title: Arbuscular mycorrhizal fungal composition across US citrus orchards, management strategies, and disease severity spectrum

abstract: Arbuscular mycorrhizal fungi (AMF) remain understudied in perennial cropping systems. Citrus is a globally grown fruit tree and under threat by the pandemic Huanglongbing (HLB) disease. Here, we assessed in what capacity geographical location, management strategies and disease affect AMF citrus root communities. Root samples were collected from 88 trees in ten orchards located in the two major citrus producing states in the US. Orchards were selected based on conventional or organic practices in California and based on HLB symptom severity in Florida. We used AMF-specific amplicon sequencing primers to capture community composition and diversity. Taxa names were assigned based on a phylogenetic analysis that comprised a backbone of AMF references sequences from Mycobank and virtual taxa from the MaarjAM database. AMF were detected in 78% of citrus root samples with taxa belonging to six known (Dominikia, Funneliformis, Glomus, Rhizophagus, Sclerocystis, Septoglomus) and unknown Glomeraceae genera. Geographical location affected AMF community composition but not richness, whereas management practice and disease influenced both richness and composition. Our approach indicated that perennial agroecosystems share a set of AMF generalist and specialist taxa. Some taxa could improve environmental fitness and be exploited for agricultural purposes.


title: The RNA Virome of Echinoderms

abstract: Echinoderms are a phylum of marine invertebrates that include model organisms, keystone species, and animals commercially harvested for seafood. Despite their scientific, ecological, and economic importance, there is little known about the diversity of RNA viruses that infect echinoderms compared to other invertebrates. We screened over 900 transcriptomes and viral metagenomes to characterize the RNA virome of 38 echinoderm species from all five classes (Crinoidea, Holothuroidea, Asteroidea, Ophiuroidea and Echinoidea). We identified 347 viral genome fragments that were classified to genera and families within nine viral orders - Picornavirales, Durnavirales, Martellivirales, Nodamuvirales, Reovirales, Amarillovirales, Ghabrivirales, Mononegavirales, and Hepelivirales. We compared the relative viral representation across three life stages (embryo, larvae, adult) and characterized the gene content of contigs which encoded complete or near-complete genomes. The proportion of viral reads in a given transcriptome was not found to significantly differ between life stages though the majority of viral contigs were discovered from transcriptomes of adult tissue. This study illuminates the biodiversity of RNA viruses from echinoderms, revealing the occurrence of viral groups in natural populations.

category: microbiology


title: Chaperones facilitate heterologous expression of naturally evolved putative de novo proteins

abstract:
Over the past decade, evidence has accumulated that new protein coding genes can emerge de novo from previously non-coding DNA. Most studies have focused on large scale computational predictions of de novo protein coding genes across a wide range of organisms. In contrast, experimental data concerning the folding and function of de novo proteins is scarce. This might be due to difficulties in handling de novo proteins in vitro, as most are predicted to be short and disordered. Here we propose a guideline for the effective expression of eukaryotic de novo proteins in Escherichia coli.

We used 11 sequences from Drosophila melanogaster and 10 from Homo sapiens, that are predicted de novo proteins from former studies, for heterologous expression. The candidate de novo proteins have varying secondary structure and disorder content. Using multiple combinations of purification tags, E. coli expression strains and chaperone systems, we were able to increase the number of solubly expressed putative de novo proteins from 30 % to 62 %. Our findings indicate that the best combination for expressing putative de novo proteins in E.coli is a GST-tag with T7 Express cells and co-expressed chaperones. We found that, overall, proteins with higher predicted disorder were easier to express.

category: molecular biology


title: More persistent bacterial than fungal associations in the microbiota of a pest

abstract: The invasive fly Drosophila suzukii is a pest that can infest a diverse range of intact, ripening fruits, using its serrated ovipositor. This constitutes a different niche compared to the rotting fruits its ancestors use, especially because these intact fruits have limited quantities of microbes and soluble nutrients for the developing larvae. To investigate the potential role of microbial associations in the niche expansion of this invasive fly, we characterized the bacterial and fungal communities of D. suzukii and various wild fruits from which they developed. To assess cross-generational microbial associations, we also lab-reared fly populations and characterized their microbial communities. Diversity metrics of microbial communities differed significantly between flies and fruits. Different fruit types varied substantially in microbial composition, while flies showed relatively uniform bacterial communities, irrespective of the fruit source they developed on. After lab-rearing, bacterial communities still showed considerable overlap with those of wild flies. Fungal communities of flies and fruits showed larger resemblance, with a substantial overlap between wild flies and the corresponding fruits on which they had developed. Our study thus reports that the fungal community structure in these pests largely reflects those on the breeding substrates, while these flies might have formed more persistent associations with bacteria and transmit these across generations rather than obtaining them from their food source.

category: ecology


title: ABA-IMPORTING TRANSPORTER 1.1 activity in the endosperm of tomato seeds restrains germination under salinity stress

abstract: The plant hormone abscisic acid (ABA) has a central role in the regulation of seed maturation and dormancy. ABA also restrains germination under abiotic-stress conditions. Here we show in tomato (Solanum lycopersicum) that the ABA importer ABA-IMPORTING TRANSPORTER 1.1 (AIT1.1) has a role in radicle emergence following imbibition. AIT1.1 expression was upregulated during imbibition, and CRISPR/Cas9-derived ait1.1 mutant seeds exhibited faster radicle emergence, increased germination and partial resistance to ABA. AIT1.1 was highly expressed in the endosperm, but not in the embryo, and ait1.1 isolated embryos did not show resistance to ABA. On the other hand, loss of AIT1.1 activity promoted the expression of endosperm-weakening related genes, and seed-coat scarification eliminated the promoting effect of ait1.1 on radicle emergence. Therefore, we propose that imbibition-induced AIT1.1 expression in the endosperm, mediates ABA-uptake into endosperm cells to restrain endosperm weakening. While salinity conditions strongly inhibited the wild-type (WT) M82 seed germination, it had much weaker effect on ait1.1 germination. We suggest that this AIT1.1 function was evolved to inhibit germination under unfavorable conditions, such as salinity. Unlike other ABA mutants, ait1.1 exhibited normal seed longevity, and therefore, the ait1.1 allele may have a potential for improving seed germination in crops.

category: plant biology


title: Arabidopsis PFA-DSP-type phosphohydrolases target specific inositol pyrophosphate messengers

abstract: Inositol pyrophosphates are signaling molecules containing at least one phosphoanhydride bond that regulate a wide range of cellular processes in eukaryotes. With a cyclic array of phosphate esters and diphosphate groups around myo-inositol, these molecular messengers possess the highest charge density found in nature. Recent work deciphering inositol pyrophosphate biosynthesis in Arabidopsis revealed important functions of these messengers in nutrient sensing, hormone signaling and plant immunity. However, despite the rapid hydrolysis of these molecules in plant extracts, very little is known about the molecular identity of the phosphohydrolases that convert these messengers back to their inositol polyphosphate precursors. Here, we investigate whether Arabidopsis Plant and Fungi Atypical Dual Specificity Phosphatases (PFA-DSP1-5) catalyze inositol pyrophosphate phosphohydrolase activity. We find that recombinant proteins of all five Arabidopsis PFA-DSP homologs display phosphohydrolase activity with a high specificity for the 5-{beta}-phosphate of inositol pyrophosphates. We further show that heterologous expression of Arabidopsis PFA-DSP1-5 rescues wortmannin-sensitivity and deranged inositol pyrophosphate homeostasis caused by the deficiency of the PFA-DSP-type inositol pyrophosphate phosphohydrolase Siw14 in yeast. Heterologous expression in Nicotiana benthamiana leaves provided evidence that Arabidopsis PFA-DSP1 also displays 5-{beta}-phosphate specific inositol pyrophosphate phosphohydrolase activity in planta. Our findings lay the biochemical basis and provide the genetic tools to uncover the roles of inositol pyrophosphates in plant physiology and plant development.


title: Increased gut microbial mucin foraging promotes clearance of a parasitic worm

abstract:
BACKGROUND & AIMSHost-secreted gastrointestinal mucus plays a key role in the expulsion of intestinal nematode parasites. A balance between mucin secretion by the host and the gut microbial mucin foraging is essential to maintain the intestinal homeostasis, yet little is known about how changes in the mucin-microbiome interactions affect worm infection. Here, we aimed to examine how increased mucin foraging activity by the microbiome changes the course of the parasitic infection by modulating the host immune responses.

METHODSWe employed a gnotobiotic mouse model containing a 14-member synthetic human gut microbiota that facilitates functional interpretations, including diet-driven manipulation of the microbiota toward mucin foraging. We infected the mice with a robust murine nematode, Trichuris muris, that closely resembles human infection with Trichuris trichiura. We investigated the temporal dynamics of worm infection including worm burden and the host immune responses, and connected these readouts to the microbial changes and metabolic activity toward mucin foraging.

RESULTSThe microbial mucin foraging was further increased during worm infection only in mice with pre-enhanced mucin degrading capacity. The elevated mucin foraging coincides with a shift in host immune responses from susceptible (chronic, Th1 type) to resistant (acute, Th2 type), which promotes worm clearance. The relative abundances of mucin-generalist bacteria drammatically increased during worm clearance, but not during worm retention.

CONCLUSIONSThese results point to a mechanism whereby skewing the metabolic activity of the microbiome toward mucin glycoproteins promotes resistance to worm infection. Our study documents a clinically-relevant, novel link in the microbiome-parasite-host immune axis, which is important prerequisite knowledge in treating parasitic infections.

category: immunology


title: The mitochondrion of Plasmodium falciparum generates essential acetyl-CoA for protein acetylation

abstract: Coenzyme A (CoA) biosynthesis is an excellent target for antimalarial intervention. While most studies have focused on the use of CoA to produce acetyl-CoA in the apicoplast and the cytosol of malaria parasites, mitochondrial acetyl-CoA production is less well understood. In the current study, we performed metabolite labeling experiments to measure endogenous metabolites in Plasmodium falciparum lines with genetic deletions affecting mitochondrial dehydrogenase activity. Our results show that mitochondrial acetyl-CoA biosynthesis is essential for parasite growth and identify a catalytic redundancy between the two main ketoacid dehydrogenase enzymes, both of which are able to produce acetyl-CoA. The activity of these enzymes is dependent on the lipoate attachment enzyme LipL2, which is essential for parasite survival solely based on its role in supporting acetyl-CoA metabolism. We also find that acetyl-CoA produced in the mitochondrion is essential for the acetylation of histones and other proteins outside of the mitochondrion. Taken together, our results demonstrate that the mitochondrion is an essential de novo source of acetyl-CoA and is required for P. falciparum protein acetylation critical to parasite survival.


title: Temporal and environmental factors interact with rootstock genotype to shape leaf elemental composition in grafted grapevines

abstract: Plants take up elements through their roots and transport them to their shoot systems for use in numerous biochemical, physiological, and structural functions. Elemental composition of above-ground plant tissues, such as leaves, reflects both above- and below-ground activities of the plant genotype, as well the local environment. Perennial, grafted plants, where the root system of one individual is fused to the shoot system of a genetically distinct individual, offer a powerful experimental system in which to study the role of the root system in the elemental composition of the shoot system. We measured elemental composition of over 7000 leaves in the grapevine cultivar  Chambourcin growing ungrafted and grafted to three rootstock genotypes. Leaves were collected over multiple years and phenological stages (across the season) and along a developmental time series. Temporal components of this study had the largest effect on leaf elemental composition; and rootstock genotype interacted with year, phenological stage, and leaf age to differentially modulate leaf elemental composition. Further, the local, above-ground environment affected leaf elemental composition, an effect influenced by rootstock genotype. This work highlights the dynamic nature by which root systems interact with shoot systems to respond to temporal and environmental variation.


title: Two Interaction Surfaces between XPA and RPA Organize the Preincision Complex in Nucleotide Excision Repair

abstract: The XPA and RPA proteins fulfill essential roles in the assembly of the preincision complex in the nucleotide excision repair pathway. We have previously characterized the two interaction surfaces between XPA and RPA, with the RPA32 and RPA70AB subunits. Here we show that the mutations in the two individual interaction surfaces reduce NER activity in biochemical and cellular systems, and that combining mutations in two domains leads to an additive inhibition of NER, suggesting that they fulfill distinct roles. Our data suggest that the interaction between XPA and RPA32 is important for the initial association of XPA with NER complexes, while the interaction between XPA and RPA70 is needed for structural organization of the complex to license the dual incision reaction. SAXS analysis of complexes of XPA and RPA bound to ss/dsDNA junction substrates reveals the architecture of XPA and RPA in the preincision complex and shows that the two interaction domains between RPA and XPA are located at opposite sides of the two molecules. We propose a structure for the overall NER preincision complex that shows that the two strands of the NER bubble assume a U-shape with the two ss/dsDNA junctions localized in close proximity, with the interaction between XPA and RPA70 as one of the key organizing elements.

category: biochemistry


title: 4D Cell-Condensate Bioprinting

abstract: 4D bioprinting techniques that facilitate formation of shape-changing scaffold-free cell condensates with prescribed geometries have yet been demonstrated. Here, a simple yet novel 4D bioprinting approach is presented that enables formation of a shape-morphing cell condensate-laden bilayer system comprised of an actuation layer and a cell condensate-supporting microgel (MG) layer. The strategy produces scaffold-free cell condensates which morph over time into predefined complex shapes. With a sequential printing (i.e., MG printing first onto the preformed actuation hydrogel layer and cell-only printing inside the pre-printed MG construct second), cell condensate-laden bilayers with specific geometries are readily fabricated and can be further UV-crosslinked to form strong interlayer adhesion. Since the bilayers have tunable deformability and MG degradation can be tailored, this enables controllable morphological transformations and on-demand liberation of cell condensates. With this system, large cell condensate-laden constructs with various complex shapes were obtained through predefined conformational conversions. As a proof-of-concept study, the formation of the letter "C" and helix-shaped robust cartilage-like tissues differentiated from human mesenchymal stem cells (hMSCs) was demonstrated. This new system brings about a new versatile 4D bioprinting platform idea that is anticipated to broaden and facilitate the applications of cell condensation-based 4D bioprinting.

category: bioengineering


title: Image segmentation and separation of spectrally similar dyes in fluorescence microscopy by dynamic mode decomposition of photobleaching kinetics

abstract:
BackgroundImage segmentation in fluorescence microscopy is often based on spectral separation of fluorescent probes (color-based segmentation) or on significant intensity differences in individual image regions (intensity-based segmentation). These approaches fail, if dye fluorescence shows large spectral overlap with other employed probes or with strong cellular autofluorescence.

ResultsHere, a novel model-free approach is presented which determines bleaching kinetics based on dynamic mode decomposition (DMD) and uses the inferred photobleaching kinetics to distinguish different probes or dye molecules from autofluorescence. DMD is a data-driven computational method for detecting and quantifying dynamic events in complex spatiotemporal data. Here, DMD is used to determine photobleaching characteristics of a fluorescent sterol probe, dehydroergosterol (DHE), compared to that of cellular autofluorescence in the nematode Caenorhabditis elegans. It is shown that decomposition of those dynamic modes allows for precise image segmentation, thereby separating probe from autofluorescence without invoking a particular model for the bleaching process. In a second application, DMD of dye-specific photobleaching is used to separate two green-fluorescent dyes, an NBD-tagged sphingolipid and Alexa488-transferrin, thereby assigning them to different cellular compartments.

ConclusionsData-based decomposition of dynamic modes can be employed to analyze spatially varying photobleaching of fluorescent probes in cells and tissues for image segmentation, discrimination of probe from autofluorescence and image denoising. The new method should find wide application in analysis of dynamic fluorescence imaging data.

category: bioinformatics


title: CLEAN: Leveraging spatial autocorrelation in neuroimaging data in clusterwise inference

abstract: While clusterwise inference is a popular approach in neuroimaging that improves sensitivity, current methods do not account for explicit spatial autocorrelations because most use univariate test statistics to construct cluster-extent statistics. Failure to account for such dependencies could result in decreased reproducibility. To address methodological and computational challenges, we propose a new powerful and fast statistical method called CLEAN (Clusterwise inference Leveraging spatial Autocorrelations in Neuroimaging). CLEAN computes multivariate test statistics by modelling brain-wise spatial autocorrelations, constructs cluster-extent test statistics, and applies a refitting-free resampling approach to control false positives. We validate CLEAN using simulations and applications to the Human Connectome Project. This novel method provides a new direction in neuroimaging that paces with advances in high-resolution MRI data which contains a substantial amount of spatial autocorrelation.

category: neuroscience


title: In-vivo phase-dependent enhancement and suppression of brain oscillations by transcranial alternating current stimulation (tACS)

abstract:
Transcranial alternating current stimulation (tACS) can influence human perception and behavior, with recent evidence also suggesting its potential impact in clinical settings, but the underlying mechanisms are poorly understood. Behavioral and indirect physiological evidence indicates that phase-dependent constructive and destructive interference between the tACS electric field and ongoing brain oscillations may play an important role, but direct in-vivo validation was infeasible because stimulation artifacts impeded such assessment. Using stimulation artifact source separation (SASS), a real-time compatible artifact suppression approach, we overcame this limitation and provide direct evidence for millisecond-by-millisecond phase-dependent enhancement and suppression of ongoing brain oscillations during amplitude-modulated tACS (AM-tACS) across 29 healthy human volunteers. We found that AM-tACS enhanced and suppressed targeted brain oscillations by 11.7 {+/-} 5.14% and 10.1 {+/-} 4.07% respectively. Millisecond-precise modulation of oscillations predicted modulation of behavior (r = 0.65, p < 0.001). These results not only provide direct evidence for constructive and destructive interference as a key mechanism of AM-tACS but suggest superiority of phase-locked (closed-loop) AM-tACS over conventional (open-loop) AM-tACS to purposefully enhance or suppress brain oscillations.

SignificanceThe presented data provide direct evidence for a key mechanism underlying neurophysiological and behavioral effects of transcranial alternating current stimulation (tACS), a broadly used neuromodulation approach that yields promising clinical results but also raised controversies because of its variable effects. Our findings not only elucidate the underlying mechanisms of tACS, but also provide the rationale for closed-loop tACS protocols that will enable targeted enhancement and suppression of brain oscillations related to various brain functions such perception, memory or cognition. Towards this end, we introduce the technical prerequisites to establish millisecond-to-millisecond precise closed-loop tACS protocols that will be important to advance tACS as a neuroscientific and clinical tool, for example in the treatment of neuropsychiatric disorders.


title: Tactile Stimulation Improves Cognition, Motor, and Anxiety-Like Behaviours and Attenuates the AD Pathology in Adult APP NL-G-F/NL-G-F mice

abstract: Alzheimers Disease (AD) is one of the largest health crises in the world. There are, however, limited but expensive pharmaceutical interventions to treat AD and most of the treatment options are not for cure or prevention, but to slow down the progression of the disease. The aim of this study was to examine the effect of tactile stimulation on AD-like symptoms and pathology in APP NL-G-F/NL-G-F mice, a mouse model of AD. The results show that tactile stimulation improves the AD-like symptoms on tests of cognition, motor, and anxiety-like behaviours and these improvements are associated with reduced AD pathology in APP mice.


title: The extracellular matrix fibulin 7 maintains epidermal stem cell heterogeneity during skin aging

abstract: Tissue stem cells divide infrequently as a protective mechanism against internal and external stresses associated with aging. Here, we demonstrate that slow- and fast-cycling interfollicular epidermal stem cells in mouse skin undergo distinct aging processes. Two years of lineage tracing reveals that Dlx1+ slow-cycling clones expanded into the fast-cycling stem cell territory, while the number of Slc1a3+ fast-cycling clones gradually declined. Transcriptome analysis further indicated that the molecular properties of each stem cell population are altered with age. Mice lacking fibulin 7, an extracellular matrix (ECM), show early impairments resembling epidermal stem cell aging, such as the loss of fast-cycling clones, delayed wound healing, and increased expression of inflammation- and differentiation-related genes. Fibulin 7 interacts with structural ECM and matricellular proteins, and the overexpression of fibulin 7 in primary keratinocytes results in slower proliferation in the absence or presence of inflammatory cytokine IL-6. Thus, these results suggest that fibulin 7 plays a crucial role in maintaining tissue resilience and epidermal stem cell heterogeneity during skin aging.

category: developmental biology


title: Stereochemistry of transient protein-protein interactions in a signaling hub: exploring G3BP1-mediated regulation of CFTR deubiquitination

abstract: Intrinsically disordered proteins (IDPs) can coordinate often transient or weak interactions with multiple proteins to mediate complex signals within large, reversible protein networks. Among these, the IDP hub protein G3BP1 forms protein complexes with Caprin1 and USP10, and the resulting control of USP10 activity plays an important role in a pathogenic virulence system that targets CFTR endocytic recycling. However, while the identities of protein interactors are known for many of these IDP hub proteins, the relationship between pairwise affinities and the extent of protein recruitment and activity is not well understood. Here we describe in vitro analysis of the G3BP1 affinities, and show that substitution of G3BP1 residues F15 or F33 to tryptophan reduces affinity for both the USP10 and Caprin1 motif peptides. These same mutations significantly reduce formation of complexes by the full-length proteins. The crystal structure of G3BP1 TripleW (F15W/F33W/F124W) mutant reveals a clear reorientation of the side chain of W33, creating a steric clash with the USP10 and Caprin1 peptides. An amino-acid scan of the USP10 and Caprin1 motif peptides reveals similarities and differences in the ability to substitute residues in the core motifs as well as specific mutations with the potential to create higher affinity peptides. Taken together, these data show that small changes in 1:1 binding affinity can have significant effects on the composition of cellular interaction hubs. These specific protein mutations can be harnessed to manipulate complex protein networks, informing future investigations into roles of these networks in cellular processes.


title: Robust and tunable performance of a cell-free biosensor encapsulated in lipid vesicles

abstract: Cell-free systems have enabled the development of genetically encoded biosensors to detect a range of environmental and biological targets. By encapsulating these systems in synthetic membranes, we can reintroduce features of the cell membrane, including molecular containment and selective permeability, which together could significantly enhance sensing capabilities. Here, we demonstrate robust and tunable performance of an encapsulated fluoride riboswitch inside of lipid vesicles. The riboswitch remains active upon encapsulation in lipid vesicles and responds to fluoride added to the surrounding solution. We find the sensitivity of the encapsulated sensor can be tuned by varying membrane composition. We then show that encapsulation protects the sensor from degradation by the sample and use two types of genetically encoded outputs to detect fluoride in real-world samples. This work establishes the feasibility of vesicle-encapsulated cell-free systems to detect environmentally relevant small molecules.

category: synthetic biology


title: Brain embeddings with shared geometry to artificial contextual embeddings, as a code for representing language in the human brain

abstract: Contextual embeddings, derived from deep language models (DLMs), provide a continuous vectorial representation of language. This embedding space differs fundamentally from the symbolic representations posited by traditional psycholinguistics. Do language areas in the human brain, similar to DLMs, rely on a continuous embedding space to represent language? To test this hypothesis, we densely recorded the neural activity in the Inferior Frontal Gyrus (IFG, also known as Brocas area) of three participants using dense intracranial arrays while they listened to a 30-minute podcast. From these fine-grained spatiotemporal neural recordings, we derived for each patient a continuous vectorial representation for each word (i.e., a brain embedding). Using stringent, zero-shot mapping, we demonstrated that brain embeddings in the IFG and the DLM contextual embedding space have strikingly similar geometry. This shared geometry allows us to precisely triangulate the position of unseen words in both the brain embedding space (zero-shot encoding) and the DLM contextual embedding space (zero-shot decoding). The continuous brain embedding space provides an alternative computational framework for how natural language is represented in cortical language areas.


title: Modeling of individual neurophysiological brain connectivity

abstract:
IntroductionComputational models are often used to assess how functional connectivity (FC) patterns emerge from neuronal population dynamics and anatomical connections in the brain. However, group averaged data is often used in this context and it remains unclear whether individual predictions of FC patterns using this approach can be made. Here, we assess the value of using individualized structural data for simulation of individual whole-brain FC.

MethodsThe Jansen and Rit neural mass model was employed, where masses were coupled using individual structural connectivity (SC) obtained from diffusion weighted imaging. Simulated FC was correlated to individual magnetoencephalography-derived empirical FC. FC was estimated using both phase-based (phase lag index (PLI), phase locking value (PLV)) and amplitude-based (amplitude envelope correlation (AEC)) metrics to analyze the goodness-of-fit of different metrics for individual predictions. Prediction of individual FC was compared against the prediction of group averaged FC. We further tested whether SC of a different participant could equally well predict a participants FC pattern.

ResultsThe AEC provided a significantly better match between individually simulated and empirical FC than phase-based metrics. Simulations with individual SC provided higher correlations between simulated and empirical FC compared to using the group-averaged SC. However, using SC from other participants resulted in similar correlations between simulated and empirical FC compared to using participants own SC.

DiscussionThis work underlines the added value of FC simulations based on individual instead of group-averaged SC, and could aid in a better understanding of mechanisms underlying individual functional network trajectories in neurological disease.

Impact statementIn this work, we investigated how well individual empirical functional connectivity can be simulated using the individuals structural connectivity matrix combined with neural mass modeling. Our research highlights the potential added value of using individual simulations of functional connectivity, and could aid in a better understanding of mechanisms underlying individual functional network trajectories in neurological disease. Moreover, individualized prediction of disease trajectories could enhance patient care and may provide better treatment options.


title: Purifying selection enduringly acts on the sequence evolution of highly expressed proteins in Escherichia coli

abstract: The evolutionary speed of a protein sequence is constrained by its expression level, with highly expressed proteins evolving relatively slowly. This negative correlation between expression levels and evolutionary rates (known as the E-R anticorrelation) has already been widely observed in past macroevolution between species from bacteria to animals. However, it remains unclear whether this seemingly general law also governs recent evolution, including past and de novo, within a species. However, the advent of genomic sequencing and high-throughput phenotyping, particularly for bacteria, has revealed fundamental gaps between the two evolutionary processes and has provided empirical data opposing the possible underlying mechanisms which are widely believed. These conflicts raise questions about the generalization of the E-R anticorrelation and the relevance of plausible mechanisms. To explore the ubiquitous impact of expression level on molecular evolution, and to test the relevance of the possible underlying mechanisms, we analyzed the genome sequences of 99 strains of Escherichia coli for microevolution in nature. We also analyzed genomic mutations accumulated under laboratory conditions as a model of de novo microevolution. Here, we show that the E-R anticorrelation is significant in both past and de novo microevolution in E. coli. Our data also confirmed ongoing purifying selection acting on highly expressed genes. Ongoing selection included codon-level purifying selection, supporting the relevance of the underlying mechanisms. However, their contributions to the constraints in recent evolution might be smaller than previously expected from past macroevolution.

category: evolutionary biology


title: BayesRB: a Markov chain Monte Carlo-based polygenic genetic risk score algorithm for dichotomous traits

abstract: AO_SCPLOWBSTRACTC_SCPLOWIdentifying high-risk individuals with diseases through reliable prediction models guides screening and preventive treatment. Most complex diseases have a genetic basis influenced by multiple genes and so disease risk can be estimated using polygenic risk score (PRS) algorithms. Many PRS algorithms have been developed so far. Among them, BayesR shows good characteristics of unbiasedness, accuracy, sparseness, and robustness. It detects the associated SNPs, estimates the SNP effects, and makes prediction of disease risks based on all SNPs simultaneously. However, this method assumes that the phenotypes follow a Gaussian distribution, which cannot be met in case-control studies. Here, we made an extension of the BayesR method, called BayesRB, by adding auxiliary variables to the BayesR model. We explored the characteristics, efficacy, and accuracy of BayesRB when estimating SNP effects and predicting disease risks compared with three traditional algorithms under different conditions using both simulated data and real data from the Welcome Trust Case Control Consortium (WTCCC). For SNP effect estimation, BayesRB shows unbiasedness and sparseness for big and small effect SNPs, respectively. For disease risk prediction, BayesRB had the best performance among the methods. This study provides a theoretical basis for complex disease risk prediction and disease prevention

category: genetics


title: Rational evolution of a recombinant DNA polymerase for efficient incorporation of unnatural nucleotides by dual-site boosting

abstract: Machine learning modelling assisting function-oriented enzyme engineering is normally built on predefined protein sequence space. However, efficient defining the determinant amino acid positions upon which the combinatorial mutation library is constructed is still a challenge in protein science. Herein, we present a comprehensive investigation of modifying a recombinant DNA polymerase for efficient incorporating one unnatural nucleotide, including the identification of key sites/regions, machine learning-assisted mutants screening, and the underlying mechanism of kinetics boosting. By using hundreds of training points and only dozens of testing samples, we found that one highly engineered enzymes catalytic efficiency can be further improved by one order of magnitude by specific mutation on two sites, 485I and 451L. Compared to the position 485 which is known to dominate local conformation of B-family DNA polymerases, 451 is a split-new active site discovered by our approach. A novel allosteric regulation mechanism is underlying the apparent synergy of 485I and 451L on the kinetics boosting. As a result, a "half-closed" conformation of the binding pocket and a cooperative binding of both primer and template DNA strands on the protein accelerated the processes of substrates incorporation, molecular recognition, and releasing of incorrect nucleotides. These findings have implications in guiding the function-tuning of DNA polymerases for a broad range of biotechnological applications.


title: Differential Effects of Koisio Technology-Modulated Solutions on the Growth of Lung Fibroblast Cell Cultures and Lung Cancer Cell Cultures

abstract: Cell growth is a crucial biological property of cells, which plays key roles in several major biological processes including organ development, tissue repair and cancer development. It is of both scientific and medical significance to discover new strategies to modulate cell growth. Koisio technology is a novel technology that modulates the properties of water solely by physical approaches without additions of any external substances. In our current study we obtained the following findings regarding the effects of Koisio technology-modulated solutions on cell growth: First, compared with the lung fibroblast (L929) cell cultures cultured in normal media, the L929 cells cultured in Koisio technology-modulated media grew at approximately 20% higher speed; second, compared with the lung cancer cell cultures (LLC cells) cultured in normal media, the LLC cells cultured in Koisio technology-modulated media grew at approximately 9% lower speed; and third, compared with the telomere lengths of the L929 cells cultured in normal media, the L929 cells cultured in Koisio technology-modulated media had approximately 14% longer telomere length. Collectively, our study has provided the first evidence indicating that Koisio technology-modulated solutions affect differentially the growth of lung fibroblast cell cultures and that of lung cancer cell cultures. The capacity of the Koisio technology-modulated solutions to promote the growth of lung fibroblast cell cultures may result at least partially from its capacity to protect the telomere length.

category: cell biology


title: Uncovering the ligandome of low-density lipoprotein receptor-related protein 1 in cartilage: a top-down approach to identify therapeutic targets

abstract: The low-density lipoprotein receptor-related protein 1 (LRP1) is a cell-surface receptor ubiquitously expressed in adult tissues. It plays tissue-specific physiological roles by mediating endocytosis of a diverse range of extracellular molecules. Dysregulation of LRP1 is involved in multiple conditions including Alzheimers disease, atherosclerosis and osteoarthritis (OA). However, little information is available about the specific ligand profile (ligandome) for each tissue, which would lead to better understanding of its role in disease states. Here, we investigated adult articular cartilage where impaired LRP1-mediated endocytosis leads to tissue destruction. We used a top-down approach involving analysis of human chondrocyte secretome, direct binding assays and validation in LRP1-deficient fibroblasts, as well as a novel Lrp1 conditional knockout (KO) mouse model. We found that inhibition of LRP1-mediated endocytosis results in cell death, alteration of the entire secretome and transcriptional modulations in human chondrocytes. We have identified more than 50 novel ligand candidates and confirmed direct LRP1 binding of HGFAC, HMGB1, HMGB2, CEMIP, SLIT2, ADAMTS1, IGFBP7, SPARC and LIF. Our in vitro endocytosis assay revealed the correlation of their affinity for LRP1 and the rate of endocytosis. Moreover, a conditional LRP1 KO mouse model demonstrated a critical role of LRP1 in regulating the high-affinity ligands in cartilage in vivo. This systematic approach revealed the extent of the chondrocyte LRP1 ligandome and identified potential novel therapeutic targets for OA.


title: TBK1 phosphorylation activates LIR-dependent degradation of the inflammation repressor TNIP1

abstract:
Limitation of excessive inflammation due to selective degradation of pro-inflammatory proteins is one of the cytoprotective functions attributed to autophagy. In the current study, we highlight that selective autophagy also plays a vital role in promoting the establishment of a robust inflammatory response. Under inflammatory conditions, here TLR3-activation by poly(I:C) treatment, the inflammation repressor TNIP1 (TNFAIP3 interacting protein 1) is phosphorylated by TBK1 (Tank-binding kinase 1) activating a LIR motif that leads to the selective autophagy-dependent degradation of TNIP1, supporting expression of pro-inflammatory genes and proteins. Thus, similarly as in cancer, autophagy may play a dual role in controlling inflammation depending on the exact state and timing of the inflammatory response.

SummaryAutophagy is well known for its anti-inflammatory effects. Here, we highlight that selective, autophagy-dependent degradation of the inflammation repressor TNIP1 supports pro-inflammatory gene and protein expression. Similarly as in cancer, autophagy appears to play a dual role in controlling inflammation.


title: Reconstitution of renal cyst formation in 3D culture reveals a role for AMOT and Yap1 in determining cyst size.

abstract: Despite substantial progress in identifying and understanding causative mutations in autosomal dominant polycystic kidney disease (ADPKD), little is known about subsequent cellular events leading to cyst formation. In prior studies we reported that Cadherin 8, a type II Cadherin, expression is sufficient to induce cyst emergence from HK-2 cells grown as tubule arrays in collagen matrix (1). However, emergent cysts did not exhibit the luminal enlargement observed in ADPKD. In this communication, we reconstitute cyst emergence with consequent cyst lumen expansion in 3D culture by stable co-expression of Cadherin 8 in combination with a constitutively active mutant of YAP1, the key effector of the HIPPO pathway. Specifically, immortalized cells derived from ADPKD cyst epithelia formed cysts with substantially larger lumen sizes when transduced with YAP1-5SA. Conversely, expression of the YAP1 inhibitor, AMOTL1, in these cells resulted in their forming cysts with smaller lumens than control cells. Our data show that cyst formation results from a sequential two-step process consisting of cyst initiation and subsequent cyst expansion. Taken together, cyst initiation induced by Cadherin 8 expression is proposed to result from decreased cell-cell adhesion while cyst expansion is driven by increased Yap1 activity.


title: LITOS - a versatile LED illumination tool for optogenetic stimulation

abstract: Optogenetics has become a key tool to manipulate biological processes with high spatio-temporal resolution. Recently, a number of commercial and open-source multi-well illumination devices have been developed to provide throughput in optogenetics experiments. However, available commercial devices remain expensive and lack flexibility, while open-source solutions require programming knowledge and/or include complex assembly processes. We present a LED Illumination Tool for Optogenetic Stimulation (LITOS) based on an assembled printed circuit board controlling a commercially available 32x64 LED matrix as illumination source. LITOS can be quickly assembled without any soldering, and includes an easy-to-use interface, accessible via a website hosted on the device itself. Complex light stimulation patterns can easily be programmed without coding expertise. LITOS can be used with different formats of multi-well plates, petri dishes, and flasks. We validated LITOS by measuring the activity of the MAPK/ERK signaling pathway in response to different dynamic light stimulation regimes using FGFR1 and Raf optogenetic actuators. LITOS can uniformly stimulate all the cells in a well and allows for flexible temporal stimulation schemes. LITOSs ease of use aims at democratizing optogenetics in any laboratory.


title: Cyclin CLB2 mRNA localization determines efficient protein synthesis to orchestrate bud growth and cell cycle progression

abstract: mRNA localization to subcellular compartments has been reported across all kingdoms of life and it is generally believed to promote asymmetric protein synthesis and localization. In striking contrast to previous observations, we show that in S. cerevisiae the B-type cyclin CLB2 mRNA is localized and translated in the yeast bud, while the Clb2 protein, a key regulator of mitosis progression, is concentrated in the mother nucleus. Using single-molecule RNA imaging in fixed (smFISH) and living cells (MS2 system), we show that the CLB2 mRNA is transported to the yeast bud by the She2-She3 complex, via an mRNA ZIP-code situated in the coding sequence. In CLB2 mRNA localization mutants, Clb2 protein synthesis in the bud is decreased resulting in changes in cell cycle distribution and genetic instability. Altogether, we propose that CLB2 mRNA localization acts as a sensor for bud development to couple cell growth and cell cycle progression, revealing a novel function for mRNA localization.


title: Ligand-mediated structural dynamics of a mammalian pancreatic KATP channel

abstract: Regulation of pancreatic KATP channels involves orchestrated interactions of channel subunits, Kir6.2 and SUR1, and their ligands. How ligand interactions affect channel conformations and activity is not well understood. To elucidate the structural correlates pertinent to ligand interactions and channel gating, we compared cryo-EM structures of channels in the presence and absence of pharmacological inhibitors and ATP, focusing on channel conformational dynamics. We found pharmacological inhibitors and ATP enrich a channel conformation in which the Kir6.2 cytoplasmic domain is closely associated with the transmembrane domain relative to one where the Kir6.2 cytoplasmic domain is extended away into the cytoplasm. This conformation change remodels a network of intra and inter-subunit interactions as well as both the ATP and PIP2 binding pockets. The structures resolved key contacts between the distal N-terminus of Kir6.2 and SUR1s ABC module involving residues implicated in channel function. A SUR1 residue, K134, is identified to directly contribute to the PIP2 binding pocket. Molecular dynamics simulations revealed two Kir6.2 residues, K39 and R54, that mediate both ATP and PIP2 binding, suggesting a mechanism for competitive gating by ATP and PIP2.


title: A Duplex Structure of SARM1 Octamers Induced by a New Inhibitor

abstract: In recent years, there has been growing interest in SARM1 as a potential breakthrough drug target for treating various pathologies of axon degeneration. SARM1-mediated axon degeneration relies on its TIR domain NADase activity, but recent structural data suggest that the non-catalytic ARM domain could also serve as a pharmacological site as it has an allosteric inhibitory function. Here, we screened for synthetic small molecules that inhibit SARM1 by stabilizing the ARM-dependent inactive, compact octamer ring conformation, and tested a selected set of these compounds in a DRG axon degeneration assay. Using cryo-EM, we found that one of the newly discovered inhibitors, a Calmidazolium designated TK106, not only stabilizes the previously reported inhibited conformation of the octamer, but also promotes the formation of a meta-stable structure: a duplex of octamers (16 protomers), which we have now determined to 4.0 [A] resolution. In the duplex, each ARM domain protomer is not only engaged in lateral interactions with neighboring protomers but is further stabilized by contralateral contacts with the opposing octamer ring. Mutagenesis of the duplex contact sites leads to SARM1 activation in cultured cells. Based on our data we propose that the duplex assembly constitutes an additional auto-inhibition mechanism that tightly prevents pre-mature activation and axon degeneration.


title: Using Biometric Data to Measure and Predict Emotional Engagement of Video Games

abstract: Measurement and prediction of engagement in video games are very important because these are indicators to guide the development of game applications. Existing methods to predict game engagement are mostly based on subjective evaluations. This paper presents results correlating subjective and biometric data to show the potential of using biometric measures for assessment and prediction of engagement. Using three different games, we measured the biometric responses of participants and analyzed the responses using statistical and data mining methods. We compared the results with those obtained using subjective evaluations. Our results show that biometric measurements do correlate with subjective measures and better predict the self-reported engagement of a game.


title: Cholesterol in the cargo membrane reduces kinesin-1 binding to microtubules in the presence of tau

abstract: Intracellular cargos are often membrane-bound and transported by microtubule-based motors in the presence of microtubule-associated proteins (MAPs). Whereas increasing evidence reveals how MAPs impact the interactions between motors and microtubules, critical questions remain about the impact of the cargo membrane on transport. Here we combined in vitro optical trapping with theoretical approaches to determine the effect of a lipid cargo membrane on kinesin-based transport in the presence of MAP tau. Attaching kinesins to a fluid lipid membrane decreases the inhibitory effect of tau in comparison to membrane-free cargos. Adding cholesterol, which reduces kinesin diffusion in the cargo membrane, amplifies the inhibitory effect of tau on kinesin in a dosage-dependent manner. Our findings can be understood in a framework in which kinesin diffusion in the cargo membrane counteracts binding-site occlusion by tau. Our study establishes a direct link between the physical properties of cargo membrane and MAP-based regulation of kinesin-1.

category: biophysics


title: Identification of potential inhibitors of cutaneous Melanoma and Non-Melanoma skin cancer cells through in vitro and in silico screening of a small library of Phenolic compounds

abstract: Melanoma and non-melanoma skin cancers are the most-lethal and commonest forms of skin cancers, that affecting one-fifth of the US population. With the aim of identifying new lead compounds as starting point for attaining cost-effective therapies, a small library of about 90 molecules was screened in vitro against A375, SKMEL-28, A431, SCC-12 skin cancer cell lines. About 35 of them, mainly dihydroquinolines, C-C and C-N linked biphenyls, and substituted methylgallate or aniline derivatives, displayed low-micromolar range activities, primarily against the A431 and SCC-12 squamous carcinoma cell lines, with only a handful of these compounds displaying any activity against the A375 and SKMEL-28 melanoma cell lines. Compounds 11 (A431: IC50 = 5.0 {micro}M, SCC-12: IC50 = 2.9 {micro}M, SKMEL-28: IC50 = 4.9 {micro}M, A375: IC50 = 6.7 {micro}M) and 13 (A431: IC50 = 5.0 {micro}M, SCC-12: IC50 = 3.3 {micro}M, SKMEL-28: IC50 = 13.8 {micro}M, A375: IC50 = 17.1 {micro}M) were the most active across all these cell lines. Furthermore, many of the hit compounds showed little to no activity against mammalian nontumorigenic immortalized HaCaT cells, with a far better selectivity index than cisplatin (a well-known anticancer agent used as a positive control). Compounds 11 and 13 significantly and dose-dependently induced apoptosis of SCC-12 and SK-MEL-28 cells as evidenced by the downregulation of Bcl-2 and upregulation of Bax protein expression levels, and by cleaved caspase-3, caspase-9 and PARP levels. Both agents also significantly reduced scratch wound healing, colony formation, and activated expression levels of major cancer molecular targets such as RSK/AKT/ERK1/2 and S6K1. To provide a better attribute profile for each of the hit molecules, in-silico target(s) prediction, pharmacokinetic and ADMET studies are also reported, together with some preliminary structure-activity relationship outlines. The SwissTargetPrediction web-based tool identified CDK8, CLK4, nuclear receptor ROR, tyrosine protein-kinase Fyn/LCK, ROCK1/2, and PARP, all of which are dysregulated in skin cancers, as likely targets for these hit compounds. Furthermore, the SwissADME web_tool predicted these compounds to exhibit high GI tract absorption, good skin permeation, and a viable biodegradability profile. To summarize, these data highlight the promising anticancer potential of these small molecules leads, warranting further investigation and/or optimization towards obtaining clinical candidates for combatting both melanoma and non-melanoma skin cancers.

category: pharmacology and toxicology


title: Evaluation of Postgraduate Educational Environment of Doctors Training in Psychiatry: a mixed method study

abstract:
IntroductionEducational Environment (EE) is of paramount importance in Medical Education, but can be intangible and hard to clearly determine. Professional satisfaction and patient care improve in a pleasant learning environment; where postgraduate physicians are encouraged, suitably supervised, and fostered. A negative learning environment can be detrimental to trainees and teams morale and can jeopardize the multidisciplinary working relationship.

ObjectivesThe objective of this study was to measure the Educational Environment (EE) of Psychiatry postgraduate training in the Midwest of Ireland training Deanery; what aspects of training are working well and what areas are seen as not optimal.

MethodsThis study took place between April and June 2021. A mixed methods approach was adopted, using the Postgraduate Hospital Educational Environment Measure (PHEEM) and semi-structured one-to-one interviews.

ResultsResponse rate was 88% (n=22). The total PHEEM score was 105.64{+/-}23.52, indicating a postgraduate EE with more positive than negative aspects, but with room for improvement. There were no differences in overall PHEEM and subscale scores between trainees gender, training grades or years of working experience. Three themes were identified that contribute to trainees perception of EE: the commitment of the trainees supervisors to the role they play in trainees overall development, the clinical workload of the trainee, and the day-to-day working conditions of the trainee. Definite disparities between work placements were evident in the collected data across these three themes.

ConclusionsAlthough the training program had an overall positive EE, specific answers and interview themes indicated some areas of weakness that may contribute to trainee dissatisfaction and possible burnout. Planned interventions targeting these areas and tracking changes in EE and burnout rates over time may be useful measures going forward.

Declaration of InterestNone

category: scientific communication and education


title: Regulation strategies for two-output biomolecular networks

abstract: Feedback control theory allows the development of self-regulating systems with desired performance which are predictable and insensitive to disturbances. Feedback regulatory topologies are used by many natural systems and have been of key importance in the design of reliable synthetic bio-devices operating in complex biological environments. Here, we study control schemes for biomolecular processes with two outputs of interest, expanding previous traditional concepts describing one-output systems. This is a step forward in building bio-devices capable of sophisticated functions. Regulation of such processes may unlock new design possibilities but it can be challenging due to coupling interactions while potential disturbances applied on one of the outputs may affect both. We therefore propose architectures for robustly manipulating the ratio and linear combinations of the outputs as well as each of the output independently. To demonstrate their characteristics, we apply these architectures to a simple process of two mutually activated biomolecular species. We also highlight the potential for experimental implementation by exploring synthetic realizations both in vivo and in vitro.


title: Early Tactile Stimulation Influences the Development of Alzheimer Disease in Gestationally Stressed APPNL-G-F/ NL-G-F Adult mice

abstract: Alzheimer Disease (AD) is associated with cerebral plaques and tangles, reduced synapse number, and shrinkage in several brain areas and these morphological effects are associated with the onset of compromised cognitive, motor, and anxiety-like behaviours. The focus of this study was to examine the effect of neonatal tactile stimulation on AD-like behavioural and neurological symptoms on APP NL-G-F/NL-G-F mice, a mouse model of AD. Our findings indicate that neonatal tactile stimulation improves cognition, motor skills, and anxiety-like symptoms in both gestationally stressed and non-stressed adult APP mice and that these alterations are associated with reduced A{beta} plaque formation. Thus, tactile stimulation appears to be a promising non-invasive preventative strategy for slowing the onset of dementia in aging animals.


title: Unbiased proteomic analysis detects painful systemic inflammatory profile in the serum of nerve injured mice

abstract: Neuropathic pain is a complex, debilitating disease that results from injury to the somatosensory nervous system. The presence of systemic chronic inflammation has been observed in chronic pain patients, but whether it plays a causative role remains unclear. This study aims to determine the perturbation of systemic homeostasis by an injury to peripheral nerve and its involvement in neuropathic pain. We assessed the proteomic profile in the serum of mice at 1-day and 1-month following partial sciatic nerve injury (PSNL) or sham surgery. We also assessed mouse mechanical and cold sensitivity in naive mice after receiving intravenous administration of serum from PSNL or sham mice. Mass spectrometry-based proteomic analysis revealed that PSNL resulted in a long-lasting alteration of serum proteome, where the majority of differentially expressed proteins were in inflammation related pathways, involving cytokines/chemokines, autoantibodies and complement factors. While transferring sham serum to naive mice did not change their pain sensitivity, PSNL serum significantly lowered mechanical thresholds and induced cold hypersensitivity in naive mice. With broad anti-inflammatory properties, bone marrow cell extracts (BMCE) not only partially restored serum proteomic homeostasis, but also significantly ameliorated PSNL-induced mechanical allodynia, and serum from BMCE-treated PSNL mice no longer induced hypersensitivity in naive mice. These findings clearly demonstrate that nerve injury has a long-lasting impact on systemic homeostasis, and nerve injury associated systemic inflammation contributes to the development of neuropathic pain.


title: Temporal responses of bumblebee gustatory neurons encode sugar identity

abstract: The sense of taste permits the recognition of valuable nutrients and the avoidance of potential toxins. Models of gustatory coding propose that within modalities (e.g. sweet, bitter, etc.), taste ligands are not distinct stimuli. However, these models are based on data from mice or flies that have omnivorous, non-specialist diets. A specialist feeder might, however, be expected to have acuity within modality if stimulus resolution was critical to survival. Previously, we found that bumblebees have a specialized mechanism for sensing sugars whereby two gustatory receptor neurons (GRNs) within the galeal sensilla of the bees mouthparts exhibit burst of spikes. Here, we show that the temporal firing patterns of these GRNs separate sugars into four distinct groups that correlate with sugar nutritional value and palatability. We also identified a third GRN that responded to stimulation with relatively high concentrations of fructose, sucrose, and maltose. Sugars that were non-metabolizable or toxic suppressed the responses of bursting GRNs to sucrose. These abilities to encode information about sugar value are a refinement to the bumblebees sense of sweet taste that could be an adaptation that enables precise calculations of the nature and nutritional value of floral nectar.


title: Temporal responses of bumblebee gustatoryneurons to sugars


title: Social deficits induced by pervasive environmental stressors are prevented by microbial or dopaminergic modulation

abstract: Environmental toxicant exposure, including air pollution, is increasing worldwide. However, toxicant exposures are not equitably distributed. Rather, low-income and minority communities bear the greatest burden, along with higher levels of psychosocial stress. Both air pollution and maternal stress during pregnancy have been linked to neurodevelopmental disorders such as autism, but biological mechanisms and targets for therapeutic intervention remain poorly understood. We demonstrate that combined prenatal exposure to air pollution (diesel exhaust particles, DEP) and maternal stress (MS) in mice induces social behavior deficits only in male offspring, in line with the male bias in autism. These behavioral deficits are accompanied by changes in microglia and dopaminergic circuits in the brain, along with changes in the structure of the gut epithelium and microbiome. Importantly, DEP/MS-induced social deficits in males are prevented by shifting the gut microbiome by cross-fostering at birth and reversed by chemogenetic activation of the dopamine system.


title: Rapidly evolving genes underlie Aedes aegypti mosquito reproductive resilience during drought

abstract: Female Aedes aegypti mosquitoes impose a severe global public health burden as vectors of multiple viral pathogens. Under optimal environmental conditions, Aedes aegypti females have access to human hosts that provide blood proteins for egg development, conspecific males that provide sperm for fertilization, and freshwater that serves as an egg-laying substrate suitable for offspring survival. As global temperatures rise, Aedes aegypti females are faced with climate challenges like intense droughts and intermittent precipitation, which create unpredictable, suboptimal conditions for egg-laying. Here we show that under drought-like conditions simulated in the laboratory, females retain mature eggs in their ovaries for extended periods, while maintaining the viability of these eggs until they can be laid in freshwater. Using transcriptomic and proteomic profiling of Aedes aegypti ovaries, we identify two previously uncharacterized genes named tweedledee and tweedledum, each encoding a small, secreted protein that both show ovary-enriched, temporally-restricted expression during egg retention. These genes are mosquito-specific, linked within a syntenic locus, and rapidly evolving under positive selection, raising the possibility that they serve an adaptive function. CRISPR-Cas9 deletion of both tweedledee and tweedledum demonstrates that they are specifically required for extended retention of viable eggs. These results highlight an elegant example of taxon-restricted genes at the heart of an important adaptation that equips Aedes aegypti females with "insurance" to flexibly extend their reproductive schedule without losing reproductive capacity, thus allowing this species to exploit unpredictable habitats in a changing world.


title: Brain signal predictions from multi-scale networks using a linearized framework

abstract:
AO_SCPLOWBSTRACTC_SCPLOWSimulations of neural activity at different levels of detail have become ubiquitous in modern neurosciences, aiding the interpretation of experimental data and underlying neural mechanisms at the level of cells and circuits. Extracellular electric measurements of brain signals that reflect transmembrane currents throughout the neural tissue remain commonplace. The lower frequencies ([lsim] 300 Hz or so) of measured signals generally stem from synaptic activity driven by recurrent interactions among neural populations and computational models should also incorporate accurate predictions of such signals. Due to limited computational resources, large scale neuronal network models ({gtrsim} 106 neurons or so) often require reducing the level of biophysical detail and account mainly for times of action potentials ( spikes) or spike rates, and corresponding extracellular signal predictions have thus poorly accounted for their biophysical origin.

Here we propose a computational framework for predicting spatiotemporal filter kernels for such extracellular signals stemming from synaptic activity, accounting for the biophysics of neurons, populations, and recurrent connections. Signals are obtained by convolving population spike rates by appropriate kernels for each connection pathway and summing the contributions. Our main results are that kernels derived via linearized synapse and membrane dynamics, distributions of cells, conduction delay, and volume conductor model allow for accurately capturing the spatiotemporal dynamics of ground truth extracellular signals. One particular observation is that changes in the effective membrane time constants caused by persistent synapse activation must be accounted for.

The work also constitutes a major advance in computational efficacy of accurate, biophysics-based signal predictions from large-scale spike and rate-based neuron network models drastically reducing signal prediction times compared to biophysically detailed network models. This work also provides insight into how experimentally recorded low-frequency extracellular signals of neuronal activity may be approximately linearly dependent on spiking activity. A new software tool LFPykernels serves as a reference implementation of the framework.

Author summaryUnderstanding the brains function and activity in healthy and pathological states across spatial scales and times spanning entire lives is one of humanitys great undertakings. In experimental and clinical work probing its activity using a variety of electric and magnetic measurement devices are routinely performed, however interpreting the signals measured extracellularly remains arduous due to multiple factors, like the large number of neurons contributing to the signals and complex interactions occurring in recurrently connected neuronal circuits. To understand how neurons give rise to such signals, mechanistic modeling combined with forward models derived using volume conductor theory has proven to be successful, but this approach currently does not scale to the systems level (encompassing millions of neurons or more) where simplified or abstract neuron representations typically are used. Motivated by experimental findings implying approximately linear relationships between times of neuronal action potentials and extracellular population signals, we provide a biophysics-based method for computing causal filters relating spikes and extracellular signals that can be applied with spike times or rates of large-scale neuronal network models for predictions of population signals without relying on ad hoc approximations.


title: Stage dependent differential influence of metabolic and structural networks on memory across Alzheimer's disease continuum

abstract:
BackgroundLarge-scale neuronal network breakdown underlies memory impairment in Alzheimers disease (AD). However, the differential trajectories of the relationships between network organization and memory across pathology and cognitive stages in AD remain elusive. We determined whether and how the influences of individual-level structural and metabolic covariance network integrity on memory varied with amyloid pathology across clinical stages without assuming a constant relationship.

Methods708 participants from the Alzheimers Disease Neuroimaging Initiative were studied. Individual-level structural and metabolic covariance scores in higher-level cognitive and hippocampal networks were derived from magnetic resonance imaging and [18F]fluorodeoxyglucose positron emission tomography using seed-based partial least square analyses. The non-linear associations between network scores and memory across cognitive stages in each pathology group were examined using sparse varying coefficient modelling.

ResultsWe showed that the associations of memory with structural and metabolic networks in the hippocampal and default mode regions exhibited pathology-dependent differential trajectories across cognitive stages using sparse varying coefficient modelling. In amyloid pathology group, there was an early influence of hippocampal structural network deterioration on memory impairment in the preclinical stage, and a biphasic influence of the angular gyrus-seeded default mode network metabolism on memory in both preclinical and dementia stages. In non-amyloid pathology groups, in contrast, the trajectory of the hippocampus-memory association was opposite and weaker overall, while no metabolism covariance networks were related to memory. Key findings were replicated in a larger cohort of 1280 participants.

ConclusionsOur findings highlight potential windows of early intervention targeting network breakdown at the preclinical AD stage.


title: Astrocyte-targeted gene delivery of interleukin 2 specifically increases brain-resident regulatory T cell numbers and protects against pathological neuroinflammation

abstract: The ability of immune-modulating biologics to prevent and reverse pathology has transformed recent clinical practice. Full utility in the neuroinflammation space, however, requires identification of both effective targets for local immune-modulation and a delivery system capable of crossing the blood-brain-barrier. The recent identification and characterization of a small population of regulatory T cells (Tregs) resident in the brain presents one such potential therapeutic target. Here we identified brain IL2 levels as a limiting factor for brain-resident Tregs. We developed a gene-delivery approach for astrocytes, with a small-molecule on-switch to allow temporal control, and enhanced production in reactive astrocytes to spatially-direct delivery to inflammatory sites. Mice with brain-specific IL2 delivery were protected from traumatic brain injury, stroke and multiple sclerosis models, without impacting the peripheral immune system. These results validate brain-specific IL2 gene-delivery as effective protection against neuroinflammation, and provide a versatile platform for delivery of diverse biologics to neuroinflammatory patients.


title: Chronic obstructive pulmonary disease and cigarette smoke exposure lead to dysregulated MAIT cell activation by bronchial epithelial cells

abstract: Chronic obstructive pulmonary disease (COPD) is associated with airway inflammation, increased infiltration by CD8+ T lymphocytes, and infection-driven exacerbations. COPD is most commonly caused by cigarette smoke (CS), however the mechanisms driving development of COPD in some smokers but not others are incompletely understood. Lung-resident mucosal-associated invariant T (MAIT) cells play a role in both microbial infections and inflammatory diseases. MAIT cell frequency is reduced in the peripheral blood of individuals with COPD, however the role of MAIT cells in COPD pathology is unknown. Here, we examined MAIT cell activation in response to CS-exposed primary human bronchial epithelial cells (BEC) from healthy, COPD, or smoker donors. We observed significantly higher MAIT cell responses to COPD BEC than healthy BEC. However, COPD BEC stimulated a smaller fold-increase in MAIT cell response despite increased microbial infection. For all donor groups, CS-exposed BEC elicited reduced MAIT cell responses; conversely, CS exposure increased ligand-mediated MR1 surface translocation in healthy and COPD BEC. Our data demonstrate MAIT cell activation is dysregulated in the context of CS and COPD. MAIT cells could contribute to CS- and COPD-associated inflammation through both inappropriate activation and reduced early recognition of bacterial infection, contributing to microbial persistence and COPD exacerbations.


title: Heterogeneity of Inflammation-associated Synovial Fibroblasts in Rheumatoid Arthritis and Its Drivers

abstract: Inflammation of non-barrier immunologically quiescent tissues is associated with a massive influx of blood-borne innate and adaptive immune cells. Cues from the latter are likely to alter and expand the spectrum of states observed in cells that are constitutively resident. However, local communications between immigrant and resident cell types in human inflammatory disease remain poorly understood. Here, we explored heterogeneity of synovial fibroblasts (FLS) in inflamed joints of rheumatoid arthritis (RA) patients using paired single cell RNA and ATAC sequencing (scRNA/ATAC-seq), multiplexed imaging, and spatial transcriptomics along with in vitro modeling of cell extrinsic factor signaling. These analyses suggest that local exposures to myeloid and T cell derived cytokines, TNF, IFN{gamma}, IL-1{beta}, or lack thereof, drive six distinct FLS states some of which closely resemble fibroblast states in other disease-affected tissues including skin and colon. Our results highlight a role for concurrent, spatially distributed cytokine signaling within the inflamed synovium.


title: Selective endocytosis controls slit diaphragm maintenance and dynamics.

abstract: The kidneys generate about 180 liters of primary urine per day by filtration of plasma. An essential part of the filtration barrier is the slit diaphragm, a multiprotein complex containing nephrin as major component. Filter dysfunction typically manifests with proteinuria and mutations in endocytosis regulating genes were discovered as causes of proteinuria. However, it is unclear how endocytosis regulates the slit diaphragm and how the filtration barrier is maintained without either protein leakage or filter clogging. Here we study nephrin dynamics in podocyte-like nephrocytes of Drosophila and show that selective endocytosis either by dynamin- or flotillin-mediated pathways regulates a stable yet highly dynamic architecture. Short-term manipulation of endocytic functions indicates that dynamin-mediated endocytosis of ectopic nephrin restricts slit diaphragm formation spatially while flotillin-mediated turnover of nephrin within the slit diaphragm is needed to maintain filter permeability by shedding of molecules bound to nephrin in endosomes. Since slit diaphragms cannot be studied in vitro and are poorly accessible in mouse models, this is the first analysis of their dynamics within the slit diaphragm multiprotein complex. Identification of the mechanisms of slit diaphragm maintenance will help to develop novel therapies for proteinuric renal diseases that are frequently limited to symptomatic treatment.


title: FtsZ is essential until the late stage of constriction

abstract: 1There has been recent debate as to the source of constriction force during cell division. FtsZ can generate a constriction force on tubular membranes in vitro, suggesting it may generate the constriction force in vivo. However, another study showed that mutants of FtsZ did not affect the rate of constriction, whereas mutants of the PG assembly did, suggesting that PG assembly may push the constriction from the outside. Supporting this model, two groups found that cells that have initiated constriction can complete septation while the Z ring is poisoned with PC190723. PC19 arrests treadmilling but leaves FtsZ in place. We sought to determine if a fully assembled Z ring is necessary during constriction. To do this, we used a temperature sensitive FtsZ mutant, FtsZ84. FtsZ84 behaves as wild type at 30{degrees} C, but it disassembles from the Z ring within one min upon a temperature jump to 42{degrees} C. Following the temperature jump we found that cells in early constriction stop constricting. Cells that had progressed to the later stage of division finished constriction without a Z ring. These results show that in Escherichia coli, an assembled Z ring is essential for constriction except in the final stage, contradicting the simplest interpretation of previous studies using PC19.


title: IFT20 governs mesenchymal stem cell fate through positively regulating TGF-β-Smad2/3-Glut1 signaling mediated glucose metabolism

abstract: Aberrant lineage allocation of mesenchymal stem cells (MSCs) could cause bone marrow osteoblast-adipocyte imbalance, and glucose as an important nutrient is required for the maintenance of the MSCs fate and function. Intraflagellar transport 20 (IFT20) is one of the IFT complex B protein which regulates osteoblast differentiation, and bone formation, but how IFT20 regulates MSCs fate remains undefined. Here, we demonstrated that IFT20 controls MSC lineage allocation through regulating glucose metabolism during skeletal development. IFT20 deficiency in the early stage of MSCs caused significantly shortened limbs, decreased bone mass and significant increase in marrow fat. However, deletion of IFT20 in the later stage of MSCs and osteocytes just slightly decreased bone mass and bone growth and increased marrow fat. Additionally, we found that loss of IFT20 in MSCs promotes adipocyte formation, which enhances RANKL expression and bone resorption. Conversely, ablation of IFT20 in adipocytes reversed these phenotypes. Mechanistically, loss of IFT20 in MSCs significantly decreased glucose tolerance and suppressed glucose uptake and lactate and ATP production. Moreover, loss of IFT20 significantly inhibited TGF-{beta}-Smad2/3 signaling and decreased the binding activity of Smad2/3 to Glut1 promoter to downregulate Glut1 expression. These findings indicate that IFT20 plays essential roles for preventing MSC lineage allocation into adipocytes through controlling TGF-{beta}-Smad2/3-Glut1 mediated glucose metabolism.


title: Hidden diversity - DNA metabarcoding reveals hyper-diverse benthic invertebrate communities

abstract: Freshwater ecosystems, such as streams, are facing increasing pressures from agricultural land use. Aquatic insects and other macroinvertebrates have historically been used as indicators of ecological condition and water quality in freshwater biomonitoring programs; however, many of these protocols use coarse taxonomic resolution (e.g., family) when identifying macroinvertebrates. The use of family-level identification can mask species-level diversity, as well as patterns in community composition in response to environmental variables. Recent literature stresses the importance of robust biomonitoring to detect trends in insect decline globally, though most of these studies are carried out in terrestrial habitats. Here, we incorporate molecular identification (DNA metabarcoding) into a stream biomonitoring sampling design to explore the diversity and variability of aquatic macroinvertebrate communities at small spatial scales. We sampled twenty southern Ontario streams in an agricultural landscape for aquatic macroinvertebrates and, using DNA metabarcoding, revealed incredibly rich benthic communities which were largely comprised of rare taxa detected only once per stream despite multiple biological replicates. In addition to numerous rare taxa, our species pool estimates indicated that after 240 samples from twenty streams, there was a large proportion of taxa present which remained undetected by our sampling regime. When comparing different levels of taxonomic resolution, we observed that using OTUs revealed over ten times more taxa than family-level identification. A single insect family, the Chironomidae, contained over one third of the total number of OTUs detected in our study. Within-stream dissimilarity estimates were consistently high for all taxonomic groups (invertebrate families, invertebrate OTUs, chironomid OTUs), indicating stream communities are very dissimilar at small spatial scales. While we predicted that increased land use would homogenize benthic communities, this was not supported as within-stream dissimilarity was unrelated to land use.


title: Social media mining and photo-identification detects the shift of long-term seasonal foraging habitat for a juvenile loggerhead sea turtle

abstract: Animal imagery uploaded on social media has been identified as an important tool in wildlife research and conservation and has been used in a variety of recent studies. Here a case study is presented, where a detailed analysis of social media content revealed a shift of a long-term foraging habitat for a juvenile loggerhead sea turtle (Caretta caretta) in Greece. In particular, this individual was a long term resident of Zakynthos island, Greece, from 2016 until 2020 (5 consecutive summer seasons), regularly foraging on a nearshore reef, with no observations of it being made during the 2021 season. However regular social media image mining combined with photo-identification, detected this individual foraging in the Gulf of Corinth in August 2021, more that 200km away from his previous foraging habitat. This case study (i) shows the possibility for juvenile loggerheads to shift their foraging site even after long term use, with implications in capture-mark-recapture studies and (ii) once more highlights the usefulness of social media mining and citizen science in diverse aspects of sea turtle studies.


title: Experimental and theoretical support for costs of plasticity and phenotype in a nematode cannibalistic trait

abstract: Developmental plasticity is the ability of a genotype to express multiple phenotypes under different environmental conditions and has been shown to facilitate the evolution of novel traits. However, while associated costs of both plasticity and phenotype have been theoretically predicted, empirically such costs remain poorly documented and little understood. Here, we use a plasticity model system, hermaphroditic nematode Pristionchus pacificus, to experimentally measure these costs in wild isolates under controlled laboratory conditions. P. pacificus can develop either a bacterial feeding or predatory mouth morph in response to different external stimuli, with natural variation of mouth-morph ratios between strains. We first demonstrated the cost of phenotype by analyzing fecundity and developmental speed in relation to mouth morphs across the P. pacificus phylogenetic tree. Then, we exposed three P. pacificus strains to two distinct microbial diets that induce strain-specific mouth-form ratios. Our results indicate that a highly-plastic strain does shoulder a cost of plasticity, i.e., the diet-induced predatory mouth morph is associated with reduced fecundity and slower developmental speed. In contrast, a non-plastic strain suffers from the cost of phenotype in unfavorable conditions, but shows increased fitness and higher developmental speed under favorable conditions. Furthermore, we computationally illustrate the consequences of the costs of plasticity and phenotype on the population dynamics in spatially-homogeneous and spatially-structured populations using empirically-derived life history parameters for modeling. This study provides comprehensive support for the costs of plasticity and phenotype based on empirical and modeling approaches.


title: Transcriptome and DNA methylome dynamics reveal differential characteristics of inflorescence development between two ecotypes in Panicum hallii

abstract:
The morphological diversity of the inflorescence determines flower and seed production, which is critical for plant adaptation and fitness. Cytosine methylation is an epigenetic mark that contributes to gene expression regulation during inflorescence development. Panicum hallii is a wild perennial grass in the subfamily Panicoideae that has been developed as a model to study perennial grass biology and adaptive evolution. Highly divergent inflorescences have evolved between the two major ecotypes in P. hallii, the upland ecotype with compact inflorescence and large seed and the lowland ecotype with an open inflorescence and small seed. Here we performed a comparative transcriptome and DNA methylome analysis across different stages of inflorescence between these two divergent ecotypes of P. hallii. Global transcriptome analysis identified differentially expressed genes (DEGs) involved in panicle divergence, stage-specific expression, and co-expression modules underlying inflorescence development. Comparing DNA methylome profiles revealed a remarkable level of differential DNA methylation associated with the evolution of the P. hallii inflorescence. We found that most differentially methylated regions (DMRs) occurred within the flanking regulatory regions of genes, especially the promoter. Integrative analysis of DEGs and DMRs characterized the global features of DMR-associated DEGs in the divergence of P. hallii inflorescence, which includes homologs of important inflorescence and seed developmental genes that have been previously identified in domesticated crops. Evolutionary analysis measured by Ka/Ks ratio suggested that most DMR-associated DEGs are under relatively strong purifying selection. This study provides insights into the transcriptome and epigenetic landscape of inflorescence divergence in P. hallii and a novel genomic resource for perennial grass biology.

One sentence summaryA comparative transcriptome and DNA methylome analysis of inflorescence between upland and lowland ecotypes reveal gene expression and DNA methylation variation underlying inflorescence divergence in Panicum hallii.


title: Genomic resolution of cryptic species diversity in chipmunks

abstract: Discovery of cryptic species is essential to understanding the process of speciation and assessing the impacts of anthropogenic stressors. Here, we used genomic data to test for cryptic species diversity within an ecologically well-known radiation of North American rodents, western chipmunks (Tamias). We assembled a de novo reference genome for a single species (Tamias minimus) combined with new and published targeted sequence-capture data for 21,551 autosomal and 493 X-linked loci sampled from 121 individuals spanning 22 species. We identified at least two cryptic lineages corresponding with an isolated subspecies of least chipmunk (T. minimus grisescens) and with a restricted subspecies of the yellow-pine chipmunk (T. amoenus cratericus) known only from around the extensive Craters of the Moon lava flow. Additional population-level sequence data revealed that the so-called Crater chipmunk is a distinct species that is abundant throughout the coniferous forests of southern Idaho. This cryptic lineage does not appear to be most closely related to the ecologically and phenotypically similar yellow-pine chipmunk but does show evidence for recurrent hybridization with this and other species.


title: Genomic patterns of divergence in the early and late steps of speciation of the deep-sea vent thermophilic worms of the genus Alvinella.

abstract:
BackgroundThe transient and fragmented nature of the deep-sea hydrothermal environment made of ridge subduction, plate collision and the emergence of new rifts is currently acting to the separation of vent populations, local adaptation and is likely to promote bursts of speciation and species specialization. The tube-dwelling worms Alvinella pompejana called the Pompeii worm and its sister species A. caudata live syntopically on the hottest part of deep-sea hydrothermal chimneys along the East Pacific Rise. They are exposed to extreme thermal and chemical gradients, which vary greatly in space and time, and thus represent ideal candidates for understanding the evolutionary mechanisms at play in the vent fauna evolution.

ResultsIn the present study, we explored genomic patterns of divergence in the early and late steps of speciation of these emblematic worms using transcriptome assemblies and the first draft genome to better understand the relative role of geographic isolation and habitat preference in their genome evolution. Analyses were conducted on allopatric populations of Alvinella pompejana (early stage of separation) and between A. pompejana and its syntopic species Alvinella caudata (late stage of speciation). We first identified divergent genomic regions and targets of selection as well as their position in the genome over collections of orthologous genes and, then, described the speciation dynamics by documenting the annotation of the most divergent and/or positively selected genes involved in the isolation process. Gene mapping clearly indicated that divergent genes associated with the early stage of speciation, although accounting for nearly 30% of genes, are highly scattered in the genome without any island of divergence and not involved in gamete recognition or mito-nuclear incompatibilities. By contrast, genomes of A. pompejana and A. caudata are clearly separated with nearly all genes (96%) exhibiting high divergence. This congealing effect however seems to be linked to habitat specialization and still allows positive selection on genes involved in gamete recognition, as a possible long-duration process of species reinforcement.

ConclusionOur analyses pointed out the non-negligible role of natural selection on both the early and late stages of speciation in the emblematic thermophilic worms living on the walls of deep-sea hydrothermal chimneys. They shed ligth on the evolution of gene divergence during the process of speciation and species specialization over a very long period of time.


title: Organism-wide mapping of MHC class I and II expression in mouse lemur cells and tissues

abstract: The major histocompatibility complex (MHC) class I and II glycoproteins have been associated with numerous disease phenotypes, mechanisms and outcomes. These associations can be due to allotypic polymorphism or to altered levels of allotype expression. Although well studied in a range of cell types and microenvironments, no study has encompassed all cell-types present in an individual mouse lemur. In this study the droplet-based single cell RNA sequence data from the mouse lemur cell atlas, Tabula Microcebus, were used to examine the patterns of MHC class I and II expression. The cell atlas comprises data obtained from 27 organs from four mouse lemurs, enabling comparison of expression pattern between both cell types and the individual lemurs. Patterns of gene expression showed a good concordance among the four mouse lemurs. Three primary patterns of expression were identified and associated with different cell-types. Mapping MHC expression onto existing cell trajectories of cell development and spatial gradients revealed fine scale differences in expression level and pattern in single tissues. The bioinformatic pipeline developed here is applicable to other cell atlas projects.


title: Multivariate genetic analysis of personality and cognitive traits reveals abundant pleiotropy and improves prediction

abstract:
Personality and cognition are heritable mental traits, and their genetic determinants may be distributed across interconnected brain functions. However, previous studies have employed univariate approaches which reduce complex traits to summary measures. We applied the "pleiotropy-informed" multivariate omnibus statistical test (MOSTest) to genome-wide association studies (GWAS) of 35 item and task-level measures of neuroticism and cognition from the UK Biobank (n=336,993). We identified 431 significant genetic loci and found evidence of abundant pleiotropy across personality and cognitive domains. Functional characterisation implicated genes with significant tissue-specific expression in all tested brain tissues and enriched in brain-specific gene-sets. We conditioned independent GWAS of the Big 5 personality traits and cognition on our multivariate findings, which boosted genetic discovery in other personality traits and improved polygenic prediction. These findings advance our understanding of the polygenic architecture of complex mental traits, indicating a prominence of pleiotropic genetic effects across higher-order domains of mental function.

Graphical abstract

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title: Genome-wide association and genomic prediction of resistance to Flavobacterium columnare in a farmed rainbow trout population

abstract: Columnaris disease is an emerging disease affecting farmed rainbow trout (Oncorhynchus mykiss) globally. In aquaculture breeding, genomic selection has been increasingly used to improve traits that are difficult to measure on candidate fish (such as disease resistance traits). Following a natural outbreak of columnaris disease, 3,054 exposed fish and their 81 parents (33 dams and 48 sires) were genotyped with the 57K SNP Axiom trout genotyping array. Genetic parameters of host resistance (measured as a binary survival trait) were estimated, a genome wide association study was performed, and the accuracy of pedigree-based and genomic prediction was estimated. After quality controls, 2,874 challenged fish (1,403 dead fish and 1,471 alive fish) and 78 parents genotyped for 27,907 SNPs remained. Pedigree based heritability was estimated to be 0.18 and 0.35 on the observed and underlying scale, respectively. Genomic heritability was estimated to be 0.21 and 0.43 on the observed and underlying scale, respectively. A quantitative trait loci (QTL) was detected on chromosome Omy3, significant at the genome-wide level, along with several suggestive QTLs on two other chromosomes. The additive effect on mortality proportion of the peak SNP from Omy3 was estimated to be 0.11 (0.018; se). Pedigree-based prediction accuracy was 0.59, and the use of genomic evaluation increased the prediction accuracy by at least 13.6%. Using the second iteration of a weighted genomic-based evaluation increased the prediction accuracy by 18.6% compared to the pedigree-based model. These results suggest that resistance is a suitable target trait for genetic improvement by selective breeding, and genomic selection may be a useful approach to speed up this process.

category: genomics


title: Divergent kinase WNG1 is regulated by phosphorylation of an atypical activation sub-domain

abstract: Apicomplexan parasites like Toxoplasma gondii grow and replicate within a specialized organelle called the parasitophorous vacuole. The vacuole is decorated with parasite proteins that integrate into the membrane after trafficking through the parasite secretory system as soluble, chaperoned complexes. A regulator of this process is an atypical protein kinase called WNG1. Phosphorylation by WNG1 appears to serve as a switch for membrane integration. However, like its substrates, WNG1 is secreted from the parasite dense granules, and its activity must therefore be tightly regulated until the correct membrane is encountered. Here we demonstrate that, while another member of the WNG family can adopt multiple multimeric states, WNG1 is monomeric and therefore not regulated by multimerization. Instead, we identify two phosphosites on WNG1 that are required for its kinase activity. Using a combination of in vitro biochemistry and structural modeling, we identify basic residues that are also required for WNG1 activity and therefore appear to recognize the activating phosphosites. Among these coordinating residues are the "HRD" Arg, which recognizes activation loop phosphorylation in canonical kinases. WNG1, however, is not phosphorylated on its activation loop, and its activating phosphosites instead appear to lock the kinase C-lobe into an activated conformation. These data suggest a simple model for WNG1 activation by increasing ATP concentration above a critical threshold once WNG1 traffics to the parasitophorous vacuole.


title: A microfluidics-assisted methodology for label-free isolation of CTCs with downstream methylation analysis of cfDNA in lung cancer

abstract: Lung cancer (LC) is a major cause of mortality. Late diagnosis, associated with limitations in tissue biopsies for adequate tumor characterization contribute to limited survival of lung cancer patients. Liquid biopsies have been introduced to improve tumor characterization through the analysis of biomarkers, including circulating tumour cells (CTCs) and cell-free DNA (cfDNA). Considering their availability in blood, several enrichment strategies have been developed to augment circulating biomarkers for improving diagnostic, prognostic and treatment efficacy assessment; often, however, only one biomarker is tested. In this work we developed and implemented a microfluidic chip for label-free enrichment of CTCs with a methodology for subsequent cfDNA analysis from the same cryopreserved sample. CTCs were successfully isolated in 38 of 42 LC patients with the microfluidic chip. CTCs frequency was significantly higher in LC patients with advanced disease. A cut-off of 1 CTC/mL was established for diagnosis (sensitivity=76.19%, specificity=100%) and in patients with late-stage lung cancer, the presence of [≥] 5 CTCs/mL was significantly associated with shorter overall survival. MIR129-2me and ADCY4me panel of cfDNA methylation performed well for LC detection, whereas MIR129-2me combined with HOXA11me allowed for patient risk stratification. Analysis of combinations of biomarkers enabled the definition of panels for LC diagnosis and prognosis. Overall, this study demonstrates that multimodal analysis of tumour biomarkers via microfluidic devices may significantly improve LC characterization in cryopreserved samples, constituting a reliable source for continuous disease monitoring.


title: Genomic analyses identify biological processes and functions between M1 and M2 macrophages

abstract: Macrophages can be induced by a variety of factors to change their phenotype and functions. M1 and M2 macrophages play converse roles during inflammation or other diseases. However, the mechanism and function of M1 and M2 macrophages are still not clear. This study aims to identify the different molecules and functions by analyzing the RNA-seq data. The GSE189354 was created by the Illumina HiSeq 4000 (Mus musculus). The KEGG and GO analyses indicated the Phagosome and Hematopoietic cell lineage are the major biological processes between M1 and M2 macrophages. Moreover, we further identified ten molecules including Il6, Il1b, Tlr2, Myc, Fn1, Itgax, Cxcl10, Ccl5, Cxcr4, and Pparg. Therefore, our study may provide novel knowledge of innate immunity.