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Salivary proteins of a gall-inducing aphid and their impact on early gene responses of susceptible and resistant host-plant genotypes

Successful plant colonization by parasites requires the circumvention of host defenses, and sometimes a reprogramming of host metabolism, mediated by effector molecules delivered into the host. Using transcriptomic and enzymatic approaches, we characterized salivary glands and saliva of Phloeomyzus passerinii, an aphid exhibiting an atypical feeding strategy. Plant genes responses to salivary extracts of P. passerinii and Myzus persicae were assessed with poplar protoplasts of a susceptible and a resistant genotype, and in a heterologous Arabidopsis system. We predict that P. passerinii secretes a highly peculiar saliva containing effectors potentially interfering with host defenses, biotic stress signaling and plant metabolism, notably phosphatidylinositol phosphate kinases which seemed specific to P. passerinii. Gene expression profiles indicated that salivary extracts of M. persicae markedly affected host defenses and biotic stress signaling, while salivary extracts of P. passerinii induced only weak responses. The effector-triggered susceptibility was characterized by downregulations of genes involved in cytokinin signaling and auxin homeostasis. This suggests that P. passerinii induces an intracellular accumulation of auxin in susceptible host genotypes, which is supported by histochemical assays in Arabidopsis. This might in turn affect biotic stress signaling and contribute to host tissue manipulation by the aphid.

ecology

Complement C3- and CR3-dependent microglial clearance protects photoreceptors in retinitis pigmentosa

Complement activation has been implicated as an inflammatory driver of neurodegeneration in retinal and brain pathologies. However, its involvement and influence of photoreceptor degeneration in retinitis pigmentosa (RP), an inherited, largely incurable blinding disease, is unclear. We discover that markedly upregulated retinal expression of multiple complement components coincided spatiotemporally with photoreceptor degeneration in both the rd10 mouse model and in human specimens of RP, with increased complement C3 expression and activation localizing to infiltrating microglia near photoreceptors. Genetic ablation of C3 in the rd10 background resulted in accelerated structural and functional photoreceptor degeneration and altered retinal expression of inflammatory genes. These effects were phenocopied by the genetic deletion of CR3, a microglia-expressed receptor for the C3 activation product C3b, implicating an adaptive microglial-mediation mechanism involving C3-CR3 interaction. Deficiency of either C3 or CR3 resulted in deficient microglial phagocytosis of apoptotic photoreceptors in vivo, as well as increased microglial neurotoxicity to photoreceptors in vitro. These findings demonstrate a novel adaptive role for complement activation in RP that facilitates microglial clearance of apoptotic photoreceptors, without which increased proinflammatory microglial neurotoxicity ensues. These positive contributions of complement via microglial-mediated mechanisms are important in the design of immunomodulatory therapeutic approaches to neurodegeneration.\n\nOne Sentence SummaryComplement activation mediates adaptive neuroprotection for photoreceptors by facilitating C3-CR3 dependent microglial clearance of apoptotic cells.

neuroscience

Comammox Nitrospira are the dominant ammonia oxidizers in a mainstream low dissolved oxygen nitrification reactor

Recent findings show that a subset of bacteria affiliated with Nitrospira, a genus known for its importance in nitrite oxidation for biological nutrient removal applications, are capable of complete ammonia oxidation (comammox) to nitrate. Early reports suggested that they were absent or present in low abundance in most activated sludge processes, and thus likely functionally irrelevant. Here we show the accumulation of comammox Nitrospira in a nitrifying sequencing batch reactor operated at low dissolved oxygen (DO) concentrations. Actual mainstream wastewater was used as influent after primary settling and an upstream pre-treatment process for carbon and phosphorus removal. The ammonia removal rate was stable and exceeded that of the treatment plants parallel full-scale high DO nitrifying activated sludge reactor. 16S rRNA sequencing showed a steady accumulation of Nitrospira to 53% total abundance and a decline in conventional ammonia oxidizing bacteria to <1% total abundance over 400+ days of operation. After ruling out other known ammonia oxidizers, qPCR confirmed the accumulation of comammox Nitrospira beginning around day 200, to eventually comprise 94% of all detected amoA and 4% of total bacteria by day 407. Quantitative fluorescence in-situ hybridization confirmed the increasing trend and high relative abundance of Nitrospira. These results demonstrate that comammox can be metabolically relevant to nitrogen transformation in wastewater treatment, and can even dominate the ammonia oxidizing community. Our results suggest that comammox may be an important functional group in energy efficient nitrification systems designed to operate at low DO levels.

bioengineering

Encoding of wind direction by central neurons in Drosophila

Wind is a major navigational cue for insects, but how wind direction is decoded by central neurons in the insect brain is unknown. Here, we find that walking flies combine signals from both antennae to orient to wind during olfactory search behavior. Movements of single antennae are ambiguous with respect to wind direction, but the difference between left and right antennal displacements yields a linear code for wind direction in azimuth. Second-order mechanosensory neurons share the ambiguous responses of single antenna and receive input primarily from the ipsilateral antenna. Finally, we identify a novel set of neurons, which we call wedge projection neurons, that integrate signals across the two antennae and receive input from at least three classes of second-order neurons to produce a more linear representation of wind direction. This study establishes how a feature of the sensory environment - the wind direction - is decoded by single neurons that compare information across two sensors.

neuroscience

Network topology of neural systems supporting avalanche dynamics predicts stimulus propagation and recovery

Many neural systems display avalanche behavior characterized by uninterrupted sequences of neuronal firing whose distributions of size and durations are heavy-tailed. Theoretical models of such systems suggest that these dynamics support optimal information transmission and storage. However, the unknown role of network structure precludes an understanding of how variations in network topology manifest in neural dynamics and either support or impinge upon information processing. Here, using a generalized spiking model, we develop a mechanistic understanding of how network topology supports information processing through network dynamics. First, we show how network topology determines network dynamics by analytically and numerically demonstrating that network topology can be designed to propagate stimulus patterns for long durations. We then identify strongly connected cycles as empirically observable network motifs that are prevalent in such networks. Next, we show that within a network, mathematical intuitions from network control theory are tightly linked with dynamics initiated by node-specific stimulation and can identify stimuli that promote long-lasting cascades. Finally, we use these network-based metrics and control-based stimuli to demonstrate that long-lasting cascade dynamics facilitate delayed recovery of stimulus patterns from network activity, as measured by mutual information. Collectively, our results provide evidence that cortical networks are structured with architectural motifs that support long-lasting propagation and recovery of a few crucial patterns of stimulation, especially those consisting of activity in highly controllable neurons. Broadly, our results imply that avalanching neural networks could contribute to cognitive faculties that require persistent activation of neuronal patterns, such as working memory or attention.

neuroscience

The Caenorhabditis elegans HAM-1 protein modifies G protein signaling and membrane extension to reverse the polarity of asymmetric cell division

Asymmetric divisions often produce daughter cells that differ in both fate and size. The Caenorhabditis elegans HAM-1 protein regulates both daughter cell fate and daughter cell size asymmetry (DCSA) in a subset of asymmetric divisions. Here we focus on the divisions of the Q.a and Q.p neuroblasts, which use distinct mechanisms to divide with opposite polarity. Q.a divides by a ham-1-dependent, spindle-independent, myosin-dependent mechanism to produce a smaller anterior daughter that dies, whereas Q.p divides by a ham-1-independent, spindle-dependent, myosin-independent mechanism to produce a smaller posterior daughter that dies. Despite these differences, we found that membrane extension at the posterior of Q.a and at the anterior of Q.p promoted DCSA in these cells by a Wiscott-Aldrich protein (WASp)-dependent mechanism and that in ham-1 mutant Q.a divisions, the polarity of this extension was reversed. In addition, the spindle moved posteriorly during the Q.a division in a ham-1 mutant, a phenotype normally exhibited by Q.p. We found that this spindle movement in wild-type Q.p divisions required Ga proteins that promote spindle movement in other asymmetric divisions, and GPR-1, a protein involved in linking G proteins to microtubule asters, localized to the posterior cortex of Q.p. Genetic interactions suggest that ham-1 mutant Q.a divisions also require Ga proteins function to divide with a reversed polarity. The transformation of Q.a to Q.p-like polarity in the ham-1 mutant, however, appeared incomplete: ham-1 loss did not alter the asymmetric localization of the non-muscle myosin NMY-2 to the anterior cortex of Q.a. A GFP tagged ham-1 transgene revealed that Q.a but not Q.p expressed ham-1. Finally, we show that HAM-1 has both cortical and nuclear functions in Q,a DCSA. We propose a model where HAM-1 modifies a default Q.p-type polarity by localizing WASp function to the posterior Q.a membrane and by interfering with G-protein mediated spindle movement.\n\nAuthor SummaryOne way that animals produce different cell types is by asymmetric cell division, where a cell divides to produce daughter cells that differ in fate. Much is known about the mechanisms that polarize dividing cells to generate daughters that differ in fate. Some asymmetric cell divisions also result in daughters that differ in size, and the mechanisms that regulate how cells generate an asymmetric cleavage plane are poorly understood. In neural progenitors of the nematode Caenorhabditis elegans, two distinct mechanisms generate daughter cells of different size. One type requires movement of the mitotic spindle, which then defines the plane of the cell division. The other is spindle-independent. Here, we study two cells that divide with opposite polarities using these two mechanisms. We find that in the absence of the protein HAM-1, which has been reported to regulate gene transcription, the cell that normally divides using a spindle-independent mechanism now divides with a reversed polarity using a spindle-dependent mechanism. Our findings suggest that HAM-1 plays a key role in defining the mechanism by which a progenitor divides to produce daughter cells of different sizes and that both localization to the cell periphery and nucleus are important for its function.

developmental biology

Metagenomic unmapped reads provide important insights into human microbiota and disease associations

We developed a computational pipeline, MicroPro, for metagenomic data analyses that take into account all the reads from known and unknown microbial organisms and for associating viruses with complex diseases. We utilized MicroPro to analyze metagenomics data related to three diseases: colorectal cancer, type-2 diabetes and liver cirrhosis, and showed that including reads from unknown organisms will markedly increase the prediction accuracy of the disease status based on metagenomics data. We identified new microbial organisms associated with these diseases. Viruses were shown to play important roles in colorectal cancer and liver cirrhosis, but not in type-2 diabetes. MicroPro is available at https://github.com/zifanzhu/MicroPro.

bioinformatics

The neural dynamics of hierarchical Bayesian inference in multisensory perception

Transforming the barrage of sensory signals into a coherent multisensory percept relies on solving the binding problem - deciding whether signals come from a common cause and should be integrated, or instead be segregated. Human observers typically arbitrate between integration and segregation consistent with Bayesian Causal Inference, but the neural mechanisms remain poorly understood. We presented observers with audiovisual sequences that varied in the number of flashes and beeps. Combining Bayesian modelling and EEG representational similarity analyses, we show that the brain initially represents the number of flashes and beeps and their numeric disparity mainly independently. Later, it computes them by averaging the forced-fusion and segregation estimates weighted by the probabilities of common and independent cause models (i.e. model averaging). Crucially, prestimulus oscillatory alpha power and phase correlate with observers prior beliefs about the worlds causal structure that guide their arbitration between sensory integration and segregation.

neuroscience

A Rap1 binding site and lipid-dependent helix in talin F1 domain cooperate in integrin activation

Rap1 GTPases bind effectors, such as RIAM, to enable talin1 to induce integrin activation. In addition, Rap1 binds directly to the talin1 F0 domain (F0); however, this interaction makes a negligible contribution to integrin activation in CHO cells or platelets. Here, we show that talin1 F1 domain contains a previously undetected Rap1 binding site of similar affinity to that in F0. A structure-guided point mutant (R118E) in F1, which blocks Rap1 binding, abolishes the capacity of Rap1 to potentiate talin1-induced integrin activation. The capacity of F1 to mediate Rap1-dependent integrin activation depends on a unique loop in F1 that transforms into an amphipathic helix upon binding to membrane lipids. Basic membrane-facing residues of this helix are critical as charge reversal mutations led to dramatic suppression of talin1-dependent activation. Thus, a novel Rap1 binding site and a lipid-dependent amphipathic helix in talin1 F1 cooperate to enable a direct Rap1-talin1 interaction to cause integrin activation.\n\nSummaryThis work reveals that Rap1 GTPases bind directly to talin1 F1 domain and by cooperating with a unique lipid-dependent amphipathic helix in the F1 domain effects talin1-mediated integrin activation.

cell biology

Mangrove forest structure and composition along urban gradients in Puerto Rico

Urban forests are repeatedly characterized as distinct in composition and structure in comparison with their non-urban counterparts. This holds true for mangroves, although previous studies lack quantified representations of urbanness as well as any inclusion of hydrology or water chemistry, which are important influences on mangrove forest structure, composition, and function. This study uses LiDAR and ground-based measurements of mangroves within well quantified urban gradients in Puerto Rico to test for the relative importance of urbanization alongside flooding metrics and surface water chemistry in explaining observed patterns of forest structure and composition. In simple regression, urban metrics were the most powerful predictors of forest composition but not structure. Results show higher tree diversity but lower mangrove diversity in the most urban forests. Structural measurements, however, were best explained by flooding, surface water chemistry, and non-urban land cover metrics. Nitrogen concentrations best explained stem density and tree size, while flooding metrics best explained stand biomass and basal area, and surrounding vegetation cover best explained canopy cover and height metrics. In multiple regression, land cover and surface water chemistry were more important than flooding, with population density again being the most important variable in explaining mangrove forest diversity. Results show that urbanization is an important influence on mangrove composition and basal area, leading to higher tree diversity and lower basal area, consistent with patterns in terrestrial forests. But urban mangrove forests are also lower in mangrove diversity and tend to have representation only by Laguncularia racemosa. Nitrogen concentrations and surrounding vegetation cover, both of which are indirectly influenced by urbanization, were positively related to tree size and canopy cover and height, respectively. These tests suggest urbanization is an important influence on mangrove forest structure and composition, but that flooding and water chemistry must also be considered when managing these forests.

ecology

Detailed analysis of paternal knockout Grb10 mice suggests effects on social stability, rather than social dominance

Imprinted genes are highly expressed in monoaminergic regions of the midbrain and their functions in this area are thought to have an impact on mammalian social behaviors. One such imprinted gene is Grb10, of which the paternal allele is currently recognized as mediating social dominance behavior. However, there has been no detailed study of social dominance in Grb10+/p mice. Moreover, the original study examined tube-test behavior in isolated mice 10 months of age. Isolation testing favors more territorial and aggressive behaviors, and does not address social dominance strategies employed in group housing contexts. Furthermore, isolation stress impacts midbrain function and dominance related behavior, often through alterations in monoaminergic signaling. Thus, we undertook a systematic study of Grb10+/p social rank and dominance behavior within the cage group, using a number of convergent behavioral tests. We examined both male and female mice to account for sex differences, and tested cohorts aged 2, 6, and 10 months to examine any developments related to age. We found group-housed Grb10+/p mice do not show evidence of enhanced social dominance, but cages containing Grb10+/p and wildtype mice lacked the normal correlation between three different measures of social rank. Moreover, a separate study indicated isolation stress induced inconsistent changes in tube test behavior. Taken together, these data suggest future research on Grb10+/p mice should focus on social stability, rather than dominance per se.

animal behavior and cognition

Concerning suppression and facilitation of motion perception in humans

Here we consider some topics from a commentary by Tzvetanov (2018) on our article entitled \"Suppression and facilitation of human neural responses\" (Schallmo et al., 2018). The author raises two main points of criticism, which we will summarize thus: 1) psychophysical response bias is not adequately modeled, and 2) other computational models may be better suited to describe the psychophysical motion discrimination data. Both of these points are reasonable in principle, but we disagree with the author in a few areas. We provide some discussion of both issues in order to further elevate the scientific dialogue.

neuroscience

Sex-dependent differences in pain and sleep in a porcine model of Neurofibromatosis type 1

Neurofibromatosis Type 1 (NF1) is an autosomal dominant genetic disorder resulting from germline mutations in the NF1 gene, which encodes neurofibromin. Patients experience a variety of symptoms, but pain in the context of NF1 remains largely underrecognized. Here, we characterize nociceptive signaling and pain behaviors in a miniswine harboring a disruptive NF1 mutation (exon 42 deletion). We explore these phenotypes in relationship to collapsin response mediator protein 2 (CRMP2), a known interactor of neurofibromin. Mechanistically, we found two previously unknown phosphorylated residues of CRMP2 in NF1+/ex42del pig dorsal root ganglia (DRGs) and replicated increased voltage-gated calcium channel currents in NF1+/ex42del pig DRGs previously described in rodent models of NF1. We present the first characterization of pain-related behaviors in a pig model of NF1, identifying unchanged agitation scores, lower tactile thresholds (allodynia), and decreased response latencies to thermal laser stimulation (hyperalgesia) in the NF1 mutant animals; NF1+/ex42del pigs demonstrated sexually dimorphic behaviors. NF1+/ex42del pigs showed reduced sleep quality and increased resting, two health-related quality of life symptoms found to be comorbid in people with NF1 pain. Finally, we show decreased depolarization-evoked calcium influx in both wildtype and NF1+/ex42del pig DRGs treated with CRMP2 phosphorylation inhibitor (5)-lacosamide. Our data supports use of NF1+/ex42del pigs as an ideal model for studying NF1-associated pain and are a better model for understanding the pathophysiology of NF1 compared to rodents. Moreover, our findings demonstrate that interfering with CRMP2 phosphorylation might be a promising therapeutic strategy for NF1-related pain management.

neuroscience

Identification of novel common variants associated with chronic pain using conditional false discovery rate analysis with major depressive disorder and assessment of pleiotropic effects of LRFN5.

Chronic pain is highly prevalent worldwide, with a significant socioeconomic burden, and also contributes to excess mortality. Chronic pain is a complex trait that is moderately heritable and genetically, as well as phenotypically, correlated with major depressive disorder (MDD). Use of the Conditional False Discovery Rate (cFDR) approach, which leverages pleiotropy identified from existing GWAS outputs, has been successful in discovering novel associated variants in related phenotypes. Here, genome-wide association study outputs for both von Korff chronic pain grade as a quasi-quantitative trait and for MDD were used to identify variants meeting a cFDR threshold for each outcome phenotype separately, as well as a conjunctional cFDR (ccFDR) threshold for both phenotypes together. Using a moderately conservative threshold, we identified a total of 11 novel single nucleotide polymorphisms (SNPs), six of which were associated with chronic pain grade and nine of which were associated with MDD. Four SNPs on chromosome 14 were associated with both chronic pain grade and MDD. SNPs associated only with chronic pain grade were located within SLC16A7 on chromosome 12. SNPs associated only with MDD were located either in a gene-dense region on chromosome 1 harbouring LINC01360, LRRIQ3, FPGT and FPGT-TNNI3K, or within/close to LRFN5 on chromosome 14. The SNPs associated with both outcomes were also located within LRFN5. Several of the SNPs on chromosomes 1 and 14 were identified as being associated with expression levels of nearby genes in the brain and central nervous system. Overall, using the cFDR approach, we identified several novel genetic loci associated with chronic pain and we describe likely pleiotropic effects of a recently identified MDD locus on chronic pain.\n\nAuthor SummaryGenetic variants explaining variation in complex traits can often be associated with more than one trait at once ( pleiotropy). Taking account of this pleiotropy in genetic studies can increase power to find sites in the genome harbouring trait-associated variants. In this study we used the suspected underlying pleiotropy between chronic pain and major depressive disorder to discover novel variants associated with chronic pain, and to investigate genetic variation that may be shared between the two disorders.

genetics

Rapid single-cell cytometry data visualization with EmbedSOM

Efficient unbiased data analysis is a major challenge for laboratories handling large cytometry datasets. We present EmbedSOM, a non-linear embedding algorithm based on FlowSOM that improves the analyses by providing high-performance visualization of complex single cell distributions within cellular populations and their transition states. The algorithm is designed for linear scaling and speed suitable for interactive analyses of millions of cells without downsampling. At the same time, the visualization quality is competitive with current state-of-art algorithms. We demonstrate the properties of EmbedSOM on workflows that improve two essential types of analyses: The native ability of EmbedSOM to align population positions in embedding is used for comparative analysis of multi-sample data, and the connection to FlowSOM is exploited for simplifying the supervised hierarchical dissection of cell populations. Additionally, we discuss the visualization of the trajectories between cellular states facilitated by the local linearity of the embedding.

bioinformatics

Performance - Based Clustering Enables The Study Of Physiological Features Supporting Sustained Attention Capacities

In the present study, we investigated different sustained attention performance profiles in the general adult population and if age is a determinant factor among these profiles. We also reported some specificities in terms of brain oscillations. The sustained attention to response task was applied combined with electrophysiological recordings in 59 adults, aged from 19 to 86 years. We used a hierarchical cluster analysis to group individuals based on similarity of levels and patterns of performance across variables of interest. We focused on the most common attentional-related variables, which allowed us to identify four distinct clusters showing specific sustained attention profiles. Furthermore, our analysis clearly revealed that age was not the determinant factor of these profiles. Finally, we highlighted specificities in terms of brain oscillations. Subjects from cluster 1- the \"high-performers\" - demonstrated a globally increased theta-gamma coupling maintained over time and an increase of theta activity at the FC6 and F8 electrodes. Subjects from cluster 2, who adopted a more cautious response strategy, presented a higher level of modulation exerted by the electrode FT7 over Oz and a higher theta-gamma coupling at the Oz. This result suggests that cluster-based method to useful in understanding specific mechanisms underlying sustained attention features.

neuroscience

A benchmark of computational CRISPR-Cas9 guide design methods

The popularity of CRISPR-based gene editing has resulted in an abundance of tools to design CRISPR-Cas9 guides. This is also driven by the fact that designing highly specific and efficient guides is a crucial, but not trivial, task in using CRISPR for gene editing. Here, we thoroughly analyse the performance of 17 design tools. They are evaluated based on runtime performance, compute requirements, and guides generated. To achieve this, we implemented a method for auditing system resources while a given tool executes, and tested each tool on datasets of increasing size, derived from the mouse genome. We found that only five tools had a computational performance that would allow them to analyse an entire genome in a reasonable time, and without exhausting computing resources. There was wide variation in the guides identified, with some tools reporting every possible guide while others filtered for predicted efficiency. Some tools also failed to exclude guides that would target multiple positions in the genome. We also considered a collection of over a thousand guides for which experimental data is available. For the tools that attempt to filter based on efficiency, 65% to 85% of the guides they reported were experimentally found to be efficient, but with limited overlap in the sets produced by different tools. Our results show that CRISPR-Cas9 guide design tools need further work in order to achieve rapid whole-genome analysis and that improvements in guide design will likely require combining multiple approaches.

bioinformatics

Genome-wide association study of alcohol consumption in Russian population

Liability to alcohol dependence is heritable, but little is known about its complex polygenic architecture. We performed a genome-wide association study (GWAS) of self-reported alcohol consumption in 1798 of Russian individuals. No SNP reached genome-wide significance for any alcohol drinking patterns: never drinking, everyday drinking, once per week drinking and once per month drinking. Polymorphisms in previously reported genes of KLB and AUTS2 were significant associated with everyday drinking and once per week drinking patterns, respectively. We also found associations of genes involved in nervous system function and mental disorders with some alcohol drinking patterns. This study identifies novel gene associations that should be the focus of future studies investigating the neurobiology of alcohol consumption.

genetics

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