title: Respiration, heartbeat, and conscious tactile perception

abstract:
Previous studies have shown that timing of sensory stimulation during the cardiac cycle interacts with perception. Given the natural coupling of respiration and cardiac activity, we investigated here their joint effects on tactile perception. Forty-one healthy female and male human participants reported conscious perception of finger near-threshold electrical pulses (33% null trials) and decision confidence while electrocardiography, respiratory activity, and finger photoplethysmography were recorded. Participants adapted their respiratory cycle to expected stimulus onsets to preferentially occur during late inspiration / early expiration. This closely matched heart rate variation (sinus arrhythmia) across the respiratory cycle such that most frequent stimulation onsets occurred during the period of highest heart rate probably indicating highest alertness and cortical excitability. Tactile detection rate was highest during the first quadrant after expiration onset. Inter-individually, stronger respiratory phase-locking to the task was associated with higher detection rates. Regarding the cardiac cycle, we confirmed previous findings that tactile detection rate was higher during diastole than systole and newly specified its minimum at 250 - 300 ms after the R-peak corresponding to the pulse wave arrival in the finger. Expectation of stimulation induced a transient heart deceleration which was more pronounced for unconfident decision ratings. Inter-individually, stronger post-stimulus modulations of heart rate were linked to higher detection rates. In summary, we demonstrate how tuning to the respiratory cycle and integration of respiratory-cardiac signals are used to optimize performance of a tactile detection task.

Significance statementMechanistic studies on perception and cognition tend to focus on the brain neglecting contributions of the body. Here, we investigated how respiration and heartbeat influence tactile perception: Respiration phase-locking to expected stimulus onsets corresponds to highest heart rate (and presumably alertness/cortical excitability) and correlates with detection performance. Tactile detection varies across the heart cycle with a minimum when the pulse reaches the finger and a maximum in diastole. Taken together with our previous finding of unchanged early ERPs across the cardiac cycle we conclude that these effects are not a peripheral physiological artifact but a result of cognitive processes that model our bodys internal state, make predictions to guide behavior, and might also tune respiration to serve the task.


title: Mechanosensory input shapes Drosophila motor behavior through Patterned Spontaneous Network Activity

abstract:
Neural activity sculpts circuit wiring in many animals. In vertebrates, patterned spontaneous network activity (PaSNA) generates sensory maps and establishes local circuits 1-3. However, it remains unclear how PaSNA might shape neuronal circuits and behavior in invertebrates. Previous work in the developing Drosophila embryo discovered spontaneous muscle activity that did not require synaptic transmission, and hence was myogenic, preceding PaSNA 4-6. These studies, however, monitored muscle movement, not neural activity, and were therefore unable to observe how myogenic activity might relate to subsequent neural network engagement. Here we use calcium imaging to directly record neural activity and characterize the emergence of PaSNA. We demonstrate that the spatiotemporal properties of PaSNA are highly stereotyped across embryos, arguing for genetic programming. Consistent with previous observations, we observe neural activity well before it becomes patterned, initially emerging during the myogenic stage. Remarkably, inhibition of mechanosensory input as well as inhibition of muscle contractions results in premature and excessive PaSNA, demonstrating that muscle movement serves as a brake on this process. Finally, using an optogenetic strategy to selectively disrupt mechanosensory inputs during PaSNA, followed by quantitative modeling of larval behavior, we demonstrate that mechanosensory modulation during development is required for proper larval foraging. This work thus provides a foundation for using the Drosophila embryo to study the role of PaSNA in circuit formation, provides mechanistic insight into how PaSNA is entrained by motor activity, and demonstrates that spontaneous network activity is essential for locomotor behavior. These studies argue that sensory feedback during the earliest stages of circuit formation can sculpt locomotor behaviors through innate motor learning.

HighlightsO_LIPaSNA in the Drosophila embryonic CNS is spatiotemporally stereotyped
C_LIO_LIMechanosensory neurons negatively modulate PaSNA
C_LIO_LIEmbryonic PaSNA is required for larval locomotor behavior
C_LI

category: neuroscience


title: Mechanosensory input during circuit formation shapes Drosophila motor behavior through Patterned Spontaneous Network Activity


title: Meta-learning local synaptic plasticity for continual familiarity detection

abstract: Over the course of a lifetime, a continual stream of information is encoded and retrieved from memory. To explore the synaptic mechanisms that enable this ongoing process, we consider a continual familiarity detection task in which a subject must report whether an image has been previously encountered. We design a class of feedforward neural network models endowed with biologically plausible synaptic plasticity dynamics, the parameters of which are meta-learned to optimize familiarity detection over long delay intervals. After training, we find that anti-Hebbian plasticity leads to better performance than Hebbian and replicates experimental results from the inferotemporal cortex, including repetition suppression. Unlike previous models, this network both operates continuously without requiring any synaptic resets and generalizes to intervals it has not been trained on. We demonstrate this not only for uncorrelated random stimuli but also for images of real-world objects. Our work suggests a biologically plausible mechanism for continual learning, and demonstrates an effective application of machine learning for neuroscience discovery.


title: Why humans are stronger but not faster after isometric strength training: specific neural, not muscular, motor unit adaptations

abstract: While maximal force increases following short-term isometric strength training, the rate of force development (RFD) may remain relatively unaffected. The underlying neural and muscular mechanisms during rapid contractions after strength training are largely unknown. Since strength training increases the neural drive to muscles, it may be hypothesized that there are distinct neural or muscular adaptations determining the change in RFD independently of an increase in maximal force. Therefore, we examined motor unit population data during the rapid generation of force before and after four weeks of strength training. We observed that strength training did not change the RFD because it did not influence the number of motor units recruited per second or their initial discharge rate during rapid contractions. While strength training did not change motoneuron behaviour in the force increase phase of rapid contractions, it increased the discharge rate of motoneurons (by [~]4 spikes/s) when reaching the plateau phase ([~]150 ms) of the rapid contractions, determining an increase in maximal force production. Computer simulations with a motor unit model that included neural and muscular properties, closely matched the experimental observations and demonstrated that the lack of change in RFD following training is primarily mediated by an unchanged maximal recruitment speed of motoneurons. These results demonstrate that maximal force and contraction speed are determined by different adaptations in motoneuron behaviour following strength training and indicate that increases in the recruitment speed of motoneurons are required to evoke training-induced increases in RFD.


title: Temporal Window based Feature Extraction Technique for Motor-Imagery EEG Signal Classification

abstract: Electroencephalogram (EEG) based motor-imagery classification is one of the most popular Brain Computer Interface (BCI) research areas due to its portability and low cost. In this paper, we have compared Wavelet Energy-entropy based different prediction models and empirically proven that temporal window based approach in motor-imagery classification provides more consistent and better results than popular filter-bank approach. In order to examine the robustness and stability of the proposed method, we have also employed multiple types of classifiers at the end and found that mix-bagging (bagging ensemble learning with multiple types of learners) technique out-smarts other frequently used classifiers. In our study, BCI Competition II Data-set III has been used with four experimental setup: (a) The whole signal (for each trial) as one segment, (b) The whole signal (for each trial) is divided into non-overlapping segments, (c) The whole signal (for each trial) is divided into overlapping segments, and (d) The filter-bank approach where the whole signal (each trial) is segmented based on different frequency bands. The result obtained from the experiment (c) i.e. 91.43% classification accuracy which outperforms the other approaches not only in this paper but to best of our knowledge it is the highest performance for this dataset so far.


title: Opponent vesicular transporters regulate the strength of glutamatergic neurotransmission in a C. elegans sensory circuit

abstract: At chemical synapses, neurotransmitters are packaged into synaptic vesicles that release their contents in response to depolarization. Despite its central role in synaptic function, regulation of the machinery that loads vesicles with neurotransmitters remains poorly understood. We find that synaptic glutamate signaling in a C. elegans chemosensory circuit is regulated by antagonistic interactions between the canonical vesicular glutamate transporter EAT-4/VGLUT and another vesicular transporter, VST-1. Loss of VST-1 strongly potentiates glutamate release from chemosensory BAG neurons and disrupts chemotaxis behavior. Analysis of the circuitry downstream of BAG neurons shows that excess glutamate release disrupts behavior by inappropriately recruiting RIA interneurons to the BAG-associated chemotaxis circuit. Our data indicate that in vivo the strength of glutamatergic synapses is controlled by regulation of neurotransmitter packaging into synaptic vesicles via functional coupling of VGLUT and VST-1.


title: Prenatal cadmium exposure does not induce greater incidence or earlier onset of autoimmunity in the offspring

abstract: We previously demonstrated that exposure of adult mice to environmental levels of cadmium (Cd) alters the immune cell development and function with increases in anti-streptococcal antibody levels, as well as decreases in splenic natural regulatory T cells (nTreg) in the adult female offspring. Based on these data, we hypothesized that prenatal Cd exposure could predispose an individual to developing autoimmunity as adults. To test this hypothesis, the effects of prenatal Cd on the development of autoimmune diabetes and arthritis were investigated. Non-obese diabetic (NOD) mice were exposed to Cd in a manner identical to our previous studies, and the onset of diabetes was assessed in the offspring. Our results showed a similar time-to-onset and severity of disease to historical data, and there were no statistical differences between Cd-exposed and control offspring. Numerous other immune parameters were measured and none of these parameters showed biologically relevant differences between Cd-exposed and control animals. To test whether prenatal Cd-exposure affected development of autoimmune arthritis, we used SKG mice. While the levels of arthritis were similar between Cd-exposed and control offspring of both sexes, the pathology of arthritis determined by micro-computed tomography (CT) between Cd-exposed and control animals, showed some statistically different values, especially in the female offspring. However, the differences were small and thus, the biological significance of these changes is open to speculation. Overall, based on the results from two autoimmune models, we conclude that prenatal exposure to Cd did not lead to a measurable propensity to develop autoimmune disease later in life.

category: immunology


title: Effect of aqueous extract of Antiaris africana stem bark on phagocytic activities of human neutrophils ex-vivo.

abstract: The immune system is one of the most complex biological systems in the body. During infection, the immune system is under attack by a large number of viruses, bacteria, fungi and parasites. Immune response firstly involves, recognition of the pathogen or foreign object and secondly, a reaction to eliminate it. Aqueous extract of Antiaris africana is used to study their immune modulator activity. This plant has its various parts used in folk medicines. The mechanism of action has not been fully elucidated. Therefore, this research work studies the effect of aqueous extract of Antiaris Africana stem bark on phagocytic activities of neutrophil isolated from apparently healthy individual using a non-subjective commercial colourimetric assay kit obtained from Cell-Biolab Inc., USA. The purity and viability of isolated neutrophils were >90% and >95% respectively. The extract enhances neutrophil phagocytosis at 1.0, 5.0, 10.0, 15.0, 20.0 and 25 g/ml by 2.5%, 11.6%, 18.4%, 24.4%, 31.2% and 38.2% respectively, compared to the control (100%). Hence, it was observed that neutrophil phagocytosis increases with increased extract concentrations. It can be concluded from the study that enhancement of phagocytosis may be the possible mechanism of action of the plant as an immune modulator.


title: Application of high dimensional flow cytometry and unsupervised analysis to define the immune cell landscape of early childhood respiratory and blood compartments

abstract: The cellular landscape of the paediatric respiratory system remains largely uncharacterised and as a result, the mechanisms of highly prevalent childhood respiratory diseases remain poorly understood. A major limitation in defining mechanisms of disease has been the availability of tissue samples collected in early life, as well as technologies that permit deep immune analysis from limited sample volumes. In this work, we developed new experimental methods and applied unsupervised analytical tools to profile the local (bronchoalveolar lavage) and systemic (whole blood) immune response in childhood respiratory disease. We quantified and comprehensively phenotyped immune cell populations across blood and lung compartments in young children (under 6 years of age), showed that inflammatory cells in the BAL express higher levels of activation and migration markers relative to their systemic counterparts, and applied new analytical tools to reveal novel tissue-resident macrophage and infiltrating monocyte populations in the paediatric lung. To our knowledge, this is the first description of the use of these methods for paediatric respiratory samples. Combined with matched analysis of the systemic immune cell profile, the application of these pipelines will increase our understanding of childhood lung disease with potential to identify clinically relevant disease biomarkers.


title: Neural networks and extreme gradient boosting predict multiple thresholds and trajectories of microbial biodiversity responses due to browning

abstract: Ecological association studies often assume monotonicity such as between biodiversity and environmental properties although there is growing evidence that non-monotonic relations dominate in nature. Here we apply machine learning algorithms to reveal the non-monotonic association between microbial diversity and an anthropogenic induced large scale change, the browning of freshwaters, along a longitudinal gradient covering 70 boreal lakes in Scandinavia. Measures of bacterial richness and evenness (alpha diversity) showed non-monotonic trends in relation to environmental gradients, peaking at intermediate levels of browning. Depending on the statistical methods, variables indicative for browning could explain 5% of the variance in bacterial community composition (beta diversity) when applying standard methods assuming monotonic relations and up to 45 % with machine learning methods (i.e. extreme gradient boosting and feed-forward neural networks) taking non-monotonicity into account. This non-monotonicity observed at the community level was explained by the complex interchangeable nature of individual taxa responses as shown by a high degree of non-monotonic responses of individual bacterial sequence variants to browning. Furthermore, the non-monotonic models provide the position of thresholds and predict alternative bacterial diversity trajectories in boreal freshwater as a result of ongoing climate and land use changes, which in turn will affect entire ecosystem metabolism and likely greenhouse gas production.

category: microbiology


title: Post-transcriptional regulation of Leishmania fitness gain

abstract: The protozoan parasite Leishmania donovani causes fatal human visceral leishmaniasis in absence of treatment. Genome instability has been recognized as a driver in Leishmania fitness gain in response to environmental change or chemotherapy. How genome instability generates beneficial phenotypes despite potential deleterious gene dosage effects is unknown. Here we address this important open question applying experimental evolution and integrative systems approaches on parasites adapting to in vitro culture. Phenotypic analyses of parasites from early and late stages of culture adaptation revealed an important fitness tradeoff, with selection for accelerated growth in promastigote culture (fitness gain) impairing infectivity (fitness costs). Comparative genomics, transcriptomics and proteomics analyses revealed a complex regulatory network driving parasite fitness, with genome instability causing highly reproducible, gene dosage-dependent changes in protein abundance linked to post-transcriptional regulation. These in turn were associated with a gene dosage-independent reduction in abundance of flagellar transcripts and a coordinated increase in abundance of coding and non-coding RNAs implicated in ribosomal biogenesis and protein translation. We correlated differential expression of small nucleolar RNAs (snoRNAs) with changes in rRNA modification, providing first evidence that Leishmania fitness gain in culture may be controlled by post-transcriptional and epitranscriptomic regulation. Our findings propose a novel model for Leishmania fitness gain in culture, where differential regulation of mRNA stability and the generation of fitness-adapted ribosomes may potentially filter deleterious from beneficial gene dosage effects and provide proteomic robustness to genetically heterogenous, adapting parasite populations. This model challenges the current, genome-centric approach to Leishmania epidemiology and identifies the Leishmania transcriptome and non-coding small RNome as potential novel sources for the discovery of biomarkers that may be associated with parasite phenotypic adaptation in clinical settings.


title: Experimental evolution reveals post-transcriptional regulation as a novel driver of Leishmania fitness gain


title: Integrative genome-scale metabolic modeling reveals versatile metabolic strategies for methane utilization in Methylomicrobium album BG8

abstract: Methylomicrobium album BG8 is an aerobic methanotrophic bacterium that can mitigate environmental methane emission, and is a promising microbial cell factory for the conversion of methane to value-added chemicals. However, the lack of a genome-scale metabolic model (GEM) of M. album BG8 has hindered the development of systems biology and metabolic engineering of this methanotroph. To fill this gap, a high-quality GEM was constructed to facilitate a system-level understanding on the biochemistry of M. album BG8. Next, experimental time-series growth and exometabolomics data were integrated into the model to generate context-specific GEMs. Flux balance analysis (FBA) constrained with experimental data derived from varying levels of methane, oxygen, and biomass were used to model the metabolism of M. album BG8 and investigate the metabolic states that promote the production of biomass and the excretion of carbon dioxide, formate, and acetate. The experimental and modeling results indicated that the system-level metabolic functions of M. album BG8 require a ratio > 1:1 between the oxygen and methane specific uptake rates for optimal growth. Integrative modeling revealed that at a high ratio of oxygen-to-methane uptake flux, carbon dioxide and formate were the preferred excreted compounds; at lower ratios, however, acetate accounted for a larger fraction of the total excreted flux. The results of this study reveal a trade-off between biomass production and organic compound excretion and provide evidence that this trade-off is linked to the ratio between the oxygen and methane specific uptake rates.


title: SAF-A promotes origin licensing and replication fork progression to ensure robust DNA replication

abstract: The organisation of chromatin is closely intertwined with biological activities of chromosome domains, including transcription and DNA replication status. Scaffold attachment factor A (SAF-A), also known as Heteronuclear Ribonucleoprotein Protein U (HNRNPU), contributes to the formation of open chromatin structure. Here we demonstrate that SAF-A promotes the normal progression of DNA replication, and enables resumption of replication after inhibition. We report that cells depleted for SAF-A show reduced origin licensing in G1 phase, and consequently reduced origin activation frequency in S phase. Replication forks progress slowly in cells depleted for SAF-A, also contributing to reduced DNA synthesis rate. Single-cell replication timing analysis revealed that the boundaries between early- and late-replicating domains are blurred in cells depleted for SAF-A. Associated with these defects, SAF-A-depleted cells show elevated {gamma}H2A phosphorylation and tend to enter quiescence. Overall we find that SAF-A protein promotes robust DNA replication to ensure continuing cell proliferation.

category: cell biology


title: α1-COP delivers sphingolipid modifiers and controls plasmodesmal callose deposition in Arabidopsis

abstract:
Callose is a plant cell wall polymer in the form of {beta}-1,3-glucan, which regulates symplasmic channel size at plasmodesmata (PD). It plays a crucial role in a variety of processes in plants through the regulation of intercelluar symplasmic continuity. However, how to maintain callose homeostasis at PD in the molecular levels is poorly understood. To further elucidate the mechanism of PD callose homeostasis, we screened and identified an Arabidopsis mutant plant that exhibited excessive callose deposition at PD. Based on the Next-generation sequencing (NGS)-based mapping, other mutant allele analysis, and complementation assay, the mutated gene was shown to be 1-COP, which encodes a member of the COPI coatomer complex comprised of , {beta}, {beta}', {gamma}, {delta}, {varepsilon}, and {zeta} subunits. Since there is no report on the link between COPI and callose/PD, it was extremely curious to know the roles of 1-COP or COPI in PD regulation through callose deposition. Here, we report that loss-of-function of 1-COP directly elevates the callose accumulation at PD by affecting subcellular protein localization of callose degradation enzyme PdBG2. This process is linked to ERH1, an inositol phosphoryl ceramide synthase (IPCS), and glucosylceramide synthase (GCS) functions through physical interactions with the 1-COP protein. In addition, the loss-of-function of 1-COP also alters the subcellular localization of ERH1 and GCS proteins, results in a reduction of GlcCers and GlcHCers molecules, which are the key SL species for lipid raft formation. According to our findings, we propose that 1-COP protein, together with the SL modifiers controlling lipid raft compositions, regulates the function of GPI-anchored PD proteins and hence the callose turnover at PD and symplastic movement of biomolecules. Our findings provide the first key clue to link the COPI-mediated intracellular trafficking pathway to the callose-mediated intercellular signaling pathway through PD.

One-sentence summaryPlant-specific coatomer protein functions as a negative regulator of callose accumulation by regulating the translocation of sphingolipid enzymes.


title: A beta-glucosidase of an insect herbivore determines both toxicity and deterrence of a dandelion defense metabolite

abstract: Gut enzymes can metabolize plant defense metabolites and thereby affect the growth and fitness of insect herbivores. Whether these enzymes also influence herbivore behavior and feeding preference is largely unknown. We studied the metabolization of taraxinic acid {beta}-D-glucopyranosyl ester (TA-G), a sesquiterpene lactone of the common dandelion (Taraxacum officinale) that deters its major root herbivore, the common cockchafer larva (Melolontha melolontha). We demonstrate that TA-G is rapidly deglycosylated and conjugated to glutathione in the insect gut. A broad-spectrum M. melolontha {beta}-glucosidase, Mm_bGlc17, is sufficient and necessary for TA-G deglycosylation. Using plants and insect RNA interference, we show that Mm_bGlc17 reduces TA-G toxicity. Furthermore, Mm_bGlc17 is required for the preference of M. melolontha larvae for TA-G deficient plants. Thus, herbivore metabolism modulates both the toxicity and deterrence of a plant defense metabolite. Our work illustrates the multifacteted roles of insect digestive enzymes as mediators of plant-herbivore interactions.

category: ecology


title: Dependence of an aquatic insect population on contemporaneous primary production

abstract:
O_LICharacterizing the dynamics of energy flow through ecosystems requires quantifying the degree to which primary and secondary production are coupled. This coupling is expected to be tight in ecosystems with high internal production relative to external carbon and energy inputs.
C_LIO_LIWe experimentally quantified the dependence of aquatic insect emergence on fresh primary production, specifically for the midge population in Lake Myvatn, Iceland. Using field mesocosms, we manipulated algal primary production by reducing light availability via shading. We then used dissolved oxygen incubations to estimate fluxes of carbon through photosynthesis (i.e., gross primary production or "GPP") over the course of the experiment.
C_LIO_LIWe found that elevated GPP was associated with higher emergence rates of adults, as judged both by comparison of emergence across the experimental shading treatments and estimates of in situ GPP within the mesocosms. Furthermore, larger adults emerged earlier than smaller ones, suggesting that asymmetries in resource availability among individuals affected the timing of emergence. Nonetheless, midge emergence was substantial under light-limiting conditions, indicating that while midges benefit from primary production contemporaneous with larval development, they are also capable of completing their life cycles on carbon already existing in the organic matter pool.
C_LIO_LIOur results show that even in systems with limited allochthonous inputs, contemporaneous primary production may be not necessary for high secondary production and insect emergence. Instead, consumers can develop from consumption of biomass derived from past autochthonous primary production. This suggests that primary production and consumer dynamics can be partially decoupled in time in systems that depend on internal production.
C_LI


title: Functional diversity alters the effects of a pulse perturbation on the dynamics of tritrophic food webs

abstract: Biodiversity decline causes a loss of functional diversity, which threatens ecosystems through a dangerous feedback loop: this loss may hamper ecosystems ability to buffer environmental changes, leading to further biodiversity losses. In this context, the increasing frequency of climate and human-induced excessive loading of nutrients causes major problems in aquatic systems. Previous studies investigating how functional diversity influences the response of food webs to disturbances have mainly considered systems with at most two functionally diverse trophic levels. Here, we investigate the effects of a nutrient pulse on the resistance, resilience and elasticity of a tritrophic--and thus more realistic--plankton food web model depending on its functional diversity. We compare a non-adaptive food chain with no diversity to a highly diverse food web with three adaptive trophic levels. The species fitness differences are balanced through trade-offs between defense/growth rate for prey and selectivity/half-saturation constant for predators. We showed that the resistance, resilience and elasticity of tritrophic food webs decreased with larger perturbation sizes and depended on the state of the system when the perturbation occured. Importantly, we found that a more diverse food web was generally more resistant, resilient, and elastic. Particularly, functional diversity dampened the probability of a regime shift towards a non-desirable alternative state. In addition, despite the complex influence of the shape and type of the dynamical attractors, the basal-intermediate interaction determined the robustness against a nutrient pulse. This relationship was strongly influenced by the diversity present and the third trophic level. Overall, using a food web model of realistic complexity, this study confirms the destructive potential of the positive feedback loop between biodiversity loss and robustness, by uncovering mechanisms leading to a decrease in resistance, resilience and elasticity as functional diversity declines.


title: Mutations in a β-group of solute carrier gene are responsible for egg and eye coloration of the brown egg 4 (b-4) mutant in the silkworm, Bombyx mori

abstract:
The brown egg 4 (b-4) is a recessive mutant in the silkworm (Bombyx mori), whose egg and adult compound eyes exhibit a reddish-brown color instead of normal purple and black, respectively. By double digest restriction-site associated DNA sequencing (ddRAD-seq) analysis, we narrowed down a region linked to the b-4 phenotype to approximately 1.1 Mb that contains 69 predicted gene models. RNA-seq analysis in a b-4 strain indicated that one of the candidate genes had a different transcription start site, which generates a short open reading frame. We also found that exon skipping was induced in the same gene due to an insertion of a transposable element in other two b-4 mutant strains. This gene encoded a putative amino acid transporter that belongs to the {beta}-group of solute carrier (SLC) family and is orthologous to Drosophila eye color mutant gene, mahogany (mah). Accordingly, we named this gene Bmmah. We performed CRISPR/Cas9-mediated gene knockout targeting Bmmah. Several adult moths in generation 0 (G0) had totally or partially reddish-brown compound eyes. We also established three Bmmah knockout strains, all of which exhibit reddish-brown eggs and adult compound eyes. Furthermore, eggs from complementation crosses between the b-4 mutants and the Bmmah knockout mutants also exhibited reddish-brown color, which was similar to the b-4 mutant eggs, indicating that Bmmah is responsible for the b-4 phenotypes.

HighlightO_LIResponsible region for the brown egg 4 (b-4) mutation was narrowed down by double digest restriction-site associated DNA sequencing (ddRAD-seq).
C_LIO_LIThe gene structure was disrupted in one of the candidate genes, Bombyx mori mahogany (Bmmah), in the b-4 mutant strains.
C_LIO_LICRISPR/Cas9-mediated gene knockout and complementation test confirmed that the Bmmah is responsible for the b-4 phenotypes.
C_LIO_LIThe Bmmah encoded a putative amino acid transporter that belongs to the {beta}-group of solute carrier family.
C_LIO_LIThe Bmmah gene is essential for normal colorization of eggs, compound eyes, and ganglions.
C_LI

Graphical abstract

O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=76 SRC="FIGDIR/small/436376v1_ufig1.gif" ALT="Figure 1">
View larger version (36K):
org.highwire.dtl.DTLVardef@10d1d56org.highwire.dtl.DTLVardef@12df5org.highwire.dtl.DTLVardef@1703701org.highwire.dtl.DTLVardef@2b5bcf_HPS_FORMAT_FIGEXP  M_FIG C_FIG

category: genetics


title: Disease-specific eQTL screening reveals an anti-fibrotic effect of AGXT2 in nonalcoholic fatty liver disease

abstract:
Background & AimsNonalcoholic fatty liver disease (NAFLD) poses an impending clinical burden. Genome-wide association studies have revealed a limited contribution of genomic variants to the disease, requiring alternative but robust approaches to identify disease-associated variants and genes. We carried out a disease-specific expression quantitative trait loci (eQTL) screen to identify novel genetic factors that specifically act on NAFLD progression on the basis of genotype.

MethodsWe recruited 125 Korean biopsy-proven NAFLD patients and healthy individuals and performed eQTL analyses using 21,272 transcripts and 3,234,941 genotyped and imputed SNPs. We then selected eQTLs that were detected only in the NAFLD group, but not in the control group (i.e., NAFLD-eQTLs). An additional cohort of 162 Korean NAFLD individuals was used for replication. The function of the selected eQTL toward NAFLD development was validated using HepG2, primary hepatocytes and NAFLD mouse models.

ResultsThe NAFLD-specific eQTL screening yielded 242 loci. Among them, AGXT2, encoding alanine-glyoxylate aminotransferase 2, displayed decreased expression in NAFLD patients homozygous for the non-reference allele of rs2291702, compared to no-NAFLD subjects with the same genotype (P = 4.79 x 10-6). This change was replicated in an additional 162 individuals, yielding a combined P-value of 8.05 x 10-8 from a total of 245 NAFLD patients and 48 controls.

Knockdown of AGXT2 induced palmitate-overloaded hepatocyte death by increasing ER stress, and exacerbated NAFLD diet-induced liver fibrosis in mice. However, overexpression of AGXT2 reversely attenuated liver fibrosis and steatosis as well.

ConclusionsWe implicate a new molecular role of AGXT2 in NAFLD. Our overall approach will serve as an efficient tool for uncovering novel genetic factors that contribute to liver steatosis and fibrosis in patients with NAFLD.

Lay summaryElucidating causal genes for NAFLD has been challenging due to limited tissue availability and the polygenic nature of the disease. Using liver and blood samples from 125 biopsy-proven NAFLD and no-NAFLD Korean individuals and an additional 162 individuals for replication, we devised a new analytic method to identify causal genes. Among the candidates, we found that AGXT2-rs2291702 protects against liver fibrosis in a genotype-dependent manner with the potential for therapeutic interventions. Our approach enables the discovery of NAFLD causal genes that act on the basis of genotype.


title: Functional variants in hematopoietic transcription factor footprints and their roles in the risk of immune system diseases

abstract: Genome-wide association studies (GWAS) have been performed to identify thousands of variants in the human genome as disease risk markers, but functional variants that actually affect gene regulation and their genomic features remain largely unknown. Here we performed a comprehensive survey of functional variants in the regulatory elements of the human genome. We integrated hematopoietic transcription factor (TF) footprints datasets generated by ENCODE project with multiple quantitative trait locus (QTL) datasets (eQTL, caQTL, bQTL, and hQTL) and investigated the associations of functional variants and immune system disease risk. We identified candidate regulatory variants highly linked with GWAS lead variants and found that they were strongly enriched in active enhancers in hematopoietic cells, emphasizing the clinical relevance of enhancers in disease risk. Moreover, we found some strong relationships between traits and hematopoietic cell types or TFs. We highlighted some credible regulatory variants and found that a variant, rs2291668, which potentially functions in the molecular pathogenesis of multiple sclerosis, is located within a TF footprint present in a protein-coding exon of the TNFSF14 gene, indicating that protein-coding exons as well as noncoding regions can possess clinically relevant regulatory elements. Collectively, our results shed light on the molecular pathogenesis of immune system diseases. The methods described in this study can readily be applied to the study of the risk factors of other diseases.

category: genomics


title: From temporal network data to the dynamics of social relationships

abstract: Networks are well-established representations of social systems, and temporal networks are widely used to study their dynamics. Temporal network data often consist in a succession of static networks over consecutive time windows whose length, however, is arbitrary, not necessarily corresponding to any intrinsic timescale of the system. Moreover, the resulting view of social network evolution is unsatisfactory: short time windows contain little information, whereas aggregating over large time windows blurs the dynamics. Going from a temporal network to a meaningful evolving representation of a social network therefore remains a challenge. Here we introduce a framework to that purpose: transforming temporal network data into an evolving weighted network where the weights of the links between individuals are updated at every interaction. Most importantly, this transformation takes into account the interdependence of social relationships due to the finite attention capacities of individuals: each interaction between two individuals not only reinforces their mutual relationship but also weakens their relationships with others. We study a concrete example of such a transformation and apply it to several data sets of social interactions. Using temporal contact data collected in schools, we show how our framework highlights specificities in their structure and temporal organization. We then introduce a synthetic perturbation into a data set of interactions in a group of baboons to show that it is possible to detect a perturbation in a social group on a wide range of timescales and parameters. Our framework brings new perspectives to the analysis of temporal social networks.

category: animal behavior and cognition


title: A method for intuitively extracting macromolecular dynamics from structural disorder

abstract: Macromolecular dynamics manifest as disorder in structure determination, which is subsequently accounted for by displacement parameters (also called temperature factors, or B-factors) or alternate conformations. Though B-factors contain detailed information about structural dynamics, they are the total of multiple sources of disorder, making them difficult to interpret and thus little-used in structural analysis. We report here an approach for decomposing molecular disorder into a parsimonious hierarchical series of contributions, providing an intuitive basis for quantitative structural-dynamics analysis. We demonstrate the decomposition of disorder on example SARS-CoV-2 and STEAP4 structures, from both crystallographic and cryo-electron microscopy data, and reveal how understanding of the macromolecular disorder leads to deeper understanding of molecular motions and flexibility, and suggests hypotheses for molecular mechanisms.

category: biochemistry


title: Turning movements in real life capture subtle longitudinal and preataxic changes in cerebellar ataxia

abstract:
OBJECTIVESClinical and regulatory acceptance of upcoming molecular treatments in degenerative ataxias might greatly benefit from ecologically valid endpoints which capture change in ataxia severity in patients real life. This longitudinal study aimed to unravel quantitative motor biomarkers in degenerative ataxias in real life turning movements which are sensitive for changes both longitudinally and at the preataxic stage.

METHODSCombined cross-sectional (n=30) and longitudinal (n=14, 1-year interval) observational study in degenerative cerebellar disease (including 8 pre-ataxic mutation carriers) compared to 23 healthy controls. Turning movements were assessed by three body-worn inertial sensors in three conditions: (1) instructed laboratory assessment, (2) supervised free walking, and (3) unsupervised real-life movements.

RESULTSMeasures which quantified dynamic balance during turning - lateral velocity change (LVC) and outward acceleration -, but not general turning measures such as speed, allowed differentiating ataxic against healthy subjects in real life with high effect size ({delta}=0.68), with LVC also differentiating preataxic against healthy subjects ({delta}=0.53). LVC was highly correlated with clinical ataxia severity (SARA score, effect size {rho}=0.79) and subjective balance confidence (ABC score, {rho}=0.66). Moreover, LVC in real life - but not general turning measures, gait measures, or the SARA score - allowed detecting significant longitudinal change in one-year follow-up with high effect size (rprb=0.66).

CONCLUSIONSMeasures of turning allow to capture specific changes of dynamic balance in degenerative ataxia in real life, with high sensitivity to longitudinal differences in ataxia severity and to the preataxic stage. They thus present promising ecologically valid motor biomarkers for capturing change in real life, even in the highly treatment-relevant early stages of degenerative cerebellar disease.

category: bioengineering


title: A novel method for generating 3D constructs with branched vascular networks using multi-materials bioprinting and direct surgical anastomosis

abstract: Vessels pervade almost all body tissues, and significantly influence the pathophysiology of human body. Previous attempts to establish multi-scale vascular connection and function in 3D model tissues using bioprinting have had limited success due to the incoordination between cell-laden materials and stability of the perfusion channel. Here, we report a methodology to fabricate centimetre-scale vascularized soft tissue with high viability and accuracy using multi-materials bioprinting involving inks with low viscosity and a customized multistage-temperature-control printer. The tissue formed was perfused with branched vasculature with well-formed 3D capillary network and lumen, which would potentially supply the cellular components with sufficient nutrients in the matrix. Furthermore, the same methodology was applied for generating liver-like tissue with the objective to fabricate and mimic a mature and functional liver tissue, with increased functionality in terms of synthesis of liver specific proteins after in vitro perfusion and in vivo subperitoneal transplantation in mice. Moreover, to establish immediate blood perfusion, an elastic layer was printed wrapping sacrificial ink to support the direct surgical anastomosis of the carotid artery to the jugular vein. Our findings highlight the support extended by vasculature network in soft hydrogels which helps to sustain the thick and dense cellularization in engineered tissues.


title: A highly accurate model for screening prostate cancer using propensity index panel of ten genes

abstract:
Prostate-specific antigen (PSA) is a key biomarker, which is commonly used to screen patients of prostate cancer. There is a significant number of unnecessary biopsies that are performed every year, due to poor accuracy of PSA based biomarker. In this study, we identified alternate biomarkers based on gene expression that can be used to screen prostate cancer with high accuracy. All models were trained and test on gene expression profile of 500 prostate cancer and 51 normal samples. Numerous feature selection techniques have been used to identify potential biomarkers. These biomarkers have been used to develop various models using different machine learning techniques for predicting samples of prostate cancer. Our logistic regression-based model achieved highest AUROC 0.91 with accuracy 82.42% on validation dataset. We introduced a new approach called propensity index, where expression of gene is converted into propensity. Our propensitybased approach improved the performance of classification models significantly and achieved AUROC 0.99 with accuracy 96.36% on validation dataset. We also identified and ranked selected genes which can be used to discriminate prostate cancer patients from health individuals with high accuracy. It was observed that single gene-based biomarkers can only achieve accuracy around 90%. In this study, we got best performance using a panel of 10 genes; random forest model using propensity index.

HighlightsO_LIApplication of Machine learning techniques to identify Biomarkers for PRAD cancer.
C_LIO_LIHighly accurate models developed for classifying prostate cancer vs. normal sample.
C_LIO_LIIntroducing Propensity index concept for enhancing model performance.
C_LIO_LITop 10 genes identified using feature selection techniques.
C_LI

category: bioinformatics


title: The Central Importance of Hub Proteins in a Disease-Gene Network Model: A New Paradigm of Chronic Myeloid Leukemia Disease Study

abstract:
BackgroundThe network biology of disease-gene association provides a holistic framework to decipher the intrinsic complexity of disease signaling pathways into cellular communication level. Different types of studies including large-scale genome-wide association, multifactor dimensional reduction analysis, whole genome, or exome-based sequencing strategies of diseases are striving to connect genes to diseases. Indeed, these approaches have had some accomplishments, but the cellular communication level needs a more streamlining outcome to understand the mechanistic impact of context. The higher-order combination of disease-gene interaction has a great potential to decipher the intricateness of diseases. The molecular interaction pattern of diseases at the genomic and proteomic level offers a revolutionized platform not only to understand the complexity of particular disease modules and pathways but also leading towards design novel therapeutics.

ResultsThe enrichment and topology analysis was performed by JEPETTO a plugin of Cytoscape software. We identified the chronic myeloid leukemia (CML) disease signaling pathways that appeared first in the ranking order based on XD-score among the bone, breast, and colon genes set and second at kidney and liver. This result validates the highest proximity between CML and five cancerous tissue gene set clusters. The topology analysis also supports the results while (p<0.0001) is considered to be extremely significant between CML and fives cancerous tissues genes set. Enrichment analysis identified that abl-gene acts as an overlapping node which is the major gene for inducing various mutations in CML. Amazingly, we identified 56 common path expansion/added genes among these five cancerous tissues which can be considered the direct cofactors of CML disease. By relative node degree, resolution, possible ligand, stoichiometry, Q-mean, and Z-score analysis we found 11 hubs proteins like SMAD3, GRB2, TP53, SMAD4, RB1, HDAC1, RAF1, ABL1, SHC1, TGFBR1, RELA which can be regarded for further drug target identification.

ConclusionsOur proposed network analysis reflects on the gene set interaction pattern of disease signaling pathways of humans. The integrated multidrug computational and experimental approaches boost up to improve the novel drug target approach. Besides, such a trove can yield unprecedented insights to lead to an enhanced understanding of potential application both in drug target optimization and for drug dislodging.


title: Molecular insights into the μ-opioid receptorselective signaling

abstract: GPCR functional selectivity has opened new opportunities for the design of safer drugs. Ligands orchestrate GPCR signaling cascades by modulating the receptor conformational landscape. Our study provides insights into the dynamic mechanism enabling opioid ligands to preferentially activate the G protein over the {beta}-arrestin pathways through the -opioid receptor (OR). We combined functional assays in living cells, solution NMR spectroscopy and enhanced-sampling molecular dynamic simulations to identify the specific OR conformations induced by G protein-biased agonists. In particular, we describe the dynamic and allosteric communications between the ligand-binding pocket and the receptor intracellular domains, through conserved motifs in class A GPCRs. Most strikingly, the biased agonists triggered OR conformational changes in the intracellular loop 1 and helix 8 domains, which may impair {beta}-arrestin binding or signaling. The findings may apply to other GPCR families and provide key molecular information that could facilitate the design of biased ligands.


title: Identifying Differential Methylation in Cancer Epigenetics via a Bayesian Functional Regression Model

abstract: DNA methylation plays an essential role in regulating gene activity, modulating disease risk, and determining treatment response. Researchers can obtain insight into methylation patterns at a single nucleotide level utilizing next-generation sequencing technologies. However, complex features inherent in the data obtained via these technologies pose challenges beyond the typical big data problems. Identifying differentially methylated cytosines (dmc) or regions is one of such challenges. Current methodologies for identifying dmcs fall short in handling low read-depth data and missing values, capturing functional data patterns, granting multiple covariates (categorical, continuous, or combination), and multiple group comparisons. We have developed an efficient method to identify dmcs based on a Bayesian functional regression approach, termed DMCFB, that tackles these shortcomings. Through simulation studies, we establish that DMCFB outperforms current methods and results in better smoothing, and efficient imputation. We apply the proposed method to analyze a dataset containing patients with acute promyelocytic leukemia and control samples. With DMCFB, we discovered many new dmcs, and more importantly, exhibited enhanced consistency of differential methylation within islands and at their adjacent shores. Furthermore, we detected differential methylation at more of the binding sites of the fused gene involved in this cancer.


title: A synthetic tubular molecular transport system

abstract: We report the bottom-up construction of a macromolecular transport system in which molecular pistons diffusively move through micrometer-long, hollow filaments. The pistons can cover micrometer distances in fractions of seconds. We built the system using multi-layer DNA origami and analyzed the structures of the components using transmission electron microscopy. We studied the motion of the pistons along the tubes using single-molecule fluorescence microscopy and performed Langevin simulations to reveal details of the free energy surface that directs the motions of the pistons. The tubular transport system achieves diffusivities and displacement ranges known so far only from natural molecular motors and realizes mobility improvements over five orders of magnitude compared to previous artificial random walker designs. Electric fields can also be employed to actively pull the pistons along the filaments, thereby realizing a nanoscale electric rail system. Our system presents a platform for artificial motors that move autonomously driven by chemical fuels and for performing nanotribology studies, and it could form a basis for future molecular transportation networks.

category: biophysics


title: Cold Adaptation Leads To Repolarization Gradients Development In The Rainbow Trout Heart

abstract:
IntroductionThermal adaptation in fish is accompanied by morphological and electrophysiological changes in the myocardium. Little is known regarding changes of spatiotemporal organization of ventricular excitation and repolarization processes with acclimatization. We aimed to evaluate transmural and apicobasal heterogeneity of depolarization and repolarization characteristics in the in-situ heart of rainbow trout in seasonal acclimatization.

MethodsThe experiments were done in the summer-acclimatized (SA, 18{degrees}C, n=8) and winter-acclimatized (WA, 3{degrees}C, n=8) rainbow trout. 24 unipolar electrograms were recorded with plunge needle electrodes (eight lead terminals each) impaled into the ventricular wall. Activation time (AT), end of repolarization time (RT), and activation-repolarization interval (ARI, a surrogate for action potential duration) were determined as dV/dt min during QRS-complex, dV/dt max during T-wave, and RT-AT difference, respectively.

ResultsThe SA fish demonstrated relatively flat apicobasal and transmural AT and especially ARI profiles. In the WA animals, ATs and ARIs were longer as compared to SA animals (p[≤]0.001), ARIs were shorter in the compact layer than in the spongy layer (p[≤]0.050), and within the compact layer, the apical region had shorter ATs and longer ARIs as compared to the basal region (p[≤]0.050). In multiple linear regression analysis, ARI duration was associated with cardiac cycle duration and AT in SA and WA animals. The WA animals demonstrated additionally an independent association of ARIs with spatial localization across the ventricle.

ConclusionAdaptation to cold conditions in rainbow trout was associated with a spatial ventricular remodeling leading to the development of repolarization gradients typically observed in mammalian myocardium.

SUMMARY STATEMENTThe study gives an example of thermal adaptation in fish realized at the level of spatiotemporal organization of myocardial depolarization and repolarization.

category: physiology


title: Accurate and efficient time-domain classification with adaptive spiking recurrent neural networks

abstract: Inspired by more detailed modeling of biological neurons, Spiking neural networks (SNNs) have been investigated both as more biologically plausible and potentially more powerful models of neural computation, and also with the aim of extracting biological neurons energy efficiency; the performance of such networks however has remained lacking compared to classical artificial neural networks (ANNs). Here, we demonstrate how a novel surrogate gradient combined with recurrent networks of tunable and adaptive spiking neurons yields state-of-the-art for SNNs on challenging benchmarks in the time-domain, like speech and gesture recognition. This also exceeds the performance of standard classical recurrent neural networks (RNNs) and approaches that of the best modern ANNs. As these SNNs exhibit sparse spiking, we show that they theoretically are one to three orders of magnitude more computationally efficient compared to RNNs with comparable performance. Together, this positions SNNs as an attractive solution for AI hardware implementations.


title: Microglial refinement of spinal cord sensory circuitry regulates normal maturation of dynamic touch.

abstract:
Sensory systems are shaped in postnatal life by the refinement of synaptic connections. In the dorsal horn of the spinal cord, sensory circuits undergo postnatal activity dependent reorganisation, including the retraction of primary afferent A-fibres from superficial to deeper laminae which is accompanied by decreases in cutaneous sensitivity. Here we show that microglia, the resident immune cells in the CNS, phagocytose A-fibre terminals in superficial laminae in the first weeks of life. Genetic perturbation of microglial engulfment at that time prevents the normal process of A-fibre retraction, resulting in increased sensitivity of dorsal horn cells to dynamic tactile cutaneous stimulation, and behavioural hypersensitivity to dynamic touch. Thus, functional microglia are necessary for normal postnatal development of dorsal horn sensory circuits. In the absence of microglial engulfment, superfluous A-fibre projections remain in the dorsal horn and the balance of sensory connectivity is disrupted, leading to lifelong hypersensitivity to dynamic touch.

Impact statementMicroglia phagocytose superfluous A-fibres in the superficial spinal dorsal horn during normal development, the disruption of which leads to long term aberrant dynamic touch processing and behaviour.


title: Microglial refinement of A-fibre projections in the postnatal spinal cord dorsal horn is required for normal maturation of dynamic touch.


title: Single cell chromatin accessibility reveals regulatory elements and developmental trajectories in the embryonic forebrain

abstract: A comprehensive characterization of epigemonic organization in the embryonic mouse forebrain will enhance our understanding of neurodevelopment and provide insight into mechanisms of neurological disease. We collected single-cell chromatin accessibility profiles from four distinct neurogenic regions of the embryonic mouse forebrain using single nuclei ATAC-Seq (snATAC-Seq). We identified thousands of differentially accessible peaks, many restricted to distinct progenitor cell types or brain regions. We integrated snATAC-Seq and single cell transcriptome data to characterize changes of chromatin accessibility at enhancers and promoters with associated transcript abundance. Multi-modal integration of histone modifications (CUT&Tag and CUT&RUN), promoter-enhancer interactions (Capture-C) and high-order chromatin structure (Hi-C) extended these initial observations. This dataset reveals a diverse chromatin landscape with region-specific regulatory mechanisms and genomic interactions in distinct neurogenic regions of the embryonic mouse brain and represents an extensive public resource of a  ground truth epigenomic landscape at this critical stage of neurogenesis.


title: An epigenome atlas of neural progenitors within the embryonic mouse forebrain


title: Genome-wide screen identifies curli amyloid fibril as a bacterial component promoting host neurodegeneration

abstract: Growing evidence indicate that gut microbiota play a critical role in regulating the progression of neurodegenerative diseases, such as Parkinsons disease (PD). The molecular mechanism underlying such microbe-host interaction is unclear. In this study, by feeding C. elegans expressing human -syn with E. coli knockout mutants, we conducted a genome-wide screen to identify bacterial genes that promote host neurodegeneration. The screen yielded 38 genes that fall into several genetic pathways, including curli formation, lipopolysaccharide assembly, adenosylcobalamin biosynthesis among others. We then focused on the curli amyloid fibril and found that genetically deleting or pharmacologically inhibiting the curli major subunit CsgA in E. coli reduced -syn-induced neuronal death, restored mitochondrial health, and improved neuronal functions. CsgA secreted by the bacteria colocalized with -syn inside neurons and promoted -syn aggregation through cross-seeding. Similarly, curli also promoted neurodegeneration in C. elegans models of AD, ALS, and HD and in human neuroblastoma cells.


title: Polycomb repressive complex 2 coordinates with Sin3 histone deacetylase complex to epigenetically reprogram genome-wide expression of effectors and regulate pathogenicity in Magnaporthe oryzae

abstract: The strict suppression and reprogramming of gene expression are necessary at different development stages and/or in response to environment stimuli in eukaryotes. In Rice Magnaporthe oryzae pathosystem, effectors from pathogen are kept transcriptionally silenced in the vegetative growth stage and are highly expressed during invasive growth stage to adapt to the host environment. However, the mechanism of how such effectors are stably repressed in the vegetative stage and its roles during rice blast infection remain unclear so far. Here, we showed that all subunits of Polycomb Repressive Complex 2 are required for such repression by direct H3K27me3 occupancy and pathogenic process in M. oryzae. Suppression of polycomb-mediated H3K27me3 causes an improper induction of effectors during vegetative growth thus simulating a host environment. Notably, the addition subunit P55 not only acts as the bridge to connect with core subunits to form a complex in M. oryzae, but also recruits Sin3 histone deacetylase complex to prompt H3K27me3 occupancy for stable maintenance of transcriptional silencing of the target genes in the absence of PRC1. In contrast, during invasive growth stage, the repressed state of effectors chromatin can be partially erased during pathogenic development resulting in transcriptional activation of effectors therein. Overall, Polycomb repressive complex 2 coordinates with Sin3 histone deacetylase complex to epigenetically reprogram genome-wide expression of effectors, which act as molecular switch to memorize the host environment from vegetative to invasive growth, thus contributing to the infection of rice blast.


title: Slippery when wet: cross-species transmission of divergent coronaviruses in bony and jawless fish and the evolutionary history of the Coronaviridae

abstract: The Nidovirales comprise a genetically diverse group of positive-sense single-stranded RNA virus families that infect a range of invertebrate and vertebrate hosts. Recent metagenomic studies have identified nido-like virus sequences, particularly those related to the Coronaviridae, in a range of aquatic hosts including fish, amphibians and reptiles. We sought to identify additional members of the Coronaviridae in both bony and jawless fish through a combination of total RNA sequencing (meta-transcriptomics) and data mining of published RNA sequencing data, and from this reveal more of the long-term patterns and processes of coronavirus evolution. Accordingly, we identified a number of divergent viruses that fell within the Letovirinae subfamily of the Coronaviridae, including those in a jawless fish - the pouched lamprey. By mining fish transcriptome data we identified additional virus transcripts matching these viruses in bony fish from both marine and freshwater environments. These new viruses retained sequence conservation in the RNA-dependant RNA polymerase across the Coronaviridae, but formed a distinct and diverse phylogenetic group. Although there are broad-scale topological similarities between the phylogenies of the major groups of coronaviruses and their vertebrate hosts, the evolutionary relationships of viruses within the Letovirinae does not mirror that of their hosts. For example, the coronavirus found in the pouched lamprey fell within the phylogenetic diversity of bony fish letoviruses, indicative of past host switching events. Hence, despite possessing a phylogenetic history that likely spans the entire history of the vertebrates, coronavirus evolution has been characterised by relatively frequent cross-species transmission, particularly in hosts that reside in aquatic habitats.


title: Introduction bias: Imbalance in species introductions may obscure the identification of traits associated with invasiveness

abstract:
1The introduction stage is usually overlooked in trait-based studies of invasiveness, implicitly assuming that species introductions are random. However, human activities promote the movement of specific types of species. Thus, species deliberately introduced for distinct purposes (e.g. gardening, forestry) or as contaminants of human commodities (e.g. stowaway) will likely show particular traits. If species with certain traits have been preferentially introduced (i.e. introduction bias), some traits may have been mistakenly linked to species invasion abilities due to their influence on introduction probability.

In this work, we propose a theoretical framework with different scenarios of introduction bias. The introduction scenarios are: (1) Random introduction, independent from traits; (2) Biologically biased introduction, following the worldwide distribution of the trait; and (3) Human biased introduction, following a theoretical introduction pathway that favours the introduction of species with high values of the trait. We evaluate how the introduced trait distributions in these scenarios may affect trait distributions in naturalized and invasive species pools under different hypothesized associations between traits and the probabilities of naturalization and invasion. The aim of this work is to identify situations where ignoring introduction bias may lead to spurious correlations being found between species traits and species ability to become naturalized or invasive.

Our framework strongly points to the need to evaluate the traits of species that have become naturalized or invasive along with the traits of species that have failed to do so in order to unravel any existing introduction bias that may confound the correlation between species traits and invasion success. Overlooking a possible introduction bias may lead to the overestimation of the correlation between the trait and the species invasion ability, especially in cases when the pool of introduced species shows extreme values of the trait distribution (as compared to a random introduction). Trait-based studies that deserve special attention to avoid undesired effects of introduction bias on their findings are: those that investigate naturalization using only the pool of naturalized species, and those studies that examine invasiveness by comparing invasive species with native species.


title: The role of DDK and Treslin-MTBP in coordinating replication licensing and pre-Initiation Complex formation

abstract: Treslin/Ticrr is required for the initiation of DNA replication and binds to MTBP (Mdm2 Binding Protein). Here we show that in Xenopus egg extract, MTBP forms an elongated tetramer with Treslin containing two molecules of each protein. Immunodepletion and add-back experiments show that Treslin-MTBP is rate-limiting for replication initiation. It is recruited onto chromatin before S phase starts and recruitment continues during S phase. We show that DDK activity both increases and strengthens the interaction of Treslin-MTBP with licensed chromatin. We also show that DDK activity cooperates with CDK activity to drive the interaction of Treslin-MTBP with TopBP1 which is a regulated crucial step in pre-Initiation Complex formation. These results suggest how DDK works together with CDKs to regulate Treslin-MTBP and plays a crucial in selecting which origins will undergo initiation.


title: Population diversity of cassava mosaic begomoviruses increases over the course of serial vegetative propagation

abstract: Cassava mosaic disease (CMD) represents a serious threat to cassava, a major root crop for more than 300 million Africans. CMD is caused by single-stranded DNA begomoviruses that evolve rapidly, making it challenging to develop durable disease resistance. In addition to the evolutionary forces of mutation, recombination, and reassortment, factors such as climate, agriculture practices, and the presence of DNA satellites may impact viral diversity. To gain insight into the factors that alter and shape viral diversity in planta, we used high-throughput sequencing to characterize the accumulation of nucleotide diversity after inoculation of infectious clones corresponding to African cassava mosaic virus (ACMV) and East African cassava mosaic Cameroon virus (EACMCV) in the susceptible cassava landrace Kibandameno. We found that vegetative propagation had a significant effect on viral nucleotide diversity, while temperature and a satellite DNA did not have measurable impacts in our study. EACMCV diversity increased linearly with the number of vegetative propagation passages, while ACMV diversity increased for a time and then decreased in later passages. We observed a substitution bias toward C[->]T and G[->]A for mutations in the viral genomes consistent with field isolates. Non-coding regions excluding the promoter regions of genes showed the highest levels of nucleotide diversity for each genome component. Changes in the 5 intergenic region of DNA-A resembled the sequence of the cognate DNA-B sequence. The majority of nucleotide changes in coding regions were non-synonymous, most with predicted deleterious effects on protein structure, indicative of relaxed selection pressure over 6 vegetative passages. Overall, these results underscore the importance of knowing how cropping practices affect viral evolution and disease progression.

category: plant biology


title: Comparative performance analysis of mulberry silkworm (Bombyx mori L.) races for integration of superior yield and maximize profit in West Bengal

abstract:
India has a prosperous and glorious history in silk production and its silk trade dates back to 15th century. Sericulture is practiced in many regions of India, where West Bengal ranks third in mulberry silk production. About 2000 villages are engaged in mulberry cultivation with plantation area of 37,883 acres. But nowadays, farmers have lack their interest in this sector due to low cost benefit ratio, high investment cost in terms of silk worm rearing, land uses and lack of proper knowledge on different races of Bombyx mori. Therefore, the present study has been aiming to find out the comparative performance of bivoltine, multivoltine, and F1 variety of B. mori by analysed the cocoon, post-cocoon characters, and silk related traits for identifying the best superior races of B. mori. The results showed that feeding habits of silkworm larvae of three races had significant effect on cocoon parameters. The average weight of ten 5th instar larvae of bivoltine was higher in comparison with multivoltine and F1 variety. Similar trends were obtained in the average length of silk thread from a single cocoon in bivoltine races, higher by 30% and 77.14% from F1 and multivoltine, respectively (P<0.05). We also inquired about capital investment and profit-making of three varieties. Net profit for bivoltine was significantly increased by 15.65% and 10.21% than multivoltine and F1 varieties, respectively.The heatmap analysis revealed that the bivoltine races of B. mori were separately clustered based on the positive correlation of measured variables mostly length of silk thread, renditta, dry cocoon weight, the average weight of larvae, present market price, leaves for rearing, net profit and selling price of cocoon per acre farmland; whereas, the multivoltine and F1 variety clustered in a separate group. From our findings, it is clear that the culture of bivoltine is preferable for the farmers who dont have enough landed property and also profitable in terms of cocoon, post cocoon and silk traits. Therefore, it is recommended that the farming of bivoltine silkworm is more gainfulcompared to F1 and multivoltine variety, and capable of more income generation than other traditional agricultural crops.

O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=191 SRC="FIGDIR/small/436391v1_ufig1.gif" ALT="Figure 1">
View larger version (53K):
org.highwire.dtl.DTLVardef@1bb1e89org.highwire.dtl.DTLVardef@1d1bb69org.highwire.dtl.DTLVardef@6727f3org.highwire.dtl.DTLVardef@6ff918_HPS_FORMAT_FIGEXP  M_FIG O_FLOATNOFig.C_FLOATNO Graphical abstract represents the comparative performance of bivoltine, multivoltine and F1 races of B. mori on the aspect of biological and economic traits in tropical climate condition.

C_FIG

category: zoology


title: Refinement of corticospinal neuron activity during skilled motor learning

abstract: The learning of motor skills relies on plasticity of the primary motor cortex as task acquisition drives the remodeling of cortical motor networks1,2. Large scale cortical remodeling of evoked motor outputs occurs in response to the learning of skilled, corticospinal-dependent behavior, but not simple, unskilled tasks1. Here we determine the response of corticospinal neurons to both skilled and unskilled motor training and assess the role of corticospinal neuron activity in the execution of the trained behaviors. Using in vivo calcium imaging, we found that refinement of corticospinal activity correlated with the development of skilled, but not unskilled, motor expertise. Animals that failed to learn our skilled task exhibited a limited repertoire of dynamic movements and a corresponding absence of network modulation. Transection of the corticospinal tract and aberrant activation of corticospinal neurons show the necessity for corticospinal network activity patterns in the execution of skilled, but not unskilled, movement. We reveal a critical role for corticospinal network modulation in the learning and execution of skilled motor movements. The integrity of the corticospinal tract is essential to the recovery of voluntary movement after central nervous system injuries and these findings should help to shape translational approaches to motor recovery.


title: New Records of California Serogroup Virus in Aedes Mosquitoes and First Detection in Simulioidae Flies from Northern Canada and Alaska

abstract: An expected consequence of climate warming is an expansion of the geographic distribution of biting insects and associated arthropod-borne diseases (arboviruses). Emerging and reemerging arboviruses that can affect human health are likely to pose significant consequences for Northern communities where access to health resources is limited. In the North American Arctic, little is known about arboviruses. Thus, in 2019, we sampled biting insects in Nunavik (Kuujjuaq), Nunavut (Igloolik, Karrak Lake and Cambridge Bay), Northwest Territories (Igloolik and Yellowknife) and Alaska (Fairbanks). The main objective was to detect the presence of California serogroup viruses (CSGv) - a widespread group of arboviruses across North America and that is known to cause a wide range of symptoms, ranging from mild febrile illness to fatal encephalitis. Biting insects were captured twice daily for a 7-day period in mid-summer, using a standardized protocol consisting of 100 figure-eight movements of a sweep net. Captured specimens were separated by genus (mosquitoes) or by superfamily (other insects), and then grouped into pools of 75 by geographical locations. In total, 5079 Aedes mosquitoes and 1014 Simulioidae flies were caught. We report the detection of CSGv RNA in mosquitoes captured in Nunavut (Karrak Lake) and Nunavik (Kuujjuaq). We also report, for the first time in North America, the presence of CSGv RNA in Simulioidae flies. These results highlight the potential of biting insects for tracking any future emergence of arboviruses in the North, thereby providing key information for public health in Northern communities.


title: LPS core type diversity in the Escherichia coli species and associations with phylogeny and virulence gene repertoire.

abstract:
Escherichia coli is a very versatile species for which diversity has been explored from various perspectives highlighting, for example, phylogenetic groupings, pathovars as well as a wide range of O serotypes. The highly variable O-antigen, the most external part of the lipopolysaccharide component of the outer membrane of E. coli, is linked to the innermost lipid A through the core region of LPS of which 5 different structures, denominated K-12, R1, R2, R3 and R4, have been characterized so far. The aim of the present study was to analyze the prevalence of these LPS core types in the E. coli species and explore their distribution in the different E. coli phylogenetic groups and in relationship with the virulence gene repertoire. Results indicated an uneven distribution of core types between the different phylogroups, with phylogroup A strains being the most diverse in terms of LPS core types while phylogroups B1, D and E strains were dominated by the R3 type and phylogroups B2 and C strains being dominated by the R1 type. Strains carrying the LEE virulence operon were mostly of the R3 type whatever the phylogroup while, within phylogroup B2, strains carrying a K-12 core all belonged to the complex STc131, one of the major clone of extra-intestinal pathogenic E. coli (ExPEC) strains. The origin of this uneven distribution is discussed but remains to be explained, as well as the consequences of carrying a specific core type on the physiology of the bacteria.

IMPACT STATEMENTThe diversity of the E. coli species in terms of type of infections is well known, and its surface O-antigen which shows some correspondence to pathogenicity. This study is the first one to report in detail the diversity and distribution of the LPS core types in the E. coli species using whole genome sequences. This distribution of the 5 know core types is analyzed in the different phylogroups along with their association with specific virulence gene repertoire. Results indicate a non-random distribution of LPS core types in the E. coli species and, most interestingly, preferential association of certain core types with either some phylogenetic clades or with particular virulence gene repertoires. This work is a first step towards the identification of the origin of this diversity as well as towards the exploration of the physiological properties associated with specific core types.

DATA SUMMARYComplete list of strains with associated data is available in supplementary table S1.


title: An autoregulation loop in fust-1 for circular RNA regulation in Caenorhabditis elegans

abstract: Circular RNAs (circRNAs) are always expressed tissue-specifically, suggestive of specific factors that regulate their biogenesis. Here, taking advantage of available mutation strains of RNA binding proteins (RBPs) in Caenorhabditis elegans, I performed a screening of circRNA regulation in thirteen conserved RBPs. Among them, loss of FUST-1, the homolog of FUS (Fused in Sarcoma), caused downregulation of multiple circRNAs. By rescue experiments, I confirmed FUST-1 as a circRNA regulator. Further, I showed that FUST-1 regulates circRNA formation without affecting the levels of the cognate linear mRNAs. When recognizing circRNA pre-mRNAs, FUST-1 can affect both exon-skipping and circRNA in the same genes. Moreover, I identified an autoregulation loop in fust-1, where FUST-1, isoform a promotes the skipping of exon 5 of its own pre-mRNA, which produces FUST-1, isoform b with different N-terminal sequences. FUST-1, isoform a is the functional isoform in circRNA regulation. Although FUST-1, isoform b has the same functional domains as isoform a, it cannot regulate either exon-skipping or circRNA formation.


title: Network medicine links SARS-CoV-2/COVID-19 infection to brain microvascular injury and neuroinflammation in dementia-like cognitive impairment

abstract:
BackgroundDementia-like cognitive impairment is an increasingly reported complication of SARS-CoV-2 infection. However, the underlying mechanisms responsible for this complication remain unclear. A better understanding of causative processes by which COVID-19 may lead to cognitive impairment is essential for developing preventive interventions.

MethodsIn this study, we conducted a network-based, multimodal genomics comparison of COVID-19 and neurologic complications. We constructed the SARS-CoV-2 virus-host interactome from protein-protein interaction assay and CRISPR-Cas9 based genetic assay results, and compared network-based relationships therein with those of known neurological manifestations using network proximity measures. We also investigated the transcriptomic profiles (including single-cell/nuclei RNA-sequencing) of Alzheimers disease (AD) marker genes from patients infected with COVID-19, as well as the prevalence of SARS-CoV-2 entry factors in the brains of AD patients not infected with SARS-CoV-2.

ResultsWe found significant network-based relationships between COVID-19 and neuroinflammation and brain microvascular injury pathways and processes which are implicated in AD. We also detected aberrant expression of AD biomarkers in the cerebrospinal fluid and blood of patients with COVID-19. While transcriptomic analyses showed relatively low expression of SARS-CoV-2 entry factors in human brain, neuroinflammatory changes were pronounced. In addition, single-nucleus transcriptomic analyses showed that expression of SARS-CoV-2 host factors (BSG and FURIN) and antiviral defense genes (LY6E, IFITM2, IFITM3, and IFNAR1) was significantly elevated in brain endothelial cells of AD patients and healthy controls relative to neurons and other cell types, suggesting a possible role for brain microvascular injury in COVID-19-mediated cognitive impairment. Notably, individuals with the AD risk allele APOE E4/E4 displayed reduced levels of antiviral defense genes compared to APOE E3/E3 individuals.

ConclusionOur results suggest significant mechanistic overlap between AD and COVID-19, strongly centered on neuroinflammation and microvascular injury. These results help improve our understanding of COVID-19-associated neurological manifestations and provide guidance for future development of preventive or treatment interventions.

category: systems biology


title: Revealing Notch-dependencies in synaptic targets associated with Alzheimer's disease

abstract:
Alzheimers disease (AD) is a progressive neurodegenerative disorder and the major cause of dementia. There is evidence that synaptic dysfunction and perturbation of Excitatory/Inhibitory (E/I) balance arise at the early stages of AD, altering the normal neural network activity, and leading to cognitive decline. Recent studies have identified Notch signaling as a contributor of neurodegenerative advancement including AD pathophysiology. As part of the efforts to understand molecular mechanisms and players involved in cognitive decline, we employed transgenic mouse models with Notch1 and RBPJK loss of function (LOF) in pyramidal neurons of the CA fields. Using bulk RNAseq. We have investigated the differential expression of Notch-dependent genes either upon environmental enrichment (EE) or upon Kainate injury (KA). We found a substantial genetic diversity in absence of both Notch1 receptor or Rbpjk transcriptional activator. Among differentially expressed genes, we observed a significant upregulation of Gabra2a in both knockout models, suggesting a role for Notch signaling in the modulation of E/I balance. Upon neuroexcitotoxic stimulation, loss of Rbpjk results in decreased expression of synaptic proteins with neuroprotective effects. We confirmed Nptx2, Npy, Pdch8, TncC as direct Notch1/Rbpjk targets and Bdnf and Scg2 as indirect targets. Finally, we translate these findings into human entorhinal cortex containing the hippocampal region from Alzheimers Disease patients performing targeted transcripts analysis. We observe an increased trend for Rbpjk and the ligand DNER but not Notch1 expression. On the other hand, neuron-specific targets, Nptx2, Npy, BDNF and Gabra2a are upregulated during the mild-moderate stage, and decline in the severe phase of the disease. These findings identify Notch as a promising signaling cascade to fine-tune in order to ameliorate synaptic transmission and memory deficits that occur during early phase of the Alzheimers Disease.

HighlightsO_LILoss of canonical and/or non-canonical Notch1 signaling in pyramidal neurons of the hippocampal CA field mainly affects the post-synaptic compartment.
C_LIO_LIIn both RBPJKcKO and Notch1cKO mouse models there is upregulation of GABAergic receptor subunit alpha2 (Gabra2a).
C_LIO_LIThe plasticity genes: Npy, Nptx2,Pcdh8 and TncC with neuroprotective functions and known association with Alzheimers Disease are direct Notch/Rbpjk targets.
C_LIO_LIDuring the mild-moderate stage of AD dementia, Notch canonical signaling promotes the expression of neuroprotective proteins, in the attempt of mitigating the effect of the excitatory-inhibitory imbalance. This activity is not observed during severe stages of the disease.
C_LI


title: Protease-activatable biosensors of SARS-CoV-2 infection for cell-based drug, neutralisation and virological assays

abstract:
Efforts to define serological correlates of protection against COVID-19 have been hampered by the lack of a simple, scalable, standardised assay for SARS-CoV-2 infection and antibody neutralisation. Plaque assays remain the gold standard, but are impractical for high-throughput screening. In this study, we show that expression of viral proteases may be used to quantitate infected cells. Our assays exploit the cleavage of specific oligopeptide linkers, leading to the activation of cell-based optical biosensors. First, we characterise these biosensors using recombinant SARS-CoV-2 proteases. Next, we confirm their ability to detect viral protease expression during replication of authentic virus. Finally, we generate reporter cells stably expressing an optimised luciferase-based biosensor, enabling viral infection to be measured within 24 h in a 96- or 384-well plate format, including variants of concern. We have therefore developed a luminescent SARS-CoV-2 reporter cell line, and demonstrated its utility for the relative quantitation of infectious virus and titration of neutralising antibodies.

Author summaryTechniques for measuring infection with SARS-CoV-2 in the laboratory are laborious and time-consuming, and different laboratories use different approaches. There is therefore no generally agreed way to quantitate neutralising antibodies against SARS-CoV-2, which block infection with the virus and protect people from COVID-19. In this study, we describe a new way to measure SARS-CoV-2 infection, which is much simpler and faster than existing methods. It relies on the production of a specific protease enzyme by the virus, which is able to cleave and activate an engineered protein biosensor in infected cells. This biosensor emits light in the presence of viral infection, and the amount of light released is used as a readout for the amount of infectious SARS-CoV-2 present. The signal is very sensitive, so the number of infected cells required is very small, and the method can be scaled-up to test many samples at once. In particular, we demonstrate how it can be used to detect different variants of SARS-CoV-2, and quantitate neutralising antibodies against these viruses.


title: A protease-activatable luminescent biosensor andreporter cell line for authentic SARS-CoV-2 infection


title: CVnCoV protects human ACE2 transgenic mice from ancestral B BavPat1 and emerging B.1.351 SARS-CoV-2

abstract: The ongoing severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) pandemic necessitates the fast development of vaccines as the primary control option. Recently, viral mutants termed "variants of concern" (VOC) have emerged with the potential to escape host immunity. VOC B.1.351 was first discovered in South Africa in late 2020, and causes global concern due to poor neutralization with propensity to evade preexisting immunity from ancestral strains. We tested the efficacy of a spike encoding mRNA vaccine (CVnCoV) against the ancestral strain BavPat1 and the novel VOC B.1.351 in a K18-hACE2 transgenic mouse model. Naive mice and mice immunized with formalin-inactivated SARS-CoV-2 preparation were used as controls. mRNA-immunized mice developed elevated SARS-CoV-2 RBD-specific antibody as well as neutralization titers against the ancestral strain BavPat1. Neutralization titers against VOC B.1.351 were readily detectable but significantly reduced compared to BavPat1. VOC B.1.351-infected control animals experienced a delayed course of disease, yet nearly all SARS-CoV-2 challenged naive mice succumbed with virus dissemination and high viral loads. CVnCoV vaccine completely protected the animals from disease and mortality caused by either viral strain. Moreover, SARS-CoV-2 was not detected in oral swabs, lung, or brain in these groups. Only partial protection was observed in mice receiving the formalin-inactivated virus preparation. Despite lower neutralizing antibody titers compared to the ancestral strain BavPat1, CVnCoV shows complete disease protection against the novel VOC B.1.351 in our studies.


title: High rates of plasmid cotransformation in E. coli overturn the clonality myth and reveal colony development

abstract: DNA transformation methods, pioneered by Griffith in 1928 and made commonplace by Hanahan in the 1980s 1, ushered in the dawn of molecular cloning of DNA. It is accepted that a typical transformation produces clonal bacterial colonies. To the contrary, using low concentrations of several fluorescent plasmids, under the same selective antibiotic, we find that E. coli bacteria readily accept multiple plasmids, resulting in widespread aclonality and surprisingly uncover a complex pattern of colony development. Cotransformation of plasmids occurs by either CaCl2 or by electroporation methods of bacterial transformation. A bacterium rod transformed with three plasmids - each expressing a high level of a unique fluorescent protein - and replated on agar, appears to reassign a random number of the three fluorescent plasmids to its daughter cell during cell division until an equilibrium is reached whereby ensuing progeny carry a specific distribution of the three plasmids. Thus, the potential to follow multiple lineage tracings in a bacteria colony simultaneously lends itself to mosaic analysis of gene function. We observe that clonally related bacterium rods self-organize in a fractal growth pattern can remain linked during colony development revealing a potential target against microbiota growth.

category: molecular biology


title: An mRNA vaccine against SARS-CoV-2: Lyophilized, liposome-based vaccine candidate EG-COVID induces high levels of virus neutralizing antibodies

abstract: In addition to the traditional method of vaccine development, the mRNA coronavirus vaccine, which is attractive as a challenging vaccination, recently opened a new era in vaccinology. Here we describe the EG-COVID which is a novel liposome-based mRNA candidate vaccine that encodes the spike (S) protein of SARS-CoV-2 with 2P-3Q substitution in European variant. We developed the mRNA vaccine platform that can be lyophilized using liposome-based technology. Intramuscular injection of the EG-COVID elicited robust humoral and cellular immune response to SARS-CoV-2. Furthermore, sera obtained from mice successfully inhibited SARS-CoV-2 viral infection into Vero cells. We developed EG-COVID and found it to be effective based on in vitro data, and we plan to initiate a clinical trial soon. Since EG-COVID is a lyophilized mRNA vaccine that is convenient for transportation and storage, accessibility to vaccines will be significantly improved.


title: Developmental timing scales wing patterning between avian species

abstract: A fundamental question in biology is how species-specific rates of embryonic development are controlled in differently sized species. To address this problem, we compared wing development in the quail and the larger chick. We reveal that pattern formation (humerus to digits) is faster in the quail wing as determined by the earlier activation of 5 Hox genes, termination of developmental organisers (Shh and Fgf8) and the laying down of the skeleton (Sox9). Using interspecies tissue grafts, we show that developmental timing can be reset during a critical window in which retinoic acid signalling is active. Accordingly, retinoic acid can switch developmental timing between the quail and chick, and also between the chick and the larger turkey. We show that the incremental growth rate is equivalent between all three species, suggesting that differences in the expansion of the skeletal pattern are governed primarily by the tempo of development. Our findings have implications for how development is timed both within and between different species.

category: developmental biology


title: Species-specific developmental timing dictates expansion of the avian wing skeletal pattern


title: Origin of diversity in spatial social dilemmas

abstract: Cooperative investments in social dilemmas can spontaneously diversify into stably co-existing high and low contributors in well-mixed populations. Here we extend the analysis to emerging diversity in (spatially) structured populations. Using pair approximation we derive analytical expressions for the invasion fitness of rare mutants in structured populations, which then yields a spatial adaptive dynamics framework. This allows us to predict changes arising from population structures in terms of existence and location of singular strategies, as well as their convergence and evolutionary stability as compared to well-mixed populations. Based on spatial adaptive dynamics and extensive individual based simulations, we find that spatial structure has significant and varied impacts on evolutionary diversification in continuous social dilemmas. More specifically, spatial adaptive dynamics suggests that spontaneous diversification through evolutionary branching is suppressed, but simulations show that spatial dimensions offer new modes of diversification that are driven by an interplay of finite-size mutations and population structures. Even though spatial adaptive dynamics is unable to capture these new modes, they can still be under-stood based on an invasion analysis. In particular, population structures alter invasion fitness and can open up new regions in trait space where mutants can invade, but that may not be accessible to small mutational steps. Instead, stochastically appearing larger mutations or sequences of smaller mutations in a particular direction are required to bridge regions of unfavourable traits. The net effect is that spatial structure tends to promote diversification, especially when selection is strong.

category: evolutionary biology


title: Principles of RNA recruitment to viral ribonucleoprotein condensates in a segmented dsRNA virus

abstract: Rotaviruses transcribe eleven distinct protein-coding RNAs that must be stoichiometrically co-packaged prior to their replication to make an infectious virion. During infection, rotavirus transcripts accumulate in cytoplasmic ribonucleoprotein (RNP) condensates, termed viroplasms. Understanding the mechanisms of viroplasm assembly and RNA enrichment within is crucial to gaining greater insight into their function and stoichiometric assortment of individual transcripts. We analysed the subcellular distribution of individual RV transcripts and viroplasm transcriptome by combining multiplexed DNA-barcoded single-molecule RNA FISH of infected cells. Using DNA-PAINT microscopy, we provide evidence of the early onset of viral transcript oligomerisation that occurs prior to the formation of viroplasms. We demonstrate that viral sequences lacking the conserved terminal regions fail to undergo enrichment in rotavirus RNP condensates. We show that individual viral transcripts exhibit variable propensities to partition into viroplasms, irrespective of their absolute numbers in cells, suggesting a selective RNA enrichment mechanism distinct from other known cellular RNP granules. We suggest that rotavirus replication factories represent unique RNP condensates enriched in eleven types of cognate transcripts that may facilitate the assembly of a multi-segmented RNA genome.


title: Benchtop Carbon Fiber Microelectrode Array Fabrication Toolkit

abstract:
BackgroundConventional neural probes are primarily fabricated in a cleanroom, requiring the use of multiple expensive and highly specialized tools.

New methodWe propose a cleanroom "light" fabrication process of carbon fiber neural electrode arrays that can be learned quickly by an inexperienced cleanroom user. This carbon fiber electrode array fabrication process requires just one cleanroom tool, a parylene-c deposition machine, that can be learned quickly or outsourced to a commercial processing facility at marginal cost. Our fabrication process also includes hand-populating printed circuit boards, insulation, and tip optimization.

ResultsThe three different tip optimizations explored here (Nd:YAG laser, blowtorch, and UV laser) result in a range of tip geometries and 1kHz impedances, with blowtorched fibers resulting in the lowest impedance. While previous experiments have proven laser and blowtorch electrode efficacy, this paper also shows UV laser cut fibers can record neural signals in vivo.

Comparison with existing methodsExisting carbon fiber arrays either do not have individuated electrodes in favor of bundles or require cleanroom fabricated guides for population and insulation. The proposed arrays use only tools that can be used at a benchtop for fiber population.

ConclusionsThis carbon fiber electrode array fabrication process allows for quick customization of bulk array fabrication at a reduced price compared to commercially available probes.


title: HolistiC: Leveraging Hi-C and Whole Genome Shotgun Sequencing for Double Minute Chromosome Discovery

abstract:
Double minute chromosomes are acentric extrachromosomal DNA artifacts that are frequently observed in the cells of numerous cancers. They are highly amplified and contain oncogenes and drug resistance genes, making their presence a challenge for effective cancer treatment. Algorithmic discovery of double minutes (DM) can potentially improve bench-derived therapies for cancer treatment. A hindrance to this task is that DMs evolve, yielding circular chromatin that shares segments from progenitor double minutes. This creates double minutes with overlapping amplicon coordinates. Existing DM discovery algorithms use whole genome shotgun sequencing in isolation, which can potentially incorrectly classify DMs that share overlapping coordinates. In this study, we describe an algorithm called " HolistIC" that can predict double minutes in tumor genomes by integrating whole genome shotgun sequencing (WGS) and Hi-C sequencing data. The consolidation of these sources of information resolves ambiguity in double minute amplicon prediction that exists in DM prediction with WGS data used in isolation. We implemented and tested our algorithm on the tandem Hi-C and WGS datasets of three cancer datasets and a simulated dataset. Results on the cancer datasets demonstrated HolistICs ability to predict DMs from Hi-C and WGS data in tandem. The results on the simulated data showed the HolistIC can accurately distinguish double minutes that have overlapping amplicon coordinates, an advance over methods that predict extrachromosomal amplification using WGS data in isolation.

AvailabilityOur software is available at http://www.github.com/mhayes20/HolistIC.