title: PatchPerPixMatch for Automated 3d Search of Neuronal Morphologies in Light Microscopy

abstract:
Studies of individual neurons in the Drosophila nervous system are facilitated by transgenic lines that sparsely and repeatably label respective neurons of interest. Sparsity can be enhanced by means of intersectional approaches like the split-GAL4 system, which labels the positive intersection of the expression patterns of two (denser) GAL4 lines. To this end, two GAL4 lines have to be identified as labelling a neuron of interest. Current approaches to tackling this task include visual inspection, as well as automated search in 2d projection images, of single cell multi-color flip-out (MCFO) acquisitions of GAL4 expression patterns. There is to date no automated method available that performs full 3d search in MCFO imagery of GAL4 lines, nor one that leverages automated reconstructions of the labelled neuron morphologies. To close this gap, we propose PatchPerPixMatch, a fully automated approach for finding a given neuron morphology in MCFO acquisitions of Gen1 GAL4 lines. PatchPerPixMatch performs automated instance segmentation of MCFO acquisitions, and subsequently searches for a target neuron morphology by minimizing an objective that aims at covering the target with a set of well-fitting segmentation fragments. Patch-PerPixMatch is computationally efficient albeit being full 3d, while also highly robust to inaccuracies in the automated neuron instance segmentation. We are releasing PatchPerPixMatch search results for ~30,000 neuron morphologies from the Drosophila hemibrain in ~20,000 MCFO acquisitions of ~3,500 Gen1 GAL4 lines.

Codehttps://github.com/Kainmueller-Lab/PatchPerPixMatch

Resultshttps://pppm.janelia.org


title: AlphaPept, a modern and open framework for MS-based proteomics

abstract: In common with other omics technologies, mass spectrometry (MS)-based proteomics produces ever-increasing amounts of raw data, making their efficient analysis a principal challenge. There is a plethora of different computational tools that process the raw MS data and derive peptide and protein identification and quantification. During the last decade, there has been dramatic progress in computer science and software engineering, including collaboration tools that have transformed research and industry. To leverage these advances, we developed AlphaPept, a Python-based open-source framework for efficient processing of large high-resolution MS data sets. Using Numba for just-in-time machine code compilation on CPU and GPU, we achieve hundred-fold speed improvements while maintaining clear syntax and rapid development speed. AlphaPept uses the Python scientific stack of highly optimized packages, reducing the code base to domain-specific tasks while providing access to the latest advances in machine learning. We provide an easy on-ramp for community validation and contributions through the concept of literate programming, implemented in Jupyter Notebooks of the different modules. A framework for continuous integration, testing, and benchmarking enforces solid software engineering principles. Large datasets can rapidly be processed as shown by the analysis of hundreds of cellular proteomes in minutes per file, many-fold faster than the data acquisiton. The AlphaPept framework can be used to build automated processing pipelines using efficient HDF5 based file formats, web-serving functionality and compatibility with downstream analysis tools. Easy access for end-users is provided by one-click installation of the graphical user interface, for advanced users via a modular Python library, and for developers via a fully open GitHub repository.

category: bioinformatics


title: Crowding-induced phase separation of nuclear transport receptors in FG nucleoporin assemblies

abstract: The rapid (< 1 ms) transport of biological material to and from the cell nucleus is regulated by the nuclear pore complex (NPC). At the core of the NPC is a permeability barrier consisting of intrinsically disordered Phe-Gly (FG) nucleoporins (FG Nups). Various types of nuclear transport receptors (NTRs) facilitate transport by partitioning in the FG Nup assembly, overcoming the barrier by their affinity to the FG Nups, and comprise a significant fraction of proteins in the NPC barrier. In previous work, we revealed that the experimental binding of the NTRs NTF2 and - the larger - Imp{beta} to different planar assemblies of FG Nups follows a universal physical law defined by negative cooperativity, which was further validated by a minimal physical model that treated the FG Nups as flexible homopolymers and the NTRs as uniformly cohesive spheres Zahn et al. (2016). Here, we build upon our original study by first parametrizing our model to experimental data, and next to predict the effects of crowding by different types of NTRs. We show how varying the amounts of one type of NTR modulates how the other NTR penetrates the FG Nup assembly. Notably, at similar and physiologically relevant NTR concentrations, our model predicts demixed phases of NTF2 and Imp{beta} within the FG Nup assembly. The functional implication of NTR phase separation is that NPCs may sustain separate transport pathways that are determined by inter-NTR competition.

category: biophysics


title: Emotional states as distinct configurations of functional brain networks

abstract: The conceptualization of emotional states as patterns of interactions between large-scale brain networks has recently gained support. Yet, few studies have directly examined the brains network structure during emotional experiences. Here, we investigated the brains functional network organization during experiences of sadness, amusement, and neutral states elicited by movies, in addition to a resting-state. We tested the effects of the experienced emotion on individual variability in the brains functional connectome. Next, for each state, we defined a community structure of the brain and quantified its segregation and integration. Our results show that emotional states increase the similarity between and within individuals in the brains functional connectome. Second, in the brains modular organization, sadness, relative to amusement, was associated with higher modular integration and increased connectivity of cognitive control networks: the salience and fronto-parietal networks. Last, in both the functional connectome and the emotional report, we found higher similarity among women. Our results suggest that the experience of emotion is linked to a reconfiguration of whole-brain distributed, not emotion-specific, functional networks and that the brains topological structure carries information about the subjective emotional experience.

category: neuroscience


title: Trial-wise exposure to visual appetitive cues increases physiological arousal but not temporal discounting.

abstract: Humans and many animals devalue future rewards as a function of time (temporal discounting). Increased discounting has been linked to various psychiatric conditions, including substance-use-disorders, behavioral addictions and obesity. Despite its high intra-individual stability, temporal discounting is partly under contextual control. One prominent manipulation that has been linked to increases in discounting is the exposure to highly arousing appetitive cues. However, results from trial-wise cue exposure studies appear highly mixed, and changes in physiological arousal were not adequately controlled. Here we tested the effects of appetitive (erotic), aversive and neutral visual cues on temporal discounting in thirty-five healthy male participants. The contribution of single-trial physiological arousal was assessed using comprehensive monitoring of autonomic activity (pupil size, heart rate, electrodermal activity). Physiological arousal was elevated following aversive and in particular erotic cues. In contrast to our pre-registered hypothesis, if anything, we observed decreased temporal discounting following erotic cue exposure. Aversive cues tended to increase decision noise. Computational modeling revealed that trial-wise arousal only accounted for minor variance over and above aversive and erotic condition effects, arguing against a general effect of physiological arousal on temporal discounting.


title: High consistency of trophic niches in soil microarthropod species (Oribatida, Acari) across soil depth and forest type

abstract: Individuals of species may differ in resource use within and between populations. High intraspecific variation in resource use may hamper the co-existence of species in natural communities. To better understand the intraspecific variation in trophic niches of oribatid mites (Oribatida, Acari), we quantified stable isotope ratios of carbon ({delta}13C) and nitrogen ({delta}15N) of 40 Oribatida species that co-occurred in litter and soil of five forest types (European beech, Douglas fir, Norway spruce, two beech-conifer mixed forests) covering a range of environmental conditions. We found that although stable isotopes in litter and soil varied among forest types, {delta}13C and {delta}15N values of Oribatida and their trophic niches were remarkably stable between litter and soil, and also among forest types. We considered four trophic guilds of Oribatida representing the guild composition of the regional species pool; notably, trophic niches of Oribatida guilds also did not vary with soil depth. Furthermore, {delta}13C of Oribatida was more enriched (detrital shift) in European beech than in coniferous forests, but {delta}15N of Oribatida did not vary among forest types, indicating that basal resources of Oribatida are variable, but trophic positions are highly consistent across forest ecosystems. We conclude that trophic positions of Oribatida species and guilds are consistent across different forest types, and Oribatida species occupy virtually identical trophic niches irrespective of the soil depth they are colonizing. Overall, the results suggest that low intraspecific variability facilitates Oribatida niche differentiation and species coexistence.

category: ecology


title: Disentangling key species interactions in diverse and heterogeneous communities: A Bayesian sparse modeling approach

abstract: 1Modeling species interactions in diverse communities traditionally requires a prohibitively large number of species-interaction coefficients, especially when considering environmental dependence of parameters. We implemented Bayesian variable selection via sparsity-inducing priors on non-linear species abundance models to determine which species-interactions should be retained and which can be represented as an average heterospecific interaction term, reducing the number of model parameters. We evaluated model performance using simulated communities, computing out-of-sample predictive accuracy and parameter recovery across different input sample sizes. We applied our method to a diverse empirical community, allowing us to disentangle the direct role of environmental gradients on species intrinsic growth rates from indirect effects via competitive interactions. We also identified a few neighboring species from the diverse community that had non-generic interactions with our focal species. This sparse modeling approach facilitates exploration of species-interactions in diverse communities while maintaining a manageable number of parameters.


abstract:
The combined toxicity test of polyester and tetra ethylene glycol on Daphnia magna. Globally, wide use of plastics and its increased production has led to a mounting amount of plastic waste entering the natural ecosystems. Due to their small size, plastic particles might be ingested by organisms at the lower end of the food chain and can be transferred by feeding to top consumers. Consequently, plastic pollution in aquatic environments and its potential impact on aquatic life has recently been recognized as an issue of considerable concern for ecosystem. I produced microplastics from 100% polyester thread from Houjix, cut it finely and used a dissecting needle to cut into a size of 5mm or less through a microscope. I also included ethylene glycol to investigate its toxic effects on D. magna. Since my aim was also to compare the toxicity effect of both chemicals, I used different concentrations individually and then in combinations to determine the potential toxic effects of polyester and tetra ethylene glycol (combined and separately) on the life (survival, death) of D. magna.

Microplastics from 100% polyester thread from Houjix were produced, into a size of 5mm or less through a microscope. Tetra ethylene glycol was also used to investigate its toxic effects on D. magna. The toxicity effect of both chemicals using different concentrations individually and then in combinations were employed to determine the potential toxic effects of polyester and tetra ethylene glycol (combined and separately) on the life of D. magna. The study exhibited that the IC50 of TEG was higher as compared to polyester which suggests that polyester was more adverse than TEG. Moreover, when TEG and polyester were treated in combination, IC50 value was lower (Figure 3) than the IC50 value of TEG and polyester separately. In other words, the TEG and polyester in combination exhibited the lowest IC50 value in this study. These results suggest that TEG and polyester in combination had adverse effects on the growth and development of D. magna

O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=122 SRC="FIGDIR/small/453624v1_fig3.gif" ALT="Figure 3">
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org.highwire.dtl.DTLVardef@10f7bcorg.highwire.dtl.DTLVardef@1f85fe1org.highwire.dtl.DTLVardef@15ed2b7org.highwire.dtl.DTLVardef@5c161d_HPS_FORMAT_FIGEXP  M_FIG O_FLOATNOfigure 3.C_FLOATNO polyester and TEG treated on D. magna

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title: Leveraging gene co-regulation to identify gene sets enriched for disease heritability

abstract: Identifying gene sets that are associated to disease can provide valuable biological knowledge, but a fundamental challenge of gene set analyses of GWAS data is linking disease-associated SNPs to genes. Transcriptome-wide association studies (TWAS) can be used to detect associations between the genetically predicted expression of a gene and disease risk, thus implicating candidate disease genes. However, causal disease genes at TWAS-associated loci generally remain unknown due to gene co-regulation, which leads to correlations across genes in predicted expression. We developed a new method, gene co-regulation score (GCSC) regression, to identify gene sets that are enriched for disease heritability explained by the predicted expression of causal disease genes in the gene set. GCSC regresses TWAS chi-square statistics on gene co-regulation scores reflecting correlations in predicted gene expression; GCSC determines that a gene set is enriched for disease heritability if genes with high co-regulation to the gene set have higher TWAS chi-square statistics than genes with low co-regulation to the gene set, beyond what is expected based on co-regulation to all genes. We verified via simulations that GCSC is well-calibrated, and well-powered to identify gene sets that are enriched for disease heritability explained by predicted expression. We applied GCSC to gene expression data from GTEx (48 tissues) and GWAS summary statistics for 43 independent diseases and complex traits (average N =344K), analyzing a broad set of biological pathways and specifically expressed gene sets. We identified many enriched gene sets, recapitulating known biology. For Alzheimers disease, we detected evidence of an immune basis, and specifically a role for antigen presentation, in analyses of both biological pathways and specifically expressed gene sets. Our results highlight the advantages of leveraging gene co-regulation within the TWAS framework to identify gene sets associated to disease.

category: genetics


title: Population colonization history influences behavioral responses of European starlings in personality tests

abstract:
To understand the processes involved in biological invasions, the genetic, morphological, physiological and behavioral characteristics of invasive populations need to be understood.

Many invasive species have been reported to be flying species. In birds, both invaders and migrants encounter novel situations, therefore one could expect that both groups might react similarly to novelty.

Here we analyzed the behavioral responses of individuals from three populations of European starling Sturnus vulgaris: a population settled for centuries in a rural region, a population that recently colonized an urban area, and a population of winter migrant birds. We conducted a social isolation test, a novel environment test, a novel food test and a novel object test to explore their reactions towards novelty. We identified and characterized different behavioral profiles for each test.

The group of migratory adults appeared to be less anxious in social isolation than the group of urban young. Urban and migrant groups entered the novel environment sooner than rural birds. Shy, bold and intermediate individuals were observed in all three groups when presented with novel food. Finally, the proportion of shy individuals which did not touch the novel object was higher than the proportion of bold individuals in the rural group. Our study emphasizes that neophilia or boldness present in migrant and invasive populations may facilitate the occupation of novel habitats. Our analysis also suggests that mixed reactions of neophobia ensure behavioral flexibility in a gregarious invasive species.

Significant statementIn this paper, we show that an invasive species like European starling, Sturnus vulgaris, presents an important flexibility in neophobia and in reaction towards social isolation. These variations depend on the settlement history of populationseven when the birds had been wild-caught as nestlings and hand-raised in standard conditions. This is significant because it highlights possible scenarios of colonization processes.

We believe that this manuscript is appropriate for publication by Behavioral Ecology and Sociobiology because it places individuals behavior in the core mechanisms of an ecological phenomenom as biological invasions. Our manuscript enlarges the paradigms related to the ways of coping with novelty in animals.

This manuscript has not been published and is not under consideration for publication elsewhere.

category: animal behavior and cognition


title: Important Docking study of Structure of Plasmodium falciparum thioredoxin reductase-thioredoxin complex: the case of potent drug Telatinib, a small molecule angiogenesis inhibitor

abstract: BackgroundOver the last decades, malaria parasites have been rapidly developing resistance against antimalarial drugs, which underlines the need for novel drug targets. Thioredoxin reductase (TrxR) is crucially involved in redox homeostasis and essential for Plasmodium falciparum. In this communication, we report first time important Docking study by in Silico approach, using AutoDock Vina. After a selective analysis of over 300 drugs, processed with Pyrx (a Virtual Screening software into the active site of protein (ID PDB 4J56 Thioredoxin reductase 2 Chain A), we noticed excellent value of Binding Energy of Telatinib estimated by Pyrx software. These results are comparable to the crystallized ligand FAD (FLAVIN-ADENINE DINUCLEOTIDE) completed in the above-mentioned protein. Indeed, from the results of Autodock Vina, Telatinib an inhibitor of tyrosine kinases, has excellent a Binding affinity value, ca. -12 kcal/mol.


title: A Combined Spectroscopic and Molecular Modeling Study on Structure-Function-Dynamics under Chemical Modification: Alpha-Chymotrypsin with Formalin Preservative

abstract: Enzyme conformations can be altered via modification of its amino acid residues, side chains and large-scale domain modifications, which are closely linked to its function. Herein, we have addressed the role of residue modification in catalytic activity and molecular recognition of an enzyme alpha-chymotrypsin (CHT) in presence of covalent cross-linker formalin. Optical spectroscopy studies exhibit reduced catalytic activity of the enzyme with increased formalin concentration. Polarization gated anisotropy studies of a fluorophore 8-anilino-1- napthelenesulfonic acid (ANS) in CHT show a dip rise pattern in presence of formalin which is consistent with the generation of multiple ANS binding sites in the enzyme owing to modifications of its local amino acid residues. Molecular docking study on minimal local residue modifications in CHT reveals formation of a stable enzyme-substrate complex even with the serine-histidine cross-linked enzyme which prohibits product formation giving rise to reduced catalytic activity.


title: A General Model for Scaling Basal Metabolic Rate, Glomerular Filtration Rate and Drug Clearance from Birth to Adulthood

abstract: Understanding the maturation process of human physiology and metabolism has broad medical and pharmaceutical implications. Age and bodyweight are frequently considered as separate variables in modeling the dynamical changes of human organ functions and of drug clearance from birth to adulthood. The objective of this study is to propose a unified, continuous and bodyweight-only equation to quantify the changes of human basal metabolic rate (BMR), glomerular filtration rate (GFR) and drug clearance (CL) from infancy to adulthood. The BMR datasets were retrieved from a comprehensive historical database of male and female subjects (0.02 to 64 years). The CL datasets for 17 drugs and the GFR dataset were generated from age-incorporated maturation-and-growth models with reported parameter values. The model used in the simulation is independent of the proposed model. A statistical approach was used to simulate the model generated CL and GFR data for a hypothetical population with 26 age groups (ranging from 0 to 20 years). Besides, individual CL data for one drug, and sparse PBPK-modeled CL values for two drugs were also included for analysis. A 4-parameter, mixed-allometry equation with two power-law functions of bodyweight was proposed and evaluated as a general model using nonlinear regression and dimensionless analysis. All datasets universally reveal biphasic curves with two distinct linear segments on log-log plots. Compared with simple allometry, the biphasic model fits satisfactorily to all datasets (based on Akaikes Information Criterion and residual plots). The biphasic equation consists of two reciprocal allometric terms that asymptotically determine the overall curvature. The fitting results show a superlinear scaling phase (slope >1; ca. 1.5 - 3.5) below the characteristic bodyweight at the phase transition; and above which, a sublinear scaling phase (slope <1; ca. 0.5 - 0.7) is evident. The phase-transition bodyweight is ranging from 5 to 20 kg (corresponding to 0.5 - 9 years) and the mean value is around 10 kg ([~]2 years) for all data sets. The dimensionless analysis generalizes, and offers quantitative realization of, the maturation and growth process. In conclusion, the proposed mixed-allometry equation is a generic model that quantitatively describes the phase transition occurring in the human maturation process of BMR, GFR and drug CL.

category: pharmacology and toxicology


title: A General Biphasic-Bodyweight Model for Scaling Basal Metabolic Rate, Glomerular Filtration Rate and Drug Clearance from Birth to Adulthood


title: Cytotoxic Effect of Silver Ions in Combination with Peanut's leaf extract on Cells

abstract:
As modern people suffered to various infectious diseases such as MERS and Covid 19, people interest in nature-driven health care has increased. Accordingly, expectations for natural therapeutics that can have a beneficial effect on the human body without being processed have increased. Buckwheat, peanut, and pine are representatives. Among them, peanuts contain polyphenols and flavonoids which are used as nutritional foods in various forms. For example, resveratrol is activated by the CYP1B1 enzyme in peanut sprouts and converted to piceatannol that can act on anticancer activity. Accordingly, increasing the content of polyphenols in peanuts makes possible to produce useful substances that are harmless to the human body as well as the environment. Therefore, I conducted research to find an effective way to increase the content of polyphenols. This study projects an effective way to secure peanuts with high polyphenol content based on the characteristics that the content of polyphenols increases when plants are wounded. Comparative studies were conducted through wounding, and it was confirmed that the polyphenol content increased in the wounded plants. Subsequently, it was confirmed that the content of polyphenol increased through the DPPH experiment, and the content of flavonoids also increased. Using the data of this study can be used to produce peanuts with high polyphenol content. To find an effective method for cultivating peanuts containing high concentration of phenolic compounds, I compared two groups of plants with different conditions. First group was consisted of normal plants with no treatment and second group was consisted of wounded plants. I treated by using these conditions in each group for two days and the results showed that group 2 has high concentration of flavonoid and phenolic compounds.

To verify this result, I conducted DPPH assay which provides convincing evidence that group 2 has justifiable anti-inflammatory effects. However, due to the difference of the effects in group 1 and 2 was not that standing out, successively added silver ion to observe synergic effect of anti-inflammatory substances. Combined phenolic compound and silver ion showed dramatic effects in nitric oxide (NO) assay for increasing anti-inflammatory effects compared to other examined groups.


title: Overexpression of the gene encoding neurosecretory protein GL precursor prevents excessive fat accumulation in the adipose tissue of mice fed a long-term high-fat diet

abstract: We previously identified a novel small hypothalamic protein, neurosecretory protein GL (NPGL), which induces feeding behavior and fat accumulation in rodents depending on their diet. In the present study, we explored the effects of NPGL on feeding behavior and energy metabolism in mice placed on a long-term high-fat diet with 60% calories from fat (HFD 60). Overexpression of the NPGL precursor gene (Npgl) over 18 weeks increased food intake and body mass. The weekly body mass gain of Npgl-overexpressing mice was higher than that of controls until 7 weeks from induction of overexpression, after which it ceased to be so. Oral glucose tolerance tests showed that Npgl overexpression maintained glucose tolerance and increased blood insulin levels, and intraperitoneal insulin tolerance tests showed that it maintained insulin sensitivity. At the experimental endpoint, Npgl overexpression was associated with increased mass of the perirenal white adipose tissue (WAT) and decreased mass of the epididymal WAT (eWAT), resulting in little effect on the total WAT mass. These results suggest that under long-term HFD 60 feeding, Npgl overexpression may play a role in avoiding metabolic disturbance both by accelerating energy storage and by suppressing excess fat accumulation in certain tissues, such as the eWAT.

category: physiology


title: A Novel Hypothalamic Factor, Neurosecretory Protein GM, Causes Fat Deposition in Chicks

abstract: We recently discovered a novel cDNA encoding the precursor of a small secretory protein, neurosecretory protein GM (NPGM), in the mediobasal hypothalamus of chickens. Although our previous study showed that subcutaneous infusion of NPGM for 6 days increased body mass in chicks, the chronic effect of intracerebroventricular (i.c.v.) infusion of NPGM remains unknown. In this study, chronic i.c.v. infusion of NPGM for 2 weeks significantly increased body mass, water intake, and the mass of abdominal fat in chicks, whereas NPGM did not affect food intake, muscle mass, or blood glucose concentration. Morphological analyses revealed that fat accumulation occurred in both liver and abdominal fat. These results indicate that NPGM may participate in fat storage in chicks.


title: Variability of pollen grains quality in oat amphiploids and their parental species

abstract: The reproductive potential of oat species and their hybrid progeny (amphiploids) was evaluated during three vegetation seasons. Morphotypes and viability of pollen grains were described by means of correlations and regression, while relationships between taxa were analysed with the use of numerical taxonomy methods. Size of pollen grains varied between the growing seasons, but the relations between the taxa appeared to be stable. Viability of pollen grains was environmentally modified and showed no correlation with pollen length. In an ordination space, amphiploids were discriminated from parental species. In both group of plants, a positive correlation between the pollen size and the level of ploidy was maintained; however, along a regression line, amphiploids were located among species with a high level of ploidy and were extreme units deviating from the regression line. Developmental anomalies of pollen grains had a low frequency, with the formation of micrograins being the most common event. Such a pattern of development can prove that some pollen grains were chromosomally unbalanced. Anomalous morphotypes of pollen were more common in hybrid types than in species, including pollens with many poruses, which were found only in amphiploids. Frequencies of multiporate grains and micropollens were strongly correlated. In an ordination space, monoporate types (species) were discriminated from multiporate types (amphiploids). In general, the high level of pollen viability in amphiploids can prove their genomic stabilisation through many generations of their reproduction.

category: plant biology


title: Comprehensive multi-omics single-cell data integration reveals greater heterogeneity in the human immune system

abstract: Single-cell transcriptomics enables the definition of diverse human immune cell types across multiple tissues and disease contexts. Still, deeper biological understanding requires comprehensive integration of multiple single-cell omics (transcriptomic, proteomic, and cell-receptor repertoire). To improve the identification of diverse cell types and the accuracy of cell-type classification in multi-omics single-cell datasets, we developed SuPERR-seq, a novel analysis workflow to increase the resolution and accuracy of clustering and allow for the discovery of previously hidden cell subsets. In addition, SuPERR-seq accurately removes cell doublets and prevents widespread cell-type misclassification by incorporating information from cell-surface proteins and immunoglobulin transcript counts. This approach uniquely improves the identification of heterogeneous cell types in the human immune system, including a novel subset of antibody-secreting cells in the bone marrow.

category: systems biology


title: Global, Low Amplitude Cortical State Predicts Response Outcomes in a Selective Detection Task

abstract: Spontaneous neuronal activity strongly impacts stimulus encoding and behavioral responses. We sought to determine the effects of neocortical prestimulus activity on stimulus detection. We trained mice in a selective whisker detection task, in which they learned to respond (lick) to target stimuli in one whisker field and ignore distractor stimuli in the contralateral whisker field. During expert task performance, we used widefield Ca2+ imaging to assess prestimulus and post-stimulus neuronal activity broadly across frontal and parietal cortices. We found that lower prestimulus activity correlated with enhanced stimulus detection: lower prestimulus activity predicted response versus no response outcomes and faster reaction times. The activity predictive of trial outcome was distributed through dorsal neocortex, rather than being restricted to whisker or licking regions. Using principal component analysis, we demonstrate that response trials are associated with a distinct and less variable prestimulus neuronal subspace. For single units, prestimulus choice probability was weak yet distributed broadly, with lower than chance choice probability correlating with stronger sensory and motor encoding. These findings support a low amplitude, low variability, optimal prestimulus cortical state for stimulus detection that presents globally and predicts response outcomes for both target and distractor stimuli.


title: Heat-inactivated modified vaccinia virus Ankara boosts Th1-biased cellular and humoral immune responses as a vaccine adjuvant by activating the STING-mediated cytosolic DNA-sensing pathway

abstract:
BackgroundProtein or peptide-based subunit vaccines are promising platforms for combating human cancers and infectious diseases. However, one primary concern regarding subunit vaccines is the relatively weak immune responses induced by proteins or peptides. Therefore, developing novel and effective vaccine adjuvants is critical for the success of subunit vaccines. Modified vaccinia virus (MVA) is a safe and effective vaccine against smallpox and monkeypox. In this study, we explored the potential of heat-inactivated MVA (heat-iMVA) as a novel vaccine adjuvant.

MethodsWe co-administered heat-iMVA with a model antigen, chicken ovalbumin (OVA), either intramuscularly or subcutaneously twice, two weeks apart, and analyzed anti-OVA specific CD8+ and CD4+ T cells in the spleens and skin draining lymph nodes (dLNs) and serum anti-OVA IgG1 and IgG2c antibodies. We also compared the adjuvanticity of heat-iMVA with several known vaccine adjuvants, including complete Freunds adjuvant (CFA) and AddaVax, an MF59-like preclinical grade nano-emulsion. In addition, we tested whether co-administration of heat-iMVA plus tumor neoantigen peptides or irradiated tumor cells improves antitumor efficacy in a B16-F10 therapeutic vaccination model. Using Stimulator of Interferon Genes (STING) or Batf3-deficient mice, we evaluated the contribution of the STING pathway and Batf3-dependent CD103+/CD8 DCs in heat-iMVA-induced immunity.

ResultsCo-administration of protein- or peptide-based immunogens with heat-iMVA dramatically enhances Th1-biased cellular and humoral immune responses. This adjuvant effect of heat-iMVA is dependent on the STING-mediated cytosolic DNA-sensing pathway, and the antigen-specific CD8+ T cell response requires Batf3-dependent CD103+/CD8+ dendritic cells (DCs). Heat-iMVA infection of bone marrow-derived DCs (BMDCs) promoted antigen cross-presentation, whereas live MVA infection did not. RNA-seq analyses revealed that heat-iMVA is a more potent activator of the STING pathway than live MVA. Additionally, combining tumor neoantigen peptides or irradiated tumor cells with heat-iMVA delayed tumor growth and extended the median survival in B16-F10 therapeutic vaccination models.

ConclusionsHeat-iMVA induces type I interferon (IFN) production and antigen cross-presentation via a STING-dependent mechanism in DCs. Co-administration of heat-iMVA with peptide antigen generates strong Th1-biased cellular and humoral immunity. Collectively, our results demonstrate that heat-iMVA is a safe and potent vaccine adjuvant.

category: immunology


title: Specialized subsets of innate-like T cells and dendritic cells protect from lethal pneumococcal infection in the lung

abstract: Innate-like T cells, including invariant natural killer T (iNKT) cells, mucosal-associated invariant T (MAIT) cells and {gamma}{delta} T cells, are present in various barrier tissues, including the lung. They carry out protective responses during infections, but the mechanisms for protection are not completely understood. Here, we investigated their roles during pulmonary infection with Streptococcus pneumoniae. Following infection, innate-like T cells rapidly increased in lung tissue, in part through recruitment, but TCR activation and cytokine production occurred mostly in IL-17-producing NKT17 and {gamma}{delta} T cells. NKT17 cells were preferentially located outside the vasculature prior to infection, as were CD103+ dendritic cells (cDC1), which were important both for antigen presentation to NKT17 cells and {gamma}{delta} T cell activation. Whereas IL-17A-producing {gamma}{delta} T cells also were numerous, GM-CSF was exclusive to NKT17 cells and contributed to iNKT cell-mediated protection. These studies demonstrate how particular cellular interactions and responses of functional subsets of innate-like T cells contribute to protection from pathogenic lung infection.


title: Bats host the most virulent--but not the most dangerous--zoonotic viruses

abstract:
Identifying virus characteristics associated with the largest public health impacts on human populations is critical to informing zoonotic risk assessments and surveillance strategies. Efforts to assess "zoonotic risk" often use trait-based analyses to identify which viral and reservoir host groups are most likely to source zoonoses but have not fully addressed how and why the impacts of zoonotic viruses vary in terms of disease severity ( virulence), capacity to spread within human populations ( transmissibility), or total human mortality ( death burden). We analyzed trends in human case fatality rates, transmission capacities, and total death burdens across a comprehensive dataset of mammalian and avian zoonotic viruses. Bats harbor the most virulent zoonotic viruses even when compared to birds, which alongside bats, have been hypothesized to be "special" zoonotic reservoirs due to molecular adaptations that support the physiology of flight. Reservoir host groups more closely related to humans--in particular, Primates--harbor less virulent, but more highly transmissible viruses. Importantly, disproportionately high human death burden, arguably the most important metric of zoonotic risk, is not associated with any animal reservoir, including bats. Our data demonstrate that mechanisms driving death burdens are diverse and often contradict trait-based predictions. Ultimately, total human mortality is dependent on context-specific epidemiological dynamics, which are shaped by a combination of viral traits and conditions in the animal host population and across and beyond the human-animal interface. Understanding the conditions that predict high zoonotic burden in humans will require longitudinal studies of epidemiological dynamics in wildlife and human populations.

Significance statementThe clear need to mitigate zoonotic risk has fueled increased viral discovery in specific reservoir host taxa. We show that a combination of viral and reservoir traits can predict zoonotic virus virulence and transmissibility in humans, supporting the hypothesis that bats harbor exceptionally virulent zoonoses. However, pandemic prevention requires thinking beyond zoonotic capacity, virulence, and transmissibility to consider collective  burden on human health. For this, viral discovery targeting specific reservoirs may be inefficient as death burden correlates with viral, not reservoir, traits, and depends on context-specific epidemiological dynamics across and beyond the human-animal interface. These findings suggest that longitudinal studies of viral dynamics in reservoir and spillover host populations may offer the most effective strategy for mitigating zoonotic risk.


title: Identification of a divergent basal body assembly protein involved in land plant spermatogenesis

abstract: Oogamy is a form of sexual reproduction and evolved independently in animals, fungi, and plants. In streptophyte plants, Charophyceae, Coleochaetophyceae, bryophytes, lycophytes, ferns (monilophytes), and some gymnosperms (Cycads and Ginkgo) utilize spermatozoids as the male gamete. Plant spermatozoids commonly possess characteristic structures such as the spline, which consists of a microtubule array, the multilayered structure (MLS) in which the uppermost layer is continuum of the spline, and multiple flagella. However, the molecular mechanisms underpinning plant spermatogenesis remain to be elucidated. To identify the genes involved in plant spermatogenesis, we performed computational analyses and successfully found deeply divergent BLD10s by combining multiple methods and omics-data. We then validated the functions of candidate genes in the liverwort Marchantia polymorpha and the moss Physcomitrium patens and found that MpBLD10 and PpBLD10 are required for normal basal body and flagella formation. Mpbld10 mutants exhibited defects in remodeling of the cytoplasm and nucleus during spermatozoid formation, thus MpBLD10 should be involved in chromatin reorganization and elimination of the cytoplasm during spermiogenesis. Streptophyte BLD10s are orthologous to BLD10/CEP135 family proteins, which function in basal body assembly, but we found that BLD10s evolved especially fast in land plants and MpBLD10 might obtain additional functions in spermatozoid formation through the fast molecular evolution. This study provides a successful example of combinatorial study from evolutionary and molecular genetic perspectives that elucidated a function of the key protein of the basal body formation that fast evolved in land plants.

category: evolutionary biology


title: Phylogenetic distribution and expression pattern analyses identified a divergent basal body assembly protein involved in land plant spermatogenesis


title: SOCIAL INFORMATION AND BIOLOGICAL INVASIONS: CHORUS SONGS ARE MORE ATTRACTIVE TO EUROPEAN STARLINGS IN MORE RECENTLY ESTABLISHED POPULATIONS.

abstract: When biological invasions by animals occur, the individuals arriving in novel environments can be confronted with unpredictable or unfamiliar resources and may need social interaction to improve survival in the newly colonized areas. Gathering with conspecifics and using social information about their activities may reveal the location of suitable feeding and breeding sites. This could compensate for the absence of individual information about new habitats and constitute an advantage for new settlers. If a tendency to gather in response to social stimuli is transmitted from one generation to the next, and if the benefit of gathering is lower in long time established populations, there should be behavioural differences in receptivity to social cues in populations with different colonizing histories. We hypothesized that individuals of a social species like the European starling from relatively recently-established populations would be more responsive to social cues than individuals belonging to long-established populations. We conducted playback experiments using a starling chorus to test its acoustic attractiveness to populations of starlings with different colonizing histories. We compared the reaction of individuals from two populations in rural Brittany, western France, established for a long time, with three more recently settled ones: two populations from a propagation front in southern Italy and one urban population from Rennes city in Brittany. Our data supported our hypothesis: individuals from more recent populations were more responsive to the acoustic stimulus, and gave more calls in flight than individuals from populations with an older settlement history. We discuss the different behavioural responses we observed in the different populations and the potential effects of habitat characteristics and starling densities.


title: Habituation, task solving and memorization may facilitate biological invasions: the Starling example

abstract:
Invasions ecology deals more and more with behavioural characteristics of invasive species. Particularly, research have focused on the personality of invaders and on their way of coping with novelty in new habitats. Traits of neophobia may limit individuals in their exploration of novel objects or the consumption of novel foods, they may stop the access to valuable ressources. Actually, in novel environments like cities, food can be unreachable in throwaway dishes with lids or hidden in the garbage or even close to frightening objects. Animals may either left the place and waste these resources, or they can express low neophobia from the beginning and manipulate the objects to reach food. They may also habituate progressively to the context and use the ressources.

Here we analyzed the behavioural responses of individuals from three populations of European starling Sturnus vulgaris: a population anciently settled in a rural region, a population that has recently colonized a urban area and a population of wintering migrant birds.

We used a series of tests in order to explore if individuals would habituate to a novel object and if they could remember it eight months later. We explored if individuals would be less neophobic when confronted to two novel objects successively and we tested them in a learning task involving a novel object and an attractive food. Our results show that Sturnus vulgaris habituates rapidly to novel objects and that categorization facilitates neophobia lost when confronted to two different novel objects. Initially young birds appeared to be more skilled than adults in the learning task. Individuals from this species seem to be able to remember an object durably. We suggest that habituation, task solving and memorization are three mechanisms enhancing biological invasions.


title: Driving Native-like Zonal Enthesis Formation in Engineered Ligaments Using Mechanical Boundary Conditions and β-Tricalcium Phosphate

abstract: Fibrocartilaginous entheses are structurally complex tissues that translate load from elastic ligaments to stiff bone via complex zonal organization with gradients in organization, mineralization, and cell phenotype. Currently, these gradients, necessary for long-term mechanical function, are not recreated in soft tissue-to-bone healing or engineered replacements, leading to high failure rates. Previously, we developed a culture system which guides ligament fibroblasts to develop aligned native-sized collagen fibers using high density collagen gels and mechanical boundary conditions. These constructs hold great promise as ligament replacements, however functional ligament-to-bone attachments, or entheses, are required for long-term function in vivo. The objective of this study was to investigate the effect of compressive mechanical boundary conditions and the addition of beta tricalcium phosphate ({beta}TCP), a known osteoconductive agent, on the development of zonal ligament-to-bone entheses. We found that compressive boundary clamps, that restrict cellular contraction and produce a zonal tensile-compressive environment, guide ligament fibroblasts to produce 3 unique zones of collagen organization, and zonal accumulation of glycosaminoglycans (GAGs), type II and type X collagen by 6 weeks of culture, ultimately resulting in similar organization and composition as immature bovine entheses. Further, {beta}TCP under the clamp enhanced the maturation of these entheses, leading to increased GAG accumulation, sheet-like mineralization, and significantly improved tensile moduli, suggesting the initiation of endochondral ossification. This culture system produced some of the most organized entheses to date, closely mirroring early postnatal enthesis development, and provides an in vitro platform to better understand the cues that drive enthesis maturation in vivo.

category: bioengineering


title: SegmA: Residue Segmentation of cryo-EM density maps

abstract: 1The cryo-EM resolution revolution enables the development of algorithms for direct de-novo modelling of protein structures from given cryo-EM density maps. Deep Learning tools have been applied to locate structure patterns, such as rotamers, secondary structures and C atoms. We present a deep neural network (nicknamed SegmA) for the residue type segmentation of a cryo-EM density map. The network labels voxels in a cryo-EM map by the residue type (amino acid type or nucleic acid) of the sampled macromolecular structure. It also provides a visual representation of the density map by coloring the different types of voxels by their assigned colors. SegmAs algorithm is a cascade of CNNs and group rotational equivariant CNNs. A data gathering algorithm was designed for creating datasets that will give best results when used for SegmAs training. At resolution of 3.2{degrees}A SegmAs accuracy is 80% for nucleotides. Amino acids which can be seen by eye, such as LEU, ARG and PHE, are detected by SegmA with about 70% accuracy. In addition SegmA detects regions where the exact labeling is of low confidence due to resolution, noise, etc. Removing those "unconfident" regions increases the amino acid detection accuracy to 80% The SegmA open code is available at https://github.com/Mark-Rozanov/SegmA_3A/tree/master.


title: Artificial Intelligence Resolves Kinetic Pathways of Magnesium Binding to RNA

abstract: Magnesium is an indispensable cofactor in countless vital processes. In order to understand its functional role, the characterization of the binding pathways to biomolecules such as RNA is crucial. Despite the importance, a molecular description is still lacking since the transition from the water-mediated outer-sphere to the direct inner-sphere conformation is on the millisecond timescale and therefore out of reach for conventional simulation techniques. To fill this gap, we use transition path sampling to resolve the binding pathways and to elucidate the role of the solvent in the reaction. The results reveal that the molecular void provoked by the leaving phosphate oxygen of the RNA is immediately filled by an entering water molecule. In addition, water molecules from the first and second hydration shell couple to the concerted exchange. To capture the intimate solute-solvent coupling, we perform a committor analysis as basis for a machine learning algorithm that derives the optimal deep learning model from thousands of scanned architectures using hyperparameter tuning. The results reveal that the properly optimized deep network architecture recognizes the important solvent structures, extracts the relevant information and predicts the commitment probability with high accuracy. Our results provide a quantitative description of solute-solvent coupling which is ubiquitous for kosmotropic ions and governs a large variety of biochemical reactions in aqueous solutions.


title: MetaBinner: a high-performance and stand-alone ensemble binning method to recover individual genomes from complex microbial communities

abstract: Binning is an essential procedure during metagenomic data analysis. However, the available individual binning methods usually do not simultaneously fully use different features or biological information. Furthermore, it is challenging to integrate multiple binning results efficiently and effectively. Therefore, we developed an ensemble binner, MetaBinner, which generates component results with multiple types of features and utilizes single-copy gene (SCG) information for k-means initialization. It then utilizes a two-step ensemble strategy based on SCGs to integrate the component results. Extensive experimental results over three large-scale simulated datasets and one real-world dataset demonstrate that MetaBinner outperforms other state-of-the-art individual binners and ensemble binners. MetaBinner is freely available at https://github.com/ziyewang/MetaBinner.


title: Modelling time evolution of in blood alcohol concentration

abstract: A theoretical model based on mass conservation is proposed to predict blood alcohol concentration (BAC) over time. The proposed model takes as input the body parameters, the data timing for each drink, as well as his alcoholic strength and ingested amount. Three test cases with variations are presented and discussed. The results given are obtained by solving numerically the equation proposed. The solution predicts a well located alcohol peak and a reasonable time of alcohol body cleaning. This model represents a first order approach to a complex problem. Similar scenarios, like, for instance, drug concentrations can be modelled by using the same concept. The proposed model has been implemented on easy-to-use program COGORZA, which source code is available online at https://github.com/tonibois/Cogorza.


title: Role of non-specific interactions in the phase-separation and maturation of macromolecules

abstract:
Phase separation of biomolecules could be mediated by both specific and non-specific interactions. How the interplay between non-specific and specific interactions along with polymer entropy influences phase separation is an open question. We address this question by simulating self-associating molecules as polymer chains with a short core stretch that forms the specifically interacting functional interface, and longer non-core regions that participate in non-specific/promiscuous interactions. Our results show that the interplay of specific (strength,{epsilon} sp) and non-specific interactions (strength,{epsilon} ns) could result in phase separation of polymers and its transition to solid-like aggregates (mature state). In the absence of{epsilon} ns, the polymer chains do not dwell long enough in the vicinity of each other to undergo phase separation and transition into a mature state. On the other hand, in the limit of strong{epsilon} ns, the assemblies cannot transition into the mature state and form a non-specific assembly, suggesting an optimal range of interactions favoring mature multimers. In the scenario where only a fraction (Nfrac) of the non-core regions participate in attractive interactions, we find that a slight modifications to either{epsilon} ns or Nfrac can result in a dramatically altered self-assembled states. Using a combination of heterogeneous and homogeneous mix of polymers, we establish how this interplay between interaction energies dictates the propensity of biomolecules to find the correct binding partner at dilute concentrations in crowded environments.

Author SummaryBiological function relies on the ability of biomolecules to bind to specific interaction partners. In the crowded cellular milieu, the process of biomolecules binding to specific interaction partners to carry out a function is non-trivial. A mere diffusion-limited meeting of interaction partners in space does not ensure biomolecular function. Rather, even when in contact these molecules have to find the correct orientations to carry out function. Further, for dynamic biomolecules such as polymers, the functional configuration is often one of several possible configurations. In this scenario, assuming the functional configuration after binding involves overcoming of a significant entropic barrier. Therefore, the interacting biomolecules have to dwell in contact long enough before they reorganize to find the functional orientation! While functional contacts offer an enthalpic gain, they are often only a small fraction of all protein-protein interactions. Therefore, in this paper, we study the role played by non-functional, promiscuous interactions in shaping the thermodynamics and kinetics of formation of specific interactions. Our results suggest that there exists an optimal range of non-specific interaction strengths which promotes the process of biomolecular complexes finding the functional configurations.


title: Oncogenic c-Myc induces replication stress by increasing cohesins chromatin occupancy

abstract: Oncogene-induced replication stress is a major driver of genomic instability in cancer cells, with a central role in both cancer initiation and progression (1). Despite its critical role in cancer development, the mechanisms that lay at the basis of oncogene-induced replication stress remains poorly understood. Here, we investigate the mechanism of c-Myc-induced replication stress. Our data shows that c-Myc induces replication stress by increasing the amount of cohesins bound to chromatin in the G1 phase of the cell cycle. This is independent of previously suggested mechanisms involving deregulation of replication initiation and transcriptional interference. Restoring the amount of chromatin-bound cohesins to control levels, or preventing the accumulation of cohesins at CTCF sites, in cells experiencing oncogenic c-Myc activity prevents replication stress. Increased cohesins chromatin occupancy correlates with a c-Myc-dependent increase in the levels of the cohesion loader Mau2. Preventing c-Myc-induced increase in Mau2 reduces oncogene-induced replication stress. Together our data support a novel mechanism for oncogene-induced replication stress. Since c-Myc activation is a crucial event in many human cancers (2), identifying the mechanisms through which this oncogene promotes replication stress provides critical insights into cancer biology.

category: cancer biology


title: Supra-physiological levels of gibberellins/DELLAs modify the root cell size/number and the root architecture in root tips of A. thaliana seedlings. Connections to the root hair patterning and abundance

abstract: A previous study (McCarthy-Suarez, 2021) showed that growing A. thaliana seedlings for 5 days under excessive levels of gibberellins (GAs)/DELLAs altered the arrangement, shape and frequency of root hairs in root tips. Because no changes in the distribution or number of root hairs occurred when the gai-1 (gibberellin-insensitive-1) DELLA was over-expressed at the root epidermis, it was concluded that the GAs/DELLAs might regulate the root hair patterning and abundance in A. thaliana seedlings by acting from the root sub-epidermal tissues. In the present study, microscopy analyses showed that excessive levels of GAs/DELLAs also modified the size and number of root tip cells in A. thaliana seedlings. While excessive DELLAs shortened and widened the root epidermal, cortical, endodermal and pericycle cells, excessive GAs, excepting the epidermal cells, generally narrowed them. However, no changes of root cell size occurred when gai-1 was over-expressed at the root epidermis. In addition, high levels of DELLAs often induced extra cells at the root epidermis, cortex, endodermis and pericycle, whereas high levels of GAs sometimes induced extra cells at the root cortex and pericycle. On the other hand, excessive levels of DELLAs enhanced the outgrowth of lateral roots in root tips, unlike excessive levels of GAs. Thus, the results of this study suggest that supra-physiological levels of GAs/DELLAs might modify the size/number of root tip cells by acting from the root sub-epidermal tissues. This, in turn, might impact on the patterning and abundance of root hairs and on the root architecture.


title: IQD1 involvement in hormonal signaling and general defense responses against Botrytis cinerea

abstract:
IQ Domain 1 (IQD1) is a novel calmodulin-binding protein in A. thaliana, which was found to be a positive regulator of glucosinolate (GS) accumulation and plant defense responses against insects. We demonstrate here that the IQD1 overexpressing line (IQD1OXP) is more resistant also to the necrotrophic fungus Botrytis cinerea, whereas an IQD1 knockout line (iqd1-1) is much more sensitive. Furthermore, we show that IQD1 is upregulated by Jasmonic acid (JA) and downregulated by Salicylic acid (SA). Comparison of whole transcriptome expression between iqd1-1 and wild type revealed a substantial downregulation of genes involved in plant defense and hormone regulation. Further examination revealed a marked reduction of SA/JA signaling and increase in ethylene signaling genes in the iqd1-1 line. Moreover, quantification of SA, JA and abscisic acids in IQD1OXP and iqd1-1lines compared to WT showed a significant reduction in endogenous JA levels in the knockout line simultaneously with increased SA levels. Epistasis relations between IQD1OXP and mutants defective in plant-hormone signaling indicated that IQD1 acts upstream or parallel to the hormonal pathways (JA/ET and SA) in defense response against B. cinerea and in regulating GS accumulation and it is dependent on JAR1 controlling indole glucosinolate accumulation. As a whole, our results suggest that IQD1 is an important defensive protein against Botrytis cinerea in A. thaliana and is integrated into several important pathways such as plant microbe perception and hormone signaling.

SIGNIFICANCE STATEMENTIQD1 is involved in glucosinolate accumulation and in general defense responses. JA activates IQD1 that acts upstream or parallel to JA/ET and SA signaling pathway while controlling glucosinolate accumulation and defense against Botrytis cinerea and it is dependent on JAR1 controlling indole glucosinolate accumulation.


title: Software for Non-Parametric Image Registration of 2-Photon Imaging Data

abstract: Functional 2-photon microscopy is a key technology for imaging neuronal activity. The recorded image sequences, however, can contain non-rigid movement artifacts which requires high-accuracy movement correction. Variational optical flow (OF) estimation is a group of methods for motion analysis with established performance in many computer vision areas. However, it has yet to be adapted to the statistics of 2-photon neuroimaging data. In this work, we present the motion compensation method Flow-Registration that outperforms previous alignment tools and allows to align and reconstruct even low signal-to-noise ratio 2-photon imaging data and is able to compensate high-divergence displacements during local drug injections. The method is based on statistics of such data and integrates previous advances in variational OF estimation. Our method is available as an easy-to-use ImageJ / FIJI plugin as well as a MATLAB toolbox with modular, object oriented file IO, native multi-channel support and compatibility with existing 2-photon imaging suites.


title: Reward-dependent selection of feedback gains impacts rapid motor decisions

abstract:
Target reward influences motor planning strategies through modulation of movement vigor. Considering current theories of sensorimotor control suggesting that movement planning consists in selecting a goal-directed control strategy, we sought to investigate the influence of reward on feedback control. Here we explored this question in three human reaching experiments. First, we altered the explicit reward associated with the goal target and found an overall increase in feedback gains for higher target rewards, highlighted by larger velocities, feedback responses to external loads, and background muscle activity. Then, we investigated whether the differences in target rewards across multiple goals impacted rapid motor decisions during movement. We observed idiosyncratic switching strategies dependent on both target rewards and, surprisingly, the feedback gains at perturbation onset: the more vigorous movements were less likely to switch to a new goal following perturbations. To gain further insight into a causal influence of the feedback gains on rapid motor decisions, we demonstrated that biasing the baseline activity and reflex gains by means of a background load evoked a larger proportion of target switches in the direction opposite to the background load associated with lower muscle activity. Together, our results demonstrate an impact of target reward on feedback control and highlight the competition between movement vigor and flexibility.

Significance statementHumans can modulate their movement vigor based on the expected reward. However, a potential influence of reward on feedback control has not been documented. Here we investigated reaching control strategies in different contexts associated with explicit rewards for one or multiple goals, while exposed to external perturbations. We report two strategies: reward could either increase feedback gains, or promote flexible switches between goals. The engagement of peripheral circuits in the modulation of feedback gains was confirmed by the application of a background load that biased feedback vigor directionally, evoking differences in switching behavior in the opposite direction. We conclude that feedback vigor and flexible changes in goal are two competing mechanisms to be selected when interacting with a dynamic environment.


title: N-VEGF, a proteolytic product of the long isoform of VEGF-A, L-VEGF, shuttles to the nucleus to activate cellular stress survival circuits

abstract: Vascular endothelial growth factor A (VEGF-A) is a secreted protein that stimulates angiogenesis in response to hypoxia. Under hypoxic conditions, a non-canonical long isoform called L-VEGF is concomitantly expressed with VEGF-A. Once translated, L-VEGF it is proteolytically cleaved to generate N-VEGF and VEGF-A. Interestingly, while VEGF-A is secreted and affects the surrounding cells, N-VEGF is mobilized to the nucleus. This suggests that N-VEGF participates in transcriptional response to hypoxia. In this study, we performed a series of complementary experiments to examine the functional role of N-VEGF. Strikingly, we found that the mere expression of N-VEGF followed by its hypoxia-independent mobilization to the nucleus was sufficient to induce key genes associated with angiogenesis, such as Hif1, VEGF-A isoforms, as well as genes associated with cell survival under hypoxia. Complementarily, when N-VEGF was genetically depleted, key hypoxia-induced genes were downregulated and cells were significantly susceptible to hypoxia-mediated apoptosis. This is the first reports of N-VEGF serving as an autoregulatory arm of VEGF-A. Further experiments will be needed to determine the role of N-VEGF in cancer and embryogenesis.

category: molecular biology


title: N-VEGF, the forgotten isoform of VEGF-A, activate cellular stress survival circuits


title: N-VEGF, the autoregulatory arm of VEGF-A


title: The first crested duck genome reveals clues to genetic compensation and crest cushion formation

abstract: The Chinese crested (CC) duck is a unique indigenous waterfowl breed with a phenotypic crest trait that affects its high survival rate. Therefore, the CC duck is an ideal model to investigate the genetic compensation response to maintain genetic stability. In the present study, we first generated a chromosome-level genome of CC ducks. Comparative genomics revealed genes related to tissue repair, immune function, and tumors were under strong positive selection, which suggested that these adaptive changes might enhance cancer resistance and immune response to maintain the genetic stability of CC ducks. We sub-assembled a Chinese spot-billed duck genome and detected genome-assembled structure variants among three ducks. Functional analysis revealed that a large number of structural variants were related to the immune system, which strongly suggests the occurrence of genetic compensation in the anti-tumor and immune systems to further support the survival of CC ducks. Moreover, we confirmed that the CC duck originated from the mallard ducks. Finally, we revealed the physiological and genetic basis of crest traits and identified a causative mutation in TAS2R40 that leads to crest formation. Overall, the findings of this study provide new insights into the role of genetic compensation in adaptive evolution.

category: genomics


title: IRI-CCE: A Platform for Evaluating CRISPR-based Genome Editing Tools and Its Components

abstract: Rapid assessment of CRISPR/Cas (Clustered Regularly Interspaced Short Palindromic Repeats/CRISPR associated Cas protein)-based genome editing (GE) tools and their components are critical aspects for successful applications in different organisms. In many bacteria, double-stranded breaks (DSBs) generated by CRISPR/Cas tool generally cause cell death due to the lack of an efficient non-homologous end-joining pathway and restricts its use. CRISPR-based DSB-free base editors (BEs) have been applied for precise nucleotide editing in bacteria, which does not need to make DSBs. However, optimization of newer BE tools in bacteria is challenging owing to the toxic effects of BE reagents expressed using strong promoters. Improved variants of two main BEs capable of converting C-to-T (CBE) and A-to-G (ABE) have been recently developed but yet to be tested in bacteria. Here, we report a platform for in vivo rapid investigation of CRISPR-BE components in Escherichia coli (IRI-CCE) comprising different combinations of promoters/terminators. We demonstrate the use of IRI-CEE to characterize different variants of CBEs (PmCDA1, evoCDA1, APOBEC3A) and ABEs (ABE8e, ABE9e), exhibiting that each independent BE has its specific editing pattern for a given target site and promoter type. Additionally, the IRI-CCE platform offers a rapid way to screen functional gRNAs. In summary, CRISPR-BE components expressed by promoters of different strengths in the IRI-CCE allow an analysis of various BE tools, including cloned biopart modules and gRNAs.


title: IRI-CCE: A Platform for Evaluating CRISPR-based Base Editing Tools and Its Components


title: The high-throughput gene prediction of more than 1,700 eukaryote genomes using the software package EukMetaSanity

abstract: Gene prediction and annotation for eukaryotic genomes is challenging with large data demands and complex computational requirements. For most eukaryotes, genomes are recovered from specific target taxa. However, it is now feasible to reconstruct or sequence hundreds of metagenome-assembled genomes (MAGs) or single-amplified genomes directly from the environment. To meet this forth-coming wave of eukaryotic genome generation, we introduce EukMetaSanity, which combines state-of-the-art tools into three pipelines that have been specifically designed for extensive parallelization on high-performance computing infrastructure. EukMetaSanity performs an automated taxonomy search against a protein database of 1,482 species to identify phylogenetically compatible proteins to be used in downstream gene prediction. We present the results for intron, exon, and gene locus prediction for 112 genomes collected from NCBI, including fungi, plants, and animals, along with 1,669 MAGs and demonstrate that EukMetaSanity can provide reliable preliminary gene predictions for a single target taxon or at scale for hundreds of MAGs. EukMetaSanity is freely available at https://github.com/cjneely10/EukMetaSanity.


title: First record of Temnothorax convexus (Forel, 1894) in Portugal (Hymenoptera: Formicidae) with an updated checklist of ants from the country

abstract: The arboreal ant Temnothorax convexus (Forel, 1894) is reported for the first time in Portugal. A single colony was found nesting inside an abandoned gall near Lisbon. A full morphometric evaluation of the specimens is provided, including a small sample from the recently discovered population in South Iberia. High-definition photographs of the worker caste are given, together with a comparison with the most similar species in Iberia and an update of the Portuguese ant checklist.

category: zoology


title: Age- and sex-related topological organisation of human brain functional networks and their relationship to cognition

abstract:
BACKGROUNDAge and sex associated with changes in functional brain network topology and cognition in large population of older adults have been poorly understood. We explored this question further by examining differences in 11 resting-state graph theory measures with respect to age, sex, and their relationships with cognitive performance in 17,127 UK Biobank participants (mean=62.83{+/-}7.41 years).

METHODSBrain connectivity toolbox was used to derive the graph theory measures that assessed network integration, segregation, and strength. Multiple linear regression was performed the relationship between age, sex, cognition, and network measures. Subsequently, multivariate analysis was done to further examine the joint effect of the network measures on cognitive functions.

RESULTSAge was associated with an overall decrease in the effectiveness of network communication (i.e. integration) and loss of functional specialisation (i.e. segregation) of specific brain regions. Sex differences were also observed, with women showing more efficient networks which were less segregated than in men (FDR adjusted p<.05). Age-related changes were also more apparent in men than women, which suggests that men may be more vulnerable to cognitive decline with age. Interestingly, while network segregation and strength of limbic network were only nominally associated with cognitive performance, the network measures collectively were significantly associated with cognition (FDR adjusted p[≤].002). This may imply that individual measures may be inadequate to capture much of the variance in neural activity or its output and need further refinement.

CONCLUSIONThe complexity of the functional brain organisation may be shaped by an individuals age and sex, which ultimately may influence cognitive performance of older adults. Age and sex stratification may be used to inform clinical neuroscience research to identify older adults at risk of cognitive dysfunction.


title: Opposing roles of blood-borne monocytes and tissue-resident macrophages in limbal stem cell damage after ocular injury

abstract:
Limbal stem cell (LSC) deficiency is a frequent and severe complication after chemical injury to the eye. Previous studies have assumed that this is mediated directly by the caustic agent. Here we show that LSC damage occurs through immune cell mediators, even without direct injury to LSCs. In particular, pH elevation in the anterior chamber (AC) causes acute uveal stress, release of inflammatory cytokines at the basal limbal tissue, and subsequent LSC loss. Peripheral CCR2+ CX3CR1- monocytes are the key mediators of LSC damage, through the upregulation of tumor necrosis factor alpha (TNF-) at the limbus. In contrast to peripherally-derived monocytes, CX3CR1+ CCR2- tissue-resident macrophages have a protective role and their depletion prior to injury exacerbates LSC loss and increases LSC vulnerability to TNF--mediated apoptosis independently of CCR2+ cell infiltration into the tissue. Consistently, repopulation of the tissue by new resident macrophages not only restores the protective M2-like phenotype of macrophages but also suppresses LSC loss after exposure to inflammatory signals. These findings may have clinical implication in patient with chemical burns.

SignificanceLimbal stem cell (LSC) loss after chemical burn is a significant clinical problem that has long been thought to be the result of direct chemical injury. This study demonstrates the existence of competing inflammatory mechanism responsible for LSC death, mediated by infiltrating peripheral monocytes that antagonize and overcome the protective role of tissue-resident macrophages. Thus, enhancing the role of tissue-resident macrophages while suppressing that of infiltrating monocytes could be a novel therapeutic strategy for LSC survival.


title: A comprehensive collection of transcriptome data to support life cycle analysis of the poplar rust fungus Melampsora larici-populina

abstract: Melampsora larici-populina is an obligate biotrophic plant pathogen responsible for the poplar rust disease. This fungus belongs to the taxonomical order Pucciniales and exhibits a complex heteroecious and macrocyclic life cycle, i.e. it has the capacity to infect two unrelated host plants, larch and poplar, and to form five distinct spore types through the year. The M. larici-populina genome has been sequenced and annotated in 2011 and since, different transcriptomic analyses were conducted at different stages with oligoarrays and later on with RNA-Seq covering most of its life cycle. Here, we collected published transcriptome data for the poplar rust fungus, transposed them for the version 2 of the genome now available at the Joint Genome Institute Mycocosm website and performed normalization of different oligoarray datasets on one hand, and of RNA-Seq on the other hand. We report a comprehensive normalized dataset for this fungus, made available for the community, which allows life cycle transcriptomics analysis.

category: microbiology


title: Distinct mechanisms underlie H2O2 sensing in C. elegans head and tail

abstract:
Environmental oxidative stress threatens cellular integrity and should therefore be avoided by living organisms. Yet, relatively little is known about environmental oxidative stress perception. Here, using microfluidics, we showed that like I2 pharyngeal neurons, the tail phasmid PHA neurons function as oxidative stress sensing neurons in C. elegans, but display different responses to H2O2 and light. We uncovered that different but related receptors, GUR-3 and LITE-1, mediate H2O2 signaling in I2 and PHA neurons. Still, the peroxiredoxin PRDX-2 is essential for both, and might promote H2O2-mediated receptor activation. Our work demonstrates that C. elegans can sense a broad range of oxidative stressors using partially distinct H2O2 signaling pathways in head and tail sensillae, and paves the way for further understanding of how the integration of these inputs translates into the appropriate behavior.

Graphical abstract

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category: cell biology


title: LAMP2A regulates the loading of proteins into exosomes.

abstract: Exosomes are extracellular vesicles of endosomal origin released by virtually all cell types across metazoans. Exosomes are active vehicles of intercellular communication and can transfer lipids, RNAs and proteins between different cells, tissues or organs. However, the mechanisms that regulate the selective loading of cytosolic proteins into these vesicles are still largely unknow. Here we describe a mechanism whereby proteins containing a pentapeptide sequence, biochemically related to the KFERQ-motif, are loaded into a subpopulation of exosomes in a process that is dependent on the membrane protein LAMP2A. Moreover, this mechanism is independent of the ESCRT machinery components TSG101 and VPS4b and dependent on HSC70, CD63, Alix, Syntenin-1, Rab31 and ceramides. The transcription factor and master regulator of hypoxia HIF1A is loaded into exosomes by this mechanism to transport hypoxia signaling to normoxic cells. Additionally, by tagging fluorescent proteins with KFERQ-like sequences we were able to follow inter-organ transfer of exosomes in zebrafish larvae. Our findings identify LAMP2A as a key component in exosome biogenesis while opening new avenues for exosome engineering by allowing the loading of bioactive proteins by tagging them with KFERQ-like motifs.


title: AGO1 regulates major satellite transcripts and H3K9me3 distribution at pericentromeric regions in mESCs

abstract:
Argonaute proteins (AGOs), that play an essential role in cytosolic post-transcriptional gene silencing, have been also reported to function in nuclear processes like transcriptional activation or repression, alternative splicing and, chromatin organization. As most of these studies have been conducted in human cancer cell lines, the relevance of AGOs nuclear functions in the context of mouse early embryonic development remains uninvestigated. Here, we examined a possible role of the AGO1 protein on the distribution of constitutive heterochromatin in mouse Embryonic Stem Cells (mESCs). We observed a specific redistribution of the repressive histone mark H3K9me3 and the heterochromatin protein HP1, away from pericentromeric regions upon Ago1 depletion. Furthermore, we demonstrated that major satellite transcripts are strongly upregulated in Ago1_KO mESCs and that their levels are partially restored upon AGO1 rescue. We also observed a similar redistribution of H3K9me3 and HP1 in Drosha_KO mESCs, suggesting a role for microRNAs (miRNAs) in the regulation of heterochromatin distribution in mESCs. Finally, we showed that specific miRNAs with complementarity to major satellites can partially regulate the expression of these transcripts.

Summary blurbDepletion of AGO1 in mESCs leads to a redistribution of H3K9me3 and HP1 away from pericentromeric regions and is accompanied by an upregulation of major satellites transcripts.


title: AGO1 regulates pericentromeric regions in mouse embryonic stem cells


title: Intermittent hypoxia enhances the expression of HIF1A by increasing the quantity and catalytic activity of KDM4A-C and demethylating H3K9me3 at the HIF1A locus

abstract: Cellular oxygen-sensing pathways are primarily regulated by hypoxia inducible factor-1 (HIF-1) in chronic hypoxia and are well studied. Intermittent hypoxia also occurs in many pathological conditions, yet little is known about its biological effects. In this study, we investigated how two proposed cellular oxygen sensing systems, HIF-1 and KDM4A-C, respond to cells exposed to intermittent hypoxia and compared to chronic hypoxia. We found that intermittent hypoxia increases HIF-1 activity through a pathway distinct from chronic hypoxia, involving the KDM4A, -B and -C histone lysine demethylases. Intermittent hypoxia increases the quantity and activity of KDM4A-C resulting in a decrease in H3K9 methylation. This contrasts with chronic hypoxia, which decreases KDM4A-C activity, leading to hypermethylation of H3K9. Demethylation of histones bound to the HIF1A gene in intermittent hypoxia increases HIF1A mRNA expression, which has the downstream effect of increasing overall HIF-1 activity and expression of HIF target genes. This study highlights how multiple oxygen-sensing pathways can interact to regulate and fine tune the cellular hypoxic response depending on the period and length of hypoxia.


title: Taxonomic repositioning of twelve Xanthomonas campestris, seven Xanthomonas axonopodis and one Pseudomonas cissicola reference pathovars to Xanthomonas citri

abstract: Here on the basis of phylo-taxonogenomics criteria we present amended description of 20 pathovars to Xanthomonas citri majority (18/20) of which were first reported from India. 7/20 are currently classified as X. axonopodis, 12/20 as X. campestris and 1/20 as Pseudomonas cissicola. Here, we have generated genome sequence data for 4 pathovars and genomes of remaining 16 were used from the published data. Genome based investigation reveals that all these pathovars belong to X. citri and not to X. axonopodis or X. campestris as previously reported. Present proposal is to aid in resolving the taxonomic confusion of the X. ctiri pathovars and prevent future usage of invalid names.


title: Low affinity integrin states have faster binding kinetics than the high affinity state

abstract: Integrin conformational ensembles contain two low-affinity states, bent-closed and extended-closed, and an active, high-affinity, extended-open state. It is widely thought that integrins must be activated before they bind ligand; however, one model holds that activation follows ligand binding. As ligand-binding kinetics are not only rate limiting for cell adhesion but also have important implications for the mechanism of activation, we measure them here for integrins 4{beta}1 and 5{beta}1 and show that the low-affinity states bind substantially faster than the high-affinity state. On and off-rate measurements are similar for integrins on cell surfaces and ectodomain fragments. Although the extended-open conformations on-rate is [~]20-fold slower, its off-rate is [~]25,000-fold slower, resulting in a large affinity increase. The tighter ligand-binding pocket in the open state may slow its on-rate. These kinetic measurements, together with previous equilibrium measurements of integrin conformational state affinity and relative free energy on intact cells, are key to a definitive understanding of the mechanism of integrin activation.

category: biophysics


title: The cryo-EM structure of the chloroplast ClpP complex reveals an interaction with the co-chaperonin complex that inhibits ClpP proteolytic activity

abstract: Protein homeostasis in plastids is strategically regulated by the protein quality control system involving multiple chaperones and proteases, among them the Clp protease. We determined the structure of the chloroplast ClpP complex from Chlamydomonas reinhardtiiby cryo-EM. ClpP contains two heptameric catalytic rings without any symmetry. The top ring contains one ClpR6, three ClpP4 and three ClpP5 subunits while the bottom ring is composed of three ClpP1C subunits and one each of the ClpR1-4 subunits. ClpR3, ClpR4 and ClpT4 subunits connect the two rings and stabilize the complex. The chloroplast Cpn11/20/23 co-chaperonin, a co-factor of Cpn60, forms a cap on the top of ClpP by protruding mobile loops into hydrophobic clefts at the surface of the top ring. The co-chaperonin repressed ClpP proteolytic activity in vitro. By regulating Cpn60 chaperone and ClpP protease activity, the co-chaperonin may play a role in coordinating protein folding and degradation in the chloroplast.


title: Miniature inverted-repeat transposable elements drive rapid microRNA diversification in angiosperms

abstract: MicroRNAs (miRNAs) are rapidly evolving endogenous small RNAs programing organism function and behavior. Although models for miRNA origination have been proposed based on sporadic cases, the genomic mechanisms driving swift diversification of the miRNA repertoires in plants remain elusive. Here, by comprehensively analyzing 20 phylogenetically representative plant species, we identified miniature inverted-repeat transposable elements (MITEs) as the predominant genomic sources for de novo miRNAs in angiosperms. Our data illustrated a transposition-transcription process whereby properly sized MITEs transposed into active genic regions could be converted into new miRNAs, termed MITE-miRNAs, in as few as 20 generations. We showed that this molecular domestication mechanism leads to a possible evolutionary arms race between the MITEs and the host genomes that rapidly and continuously changes the miRNA repertoires. We found that the MITE-miRNAs are selected for targeting genes associated with plant adaptation and habitat expansion, thereby constituting a genomic innovation potentially underlying angiosperm megadiversity.


title: Inhibition of striatal SEZ6 by miR-3594-5p is a drug-specific marker for late-stage heroin intake escalation

abstract: Escalation of drug use is a hallmark stage in the transition to addiction and uncovering its underlying brain molecular mechanisms constitutes a considerable challenge. Here, we report in rats with extended access to heroin for self-administration that miR-3594-5p was upregulated in the dorsal striatum at late, but not early, stages during escalation when excessive heroin intake plateaued. Striatal miR-3594-5p bound directly to the 3UTR region of Sez6 transcript and inhibited its expression, thereby decreasing the mature form of the translated SEZ6 protein. This miR-3594-5p/Sez6 interaction was specific to heroin, as it was not observed with cocaine, and correlated with the severity of heroin intake escalation. Our findings reveal that miRNA alterations during escalation of drug self-administration are spatially and temporally regulated and drug-specific.

category: neuroscience


title: Connectivity between the hippocampus and default mode network during the relief, but not elicitation, of curiositysupports curiosity-enhanced memory enhancements

abstract:
Consistent with the idea that curiosity enhances information seeking, it has been shown that activity within both the dopaminergic circuit and hippocampus supports curiosity-enhanced learning. However, the role of whole-brain mechanisms involved in cognitive control (fronto-parietal network; FPN) and memory integration (default mode network; DMN) that might underpin curiosity states and their effects on memory remain elusive. We hypothesised that the FPN and DMN should distinguish between high- and low-curiosity conditions and be recruited more heavily for later remembered information associated with high-curiosity. Here, we used functional magnetic resonance imaging whilst participants completed a trivia paradigm, in which we presented trivia questions associated with high- and low-curiosity, followed by the associated answer. After a short delay, we tested memory for trivia answers. We adopted a network-based parcellation of the brain into subnetworks of the FPN and DMN to examine how neural activity within, and functional connectivity between, each subnetwork predicts curiosity-enhanced memory. Across elicitation and relief of curiosity, we found focal recruitment of FPNA and widespread recruitment of DMN subnetworks in support of curiosity and curiosity-enhanced memory. Most importantly, during the elicitation of curiosity, functional subcortical connectivity and across cortical networks, but not subcortical-cortical coupling, correlated with curiosity-enhanced memory. However, during the relief of curiosity, coupling between subcortical regions and DMNA emerged in support of curiosity-enhanced memory. Taken together, our results provide the first evidence about how neuromodulatory mechanisms via the hippocampal-dopaminergic circuit trigger states of curiosity and thereby communicate to higher-order cortical regions to facilitate curiosity-enhanced memory.

Significant statementDoes neural activity within, and functional connectivity between, the dopaminergic-hippocampal network, fronto-parietal network (FPN), and default mode network (DMN) underpin curiosity states and their effects on memory? Here, we show how the dopaminergic system together with the hippocampus interact specifically with subnetwork DMNA potentially reflecting how subcortical regions support the enhancement of memory intergration of semantic information associated with curiosity. As DMNA (the core DMN subnetwork) was also functionally coupled with the whole DMN network and the semantic control network (FPNA), these findings provide a plausible neuromodulatory mechanism through which hippocampal-dopaminergic input triggers curiosity and then communicates to higher-order brain regions via DMNA to facilitate curiosity-enhanced memory.


title: Quantitative Profiling of Adaptation to Cyclin E Overproduction

abstract: Cyclin E/CDK2 drives cell cycle progression from G1 to S phase. Cyclin E overproduction is toxic to mammalian cells, although the gene encoding cyclin E (CCNE1) is overexpressed in some cancers. To gain insight into how cancer cells tolerate high cyclin E, we extensively characterized non-transformed epithelial cells throughout a time course of chronic cyclin E overproduction. Cells overproducing human cyclin E, but not cyclin D or cyclin A, briefly experienced truncated G1 phases, then endured a transient period of DNA replication origin underlicensing, replication stress, and severely impaired proliferation. Individual cells displayed substantial intercellular heterogeneity in cell cycle dynamics and CDK activity. Each phenotype improved rapidly despite maintaining high cyclin E-associated activity. Transcriptome analysis revealed that adapted cells downregulated a cohort of G1-regulated genes. Withdrawing cyclin E induction only partially reversed the intermediate licensing phenotype of adapted cells indicating that adaptation is at least partly independent of mutations. This study provides evidence that mammalian cyclin E/CDK inhibits origin licensing by an indirect mechanism through premature S phase onset and provides further insight into the relationship between CDK activity and licensing in mammals. It serves as an example of specific oncogene adaptation that may recapitulate molecular changes during tumorigenesis.


title: The northern gene flow into southeastern East Asians inferred from genome-wide array genotyping

abstract: The population history of Southeast China remains poorly understood due to the sparse sampling of present-day populations and far less modeling with ancient genomic data. We here newly reported genome-wide genotyping data from 207 present-day Han Chinese and Hmong-Mien-speaking She people from Fujian and Taiwan, southeast China. We co-analyzed with 66 early-Neolithic to Iron-Age ancient Fujian and Taiwan individuals obtained from literature to explore the genetic continuity and admixture based on the genetic variations of high-resolution time transect. We found the genetic differentiation between northern and southern East Asians defined by a north-south East Asian genetic cline and the studied southern East Asians were clustered in the southern end of this cline. We also found that southeastern coastal continental modern East Asians harbored the genetic differentiation with other southern Tai-Kadai, Hmong-Mien, Austronesian and Austroasiatic speakers, as well as geographically close Neolithic-to-Iron Age populations, but relatedly close to post-Neolithic Yellow River ancients, which suggested the influence of southward gene flow on the modern southern coastal gene pool. Besides, we also identified one new Hmong-Mien genetic cline in East Asia with the coastal Fujian She localizing at the intersection position between Hmong-Mien and Han clines in the principal component analysis. She people show stronger genetic affinity with southern East Asian indigenous populations with the main ancestry deriving from Hanben-related populations. The southeastern Han Chinese could be modeled with the primary ancestry deriving from the group related to the Yellow River Basin millet farmers and the remaining from groups related to southeastern ancient indigenous rice farmers, which was consistent with the northern China origin of modern southeastern Han Chinese and in line with the historically and archaeologically attested southward migrations of Han people and their ancestors. Interestingly, f4-statistics and three-way admixture model results showed both coastal ancient sources related to Austronesian speakers and inland ancient sources related to Austroasiatic speakers complexed the modern observed fine-scale genetic structure here. Our estimated north-south admixture time ranges based on the decay of the linkage disequilibrium spanned from the Bronze age to historic periods, suggesting the recent large-scale population migrations and subsequent admixture participated in the formation of modern Han in Southeast Asia.

category: genetics


title: Fusion-oncogenes are associated with increased metastatic capacity and persistent disease in pediatric thyroid cancers

abstract:
BackgroundIn 2014, data from a comprehensive multiplatform analysis of 496 adult papillary thyroid cancer samples reported by The Cancer Genome Atlas project suggested that reclassification of thyroid cancer into molecular subtypes, RAS-like and BRAF-like, better reflects clinical behavior than sole reliance on pathological classification. The aim of this study was to categorize the common oncogenic variants in pediatric differentiated thyroid cancer and investigate if mutation subtype classification correlated with the risk of metastasis and response to initial therapy in pediatric DTC.

MethodsSomatic cancer gene panel analysis was completed on DTC from 131 pediatric patients. DTC were categorized into RAS-mutant (H-K-NRAS), BRAF-mutant (BRAF p.V600E) and RET/NTRK fusion (RET, NTRK1 and NTRK3 fusions) to determine differences between subtype classification in regard to pathological data (AJCC TNM) as well as response to therapy 1-year after initial treatment had been completed.

ResultsMutation-based subtype categories were significant in most variables, including age at diagnosis, metastatic behavior, and the likelihood of remission at 1-year. Patients with RET/NTRK fusions were significantly more likely to have advanced lymph node and distant metastasis and less likely to achieve remission at one year than patients within RAS- or BRAF-mut subgroups.

ConclusionsOur data supports that genetic subtyping of pediatric DTC more accurately reflects clinical behavior than sole reliance on pathological classification with patients with RET/NTRK fusions having worse outcomes than those with BRAF-mutant disease. Future trials should consider inclusion of molecular subtype into risk stratification.


title: Evaluating Differences in Elastic Modulus of Regenerated and Uninjured Mouse Digit Bone through microCT Density-Elasticity Calculation and Nanoindentation Testing

abstract: Bone is an essential, healing structure in vertebrates that ensures daily function. However, the regenerative capacity of bone declines with age, compromising quality of life in the elderly and increasing cost of care. Here, for the first time, the elasticity of regenerated bone in a mouse digit amputation model is evaluated in order to better investigate biomechanics of skeletal regeneration. Amputation of the distal one third of the digit (third phalangeal element - P3) results in de novo regeneration of the digit, where analyzing the structural quality of this regenerated bone is a challenging task due to its small scale and triangular shape. To date, the evaluation of structural quality of the P3 bone has primarily focused on mineral density and bone architecture. This work describes an image-processing based method for assessment of elasticity in the whole P3 bone by using microcomputed tomography-generated mineral density data to calculate spatially discrete elastic modulus values across the entire P3 bone volume. Further, we validate this method through comparison to nanoindentation-measured values for elastic modulus. Application to a set of regenerated and unamputated digits shows that regenerated bone has a lower elastic modulus compared to the uninjured digit, with a similar trend for experimental hardness values. This method will be impactful in predicting and evaluating the regenerative outcomes of potential treatments and heightens the utility of the P3 regenerative model.