institute for Brain Science) for experiments that used anterograde tracer injections into the right isocortex in mice. For each eligible experiment (N=607), CRP and CST projection strength were quantified by the tracer volume reaching the reticular formation motor nuclei (RFmotor) and pyramids respectively. Tracer density in each brain voxel was also correlated with RFmotor versus pyramids projection strength to explore the relative trajectories of the CRP and CST. We found significant CRP projections originating from the primary and secondary motor cortices, anterior cingulate, primary somatosensory cortex and medial prefrontal cortex. Compared with the CST, the CRP had stronger projections from each region except the primary somatosensory cortex. Ipsilateral projections were stronger than contralateral for both tracts (above the pyramidal decussation), but the CRP projected more bilaterally than the CST. The estimated CRP trajectory was anteromedial to the CST in the internal capsule and dorsal to the CST in the brainstem. Our findings reveal a widespread distribution of CRP origins and confirm strong bilateral CRP projections, theoretically increasing the potential for partial sparing after brain lesions and contralesional compensation after unilateral injury.

SIGNIFICANCEThe corticoreticular pathway (CRP) provides volitional input to brainstem nuclei that generate walking command signals, facilitate balance and direct limb movements. Upregulation of this pathway appears to be a central mechanism of movement recovery after brain and spinal cord injury, but its anatomy is not well understood. We showed that the mouse CRP originates from widespread parts of the cortex, including non-motor regions, that it projects strongly to both sides of the brainstem, and that its projections are more distributed and bilateral than the corticospinal tract. These findings suggest that the CRP may be particularly resilient to complete disruption.


title: The transcriptome of rat hippocampal subfields

abstract: The hippocampus comprises several neuronal populations such as CA1, CA2, CA3, and the dentate gyrus (DG), which present different neuronal origins, morphologies, and molecular mechanisms. Laser capture microdissection (LCM) allows selectively collecting samples from target regions and eliminating unwanted cells to obtain more specific results. LCM of hippocampus neuronal populations coupled with RNA-seq analysis has the potential to allow the exploration of the molecular machinery unique to each of these subfields. Previous RNA-seq investigation has already provided a molecular blueprint of the hippocampus, however, there is no RNA-seq data specific for each of the rat hippocampal regions. Serial tissue sections covering the hippocampus were produced from frozen brains of adult male Wistar rats, and the hippocampal subfields CA1, CA2, CA3, and DG were identified and isolated by LCM. Total RNA was extracted from samples, and cDNA libraries were prepared and run on a HiSeq 2500 platform. Reads were aligned using STAR, and the DESeq2 statistics package was used to estimate gene expression. We found evident segregation of the transcriptomic profile from different regions of the hippocampus and the expression of known, as well as novel, specific marker genes for each region. Gene ontology enrichment analysis of CA1 subfield indicates an enrichment of actin regulation and postsynaptic membrane AMPA receptors genes indispensable for long-term potentiation. CA2 and CA3 transcripts were found associated with the increased metabolic processes. DG expression was enriched for ribosome and spliceosome, both required for protein synthesis and maintenance of cell life. The present findings contribute to a deeper understanding of the differences in the molecular machinery expressed by the rat hippocampal neuronal populations, further exploring underlying mechanisms responsible for each subflied specific functions.


title: Modular, Cascade-like Transcriptional Program of Regeneration in Stentor

abstract: The giant ciliate Stentor coeruleus is a classical model system for studying regeneration and morphogenesis at the level of a single cell. The anterior of the cell is marked by an array of cilia, known as the oral apparatus, which can be induced to shed and regenerate in a series of reproducible morphological steps, previously shown to require transcription. If a cell is cut in half, each half will regenerate an intact cell, including a new oral apparatus in the posterior half. We used RNAseq to assay the dynamic changes in Stentors transcriptome during regeneration, after both oral apparatus shedding and bisection, allowing us to identify distinct temporal waves of gene expression including kinases, RNA binding proteins, centriole biogenesis factors, and orthologs of human ciliopathy genes implicated in Meckel and Joubert syndromes. By comparing transcriptional profiles of different regeneration events in the same species, we were able to identify distinct modules of gene expression corresponding to oral apparatus regeneration, posterior holdfast regeneration, and recovery after wounding. By measuring gene expression in cells in which translation is blocked, we show that the sequential waves of gene expression involve a cascade mechanism in which later waves of expression are triggered by translation products of early-expressed genes. Among the early-expressed genes, we identified an E2F transcription factor and the conserved RNA binding protein Pumilio as potential regulators of regeneration based on the expression pattern of their predicted target genes. This work allows us to classify regeneration genes into groups based on their potential role for regeneration in distinct cell regeneration paradigms, and provides new insight into how a single cell can coordinate complex morphogenetic pathways to regenerate missing structures.

category: cell biology


title: SLC1A5 provides glutamine and asparagine necessary for bone development in mice

abstract: Osteoblast differentiation is sequentially characterized by high rates of proliferation followed by increased protein and matrix synthesis, processes that require substantial amino acid acquisition and production. How osteoblasts obtain or maintain intracellular amino acid production is poorly understood. Here we identify Slc1a5 as a critical amino acid transporter during bone development. Using a genetic and metabolomic approach, we show Slc1a5 acts cell autonomously in osteoblasts to import glutamine and asparagine. Deleting Slc1a5 or reducing either glutamine or asparagine availability prevents protein synthesis and osteoblast differentiation. Mechanistically, glutamine and asparagine metabolism support amino acid biosynthesis. Thus, osteoblasts depend on Slc1a5 to provide glutamine and asparagine, which are subsequently used to produce non-essential amino acids and support osteoblast differentiation and bone development.

category: developmental biology


title: A rare natural lipid induces neuroglobin expression to prevent amyloid oligomers toxicity and retinal neurodegeneration.

abstract:
Most neurodegenerative diseases such as Alzheimers disease are proteinopathies linked to the toxicity of amyloid oligomers. Treatments to delay or cure these diseases are lacking. Using budding yeast, we report that the natural lipid tripentadecanoin induces expression of the nitric oxide oxidoreductase Yhb1 to prevent the formation of protein aggregates during aging and extends replicative lifespan. In mammals, tripentadecanoin induces expression of the Yhb1 orthologue, neuroglobin, to protect neurons against amyloid toxicity. Tripentadecanoin also rescues photoreceptors in a mouse model of retinal degeneration and retinal ganglion cells in a Rhesus monkey model of optic atrophy. Together, we propose that tripentadecanoin affects p-bodies to induce neuroglobin expression and offers a potential treatment for proteinopathies and retinal neurodegeneration.

One Sentence SummaryThe natural lipid tripentadecanoin is cytoprotective against amyloid oligomer toxicity and retinal neurodegeneration by inducing YHBI/neuroglobin expression in yeast and mammals.


title: LSD induces increased signalling entropy in rats' prefrontal cortex

abstract: Psychedelic drugs are gaining attention from the scientific community as potential new compounds for the treatment of psychiatric diseases such as mood and substance use disorders. The 5-HT2A receptor has been identified as the main molecular target, and early studies pointed to an effect on the expression of neuroplasticity genes. Analysing RNA-seq data from the prefrontal cortex of rats chronically treated with lysergic acid diethylamide (LSD), we describe the psychedelic-induced rewiring of gene co-expression networks, which become less centralized but more complex, with an overall increase in signalling entropy, typical of highly plastic systems. Intriguingly, signalling entropy mirrors, at the molecular level, the increased brain entropy reported through neuroimaging studies in human, suggesting the underlying mechanisms of higher-order phenomena. Moreover, from the analysis of network topology we identify potential transcriptional regulators and imply different cell types in psychedelics activity.

category: bioinformatics


title: Uncovering the Genetic Profiles Underlying the Intrinsic Organization of the Human Cerebellum

abstract: The functional diversity of the human cerebellum is largely believed to be derived more from its extensive connections rather than being limited to its mostly invariant architecture. However, whether and how the determination of cerebellar connections in its intrinsic organization interact with microscale gene expression is still unknown. Here we decode the genetic profiles of the cerebellar functional organization by investigating the genetic substrates simultaneously linking cerebellar functional heterogeneity and its drivers, i.e., the connections. We not only identified 443 network-specific genes but also discovered that their co-expression pattern correlated strongly with intra-cerebellar functional connectivity (FC). Ninety of these genes were also linked to the FC of cortico-cerebellar cognitive-limbic networks. To further discover the biological functions of these genes, we performed a "virtual gene knock-out" by observing the change in the coupling between gene co-expression and FC and divided the genes into two subsets, i.e., a positive gene contribution indicator (GCI+) involved in cerebellar neurodevelopment and a negative gene set (GCI-) related to neurotransmission. A more interesting finding is that GCI- is significantly linked with the cerebellar connectivity-behavior association and many recognized brain diseases that are closely linked with the cerebellar functional abnormalities. Our results could collectively help to rethink the genetic substrates underlying the cerebellar functional organization and offer possible micro-macro interacted mechanistic interpretations of the cerebellum-involved high order functions and dysfunctions in neuropsychiatric disorders.


title: Hippocampal place cells use vector computations to navigate

abstract: One function of the Hippocampal Cognitive Map is to provide information about salient locations in familiar environments such as those containing reward or danger, and to support navigation towards or away from those locations1. Although much is known about how the hippocampus encodes location in world-centred coordinates, how it supports flexible navigation is less well understood. We recorded from CA1 place cells while rats navigated to a goal or freely foraged on the honeycomb maze2. The maze tests the animals ability to navigate using indirect as well as direct paths to the goal and allows the directionality of place cells to be assessed at each choice point during traversal to the goal. Place fields showed strong directional polarization in the navigation task, and to a lesser extent during random foraging. This polarization was characterized by vector fields which converged to sinks distributed throughout the environment. The distribution of these convergence sinks was centred near the goal location, and the population vector field converged on the goal, providing a strong navigational signal. Changing the goal location led to the movement of ConSinks and vector fields towards the new goal and within-days, the ConSink distance to the goal decreased with continued training. The honeycomb maze allows the independent assessment of spatial representation and spatial action in place cell activity and shows how the latter depends on the former. The results suggest a vector-based model of how the hippocampus supports flexible navigation, allowing animals to select optimal paths to destinations from any location in the environment.


title: Timed global reorganization of protein synthesis during neocortex neurogenesis at codon resolution

abstract: Translation modulates the timing and amplification of gene expression after transcription. Brain development requires uniquely complex gene expression patterns, but large-scale measurements of translation directly in the prenatal brain are lacking. We measure the reactants, synthesis, and products of translation spanning mouse neocortex neurogenesis, and discover a transient window of dynamic regulation at mid-gestation. Timed translation upregulation of chromatin binding proteins like Satb2, which is essential for neuronal subtype differentiation, restricts protein expression in neuronal lineages despite broad transcriptional priming in progenitors. In contrast, translation downregulation of ribosomal proteins sharply decreases ribosome number, coinciding with a major shift in protein synthesis dynamics at mid-gestation. Changing levels of eIF4EBP1, a direct inhibitor of ribosomal protein translation, are concurrent with ribosome downregulation and controls Satb2 fate acquisition during neuronal differentiation. Thus, the refinement of transcriptional programs by translation is central to the molecular logic of brain development. Modeling of the developmental neocortex translatome is provided as an open-source searchable resource: https://shiny.mdc-berlin.de/cortexomics/.


title: A critical period of translational control during brain development at codon resolution


title: Contextual gating of motivationally-relevant stimuli in the mouse nucleus accumbens

abstract: Neural activity in the nucleus accumbens (NAc) is thought to track fundamentally value-centric quantities such as current or future expected reward, reward prediction errors, the value of work, opportunity cost, and approach vigor. However, the NAc also contributes to flexible behavior in ways that are difficult to explain based on value signals alone, raising the question of if and how non-value signals are encoded in NAc. We recorded NAc neural ensembles while head-fixed mice performed a biconditional discrimination task where context-setting cues modulated the stimulus-outcome association of subsequently presented reward-predictive cues. We extracted single-unit and population-level correlates of task features, and found value-independent coding for the context cues. This context signal occupied a subspace orthogonal to outcome-predictive representations, and was predictive of subsequent behaviorally-relevant coding. Together, these findings support a circuit-level gating model for how the NAc contributes to behavioral flexibility and provide a novel population-level perspective from which to view NAc computations.


title: Context coding in the mouse nucleus accumbens modulates motivationally relevant information


title: How does the brain represent the semantic content of an image?

abstract: Using deep neural networks (DNNs) as models to explore the biological brain is controversial, which is mainly due to the impenetrability of DNNs. Inspired by neural style transfer, we circumvented this problem by using deep features that were given a clear meaning--the representation of the semantic content of an image. Using encoding models and the representational similarity analysis, we quantitatively showed that the deep features which represented the semantic content of an image mainly predicted the activity of voxels in the early visual areas (V1, V2, and V3) and these features were essentially depictive but also propositional. This result is in line with the core viewpoint of the grounded cognition to some extent, which suggested that the representation of information in our brain is essentially depictive and can implement symbolic functions naturally.


title: P2Y6 receptor signaling in natural killer cells impairs insulin sensitivity in obesity

abstract: Natural killer (NK) cells contribute to the development of obesity-associated insulin resistance and have previously been shown to up-regulate the expression of the P2Y purinoreceptor 6 (P2Y6R) upon high fat diet (HFD)-induced obesity. Here, we reveal that NK cell-specific inactivation of the P2Y6R gene improves insulin sensitivity in obese mice and reduces the expression of chemokines in adipose tissue infiltrating NK-cells. Obese mice lacking P2Y6R specifically in NK cells exhibited a reduction in adipose tissue inflammation, exhibited improved insulin-stimulated suppression of lipolysis in adipose tissue and a reduction in hepatic glucose production, leading to an overall improvement of systemic insulin sensitivity. In contrast, myeloid lineage specific P2Y6R inactivation does not affect energy or glucose homeostasis in obesity. Collectively, we show that P2Y6R signaling in NK cells contributes to the development of obesity-associated insulin resistance and thus might be a future target for the treatment of obesity-associated insulin resistance and type 2 diabetes.

category: immunology


title: Moving Beyond the 'CAP' of the Iceberg: Intrinsic Connectivity Networks in fMRI are Continuously Engaging and Overlapping

abstract:
Resting-state functional magnetic resonance imaging is currently the mainstay of functional neuroimaging and has allowed researchers to identify intrinsic connectivity networks (aka functional networks) at different spatial scales. However, little is known about the temporal profiles of these networks and whether it is best to model them as continuous phenomena in both space and time or, rather, as a set of temporally discrete events. Both categories have been supported by series of studies with promising findings. However, a critical question is whether focusing only on time points presumed to contain isolated neural events and disregarding the rest of the data is missing important information, potentially leading to misleading conclusions. In this work, we argue that brain networks identified within the spontaneous blood oxygenation level-dependent (BOLD) signal are not limited to temporally sparse burst moments and that these event present time points (EPTs) contain valuable but incomplete information about the underlying functional patterns.

We focus on the default mode and show evidence that is consistent with its continuous presence in the BOLD signal, including during the event absent time points (EATs), i.e., time points that exhibit minimum activity and are the least likely to contain an event. Moreover, our findings suggest that EPTs may not contain all the available information about their corresponding networks. We observe distinct default mode connectivity patterns obtained from all time points (AllTPs), EPTs, and EATs. We show evidence of robust relationships with schizophrenia symptoms that are both common and unique to each of the sets of time points (AllTPs, EPTs, EATs), likely related to transient patterns of connectivity. Together, these findings indicate the importance of leveraging the full temporal data in functional studies, including those using event-detection approaches.


title: Norepinephrine activates β1-adrenergic receptors localized to the inner nuclear membrane in cortical astrocytes

abstract: Studies in cardiomyocytes have established that adrenergic receptors, conventionally thought to initiate signaling events exclusively from the plasma membrane, can also localize to and signal from the nuclear membrane. Activation of these receptors by their endogenous cationic ligands requires transmembrane uptake mediated by organic cation transporter 3 (OCT3). We have demonstrated that OCT3 is densely localized to outer nuclear membranes in neurons and astrocytes, suggesting that nuclear adrenergic signaling is also present in the central nervous system. In this study, we examined the subcellular localization of {beta}1-adrenergic receptors, their G-protein signaling partners, and catecholamine transporters in mouse astrocytes. We identified a population of {beta}1-adrenergic receptors localized to astrocyte inner nuclear membranes. We demonstrated that key components of Gs-mediated signaling are localized to the nuclear compartment and identified OCT3 and other catecholamine transporters localized to plasma and nuclear membranes. Treatment of astrocytes with norepinephrine induced rapid increases in nuclear PKA activity which were blocked by pretreatment with inhibitors of catecholamine transport. These data indicate that nuclear {beta}1-adrenergic receptors are functionally coupled to Gs-coupled signaling mediators and that their activation by norepinephrine requires transporter-mediated uptake. These receptors represent a powerful mechanism by which norepinephrine may alter astrocyte gene expression and brain function.


title: Land-surface evapotranspiration derived from a first-principles primary production model

abstract:
We propose an application of eco-evolutionary optimality theory in the context of monitoring and modelling physical land-surface processes. Evapotranspiration (ET) links the water and carbon cycles in the atmosphere, hydrosphere, and biosphere. We develop an ET modelling framework based on the hypothesis that canopy conductance acclimates to plant growth conditions so that the total costs of maintaining carboxylation and transpiration capacities are minimized. This is combined with the principle of co-ordination between the light- and Rubisco-limited rates of photosynthesis to predict gross primary production (GPP). Transpiration (T) is predicted from GPP via canopy conductance. No plant type- or biome-specific parameters are required. ET is estimated from T by calibrating a site-specific (but time-invariant) ratio of modelled average T to observed average ET. Predicted seasonal cycles of GPP were well supported by (weekly) GPP data at 20 widely distributed eddy-covariance flux sites (228 site-years), with correlation coefficients (r) = 0.81 and root-mean-square error (RMSE) = 18.7 gC/week and Nash-Sutcliffe efficiency coefficient (NSE) = 0.61. Seasonal cycles of ET were also well supported, with r = 0.85, RMSE = 5.5 mm week-1 and NSE = 0.66. Estimated T/ET ratios (0.52-0.92) showed significant positive relationships to radiation, precipitation and green vegetation cover and negative relationships to temperature and modelled T (r = 0.84). Although there are still uncertainties to be improved in the current framework, particularly in estimating T/ET, we see the application of eco-evolutionary principles as a promising direction for water resources research.

HighlightsO_LIBuilding an evapotranspiration estimation framework based on a priori primary productivity model (the P model).
C_LIO_LIAssessing the contribution of environmental indicators to the ratio of transpiration to evapotranspiration.
C_LIO_LIProving the reliability of this approach to estimate evapotranspiration.
C_LI

category: ecology


title: Adaptive shifts underlie the divergence in wing morphology in bombycoid moths

abstract: The evolution of flapping flight is linked to the prolific success of insects. Across Insecta, wing morphology diversified, strongly impacting aerodynamic performance. In the presence of ecological opportunity, discrete adaptive shifts and early bursts are two processes hypothesized to give rise to exceptional morphological diversification. Here, we use the sister-families Sphingidae and Saturniidae to answer how the evolution of aerodynamically important traits is linked to clade divergence and through what process(es) these traits evolve. Many agile Sphingidae evolved hover-feeding behaviors, while adult Saturniidae lack functional mouth parts and rely on a fixed energy budget as adults. We find that Sphingidae underwent an adaptive shift in wing morphology coincident with life history and behavior divergence, evolving small high aspect-ratio wings advantageous for power reduction that can be moved at high frequencies, beneficial for flight control. In contrast, Saturniidae, which do not feed as adults, evolved large wings and morphology which surprisingly does not reduce aerodynamic power, but could contribute to their erratic flight behavior, aiding in predator avoidance. We suggest that after the evolution of flapping flight, diversification of wing morphology can be potentiated by adaptative shifts, shaping the diversity of wing morphology across insects.

category: evolutionary biology


title: Genomic history and forensic characteristics of Sherpa highlanders on the Tibetan Plateau inferred from high-resolution genome-wide InDels and SNPs

abstract: Sherpa people, one of the high-altitude hypoxic adaptive populations, mainly reside in Nepal and the southern Tibet Autonomous Region. The genetic origin and detailed evolutionary profiles of Sherpas remain to be further explored and comprehensively characterized. Here we analyzed the newly-generated InDel genotype data from 628 Dingjie Sherpa people by merging with 4222 worldwide InDel profiles and collected genome-wide SNP data (approximately 600K SNPs) from 3324 individuals in 382 modern and ancient populations to explore and reconstruct the fine-scale genetic structure of Sherpas and their relationships with nearby modern and ancient East Asians based on the shared alleles and haplotypes. The forensic parameters of 57 autosomal InDels (A-InDels) included in our used new-generation InDel amplification system showed that this updated InDel panel is informative and polymorphic in Sherpas, suggesting that it can be used as the supplementary tool for forensic personal identification and parentage testing in the highland East Asians. Descriptive findings from the PCA, ADMIXTURE and TreeMix-based phylogeny suggested that Sherpas showed excess allele sharing with neighboring Tibeto-Burman Tibetans. Furthermore, patterns of allele sharing in f-statistics demonstrated that Sherpa people had a different evolutionary history compared with their neighbors from Nepal (Newar and Gurung) but showed genetic similarity with 2700-year-old Chokhopani and modern Tibet Tibetans. QpAdm/qpGraph-based admixture sources and models further showed that Sherpa, core Tibetans and Chokhopani formed one clade which could be fitted as having the main ancestry from late Neolithic Qijia millet farmers and other deep ancestries from early Asians. Chromosome painting profiles and shared IBD fragments inferred from FineStructure and ChromoPainter not only confirmed the abovementioned genomic affinity patterns but also revealed the fine-scale microstructures among Sino-Tibetan speakers. Finally, natural-selection signals revealed via iHS, nSL, and iHH12 showed signatures associated with disease susceptibility in Sherpa people. Generally, we provided the comprehensive landscape of admixture and evolutionary history of Sherpa people based on the shared alleles and haplotypes from the low-density forensic markers and high-density genome-wide SNP data. The more detailed genetic landscape of Sherpa people should be further confirmed and characterized via ancient genomes or single-molecule real-time sequencing technology.

category: genetics


title: Sex-specific effects of polygenic risk for schizophrenia on lifespan cognitive functioning in healthy individuals

abstract: Polygenic risk for schizophrenia has been associated with lower cognitive ability and age-related cognitive change in healthy individuals. Despite well-established neuropsychological sex differences in schizophrenia patients, genetic studies on sex differences in schizophrenia in relation to cognitive phenotypes are scarce. Here, we investigated whether the effect of a polygenic risk score (PRS) for schizophrenia on childhood, midlife and late life cognitive function in healthy individuals is modified by sex, and if PRS is linked to accelerated cognitive decline. Using a longitudinal data set from healthy individuals aged 25-100 years (N = 1,459) spanning a 25-year period, we found that PRS was associated with lower cognitive ability (episodic memory, semantic memory, visuospatial ability), but not with accelerated cognitive decline. A significant interaction effect between sex and PRS was seen on cognitive task performance, and sex-stratified analyses showed that the effect of PRS was male-specific. In a sub-sample, we observed a male-specific effect of the PRS on school performance at age 12 (N = 496). Our findings of sex-specific effects of schizophrenia genetics on cognitive functioning across the life-span indicate that the effects of underlying disease genetics on cognitive functioning is dependent on biological processes that differ between the sexes.

category: genomics


title: Bioaffinity-based Surface Immobilization of Antibodies to Capture Endothelial Colony-forming Cells

abstract:
Maximizing the re-endothelialization of vascular implants such as prostheses or stents has the potential to significantly improve their long-term performance. Endothelial progenitor cell capture stents with surface-immobilized antibodies show significantly improved endothelialization in the clinic. However, most current antibody-based stent surface modification strategies rely on antibody adsorption or direct conjugation via amino or carboxyl groups which leads to poor control over antibody surface concentration and/or molecular orientation, and ultimately bioavailability for cell capture. Here, we assess the utility of a bioaffinity-based surface modification strategy consisting of a surface-conjugated cysteine-tagged protein G molecules that immobilize Immunoglobulin G (IgG) antibodies via the Fc domain to capture circulating endothelial colony-forming cells (ECFCs). The cysteine-tagged protein G was grafted onto aminated substrates at different concentrations as detected by an enzyme-linked immunosorbent assay and fluorescence imaging. Different IgG antibodies were successfully immobilized on the protein G-modified surfaces and higher antibody surface concentrations were achieved compared to passive adsorption methods. Surfaces with immobilized antibodies targeting endothelial surface proteins, such as CD144, significantly enhanced the capture of circulating ECFCs in vitro compared to surfaces with non-endothelial specific antibodies such as anti-CD14. This work presents a potential avenue for enhancing the clinical performance of vascular implants by using covalent grafting of protein G to immobilize IgG antibodies more effectively.

Table of Contents

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category: bioengineering


title: 3D UNet with GAN discriminator for robust localisation of the fetal brain and trunk in MRI with partial coverage of the fetal body

abstract: In fetal MRI, automated localisation of the fetal brain or trunk is a prerequisite for motion correction methods. However, the existing CNN-based solutions are prone to errors and may require manual editing. In this work, we propose to combine a multi-label 3D UNet with a GAN discriminator for localisation of both fetal brain and trunk in fetal MRI stacks. The proposed method is robust for datasets with both full and partial coverage of the fetal body.


title: Quantitative Mining of Compositional Heterogeneity in Cryo-EM Datasets of Ribosome Assembly Intermediates

abstract: Macromolecular complexes are dynamic entities whose function is often intertwined with their many structural configurations. Single particle cryo-electron microscopy (cryo-EM) offers a unique opportunity to characterize macromolecular structural heterogeneity by virtue of its ability to place distinct populations into different groups through computational classification. However, current workflows are limited, and there is a dearth of tools for surveying the heterogeneity landscape, quantitatively analyzing heterogeneous particle populations after classification, deciding how many unique classes are represented by the data, and accurately cross-comparing reconstructions. Here, we develop a workflow that contains discovery and analysis modules to quantitatively mine cryo-EM data for a set of structures with maximal diversity. This workflow was applied to a dataset of E. coli 50S ribosome assembly intermediates, which is characterized by significant structural heterogeneity. We identified new branch points in the assembly process and characterized the interactions of an assembly factor with immature intermediates. While the tools described here were developed for ribosome assembly, they should be broadly applicable to the analysis of other heterogeneous cryo-EM datasets.

category: biophysics


title: How Communication Pathways Bridge Local and Global Conformations in an IgG4 Antibody: a Molecular Dynamics Study

abstract:
The affinity of an antibody for its antigen is primarily determined by the specific sequence and structural arrangement of the complementarity-determining regions (CDRs). Recently, however, evidence has accumulated that points toward a nontrivial relation between the CDR and distal sites on the antibody structure: variations in the binding strengths have been observed upon mutating amino acids separated from the paratope by several nanometers, thus suggesting the existence of a communication network within antibodies whose extension and relevance might be deeper than insofar expected. In this work, we test this hypothesis by means of molecular dynamics (MD) simulations of the IgG4 monoclonal antibody pembrolizumab, an approved drug that targets the programmed cell death protein 1 (PD-1). The molecule is simulated in both the apo and holo states, totalling 4s of MD trajectory. The analysis of these simulations shows that the bound antibody explores a restricted range of conformations with respect to the apo one, and that the global conformation of the molecule correlates with that of the CDR; a pivotal role in this relationship is played by the relatively short hinge, which mechanically couples Fab and Fc domains. These results support the hypothesis that pembrolizumab behaves as a complex machinery, with a multi-scale hierarchy of global and local conformational changes that communicate with one another. The analysis pipeline developed in this work is general, and it can help shed further light on the mechanistic aspects of antibody function.

SynopsisAntigen binding restricts the conformational variability of the therapeutic antibody pembrolizumab in an interplay between the paratope and hinge region, mediated by a full-scale interaction network.

Graphical TOC Entry

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title: Why are SNAREpins rod-shaped?

abstract: SNARE proteins are the core components of the cellular machineries that fuse membranes for neurotransmitter or hormone release and other fundamental processes. Fusion is accomplished when SNARE proteins hosted by apposing membranes form SNARE complexes called SNAREpins, but the mechanism of fusion remains unclear. Computational simulations of SNARE-mediated membrane fusion are challenging due to the millisecond timescales of physiological membrane fusion. Here we used ultra-coarse-grained (UCG) simulations to investigate the minimal requirements for a molecular intracellular fusogen, and to elucidate the mechanisms of SNARE-mediated fusion. We find fusion by simple body forces that push vesicles together is highly inefficient. Inter-vesicle fusogens with different aspect ratios can fuse vesicles only if they are rodlike, of sufficient length to clear the fusogens from the fusion site by entropic forces. Simulations with rod-shaped SNAREpin-like fusogens fused 50-nm vesicles on ms timescales, driven by entropic forces along a reproducible fusion pathway. SNARE-SNARE and SNARE-membrane entropic forces cleared the fusion site and pressed the vesicles into an extended contact zone (ECZ), drove stalk nucleation at the high curvature ECZ boundary, and expanded the stalk into a long-lived hemifusion diaphragm in which a simple pore completed fusion. Our results provide strong support for the entropic hypothesis of SNARE-mediated membrane fusion, and implicate the rodlike structure of the SNAREpin complex as a necessity for entropic force production and fusion.


title: Dynamic Self-Reinforcement of Gene Expression Determines Acquisition and Retention of Cellular Mechanical Memory

abstract: Mechanotransduction describes activation of gene expression by changes in the cells physical microenvironment. Recent experiments show that mechanotransduction can lead to long-term "mechanical memory", where cells cultured on stiff substrates for sufficient time (priming phase) maintain altered phenotype after switching to soft substrates (dissipation phase), as compared to unprimed controls. The timescale of memory acquisition and retention is orders of magnitude larger than the timescale of mechanosensitive cellular signaling, and memory retention time changes continuously with priming time. We develop a model that captures these features by accounting for positive reinforcement in mechanical signaling. The sensitivity of reinforcement represents the dynamic transcriptional state of the cell composed of protein lifetimes and 3D chromatin organization. Our model provides a single framework connecting microenvironment mechanical history to cellular outcomes ranging from no memory to terminal differentiation. Predicting cellular memory of environmental changes can help engineer cellular dynamics through changes in culture environments.


title: Alcohol and Vapourized Nicotine Co-Exposure During Adolescence Contribute Differentially to Sex-Specific Behavioural Effects in Adulthood

abstract:
IntroductionCo-occurrence of e-cigarette use and alcohol consumption during adolescence is frequent. However, little is known about their long-lasting effects when combined. Here, we examined whether adolescent co-exposure to alcohol drinking and vapourized nicotine would impact reward- and cognition-related behaviours in adult male and female rats during adulthood.

MethodsFour groups of male and female Sprague Dawley rats (n=8-11/group/sex) received either nicotine (JUUL 5% nicotine pods) or vehicle vapour daily between postnatal days 30-46, while having continuous voluntary access to ethanol and water during this time in a two-bottle preference design. Upon reaching adulthood, rats underwent behavioural testing utilizing Pavlovian conditioned approach testing, fear conditioning and a two-bottle alcohol preference test.

ResultsA sex-dependent effect was found in the two-bottle preference test in adulthood such that females had a higher intake and preference for alcohol compared to males regardless of adolescent exposure; both male and female adult rats had greater alcohol preference compared to adolescents. Male rats exposed to vapourized nicotine with or without alcohol drinking during adolescence exhibited altered reward-related learning in adulthood, evidenced by enhanced levels of sign-tracking behaviour. Male rats that drank alcohol with or without nicotine vapour in adolescence showed deficits in associative fear learning and memory as adults. In contrast, these effects were not seen in female rats exposed to alcohol and nicotine vapour during adolescence.

ConclusionsThe present study provides evidence that co-exposure to alcohol and vapourized nicotine during adolescence in male, but not female, rats produces longterm changes in reward- and cognition-related behaviours.

ImplicationsThese findings enhance our understanding of the effects of alcohol drinking and nicotine vapour exposure in adolescence. Moreover, they highlight potential sex differences that exist in the response to alcohol and nicotine vapour, underscoring the need for follow-up studies elucidating the neurobiological mechanisms that drive these sex differences, as well as the long-term effects of alcohol and nicotine vapour use.


title: Mice are not automatons; subjective experience in premotor circuits guides behavior

abstract: Subjective experience is a powerful driver of decision-making and continuously accrues. However, most neurobiological studies constrain analyses to task-related variables and ignore how continuously and individually experienced internal, temporal, and contextual factors influence adaptive behavior during decision-making and the associated neural mechanisms. We show mice rely on learned information about recent and longer-term subjective experience of variables above and beyond prior actions and reward, including checking behavior and the passage of time, to guide self-initiated, self-paced, and self-generated actions. These experiential variables were represented in secondary motor cortex (M2) activity and its projections into dorsal medial striatum (DMS). M2 integrated this information to bias strategy-level decision-making, and DMS projections used specific aspects of this recent experience to plan upcoming actions. This suggests diverse aspects of experience drive decision-making and its neural representation, and shows premotor corticostriatal circuits are crucial for using selective aspects of experiential information to guide adaptive behavior.


title: Intracortical human recordings reveal intensity coding for the pain of others in the insula

abstract: Based on neuroimaging data, the insula is considered important for people to empathize with the pain of others, whether that pain is perceived through facial expressions or the sight of limbs in painful situations. Here we present the first report of intracranial electroencephalographic (iEEG) recordings from the insulae collected while 7 presurgical epilepsy patients rated the intensity of a womans painful experiences viewed in movies. In two separate conditions, pain was deduced from seeing facial expressions or a hand being slapped by a belt. We found that broadband activity in the 20-190 Hz range correlated with the trial-by-trial perceived intensity in the insula for both types of stimuli. Using microwires at the tip of a selection of the electrodes, we additionally isolated 8 insular neurons with spiking that correlated with perceived intensity. Within the insula, we found a patchwork of locations with differing selectivities within our stimulus set, some representing intensity only for facial expressions, others only for the hand being hit, and others for both. That we found some locations with intensity coding only for faces, and others only for hand across simultaneously recorded locations suggests that insular activity while witnessing the pain of others cannot be entirely reduced to a univariate salience representation. Psychophysics and the temporal properties of our signals indicate that the timing of responses encoding intensity for the sight of the hand being hit are best explained by kinematic information; the timing of those encoding intensity for facial expressions are best explained by shape information in the face. In particular, the furrowing of the eyebrows and the narrowing of the eyes of the protagonist in the movies suffice to predict both the rating of and the timing of the neuronal response to the facial expressions. Comparing the broadband activity in the iEEG signal with spiking activity and an fMRI experiment with similar stimuli revealed a consistent spatial organization for the representation of intensity from our hand stimuli, with stronger intensity representation more anteriorly and around neurons with intensity coding. In contrast, for the facial expressions, we found that the activity at the three levels of measurement do not coincide, suggesting a more disorganized representation. Together, our intracranial recordings indicate that the insula encodes, in a partially intermixed layout, both static and dynamic cues from different body parts that reflect the intensity of pain experienced by others.


title: Intracranial human recordings reveal intensity coding for the pain of others in the insula


title: Repertoire analyses reveal TCR sequence features that influence T cell fate

abstract: T cells acquire a regulatory phenotype when their T cell receptors (TCRs) experience an intermediate-high affinity interaction with a self-peptide presented on MHC. Using TCR sequences from FACS-sorted human cells, we identified TCR features that shape affinity to these self-peptide-MHC complexes, finding that 1) CDR3{beta} hydrophobicity and 2) certain TRBV genes promote Treg fate. We developed a scoring system for TCR-intrinsic regulatory potential (TiRP) and found that within the tumor microenvironment clones exhibiting Treg-Tconv plasticity had higher TiRP than expanded clones maintaining the Tconv phenotype. To elucidate drivers of these predictive TCR features, we examined the two elements of the Treg TCR ligand separately: the self-peptide via murine Tregs, and the human MHC II molecule via human memory Tconvs. These analyses revealed that CDR3{beta} hydrophobicity promotes reactivity to self-peptides, while TRBV gene usage shapes the TCRs general propensity for MHC II-restricted activation.


title: An Open-Source Modular Framework for Automated Pipetting and Imaging Applications

abstract:
The number of samples in biological experiments are continuously increasing, but complex protocols and human experimentation in many cases lead to suboptimal data quality and hence difficulties in reproducing scientific findings. Laboratory automation can alleviate many of these problems by precisely reproducing machine-readable protocols. These instruments generally require high up-front investments and due to lack of open APIs they are notoriously difficult for scientists to customize and control outside of the vendor-supplied software.

Here, we demonstrate automated, high-throughput experiments for interdisciplinary research in life science that can be replicated on a modest budget, using open tools to ensure reproducibility by combining the tools Openflexure, Opentrons, ImJoy and UC2. Our automated sample preparation and imaging pipeline can easily be replicated and established in many laboratories as well as in educational contexts through easy-to-understand algorithms and easy-to-build microscopes. Additionally, the creation of feedback loops, with later pipetting or imaging steps depending on analysis of previously acquired images, enables the realization of smart microscopy experiments, featuring completely autonomously performed experiments. All documents and source-files are publicly available (https://beniroquai.github.io/Hi2) to prove the concept of smart lab automation using inexpensive, open tools. We believe this democratizes access to the power and repeatability of automated experiments.


title: Predator avoidance and foraging for food shape synchrony and response to perturbations in trophic metacommunities

abstract: The response of species to perturbations strongly depends on spatial aspects in populations connected by dispersal. Asynchronous fluctuations in biomass among populations lower the risk of simultaneous local extinctions and thus reduce the regional extinction risk. However, dispersal is often seen as passive diffusion that balances species abundance between distant patches, whereas ecological constraints, such as predator avoidance or foraging for food, trigger the movement of individuals. Here, we propose a model in which dispersal rates depend on the abundance of the species interacting with the dispersing species (e.g., prey or predators) to determine how density-dependent dispersal shapes spatial synchrony in trophic metacommunities in response to stochastic perturbations. Thus, unlike those with passive dispersal, this model with density-dependent dispersal bypasses the classic vertical transmission of perturbations due to trophic interactions and deeply alters synchrony patterns. We show that the species with the highest coefficient of variation of biomass governs the dispersal rate of the dispersing species and determines the synchrony of its populations. In addition, we show that this mechanism can be modulated by the relative impact of each species on the growth rate of the dispersing species. Species affected by several constraints disperse to mitigate the strongest constraints (e.g., predation), which does not necessarily experience the highest variations due to perturbations. Our approach can disentangle the joint effects of several factors implied in dispersal and provides a more accurate description of dispersal and its consequences on metacommunity dynamics.


title: Automated classification of bat echolocation call recordings with artificial intelligence

abstract: Acoustic recorders are commonly used to remotely monitor and collect data on bats (Order Chiroptera). These efforts result in many acoustic recordings that must be classified by a bat biologist with expertise in call classification in order to obtain useful information. The rarity of this expertise and time constraints have prompted efforts to automatically classify bat species in acoustic recordings using a variety of learning methods. There are several software programs available for this purpose, but they are imperfect and the United States Fish and Wildlife Service often recommends that a qualified acoustic analyst review bat call identifications even if using these software programs. We sought to build a model to classify bat species using modern computer vision techniques. We used images of bat echolocation calls (i.e., plots of the pulses) to train deep learning computer vision models that automatically classify bat calls to species. Our model classifies 10 species, five of which are protected under the Endangered Species Act. We evaluated our models using standard model validation procedures, but we also performed two out-of-distribution tests. For the out-of-distribution tests, an entire dataset was withheld from the procedure before splitting the data into training and validation sets. We found that our validation accuracy (93%) and out-of-distribution accuracy (90%) were higher than when we used Kaleidoscope Pro and BCID software (65% and 61% accuracy, respectively) to evaluate the same calls. Our results suggest that our approach is effective at classifying bat species from acoustic recordings, and our trained model will be incorporated into new bat call identification software: WEST-EchoVision.


title: Polygenic variation in sexual investment across an ephemerality gradient in Daphnia pulex

abstract: Species across the tree of life can switch between asexual and sexual reproduction. In facultatively sexual species, the ability to switch between reproductive modes is often environmentally dependent and subject to local adaptation. However, the ecological and evolutionary factors that influence the maintenance and turnover of polymorphism associated with facultative sex remain unclear. To address this basic question, we studied the ecological and evolutionary dynamics of polymorphism in reproductive strategy in a metapopulation of the model facultative sexual, Daphnia pulex, located in the southern United Kingdom. We found that patterns of clonal diversity, but not genetic diversity varied with ephemerality. Reconstruction of a multi-year pedigree demonstrated the co-existence of clones that were found to differ in their investment into male production. Mapping of quantitative variation in male production using lab-generated and field-collected individuals identified multiple putative QTL underlying this trait, and we identified a plausible candidate gene. The evolutionary history of these QTL suggests that they are relatively young, and male limitation in this system is a rapidly evolving trait. Our work highlights the dynamic nature of the genetic structure and composition of facultative sex across space and time and suggests that quantitative genetic variation in reproductive strategy can undergo rapid evolutionary turnover.


title: utR.annotation: a tool for annotating genomic variants that could influence post-transcriptional regulation

abstract:
SummaryWhole genome sequencing of patient populations is identifying thousands of new variants in UnTranslated Regions(UTRs). While the consequences of UTR mutations are not as easily predicted from primary sequence as coding mutations are, there are some known features of UTRs modulate their function. utR.annotation is an R package that can be used to annotate potential deleterious variants in the UTR regions for both human and mouse species. Given a CSV or VCF format variant file, utR.annotation provides information of each variant on whether and how it alters known translational regulators including:upstream Open Reading Frames (uORFs), upstream Kozak sequences, polyA signals, the Kozak sequence at the annotated translation initiation site, start codon, and stop codon, conservation scores in the variant position, and whether and how it changes ribosome loading based on a model from empirical data.

Availability and implementationutR.annotation is freely available on Bitbucket (https://bitbucket.org/jdlabteam/utr.annotation/src/master/) and CRAN (to be updated)

Supplementary informationSupplementary data are available at https://wustl.box.com/s/yye99bryfin89nav45gv91l5k35fxo7z


title: Factors Driving DNA Methylation Variation in Human Blood

abstract: Epigenetic changes are required for normal development and health, and can also underlie disease states; yet, the nature and respective contribution of factors that drive epigenetic variation in humans remain to be fully characterized. Here, we assessed how the blood DNA methylome of 958 adults is affected by genetic variation, aging, sex and 139 diverse environmental exposures, and investigated whether these effects are direct or mediated by changes in cellular composition, measured by deep immunophenotyping. We show that cellular heterogeneity and DNA sequence variation are the strongest predictors of DNA methylation levels. We identify latent cytomegalovirus infection as a major driver of DNA methylation variation and delineate three distinct effects of aging on DNA methylation, including increased dispersion consistent with epigenetic drift. Our rich dataset provides a unique resource for the design and interpretation of epigenetic studies and highlight critical factors in medical epigenomics studies.


title: Genetic Analyses of Epigenetic Predictors that Estimate Aging, Metabolic Traits, and Lifespan

abstract: Changes in DNA methylation (DNAm) are linked to aging. Here, we profile highly conserved CpGs in 339 predominantly female mice belonging to the BXD family for which we have deep longevity and genomic data. We use a  pan-mammalian microarray that provides a common platform for assaying the methylome across mammalian clades. We computed epigenetic clocks and tested associations with DNAm entropy, diet, weight, metabolic traits, and genetic variation. We describe the multifactorial variance of methylation at these CpGs, and show that high fat diet augments the age-associated changes. Entropy increases with age. The progression to disorder, particularly at CpGs that gain methylation over time, was predictive of genotype-dependent life expectancy. The longer-lived BXD strains had comparatively lower entropy at a given age. We identified two genetic loci that modulate rates of epigenetic age acceleration (EAA): one on chromosome (Chr) 11 that encompasses the Erbb2/Her2 oncogenic region, and a second on Chr19 that contains a cytochrome P450 cluster. Both loci harbor genes associated with EAA in humans including STXBP4, NKX2-3, and CUTC. Transcriptome and proteome analyses revealed associations with oxidation-reduction, metabolic, and immune response pathways. Our results highlight concordant loci for EAA in humans and mice, and demonstrate a tight coupling between the metabolic state and epigenetic aging.


title: Genetic Loci and Metabolic States Associated With Murine Epigenetic Aging


title: High Bandwidth Power Electronics and Magnetic Nanoparticles for Multichannel Magnetogenetic Neurostimulation

abstract:
ObjectiveWe present a power electronic system and magnetic nanoparticles for multiplexed magnetogenetic neurostimulation with three channels spanning a wide frequency range and rapid channel switching capability. This enables selective heating of magnetic nanoparticles with different coercivity using various frequency-amplitude combinations of the magnetic field. Such multiplexed operation could provide the technical means for selective magnetogenetic neurostimulation beyond its spatial focality limits.

ApproachThe electronic system uses a hybrid of silicon metal-oxide-semiconductor and gallium-nitride field-effect transistors, which generate the required high-amplitude current up to 500 A in the sub-MHz range and the high-frequency current in the MHz range, respectively. Via three discrete resonance capacitor banks, the system generates an alternating magnetic field in the same liquid-cooled field coil at three distinct frequency channels spanning 50 kHz to 4 MHz. Fast switching between channels is achieved with high-voltage contactors connecting the coil to different capacitor banks. We characterized the system by the output channels frequencies, field strength, and switching time, as well as the systems overall operation stability. Three types of iron oxide nanoparticles with different coercivity are developed to form three magnetothermal channels. Specific absorption rate and infrared thermal imaging measurements are performed with the nanoparticles to characterize their heating and demonstrate selective actuation for all three channels.

Main resultsThe system achieved the desired target field strengths for three frequency channels (70 kA/m at 50 kHz, 10 kA/m at 500 kHz, and 1 kA/m at [≥]2 MHz), with rapid switching speed between channels on the order of milliseconds. The system can operate continuously for at least two hours at 30% duty cycle with 125 Arms load in the coil, corresponding to a stimulation protocol of cycling the three channels at target strength with 3 s pulses and 7 s interpulse intervals. The nanoparticles were heated with selectivity between 2.3x and 9x for their respective frequency channel. The systems intended use was thus validated with three distinct channels available for magnetothermal heating.

SignificanceWe describe the first combination of a power electronic system and magnetic nanoparticles that achieves three stimulation channels. Selective actuation of nanoparticles is demonstrated for each channel using the same field coil, including a novel composition responding to magnetic fields in the MHz range. This approach could improve the speed and flexibility of frequency-multiplexed magnetogenetic neural stimulation.


title: A Bayesian Multivariate Mixture Model for Spatial Transcriptomics Data

abstract: High throughput spatial transcriptomics (HST) is a rapidly emerging class of experimental technologies that allow for profiling gene expression in tissue samples at or near single-cell resolution while retaining the spatial location of each sequencing unit within the tissue sample. Through analyzing HST data, we seek to identify sub-populations within a tissue sample that reflect distinct cell types or states. Existing methods either ignore the spatial heterogeneity in gene expression profiles, fail to account for important statistical features such as skewness, or are heuristic network-based clustering methods that lack the inferential benefits of statistical modeling. To address this gap, we develop SPRUCE: a Bayesian spatial multivariate finite mixture model based on multivariate skew-normal distributions, which is capable of identifying distinct cellular sub-populations in HST data. We further implement a novel combination of Polya-Gamma data augmentation and spatial random effects to infer spatially correlated mixture component membership probabilities without relying on approximate inference techniques. Via a simulation study, we demonstrate the detrimental inferential effects of ignoring skewness or spatial correlation in HST data. Using publicly available human brain HST data, SPRUCE outperforms existing methods in recovering expertly annotated brain layers. Finally, our application of SPRUCE to human breast cancer HST data indicates that SPRUCE can distinguish distinct cell populations within the tumor microenvironment.


title: A Random Forest Classifier for Protein-Protein Docking Models

abstract: Herein, we present the results of a machine learning approach we developed to single out correct 3D docking models of protein-protein complexes obtained by popular docking software. To this aim, we generated a set of {approx}7x106 docking models with three different docking programs (HADDOCK, FTDock and ZDOCK) for the 230 complexes in the protein-protein interaction benchmark, version 5 (BM5). Three different machine-learning approaches (Random Forest, Supported Vector Machine and Perceptron) were used to train classifiers with 158 different scoring functions (features). The Random Forest algorithm outperformed the other two algorithms and was selected for further optimization. Using a features selection algorithm, and optimizing the random forest hyperparameters, allowed us to train and validate a random forest classifier, named CoDES (COnservation Driven Expert System). Testing of CoDES on independent datasets, as well as results of its comparative performance with machine-learning methods recently developed in the field for the scoring of docking decoys, confirm its state-of-the-art ability to discriminate correct from incorrect decoys both in terms of global parameters and in terms of decoys ranked at the top positions.


title: Panel Informativity Optimizer (PIO): an R package to improve cancer NGS panel informativity

abstract: Mutation detection by next generation sequencing (NGS) is routinely used for cancer diagnosis. Selecting an optimal set of genes for a given cancer is not trivial as it has to optimize informativity (i.e. the number of patients with at least one mutation in the panel), while minimizing panel length in order to reduce sequencing costs and increase sensitivity. We propose herein Panel Informativity Optimizer (PIO), an open-source software developed as an R package with a user-friendly graphical interface to help optimize cancer NGS panel informativity. Using patient-level mutational data from either private datasets or preloaded dataset of 91 independent cohort from 31 different cancer type, PIO selects an optimal set of genomic intervals to maximize informativity and panel size in a given cancer type. Different options are offered such as the definition of genomic intervals at the gene or exon level, and the use of optimization strategy at the patient or patient per kilobase level. PIO can also propose an optimal set of genomic intervals to increase informativity of custom panels. A panel tester function is also available for panel benchmarking. Using public databases, as well as data from real-life settings, we demonstrate that PIO allows panel size reduction of up to 1000kb, and accurately predicts the performance of custom or commercial panels. PIO is available online at https://vincentalcazer.shinyapps.io/Panel_informativity_optimizer/ or can be set on a locale machine from https://github.com/VincentAlcazer/PIO.


title: The Influence of Irreversibly Electroporated Cells on Post Pulse Drug Delivery to Reversibly Electroporated Cells

abstract: Electroporation can result in cell death in some proportion of a population of cells and, because the nature of the membrane disruption can vary significantly in irreversibly electroporated cells, there is uncertainty in the magnitude of and the transient behaviour of the associated permeability increases. This study numerically investigates the drug uptake by a population of cells that includes both reversibly and irreversibly electroporated cells. A theoretical continuum model is developed and simulations are conducted in conditions of low porosity (cells in tissues) and of high porosity (cells in suspension). This model estimates the permeability increases of electroporated cells using empirically based predictions of the dependence of long-lived electropore density on the local electric field magnitude. A parametric investigation investigates how the transmembrane transport characteristics of irreversibly electroporated cells (permeability and resealing rate) affect the drug uptake of the surviving cells. The results show that the magnitude and duration of the permeability increases of irreversibly electroporated cells is much more influential in low porosity tissues than in high porosity dilute suspensions. In applications of electroporation of cells in tissues, the uncertainty of irreversibly electroporated cells should be considered in regions of tissue experiencing field strengths for which the fraction of the total cells that are irreversibly electroporated exceeds about 0.1.


title: Coordination games in cancer

abstract: We propose a model of cancer initiation and progression where tumor growth is modulated by an evolutionary coordination game. Evolutionary games of cancer are widely used to model frequency-dependent cell interactions with the most studied games being the Prisoners Dilemma and public goods games. Coordination games, by their more obscure and less evocative nature, are left understudied, despite the fact that, as we argue, they offer great potential in understanding and treating cancer. In this paper we present the conditions under which coordination games between cancer cells evolve, we propose aspects of cancer that can be modeled as results of coordination games, and explore the ways through which coordination games of cancer can be exploited for therapy.

category: cancer biology


title: An empirically-driven guide on using Bayes Factors for M/EEG decoding

abstract: Bayes Factors can be used to provide quantifiable evidence for contrasting hypotheses and have thus become increasingly popular in cognitive science. However, Bayes Factors are rarely used to statistically assess the results of neuroimaging experiments. Here, we provide an empirically-driven guide on implementing Bayes Factors for time-series neural decoding results. Using real and simulated Magnetoencephalography (MEG) data, we examine how parameters such as the shape of the prior and data size affect Bayes Factors. Additionally, we discuss benefits Bayes Factors bring to analysing multivariate pattern analysis data and show how using Bayes Factors can be used instead or in addition to traditional frequentist approaches.


title: Dopamine Neurons Evaluate Natural Fluctuations in Performance Quality

abstract: Many motor skills are learned by comparing ongoing behavior to internal performance benchmarks. Dopamine neurons encode performance error in behavioral paradigms where error is externally induced, but it remains unknown if dopamine also signals the quality of natural performance fluctuations. Here we recorded dopamine neurons in singing birds and examined how spontaneous dopamine spiking activity correlated with natural fluctuations in ongoing song. Antidromically identified basal ganglia-projecting dopamine neurons correlated with recent, and not future, song variations, consistent with a role in evaluation, not production. Furthermore, dopamine spiking was suppressed following the production of outlying vocal variations, consistent with a role for active song maintenance. These data show for the first time that spontaneous dopamine spiking can evaluate natural behavioral fluctuations unperturbed by experimental events such as cues or rewards.


title: Prolonged and distributed processing of facial identity in the human brain

abstract: The recognition of facial identity is essential for social interactions. Despite extensive prior fMRI and EEG/MEG research on the neural representations of familiar faces, we know little about the spatio-temporal dynamics of face identity information. Therefore, we applied a novel multimodal approach by fusing the neuronal responses recorded in an fMRI and an EEG experiment. We analyzed the neural responses to naturally varying famous faces and traced how face identity emerges over time in different areas of the brain. We found that image invariant face identity information prevails over an extended time period (from 150 to 810 ms after stimulus onset) in the representational geometry of a broadly distributed network of parietal, temporal, and frontal areas with overlapping temporal profiles. These results challenge the current hierarchical models of face perception and suggest instead concerted and parallel activation of multiple nodes in the brains identity coding network while processing information of familiar faces.


title: Structural analysis of 3'UTRs in insect flaviviruses reveals novel determinant of sfRNA biogenesis and provides new insights into flavivirus evolution

abstract: Insect-specific flaviviruses (ISFs) circulate in nature due to vertical transmission in mosquitoes and do not infect vertebrates. ISFs include two distinct lineages - classical ISFs (cISFs) that evolved independently and dual host associated ISFs (dISFs) that are proposed to diverge from mosquito-borne flaviviruses (MBFs). Compared to pathogenic flaviviruses, ISFs are relatively poorly studied, and their molecular biology remains largely unexplored. In this study we focused on the characterisation of ISF 3UTRs and their ability to produce subgenomic flaviviral RNAs - noncoding viral RNAs that are known as important determinants of transmission and replication of pathogenetic flaviviruses. We demonstrated that cISFs and dISFs produce sfRNAs by employing a highly conserved mechanism of resistance to degradation by the cellular 5-3 exoribonuclease XRN1. We determined the secondary structures of complete 3UTRs and experimentally identified structured RNA elements that resist degradation by XRN1 (xrRNAs) in divergent representatives of cISF and dISF clades. We discovered a novel class of xrRNAs in dISFs and identified structurally divergent xrRNA in Anopheles-associated cISFs. Phylogenetic analyses based on sequences and secondary structures of xrRNAs and complete 3UTRs reveal that xrRNAs of cISFs and MBFs/dISFs evolved from a common xrRNA ancestor similar to the xrRNA of Anopheles-associated cISFs. Additionally, we found that duplications of xrRNAs occurred independently in ISF and MBF clades. Using ISF mutants deficient in the production of sfRNAs, we found that individual sfRNAs of ISFs have redundant functions. We conclude that duplicated xrRNAs were selected in the evolution of flaviviruses to ensure that sfRNA is produced if one of the xrRNAs lose XRN1 resistance due to mutations or misfolding.

category: microbiology


title: Nuclear envelope reshaping around the vacuole determines the morphology of the ribosomal DNA

abstract: The ribosomal DNA array (rDNA) of Saccharomyces cerevisiae has served as a model to address chromosome organization. In cells arrested before anaphase (mid-M), the rDNA acquires a highly structured chromosomal organization referred to as the rDNA loop, whose length can double the cell diameter. Previous works established that complexes such as condensin and cohesin are essential to attain this structure. Here, we report that the rDNA loop adopts distinct morphologies that arise as spatial adaptations to changes in the nuclear morphology triggered during the mid-M arrests. Interestingly, the formation of the rDNA loop results in the appearance of a space under the loop (SUL) which is devoid of any nuclear component yet colocalizes with the vacuole. We finally show that the formation and maintenance of the rDNA loop and the SUL require TORC1 and membrane synthesis. We propose that the rDNA-associated nuclear envelope (NE) reshapes into a loop to accommodate the vacuole, with the nucleus becoming bilobed.


title: Biological Innocuousness of a Device developed to select the Optimum Spermatozoa to be used in the Treatment of Infertility

abstract: The sperm selection assay (SSA) is a method based on chemotaxis to obtain spermatozoa at the optimum physiological state to successfully fertilize the egg. It consists of a device made of acrylic and an attractant solution which includes progesterone. We evaluate potential cytotoxicity interactions by means of Neutral Red uptake, the MTT and colony formation assays, according to ISO normative. Here we showed that even stressing the conditions of the assays, the SSA device alone or together with the progesterone solutions employed, showed to be innocuous for the cells. Suggesting that SSA could be incorporated into the ART procedures.


title: Aberrant FGF signaling promotes granule neuron precursor expansion in SHH subgroup infantile medulloblastoma

abstract: Mutations in Sonic Hedgehog (SHH) signaling pathway genes, e.g. Suppressor of Fused (SUFU), drive granule neuron precursors (GNP) to form medulloblastomas (MBSHH). However, how different molecular lesions in the Shh pathway drive transformation is frequently unclear, and in particular, SUFU mutations in the cerebellum seem distinct. In this study, we show that fibroblast growth factor 5 (FGF5) signaling is integral for many infantile MBSHH cases. We found that FGF5 expression is uniquely upregulated in infantile MBSHH tumors. Also, in mice carrying loss-of-function SUFU mutations (Sufu-cKO), FGF5 is ectopically expressed specifically along the secondary fissure where GNPs harboring preneoplastic DNA lesions are massively expanded and FGFR signaling is also ectopically activated in this region. Treatment with an FGFR antagonist rescues the severe GNP hyperplasia and restores cerebellar architecture. Thus, direct inhibition of FGF signaling may be a promising and novel therapeutic candidate for infantile MBSHH.


title: Dynamic aspects of plant water potential revealed by a microtensiometer

abstract: Water potential is a fundamental thermodynamic parameter that describes the activity of water. In this paper, we describe the continuous measurement of plant water potential, a reliable indicator of its water status, using a novel in situ sensor known as a  microtensiometer in mature grapevines under field conditions. The microtensiometer operates on the principle of equilibration of water potentials of internal liquid water with an external vapour or liquid phase. We characterised the seasonal and diurnal dynamics of trunk water potentials ({Psi}trunk) obtained from microtensiometers installed in two grapevine cultivars, Shiraz and Cabernet Sauvignon, and compared these values to pressure chamber-derived stem ({Psi}stem) and leaf ({Psi}leaf) water potentials as well as leaf stomatal conductance. Diurnal patterns of {Psi}trunk matched those of {Psi}stem and {Psi}leaf under low vapour pressure deficit (VPD) conditions, but diverged under high VPD conditions. The highest diurnal values of {Psi}trunk were observed shortly after dawn, while the lowest values were typically observed in the late afternoon. Differential responses of {Psi}trunk to VPD were observed between cultivars, with Shiraz more sensitive than Cabernet to increasing VPD over long time scales, and both cultivars had a stronger VPD response than soil moisture response. On a diurnal basis, however, time cross correlation analysis revealed that Shiraz {Psi}trunk lagged Cabernet {Psi}trunk in response to changing VPD. Microtensiometers were shown to operate reliably under field conditions over several months. To be useful for irrigation scheduling of woody crops, new thresholds of {Psi}trunk need to be developed.

category: plant biology


title: Machine Learning based Genome-Wide Association Studies for Uncovering QTL Underlying Soybean Yield and its Components

abstract: Genome-wide association study (GWAS) is currently one of the important approaches for discovering quantitative trait loci (QTL) associated with traits of interest. However, insufficient statistical power is the limiting factor in current conventional GWAS methods for characterizing quantitative traits, especially in narrow genetic bases plants such as soybean. In this study, we evaluated the potential use of machine learning (ML) algorithms such as support vector machine (SVR) and random forest (RF) in GWAS, compared with two conventional methods of mixed linear models (MLM) and fixed and random model circulating probability unification (FarmCPU), for identifying QTL associated with soybean yield components. In this study, important soybean yield component traits, including the number of reproductive nodes (RNP), non-reproductive nodes (NRNP), total nodes (NP), and total pods (PP) per plant along with yield and maturity were assessed using 227 soybean genotypes evaluated across four environments. Our results indicated SVR-mediated GWAS outperformed RF, MLM and FarmCPU in discovering the most relevant QTL associated with the traits, supported by the functional annotation of candidate gene analyses. This study for the first time demonstrated the potential benefit of using sophisticated mathematical approaches such as ML algorithms in GWAS for identifying QTL suitable for genomic-based breeding programs.


title: Automated quantification of vomeronasal glomeruli number, size, and color composition after immunofluorescent staining

abstract:
Glomeruli are neuropil rich regions of the main or accessory olfactory bulbs where the axons of olfactory or vomeronasal neurons and dendrites of mitral/tufted cells form synaptic connections. In the main olfactory system olfactory sensory neurons (OSNs) expressing the same receptor innervate one or two glomeruli. However, in the accessory olfactory system, vomeronasal sensory neurons (VSNs) expressing the same receptor can innervate up to 30 different glomeruli in the accessory olfactory bulb (AOB).

Genetic mutation disrupting genes with a role in defining the identity/diversity of olfactory and vomeronasal neurons can alter number and size of glomeruli. Interestingly, two cell surface molecules, Kirrel2 and Kirrel3, have been indicated to play a critical role in the organization of axons into glomeruli in the AOB.

Being able to quantify differences in glomeruli features such as number, size or immunoreactivity for specific markers is an important experimental approach to validate the role of specific genes in controlling neuronal connectivity and circuit formation in control or mutant animals. Since the manual recognition and quantification of glomeruli on digital images is a challenging and time-consuming task, we generated a program in Python able to identify glomeruli in digital images and quantify their properties, such as size, number, and pixel intensity. Validation of our program indicates that our script is a fast and suitable tool for high throughput quantification of glomerular features of mouse lines with different genetic makeup.


title: Familial Danish dementia young Knock-in rats expressing humanized APP and human Aβ show impaired pre and postsynaptic glutamatergic transmission

abstract: Familial British and Danish dementia (FBD and FDD) are two neurodegenerative disorders caused by mutations in the Integral membrane protein 2B (ITM2b). BRI2, the protein encoded by ITM2b, tunes excitatory synaptic transmission at both pre- and post-synaptic terminus. Too, BRI2 interacts with and modulates proteolytic processing of Amyloid-{beta} precursor Protein (APP), whose mutations cause familial forms of Alzheimer disease (FAD). To study pathogenic mechanism triggered by the Danish mutation we generated rats carrying the Danish mutation into the rat Itm2b gene (Itm2bD rats). Given the BRI2/APP interaction and the widely accepted relevance of human A{beta}, a proteolytic product of APP, to AD, Itm2bD rats were engineered to express two humanized App alleles, to produce human A{beta}. Here, we studied young Itm2bD rats to investigate early pathogenic changes. We found that peri-adolescent Itm2bD rats present subtle changes in human A{beta} levels along with decreased spontaneous glutamate release and AMPAR-mediated responses but increased short-term synaptic facilitation in the hippocampal Schaeffer-collateral pathway. These changes are like those observed in adult mice producing rodent A{beta} and carrying either the Danish or British mutations into the mouse Itm2b gene. Collectively, the data show that the pathogenic Danish mutation alters the physiological function of BRI2 at glutamatergic synapses; these functional alterations are detected across species and occur early in life. Future studies will be needed to determine whether this phenomenon represents an early pathogenic event in human dementia.


title: Single-cell dissection of live human hearts in ischemic heart disease and heart failure reveals cell-type-specific driver genes and pathways

abstract: Ischemic heart disease is the single most common cause of death worldwide with an annual death rate of over 9 million people. Genome-wide association studies have uncovered over 200 genetic loci underlying the disease, providing a deeper understanding of the causal mechanisms leading to it. However, in order to understand ischemic heart disease at the cellular and molecular level, it is necessary to identify the cell-type-specific circuits enabling dissection of driver variants, genes, and signaling pathways in normal and diseased tissues. Here, we provide the first detailed single-cell dissection of the cell types and disease-associated gene expression changes in the living human heart, using cardiac biopsies collected during open-heart surgery from control, ischemic heart disease, and ischemic and non-ischemic heart failure patients. We identify 84 cell types/states, grouped in 12 major cell types. We define markers for each cell type, providing the first extensive reference set for the live human heart. These major cell types include cardiovascular cells (cardiomyocytes, endothelial cells, fibroblasts), rarer cell types (B lymphocytes, neurons, Schwann cells), and rich populations of previously understudied layer-specific epicardial and endocardial cells. In addition, we reveal substantial differences in disease-associated gene expression at the cell subtype level, revealing t arterial pericytes as having a central role in the pathogenesis of ischemic heart disease and heart failure. Our results demonstrate the importance of high-resolution cellular subtype mapping in gaining mechanistic insight into human cardiovascular disease.

category: molecular biology


title: The endoplasmic reticulum-plasma membrane tethering protein TMEM24 is a regulator of cellular Ca2+ homeostasis

abstract: Endoplasmic reticulum (ER) - plasma membrane (PM) contacts are sites of lipid exchange and Ca2+ transport, and both lipid transport proteins and Ca2+ channels specifically accumulate at these locations. In pancreatic {beta}-cells, both lipid- and Ca2+ signaling are essential for insulin secretion. The recently characterized lipid transfer protein TMEM24 dynamically localize to ER-PM contact sites and provide phosphatidylinositol, a precursor of PI(4)P and PI(4,5)P2, to the plasma membrane. {beta}-cells lacking TMEM24 exhibit markedly suppressed glucose-induced Ca2+ oscillations and insulin secretion but the underlying mechanism is not known. We now show that TMEM24 only weakly interact with the PM, and dissociates in response to both diacylglycerol and nanomolar elevations of cytosolic Ca2+. Release of TMEM24 into the bulk ER membrane also enables direct interactions with mitochondria, and we report that loss of TMEM24 results in excessive accumulation of Ca2+ in both the ER and mitochondria and in impaired mitochondria function.


title: Gene-teratogen interactions influence the penetrance of birth defects by altering Hedgehog signaling strength

abstract: Birth defects result from interactions between genetic and environmental factors, but the mechanisms remain poorly understood. We find that mutations and teratogens interact in predictable ways to cause birth defects by changing target cell sensitivity to Hedgehog (Hh) ligands. These interactions converge on a membrane protein complex, the MMM complex, that promotes degradation of the Hh transducer Smoothened (SMO). Deficiency of the MMM component MOSMO results in elevated SMO and increased Hh signaling, causing multiple birth defects. In utero exposure to a teratogen that directly inhibits SMO reduces the penetrance and expressivity of birth defects in Mosmo-/- embryos. Additionally, tissues that develop normally in Mosmo-/- embryos are refractory to the teratogen. Thus, changes in the abundance of the protein target of a teratogen can change birth defect outcomes by quantitative shifts in Hh signaling. Consequently, small molecules that re-calibrate signaling strength could be harnessed to rescue structural birth defects.


title: Multiple mechanisms impact fluconazole resistance of mutant Erg11 proteins in Candida glabrata

abstract:
Azoles, the most commonly used antifungal drugs, specifically inhibit the fungal lanosterol -14 demethylase enzyme, which is referred to as Erg11. Inhibition of Erg11 ultimately leads to a reduction in ergosterol production, an essential fungal membrane sterol. Many Candida species, such as Candida albicans, develop mutations in this enzyme which reduces the azole binding affinity and results in increased resistance. Candida glabrata is also a pathogenic yeast that has low intrinsic susceptibility to azole drugs and easily develops elevated resistance. These azole resistant mutations typically cause hyperactivity of the Pdr1 transcription factor and rarely lie within the ERG11 gene. Here, we generated C. glabrata ERG11 mutations that were analogous to azole resistance alleles from C. albicans ERG11. Three different Erg11 forms (Y141H, S410F, and the corresponding double mutant (DM)) conferred azole resistance in C. glabrata with the DM Erg11 form causing the strongest phenotype. The DM Erg11 also induced cross-resistance to amphotericin B and caspofungin. Resistance caused by the DM allele of ERG11 imposed a fitness cost that was not observed with hyperactive PDR1 alleles. Crucially, the presence of the DM ERG11 allele was sufficient to activate the Pdr1 transcription factor in the absence of azole drugs. Our data indicate that azole resistance linked to changes in ERG11 activity can involve cellular effects beyond an alteration in this key azole target enzyme. Understanding the physiology linking ergosterol biosynthesis with Pdr1-mediated regulation of azole resistance is crucial for ensuring the continued efficacy of azole drugs against C. glabrata.

ImportanceAzole drugs target the Erg11 enzyme and lead to a reduction in fungal ergosterol, a vital sterol in yeast. Mutations in Erg11 are common among azole resistant Candida albicans clinical isolates, but not in C. glabrata, a major human pathogen. In this study, we showed that ERG11 mutations were tolerated in C. glabrata, and these mutations could confer azole resistance. We found that the strongest azole-resistant allele of ERG11 led to induction of the Pdr1 transcription factor and Cdr1 ATP-binding cassette transporter protein in the absence of drug. ERG11 mutations can cause azole resistance via altered enzymatic properties but also by triggering induction of other resistance systems owing to impacts on ergosterol biosynthesis. These data illustrate the deep connections between ergosterol biosynthesis and regulation of membrane transporter proteins via Pdr1 and the ergosterol-responsive transcription factor Upc2A.


title: The population genomics of increased virulence and antibiotic resistance in human commensal Escherichia coli over 30 years in France

abstract:
Escherichia coli is a commensal species of the lower intestine, but also a major pathogen causing intestinal and extra-intestinal infections, increasingly prevalent and resistant to antibiotics. Most studies on genomic evolution of E. coli used isolates from infections. Here instead, we whole-genome sequenced a collection of 403 commensal E. coli isolated from fecal samples of healthy adult volunteers in France (1980-2010). These isolates were distributed mainly in phylogroups A and B2 (30% each) and belonged among 152 sequence types (STs), the five most frequent being ST10 (16.3%), ST73 (6.3%), ST95 (5.0%), ST69 (4.2%) and ST59 (3.9%), and 224 O:H serotypes. ST and serotype diversity increased over time. The O1, O2, O6 and O25-groups used in bioconjugate O-antigen vaccine against extraintestinal infections were found in 23% of the strains of our collection. Extra-intestinal virulence-associated genes and antibiotic resistances increased in frequency, suggesting positive selection on these genes. Evolution of virulence genes was driven by both clonal expansion of STs with more virulence genes ("ST-driven") and increases in gene frequency within STs independently of changes in ST frequencies ("gene-driven"), whereas the evolution of resistance was dominated by increases in frequency within STs ("gene-driven"). This study provides a unique picture of the phylogenomic evolution of E. coli in its human commensal habitat over 30 years and will have implications for the development of preventive strategies.

IMPORTANCEEscherichia coli is an opportunistic pathogen with the greatest burden of antibiotic resistance, one of the main causes of nosocomial infections and an increasing concern in an ageing population. Deciphering the evolutionary dynamics of virulence and antibiotic resistance in commensal E. coli is important to understand adaptation and anticipate future changes. The gut of vertebrates is the primary habitat of E. coli and probably where selection for virulence and resistance take place. Unfortunately, most whole-genome sequenced strains are isolated from pathogenic conditions. Here instead, we whole genome sequenced 403 E. coli commensals isolated from healthy French subjects on a 30-year period. Virulence and resistance genes increased in frequency both by clonal expansion of clones carrying them and by increases in frequency within clones. Such studies should be performed worldwide to have a broader picture of E. coli evolution and adaptation in commensalism.


title: Chrysomycin A inhibits the topoisomerase I of Mycobacterium tuberculosis.

abstract: Novel anti-tuberculosis drugs are essential to manage drug resistant tuberculosis, caused by the notorious pathogen Mycobacterium tuberculosis. We recently reported the antimycobacterial activity of chrysomycin A in vitro and in infected macrophages. In this study, we report that the molecule inhibits the growth of drug resistant clinical strains of Mycobacterium tuberculosis and acts in synergy with anti-TB drugs such as ethambutol, ciprofloxacin and novobiocin. In pursuit of its mechanism of action, it was found that chrysomycin A renders bactericidal activity by interacting with DNA at specific sequences and by inhibiting topoisomerase I activity of Mycobacterium tuberculosis. It also exhibits weak inhibition of gyrase enzyme of the pathogen.

category: biochemistry