title: Lifting the ban on nuclear import activates Gdown1-mediated modulation of global transcription and facilitates adaptation to cellular stresses

abstract: Dynamic regulation of transcription is crucial for cellular response to various environmental or developmental cues. Gdown1 is a ubiquitously expressed, RNA polymerase II (Pol II) interacting protein, essential for embryonic development. It tightly binds Pol II in vitro and competitively blocks binding of TFIIF and other transcriptional regulatory factors, yet its cellular functions and regulatory circuits remain unclear. Here, we show that Gdown1 strictly localizes in the cytoplasm of mammalian somatic cells and exhibits potent resistance to the imposed driving force for nuclear localization. Combined with genetic and microscope-based approaches, two types of functionally coupled and evolutionally conserved localization regulatory motifs are identified, including the CRM1-dependent nucleus export signal (NES) and a novel Cytoplasm Anchoring Signal (CAS) which mediates nuclear pore retention. Mutagenesis of CAS alleviates the cytoplasmic retention activity thus unlocks its nucleocytoplasmic shuttling properties, and increased nuclear import of Gdown1 causes drastic reduction of Pol II levels and global transcription. Importantly, nuclear translocation of Gdown1 occurs in a stress-responsive manner and ablation of GDOWN1 significantly weakens cellular tolerance. Collectively, our work uncovers the molecular basis of the localization of Gdown1 and highlights that its controlled nuclear translocation serves as a key strategy in modulating global transcription and stress-adaptation.

category: cell biology


title: PPAR-γ activation promotes xenogenic bioroot regeneration by attenuating the xenograft induced-oxidative stress

abstract:
Objectivexenogenic organ transplantation has been considered the most promising strategy in providing possible subtitutes with physiological function of the failing organs as well as solving the problem of insufficient donor sources. However, the xenograft, suffered from immune rejection and ischemia-reperfusion injury (IRI), causes massive ROS expression and the subsequent cell apoptosis, leading to the xenograft failure. Our previous study found a positive role of PPAR-{gamma} in anti-inflammation through its immunomodulation effects, which inspires us to apply PPAR-{gamma} agonist rosiglitazone (RSG) to address survival issue of xenograft with the potential to eliminate the excessive ROS.

MethodsXenogenic bioroot was constructed by wrapping the dental follicle cells (DFC) with porcine extracellular matrix (pECM). The hydrogen peroxide (H2O2)-induced DFC was pretreated with RSG to observe its protection on the damaged biological function. Immunoflourescence staining and transmission electron microscope were used to detect the intracellular ROS level. SD rat orthotopic transplantation model and SOD1 knockout mice subcutaneous transplantation model were applied to explore the regenerative outcome of the xenograft.

ResultsRSG pretreatment significantly reduced the adverse effects of H2O2 on DFC with decreased intracellular ROS expression and alleviated mitochondrial damage. In vivo results confirmed RSG administration substantially enhanced the hosts antioxidant capacity with reduced osteoclasts formation and increased periodontal ligament like tissue regeneration efficiency, maximumly maintaining the xenograft function.

ConclusionsRSG preconditioning could preserve the biological properties of the transplanted stem cells under OS microenvironment and promote organ regeneration by attenuating the inflammatory reaction and OS injury.


title: Mechano-redox control of Mac-1 de-adhesion from ICAM-1 by protein disulfide isomerase promotes directional movement of neutrophils under flow

abstract: Macrophage-1 antigen or Mac-1 (CD11b/CD18, M{beta}2) is a leukocyte integrin essential for firm adhesion of neutrophils, lymphocytes and monocytes against flow when recruited to the endothelium. To migrate to the site of inflammation, leukocytes require coordinated adhesion and de-adhesion for directional movement. The vascular thiol isomerase, protein disulfide isomerase (PDI), was found by fluorescence microscopy to colocalize with high affinity Mac-1 at the trailing edge of stimulated neutrophils when adhered to ICAM-1 under fluid shear. From differential cysteine alkylation and mass spectrometry studies, PDI cleaves two allosteric disulfide bonds, C169-C176 and C224-C264, in the {beta}I domain of the {beta}2 subunit, and in mutagenesis and cell transfection studies, cleavage of the C224-C264 disulfide bond was shown to selectively control Mac-1 dis-engagement from ICAM-1 under fluid shear. Molecular dynamics simulations and binding of conformation-specific antibodies reveal that cleavage of the C224-C264 bond induces conformational change and mechanical stress in the {beta}I domain that allosterically alters exposure of an I domain epitope and shifts Mac-1 to a lower affinity state. From studies of neutrophil adherence to ICAM-1 under fluid shear, these molecular events promote neutrophil motility in the direction of flow at high shear stress. In summary, shear-dependent PDI cleavage of neutrophil Mac-1 C224-C264 disulfide bond triggers Mac-1 de-adherence from ICAM-1 at the trailing edge of the cell and enables directional movement of neutrophils during inflammation.

category: biochemistry


title: Novel assays monitoring direct glucocorticoid receptor protein activity exhibit high predictive power for ligand activity on endogenous gene targets

abstract: Exogenous glucocorticoids are widely used in the clinic for the treatment of inflammatory disorders and auto-immune diseases. Unfortunately, their use is hampered by many side effects and therapy resistance. Efforts to find more selective glucocorticoid receptor (GR) agonists and modulators (called SEGRAMs) that are able to separate anti-inflammatory effects via gene repression from metabolic effects via gene activation, have been unsuccessful so far. In this study, we characterized a set of functionally diverse GR ligands in A549 cells, first using a panel of luciferase-based reporter gene assays evaluating GR-driven gene activation and gene repression. We expanded this minimal assay set with novel luciferase-based read-outs monitoring GR protein levels, GR dimerization and GR Serine 211 (Ser211) phosphorylation status and compared their outcomes with compound effects on the mRNA levels of known GR target genes in A549 cells and primary hepatocytes. We found that luciferase reporters evaluating GR-driven gene activation and gene repression were not always reliable predictors for effects on endogenous target genes. Remarkably, our novel assay monitoring GR Ser211 phosphorylation levels proved to be the most reliable predictor for compound effects on almost all tested endogenous GR targets, both driven by gene activation and repression. The integration of this novel assay in existing screening platforms running both in academia and industry may therefore boost chances to find novel GR ligands with an actual improved therapeutic benefit.

category: pharmacology and toxicology


title: Membrane compartmentalization of Ect2/Cyk4/Mklp1 and NuMA/dynein/dynactin is essential for cleavage furrow formation during anaphase

abstract: In animal cells, spindle elongation during anaphase is temporally coupled with cleavage furrow formation. Spindle elongation during anaphase is regulated by NuMA/dynein/dynactin complexes that occupy the polar region of the cell membrane and are excluded from the equatorial membrane. How NuMA/dynein/dynactin are excluded from the equatorial membrane and the biological significance of this exclusion remains unknown. Here, we show that the centralspindlin (Cyk4/Mklp1) and its interacting partner RhoGEF Ect2 are required for NuMA/dynein/dynactin exclusion from the equatorial cell membrane. The Ect2-based (Ect2/Cyk4/Mklp1) and NuMA-based (NuMA/dynein/dynactin) complexes occupy mutually exclusive membrane surfaces during anaphase. The equatorial membrane enrichment of Ect2-based complexes is essential for NuMA/dynein/dynactin exclusion and proper spindle elongation. Conversely, NuMA-based complexes at the polar region of the cell membrane ensure spatially confined localization of Ect2-based complexes and thus RhoA. Overall, our work establishes that membrane compartmentalization of NuMA-based and Ect2-based complexes at the two distinct cell surfaces restricts dynein/dynactin and RhoA for coordinating spindle elongation with cleavage furrow formation.


title: Accounting for cis-regulatory constraint prioritizes genes likely to affect species-specific traits

abstract: Measuring differences in allele specific gene expression in hybrids between two different species is a powerful way to detect cis-regulatory changes underlying adaptation. However, these studies frequently identify thousands of differentially expressed genes. This makes it difficult to differentiate candidate genes most likely to explain interspecies phenotypic differences from genes whose expression levels diverge with little evolutionary constraint. Here we outline a simple strategy that leverages population-scale allele-specific RNA-seq data to identify genes that have constrained cis-regulation within species yet show divergence between species. By applying this strategy to data from human/chimpanzee hybrid cortical spheroids we identify signatures of lineage-specific selection on the expression of genes related to cellular proliferation, speech, glucose metabolism, and glycan degradation. In addition, we highlight human-derived differences in the expression of CUX1 and EDNRB that may contribute to differences in neural connectivity and brain size between humans and other primates.

category: evolutionary biology


title: Right Anterior Theta Connectivity Predicts Autistic Social Traits in Neurotypical Children

abstract: Growing evidence supports functional network alterations in autism spectrum disorder, however much less is known about the neural mechanisms underlying autistic traits in typically developing children. Using resting-state electroencephalographic (EEG) recordings, we examined whether functional connectivity could predict autistic trait expression in 127 children aged between 4-12 years. Regression models showed that right anterior theta connectivity was a significant predictor of autistic traits (p = 0.013), with increased connectivity in this region associated with greater autistic trait expression. These results corroborate similar recent findings in adults, extending this observation to a cohort of children spanning early-to-middle childhood. These findings further highlight EEG-derived functional connectivity as a sensitive physiological correlate of autistic trait expression in neurotypical children.

category: neuroscience


title: Neuroimaging within the Dominantly Inherited Alzheimer's Network (DIAN): PET and MRI

abstract: The Dominantly Inherited Alzheimer Network (DIAN) Observational Study is an international collaboration studying autosomal dominant Alzheimer disease (ADAD). This rare form of Alzheimer disease (AD) is caused by mutations in the presenilin 1 (PSEN1), presenilin 2 (PSEN2), or amyloid precursor protein (APP) genes. As individuals from these families have a 50% chance of inheriting the familial mutation, this provides researchers with a well-matched cohort of carriers vs non-carriers for case-control studies. An important trait of ADAD is that the age at symptom onset is highly predictable and consistent for each specific mutation, allowing researchers to estimate an individuals point in their disease time course prior to symptom onset. Although ADAD represents only a small proportion (approximately 0.1%) of all AD cases, studying this form of AD allows researchers to investigate preclinical AD and the progression of changes that occur within the brain prior to AD symptom onset. Furthermore, the young age at symptom onset (typically 30-60 years) means age-related comorbidities are much less prevalent than in sporadic AD, thereby allowing AD pathophysiology to be studied independent of these confounds. A major goal of the DIAN Observational Study is to create a global resource for AD researchers. To that end, the current manuscript provides an overview of the DIAN magnetic resonance imaging (MRI) and positron emission tomography (PET) protocols and highlights the key imaging results of this study to date.


title: Lagrangian Formalism in Biology: I. Standard Lagrangians and their Role in Population Dynamics

abstract: The Lagrangian formalism is developed for the population dynamics of interacting species that are described by several well-known models. The formalism is based on standard Lagrangians, which represent differences between the physical kinetic and potential energy-like terms. A method to derive these Lagrangians is presented and applied to selected theoretical models of the population dynamics. The role of the derived Lagrangians and the energy-like terms in the population dynamics is investigated and discussed. It is suggested that the obtained standard Lagrangians can be used to identify physical similarities between different population models.

category: ecology


title: Quantifying the capacity for assisted migration to achieve conservation and forestry goals under climate change

abstract: Many tree species might be threatened with extinction because they cannot disperse or adapt quickly enough to keep pace with climate change. One potential, and potentially risky, strategy to mitigate this threat is assisted migration, the intentional movement of species to facilitate population range shifts to more climatically suitable locations under climate change. The ability for assisted migration to minimize risk and maximize conservation and forestry outcomes depends on a multi-faceted decision process for determining, what, where, and how much to move. To quantify how the benefits and risks of assisted migration could affect the decision-making process, we used a dynamical vegetation model parameterized with 23 tree species in the western United States. We found that most of the modeled species are likely to experience a substantial decline in biomass, potentially facing regional extinction by 2100 under the high-emission SSP5-85 climate-change scenario. Though simulations show assisted migration had little effect on the forestry goal of total biomass across all species, its effects on the conservation goal of promoting individual species persistence were far more substantial. Among eight assisted migration strategies we tested that differ in terms of life cycle stage of movement and target destination selection criteria, the approach that conserved the highest biomass for individual species involved relocating target seedlings to areas with the highest canopy openness. Although this strategy significantly reduced extinction risk for six at-risk species compared to no action, it also slightly reduced biomass of four species, due to increasing competition. Species with relatively weak tolerance to drought, fire or high temperature were the most likely candidate groups for assisted migration. This model framework could be applied to other forest ecosystems to evaluate the efficacy of assisted migration globally.


title: Genomic demography of world's ethnic groups and their genomic identity between two individuals

abstract:
A genome-based grouping of worlds ethnic groups (EGs) is presented using a computational method developed for semantic analysis and categorization of books. For simplicity, we represent each individual as a "book" of all overlapping short strings of contextually-linked genotypes at all loci of Single Nucleotide Polymorphism, the most common type of individuals genomic variation. The study suggests that: (a) the EGs can be grouped into about 13 "genomic groups (GGs)"; (b) each GG consists of multiple EGs; (c) all African GGs emerged sequentially, followed by all non-African GGs, which emerged in a "burst" from the Middle East GG; and (d), at an individual level, approximately 99.8%, on average, of the whole genome contents are identical between any two individuals regardless of their GGs or EGs.

One Sentence SummaryAbout 99.8% of genome content is identical between two individuals among worlds ethnic populations in 13 genomic groups.


title: Development of a new 3D tracking system for multiple marmosets under free-moving conditions

abstract: Accurate assessment of social interactions in mammalian models are necessary to elucidate the pathogenesis of psychiatric and neurodegenerative diseases. The common marmoset (Callithrix jacchus) is a useful model for understanding the mechanisms of these disorders. However, behavioral measurements of free-moving group animals, including assessment of sociality have not been conducted. Here, we developed a new animal behavioral analysis system for three-dimensional (3D) trajectory and behavior of free-moving individuals. Each marmoset was identified using deep learning facial recognition (accuracy [≥] 97%). Their trajectories were tracked independently by combining video, 3D coordinates detected by light detection and ranging (lidar) systems, and facial identification. Location preferences and distances between individuals were calculated using the 3D trajectories and grooming behavior was detected by deep learning. This novel system will allow the quantification of individual captive animals within groups, facilitating the quick and automatic measurement of social behavior, and enhancing development of objective behavioral indices.

category: animal behavior and cognition


title: DTSyn: a dual-transformer-based neural network to predict synergistic drug combinations

abstract: Drug combination therapies are superior to monotherapy for cancer treatment in many ways when addressing tumor heterogeneity issue. For wet-lab experiment, screening out novel synergistic drug pairs is challenging due to the enormous searching space of possible drug pairs. Thus, computational methods have been developed to predict drug pairs with potential synergistic function. Notwithstanding the success of current models, the power of generalization to other datasets as wells as understanding of mechanism for chemical-chemical interaction or chemical-sample interaction are lack of study, hindering current algorithms from real application. In this paper, we proposed a deep neural model termed DTSyn (Dual Transformer model for drug pair Synergy prediction) based on multi-head attention mechanism to identify novel drug combinations. We designed a fine-granularity transformer for capturing chemical substructure-gene and gene-gene associations and a coarse-granularity transformer for extracting chemical-chemical and chemical-cell line interactions. DTSyn achieves highest Receiver operating characteristic area under curve (ROC AUC) of 0.73, 0.78. 0.82 and 0.81 on four different cross validation tasks, outperforming all competing methods. Further, DTSyn achieved best True Positive Rate (TPR) over five independent datasets. The ablation study showed that both transformer blocks contributed to the performance of DTSyn. In addition, DTSyn can extract interactions among chemicals and cell lines, which may represent the mechanisms of drug action. Thus, we envision our model a valuable tool to prioritize synergistic drug pairs by utilizing chemicals and transcriptome data.

category: bioinformatics


title: Pain as a Trigger for Epigenetic Modifications in Limbic Circuitry

abstract: Chronic pain involves both central and peripheral neuronal plasticity that encompasses changes in the brain, spinal cord, and peripheral nociceptors. Within the forebrain, mesocorticolimbic regions associated with emotional regulation have recently been shown to exhibit enduring gene expression changes in models of chronic pain. To better understand how such enduring transcriptional changes might be regulated within brain structures associated with processing of pain or affect, we examined epigenetic modifications associated with active or permissive transcriptional states (histone H3 lysine 4 mono and trimethylation, and histone H3 lysine 27 acetylation) in periaqueductal gray, lateral hypothalamus, nucleus accumbens, and ventral tegmental area five weeks after sciatic nerve injury to model chronic pain. For mice in chronic pain, we observed an overall trend for a reduction of these epigenetic markers in the periaqueductal gray, lateral hypothalamus, and nucleus accumbens, but not the ventral tegmental area. Moreover, we discovered that some epigenetic modifications exhibited changes associated with pain history, while others were associated with individual differences in pain sensitivity. When taken together, these results suggest that chronic pain may lead to a suppression of transcription and gene expression in key limbic brain structures and circuits, which may ultimately result in maladaptive plasticity within these systems.


title: Patient-derived recombinant autoantibodies reveal the subcellular neuroglial distribution and heterogeneous interactome of leucine-rich glioma-inactivated 1

abstract: Autoantibodies against leucine-rich glioma-inactivated 1 (LGI1) occur in patients with encephalitis who present with frequent focal seizures and a pattern of amnesia consistent with focal hippocampal damage. To investigate whether the cellular and subcellular distribution of LGI1 may explain the localisation of these features, and gain broader insights into LGI1 neurobiology, we analysed the detailed localisation of LGI1, and the diversity of its protein interactome, in mouse brains using recombinant monoclonal LGI1-antibodies derived from encephalitis patients. Combined immunofluorescence and mass spectrometry analyses showed that LGI1 is enriched in excitatory and inhibitory synaptic contact sites, most densely within CA3 regions of the hippocampus. LGI1 is secreted in both neuronal somatodendritic and axonal compartments, and occurs in oligodendrocytic, neuro- oligodendrocytic and astro-microglial protein complexes. Proteomic data support the hypothesis that destabilization of Kv1 / MAGUK complexes by autoantibodies could promote excitability, but did not reveal LGI1 complexes with postsynaptic glutamate receptors. Our results extend our understanding of regional, cellular and subcellular LGI1 expression profiles and reveal novel LGI1-associated complexes, thus providing insights into the complex biology of LGI1 and its relationship to seizures and memory loss.


title: Focal Non-invasive Deep-brain Stimulation with Temporal Interference for the Suppression of Epileptic Biomarkers

abstract:
Neurostimulation applied from deep brain stimulation (DBS) electrodes is an effective therapeutic intervention in patients suffering from intractable drug-resistant epilepsy when resective surgery is contraindicated or failed. Inhibitory DBS to suppress seizures and associated epileptogenic biomarkers could be performed with high-frequency stimulation (HFS), typically between 100 -165Hz, to various deep-seated targets such as for instance the Mesio-temporal lobe (MTL) which leads to changes in brain rhythms, specifically in the hippocampus. The most prominent alterations concern high-frequency oscillations (HFOs), namely increase in ripples, a reduction in pathological Fast Ripples (FRs), and a decrease in pathological interictal epileptiform discharges (IEDs). In the current study, we use Temporal Interference stimulation to provide a non-invasive focal DBS (130 Hz) of the MTL, specifically the hippocampus, which increases physiological ripples, and decreases the number of FRs and IEDs in a mouse model of epilepsy. Similarly, we show the inability of 130 Hz transcranial current stimulation (TCS) to achieve similar results. The method could potentially revolutionize how DBS, certainly in epilepsy, is performed, and we therefore further demonstrate the translatability to human subjects via measurements of the TI stimulation vs TCS in human cadavers. Results show the better penetration of TI fields into the human hippocampus as compared with TCS. Finally, we provide evidence of the efficacy of the specific form of Pulse-width Modulated TI (PWM-TI), implemented with square waves, which is used in this study.

One Sentence SummaryA non-invasive deep brain stimulation applied via temporal interference achieves the suppression of biomarkers of epilepsy in mice and is scaled to humans.


title: Sleep spindles favor emotion regulation over memory consolidation of stressors in PTSD

abstract: Posttraumatic stress disorder (PTSD) is a trauma-induced debilitating condition, with symptoms that revolve around a declarative memory of a severe stressor. How does the brain process declarative and emotional information of stressors in PTSD? We evaluated the role of NREM sleep spindles in this process after exposure to laboratory stress, in a cohort of human subjects with different levels of PTSD symptoms. Subjects performed two laboratory visits: 1) a stress visit which involved exposure to negatively-valent images in the morning and 2) a control visit. In both visits subjects had a sleep/nap opportunity in the afternoon monitored via electroencephalography (EEG). In the stress visit, self-reported anxiety confirmed elevated stress immediately after stressor exposure (pre-sleep) that decayed to control levels post-sleep. An image recall session took place in the late afternoon. Overall, NREM2 spindle rates were elevated in the stress visit as compared to the control visit. This increase in NREM2 spindle rates, especially over occipital cortex, was significantly greater in subjects with high vs. low PTSD symptoms. However in high-PTSD subjects, NREM2 spindle rates correlated with poorer recall accuracy of stressor images as compared to lower symptomatic individuals while surprisingly correlating with a greater reduction in anxiety levels across sleep. Thus although NREM2 spindles are known to play a role in declarative memory processes, our findings highlight an important role of NREM sleep in favoring sleep-dependent anxiety regulation over memory consolidation after exposure to stressors in PTSD and shed new light on the function of NREM2 spindles in PTSD.


title: Application of B cell immortalization for the isolation of antibodies and B cell clones from vaccine and infection settings

abstract: The isolation and characterization of neutralizing antibodies from infection and vaccine settings will inform future vaccine design, and methodologies that streamline the isolation of antibodies and the generation of B cell clones are of great interest. Retroviral transduction to express Bcl-6 and Bcl-xL in primary B cells has been shown to promote long-term B cell survival and antibody secretion in vitro, and can be used to isolate antibodies from memory B cells. The application of this methodology to B cell subsets from tissues and to B cells from individuals with chronic infection has not been extensively characterized. Here, we characterize Bcl-6/Bcl-xL B cell immortalization across multiple tissue types and B cell subsets in healthy and HIV-1 infected individuals, as well as individuals recovering from malaria. In HIV-1- and malaria-uninfected donors, naive and memory B cell subsets from PBMC and tonsil tissue transformed with similar efficiencies, and displayed similar characteristics after transformation with respect to their longevity and immunoglobulin secretion. In HIV-1-viremic individuals or in individuals after malaria infection, the CD27-CD21- memory B cell subsets transformed with lower efficiencies compared to the CD27+CD21+ populations, but following transformation B cells expanded and secreted IgG with similar efficiency. Using B cells from HIV-1-infected individuals, we combined Bcl-6/Bcl-xL B cell immortalization with a HIV-1 microneutralization assay to isolate broadly neutralizing antibodies related to VRC13 and VRC38.01. Overall, Bcl-6/Bcl-xL B cell immortalization can be used to isolate antibodies and generate B cell clones from multiple different B cell populations, albeit with different efficiencies.

category: immunology


title: The human placenta dictates the phenotype of decidual macrophages.

abstract:
During human pregnancy, placenta-derived extravillous trophoblasts (EVT) invade the decidua and communicate with maternal immune cells. The decidua can be distinguished into basalis (decB) and parietalis (decP), the latter being unaffected by placentation. By defining a novel gating strategy, we report accumulation of myeloid cells in decB. We identified a decidua basalis-associated macrophage (decBAM) population with a differential transcriptome and secretome when compared to decidua parietalis-associated macrophages (decPAMs). decBAMs are CD11chi and efficient inducers of Tregs, proliferate in situ and secrete high levels of CXCL1, CXCL5, M-CSF, and IL-10. In contrast, decPAMs exert a dendritic cell-like, motile phenotype characterized by induced expression of HLA class II molecules, enhanced phagocytosis, and the ability to activate T cells. Strikingly, EVT-conditioned media are able to convert decPAMs into a decBAM phenotype. Cumulatively, these findings assign distinct macrophage phenotypes to decidual areas depending on placentation and further highlight a critical role for EVTs in the induction of pregnancy-tolerant macrophage polarization.

O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=131 SRC="FIGDIR/small/486171v2_ufig1.gif" ALT="Figure 1">
View larger version (37K):
org.highwire.dtl.DTLVardef@1f96eb8org.highwire.dtl.DTLVardef@d3f725org.highwire.dtl.DTLVardef@6caaborg.highwire.dtl.DTLVardef@1e3dd16_HPS_FORMAT_FIGEXP  M_FIG C_FIG In this study we identified so far unrecognized, placenta-dictated immune responses at the maternal-fetal interface. Altogether we imply that placenta-derived trophoblasts induce a pregnancy-tolerant phenotype by suppressing antigen presenting cell-like functions in maternal tissue macrophages.


title: A machine learning method for estimating the probability of presence using presence-background data

abstract: Estimating the prevalence or the absolute probability of presence of a species from presence-background data has become a controversial topic in species distribution modelling. In this paper we propose a new method by combining both statistics and machine learning algorithms that helps overcome some of the known existing problems. We have also revisited the popular but highly controversial Lele and Keim (LK) method by evaluating its performance and assessing the RSPF condition it relies on. Simulations show that the LK method with unfounded model assumptions would render fragile estimation/prediction of the desired probabilities. Rather we propose the local knowledge condition, which relaxes the pre-determined population prevalence condition that has so often been used in much of the existing literature. Simulations demonstrate the performance of the CLK method utilising the local knowledge assumption to successfully estimate the probability of presence. The local knowledge extends the local certainty or the prototypical presence location assumption, and has significant implications for demonstrating the necessary condition for identifying absolute (rather than relative) probability of presence without absence data in species distribution modelling.


title: Sex differences in allometry for phenotypic traits indicate that females are not scaled males

abstract: Sex differences in the lifetime risk and expression of disease are well-known. Paradoxically, preclinical research targeted at improving treatment, increasing health span and reducing the financial burden of health care, has mostly been conducted on male animals and cells. Females are assumed to be the same or scaled versions of males, yet sex differences in the allometric relationship between phenotypic traits and body size, needed to evaluate the validity of this assumption, have not been established. We quantify allometry for 297 phenotypic traits in male and female mice, recorded in >2.1 million measurements from the International Mouse Phenotyping Consortium. We find sex differences in allometric parameters (slope, intercept, residual SD) are common. Thus, the allometric relationship varies between the sexes: females are not scaled males. Our results support a complex, trait-specific patterning of sex differences in phenotypic traits, promoting case-specific approaches to therapeutic intervention and drug dosage scaled by body weight.


title: High-density mapping of QTL controlling agronomically important traits in quinoa (Chenopodium quinoa Willd.)

abstract:
Quinoa is a pseudocereal originating from the Andean regions. In spite of quinoas long cultivation history, genetic analysis of this crop is still in its infancy. We aimed to localize QTL contributing to the phenotypic variation of agronomically important traits. We crossed the Chilean accession PI-614889 and the Peruvian accession CHEN-109, which depicted significant differences in days to flowering, days to maturity, plant height, panicle length, thousand kernel weight (TKW), saponin content, and mildew susceptibility. We observed sizeable phenotypic variation across F2 plants and F3 families grown in the greenhouse and in the field, respectively. We used Skim-seq to genotype the F2 population and constructed a high-density genetic map with 133,923 SNPs. Fifteen QTL were found for ten traits. Two significant QTL, common in F2 and F3 generations, depicted pleiotropy for days to flowering, plant height, and TKW. The pleiotropic QTL harbored several putative candidate genes involved in photoperiod response and flowering time regulation. This study presents the first high-density genetic map of quinoa that incorporates QTL for several important agronomical traits. The pleiotropic loci can facilitate marker assisted selection in quinoa breeding programs.

Key messageSkim-sequencing enabled the construction a high-density genetic map (133,923 SNPs) and fifteen QTL were detected for ten agronomically important traits.

category: genetics


title: Acoustic signatures in cavefish populations inhabiting different caves

abstract: Complex patterns of acoustic communication exist throughout the animal kingdom, including underwater. The river-dwelling and the Pachon cave-adapted morphs of the fish Astyanax mexicanus share a repertoire of sounds, but their trigger, use and meaning has changed in cavefish after their recent colonization of the subterranean environment. Here, we explored whether and how sounds produced by blind cavefishes inhabiting different Mexican caves may have evolved, too. We compared acoustic parameters of sounds produced by wild cavefish, recorded in their natural settings, in six different caves located in three mountains ranges in North-East Mexico. Multi-parametric analyses show that the six cavefish populations sampled present cave-specific acoustic signatures, as well as possible individual signatures. The variations in acoustic parameters do not seem related to fish phenotypes, phylogeography or ecological conditions. We propose that the evolution of such acoustic signatures would be neutral and occur by drift, progressively leading to the differentiation of local accents that may prevent interbreeding and thus contribute to speciation.


title: The growth rate of DNA condensate droplets increases with the size of participating subunits

abstract: Liquid-liquid phase separation (LLPS) is a common phenomenon underlying the formation of dynamic membraneless organelles in biological cells, which are emerging as major players in controlling cellular functions and health. The bottom-up synthesis of biomolecular liquid systems with simple constituents, like nucleic acids and peptides, is useful to understand LLPS in nature as well as to develop programmable means to build new amorphous materials with properties matching or surpassing those observed in natural condensates. In particular, understanding which parameters determine condensate growth kinetics is essential for the synthesis of condensates with the capacity for active, dynamic behaviors. Here we use DNA nanotechnology to study artificial liquid condensates through programmable star-shaped subunits, focusing on the effects of changing subunit size. First, we show that LLPS is achieved in a six-fold range of subunit size. Second, we demonstrate that the rate of growth of condensate droplets scales with subunit size. Our investigation is supported by a general model that describes how coarsening and coalescence are expected to scale with subunit size under ideal assumptions. Beyond suggesting a route toward achieving control of LLPS kinetics via design of subunit size in synthetic liquids, our work suggests that particle size may be a key parameter in biological condensation processes.

category: bioengineering


title: Boquila: NGS read simulator to eliminate read nucleotide bias in sequence analysis

abstract: Sequence content is heterogeneous throughout genomes. Therefore, Genome-wide NGS reads biased towards specific nucleotide profiles are affected by the genome-wide heterogeneous nucleotide distribution. Boquila generates sequences that mimic the nucleotide profile of true reads, which can be used to correct the nucleotide-based bias of genome-wide distribution of NGS reads. Boquila can be configured to generate reads from only specified regions of the reference genome. It also allows the use of input DNA sequencing to correct the bias due to the copy number variations in the genome. Boquila uses standard file formats for input and output data, and it can be easily integrated into any workflow for high-throughput sequencing applications.


title: Transcriptional dynamics of colorectal cancer risk associated variation at 11q23.1 are correlated with tuft cell abundance and marker expression in silico

abstract: Colorectal cancer (CRC) is characterised by heritable risk that is not well understood. Heritable, genetic variation at 11q23.1 is associated with increased colorectal cancer (CRC) risk, demonstrating eQTL effects on 3 cis- and 23 trans-eQTL targets. We sought to determine the relationship between 11q23.1 cis- and trans-eQTL target expression and test for potential cell-specificity. scRNAseq from 32,361 healthy colonic epithelial cells was aggregated and subject to weighted gene co-expression network analysis (WGCNA). One module (blue) included 19 trans-eQTL targets and was correlated with C11orf53 expression only. Following unsupervised clustering of single cells, the expression of 19 trans-eQTL targets was greatest and most variable in cluster number 11, which transcriptionally resembled tuft cells. 14 trans-eQTL targets were found to demarcate this cluster, 11 of which were corroborated in a second dataset. Intra-cluster WGCNA and module preservation analysis then identified twelve 11q23.1 trans-eQTL targets to comprise a network that was specific to cluster 11. Finally, linear modelling and differential abundance testing showed 11q23.1 trans-eQTL target expression was predictive of cluster 11 abundance. Our findings suggest 11q23.1 trans-eQTL targets comprise a C11orf53-related network that is likely tuft cell-specific and reduced expression of these genes correlates with reduced tuft cell abundance in silico.


title: Imputation of Low-density Marker Chip Data in Plant Breeding: Evaluation of Methods Based on Sugar Beet

abstract:
Low-density genotyping followed by imputation reduces genotyping costs while still providing high-density marker information. An increased marker density has the potential to improve the outcome of all applications that are based on genomic data. This study investigates techniques for 1k to 20k genomic marker imputation for plant breeding programs with sugar beet as an example crop, where these are realistic marker numbers for modern breeding applications.

The generally accepted  gold standard for imputation, Beagle 5.1, was compared to the recently developed software AlphaPlantImpute2 which is designed specifically for plant breeding. For Beagle 5.1 and AlphaPlantImpute2, the imputation strategy as well as the imputation parameters were optimized in this study. We found that the imputation accuracy of Beagle could be tremendously improved (0.22 to 0.67) by tuning parameters, mainly by lowering the values for the parameter for the effective population size and increasing the number of iterations performed. Separating the phasing and imputation steps also improved accuracies when optimized parameters were used (0.67 to 0.82). We also found that the imputation accuracy of Beagle decreased when more low-density lines were included for imputation. AlphaPlantImpute2 produced very high accuracies without optimization (0.89) and was generally less responsive to optimization. Overall, AlphaPlantImpute2 performed relatively better for imputation while Beagle was better for phasing. Combining both tools yielded the highest accuracies.

SummaryGenotype marker information allows the prediction of an individuals breeding value without the need to observe its actual phenotype which can accelerate the breeding progress. The more markers are genotyped, the better the genomic prediction may be. However, analyzing many markers is costly, particularly in commercial breeding programs where thousands of new individuals are genotyped. A solution to obtain information for all markers, while spending comparatively little on genotyping, is to genotype only a small fraction of markers in most individuals. Together with high-density information on other individuals, the low-density individuals can be imputed to high-density. High-density individuals are typically parents or highly influential individuals.

In this study, we compare the widely used software Beagle with the recently developed software AlphaPlantImpute2 on plant breeding data. To allow a fair comparison, we first optimized existing methods and developed new approaches. This was done to avoid comparing results of a less ideal version of one software to optimized settings of another software. After optimization, the software were evaluated in different scenarios with regards to genotyping errors, population types and number of markers based on simulated data. Simulated data were based on real marker data from a sugar beet population as input to mimic the population history of a commercial breeding population.

AlphaPlantImpute2 performs well with default parameters, while much optimization with regards to parameters and strategy was needed to boost accuracies of Beagle. A pipeline is presented which uses Beagle for phasing and AlphaPlantImpute2 for imputation. This pipeline yielded the highest accuracies and shortest run time.

Core IdeasBeagle is sensitive to parameter tuning

Best imputation accuracies could be achieved by using a combination of Beagle and AlphaPlantImpute2

The population structure influence imputation accuracy


title: Optimal inference of molecular interactions in live FRET imaging

abstract: Intensity-based live-cell fluorescence resonance energy transfer (FRET) imaging converts otherwise unobservable molecular interactions inside cells into fluorescence time-series signals. However, inferring the degree of molecular interactions from these observables is challenging, due to experimental complications such as spectral crosstalk, photobleaching, and measurement noise. Conventional methods solve this inverse problem through algebraic manipulations of the observables, but such manipulations inevitably accumulate measurement noise, limiting the scope of FRET analysis. Here, we introduce a Bayesian inference framework, B-FRET, which estimates molecular interactions from FRET data in a statistically optimal manner. B-FRET requires no additional measurements beyond those routinely conducted in standard 3-cube FRET imaging methods, and yet, by using the information contained in the data more efficiently, dramatically improves the signal-to-noise ratio (SNR). We validate B-FRET using simulated data, and then apply it to FRET data measured from single bacterial cells, a system with notoriously low SNR, to reveal signaling dynamics that are otherwise hidden in noise.

category: biophysics


title: Effects of taurine in mice and zebrafish behavioral assays with translational relevance to schizophrenia

abstract:
BackgroundAltered redox state and developmental abnormalities in glutamatergic and GABAergic transmission during development are linked to the behavioral changes associated with schizophrenia. As an amino acid that exerts antioxidant and inhibitory actions in the brain, taurine is a potential candidate to modulate biological targets relevant to this disorder. Here, we investigated in mice and zebrafish assays whether taurine prevents the behavioral changes induced by acute administration of MK-801 (dizocilpine), a glutamate NMDA receptor antagonist.

MethodsC57BL/6 mice were intraperitoneally administered with saline or taurine (50, 100 and 200 mg/kg) followed by MK-801 (0.15 mg/kg). Locomotor activity, social interaction and prepulse inhibition of the acoustic startle reflex were then assessed in different sets of animals. Zebrafish were exposed to tank water or taurine (42, 150 and 400 mg/L) followed by MK-801 (5 M); social interaction and locomotor activity were evaluated in the same test.

ResultsMK-801 induced hyperlocomotion and disrupted sensorimotor gating in mice; in zebrafish, it reduced sociability while increased locomotion. Taurine was mostly devoid of effects and did not counteract NMDA antagonism in mice or zebrafish.

DiscussionContradicting previous clinical and preclinical data, taurine did not show antipsychotic-like effects in the present study. However, it still warrants consideration as a preventive intervention in animal models of relevance to the prodromal phase of schizophrenia; further studies are thus necessary to evaluate whether and how taurine might benefit patients.


title: Toward a first principles understanding of the activation and deactivation mechanisms of class A G-protein coupled receptors and voltage-gated cation channels

abstract: We previously reported a first principles multi-scale theory called Biodynamics that attributes cellular functions to sets of coupled molecular and ionic fluxes operating in the non-equilibrium/non-linear dynamic regime. Fluxes build and decay over time and undergo dynamic non-covalent intra- and intermolecular state transitions powered principally by the storage and release of free energy to/from the H-bond networks of external and internal solvation (that we refer to as solvation dynamics) at rates governed by the desolvation and resolvation costs incurred during their entry and exit, respectively. We have thus far examined the functional state transitions of cereblon and COVID Mpro in this context, and now turn to the agonist-induced activating and deactivating state transitions of class A G-protein coupled receptors (GPCRs) and membrane potential-/dipole potential-induced activating and deactivating state transitions of voltage-gated cation channels (VGCCs). We analyzed crystal structures of the activated and deactivated forms of the human {beta}2 adrenergic receptor ({beta}2AR) and cryo-EM structures of the activated and deactivated forms of Nav1.7 channels. We postulate that activation and deactivation of the {beta}2AR is conveyed by switchable changes in transmembrane helix (TMH) orientations relative to extracellular loop 2 (ECL2) and curvature of TMH6 and TMH7, all of which are powered by solvation free energy and kickstarted by agonist binding. The known activation and deactivation mechanisms of Nav1.7 consist of S4 translations toward and away from the extracellular membrane surface, respectively, resulting in S4-S5 linker repositioning, followed by rearrangements of the S5 and S6 helices. The latter TMH conveys channel opening and closing by respectively curving away from and toward the central pore axis. We postulate that all of these rearrangements are likewise powered by solvation free energy and kickstarted by changes in the membrane and dipole potentials. The results of our study may facilitate structure-based design of GPCR agonists/antagonists and mitigation of drug-induced ion channel blockade.


title: Enhanced performance in perceptual decision making task without deprivation in mice using medial forebrain bundle stimulation

abstract: Training animals on perceptual decision making tasks is essential to many fields of neuroscience. Current protocols generally use water as a reward in water-deprived animals. This can be challenging since it requires balancing animals deprivation level with their well-being. Moreover, trial number is limited once they reach satiation. Here, we present electrical stimulation of the medial forebrain bundle (MFB) as an alternative reward in mice that avoids deprivation entirely while yielding stable motivation for thousands of trials. We conducted a comparison of MFB rewarded and water-deprived animals on two auditory discrimination tasks of increasing difficulty. MFB rewarded mice learnt the hard task faster and with higher overall accuracy levels than their water-deprived counterparts. Moreover, they performed up to 4600 trials within a session without loss of motivation. Importantly, MFB stimulation does not impact the sensory behaviour under study since psychometric parameters and response times are preserved. Finally, in accordance with the lack of deprivation, MFB mice lack signs of metabolic or behavioural stress compared to water-deprived mice (open field, home cage behaviour). Overall, using MFB stimulation as a reward is a highly promising tool for task learning since it enhances task performance whilst avoiding deprivation.


title: Large scale in vivo acquisition, segmentation and 3D reconstruction of cortical vasculature using functional ultrasound imaging.

abstract: The brain is composed of a dense and ramified vascular network comprising various sizes of arteries, veins, and capillaries. One way to assess the risk of cerebrovascular pathologies is to use computational models to predict the physiological effects of a reduction of blood supply and correlate these responses with observations of brain damage. Therefore, it is crucial to establish a detailed 3D organization of the brain vasculature, which could be used to develop more accurate in silico models. For this purpose, we have adapted our open-access functional ultrasound imaging platform previously designed for recording brain-wide activity that is now capable of fast and reproducible acquisition, segmentation, and reconstruction of the cortical vasculature. For the first time, it allows us to digitize the cortical vasculature in awake rodents with a [~]100 {micro}m3 spatial resolution. Contrary to most available strategies, our approach can be performed in vivo within minutes. Moreover, it is easy to implement since it neither requires exogenous contrast agents nor long post-processing time. Hence, we performed a cortex-wide reconstruction of the vasculature and its quantitative analysis, including i) classification of descending arteries versus ascending veins in more than 1500 vessels/animal, ii) quick estimation of their length. Importantly, we confirmed the relevance of our approach in a model of cortical stroke, which enables quick visualization of the ischemic lesion. This development contributes to extending the capabilities of ultrasound neuroimaging to understand better cerebrovascular pathologies such as stroke, vascular cognitive impairment, and brain tumors and is highly scalable for the clinic.


title: Large scale in vivo acquisition, segmentation, and 3D reconstruction of cortical vasculature using open-source functional ultrasound imaging platform


title: Reanalysis of double EphA3 knockin maps in mouse shows the importance of chemoaffinity in topographic map formation

abstract: Double visual maps in the EphA3 knockin mouse have been used extensively to investigate the mechanisms for the formation of ordered nerve connections. Here, EphA3+ and EphA3-retinal ganglion cells, forming a mosaic, each make a separate map on the superior colliculus. We constructed ordered 2D maps from EphA3 knockin Fourier-based intrinsic imaging data. Over both EphA3+/- and EphA3+/+ genotypes, the extent and location in the visual field of each projection of a double map vary considerably. Aided by computer modelling results, we suggest that all EphA3 knockin maps are examples of a single type, with the amount of EphA3 in EphA3+ retinal cells varying between animals. Previous analysis of the same dataset suggested that EphA3+/- maps represent an unstable transition between single (wild type) and double (EphA3+/+) maps, reflecting a balance between molecular and electrical signalling. In contrast, our analysis highlights the importance of molecular-based cues in establishing the retinotopic map.


title: Immune chromatin reader SP140 regulates microbiota and risk for inflammatory bowel disease

abstract: Inflammatory bowel disease (IBD) is driven by host genetics and environmental factors, including commensal microorganisms. Epigenetics facilitate integration of environmental cues for transcriptional output. However, evidence of epigenetic dysregulation directly causing host-commensal dysbiosis and IBD is lacking. Speckled Protein 140 (SP140) is an immune-restricted chromatin  reader with homology to Autoimmune Regulator (AIRE). SP140 mutations associate with three immune diseases: Crohns disease (CD), multiple sclerosis (MS) and chronic lymphocytic leukemia (CLL), but disease-causing mechanisms remain undefined. Here we identify a critical immune-intrinsic role for SP140 in preventing expansion of inflammatory Proteobacteria, including Helicobacter in mice and Enterobacteriaceae in humans. Mice harboring altered microbiota due to hematopoietic Sp140 deficiency exhibited severe colitis which was transmissible upon co-housing and ameliorated with antibiotics. SP140 was critical for calibration of macrophage microbicidal responses required for normal host-commensal crosstalk and elimination of invasive pathogens. Mutations within this epigenetic reader may constitute a predisposing event in human diseases provoked by the microbiome, such as IBD and MS.


title: Correlative SIP-FISH-SEM-Raman-NanoSIMS links identity, morphology, biochemistry, and physiology of environmental microbes

abstract: Microscopic and spectroscopic techniques are commonly applied to study microbial cells but are typically used on separate samples, resulting in population-level datasets that are integrated across different cells with little spatial resolution. To address this shortcoming, we developed a workflow that correlates several microscopic and spectroscopic techniques to generate an in-depth analysis of individual cells. By combining stable isotope probing (SIP), fluorescence in situ hybridization (FISH), scanning electron microscopy (SEM), confocal Raman microspectroscopy (Raman), and nano-scale secondary ion mass spectrometry (NanoSIMS), we illustrate how individual cells can be thoroughly interrogated to obtain information about their taxonomic identity, structure, physiology, and metabolic activity. Analysis of an artificial community demonstrated that our correlative approach was able to resolve the activity of single cells using heavy water SIP in conjunction with Raman and/or NanoSIMS and establish their taxonomy and morphology using FISH and SEM. We then applied this workflow to a sample of yet uncultured multicellular magnetotactic bacteria. In addition to establishing their identity and activity, backscatter electron microscopy (BSE), NanoSIMS, and energy-dispersive X-ray spectroscopy (EDS) were employed to characterize the magnetosomes within the cells. By integrating these techniques, we demonstrate a cohesive approach to thoroughly study environmental microbes at single cell resolution.

category: microbiology


title: Acinetobacter baumannii sampled from cattle and pigs represent novel clones

abstract: Acinetobacter baumannii is a very important human pathogen. Nonetheless, we know very little about non-human isolates of A. baumannii. Here we determine the genomic identity of 15 cattle and pig isolates, as well their antibiotic and virulence genetic determinants, and compare them to the main human clinical international clones.


title: Transcriptomics, Regulatory Syntax, and Enhancer Identification in Heterogenous Populations of Mesoderm-Induced ESCs at Single-Cell Resolution

abstract: ESCs can adopt lineage-specific gene expression programs by stepwise exposure to defined factors, resulting in the generation of functional cell types. Bulk and single cell-based assays were employed to catalogue gene expression, histone modifications, chromatin conformation, and accessibility transitions in ESC populations and individual cells acquiring a presomitic mesoderm fate and undergoing further lineage specification. These assays identified cis-regulatory regions and transcription factors presiding gene expression programs occurring at defined ESC transitions and revealed the presence of heterogeneous cell populations within discrete ESC developmental stages. The datasets were employed to identify previously unappreciated genomic elements directing the initial activation of Pax7 and myogenic and neurogenic gene expression programs. This study provides a resource for the discovery of genomic and transcriptional features of pluripotent, mesoderm-induced ESCs, and ESCs-derived cell lineages.

category: developmental biology


title: Generation of raptor diversity in Europe: linking speciation to climate changes and the ability to migrate

abstract:
AimEurope should be considered as a diversity hotspot for diurnal raptors, but just during the breeding season, as it holds the higher proportion of transcontinental migratory species of any landmass, and the area becomes depleted during the winter period. This study will test the hypothesis that the high diversification of the raptor assemblage in Europe is a recent event, occurring mainly during the Quaternary, and that closely related species sharing the same trophic niches can only coexist in sympatry during the breeding period, when food availability is higher.

LocationContinental Europe.

TaxonDiurnal birds of prey (Accipitriformes and Falconiformes).

MethodsA consensus molecular phylogeny for the 38 regular breeding species of raptors in Europe was obtained from BirdTree. For the same species, a trophic niche cluster dendrogram was constructed. Size and migratory strategy were introduced in the resulting phylogeny, where trophic groups were also identified.

ResultsA total of 16 trophic groups were identified. Multispecific trophic groups tended to be composed of reciprocal sister species, while monospecific groups (only three) were composed of highly specialized species. According to time calibrated phylogenies, the speciation events took place during the glacial cycles of the Quaternary period in a majority of cases. During the non-breeding season, the smaller species in every trophic group migrate to sub-Saharan Africa, whereas larger species are either non-migratory or perform shorter migrations within Europe and/or northern Africa.

Main conclusionsThis investigation illustrates how the rich assemblage of diurnal birds of prey in Europe, more diverse and more migratory than the North American assemblage at equivalent latitudes, has emerged recently due to the multiplication of look-alike species with similar trophic ecologies, mainly in climate refugia during cold periods. In the non-breeding season, when shared food resources are limited, smaller species migrate to Africa and alleviate competition.


title: Do amplifiers of selection maximise average fitness?

abstract: Evolutionary dynamics on graphs has remarkable features: For example, it has been shown that amplifiers of selection exist that - compared to an unstructured population - increase the fixation probability of advantageous mutations, while they decrease the fixation probability of disadvantageous mutations. So far, the theoretical literature has focused on the case of a single mutant entering a graph structured population, asking how the graph affects the probability that a mutant takes over a population and the time until this typically happens. For continuously evolving systems, the more relevant case is when mutants constantly arise in an evolving population. Typically, such mutations occur with a small probability during reproduction events. We thus focus on the low mutation rate limit. The probability distribution for the fitness in this process converges to a steady-state at long times. Intuitively, amplifiers of selection are expected to increase the populations mean fitness in the steady-state. Similarly, suppressors of selection are expected to decrease the populations mean fitness in the steady-state. However, we show that another category of graphs, called suppressor of fixation, can attain the highest population mean fitness. The key reason behind this is their ability to efficiently reject deleterious mutants. This illustrates the importance of the deleterious mutant regime for the long-term evolutionary dynamics, something that seems to have been overlooked in the literature so far.


title: Phylogenomics Illuminates the Evolutionary History of Wild Silkmoths in Space and Time (Lepidoptera: Saturniidae)

abstract: AO_SCPLOWBSTRACTC_SCPLOWWild silkmoths (Saturniidae) are one of the most emblematic and most studied families of moths. Yet, the absence of a robust phylogenetic framework based on a comprehensive taxonomic sampling impedes our understanding of their evolutionary history. We analyzed 1,024 ultraconserved elements (UCEs) and their flanking regions to infer the relationships among 338 species of Saturniidae representing all described subfamilies, tribes, and genera. We investigated systematic biases in genomic data and performed dating and historical biogeographic analyses to reconstruct the evolutionary history of wild silkmoths in space and time. Using Gene Genealogy Interrogation, we showed that saturation of nucleotide sequence data blurred our understanding of early divergences and first biogeographic events. Our analyses support a Neotropical origin of saturniids, shortly after the Cretaceous-Paleogene extinction event (ca 64.0 [stem] - 52.0 [crown] Ma), and two independent colonization events of the Old World during the Eocene, presumably through the Bering Land Bridge. Early divergences strongly shaped the distribution of extant subfamilies as they showed very limited mobility across biogeographical regions, except for Saturniinae, a subfamily now present on all continents but Antarctica. Overall, our results provide a framework for in-depth investigations into the spatial and temporal dynamics of all saturniid lineages and for the integration of their evolutionary history into further global studies of biodiversity and conservation. Rather unexpectedly for a taxonomically well-known family such as Saturniidae, the proper alignment of taxonomic divisions and ranks with our phylogenetic results leads us to propose substantial rearrangements of the family classification, including the description of one new subfamily and two new tribes.


title: Mesoscopic oblique plane microscopy (Meso-OPM) - enabling large-scale 4D isotropic cellular resolution imaging with a diffractive light sheet

abstract: Fundamental understanding of large-scale dynamic connectivity within a living organism requires volumetric imaging over a large field of view (FOV) at biologically relevant speed and resolution. However, most microscopy methods make trade-offs between FOV and resolution or imaging speed, making it challenging to observe highly dynamic processes at cellular resolution across mesoscopic scales (e.g., whole zebrafish larva). To overcome this limitation, we have developed mesoscopic oblique plane microscopy (Meso-OPM) with a diffractive light sheet. By augmenting the illumination angle of the light sheet with a transmission grating, the axial resolution was improved ~7-fold over existing methods and ~2-fold beyond the diffraction limitation of the primary objective lens. We demonstrated an unprecedented FOV up to 5.4 x 3.3 mm with resolution of 2.5x 3 x 6 m, allowing volumetric imaging of cellular structures in an uncleared brain slice with a single scan. Applying Meso-OPM for in vivo imaging of zebrafish larvae, we report here the first whole fish volumetric recordings of neuronal activity at 2 Hz volume rate and the first example of whole fish volumetric recordings of blood flow dynamics at 5 Hz with isotropic cellular resolution.


title: scAllele: a versatile tool for the detection and analysis of variants in scRNA-seq

abstract: Single-cell RNA sequencing (scRNA-seq) data contain rich information at the gene, transcript, and nucleotide levels. Most analyses of scRNA-seq have focused on gene expression profiles, and it remains challenging to extract nucleotide variants and isoform-specific information. Here, we present scAllele, an integrative approach that detects single nucleotide variants, insertions, deletions, and their allelic linkage with splicing patterns in scRNA-seq. We demonstrate that scAllele achieves better performance in identifying nucleotide variants than other commonly used tools. In addition, the read-specific variant calls by scAllele enables allele-specific splicing analysis, a unique feature not afforded by other methods. Applied to a lung cancer scRNA-seq data set, scAllele identified variants with strong allelic linkage to alternative splicing, some of which being cancer-specific. scAllele represents a versatile tool to uncover multi-layer information and novel biological insights from scRNA-seq data.


title: MultiHeadGAN: A Deep Learning Method for Low Contrast Retinal Pigment Epithelium Cells Segmentation in Fluorescent Flatmount Microscopy Images

abstract:
BackgroundRetinal pigment epithelium (RPE) aging is an important cause of vision loss. As RPE aging is accompanied by changes in cell morphological features, an accurate segmentation of RPE cells is a prerequisite to such morphology analyses. Due the overwhelmingly large cell number, manual annotations of RPE cell borders are time-consuming. Computer based methods do not work well on cells with weak or missing borders in the impaired RPE sheet regions.

MethodTo address such a challenge, we develop a semi-supervised deep learning approach, namely MultiHeadGAN, to segment low contrast cells from impaired regions in RPE flatmount images. The developed deep learning model has a multi-head structure that allows model training with only a small scale of human annotated data. To strengthen model learning effect, we further train our model with RPE cells without ground truth cell borders by generative adversarial networks. Additionally, we develop a new shape loss to guide the network to produce closed cell borders in the segmentation results.

ResultsIn this study, 155 annotated and 1,640 unlabeled image patches are included for model training. The testing dataset consists of 200 image patches presenting large impaired RPE regions. The average RPE segmentation performance of the developed model MultiHeadGAN is 85.4 (correct rate), 88.8 (weighted correct rate), 87.3 (precision), and 80.1 (recall), respectively. Compared with other state-of-the-art deep learning approaches, our method demonstrates superior qualitative and quantitative performance.

ConclusionsSuggested by our extensive experiments, our developed deep learning method can accurately segment cells from RPE flatmount microscopy images and is promising to support large scale cell morphological analyses for RPE aging investigations.


title: A Quantitative Modelling Approach for DNA Repair on a Population Scale

abstract:
Despite intensive research of DNA repair after UV in eukaryotes, a framework to quantitatively describe the dynamics in vivo is still lacking. We developed a new data-driven approach to analyse CPD repair kinetics over time in Saccharomyces cerevisiae. In contrast to other studies that consider sequencing signals as an average behaviour, we introduce a hidden axis representing independent cells where loci can transition from damaged to repaired. This permits the application of the Kolmogorov-Johnson-Mehl-Avrami model to find a region-specific and continuous representation of the entire temporal process. We correlated the parameters via a k-nearest neighbour approach to a variety of genomic features, including transcription rate and nucleosome density. The clearest link was found for the gene size, which has been unreported for budding yeast to our knowledge. The framework hence allows a comprehensive analysis of nuclear processes on a population scale.

Author SummaryAs DNA encodes our very identity, it has been subject to a plethora of studies over the last century. The advent of new technologies that permit rapid sequencing of large DNA and RNA samples opened doors to before unknown mechanisms and interactions on a genomic scale. This led to an in-depth analysis of several nuclear processes, including transcription of genes and lesion repair. However, the applied protocols do mostly not allow a high temporal resolution. Quite the contrary, the experiments yield often only some few data signals over several hours. Missing dynamics between time points are chiefly ignored, implicitly assuming that they straightforwardly transition from one to another. Here, we show that such an understanding can be flawed. We use the repair process of UV-induced DNA damage as an example to present a quantitative analysis framework that permits the representation of the entire temporal process with only three parameters. We subsequently describe how they can be linked to other heterogeneous data sets. Consequently, we evaluate a correlation to the whole kinetic process rather than to a single time point. Although the approach is exemplified using DNA repair, it can be readily applied to any other mechanism and sequencing data that represents a state transition between two states, such as damaged and repaired.


title: A high-throughput 384-well CometChip platform reveals a role for 3-methyladenine in the cellular response to etoposide-induced DNA damage

abstract: The Comet or single-cell gel electrophoresis assay is the gold standard for analysis of cellular, nuclear genome damage. However, low throughput limits its application for large-scale studies. To overcome these limitations, a 96-well CometChip platform was recently developed that increases throughput and reduces variation due to simultaneous processing and automated analysis of 96 samples. To advance throughput further, we developed a 384-well CometChip platform that allows analysis of [~]100 cells per well. The 384-well CometChip extends the capacity by 4-fold as compared to the 96-well system, enhancing application for larger DNA damage analysis studies. The overall sensitivity of the 384-well CometChip is consistent with that of the 96-well system, sensitive to genotoxin exposure and to loss of DNA repair capacity. We then applied the 384-well platform to screen a library of protein kinase inhibitors to probe each as enhancers of etoposide induced DNA damage and found that 3-methyladenine significantly increased levels of etoposide-induced DNA damage. Our results suggest that a 384-well CometChip is useful for large-scale DNA damage analyses, which may have increased potential in the evaluation of chemotherapy efficacy, compound library screens, population-based analyses of genome damage and evaluating the impact of environmental genotoxins on genome integrity.

category: cancer biology


title: The sugarless grape trait characterized by single berry phenotyping

abstract: For grape production, an important driver for the selection of varieties better adapted to climate fluctuations, especially warming, is the balance between fruit sugars and acidity. Since the past decades, temperature during ripening has constantly raised causing excessive sugars concentrations and insufficient acidity of the wine grapes in warmest regions. There is thus an increasing interest in breeding new cultivars, able to ripen at lower sugar concentration while preserving fruit acidity. However, the phenotyping of berry composition challenges both methodological and conceptual issues. Indeed, most authors predetermine either average harvest date, ripening duration, thermal time or even hexoses concentration threshold itself, to compare accessions at an hopefully similar ripe stage. Here, we have phenotyped the fruit development and composition of 6 genotypes, including 3 new disease-tolerant varieties known to produce wines with low alcoholic contents. The study was performed at single berry level from the end of green growth stage to the arrest of phloem unloading, when water and solute contents reach a maximum per berry. The results confirmed that sugarless genotypes achieve fruit ripening with 20-30% less hexoses than classical varieties, Grenache N and Merlot N, without impacting berry growth, total acidity or cations accumulation. Sugarless genotypes displayed a higher malic acid/tartaric acid balance than other genotypes with similar sucrose/H+ exchanges at the onset of ripening. Data suggest that sugarless phenotype results from a specific plasticity in the relationship between growth and the turgor imposed by organic acid accumulation and sugar loading. This opens interesting perspectives to understand the mechanism of grapevine berry growth and to breed varieties better coping with climate warming.

category: plant biology


title: Memory reactivation in slow wave sleep enhances relational learning

abstract: Memories are often strengthened by sleep, which can also boost integration and relational learning. This process can be facilitated by a technique called targeted memory reactivation (TMR), which involves re-applying cues that were associated with learned material during wake during subsequent sleep. We tested whether TMR during slow wave sleep increases the solving of inference pairs in a transitive inference task. Because the slow oscillation up-state is thought to be more important for plasticity, we also asked whether stimulation is more beneficial at this phase. Our data show that TMR can boost inference on the most difficult pairs, but only when presented during the down-to-up transition of the slow oscillation. Such stimulation was associated with classifiable replay, whereas stimulation of the up-to-down transition produced no apparent replay and led to below-chance performance. These findings demonstrate that targeted memory replay in sleep can play a role in integration and relational learning.


title: Multi-Layered Maps of Neuropil with Segmentation-Guided Contrastive Learning

abstract: Maps of the nervous system that identify individual cells along with their type, subcellular components, and connectivity have the potential to reveal fundamental organizational principles of neural circuits. Volumetric nanometer-resolution imaging of brain tissue provides the raw data needed to build such maps, but inferring all the relevant cellular and subcellular annotation layers is challenging. Here, we present Segmentation-Guided Contrastive Learning of Representations ("SegCLR"), a self-supervised machine learning technique that produces highly informative representations of cells directly from 3d electron microscope imagery and segmentations. When applied to volumes of human and mouse cerebral cortex, SegCLR enabled the classification of cellular subcompartments (axon, dendrite, soma, astrocytic process) with 4,000-fold less labeled data compared to fully supervised approaches. Surprisingly, SegCLR also enabled inference of cell types (neuron vs. glia and subtypes of each) from fragments with lengths as small as 10 micrometers, a task that can be difficult for humans to perform and whose feasibility greatly enhances the utility of imaging portions of brains in which many neuron fragments terminate at a volume boundary. These predictions were further augmented via Gaussian process uncertainty estimation to enable analyses restricted to high confidence subsets of the data.


title: A comparison of intracranial volume estimation methods and their cross-sectional and longitudinal associations with age

abstract:
Intracranial volume (ICV) is frequently used in volumetric brain magnetic resonance imaging (MRI) studies, both as an adjustment factor for head size and as a variable of interest. Associations with age have been reported in both longitudinal and cross-sectional studies, but results have varied, potentially due to differences in ICV estimation methods. Here, we compared five commonly used ICV estimation methods and their cross-sectional and longitudinal associations with age. T1-weighted cross-sectional MRI data was included for 651 healthy individuals recruited through the NORMENT Centre (mean age = 46.1 years, range = 12.0-85.8 years) and 2,410 healthy individuals recruited through the UK Biobank study (UKB, mean age = 63.2 years, range = 47.0-80.3 years), where follow-up data was also available with a mean follow-up interval of 2.3 years. ICV was estimated with FreeSurfer (eTIV and sbTIV), SPM12, CAT12, and FSL. We assessed Pearson correlations, performed Bland-Altman analysis, and tested the explained variance of sex, height, body weight, and age on pairwise differences between ICV estimation methods. We fitted regression models to test linear and non-linear cross-sectional associations between age and ICV. For the UKB dataset, we further assessed longitudinal ICV change using linear mixed-effects (LME) models. We found overall high correlations across ICV estimation method, with the lowest correlations between FSL and eTIV (r=0.87) and between FSL and CAT12 (r=0.89). Widespread proportional bias was found in the Bland-Altman analyses, i.e., agreement between methods varying as a function of head size. Body weight, age, and sex explained the most variance in the differences between ICV estimation methods, indicating possible confounding by these variables for some estimation methods. In the NORMENT dataset, cross-sectional associations with age were found only for FSL and SPM12, indicating a positive association. For the UKB dataset, we observed negative cross-sectional associations with age for all ICV estimation methods. Longitudinal associations with age were found for all ICV estimation methods, with estimated annual percentage change ranging from -0.291 % to -0.416 % across the sampled age range. This convergence of longitudinal results across ICV estimation methods, in the largest dataset to date, offers strong evidence for age-related ICV reductions in mid- to late adulthood.

HighlightsO_LICorrelations between the five assessed estimation methods were very high (r>0.90) with the exception of FSL and eTIV (r=0.87), and FSL and CAT12 (r=0.89).
C_LIO_LIExplained variance of estimated ICV differences by body weight, age, and sex indicate possible confounding for some ICV estimation methods.
C_LIO_LIPositive cross-sectional associations with age, from adolescence to old age, were observed for the SPM12 and FSL estimation methods in one dataset.
C_LIO_LIIn the other dataset, negative cross-sectional associations with age, from mid- to late adulthood, were found for all estimation methods.
C_LIO_LILongitudinal ICV changes were observed for all estimation methods, indicating an annual percentage ICV reduction of -0.29 % to -0.42 % in mid- to late adulthood.
C_LI


title: Population genetic analysis reveals the role of natural selection and phylogeography on genome-wide diversity in an extremely compact and reduced microsporidian genome

abstract:
The determinants of variation in a species genome-wide nucleotide diversity include historical, environmental, and stochastic aspects. This diversity can inform us about the species past and present evolutionary dynamics. In parasites, the mode of transmission and the interactions with the host might supersede the effects of these aspects in shaping parasite genomic diversity. We used genomic samples from ten populations of the microsporidian parasite Ordospora colligata to investigate present genomic diversity and how it was shaped by evolutionary processes, specifically, the role of phylogeography, co-phylogeography (with the host), natural selection, and transmission mode. Although very closely related microsporidia cause diseases in humans, O. colligata is specific to the freshwater crustacean Daphnia magna and has one of the smallest known eukaryotic genomes. We found an overlapping phylogeography between O. colligata and its host highlighting the long-term, intimate relationship between them. The observed geographic distribution reflects previous findings that O. colligata exhibits adaptations to colder habitats, which differentiates it from other microsporidian gut parasites of D. magna predominantly found in warmer areas. The co-phylogeography allowed us to calibrate the O. colligata phylogeny and thus estimate its mutation rate. We found patterns of more efficient purifying selection in O. colligata relative to other microsporidia sharing the same host, which likely allowed this parasite to maintain its very compact genome. We also identified regions under potential selection related to coevolution including the ribosomal protein L24, a leucyl-tRNA synthetase, and a putative ABC-like lipid transport protein. Our whole-genome study provides insights into the evolution of one of the most reduced eukaryotic genomes and shows how different processes shape genomic diversity of an obligate parasite.

Author summaryMicrosporidia are intracellular parasites that infect vertebrates, invertebrates, and even unicellular organisms. Due to their high variation in many aspects of life history and genomics, microsporidia have become a model clade for understanding evolutionary processes related to intracellular parasitism. However, the evolution of extreme genomic architectures in microsporidia and the coevolution with their hosts is still under-surveyed, especially given their role in human disease. Here, we study past and present evolutionary dynamics in a microsporidian species with one of the smallest known eukaryotic genomes, O. colligata. Close relatives of O. colligata cause death and disease in humans and agriculturally important animals. We show that purifying selection helped maintaining its reduced, compact genome and corroborate hypotheses about the evolution of different genome sizes in microsporidia. Importantly, we utilize the highly resolved phylogeny of its host to estimate the parasites mutation rate. This methodology allowed us to establish the first mutation rate estimate for a microsporidium, an estimate which is within the range of mutation rates estimated for phylogenetically related, non-parasitic fungi. Our study exemplifies how the combined knowledge about a species biology, ecology, and genomic diversity helps to resolve its evolutionary dynamics, in particular when phylogenomic information can be brought to bear for both host and parasite.


title: Holobiont transcriptomes for the critically endangered staghorn coral (Acropora cervicornis) from two environmentally distinct sites on Turneffe Atoll, Belize

abstract: Historically, staghorn coral (Acropora cervicornis) was a preeminent reef-builder in the Caribbean and Tropical Western Atlantic, where it constructed extensive thickets at 5-20 m depth that supported diverse ecosystems and provided coastal populations with food, storm protection, and income from tourism. In recent decades, A. cervicornis declined precipitously, up to 97% in some localities. To reverse its decline, widespread efforts are underway to characterize the phenotypic and genetic diversity of persisting populations with the goal of restoring them to historical levels by out-planting nursery grown specimens. To support this target, we developed transcriptomes for two A. cervicornis populations located in Turneffe Atoll Marine Reserve, Belize. These populations experience significantly different temperatures, light levels and water currents, and they harbor individuals that differ in key phenotypes. Because differentiating the gene activity of diverse taxa--i.e., coral host, algal photosymbiont, plus associated eukaryotes, bacteria, archaea, and viruses-- is critical to understanding the function of the coral holobiont, we developed a pipeline for parsing transcripts by taxon. Separate transcriptomes for each population contain complete representatives for >96% of 978 conserved metazoan single copy orthologs. The taxonomic breakdown of transcripts differed between sites, with more bacterial transcripts recovered from Calabash Caye and more symbiont transcripts from Blackbird Caye. The assembled transcriptomes will facilitate gene expression studies and in silico cloning from this endangered coral.

category: genomics


title: Effects of low intensity pulsed ultrasound stimulation on metabolic lipolysis of adipocytes

abstract: Obesity is closely related to several metabolic diseases along with abnormal increase in fat cells. Reducing size and number of fat cells, a procedure known as lipolysis, may be used to prevent obesity as a potential therapy, which also requires fundamental understanding of the mechanisms of lipolysis at molecular level upon different types of stimulations. Here, we used low intensity pulsed ultrasound (LIPUS) stimulation to investigate underlying mechanisms of the activation of lipolysis and autophagy related genes and signaling pathways of adipocytes differentiated from 3T3-L1 cells. LIPUS with the center frequency of 2 MHz was applied for 10 minutes per day for three days. After LIPUS stimulation, quantitative reverse transcription polymerase chain reaction (RT-qPCR) and Western blot were used to determine the regulation of lipolytic factors such as adipose triglyceride lipase (ATGL), hormone-sensitive lipase (HSL), and monoacylglycerol lipase (MGL). At RNA level, all three factors were upregulated while only MGL was upregulated at protein level, which presents slightly different activation pattern of lipolysis compared to widely used chemical stimulation. These results demonstrate that LIPUS stimulation can promote the lipolytic capacity of adipocytes in the differentiated state. The differences between transcriptional genes and metabolites were analyzed by transcript analysis and metabolomic profiling experiments. Cellular RNA-sequencing (RNA-Seq) showed an increase in lipolysis and immune-related genes and autophagy related genes after LIPUS stimulation. This study may provide an important experimental basis for the clinical applications and a fundamental understanding of the mechanisms of lipolysis using LIPUS stimulation.


title: Protein language models trained on multiple sequence alignments learn phylogenetic relationships

abstract: Self-supervised neural language models with attention have recently been applied to biological sequence data, advancing structure, function and mutational effect prediction. Some protein language models, including MSA Transformer and AlphaFolds EvoFormer, take multiple sequence alignments (MSAs) of evolutionarily related proteins as inputs. Simple combinations of MSA Transformers row attentions have led to state-of-the-art unsupervised structural contact prediction. We demonstrate that similarly simple, and universal, combinations of MSA Transformers column attentions strongly correlate with Hamming distances between sequences in MSAs. Therefore, MSA-based language models encode detailed phylogenetic relationships. This could aid them to separate coevolutionary signals encoding functional and structural constraints from phylogenetic correlations arising from historical contingency. To test this hypothesis, we generate synthetic MSAs, either without or with phylogeny, from Potts models trained on natural MSAs. We demonstrate that unsupervised contact prediction is indeed substantially more resilient to phylogenetic noise when using MSA Transformer versus inferred Potts models.


title: A Distinct Chromatin State Drives Therapeutic Resistance in Invasive Lobular Breast Cancer

abstract:
Most invasive lobular breast cancers (ILC) are of the luminal A subtype and strongly hormone receptor positive. Yet, they are relatively resistant to tamoxifen and are associated with inferior long-term outcomes compared to invasive ductal cancers (IDC). In this study, we sought to gain mechanistic insights into these clinical findings that are not explained by the genetic landscape of ILC and to identify strategies to improve patient outcomes. Through a comprehensive analysis of the epigenome of ILC in pre-clinical models and clinical samples we found that compared to IDC, ILC has a distinct chromatin state that is linked to gained recruitment of FOXA1, a lineage-defining pioneer transcription factor. This results in an ILC-unique FOXA1-estrogen receptor (ER) axis that promotes the transcription of genes associated with tumor progression and poor outcomes. The ILC-unique FOXA1-ER axis leads to retained ER chromatin binding after tamoxifen treatment thereby facilitating tamoxifen resistance while remaining strongly dependent on ER signaling. Mechanistically, gained FOXA1 binding was associated with the auto-induction of FOXA1 in ILC through an ILC-unique FOXA1 binding site. Targeted silencing of this regulatory site resulted in the disruption of the feed-forward loop and growth inhibition in ILC.

In summary, we show that ILC is characterized by a unique cell state and FOXA1-ER axis that dictate tumor progression and offer a novel mechanism of tamoxifen resistance. These results underscore the importance of conducting clinical trials dedicated to patients with ILC to optimize endocrine treatments in this breast cancer subtype.


title: Establishing combination PAC-1 and TRAIL regimens for treating ovarian cancer based on patient-specific pharmacokinetic profiles using in silico clinical trails

abstract: Ovarian cancer is commonly diagnosed in its late stages, and new treatment modalities are needed to improve patient outcomes and survival. We have recently established the synergistic effects of combination tumour necrosis factor-related apoptosis-inducing ligand (TRAIL) and procaspase activating compound (PAC-1) therapies in granulosa cell tumours (GCT) of the ovary, a rare form of ovarian cancer, using a mathematical model of the effects of both drugs in a GCT cell line. Here, to understand the mechanisms of combined TRAIL and PAC-1 therapy, study the viability of this treatment strategy, and accelerate preclinical translation, we leveraged our mathematical model in combination with population pharmacokinetics (PopPK) models of both TRAIL and PAC-1 to expand a realistic heterogeneous cohort of virtual patients and optimize treatment schedules. Using this approach, we investigated treatment responses in this virtual cohort and determined optimal therapeutic schedules based on patient-specific pharmacokinetic characteristics. Our results showed that schedules with high initial doses of PAC-1 were required for therapeutic efficacy. Further analysis of individualized regimens revealed two distinct groups of virtual patients within our cohort: one with high PAC-1 elimination, and one with normal PAC-1 elimination. In the high elimination group, high weekly doses of both PAC-1 and TRAIL were necessary for therapeutic efficacy, however virtual patients in this group were predicted to have a worse prognosis when compared to those in the normal elimination group. Thus, PAC-1 pharmacokinetic characteristics, particularly clearance, can be used to identify patients most likely to respond to combined PAC-1 and TRAIL therapy. This work underlines the importance of quantitative approaches in preclinical oncology.


title: Establishing combination PAC-1 and TRAIL regimens for treating ovarian cancer based on patient-specific pharmacokinetic profiles using in silico clinical trials


title: Measurement of plant water status via static uniaxial compression of the leaf lamina

abstract: Turgor pressure is an essential, but difficult to measure indicator of plant water status. Turgor has been quantified by localised compression of cells or tissues, but a simple method to perform these measurements is lacking. We hypothesized that changes in leaf turgor pressure can be monitored by uniaxially compressing the leaf lamina and measuring the mechanical stress under a constrained thickness (stress relaxation); and that changes in leaf water content can be monitored by measuring the thickness of the leaf lamina compressed under a constant force (creep). Using a custom-built leaf squeeze-flow rheometer, we performed different compression tests on leaves from thirteen plant species. The equilibrium mechanical stress measured during stress relaxation was correlated with leaf turgor pressure (R2 > 0.95) and thus with leaf water potential (R2 > 0.94); the equilibrium leaf thickness measured during creep was correlated with relative water content (R2 > 0.74). The coefficients of these relationships were related to the leaf osmotic pressure at the turgor-loss point. An idealised average-cell model suggests that, under isothermal conditions, the bulk cell stiffness during compression is largely determined by the leaf osmotic pressure. Our study presents an inexpensive, accessible and automatable method to monitor plant water status non-invasively.


title: The origin of diffuse noxious inhibitory controls

abstract:
Pain alerts us to actual or potential tissue damage. During acute pain, our central nervous system acts endogenously to modulate pain processing, thus reducing or enhancing pain perception. However, during chronic pain, the balance between inhibitory and facilitatory processes are tipped in favour of pro-pain modulation.

Diffuse noxious inhibitory controls (DNIC) is a naturally occurring pain inhibitory pathway that projects from the brainstem to the spinal cord to inhibit neuronal activity therein in a manner that is 1) subserved by noradrenaline, and 2) dysfunctional in chronicity. To harness its high therapeutic potential, we aimed to anatomically and functionally define DNIC.

Through employing an intersectional opto- and chemogenetic approach to modulate activity in brainstem noradrenergic nuclei, here we show that spinal neuronal firing observed upon DNIC activation during electrophysiological experiments, and animal pain thresholds observed during behavioural experiments, are modulated in a pro-pain manner upon opto-manipulation of A5 spinally projecting noradrenergic neurons, thus evidencing the DNIC origin.

Given the plasticity of the functional expression of DNIC in disease, and the success of back and forward translation of paradigms that evoke DNIC in pre-clinical and clinical models, our findings offer an attractive avenue of studies for disease specific analgesic interventions.


title: Novel Adult Cortical Neuron Processing and Screening method illustrates Sex- and Age-dependent effects of pharmaceutical compounds

abstract: Neurodegenerative diseases and neurotraumatic injuries are typically age-associated disorders that can reduce neuron survival, neurite outgrowth, and synaptic plasticity leading to loss of cognitive capacity, executive function, and motor control. In pursuit of reducing the loss of said neurological functions, novel compounds are sought that promote neuron viability, neuritogenesis, and/or synaptic plasticity. Current high content in vitro screenings typically use cells that are iPSC-derived, embryonic, or originate from post-natal tissues; however, most patients suffering from neurodegenerative diseases and neurotrauma are of middle-age and older. The chasm in maturity between the neurons used in drug screens and those in a target population is a barrier for translational success of in vitro results. It has been historically challenging to culture adult neurons let alone conduct screenings; therefore, age-appropriate drug screenings have previously not been plausible. We have modified Miltenyis protocol to increase neuronal yield, neuron purity, and neural viability at a reduced cost to expand our capacity to screen compounds directly in primary adult neurons. Furthermore, we have developed the first morphology-based screening system using adult cortical neurons. By using primary adult cortical neurons from mice that were 4 to 48 weeks old for screening of a library of pharmaceuticals, we have demonstrated age- and sex-dependent effects on neuritogenesis and neuron survival in vitro. Utilizing age- and sex-appropriate in vitro models to find novel compounds increasing neuron survival and neurite outgrowth, made possible by our modified adult neuron processing method, will greatly increase the relevance of in vitro screening for finding neuroprotective compounds.


title: Different astrocyte-to-neuron conversion tracing reporters affect results in mouse striatum under Ptbp1 knockdown

abstract: Conversion of astrocytes to neurons (AtN) is a promising potential strategy for the treatment of neurodegenerative diseases. Recent studies have reported that shRNA-, CasRx-, or ASO-mediated Ptbp1 suppression could reprogram resident astrocytes to neurons1-3. However, some groups have disputed the data interpretation of the reported AtN conversion events4-7. These controversies surrounding AtN conversion may due to differences in the astrocyte fate-mapping systems they applied from that in the original study, i.e., recombinant mouse strains with astrocyte specific reporter constructs versus AAV-based labeling systems. Here, we applied two AAV-based tracing systems to label astrocytes with either a GFAP-driven tdTomato reporter (AAV-GFAP::tdTomato) or GFAP-driven HA-tagged Cas13X (AAV-GFAP::Cas13X-NLS-HA-sgPtbp1) and found conflicting observations of AtN conversion in mouse striatum. Our findings indicated that inconsistent AtN outcomes may arise from different fate-mapping systems between AAV and transgenic mice, as well as through use of different reporter proteins. Thus, the complexity of astrocyte labeling systems warrants careful attention when drawing conclusions about whether AtN conversion occurs.