title: Coupling adipose tissue architecture and metabolism via cytoophidia

abstract: Tissue architecture determines its unique physiology and function. How these properties are intertwined has remained unclear. Here, we show that the metabolic enzyme CTP synthase (CTPS) form filamentous structures termed cytoophidia along the adipocyte cortex in Drosophila adipose tissue. Interestingly, loss of cytoophidia, whether due to reduced CTPS expression or a point mutation that specifically abrogates its polymerization ability, leads to downregulated Collagen-Integrin signaling, weakened adipocyte adhesion, and defective adipose architecture. Strikingly, CTPS specifically binds with Integrin subunit 2, which influences Integrin function and Collagen IV deposition. cytoophidia promote Collagen IV mRNA expression and thus its extracellular deposition to strengthen adipocyte adhesion. Remarkably, Collagen IV-Integrin signaling reciprocally regulates cytoophidium formation at a post-translational level. Together, we demonstrate that a positive feedback signaling loop containing both cytoophidia and Integrin adhesion complex couples tissue architecture and metabolism in the fly adipose.


title: Trade of commercial potting substrates: A largely overlooked means of the long-distance dispersal of plants

abstract: Although long-distance dispersal (LDD) events are considered to be rare and highly stochastic, they are disproportionately important and drive several large-scale ecological processes. The realisation of the disproportionate importance of LDD has led to an upsurge in studies of this phenomenon; yet, we still have a very limited understanding of its frequency, extent and consequences. Humanity intentionally spreads a high number of species, but a less obvious issue is that it is associated with the accidental dispersal of other plant species. Although the global trade of potted plants and horticultural substrates is capable of dispersing large quantities of propagules, this issue has hardly been studied from an ecological point of view. We used the seedling emergence method to assess the viable seed content of different types of commercial potting substrates to answer the following questions: (i) In what richness and density do substrates contain viable seeds? (ii) Does the composition of substrates influence their viable seed content? and (iii) Are there common characteristics of the species dispersed this way? We detected altogether 438 seedlings of 66 taxa and found that 1 litre of potting substrate contains an average of 13.27 seeds of 6.24 species, so an average 20-litre bag of substrate contains 265 viable seeds. There was a high variability in the seed content of the substrates, as substrates containing cattle manure contained a substantially higher number of species and seeds than substrates without manure. Based on this, this pathway of LDD is an interplay between endozoochory by grazing livestock and accidental human-vectored dispersal, implying that the diet preference of grazing animals largely determines the ability of a plant species to be dispersed this way. According to our results, potting substrates can disperse large quantities of seeds of a wide range of plant species, moreover, these dispersal events occur on very long distances in almost all cases. We conclude that this kind of human-vectored LDD may have complex effects on plant populations and communities; however, as this dispersal pathway is largely understudied and has hardly been considered as a type of LDD, its consequences are still largely unknown and further studies of the issue are of great importance.

category: ecology


title: Neoisoptera repetitively colonised Madagascar after the Middle Miocene climatic optimum

abstract: Madagascar is home to many endemic plant and animal species owing to its ancient isolation from other landmasses. This unique fauna includes several lineages of termites, a group of insects known for their key role in organic matter decomposition in many terrestrial ecosystems. How and when termites colonised Madagascar remains unknown. In this study, we used 601 mitochondrial genomes, 93 of which were generated from Madagascan samples, to infer the global historical biogeography of Neoisoptera, a lineage containing upwards of 80% of described termite species. Our results indicate that Neoisoptera colonised Madagascar between seven to ten times independently during the Miocene, between 8.4-16.6 Ma (95% HPD: 6.1-19.9 Ma). This timing matches that of the colonization of Australia by Neoisoptera. Furthermore, the taxonomic composition of the Neoisopteran fauna of Madagascar and Australia are strikingly similar, with Madagascar harbouring an additional two lineages absent from Australia. Therefore, akin to Australia, Neoisoptera colonised Madagascar during the global expansion of grasslands, possibly helped by the ecological opportunities arising from the spread of this new biome.


title: Mitochondrial antiviral-signalling protein is a client of the BAG6 protein quality control complex

abstract:
The heterotrimeric BAG6 complex coordinates the direct handover of newly synthesised tail-anchored (TA) membrane proteins from an SGTA-bound preloading complex to the endoplasmic reticulum (ER) delivery component TRC40. In contrast, defective precursors, including aberrant TA proteins, form a stable complex with this cytosolic protein quality control factor, enabling such clients to be either productively re-routed or selectively degraded. We identify the mitochondrial TA protein MAVS (mitochondrial antiviral-signalling protein) as an endogenous client of both SGTA and the BAG6 complex. Our data suggest that the BAG6 complex binds to a cytosolic pool of MAVS before its misinsertion into the ER membrane, from where it can subsequently be removed via ATP13A1-mediated dislocation. This BAG6- associated fraction of MAVS is dynamic and responds to the activation of an innate immune response, suggesting that BAG6 may modulate the pool of MAVS that is available for coordinating the cellular response to viral infection.

SUMMARY STATEMENTMitochondrial antiviral-signalling (MAVS) protein is a favoured client of the cytosolic BAG6 complex. We discuss how this dynamic interaction may modulate MAVS biogenesis at signalling membranes.

category: biochemistry


title: Miniature Structured Illumination Microscope for in vivo 3D Imaging of Brain Structures with Optical Sectioning

abstract: We present a high-resolution miniature, light-weight fluorescence microscope with electrowetting lens and onboard CMOS for high resolution volumetric imaging and structured illumination for rejection of out-of-focus and scattered light. The miniature microscope (SIMscope3D) delivers structured light using a coherent fiber bundle to obtain optical sectioning with an axial resolution of 18 m. Volumetric imaging of eGFP labeled cells in fixed mouse brain tissue at depths up to 220 m is demonstrated. The functionality of SIMscope3D to provide background free 3D imaging is shown by recording time series of microglia dynamics in awake mice at depths up to 120 m in the brain.

category: bioengineering


title: Fast volumetric imaging with line-scan confocal microscopy by an electro-tunable lens

abstract: In microscopic imaging of biological tissues, particularly real-time visualization of neuronal activities, rapid acquisition of volumetric images poses a prominent challenge. Typically, two-dimensional (2D) microscopy can be devised into an imaging system with 3D capability using any varifocal lens. Despite the conceptual simplicity, such an upgrade yet requires additional, complicated device components and suffers a reduced acquisition rate, which is critical to document neuronal dynamics properly. In this study, we implemented an electro-tunable lens (ETL) in the line-scan confocal microscopy, enabling the volumetric acquisition at the rate of 20 frames per second with the maximum volume of interest of 315 x 315 x 80 m3. The axial extent of point-spread-function (PSF) was 17.6 {+/-} 1.6 m and 90.4 {+/-} 2.1 m with the ETL operating in either stationary or resonant mode, respectively, revealing significant depth elongation by the resonant mode ETL microscopy. We further demonstrated the utilities of the ETL system by volume imaging of cleared mouse brain ex vivo samples and in vivo brains. The current study foregrounds the successful application of resonant ETL for constructing a basis for a high-performance 3D line-scan confocal microscopy system, which will enhance our understanding of various dynamic biological processes.


title: CaveCrawler: An interactive analysis suite for cavefish bioinformatics

abstract: The growing use of genomics data in diverse animal models provides the basis for identifying genomic and transcriptional differences across species and contexts. Databases containing genomic and functional data have played critical roles in the development of numerous genetic models but are lacking for most emerging models of evolution. There is a rapidly expanding use of genomic, transcriptional, and functional genetic approaches to study diverse traits of the Mexican tetra, Astyanax mexicanus. This species exists as two morphs, eyed surface populations and at least 30 blind cave populations, providing a system to study convergent evolution. We have generated a web-based analysis suite that integrates datasets from different studies to identify how gene transcription and genetic markers of selection differ between populations and across experimental contexts. Results can be processed with other analysis platforms including Gene Ontology (GO) to enable biological inference from cross-study patterns and identify future avenues of research. Furthermore, the framework that we have built A. mexicanus can readily applied to other emerging model systems.

category: bioinformatics


title: The PNUTS-PAD domain recruits MYC to the PNUTS:PP1 phosphatase complex via the oncogenic MYC-MB0 region

abstract:
Despite MYC dysregulation in most human cancers, strategies to target this potent oncogenic driver remains an urgent unmet need. Recent evidence shows the PP1 phosphatase and its regulatory subunit PNUTS control MYC phosphorylation and stability, however the molecular basis remains unclear. Here we demonstrate that MYC interacts directly with PNUTS through the MYC homology Box 0 (MB0), a highly conserved region recently shown to be important for MYC oncogenic activity. MB0 interacts with PNUTS residues 1-148, a functional unit here termed, PNUTS amino-terminal domain (PAD). Using NMR spectroscopy we determined the solution structure of PAD, and characterised its interaction with MYC. Point mutations of residues at the MYC-PNUTS interface significantly weaken their interaction both in vitro and in vivo. These data demonstrate the MB0 binding pocket of the PAD represents an attractive site for pharmacological disruption of the MYC-PNUTS interaction.

In BriefSolving the structure of MYC-PNUTS direct interaction reveals how the intrinsically disordered MYC-Box0 (MB0) region anchors into a binding pocket in the N-terminal PAD domain of PNUTS. These data provide insight into the molecular mechanism of how the PNUTS:PP1 phosphatase complex regulates MYC phosphorylation.

O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=197 SRC="FIGDIR/small/470928v1_ufig1.gif" ALT="Figure 1">
View larger version (86K):
org.highwire.dtl.DTLVardef@179b89corg.highwire.dtl.DTLVardef@47338eorg.highwire.dtl.DTLVardef@89b6f4org.highwire.dtl.DTLVardef@14a80bd_HPS_FORMAT_FIGEXP  M_FIG C_FIG HighlightsO_LIA region critical for MYC oncogenesis, MYC-Box0 (MB0), directly interacts with PNUTS
C_LIO_LIPNUTS amino-terminal domain (PAD) is a structural domain that interacts with MYC MB0
C_LIO_LIMutation of single residues at the interaction interface disrupts MYC-PNUTS binding in cells
C_LIO_LIMYC-PNUTS binding releases MYC intramolecular interactions to enable PP1substrate access
C_LI

category: cancer biology


title: Microenvironmental factors in cell segregation and heterogeneity in breast cancer development

abstract: We analyzed a quantitative model that describes the epigenetic dynamics during the growth and evolution of an avascular tumor. A gene regulatory network (GRN) formed by a set of ten genes that are believed to play an important role in breast cancer development was kinetically coupled to the microenvironmental agents: glucose, estrogens and oxygen. The dynamics of spontaneous mutations was described by a Yule-Furry master equation whose solution represents the probability that a given cell in the tissue undergoes a certain number of mutations at a given time. We assumed that mutations rate is modified by nutrients spatial gradients. The tumor mass was grown by means of a cellular automata supplemented with a set of reaction diffusion equations that described the transport of the microenvironmental agents. By analyzing the epigenetic states space described by the GRN dynamics, we found three attractors that were identified with the cellular epigenetic states: normal, precancer and cancer. For two-dimensional (2D) and three-dimensional (3D) tumors we calculated the spatial distributions of the following quantities: (i) number of mutations, (ii) mutations of each gene and, (iii) phenotypes. Using estrogens as the principal microenvironmental agent that regulates cells proliferation process, we obtained the tumor shapes for different values of the estrogen consumption and supply rates. It was found that he majority of mutations occurred in cells that were located close to the 2D tumor perimeter or close to the 3D tumor surface. Also It was found that the occurrence of different phenotypes in the tumor are controlled by the levels of estrogen concentration since they can change the individual cell threshold and gene expression levels. All the results were consistently observed for 2D and 3D tumors.


title: Oxycodone decreases anxiety-like behavior in the elevated plus-maze test in male and female rats

abstract: The prescription opioid oxycodone is widely used for the treatment of pain in humans. Oxycodone misuse is more common among people with an anxiety disorder than those without one. Therefore, oxycodone might be misused for its anxiolytic properties. We investigated if oxycodone affects anxiety-like behavior in adult male and female rats. The rats were treated with oxycodone (0.178, 0.32, 0.56, or 1 mg/kg), and anxiety-like behavior was investigated in the elevated plus-maze test. Immediately after the elevated plus-maze test, a small open field test was conducted to determine the effects of oxycodone on locomotor activity. In the elevated plus-maze test, oxycodone increased the percentage of time spent on the open arms, the percentage of open arm entries, time on the open arms, open arm entries, and the distance traveled. The males treated with vehicle had a lower percentage of open arm entries than the females treated with vehicle, and oxycodone treatment led to a greater increase in the percentage of open arm entries in the males than females. Furthermore, the females spent more time on the open arms, made more open arm entries, spent less time in the closed arms, and traveled a greater distance than the males. In the small open field test, treatment with oxycodone did not affect locomotor activity or rearing. Sex differences were observed; the females traveled a greater distance and displayed more rearing than the males. In conclusion, oxycodone decreases anxiety-like behavior in rats, and oxycodone has a greater anxiolytic-like effect in males than females.

category: pharmacology and toxicology


title: Differential recognition of opioid analgesics by μ opioid receptors: Predicted interaction patterns correlate with ligand-specific voltage sensitivity

abstract: The {micro} opioid receptor (MOR) is the key target for analgesia, but the application of opioids is accompanied by several issues. There is a wide range of opioid analgesics, differing in their chemical structure and their properties in receptor activation and subsequent effects. A better understanding of ligand-receptor interactions and resulting effects is important. Here, we calculated the respective binding modes for several opioids and analyzed fingerprints of ligand-receptor interactions. We further corroborated the binding modes experimentally by cellular assays. As ligand-induced modulation of activity due to changes in membrane potential was displayed by MOR, we further analyzed the effects of voltage sensitivity of this receptor. With a combined in silico and in vitro approach, we defined discriminating interaction patterns for the ligand-specific voltage sensitivity. With this, we present new insights for interactions likely in ligand recognition and their specific effects on activation of the MOR.


title: The ENDS of assumptions; an online tool for the Epistemic Nonparametric Drug-response Scoring

abstract:
MotivationThe drugs sensitivity analysis is often elucidated from drug dose-response curves. These curves capture the degree of cell viability (or inhibition) over a range of induced drugs, often with parametric assumptions that are rarely validated.

ResultsWe present a class of nonparametric models for the curve fitting and scoring of drug dose-responses. To allow a more objective representation of the drug sensitivity, these epistemic models devoid of any parametric assumptions attached to the linear fit, allow the parallel indexing such as IC50 and AUC. Specifically, three nonparametric models including Spline, Monotonic, and Bayesian (npS, npM, npB) and the parametric Logistic (pL) are implemented. Other indices including Maximum Effective Dose (MED) and Drug-response Span Gradient (DSG) pertinent to the npS are also provided to facilitate the interpretation of the fit. The collection of these models are implemented in an online app, standing as useful resource for drug dose-response curve fitting and analysis.

AvailabilityThe ENDS is freely available online at https://irscope.shinyapps.io/ENDS/ and source codes can be obtained from https://github.com/AmiryousefiLab/ENDS.

Supplementary informationSupplementary data are available at Bioinformatics and https://irscope.shinyapps.io/ENDS/

Contactali.amiryousefi@helisnki.fi; jing.tang@helisnki.fi.

ContributionsAA conceived the study and developed the models, AA and BW adopted and implemented the methods, JT provided the funding, AA, BW, MJ, and JT wrote the paper.


title: A nuclear import pathway exploited by viroid RNAs

abstract: The prevailing view regarding intracellular RNA trafficking in eukaryotic cells describes that RNAs transcribed in the nucleus either stay in the nucleus or cross the nuclear envelope entering the cytoplasm for function. Interestingly, emerging evidence illustrates numerous functional RNAs trafficking in the reverse direction from the cytoplasm to the nucleus. However, the mechanism underlying the RNA nuclear import has not been well elucidated. Viroids are single-stranded circular noncoding RNAs that infect plants. Using nuclear-replicating viroids as a model, we showed that cellular Importin alpha-4 is likely involved in viroid RNA nuclear import, empirically supporting the involvement of Importin-based cellular pathway in RNA nuclear import. We also confirmed the involvement of a cellular protein (Virp1) that binds both Importin alpha-4 and viroids. Furthermore, a conserved C-loop in nuclear-replicating viroids is critical for Virp1 binding. Disrupting C-loop impairs Virp1 binding, viroid nuclear accumulation and infectivity. Further, C-loop exists in a subviral satellite noncoding RNA that relies on Virp1 for nuclear import. These results have significant implications for understanding the infection process of subviral agents. In addition, our data outline a cellular pathway responsible for the nuclear import of RNAs and uncover a 3-dimensional RNA motif-based regulation over RNA nuclear import.

category: plant biology


title: A nuclear import pathway exploited by pathogenic noncoding RNAs


title: A stepwise route to domesticate rice by controlling seed shattering and panicle shape

abstract:
Asian rice (Oryza sativa L.) is consumed by more than half of the worlds population. Despite its global importance, the process of early rice domestication remains unclear. During domestication, wild rice (O. rufipogon Griff.) acquired non-seed-shattering behaviour, allowing humans to increase grain yield. Previous studies argued that the sh4 mutation triggered a reduction in seed shattering during rice domestication; but our experiments using wild introgression lines of O. rufipogon show that the domesticated sh4 allele alone is insufficient for shattering loss. Here, we identified the interaction between three key mutations associated with the interruption of abscission layer formation and panicle architecture that were causal in early rice domestication. An interruption of abscission layer formation requires both sh4 and qSH3 mutations, presenting an apparent barrier to the selection of shattering loss. We identified a causal single-nucleotide polymorphism at qSH3 within the seed-shattering gene OsSh1, which is conserved in indica and japonica subspecies but absent in the circum-aus group of rice. Through harvest experiments, we demonstrated that seed shattering alone did not significantly impact yield; rather yield increases were observed with closed panicle formation controlled by SPR3, which is further augmented by the integration of sh4 and qSH3 alleles. Complementary manipulation of seed shattering and panicle shape result in a mechanically stable panicle structure. We propose a stepwise route for the earliest phase of rice domestication, wherein selection of visible SPR3-controlled closed panicle morphology was instrumental in the sequential recruitment of sh4 and qSH3, which led to the loss of shattering.

Significance StatementRice is one of the most important crops worldwide. Loss of seed shattering in domesticated rice, previously attributed to single mutations such as those in sh4, is considered the principal genetic change which resulted in yield increases. However, we show that sh4 alone is insufficient and other genes, such as qSH3, are required to cause abscission layer disruption. The evolution of non-seed-shattering therefore required multiple mutations. Furthermore, shattering loss in genetic backgrounds of wild rice does not correspondingly increase yields. We have identified an interaction in which a second trait, closed panicle formation controlled by SPR3, that both increases the yield and facilitates recruitment of sh4 and qSH3, which synergistically augment yield, leading to a stepwise model for rice domestication.


title: Application of Parallel Reaction Monitoring in 15N labeled Samples for Quantification

abstract: Accurate relative quantification is critical in proteomic studies. The incorporation of stable isotope 15N to plant-expressed proteins in vivo is a powerful tool for accurate quantification with a major advantage of reducing preparative and analytical variabilities. However, 15N labeling quantification has several challenges. Less identifications are often observed in the heavy labeled samples because of incomplete labeling, resulting in missing values in reciprocal labeling experiments. Inaccurate quantification can happen when there is contamination from co-eluting peptides or chemical noise in the MS1 survey scan. These drawbacks in quantification can be more pronounced in less abundant but biologically interesting proteins, which often have very few identified peptides. Here we demonstrate the application of parallel reaction monitoring (PRM) to 15N labeled samples on a high resolution, high mass accuracy Orbitrap mass spectrometer to achieve reliable quantification even of low abundance proteins in samples.


title: Self-confined expression in the Arabidopsis root stem cell niche

abstract: Stem cell niches are local microenvironments that preserve their unique identity while communicating with adjacent tissues. In the primary root of Arabidopsis thaliana, the stem cell niche comprises the expression of two transcription factors, BRAVO and WOX5, among others. Intriguingly, these proteins confine their own gene expression to the niche, as evidenced in each mutant background. Here we propose through mathematical modeling that BRAVO confines its own expression domain to the stem cell niche by attenuating its WOX5-dependent diffusible activator. This negative feedback drives WOX5 action to be spatially restricted as well. The results show that WOX5 diffusion and sequestration by binding to BRAVO is sufficient to drive realistic confined BRAVO expression at the stem cell niche. We propose that attenuation of a diffusible activator can be a general mechanism to confine genetic activity to a small region while at the same time maintain signaling within it and with the surrounding cells.

category: systems biology


title: McSNAC: A software to approximate first-order signaling networks from mass cytometry data

abstract:
Mass cytometry (CyTOF) gives unprecedented opportunity to simultaneously measure up to 40 proteins in single cells, with a theoretical potential to reach 100 proteins. This high-dimensional single-cell information can be very useful to dissecting mechanisms of cellular activity. In particular, measuring abundances of signaling proteins like phospho-proteins can provide detailed information on the dynamics of single-cell signaling processes. With a proper computational analysis, timestamped CyTOF data of signaling proteins could help develop predictive and mechanistic models for signaling kinetics. These models would be useful for predicting the effects of perturbations in cells, or comparing signaling networks across cell groups. We propose our Mass cytometry Signaling Network Analysis Code, or McSNAC, a new software capable of reconstructing signaling networks and estimating their kinetic parameters from CyTOF data.

McSNAC approximates signaling networks as a network of first-order reactions between proteins. This assumption breaks down often as signaling reactions can involve binding and unbinding, enzymatic reactions, and other nonlinear constructions. Furthermore, McSNAC may be limited to approximating indirect interactions between protein species, as cytometry experiments are only able to assay a small fraction of the protein species that are involved in signaling. We carry out a series of in silico experiments here to show that 1) McSNAC is capable of accurately estimating the ground-truth model in a scalable manner when given data originating from a first-order system; 2) McSNAC is capable of qualitatively predicting outcomes to perturbations of species abundances in simple second-order reaction models and in a complex in silico nonlinear signaling network in which some proteins are unmeasured. These findings demonstrate that McSNAC can be a valuable screening tool for generating models of signaling networks from timestamped CyTOF data.


title: Smart3-ATAC: a highly sensitive method for joint accessibility and full-length transcriptome analysis in single cells

abstract: Joint single-cell measurements of gene expression and DNA regulatory element activity holds great promise as a tool to understand transcriptional regulation. Towards this goal we have developed Smart3-ATAC, a highly sensitive method which allows joint mRNA and chromatin accessibility analysis genome wide in single cells. With Smart3-ATAC, we are able to obtain the highest possible quality measurements per cell. The method combines transcriptomic profiling based on the highly sensitive Smart-seq3 protocol on cytosolic mRNA, with a novel low-loss single-cell ATAC (scATAC) protocol to measure chromatin accessibility. Compared to current droplet multiome methods, the yield of both the scATAC protocol and mRNA-seq protocol is markedly higher.


title: Assessing the impact of free-roaming dog population management through systems modelling

abstract: Free-roaming dogs can present significant challenges to public health, wildlife conservation, and livestock production. Their own welfare may also be a concern, as free-roaming dogs can experience poor health and welfare. Dog population management is widely conducted to mitigate these issues. To ensure efficient use of resources, it is critical that effective, cost-efficient, and high-welfare strategies are identified. The dog population comprises distinct subpopulations characterised by their restriction status and level of ownership, but the assessment of dog population management often fails to consider the impact of the interaction between subpopulations on management success. We present a system dynamics model that incorporates an interactive and dynamic system of dog subpopulations. We identify that methods incorporating both fertility control and responsible ownership interventions (a reduction in abandonment and an increase in shelter adoptions) have the greatest potential to reduce free-roaming dog population sizes over longer periods of time, whilst being cost-effective and improving overall welfare. We suggest that future management should be applied at high levels of coverage and should target all sources of population increase, such as abandonment, births, and free-roaming owned dogs, to ensure effective and cost-efficient reduction in free-roaming dog numbers.

category: zoology


title: Sex-specific Stress and Behavioural Responses to Human Experimenters in Rats

abstract: The sex of the experimenter may cause stress in animal models and be a major confounding factor in preclinical research. We studied the effects of the sex of the experimenter on female and male rat anxiety behaviours using thigmotaxis in the open field test, anxiety-induced changes in brain and back temperature using infra-red thermography, and alterations in plasma concentrations of stress hormones, corticosterone and oxytocin. Female rats displayed consistently exacerbated anxiety-related behaviours along with increased infrared cutaneous temperature during repeated exposure to male experimenters. Experimental stress further intensified thermal responses to a male experimenter, especially in female rats. These behavioural responses to a male experimenter in females were associated with higher circulating corticosterone and lower oxytocin levels. Similar responses were induced by a T-shirt worn by a human male. These findings suggest that emotional and physiological responses of female rats to a male experimenter are influenced by visual and olfactory cues. These results emphasize the need to standardize and report experimenter sex throughout a study to avoid ambiguity in interpretation of the results.

category: neuroscience


title: Contextual control of conditioned pain tolerance and endogenous analgesic systems: Evidence for sex-based differences in endogenous opioid engagement

abstract: The mechanisms underlying the transition from acute to chronic pain are unclear but may involve the persistence or strengthening of pain memories acquired in part through associative learning. Contextual cues, which comprise the surrounding environment where events occur, were recently described as a critical regulator of pain memory; both rodents and humans exhibit increased pain sensitivity in environments recently associated with a single painful experience. It is unknown, however, how repeated exposure to an acute painful unconditioned stimulus in a distinct context modifies pain sensitivity or the expectation of pain in that environment. To answer this question, we conditioned mice to associate distinct contexts with either repeated administration of a mild visceral pain stimulus (intraperitoneal injection of acetic acid) or vehicle injection over the course of three days. On the final day of experiments animals received either an acid injection or vehicle injection prior to being placed into both contexts. In this way, contextual control of pain sensitivity and pain expectation could be tested respectively. Both male and female mice developed context-dependent conditional pain tolerance, a phenomenon mediated by endogenous opioid signaling. However, when expecting the presentation of a painful stimulus in a given context, males exhibited conditional hypersensitivity whereas females exhibited endogenous opioid-mediated conditional analgesia. Successful determination of the brain circuits involved in this sexually dimorphic anticipatory response may allow for the manipulation of pain memories, which may contribute to the development of chronic pain states.


title: Specific plasticity loci and their synergism mediate operant	conditioning

abstract:
Despite numerous studies examining the mechanisms of operant conditioning (OC), the diversity of plasticity loci and their synergism have not been examined sufficiently. In the well-characterized feeding neural circuit of Aplysia, appetitive OC increases neuronal excitability and electrical coupling among several neurons. Here we found OC decreased the intrinsic excitability of B4 and the strength of its inhibitory connection to a key decision-making neuron, B51. The OC-induced changes were specific without affecting the B4-to-B8 inhibitory connection or excitability of another neuron critical for feeding behavior, B8. A conductance-based circuit model indicated certain sites of plasticity mediated the OC phenotype more effectively and that plasticity loci acted synergistically. This synergy was specific in that only certain combinations of loci synergistically enhanced feeding. Taken together, these results suggest modifications of diverse loci work synergistically to mediate OC.

Significance StatementThe diversity and synergism of plasticity loci mediating operant conditioning (OC) is poorly understood. Here we found that OC decreased the intrinsic excitability of a critical neuron mediating Aplysia feeding behavior and specifically reduced the strength of one of its inhibitory connections to a key decision-making neuron. A conductance-based computational model indicated that the known plasticity loci showed a surprising level of synergism to mediate the behavioral changes associated with OC. These results highlight the importance of understanding the diversity, specificity and synergy among different types of plasticity that encode memory. Also, because OC in Aplysia is mediated by dopamine (DA), the present study provides insights into specific and synergistic mechanisms of DA-mediated reinforcement of behaviors.


title: Stability and dynamics of a spectral graph model of brain oscillations

abstract: We explore the stability and dynamic properties of a hierarchical, linearized, and analytic spectral graph model for neural oscillations that integrates the structuring wiring of the brain. Previously we have shown that this model can accurately capture the frequency spectra and the spatial patterns of the alpha and beta frequency bands obtained from magnetoencephalography recordings without regionally varying parameters. Here, we show that this macroscopic model based on long-range excitatory connections exhibits dynamic oscillations with a frequency in the alpha band even without any oscillations implemented at the mesoscopic level. We show that depending on the parameters, the model can exhibit combinations of damped oscillations, limit cycles, or unstable oscillations. We determined bounds on model parameters that ensure stability of the oscillations simulated by the model. Finally, we estimated time-varying model parameters to capture the temporal fluctuations in magnetoencephalography activity. We show that a dynamic spectral graph modeling framework with a parsimonious set of biophysically interpretable model parameters can thereby be employed to capture oscillatory fluctuations observed in electrophysiological data in various brain states and diseases.


title: Age-related differences in the neural network dynamics underlying the predictability gain

abstract: Speech comprehension is often challenged by increased background noise, but can be facilitated via the semantic context of a sentence. This predictability gain relies on an interplay of language-specific semantic and domain-general brain regions. However, age-related differences in the interactions within and between semantic and domain-general networks remain poorly understood. Using functional neuroimaging, we investigated commonalities and differences in network interactions enabling processing of degraded speech in healthy young and old participants. Participants performed a sentence repetition task while listening to sentences with high and low predictable endings and varying intelligibility. Stimulus intelligibility was adjusted to individual hearing abilities. Older adults showed an undiminished behavioural predictability gain. Likewise, both groups recruited a similar set of semantic and cingulo-opercular brain regions. However, we observed age-related differences in effective connectivity for high predictable speech of increasing intelligibility. Young adults exhibited stronger connectivity between regions of the cingulo-opercular network and between left insula and the posterior middle temporal gyrus. Moreover, these interactions were excitatory in young adults but inhibitory in old adults. Finally, the degree of the inhibitory influence between cingulo-opercular regions was predictive of the behavioural sensitivity towards changes in intelligibility for high predictable sentences in older adults only. Our results demonstrate that the predictability gain is relatively preserved in older adults when stimulus intelligibility is individually adjusted. While young and old participants recruit similar brain regions, differences manifest in underlying network interactions. Together, these results suggest that ageing affects the network configuration rather than regional activity during successful speech comprehension under challenging listening conditions.


title: Age-related differences in the neural network interactions underlying the predictability gain


title: Neutralization Fingerprinting Technology for Characterizing Polyclonal Antibody Responses to Dengue Vaccines

abstract: Dengue is a major public health threat. There are four serotypes of dengue virus (DENV), therefore efforts are focused on development of safe and effective tetravalent DENV vaccines. While neutralizing antibodies contribute to protective immunity, there are still important gaps in understanding of immune responses elicited by dengue infection and vaccination, including defining immune correlates of protection. To that end, here we present a computational modeling framework for evaluating the specificities of neutralizing antibodies elicited to tetravalent DENV vaccines, based on the concept of antibody-virus neutralization fingerprints. We developed and applied this framework to samples from clinical studies of TAK-003, a tetravalent vaccine candidate currently in phase 3 trials, to characterize the effect of prior dengue infection (baseline) on the specificities of vaccine-elicited antibody responses. Our results suggested a similarity of neutralizing antibody specificities in baseline-seronegative individuals. In contrast, amplification of pre-existing neutralizing antibody specificities was predicted for baseline-seropositive individuals, thus quantifying the role of immunologic imprinting in driving antibody responses to DENV vaccines. The analysis framework proposed here can apply to studies of sequential dengue infections and other tetravalent DENV vaccines and can contribute to understanding dengue immune correlates of protection to help guide further vaccine development and optimization.

category: immunology


title: Age-elevated prostaglandin E2 enhances mortality to influenza infection

abstract: Aging impairs the immune responses to influenza A virus (IAV), resulting in increased mortality to IAV infections in older adults. With aging, there is reduced number and impaired function of alveolar macrophages (AMs), cells critical for defense against IAV. However, factors within the aged lung that impair AMs are not fully known. Using a murine model of IAV infection, we observed that aging increased the level of prostaglandin E2 (PGE2) in the bronchoalveolar lavage fluid (BALF) of aged mice compared to young mice. Blockade of the PGE2 receptor EP2 in aged mice increased AM numbers and subsequently enhanced survival to IAV. Additionally, PGE2 impaired the mitochondrial health of AMs. We also identified senescent type II alveolar epithelial cells (AECs) as a source of the aged-associated PGE2 in the lung. Our results reveal a crosstalk between AECs and AMs, via PGE2, that compromises host defense to IAV infection with aging.


title: Fungal endophytes from salt-adapted plants confer salt tolerance and promote growth in Wheat (Triticum aestivum L.) at early seedling stage

abstract: With increasing human global population, increased yield under saline conditions is a desirable trait for major food crops. Use of endophytes, isolated from halophytic hosts, seems to be an exciting approach for conferring salt tolerance to a salt sensitive crop. Therefore, in the current study, fungal endophytes were isolated from halophytic plants roots and their ability to withstand in vitro salt stress was evaluated. They could withstand upto 1M NaCl concentrations and this tolerance was independent of their host or tissue source. When inoculated on salt sensitive wheat seeds/seedlings several of the endophytes showed a positive impact on germination and biomass related parameters upon salt stress, both in vitro and under glasshouse conditions. One of the isolate from dicot plants (identified as Microsphaeropsis arundinis) could successfully colonize wheat and promote its growth under salt and no salt conditions. Amongst the fungal isolates that are known to be natural endophytes of wheat, Chaetomium globosum was the best performing isolate which has been reported as an effective biocontrol agent earlier. Based on the results of our preliminary study, we suggest that these fungal endophytes could prove beneficial for salt stress tolerance enhancement of wheat crop.

category: microbiology


title: Lactococcus lactis sb. cremoris orchestrates signal events in the gut epithelium via TLR2 to promote tissue restitution

abstract: The use of beneficial bacteria to promote gastrointestinal heath is widely practiced, however, the mechanisms whereby many of these microbes elicit their beneficial effects remain elusive. Previously, we conducted a screen for the discovery of novel beneficial microbes and identified the potent cytoprotective effects of a strain of Lactococcus lactis subsp. cremoris. Here, we show that dietary supplementation with L. lactis subsp. cremoris induced transcript enrichment of a set of genes within the colon whose functions are associated with host cell and microbe interactions. Specifically, L. lactis subsp. cremoris induced the expression of tlr2, which we show was required for L. lactis subsp. cremoris to elicit its beneficial effects on the intestine. L. lactis subsp. cremoris did not confer beneficial effects in mice deficient in TLR-2, or deficient in its adaptor protein Myd88 in chronic gut injury models. In addition to cytoprotection, culture supernatant from L. lactis subsp. cremoris accelerated epithelial migration in a cultured epithelial cell scratch wound assay; and effect that was abrogated by a TLR-2 antagonist. Furthermore, L. lactis subsp. cremoris accelerated epithelial tissue restitution following the infliction of a colonic wound biopsy in a TLR-2 and Myd88-dependent manner. Within colonic wounds, L. lactis subsp. cremoris induced the activation of signaling pathways that function in tissue restitution following injury, including the ERK signaling pathway, and of focal adhesion complex (FAC) proteins. Together, these data demonstrate that L. lactis subsp. cremoris signals via the TLR2/MyD88-axis to confer cytoprotection and accelarated tissue restituion in the gut epithelium. These data point to evolving adaptations where beneficial gut microbes moduate innate immune signaling to excert positive influnces on host physiology.


title: Synergistic collagen-condiment: Streptococcal collagen-like (Scl) protein in cell-adhesion and diabetic wound-closure matrix

abstract: Group A streptococcus (GAS), Streptococcus pyogenes manifests plethora of diseases through its explicit virulence factors. Among these, the recently deciphered MSCRAMMs, Streptococcal collagen-like (Scls) adhesins are most studied proteins in context of their biophysically stable collagenous-sequence (Gly-X-Y) despite the difference from analogous mammalian-collagen. Based on recent evidence on collagen-mimetic Scls, we elucidated biomaterial-potential of the unmodified, recombinant Scl1 (rScl1). Initially, rScl1 trimeric- assembly yielded its stability in silico than the monomeric-unit. Thereby, rScl1 matrix characterization was confirmed in vitro. rScl1 exhibited high A549 and HepG2 cell- viability--rScl1 dose incremented to 20.0 {micro}g/ml at time points up to 24 hr, and on 24 hr stored-dishes--deliberating it non-cytotoxic. Imploring cell-adhesion potential, we observed increased cell-counts tangential to rScl1-gradient. This affirmative prelude on rScl1 as a supporting-matrix cued its synergy to collagen; we discerned it through rScl1-augmented, full-thickness diabetic wound-closure in vivo and as a first, we studied > 18-month rabbit alloxan-models. We have ascertained re-epithelialization with higher type III collagen in absence of inflammation evidenced morphometrically and histologically. Finally, we correlated our observations through atomistic-evaluation of rScl1-2{beta}1-integrin interaction, surprisingly, with augmented binding-energy compared to collagen. Hence, connoting recombinant-streptococcal collagen as an  alternate; with further characterization, rScl1 can potentiate important revelations conceding homogeneous and safe, bio-available, biomaterial.


title: ABCA1 causes an asymmetric cholesterol distribution to regulate intracellular cholesterol homeostasis

abstract: Cholesterol is a major and essential component of the mammalian cell plasma membrane (PM) and the loss of cholesterol homeostasis leads to various pathologies. Cellular cholesterol uptake and synthesis are regulated by a cholesterol sensor in the endoplasmic reticulum (ER). However, it remains unclear how the PM cholesterol level is sensed. Here we show that the sensing depends on ATP-binding cassette A1 (ABCA1) and Aster-A, which cooperatively maintain the asymmetric transbilayer cholesterol distribution in the PM. ABCA1 translocates (flops) cholesterol from the inner to the outer leaflet of the PM to maintain a low inner cholesterol level. When the inner cholesterol level exceeds a threshold, Aster-A is recruited to the PM-ER contact site to transfer cholesterol to the ER. These results show unknown synergy between ABCA1 and Aster-A in intracellular cholesterol homeostasis.

category: cell biology


title: Zn2+ acts as a brake signal for axonal transport by directly inhibiting motor protein progression

abstract:
Accurate delivery of cargo over long distances through axonal transport requires precise spatiotemporal regulation. Here we discover that Zn2+, either released from lysosomes through TRPML1 or influx via depolarization, inhibits axonal transport. Zn2+-mediated inhibition is neither selective for cargo nor for cell type because elevated Zn2+ (IC50 {approx} 5 nM) reduces both lysosomal and mitochondrial motility in primary rat hippocampal neurons and HeLa cells. We further reveal that Zn2+ directly binds to microtubules and inhibits movement of kinesin motors. Loss of TRPML1 function, which causes Mucolipidosis Type IV (MLIV) disease, impairs lysosomal Zn2+ release, disrupts Zn2+-mediated regulation of axonal transport, and increases overall organellar motility. In addition, MLIV patient mutations in TRPML1 have decreased Zn2+ permeability, which parallels disease severity. Our results reveal that Zn2+ acts as a critical signal to locally pause axonal transport by directly blocking the progression of motor proteins on microtubules.

Significance StatementDisruptions in proper axonal transport have been linked to neurodevelopmental and neurodegenerative diseases. Here we discover that activation of the lysosomal channel TRPML1 arrests lysosomal trafficking. Such lysosome self-regulation mechanism is mediated via TRPML1-mediated Zn2+, not Ca2+. We further reveal that Zn2+ acts as a critical brake signal to pause axonal transport locally by directly decorating microtubules and blocking the movement of motor proteins. Dysfunction of TRPML1, the genetic cause of Mucolipidosis type IV (MLIV), blocks lysosomal Zn2+ release, causing loss of fine-tuning of lysosomal motility. Overall, this study implicates the importance of Zn2+ signals and axonal transport in the pathology of MLIV and reveals new signaling roles for Zn2+ in regulating cell processes involved with microtubule-based transport.


title: Transcription feedback dynamics in the wake of cytoplasmic degradation shutdown

abstract: In the last decade, multiple studies have shown that cells maintain a balance of mRNA production and degradation, but the mechanisms by which cells implement this balance remain unknown. Here, we monitored cells mRNA and nascent mRNA profiles immediately following an acute depletion of Xrn1 - the main 5-3 mRNA exonuclease - that was previously implicated in balancing mRNA levels. We captured the detailed dynamics of the cells adaptation to rapid degradation of Xrn1 and observed a significant accumulation of mRNA, followed by a delayed global reduction in nascent transcription and a gradual return to baseline mRNA levels. We present evidence that this transcriptional response is linked to cell cycle progression, and that it is not unique to Xrn1 depletion; rather, it is induced earlier when upstream factors in the 5-3 degradation pathway are perturbed. Our data suggest that the RNA feedback mechanism is cell-cycle-linked and monitors the accumulation of inputs to the 5-3 exonucleolytic pathway rather than its outputs.


title: CTP synthase does not form cytoophidia in Drosophila interfollicular stalks

abstract: CTP synthase (CTPS) catalyzes the final step of de novo synthesis of the nucleotide CTP. In 2010, CTPS has been found to form filamentous structures termed cytoophidia in Drosophila follicle cells and germline cells. Subsequently, cytoophidia have been reported in many species across three domains of life: bacteria, eukaryotes and archaea. Forming cytoophidia appears to be a highly conserved and ancient property of CTPS. To our surprise, here we find that polar cells and stalk cells, two specialized types of cells composing Drosophila interfollicular stalks, do not possess obvious cytoophidia. Moreover, we show that Myc level is low in these two types of cells, supporting the idea that Myc regulates cytoophidium assembly. Treatment with a glutamine analog, 6-diazo-5-oxo-l-norleucine (DON), increases cytoophidium assembly in main follicle cells, but not in polar cells or stalk cells. Our findings provide an interesting paradigm for the in vivo study of cytoophidium assembly and disassembly among different populations of follicle cells.

category: developmental biology


title: Reduction of free-roaming cat population requires high-intensity neutering in spatial contiguity to mitigate compensatory effects

abstract:
When free-roaming in natural areas, the domestic cat (Felis silvestris catus) is ranked high among the most destructive alien species. Near human dwellings, it might risk humans, impair sanitation, and suffer from poor welfare. Cats popularity as companion animals complicates their population control. Thus, culling is often replaced by a fertility control method called "Trap-Neuter-Return/Release (TNR)," which is considered more humane. Despite the extensive application of TNR, a long-term controlled study was never performed to test its effectiveness. We present a uniquely designed controlled field experiment for examining TNR effectiveness. The study was performed over a twelve-year period, divided into pre-intervention, mixed- and full-intervention phases, and spanned a 20Km2 urban area. Trends of cat, intact-female, and kitten counts, cat reproduction, and carcass reports were compared among study phases and areas with different neutering intensities. The cat population increased during the first two study phases and did not decline in highly neutered populations, presumably due to cat immigration. Expansion of high-intensity neutering to the entire city in the full-intervention phase (>70% neutering percentage) reversed cat population growth, reaching an annual ca. 7% reduction. This population reduction was limited by a rebound increase in cat reproduction and longevity. We conclude that cat population management by TNR should be performed in high-intensity, continuously, and in geographic contiguity to enable population reduction. To enhance management effectiveness and mitigate compensatory effects, we recommend further evaluating an integrated strategy that combines TNR with complementary methods (e.g., vital resource regulation, ill cat euthanasia, and adoption).

Significance StatementThough popular companion animals, domestic cats pose numerous problems when free-roaming, including predation of wildlife, hazards to humans, impaired sanitation, and a decrease in their welfare. Thus, managing their populations is essential. The Trap-Neuter-Return method (TNR, capturing, sterilizing, returning/releasing) is widely employed for managing cat populations. However, there is a lack of long-term controlled evidence for its effectiveness. We examined the outcomes of high-intensity TNR by performing a twelve-year controlled field experiment, the largest to date. Neutering over 70% of the cats caused population decline when applied over contiguous areas. However, it was limited by a rebound increase in reproduction and survival. These findings provide a robust quantification of the limitations and the long-term effectiveness of TNR.


title: A chromosomal inversion may facilitate adaptation despite periodic gene flow in a freshwater fish

abstract: Differences in genomic architecture between populations, such as chromosomal inversions, may play an important role in facilitating adaptation despite opportunities for gene flow. One system where chromosomal inversions may be important for eco-evolutionary dynamics are in freshwater fishes, which often live in heterogenous environments characterized by varying levels of connectivity and varying opportunities for gene flow. In the present study, reduced representation sequencing was used to study possible adaptation in n = 345 walleye (Sander vitreus) from three North American waterbodies: Cedar Bluff Reservoir (Kansas, USA), Lake Manitoba (Manitoba, Canada), and Lake Winnipeg (Manitoba, Canada). Haplotype and outlier-based tests revealed a putative chromosomal inversion that contained three expressed genes and was nearly fixed for alternate genotypes in each Canadian lake. These patterns exist despite several opportunities for gene flow between these proximate Canadian lakes, suggesting that the inversion may be important for facilitating adaptive divergence between the two lakes despite gene flow. Our study illuminates the importance of genomic architecture for facilitating local adaptation in freshwater fishes. Furthermore, our results provide additional evidence that inversions may facilitate local adaptation in many organisms that inhabit connected but heterogenous environments.

category: evolutionary biology


title: Historical biogeography of early diverging termite lineages (Isoptera: Teletisoptera)

abstract: Termites are social cockroaches distributed throughout warm temperate and tropical ecosystems. The ancestor of modern termites (crown-Isoptera) occurred during the earliest Cretaceous, approximately 140 million years ago, suggesting that both vicariance through continental drift and overseas dispersal may have shaped the distribution of early diverging termite lineages. We reconstruct the historical biogeography of three early diverging termite families - Stolotermitidae, Hodotermitidae, and Archotermopsidae - using the nuclear rRNA genes and mitochondrial genomes of 27 samples. Our analyses confirmed the monophyly of Stolotermitidae + Hodotermitidae + Archotermopsidae (clade Teletisoptera), with Stolotermitidae diverging from a monophyletic Hodotermitidae + Archotermopsidae approximately 100.3 Ma (94.3-110.4 Ma, 95% HPD), and with Archotermopsidae paraphyletic to a monophyletic Hodotermitidae. The Oriental Archotermopsis and the Nearctic Zootermopsis diverged 50.8 Ma (40.7-61.4 Ma, 95% HPD) before land connections between the Palearctic region and North America ceased to exist. The African Hodotermes + Microhodotermes diverged from Anacanthotermes, a genus found in Africa and Asia, 32.1 Ma (24.8-39.9 Ma, 95% HPD), and the most recent common ancestor of Anacanthotermes lived 10.7 Ma (7.3-14.3 Ma, 95% HPD), suggesting that Anacanthotermes dispersed to Asia using the land bridge connecting Africa and Eurasia [~]18-20 Ma. In contrast, the common ancestors of modern Porotermes and Stolotermes lived 20.2 Ma (15.7-25.1 Ma, 95% HPD) and 26.6 Ma (18.3-35.6 Ma, 95% HPD), respectively, indicating that the presence of these genera in South America, Africa, and Australia involved over-water dispersals. Our results suggest that early diverging termite lineages acquired their current distribution through a combination of over-water dispersals and dispersal via land bridges. We clarify the classification by resolving the paraphyly of Archotermopsidae, restricting the family to Archotermopsis and Zootermopsis, and elevating Hodotermopsinae (Hodotermopsis) as Hodotermopsidae (status novum).


title: UG/Abi: a highly diverse family of prokaryotic reverse transcriptases associated with defense functions

abstract: Reverse transcriptases (RTs) are enzymes capable of synthesizing DNA using RNA as a template. Within the last few years, a burst of research has led to the discovery of novel prokaryotic RTs with diverse antiviral properties, such as DRTs (Defense-associated RTs), which belong to the so-called group of unknown RTs (UG) and are closely related to the Abortive Infection system (Abi) RTs. In this work, we performed a systematic analysis of UG and Abi RTs, increasing the number of UG/Abi members up to 42 highly diverse groups, most of which are predicted to be functionally associated with other gene(s) or domain(s). Based on this information, we classified these systems into three major classes. In addition, we reveal that most of these groups are associated with defense functions and/or mobile genetic elements, and demonstrate the antiphage role of four novel groups. Besides, we highlight the presence of one of these systems in novel families of human gut viruses infecting members of the Bacteroidetes and Firmicutes phyla. This work lays the foundation for a comprehensive and unified understanding of these highly diverse RTs with enormous biotechnological potential.


title: Structure-driven effects on genomic DNA damage propensity at G-quadruplex sites

abstract:
Our genome contains about half a million sites capable of forming G-quadruplex (G4) structures. Such structural formations, often localised at important regulatory loci, have high capability of altering the predisposition of corresponding genomic spans to endogenous and exogenous DNA damage. In this work, we devised an approach to systematically enrich and zoom onto structure-driven effects on the propensity to undergo 9 types of DNA damage: ultraviolet radiation-induced pyrimidine-pyrimidone (6-4) photoproduct PP and cyclobutane pyrimidine dimer CPD couplings (two dyad-based subtypes in each), cisplatin-mediated G-G crosslinks, reactive oxygen species induced 8-oxoguanine damage, DNA fragmentation upon natural decay and fossilisation, breakages from artificial enzymatic cleavage and ultrasound sonication. Our results indicate that the structural effects on DNA damageability at G4 sites are not a simple combination of shielding (G4 strand) and de-shielding (opposite strand) against damaging factors, and the outcomes have different patterns and variation from one damage type to another, highly dependent on the G4 strength and relative strand localisation. The results are accompanied by electronic structure calculations, detailed structural parallels and considerations.

Graphical Abstract. An illustration of the considered damage factors acting on G-quadruplex sites, through strand-specific (two pointing thunder signs) and strand-invariant (a single pointing thunder sign) manner.

O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=151 SRC="FIGDIR/small/471014v1_ufig1.gif" ALT="Figure 1">
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category: genomics


title: Epiphany: predicting Hi-C contact maps from 1D epigenomic signals

abstract: Recent deep learning models that predict the Hi-C contact map from DNA sequence achieve promising accuracy but cannot generalize to new cell types and indeed do not capture cell-type-specific differences among training cell types. We propose Epiphany, a neural network to predict cell-type-specific Hi-C contact maps from five epigenomic tracks that are already available in hundreds of cell types and tissues: DNase I hypersensitive sites and ChIP-seq for CTCF, H3K27ac, H3K27me3, and H3K4me3. Epiphany uses 1D convolutional layers to learn local representations from the input tracks, a bidirectional long short-term memory (Bi-LSTM) layers to capture long term dependencies along the epigenome, as well as a generative adversarial network (GAN) architecture to encourage contact map realism. To improve the usability of predicted contact matrices, we trained and evaluated models using multiple normalization and matrix balancing techniques including KR, ICE, and HiC-DC+ Z-score and observed-over-expected count ratio. Epiphany is trained with a combination of MSE and adversarial (i.a., a GAN) loss to enhance its ability to produce realistic Hi-C contact maps for downstream analysis. Epiphany shows robust performance and generalization to held-out chromosomes within and across cell types and species, and its predicted contact matrices yield accurate TAD and significant interaction calls. At inference time, Epiphany can be used to study the contribution of specific epigenomic peaks to 3D architecture and to predict the structural changes caused by perturbations of epigenomic signals.


title: Long term analysis of social structure: evidence of age-based consistent associations in Alpine ibex

abstract: Despite its recognized importance for understanding the evolution of animal sociality as well as for conservation, long term analysis of social networks of animal populations is still relatively uncommon. We investigated social network dynamics in males of a gregarious mountain ungulate (Alpine ibex, Capra ibex) over ten years focusing on groups, sub-groups and individuals, exploring the dynamics of sociality over different scales. Despite the social structure changing between seasons, the Alpine ibex population was highly cohesive: fission-fusion dynamics lead almost every male in the population to associate with each other male at least once. Nevertheless, we found that male Alpine ibex showed preferential associations that were maintained across seasons and years. Age seemed to be the most important factor driving preferential associations while other characteristics, such as social status, appeared less crucial. We also found that centrality measures were influenced by age and were also related to individual physical condition. The multi-scale and long-term frame of our study helped us show that ecological constrains, such as resource availability, may play a role in shaping associations in a gregarious species, but they cannot solely explain sociality and preferential association that are likely also to be driven by life-history linked physiological and social needs. Our results highlight the importance of long-term studies based on individually recognizable subjects to help us build on our understanding of the evolution of animal sociality.

category: animal behavior and cognition


title: Long term analysis of social structure: evidence of age-based consistent associations in male Alpine ibex


title: Fractal scaling of C. elegans behavior is shaped by insulin signaling

abstract: Fractal scaling governs the complex behavior of various animal species and, in humans, can be altered by neurodegenerative diseases and aging1. However, the mechanism underlying fractal scaling remains unknown. Here, we videorecorded C. elegans that had been cultured in a microfluidic device for 3 days and analyzed temporal patterns of C. elegans actions by fractal analyses. The residence-time distribution of C. elegans shared a common feature with those of human and mice2-4. Specifically, the residence-time power-law distribution of the active state changed to an exponential-like decline at a longer time scale, whereas this change did not occur in the inactive state. The exponential-like decline disappeared in starved C. elegans but was restored by culturing animals with glucose. The exponential-like decline similarly disappeared in insulin-signaling daf-2 and daf-16 mutants. Therefore, we conclude that insulin signaling regulates fractal scaling of C. elegans behavior. Our findings indicate that neurosensory modulation of C. elegans behavior by insulin signaling is achieved by regulation of fractal scaling. In humans, diabetes mellitus is associated with depression, bipolar disorder, and anxiety disorder5, which affect daily behavioral activities. We hypothesize that comorbid behavioral defects in patients with diabetes may be attributed to altered fractal scaling of human behavior.


title: A Substrate-triggered μ-Peroxodiiron(III) Intermediate in the 4-Choro-L-Lysine-Fragmenting Heme-Oxygenase-like Diiron Oxidase (HDO) BesC: Substrate Dissociation from, and C4 Targeting by, the Intermediate

abstract: The enzyme BesC from the {beta}-ethynyl-L-serine biosynthetic pathway in Streptomyces cattleya fragments 4-chloro-L-lysine (produced from L-Lysine by BesD) to ammonia, formaldehyde, and 4-chloro-L-allylglycine and can analogously fragment L-Lys itself. BesC belongs to the emerging family of O2-activating non-heme-diiron enzymes with the "heme-oxygenase-like" protein fold (HDOs). Here we show that binding of L-Lys or an analog triggers capture of O2 by the proteins diiron(II) cofactor to form a blue {micro}-peroxodiiron(III) intermediate analogous to those previously characterized in two other HDOs, the olefin-installing fatty acid decarboxylase, UndA, and the guanidino-N-oxygenase domain of SznF. The [~] 5- and [~] 30-fold faster decay of the intermediate in reactions with 4-thia-L-Lys and (4RS)-chloro-DL-lysine than in the reaction with L-Lys itself, and the primary deuterium kinetic isotope effects (D-KIEs) on decay of the intermediate and production of L-allylglycine in the reaction with 4,4,5,5-[2H]-L-Lys, imply that the peroxide intermediate or a successor complex with which it reversibly interconverts initiates the oxidative fragmentation by abstracting hydrogen from C4. Surprisingly, the sluggish substrate L-Lys can dissociate after triggering the intermediate to form, thereby allowing one of the better substrates to bind and react. Observed linkage between Fe(II) and substrate binding suggests that the triggering event involves a previously documented (in SznF) ordering of the dynamic HDO architecture that contributes one of the iron sites, a hypothesis consistent with the observation that the diiron(III) product cluster produced upon decay of the intermediate spontaneously degrades, as it has been shown to do in all other HDOs studied to date.


title: A Substrate-triggered μ-Peroxodiiron(III) Intermediate in the 4-Chloro-L-Lysine-Fragmenting Heme-Oxygenase-like Diiron Oxidase (HDO) BesC: Substrate Dissociation from, and C4 Targeting by, the Intermediate


title: Dataset-adaptive minimizer order reduces memory usage in k-mer counting

abstract: The rapid, continuous growth of deep sequencing experiments requires development and improvement of many bioinformatics applications for analysis of large sequencing datasets, including k-mer counting and assembly. Several applications reduce RAM usage by binning sequences. Binning is done by employing minimizer schemes, which rely on a specific order of the minimizers. It has been demonstrated that the choice of the order has a major impact on the performance of the applications. Here we introduce a method for tailoring the order to the dataset. Our method repeatedly samples the dataset and modifies the order so as to flatten the k-mer load distribution across minimizers. We integrated our method into Gerbil, a state-of-the-art memory efficient k-mer counter, and were able to reduce its memory footprint by 30% - 50% for large k, with only minor increase in runtime. Our tests also showed that the orders produced by our method produced superior results when transferred across datasets from the same species, with little or no order change. This enables memory reduction with essentially no increase in runtime.


title: ABC Transporters are billion-year-old Maxwell Demons

abstract: ABC transporters are a broad family of biological machines, found in most prokaryotic and eukaryotic cells, performing the crucial import or export of substrates through both plasma and organellar membranes, and maintaining a steady concentration gradient driven by ATP hydrolysis. Building upon the present biophysical and biochemical characterization of ABC transporters, we propose here a model whose solution reveals that these machines are an exact molecular realization of the Maxwell Demon, a century-old abstract device that uses an energy source to drive systems away from thermodynamic equilibrium. In particular, the Maxwell Demon does not perform any direct mechanical work on the system, but simply selects which spontaneous processes to allow and which ones to forbid based on information that it collects and processes. In the molecular model introduced here, the different information-processing steps that characterize Maxwell Demons (measurement, feedback and resetting) are features that emerge from the biochemical and structural properties of ABC transporters, allowing us to develop an explicit bridge between the molecular level description and the higher-level language of information theory.

category: biophysics


title: Tumor Treating Fields Suppression of Ciliogenesis Enhances Temozolomide Toxicity

abstract: Tumor Treating Fields (TTFields) are low intensity, alternating intermediate frequency (200kHz) electrical fields that extend survival of glioblastoma patients receiving maintenance temozolomide (TMZ) chemotherapy. How TTFields exert efficacy on cancer over normal cells, or interact with TMZ is unclear. Primary cilia are microtubule-based organelles triggered by extracellular ligands, mechanical and electrical field stimulation, and are capable of promoting cancer growth and TMZ chemoresistance. We found in both low and high grade patient glioma cell lines that TTFields ablated cilia within 24 hours. Halting TTFields treatment led to recovered frequencies of elongated cilia. Cilia on normal primary astrocytes, neurons, and multiciliated/ependymal cells were less affected by TTFields. The TTFields-mediated loss of glioma cilia was partially rescued by chloroquine pretreatment, suggesting the effect is in part due to autophagy activation. We also observed death of ciliated cells during TTFields by live imaging. Notably, TMZ-induced stimulation of ciliogenesis in both adherent cells and gliomaspheres was blocked by TTFields. Moreover, the inhibitory effects of TTFields and TMZ on tumor cell recurrence correlated with the relative timing of TMZ exposure to TTFields and ARL13B+ cilia. Finally, TTFields disrupted cilia in patient tumors treated ex vivo. Our findings suggest TTFields efficacy may depend on the degree of tumor ciliogenesis and relative timing of TMZ treatment.


title: CV-containing vesicle budding from chloroplast inner envelope membrane is mediated by clathrin but inhibited by GAPC

abstract: Clathrin-mediated vesicular formation and trafficking are highly conserved in eukaryotic cells and are responsible for molecular cargo transport and signal transduction among organelles. It remains largely unknown whether clathrin-coated vesicles can be generated from chloroplasts. CHLOROPLAST VESICULATION (CV)-containing vesicles (CVVs) generate from chloroplasts and mediate chloroplast degradation under abiotic stress. In this study, we showed that CV interacted with the clathrin heavy chain (CHC) and induced vesicle budding from the chloroplast inner envelope membrane. Defects on CHC2 and the dynamin-encoding DRP1A gene affected CVV budding and releasing from chloroplast. CHC2 is also required for CV-induced chloroplast degradation and hypersensitivity to water stress. Moreover, GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE (GAPC) interacts with CV and impairs the CV-CHC2 interaction. GAPC1 overexpression inhibited CV-mediated chloroplast degradation and hypersensitivity to water stress. CV silencing alleviated the hypersensitivity of gapc1gapc2 plant to water stress. Together, our work revealed a pathway of clathrin-assisted CVV budding from the chloroplast inner envelope membrane, which mediated the stress-induced chloroplast degradation and stress response.


title: A Non-Canonical Function of Arabidopsis ERECTA Proteins in Gibberellin Signaling

abstract:
The Arabidopsis ERECTA family (ERf) of leucine-rich repeat receptor-like kinases (LRR-RLKs), comprising ERECTA (ER), ERECTA-LIKE 1 (ERL1) and ERECTA-LIKE 2 (ERL2), control epidermal patterning, inflorescence architecture, stomata development, and hormonal signaling. Here we show that the er/erl1/erl2 triple mutant exhibits impaired gibberellin (GA) biosynthesis and perception alongside broad transcriptional changes. ERf proteins interact in the nucleus, via kinase domains, with the SWI3B subunit of the SWI/SNF chromatin remodeling complex (CRCs). The er/erl1/erl2 triple mutant exhibits reduced SWI3B protein level and affected nucleosomal chromatin structure. The ER kinase phosphorylates SWI3B in vitro, and the inactivation of all ERf proteins leads to the decreased phosphorylation of SWI3B protein in vivo. Correlation between DELLA overaccumulation and SWI3B proteasomal degradation together with the physical interaction of SWI3B with DELLA proteins explain the lack of RGA accumulation in the GA- and SWI3B-deficient erf mutant plants. Co-localization of ER and SWI3B on GID1 (GIBBERELLIN INSENSITIVE DWARF 1) DELLA target gene promoter regions and abolished SWI3B binding to GID1 promoters in er/erl1/erl2 plants supports the conclusion that ERf-SWI/SNF CRC interaction is important for transcriptional control of GA receptors. Thus, the involvement of ERf proteins in transcriptional control of gene expression, and observed similar features for human HER2 (Epidermal Growth Family Receptor-member), indicate an exciting target for further studies of evolutionarily conserved non-canonical functions of eukaryotic membrane receptors.

ONE SENTENCE SUMMARYERECTA leucine-rich receptor-like kinase and SWI3B subunit of SWI/SNF chromatin remodeling complex cooperate in direct transcriptional control of GID1 genes in Arabidopsis.


title: In vitro neurons learn and exhibit sentience when embodied in a simulated game-world

abstract: Integrating neurons into digital systems to leverage their innate intelligence may enable performance infeasible with silicon alone, along with providing insight into the cellular origin of intelligence. We developed DishBrain, a system which exhibits natural intelligence by harnessing the inherent adaptive computation of neurons in a structured environment. In vitro neural networks from human or rodent origins, are integrated with in silico computing via high-density multielectrode array. Through electrophysiological stimulation and recording, cultures were embedded in a simulated game-world, mimicking the arcade game  Pong. Applying a previously untestable theory of active inference via the Free Energy Principle, we found that learning was apparent within five minutes of real-time gameplay, not observed in control conditions. Further experiments demonstrate the importance of closed-loop structured feedback in eliciting learning over time. Cultures display the ability to self-organise in a goal-directed manner in response to sparse sensory information about the consequences of their actions.

category: synthetic biology


title: NRF2-dependent epigenetic regulation can promote the hybrid epithelial/mesenchymal phenotype

abstract: The epithelial-mesenchymal transition (EMT) is a cellular process critical for wound healing, cancer metastasis and embryonic development. Recent efforts have identified the role of hybrid epithelial/mesenchymal states, having both epithelial and mesehncymal traits, in enabling cancer metastasis and resistance to various therapies. Also, previous work has suggested that NRF2 can act as phenotypic stability factor to help stablize such hybrid states. Here, we incorporate a phenomenological epigenetic feedback effect into our previous computational model for EMT signaling. We show that this type of feedback can stabilize the hybrid state as compared to the fully mesenchymal phenotype if NRF2 can influence SNAIL at an epigenetic level, as this link makes transitions out of hybrid state more difficult. However, epigenetic regulation on other NRF2-related links do not significantly change the EMT dynamics. Finally, we considered possible cell division effects in our epigenetic regulation model, and our results indicate that the degree of epigenetic inheritance does not appear to be a critical factor for the hybrid E/M state stabilizing behavior of NRF2.


title: Universality and non-universality of the growth law

abstract: An approximately linear relationship between the fraction of ribosomal proteins in the proteome ({phi}R) and the growth rate () holds in proliferating cells when the nutrient quality changes, often referred to as a growth law. While a simple model assuming a constant translation speed of ribosomes without protein degradation can rationalize this growth law, real protein synthesis processes are more complex. This work proposes a general theoretical framework of protein synthesis, taking account of heterogeneous translation speeds among proteins and finite protein degradation. We introduce ribosome allocations as the fraction of active ribosomes producing certain proteins, with two correlation coefficients respectively quantifying the correlation between translation speeds and ribosome allocations, and between protein degradation rates and mass fractions. We prove that the growth law curve generally follows{phi} R = ( + c1)/(c2 + c3) where c1, c2, and c3 are constants depending on the above correlation coefficients and the translation speed of ribosomal proteins. Our theoretical predictions of{phi} R agree with existing data of Saccharomyces cerevisiae. We demonstrate that when different environments share similar correlation coefficients, the growth law curve is universal and up-bent relative to a linear line in slow-growth conditions, which appears valid for Escherichia coli. However, the growth law curve is non-universal and environmental-specific when the environments have significantly different correlation coefficients. Our theories allow us to estimate the translation speeds of ribosomal and non-ribosomal proteins based on the experimental growth law curves.


title: Pupillary dynamics of optimal effort

abstract: While a substantial body of work has shown that cognitive effort is aversive and costly, a separate line of research on intrinsic motivation suggests that people spontaneously seek challenging tasks. According to one prominent account of intrinsic motivation, the Learning Progress Motivation theory, the preference for difficult tasks reflects the dynamic range that these tasks yield for changes in task performance (Oudeyer, Kaplan & Hafner, 2007). Here we test this hypothesis, by asking whether greater engagement with intermediately difficult tasks, indexed by subjective ratings and objective pupil measurements, is a function of trial-wise changes in performance. In a novel paradigm, we determined each individuals capacity for task performance and used difficulty levels that are too low, intermediately challenging or high for that individual. We demonstrated that challenging tasks resulted in greater liking and engagement scores compared with easy tasks. Pupil size tracked objective task difficulty, where challenging tasks were associated with greater pupil responses than easy tasks. Most importantly, pupil responses were predicted by trial-to-trial changes in average accuracy as well as learning progress (derivative of average accuracy), while greater pupil responses also predicted greater subjective engagement scores. Together, these results substantiate the Learning Progress Motivation hypothesis stating that the link between task engagement and cognitive effort is mediated the dynamic range for changes in task performance.


title: Learning progress mediates the link between cognitive effort and task engagement


title: Sensory-thresholded switch of neural firing states in a computational model of the ventromedial hypothalamus

abstract: The mouse ventromedial hypothalamus (VMH) is both necessary and sufficient for defensive responses to predator and social threats. Defensive behaviors typically involve cautious approach toward potentially threatening stimuli aimed at obtaining information about the risk involved, followed by sudden avoidance and flight behavior to escape harm. In vivo neural recording studies in mice have identified two major populations of VMH neurons that either increase their firing activity as the animal approaches the threat (called Assessment+ cells) or increase their activity as the animal flees the threat (called Flight+ cells). Interestingly, Assessment+ and Flight+ cells abruptly decrease and increase their firing activity, respectively, at the decision point for flight, creating an escape-related "switch" in functional state. This suggests that the activity of the two cell types in VMH is coordinated and could result from local circuit interactions. Here, we used computational modelling to test if a local inhibitory feedback circuit could give rise to key features of the neural activity seen in VMH during the approach-to-flight transition. Starting from a simple dual-population inhibitory feedback circuit receiving repeated trains of monotonically increasing sensory input to mimic approach to threat, we tested the requirement for balanced sensory input, balanced feedback, short-term synaptic plasticity, rebound excitation, and inhibitory feedback exclusivity to reproduce an abrupt, sensory-thresholded reciprocal firing change that resembles Assessment+ and Flight+ cell activity seen in vivo. Our work demonstrates that a relatively simple local circuit architecture is sufficient for the emergence of firing patterns similar to those seen in vivo and suggests that a reiterative process of experimental and computational work may be a fruitful avenue for better understanding the functional organization of mammalian instinctive behaviors at the circuit level.


title: Spectral distribution dynamics across different attentional priority states

abstract: Anticipatory covert spatial attention improves performance on tests of visual detection and discrimination, and shifts are accompanied by decreases and increases of alpha-band power at EEG electrodes corresponding to the attended and unattended location, respectively. Although the increase at the unattended location is often interpreted as an active mechanism (e.g., inhibiting processing at the unattended location), most experiments cannot rule out the alternative possibility that it is a secondary consequence of selection elsewhere. To adjudicate between these accounts, we designed a Posner-style cuing task in which male and female human participants made orientation judgments of targets appearing at one of four locations: up, down, right, or left. Critically, trials were blocked such that within a block the locations along one meridian alternated in status between attended and unattended, and targets never appeared at the other two, making them irrelevant. Analyses of the concurrently measured EEG signal were carried out on traditional narrowband alpha (8-14 Hz), as well as on two components resulting from the decomposition of this signal: periodic alpha; and the slope of the aperiodic 1/f-like component. Although data from right-left blocks replicated the familiar pattern of lateralized asymmetry in narrowband alpha power, with neither alpha signal could we find evidence for any difference in the time course at unattended versus irrelevant locations, an outcome consistent with the secondary-consequence interpretation of attention-related dynamics in the alpha band. Additionally, 1/f slope was lower at attended and unattended locations, relative to irrelevant, suggesting a tonic adjustment of physiological state.


title: Phage resistance accompanies reduced fitness of uropathogenic E. coli in the urinary environment

abstract:
Urinary tract infections (UTIs) are among the most common infections treated worldwide each year and are primarily caused by uropathogenic E. coli (UPEC). Rising rates of antibiotic resistance among uropathogens have spurred consideration of alternative strategies such as bacteriophage (phage) therapy; however, phage-bacterial interactions within the urinary environment are poorly defined. Here, we assess the activity of two phages, HP3 and ES17, against clinical UPEC isolates using in vitro and in vivo models of UTI. In both bacteriologic medium and pooled human urine, we identified phage resistance arising within the first 6-8 hours of coincubation. Whole genome sequencing revealed that UPEC resistant to HP3 and ES17 harbored mutations in genes involved in lipopolysaccharide (LPS) biosynthesis. These mutations coincided with several in vitro phenotypes, including alterations to adherence to and invasion of human bladder epithelial HTB-9 cells, and increased biofilm formation. Interestingly, these phage-resistant UPEC demonstrated reduced growth in pooled human urine, which could be partially rescued by nutrient supplementation, and were more sensitive to several outer membrane targeting antibiotics than parental strains. Additionally, these phage-resistant UPEC were attenuated in a murine UTI model. In total, our findings suggest that while resistance to phages, such as LPS-targeted HP3 and ES17, may readily arise in the urinary environment, phage resistance is accompanied by fitness costs rendering UPEC more susceptible to host immunity or antibiotics.

IMPORTANCEUTIs are one of the most common causes of outpatient antibiotic use, and rising antibiotic resistance threatens the ability to control these infections unless alternative treatments are developed. Bacteriophage (phage) therapy is gaining renewed interest, however, much like antibiotics, bacteria can readily become resistant to phage. For successful UTI treatment, we must predict how bacteria will evade killing by phage and identify the downstream consequences of phage-resistant bacterial infections. In our current study, we found that while phage-resistant mutant bacteria quickly emerged, these mutations left bacteria less capable of growing in human urine and colonizing the murine bladder. These results suggest that phage therapy poses a viable UTI treatment if phage resistance confers fitness costs for the uropathogen. These results have implications for developing cocktails of phage with multiple different bacterial targets, each of which is only evaded at the cost of bacterial fitness.


title: Nucleophagy contributes to genome stability though TOP2cc and nucleolar components degradation

abstract: The nuclear architecture of mammalian cells can be altered as a consequence of anomalous accumulation of nuclear proteins or genomic alterations. Most of the knowledge about nuclear dynamics comes from studies on cancerous cells. How normal, healthy cells maintain genome stability avoiding accumulation of nuclear damaged material is less understood. Here we describe that primary mouse embryonic fibroblasts develop a basal level of nuclear buds and micronuclei, which increase after Etoposide-induced DNA Double-Stranded Breaks. These nuclear buds and micronuclei co-localize with autophagic proteins BECN1 and LC3 and with acidic vesicles, suggesting their clearance by nucleophagy. Some of the nuclear alterations also contain autophagic proteins and Type II DNA Topoisomerases (TOP2A and TOP2B), or nucleolar protein Fibrillarin, implying they are also targets of nucleophagy. We propose that a basal nucleophagy contributes to genome and nuclear stability and also in response to DNA damage and nucleolar stress.


title: Neighbor-specific gene expression revealed from physically interacting cells during mouse embryonic development

abstract: Cells continuously communicate with the neighboring cells during development. Direct interaction of different cell types can induce molecular signals dictating lineage specification and cell fate decisions. The current single cell RNAseq (scRNAseq) technology cannot study cell contact dependent gene expression due to the loss of spatial information. To overcome this issue and determine cell contact specific gene expression during embryogenesis, we performed RNA sequencing of physically interacting cells (PICseq) and assessed alongside our single cell transcriptomes (scRNAseq) derived from developing mouse embryos between embryonic day (E) 7.5 and E9.5. Analysis of PICseq data identifies an interesting suite of gene expression signatures depending on neighboring cell types. For instance, neural progenitor (NP) cells expressed Nkx2-1 when interacting with definitive endoderm (DE) and DE cells expressed Gsc when interacting with NP. Based on the identified cell contact specific genes, we devised a means to predict the neighboring cell types from individual cell transcriptome. We further developed spatial-tSNE to show the pseudo-spatial distribution of cells in a 2-dimensional space. In sum, we suggest an approach to study contact specific gene regulation during embryogenesis.


title: Aboveground impacts of a belowground invader: how invasive earthworms alter aboveground arthropod communities in a northern North American forest

abstract: Declining arthropod communities have recently gained a lot of attention with climate and land-use change among the most-frequently discussed drivers. Here, we focus on a seemingly underrepresented driver of arthropod-community decline: biological invasions. For [~]12,000 years, earthworms have been absent from wide parts of northern North America, but they have been re-introduced with dramatic consequences. Most studies investigating earthworm-invasion impacts focus on the belowground world, resulting in limited knowledge on aboveground-community changes. We present observational data on earthworm, plant, and aboveground-arthropod communities in 60 plots, distributed across areas with increasing invasion status (low, medium, high) in a Canadian forest. We analyzed how earthworm-invasion status and biomass impact aboveground arthropod community abundance, biomass, and species richness, and how earthworm impacts cascade across trophic levels. We sampled [~]13,000 arthropods, dominated by Hemiptera, Diptera, Araneae, Thysanoptera, and Hymenoptera. Total arthropod abundance, biomass, and species richness declined significantly from areas of low to those with high invasion status with reductions of 61, 27, and 18%, respectively. Structural Equation Models unraveled that earthworms directly and indirectly impact arthropods across trophic levels. We show that earthworm invasion can alter aboveground multitrophic arthropod communities and suggest that belowground invasions can be important drivers of aboveground-arthropod decline.

category: ecology


title: Looking from the top: enhanced top-down sensorimotor processing in somatic anxiety

abstract: Functional neuroimaging research on anxiety has traditionally focused on brain networks associated with the psychological aspects of anxiety. In this study, instead, we target the somatic aspects of anxiety. Motivated by the growing appreciation that top-down cortical processing plays a crucial role in perception and action, we characterize effective connectivity among hierarchically organized sensorimotor regions and its association with (trait) anxiety. We selected 164 participants from the Human Connectome Project based on psychometric measures. We used their resting-state functional MRI data and Dynamic Causal Modeling (DCM) to assess effective connectivity within and between key regions in the exteroceptive, interoceptive, and motor hierarchy. Using hierarchical modeling of between-subject effects in DCM with Parametric Empirical Bayes we first established the architecture of effective connectivity in sensorimotor networks and then tested for an association with fear somatic arousal (FSA) and fear affect (FA) scores. To estimate the out of sample effect sizes, we implemented a leave-one-out cross validation analysis. At the group level, the top-down connections to exteroceptive cortices were inhibitory in nature whereas in interoceptive and motor cortices they were excitatory. With increasing FSA scores, the pattern of top-down effective connectivity was enhanced in all three networks: an observation that corroborates well with anxiety phenomenology. The effect sizes of anxiety associated changes in effective connectivity were sufficiently large to predict whether a new participant has mild or severe somatic anxiety. Interestingly, the enhancement in top-down processing in sensorimotor cortices were associated with FSA but not FA scores, thus establishing the (relative) dissociation between somatic and cognitive dimensions of anxiety. Overall, enhanced top-down effective connectivity in sensorimotor cortices emerges as a promising and quantifiable candidate marker of trait somatic anxiety. These results pave the way for a novel and quantitative approach to the neural underpinnings of anxiety, which speak to anxiety as an embodied phenomenon and the importance of top-down cortical processing.


title: Identification of Six Thiolases and their Effects on Fatty Acid and Ergosterol Biosynthesis in Aspergillus oryzae

abstract:
Thiolase plays important roles in lipid metabolism. It can be divided into degradative thiolases (Thioase I) and biosynthetic thiolases (thiolases II), which are involved in fatty acid {beta}-oxidation and acetoacetyl-CoA biosynthesis, respectively. The Saccharomyces cerevisiae (S. cerevisiae) genome harbors only one gene each for thioase I and thiolase II, namely, Pot1 and Erg10, respectively. In this study, six thiolases (named AoErg10A-AoErg10F) were identified in Aspergillus oryzae (A. oryzae) genome using bioinformatics analysis. Quantitative reverse transcription-PCR (qRT-PCR) indicated that the expression of these six thiolases varied at different growth stages and under different forms of abiotic stress. Subcellular localization analysis showed that AoErg10A was located in the cytoplasm, AoErg10B and AoErg10C in the mitochondria, and AoErg10D-AoErg10F in the peroxisome. Yeast heterologous complementation assays revealed that AoErg10A, AoErg10D, AoErg10E, AoErg10F and cytoplasmic AoErg10B (AoErg10B{Delta}MTS) recovered the phenotypes of S. cerevisiae erg10 weak and lethal mutants, and that only AoErg10D-F recovered the phenotype of the pot1 mutant that cannot use oleic acid as the carbon source. Overexpression of AoErg10s either affected the growth speed or sporulation of the transgenic strains. In addition, the fatty acid and ergosterol content changed in all the AoErg10-overexpressing strains. This study revealed the function of six thiolases in A. oryzae and their effect on growth, and fatty acid and ergosterol biosynthesis, which may lay the foundation for genetic engineering for lipid metabolism in A. oryzae or other fungi.

ImportanceThiolase including thioase I and thiolase II, plays important roles in lipid metabolism. A. oryzae, one of the most industrially important filamentous fungi, has been widely used for manufacturing oriental fermented food such as sauce, miso, and sake for a long time. Besides, A. oryzae has a high capability in production of high lipid content and has been used for lipid production. Thus, it is very important to investiagte the function of thiolases in A. oryzae. In this study, six thiolase (named AoErg10A-AoErg10F) were identified by bioinformatics analysis. Unlike other reported thiolases in fungi, three of the six thiolases showed dual function of thioase I and thiolase II in S. cerevisiae, indicating the lipid metabolism is more complex in A. oryzae. The reveal of founction of these thiolases in A. oryzae can lay the foundation for genetic engineering for lipid metabolism in A. oryzae or other fungi.


title: Delta variant with P681R critical mutation revealed by ultra-large atomic-scale ab initio simulation: Implications for the fundamentals of biomolecular interactions

abstract: SARS-CoV-2 Delta variant is emerging as a globally dominant strain. Its rapid spread and high infection rate are attributed to a mutation in the spike protein of SARS-CoV-2 allowing the virus to invade human cells much faster and with increased efficiency. Particularly, an especially dangerous mutation P681R close to the furin cleavage site has been identified as responsible for increasing the infection rate. Together with the earlier reported mutation D614G in the same domain, it offers an excellent instance to investigate the nature of mutations and how they affect the interatomic interactions in the spike protein. Here, using ultra large-scale ab initio computational modeling, we study the P681R and D614G mutations in the SD2-FP domain including the effect of double mutation and compare the results with the wild type. We have recently developed a method of calculating the amino acid-amino acid bond pairs (AABP) to quantitatively characterize the details of the interatomic interactions, enabling us to explain the nature of mutation at the atomic resolution. Our most significant find is that the mutations reduce the AABP value, implying a reduced bonding cohesion between interacting residues and increasing the flexibility of these amino acids to cause the damage. The possibility of using this unique mutation quantifiers in a machine learning protocol could lead to the prediction of emerging mutations.

category: biochemistry