title: Effect of Positive Allosteric Modulation and Orthosteric Agonism of Dopamine D2 Receptors on Respiration in Mouse Models of Rett Syndrome

abstract: Rett syndrome (RTT) is an autism spectrum disorder caused by loss-of-function mutations in the methyl-CPG-binding protein 2 (Mecp2) gene. Frequent apneas and irregular breathing are prevalent in RTT, and also occur in rodent models of the disorder, including Mecp2Bird and Mecp2R168X mice. Sarizotan, a serotonin 5-HT1a and dopamine D2-like receptor agonist, reduces the incidence of apneas and irregular breathing in mouse models of RTT (Abdala et al., 2014). Targeting the 5HT1a receptor alone also improves respiration in RTT mice (Levitt et al., 2013). However, the contribution of D2 receptors in correcting these respiratory disturbances remains untested. PAOPA, a dopamine D2 receptor positive allosteric modulator, and quinpirole, a dopamine D2 receptor orthosteric agonist, were used in conjunction with whole-body plethysmography to evaluate whether activation of D2 receptors is sufficient to improve breathing disturbances in female heterozygous Mecp2Bird/+ and Mecp2R168X/+ mice. PAOPA did not significantly change apnea incidence or irregularity score in RTT mice. PAOPA also had no effect on the ventilatory response to hypercapnia (7% CO2). In contrast, quinpirole reduced apnea incidence and irregularity scores and improved the hypercapnic ventilatory response in Mecp2R168X/+ and Mecp2Bird/+ mice, while also reducing respiratory rate. These results suggest that D2 receptors do contribute to the positive effects of sarizotan in the correction of respiratory abnormalities in Rett syndrome. However, positive allosteric modulation of the D2 receptor alone is not sufficient to evoke these effects.


title: Melanocortin receptor agonist melanotan-II microinjected in the nucleus accumbens decreases appetitive and consumptive responding for food

abstract:
Rationale. Obesity is a major health problem worldwide. An understanding of the factors that drive feeding behaviors is key to the development of pharmaceuticals to decrease appetite and consumption. Proopiomelanocortin (POMC), the melanocortin peptide precursor, is essential in the regulation of body weight and ingestive behaviors. Deletion of POMC or impairment of melanocortin signaling in the brain results in hyperphagic obesity. Neurons in the hypothalamic arcuate nucleus produce POMC and project to many areas including the nucleus accumbens (NAcc), which is well established in the rewarding and reinforcing effects of both food and drugs of abuse.

ObjectiveThese studies sought to determine the role of melanocortins in the NAcc on consumption of and motivation to obtain access to standard rodent chow.

MethodsMale, C57BL/6J mice were microinjected bilaterally into the NAcc (100 nl/side) with the melanocortin receptor 3/4 agonist melanotan-II (MT-II; 0.1, 0.3, and 1 nmol), and ingestive behaviors were examined in both home cage and operant food self-administration experiments. In addition, the ability of MT-II in the NAcc to produce aversive properties or affect metabolic rate were tested.

ResultsMT-II injected into the NAcc significantly decreased consumption in both home cage and operant paradigms, and furthermore decreased appetitive responding to gain access to food. There was no development of conditioned taste avoidance or change in metabolic parameters following anorexic doses of MT-II. Conclusions. MT-II in the NAcc decreased both the motivation to eat and the amount of food consumed without inducing an aversive state or affecting metabolic rate, suggesting a role for melanocortin signaling in the ventral striatum that is selective for appetite and satiety without affecting metabolism or producing an aversive state.

category: neuroscience


title: Cis mutagenesis in vivo reveals extensive noncanonical functions of Dscam1 isoforms in neuronal wiring

abstract: Drosophila Dscam1 encodes ten thousand of cell recognition molecules via alternative splicing, which is required for nervous function. However, the underlying mechanism has not fully understood. Here we revealed extensive noncanonical functions of Dscam1 isoform diversity in neuronal wiring. We generated a series of allelic cis mutations in Dscam1, encoding normal number of isoforms albeit with altered isoform composition. Despite normal dendritic self-avoidance and self/non-self discrimination in da neurons, which is consistent with canonical self-avoidance model, these mutants exhibited strikingly distinct spectra of phenotypic defects in three classes of neurons: up to [~]60% defects in mushroom bodies, a significantly increased branching and growth in da neurons, and mild axonal branching defects in mechanosensory neurons. These data suggest that proper Dscam1 isoform composition is required for axon and dendrite growth in diverse neurons. This unprecedented splicing-tuned regulation unlocks new insights into the molecular mechanisms that Dscam1 isoform diversity is engaged in.


title: Synaptic wiring motifs in posterior parietal cortex support decision-making

abstract: The posterior parietal cortex (PPC) exhibits choice-selective activity during perceptual decision-making tasks. However, it is not known how this selective activity arises from the underlying synaptic connectivity. Here, we combined virtual reality behavior, two-photon calcium imaging, high throughput electron microscopy, and circuit modeling to analyze how synaptic connectivity between neurons in PPC relates to their selective activity. We found that excitatory pyramidal neurons preferentially target inhibitory interneurons with the same selectivity. In turn, inhibitory interneurons preferentially target pyramidal neurons with opposite selectivity, forming an opponent inhibition motif. Using circuit models, we show that opponent inhibition amplifies selective inputs and induces competition between neural populations with opposite selectivity, thereby improving the encoding of trial-type information. These results provide evidence for how synaptic connectivity in cortical circuits supports a learned decision-making task.


title: Self-avoidance alone does not explain the function of Dscam1 in mushroom body axonal wiring

abstract: Alternative splicing of Drosophila Dscam1 into 38,016 isoforms provides neurons with a unique molecular code for self-recognition and self-avoidance. A canonical model suggests that homophilic binding of identical Dscam1 isoforms on sister branches of mushroom body (MB) axons supports segregation with high fidelity, even when only a single isoform is expressed. Here we generated a series of mutant flies with a single exon 4, 6, or 9 variant, encoding 1,584, 396, or 576 potential isoforms, respectively. Surprisingly, most of the mutants in the latter two groups exhibited obvious defects in the growth, branching, and segregation of MB axonal sister branches. This demonstrates that repertoires of 396 and 576 Dscam1 isoforms were not sufficient for normal patterning of axonal branches. Moreover, reducing Dscam1 levels largely reversed the defects caused by reduced isoform diversity, suggesting a functional link between Dscam1 expression levels and isoform diversity. Taken together, these results indicate that canonical self-avoidance alone does not explain the function of Dscam1 in MB axonal wiring.


title: Lateral Orbitofrontal Cortex and Basolateral Amygdala Regulate Sensitivity to Delayed Punishment during Decision-making

abstract:
In real-world decision-making scenarios, negative consequences do not always occur immediately after a choice. This delay between action and outcome drives the underestimation, or "delay discounting", of punishment. While the neural substrates underlying sensitivity to immediate punishment have been well-studied, there has been minimal investigation of delayed consequences. Here, we assessed the role of lateral orbitofrontal cortex (LOFC) and basolateral amygdala (BLA), two regions implicated in cost/benefit decision-making, in sensitivity to delayed vs immediate punishment. The delayed punishment decision-making task (DPDT) was used to measure delay discounting of punishment in rodents. During DPDT, rats choose between a small, single pellet reward and a large, three pellet reward accompanied by a mild foot shock. As the task progresses, the shock is preceded by a delay that systematically increases or decreases throughout the session. We observed that rats avoid choices associated with immediate punishment, then shift preference toward these options when the punishment is delayed. LOFC inactivation did not influence choice of rewards with immediate punishment, but decreased choice of delayed punishment. We also found that BLA inactivation reduced choice of delayed punishment, but this was only evident when punishment was initially delivered immediately after a choice, then preceded by a delay as the task progressed. Therefore, both LOFC and BLA contribute to the delay discounting of punishment, and may serve as promising therapeutic targets to improve sensitivity to delayed punishment during decision-making.

Significance StatementNegative consequences occurring after a delay are often underestimated, which can lead to maladaptive decision-making. While sensitivity to immediate punishment during reward-seeking has been well-studied, the neural substrates underlying sensitivity to delayed punishment remain unclear. Here, we used the Delayed Punishment Decision-making Task to determine that lateral orbitofrontal cortex and basolateral amygdala both regulate the discounting of delayed punishment, suggesting that these regions may be potential targets to improve decision-making in psychopathology.


title: Schizophrenia-derived hiPSC brain microvascular endothelial cells show impairments in angiogenesis and blood-brain barrier function

abstract:
Schizophrenia (SZ) is a complex neuropsychiatric disorder, affecting 1% of the world population. Long-standing clinical observations and molecular data have pointed out a possible vascular deficiency that could be acting synergistically with neuronal dysfunction in SZ.

As SZ is a neurodevelopmental disease, the use of human induced pluripotent stem cells (hiPSC) allows disease biology modeling retaining the patients unique genetic signature. Previously, we reported a VEGF-A signaling impairment in SZ-hiPSC derived neural lineages leading to a decreased angiogenesis. Here, we present a functional characterization of SZ-derived brain microvascular endothelial-like cells (BEC), the counterpart of the neurovascular crosstalk, revealing an intrinsically defective Blood-Brain Barrier (BBB) phenotype. Transcriptomic assessment of genes related to endothelial function among three control (Ctrl BEC) and five schizophrenia patients derived BEC (SZP BEC), revealed that SZP BEC have a distinctive expression pattern of angiogenic and BBB-associated genes. Functionally, SZP BEC showed a decreased angiogenic response in vitro and higher transpermeability than Ctrl BEC. Immunofluorescence staining revealed less expression and altered distribution of tight junction proteins in SZP BEC. Moreover, SZP BECs secretome reduced barrier capacities in the brain microvascular endothelial cell line HCMEC/D3 and in an in vivo permeability assay in mice. Overall, our results describe an intrinsic failure of SZP BEC for proper barrier function. These findings are consistent with the hypothesis that traces schizophrenia origins to brain development and BBB dysfunction.

category: cell biology


title: Murine blastocysts generated by in vitro fertilization show increased Warburg metabolism and altered lactate production

abstract:
In vitro fertilization (IVF) has resulted in the birth of over 8 million children. Although most of IVF-conceived children are healthy, several studies suggest an increased risk of altered growth rate, cardiovascular dysfunction, and glucose intolerance in this population compared to naturally conceived children. However, a clear understanding of how embryonic metabolism is affected by culture condition and how embryos reprogram their metabolism is unknown.

Here, we studied oxidative stress and metabolic alteration in blastocysts conceived by natural mating or by IVF and culture in physiologic (5%) or atmospheric (20%) oxygen. We found that IVF-generated blastocyst manifest increased reactive oxygen species, oxidative damage to DNA/lipid/proteins, and reduction in glutathione. Metabolic analysis revealed IVF-generated blastocysts display decreased mitochondria respiration and increased glycolytic activity suggestive of enhanced Warburg metabolism. These findings were corroborated by altered intracellular and extracellular pH and increased intracellular lactate levels in IVF-generated embryos. Comprehensive proteomic analysis and targeted immunofluorescence showed reduction of LDH-B and MCT1, enzymes involved in lactate metabolism. Importantly, these enzymes remained downregulated in tissues of adult IVF-conceived mice, suggesting that metabolic alterations in IVF-generated embryos may result in alteration in lactate metabolism. These findings suggest that alterations in lactate metabolism is a likely mechanism involved in genomic reprogramming and could be involved in the developmental origin of health and disease.

category: developmental biology


title: Evolution and co-evolution of the suck behaviour, a postcopulatory female resistance trait that manipulates received ejaculate

abstract: Sexual conflicts over the post-mating fate of received ejaculate can favour traits in one sex that are costly to the other. Reciprocally mating hermaphrodites face unique challenges as they mate simultaneously in both the male and female role, potentially leading to receipt of unwanted ejaculate. Reciprocal mating can then give rise to postcopulatory female resistance traits that allow manipulation of received ejaculate. A putative example is the suck behaviour, observed in the flatworm genus Macrostomum. It involves the sperm recipient placing its pharynx over its own female genital opening and appearing to suck, likely removing received ejaculate after mating. The genus also contains hypodermically-inseminating species that presumably exhibit unilateral mating and have not been observed to suck. Here, we examine the evolution of the suck behaviour in Macrostomum, aiming to document the mating behaviour in 64 species. First, we provide videographic evidence that ejaculate is indeed removed during the suck behaviour in a reciprocally mating species, Macrostomum hamatum. Next, we show evolutionary positive correlations between the presence, duration and frequency of reciprocal mating behaviour and the suck behaviour, providing clear evidence that the suck behaviour co-evolves with reciprocal mating behaviour. Finally, we show an association between reproductive behaviour and reproductive morphology, suggesting that reproductive morphology can be used for inferring the behavioural mating strategy of a species. Together our study demonstrates sexual antagonistic coevolution leading to the evolution of a postcopulatory behavioural trait that functions as a female counter-adaptation allowing individuals to gain control over received ejaculate in a hermaphroditic sexual system.

category: evolutionary biology


title: A structural database of chain-chain and domain-domain interfaces of proteins

abstract: In this study, we have mined the PDB and created a structural library of 178,465 interfaces that mediate protein-protein or domain-domain interactions. Interfaces involving the same CATH fold(s) were clustered together. Our analysis of the entries in the library reveals the similarity between chain-chain and domain-domain interactions. The library also illustrates how a single protein fold can interact with multiple folds using similar interfaces. The library is hence a useful resource to study the types of interactions between protein folds. Analyzing the data in the library reveals various interesting aspects of protein-protein and domain-domain interactions such as how proteins belonging to folds that interact with many other folds also have high EC values. These data could be utilized to seek potential binding partners. It can also be utilized to investigate the different ways in which two or more folds interact with one another structurally. We constructed a statistical potential of pair preferences of amino acids across the interface for chain-chain and domain-domain interactions separately. They are quite similar further lending credence to the notion that domain-domain interfaces could be used to study chain-chain interactions. Lastly and importantly, the library includes predicted small molecule binding sites at the protein-protein interfaces. This has applications as interfaces containing small molecule binding sites can be easily targeted to prevent the interaction and perhaps form a part of a therapeutic strategy.

category: bioinformatics


title: Human blood plasma proteins modeling and binding affinities with Δ9-tetrahydrocannabinol active metabolites: In silico approach

abstract: Tetrahydrocannabinol (THC) is a key psychotropic constituent of cannabis sativa. It is also known as {Delta}9-tetrahydrocannabinol ({Delta}9-THC). Previous study suggested that owing to its high lipophilicity, it piles up in adipose tissue and it is disseminated into blood stream for prolonged time. Research suggests that numerous diseases such as multiple sclerosis, neurodegenerative disorders, epilepsy, schizophrenia, osteoporosis, cancer, glaucoma and cardiovascular disorders can be treated using this substance. However, apart from having therapeutic potential, many studies have reported detrimental outcomes along with addiction of {Delta}9-THC for short-term and long-term consumption. Thus, in this study, we determined the binding affinities of {Delta}9-THC and its two active metabolites, 11-Hydroxy-{Delta}9-tetrahydrocannabinol (11-OH-{Delta}9-THC) and 8beta,11-dihydroxy-{Delta}9-tetrahydrocannabinol (8{beta},11-diOH-{Delta}9-THC) with 401 human blood plasma proteins using molecular docking analysis. Results show that {Delta}9-THC has greater binding potential with plasma proteins as compared to other two metabolites. Overall, ADGRE5, ALB, APOA5, APOD, CP, PON1 and PON3 proteins showed the highest binding affinities with three cannabis metabolites.


title: A hybrid unsupervised approach for accurate short read clustering and barcoded sample demultiplexing in nanopore sequencing

abstract: Short nucleic acid sequences are usually attached as DNA barcodes for multiple sample sequencing and single cell protocols, which enables Oxford Nanopore sequencing to sequence multiple barcoded DNA samples on a single flow cell. However, due to the high base-calling error, short reads in Nanopore sequencing are difficult to be accurately identified by traditional tools. Here, we propose a hybrid unsupervised approach for the accurate clustering of short reads and demultiplexing of barcoded samples in Nanopore sequencing. In our approach, both the nucleic base information translated from base-calling and the raw current signal directly outputted by the flow cell are utilized. A GPU-supported parallelization strategy is proposed to ensure the runtime of our hybrid clustering. Comprehensive experiments demonstrate that our approach outperforms all the traditional unsupervised tools in short read clustering, and achieves comparable accuracy in barcoded sample demultiplexing compared with the learning-based methods.


title: Lossless end-to-end transport of small molecules through micron-length DNA nanochannels

abstract:
Designed and engineered protein and DNA nanopores can sense and characterize single molecules and control transmembrane transport of molecular species. However, designed biomolecular pores are less than 100 nm in length and are used primarily for transport across lipid membranes. Nanochannels that span longer distances could be used as conduits for molecules between non-adjacent compartments or cells. Here, we design microns-long, 7 nm diameter DNA nanochannels that small molecules can traverse according to the laws of continuum diffusion. Binding DNA origami caps to channel ends eliminates transport and demonstrates that molecules diffuse from one channel end to the other rather than permeating through channel walls. These micron-length nanochannels can also grow, form interconnects, and interface with living cells. This work thus shows how to construct multifunctional, dynamic agents that control molecular transport, opening new ways of studying intercellular signaling and modulating molecular transport between synthetic and living cells.

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category: synthetic biology


title: Fast, Efficient, and Accurate Neuro-Imaging Denoising via Deep Learning

abstract: Volumetric functional imaging is widely used for recording neuron activities in vivo, but there exist tradeoffs between the quality of the extracted calcium traces, imaging speed, and laser power. While deep-learning methods have recently been applied to denoise images, their applications to downstream analyses, such as recovering high-SNR calcium traces, have been limited. Further, these methods require temporally-linked pre-registered data with ultrafast rates. Here, we demonstrate supervised deep-denoising methods to circumvent these tradeoffs for several applications, including whole-brain imaging, large field-of-view imaging in freely moving animals, and recovering complex neurite structures in C. elegans. Our framework has 30x smaller memory footprint, and is fast in training and inference (50-70ms); it is highly accurate and generalizable, and further, only small, non-temporally-sequential, independently-acquired training datasets ([~]500 images) are needed. We envision that the framework will enable faster and long-term imaging experiments necessary to study neuronal mechanisms of many behaviors.


title: Similarity-Based Multimodal Regression

abstract: To better understand complex human phenotypes, large-scale studies have increasingly collected multiple data modalities across domains such as imaging, mobile health, and physical activity. The properties of each data type often differ substantially and require either separate analyses or extensive processing to obtain comparable features for a combined analysis. Multimodal data fusion enables certain analyses on matrix-valued and vector-valued data, but it generally cannot integrate modalities of different dimensions and data structures. For a single data modality, multivariate distance matrix regression provides a distance-based framework for regression accommodating a wide range of data types. However, no distancebased method exists to handle multiple complementary types of data. We propose a novel distance-based regression model, which we refer to as Similarity-based Multimodal Regression (SiMMR), that enables simultaneous regression of multiple modalities through their distance profiles. We demonstrate through simulation, imaging studies, and longitudinal mobile health analyses that our proposed method can detect associations in multimodal data of differing properties and dimensionalities, even with modest sample sizes. We perform experiments to evaluate several different test statistics and provide recommendations for applying our method across a broad range of scenarios.


title: Overexpressing eukaryotic elongation factor 1 alpha (eEF1A) proteins to promote corticospinal axon repair after injury

abstract: Although protein synthesis is hypothesized to have a pivotal role in axonal repair after central nervous system (CNS) injury, the role of core components of the protein synthesis machinery has not been examined. Notably, some elongation factors possess non-canonical functions that may further impact axonal repair. Here, we examined whether overexpressing eukaryotic elongation factor 1 alpha (eEF1A) proteins enhances the collateral sprouting of corticospinal tract (CST) neurons after unilateral pyramidotomy, along with the underlying molecular mechanisms. Compared with axonal regeneration from injured neurons, axonal sprouting from uninjured neurons occurs spontaneously after injury and may represent a more accessible form of axonal repair for clinical translation. We found that overexpressing eEF1A1, eEF1A2 or both proteins in CST neurons increased the levels of pS6, an indicator for mTOR activity, in neuronal somas. In contrast, the levels of pSTAT3 and pAKT were not increased. Strikingly, overexpressing eEF1A2 alone, but neither eEF1A1 alone nor both factors simultaneously, increased protein synthesis and actin rearrangement in CST neurons. While eEF1A1 overexpression only slightly enhanced CST sprouting across the midline into the denervated side in the cervical spinal after pyramidotomy, eEF1A2 overexpression substantially enhanced this sprouting. Surprisingly, co-overexpression of both eEF1A1 and eEF1A2 led to a sprouting phenotype similar to wild-type controls, suggesting an antagonistic effect of overexpressing both proteins. These data provide the first evidence that overexpressing a core component of the translation machinery, eEF1A2, enhances CST sprouting, likely by a combination of increased protein synthesis, mTOR signaling and actin cytoskeleton rearrangement.


title: The role of neuropeptides in regulating ecdysis and reproduction in the hemimetabolous insect Rhodnius prolixus

abstract:
In ecdysozoan animals, moulting entails the production of a new exoskeleton and the shedding of the old one during ecdysis. It is induced by a pulse of ecdysone that regulates the expression of different hormonal receptors and activates a peptide-mediated signalling cascade. In Holometabola, the peptidergic cascade regulating ecdysis has been well described. However, very little functional information regarding the neuroendocrine regulation of ecdysis is available for Hemimetabola, which displays an incomplete metamorphosis.

Here, we studied neuropeptides related to ecdysis regulation in the hemi-metabolous insect Rhodnius prolixus. The RNA interference-mediated reduction of ETH expression in fourth instar nymphs resulted in lethality at the expected time of ecdysis, thereby showing its crucial role in this process. Furthermore, the results revealed the involvement of ETH in the regulation of reproductive fitness. Different from holometabolous, the knockdown of ETH in adult females led to failures in egg hatching without affecting the oviposition. Most of the first instar nymphs hatched from the eggs laid by females injected with dsEH, dsCCAP and dsOKA died at the expected time of ecdysis, indicating the crucial involvement of these genes for post-embryonic development. No phenotypes were observed upon CZ knockdown in nymphs or adult females. The conservation of the role of these neuropeptides in regulating ecdysis and reproduction throughout the class Insecta is discussed.

Summary statementThe information provided here is of interest for evolutive studies on the neuroendocrine regulation of ecdysis and reproduction in insects, and the research for new targets to control pest insects.


title: Individual-based quantitative temporal beta-diversity: Novel indices for assessing community compositional shifts accounting for changes in the properties of individuals

abstract:
AimRevealing patterns of temporal biodiversity change is an urgent issue in light of the effects of global climate change. In addition, climate change is known to modify not only biodiversity but also individual life-history. Nevertheless, although the connection between individual physiology and large-scale ecological patterns is a major challenge for the mechanistic understanding of macroecology, large gaps exist between individual life-history and biodiversity. In this context, novel methods can be used to evaluate changes in individual properties and their effects on biodiversity.

InnovationNovel indices that can evaluate compositional shifts across time by explicitly considering the contributions of the life-histories (i.e., growth, mortality, and recruitment) of individuals in a community were successfully developed. By applying subset data of the Forest Inventory and Analysis database for the state of Rhode Island in the USA, changes in the contribution of individual life-histories to biodiversity change were successfully identified.

Main conclusionsThe development of the proposed novel indices not only represents methodological progress in community ecology and macroecology but also a conceptual advance, bridging studies of biodiversity and individual life-history and physiology. The individual-based diversity index opens the door to the possibility of individual-based biodiversity science, which could facilitate understanding the comprehensive effects of climate change across different hierarchies of biological organisation.

category: ecology


title: 3' RNA sequencing does not increase power or reduce costs for gene expression analysis

abstract:
BackgroundSequencing RNA transcripts for gene expression profiling is a popular and important technique with broad utility in biological sciences. We set out to comprehensively compare the two most popular methods for generating sequencing libraries for differential gene expression analysis: 3-end sequencing, which generates libraries from the 3 end of an RNA transcript; and traditional RNA sequencing, which generates libraries from whole RNA transcripts. We include three species in our experiment to test whether our findings replicate across genomes and genome assemblies.

ResultsWe found similar levels of precision and power to detect differentially expressed genes between the two methods. Notably, whole transcript RNA-seq performed better in the non-traditional model species included in our study.

ConclusionOverall, we recommended whole transcript RNA sequencing for the added benefits of alternative splicing detection, and gene-body variant detection.

category: genomics


title: In-cell penetration selection-mass spectrometry produces noncanonical peptides for antisense delivery

abstract: Peptide-mediated delivery of macromolecules in cells has significant potential therapeutic benefits, but no therapy employing cell-penetrating peptides (CPPs) has reached the market after 30 years of investigation due to challenges in the discovery of new, more efficient sequences. We developed a method for in-cell penetration selection-mass spectrometry (in-cell PS-MS) to discover peptides from a synthetic library capable of delivering macromolecule cargo to the cytosol. This method was inspired by recent in vivo selection approaches for cell-surface screening, with an added spatial dimension resulting from subcellular fractionation. A representative peptide discovered in the cytosolic extract, Pep1a, is nearly 100-fold more active toward antisense phosphorodiamidate morpholino oligomer (PMO) delivery compared to a sequence identified from a whole cell extract, which includes endosomes. Pep1a is composed of D-amino acids and two non--amino acids. Pulse-chase and microscopy experiments revealed that while the PMO-Pep1a conjugate is likely taken up by endosomes, it can escape to localize to the nucleus. In-cell PS-MS introduces a means to empirically discover unnatural synthetic peptides for subcellular delivery of therapeutically relevant cargo.

category: bioengineering


title: Classifying enthalpy-neutral DNA strand displacement cascades: trading off desired and undesired signal propagation

abstract:
Artificially designed molecular systems made of DNA can exhibit complex and programmable behaviors. One kind of building block, the enthalpy-neutral DNA strand displacement cascade, propagates signal without gaining or losing overall base pairs. This flexible and programmable component has been used for constructing molecular logic circuits, smart structures and devices, for systems with complex autonomously generated dynamics, and for diagnostics. Limiting their utility, however, these systems are susceptible to the spurious release of output even in the absence of the proper combination of inputs--so-called leak. In addition, the speed of these systems is usually affected by undesired reaction pathways such as reversible unproductive binding (toehold occlusion) or spurious displacement. We systematize the properties of the simplest enthalpy-neutral strand displacement cascades (logically linear topology). We use combinatorial arguments to show that enthalpy-neutral linear cascades can be engineered with stronger thermodynamic guarantees to leak than previously studied systematic ways to reduce leak in non-enthalpy-neutral designs. Depending on a few basic parameters, we develop a taxonomy for the desired and undesired properties and trade-offs between them. Further, we experimentally confirm the theoretical prediction of the properties on different designs. These results provide an effective guide for future designs of molecular systems.

Significance StatementMolecular control circuits embedded within chemical systems to direct molecular events have transformative applications in synthetic biology, medicine, and other fields. However, due to the complexity of molecular interactions, it is challenging to understand and formally reason about the collective functions of components within larger systems. Focusing on systems composed of one type of programmable DNA strand displacement reaction, we develop a formal framework to analyze desired and undesired properties affecting speed and correctness, and experimentally confirm the predictions. The properties are derived from structural design parameters based on combinatorial arguments (counting bonds and separate complexes). This approach, analogous to the rigorous proofs of algorithm correctness in computer science, can guide the future engineering of robust and efficient molecular algorithms.


title: Structural basis of mammalian Complex IV inhibition by steroids

abstract:
The mitochondrial electron transport chain maintains the proton motive force that powers ATP synthesis. The energy for this process comes from oxidation of NADH and succinate, with the electrons from this oxidation passed via intermediate carriers to oxygen. Complex IV (CIV), the terminal oxidase, transfers electrons from the intermediate electron carrier cytochrome c to oxygen, contributing to the proton motive force in the process. Within CIV, protons move through the K- and D-pathways during turnover. The former is responsible for transferring two protons to the enzymes catalytic site upon reduction of the site, where they eventually combine with oxygen and electrons to form water. CIV is the main site for respiratory regulation, and although previous studies showed that steroid-binding can regulate CIV activity little is known about how this regulation occurs. Here we characterize the interaction between CIV and steroids using a combination of kinetic experiments, structure determination, and molecular simulations. We show that molecules with a sterol moiety, such as glyco-diosgenin and cholesteryl hemisuccinate, reversibly inhibit CIV. Flash photolysis experiments probing the high-speed equilibration of electrons within CIV demonstrate that binding of these molecules inhibits proton uptake through the K-pathway. Single particle cryo-EM of CIV with glyco-diosgenin reveals a previously undescribed steroid-binding site adjacent to the K-pathway, and molecular simulations suggest that the steroid binding modulates the conformational dynamics of key residues and proton transfer kinetics within this pathway. The binding pose of the sterol group sheds light on possible structural gating mechanisms in the CIV catalytic cycle.

SIGNIFICANCE STATEMENTMammalian complex IV (CIV), the final complex of the mitochondrial electron transport chain, uses electrons from cytochrome c to reduce oxygen to water, driving aerobic life. Although CIV functions as the main site for respiratory regulation, there is little structural or biochemical information on how this regulation occurs. Previous studies provided evidence of CIV regulation by steroids, but the steroid binding site and regulatory mechanism remain unclear. Using single particle cryogenic electron microscopy, we discover the binding site of the steroid-derived detergent, glyco-diosgenin. Results from flash photolysis kinetic experiments with CIV in the presence of glyco-diosgenin and cholesterol hemisuccinate are combined with cryo-EM and molecular simulations to elucidate how steroid binding limits proton uptake by the complex.

category: biophysics


title: Complete mutational mapping of a GTPase switch in vivo reveals novel allosteric regulation

abstract: GTPases are highly regulated molecular switches that control signaling. Switching occurs via catalyzed GTP hydrolysis and nucleotide exchange, yet the importance of additional regulation for biological function - suggested by high GTPase conservation and centrality in protein networks - is unclear. Here we map the function of each residue in the central GTPase Gsp1/Ran in its native biological network by deep mutagenesis. 28% of 4315 assayed mutations in Gsp1/Ran show a toxic/gain-of-function (GOF) response, and 20/60 positions enriched for GOF mutations are outside the GTPase active site. Kinetic analysis shows that these sites are allosterically coupled to the active site, identifying distinct mechanisms that alter Gsp1/Ran cellular function by modulating GTPase switching. Our systematic discovery of new regulatory sites provides a functional map relevant to other GTPases such as Ras.


title: Free fatty acid receptor 4 (FFAR4) regulates cardiac oxylipin balance to promote inflammation resolution in a model of heart failure preserved ejection fraction secondary to metabolic syndrome

abstract: Free fatty acid receptor 4 (Ffar4) is a G-protein coupled receptor for long-chain fatty acids that improves metabolism and attenuates inflammation. Heart failure preserved ejection fraction (HFpEF) is a complex clinical syndrome, but a predominant subset of patients has meta-bolic syndrome (MetS). Mechanistically, systemic, non-resolving inflammation associated with MetS might promote HFpEF. Interestingly, we recently demonstrated that Ffar4 is cardioprotective in pressure overload. The beneficial effects of Ffar4 on metabolism/inflammation, the high incidence of MetS in HFpEF patients, and the cardioprotective effects of Ffar4 led us to hypothesize that loss of Ffar4 would worsen remodeling in HFpEF secondary to MetS (HFpEF-MetS). To test this, mice with systemic deletion of Ffar4 (Ffar4KO) were fed a high-fat/high-sucrose diet with L-NAME in their water (HFpEF-MetS diet) to induce HFpEF-MetS. In male Ffar4KO mice, the HFpEF-MetS diet induced similar metabolic deficits, but worsened diastolic function and microvascular rarefaction compared to wild-type mice. Conversely, in female Ffar4KO mice, the diet produced greater obesity but no worsening of HFpEF. Loss of Ffar4 in males altered the balance of inflammatory oxylipins in the heart, decreasing the eicosapentaenoic acid derived, pro-resolving oxylipin 18-hydroxyeicosapentaenoic acid (18-HEPE), while increasing the arachadonic acid derived, proinflammatory oxylipin 12-hydroxyeicosatetraenoic acid (12-HETE). This increased 12-HETE/18-HEPE ratio, reflecting a more proinflammatory state, was associated with increased macrophage numbers, which in turn correlated with worsened ventricular remodeling in male Ffar4KO hearts. In summary, our data suggest that Ffar4 controls the pro/anti-inflammatory oxylipin balance in the heart to modulate macrophage function and attenuate HFpEF remodeling.

category: physiology


title: Epitope Mapping of SARS-CoV-2 Spike Protein Reveals Distinguishable Antibody Binding Activity of Vaccinated and Infected Individuals.

abstract: A multitude of studies have attempted to characterize the antibody response of individuals to the SARS-CoV-2 virus on a linear peptide level by utilizing peptide microarrays. These studies have helped to identify epitopes that have potential to be used for diagnostic tests to identify infected individuals, however the immunological responses of individuals who have received the currently available mRNA vaccines have not been characterized. We aimed to identify linear peptides of the SARS-CoV-2 spike protein that elicited high IgA or IgG binding activity and compare the immunoreactivity of infected individuals to those who received recommended doses of either the Moderna mRNA-1273 or Pfizer BNT162b2 vaccines by utilizing peptide microarrays. Our results revealed peptide epitopes of significant IgG binding among recently infected individuals, many of which are located near functional domains implicated in the high infectivity of SARS-CoV-2. Vaccinated individuals were found to have less intense antibody binding activity than those acutely infected, yet novel markers of IgG binding were identified in the vaccinated group.

category: immunology


title: Determinants of Spike Infectivity, Processing and Neutralization in SARS-CoV-2 Omicron subvariants BA.1 and BA.2

abstract:
The SARS-CoV-2 Omicron variant rapidly outcompeted other variants and currently dominates the COVID-19 pandemic. Its enhanced transmission, immune evasion and pathogenicity is thought to be driven by numerous mutations in the Omicron Spike protein. Here, we examined the impact of amino acid changes that are characteristic for the BA.1 and/or BA.2 Omicron lineages on Spike function, processing and susceptibility to neutralization. Individual mutations of S371F/L, S375F and T376A in the ACE2 receptor-binding domain as well as Q954H and N969K in the hinge region 1 impaired infectivity, while changes of G339D, D614G, N764K and L981F moderately enhanced it. Most mutations in the N-terminal region and the receptor binding domain reduced sensitivity of the Spike protein to neutralization by sera from individuals vaccinated with the BNT162b2 vaccine or therapeutic antibodies. Our results represent a systematic functional analysis of Omicron Spike adaptations that allowed this SARS-CoV-2 variant to overtake the current pandemic.

HIGHLIGHTSO_LIS371F/L, S373P and S375F impair Spike function and revert in some BA. 1 isolates
C_LIO_LIChanges of Q954H and N969K in HR1 reduce while L981F enhances S-mediated infection
C_LIO_LIOmicron-specific mutations in the NTD and RBD of Spike reduce neutralization
C_LIO_LIN440K, G446S, E484A and Q493K confer resistance to bamlanivimab or imdevimab
C_LI

category: microbiology


title: Relative infectivity of the SARS-CoV-2 Omicron variant in human alveolar cells

abstract: With the emergence of multiple highly transmissible SARS-CoV-2 variants during the recent pandemic, the comparison of their infectivity has become a substantially critical issue for public health. However, a direct assessment of these viral characteristics has been challenging due to the lack of appropriate experimental models and efficient methods. Here, we integrated human alveolar organoids and single-cell transcriptome sequencing techniques to facilitate the evaluation. In a proof-of-concept study using the assay with four highly transmissible SARS-CoV-2 variants, including GR (B.1.1.119), Alpha (B.1.1.7), Delta (B.1.617.2), and Omicron (BA.1), a rapid evaluation of the relative infectivity was possible. Our results demonstrate that the Omicron (BA.1) variant is 3-5-fold more infectious to human alveolar cells than the other SARS-CoV-2 variants at the early phase of infection. To our knowledge, this study provides the first direct measurement of the infectivity of the Omicron variant and new experimental procedures that can be applied for monitoring newly emerging viral variants.


title: Multisite Test-Retest Reliability and Compatibility of Brain Metrics derived from FreeSurfer Versions 7.1, 6.0, and 5.3

abstract: Automatic neuroimaging segmentation and parcellation tools provide convenient and systematic methods for extracting numerous features from brain MRI scans, and are becoming standard practice for large-scale coordinated studies. One such tool, FreeSurfer, provides an easy-to-use pipeline to extract metrics describing cortical and subcortical morphometry. Over the past two decades, there have been over 25 stable releases of FreeSurfer, and different versions are used across published works. Despite this, the reliability and compatibility of metrics derived from the most recent major version releases have yet to be assessed empirically. Here, we use test-retest data from three public brain MRI datasets to assess within-version reliability and between-version compatibility across 42 regional outputs from three versions of FreeSurfer: the latest, v7.1, and two previous stable releases - v5.3, and v6.0. We find v7.1 was less compatible with older versions for measuring cortical thickness. In particular, the thickness of the cingulate gyrus had low compatibility (intraclass correlation coefficient (ICC) between 0.37 and 0.61) between versions. Temporal and frontal poles, and the medial orbitofrontal surface area metrics, also showed low to moderate compatibility with v7.1. While our work compares all three versions, our sub-comparisons between the older versions (v5.3 and v6.0) replicates earlier findings of low compatibility of pallidum and putamen volumes. Low between-version compatibility was not always indicative of low within-version reliability - all versions showed good to excellent reliability across most regional measures (ICC>0.8). Age associations, quality control metrics, and Dice coefficients in an independent sample of 106 individual scans, processed with all three versions of FreeSurfer, revealed differences in results of downstream statistical analysis. As neuroimaging studies adopt more recently released software, we provide researchers with a reference to highlight the regions and metrics that may yield findings inconsistent with published works using older FreeSurfer software. An interactive viewer for the results is provided at http://data.brainescience.org/Freesurfer_Reliability/


title: A Third Somatomotor Representation in the Human Cerebellum

abstract: Seminal neurophysiological studies in the 1940s discovered two somatomotor maps in the cerebellum - an inverted anterior lobe map and an upright posterior lobe map. Both maps have been confirmed in the human using non-invasive neuroimaging with additional hints of a third map near to the cerebellar vermis. Here we sought direct evidence for the third somatomotor map by using intensive, repeated functional MRI (fMRI) scanning of individuals performing movements across multiple body parts (tongue, hands, glutes and feet). An initial discovery sample (N=4, 4 sessions per individual including 576 separate blocks of body movements) yielded evidence for the two established cerebellar somatomotor maps, as well as evidence for a third discontinuous foot representation near to the vermis. When the left versus right foot movements were directly contrasted, the third representation could be clearly distinguished from the second representation in multiple individuals. Functional connectivity from seed regions in the third somatomotor representation confirmed anatomically-specific connectivity with the cortex, paralleling the patterns observed for the two well-established maps. All results were prospectively replicated in an independent dataset with new individuals (N=4). These collective findings provide direct support for a third somatomotor map in the vermis of the cerebellum. We discuss the relations of this candidate third map to the broader topography of the cerebellum as well as its implications for understanding the specific organization of the human cerebellar vermis where distinct zones appear functionally specialized for somatomotor and visual domains.


title: Isolation, purification, and characterisation of a phage tail-like bacteriocin from the insect pathogenic bacterium Brevibacillus laterosporus

abstract:
The gram-positive and spore-forming bacterium Brevibacillus laterosporus (Bl) belongs to the Brevibacillus brevis phylogenetic cluster. Isolates of the species have demonstrated pesticidal potency against a wide range of invertebrate pests and plant diseases. Two New Zealand isolates, Bl 1821L and Bl 1951, are under development as biopesticides for control of diamondback moth and other pests. However, due to often restricted growth of these endemic isolates, production can be an issue. During investigations of the cause of the disrupted growth, electron micrographs of crude lysate of Bl 1821L showed the presence of phages tail-like structures. PEG 8000 precipitated lysate harbouring the putative phage tail-like particles demonstrated broad-spectrum activity against several gram-positive bacteria. SDS-PAGE of purified and concentrated lysate showed a prominent protein band of [~]48 kD from where transmission electron microscopy revealed the presence of polysheath-like structures. N-terminal sequencing of the [~]48 kD protein mapped to a gene with weak predicted amino acid homology to a Bacillus PBSX phage-like element xkdK, the translated product of which shared >90% amino acid similarity to the phage tail-sheath protein of another Bl published genome, LMG15441. An xkdK homolog was also identified in the Bl 1951 genome. However, genome comparison of the region around the xkdK gene between Bl 1821L and Bl 1951 found differences including two glycine rich protein encoding genes which contain imperfect repeats (1700 bp) in Bl 1951, while a putative phage region resides in the analogous Bl 1821L region. Although comparative analysis of the genomic organisation of Bl 1821L and Bl 1951 PBSX-like region with the defective phages PBSX, PBSZ, and PBP 180 of Bacillus subtilis isolates 168 and W23, and Bacillus phage PBP180 revealed low amino acids similarity, the genes encode similar functional proteins in similar arrangements, including phage tail-sheath (XkdK), tail (XkdO), holin (XhlB), and N-acetylmuramoyl-L-alanine (XlyA). AMPA analysis identified a bactericidal stretch of 13 amino acids in the [~]48 kD sequenced protein of Bl 1821L. Assays of purified [~]48 kD protein of Bl 1821L caused a decrease of 34.2% in the number of viable cells of Bl 1951, 18 hours after treatment as compared to the control.

Significance of the studyThis study for the first time isolated, purified, and characterised putative phage tail-like bacteriocins (PTLBs) from the insect pathogenic isolates of Brevibacillus laterosporus. Identified PTLBs caused a decrease in the number of viable cells of Bl 195, 18 hours after treatment as compared to control. Therefore, it is likely that the putative PTLBs might have implications in harnessing the insecticidal potential of this useful bacterium.


title: ModA phasevarions regulate adherence of non-typeable Haemophilus influenzae to the host airway in a tissue-specific manner

abstract: Adherence of non-typeable Haemophilus influenzae (NTHi) to the host airway is an essential initial step for asymptomatic colonization of the nasopharynx, as well as development of disease. NTHi relies on strict regulation of multiple adhesins for its pathogenesis. The ModA phasevarion is a bacterial regulatory system important for virulence of NTHi. However, the role of the ModA phasevarion in adherence of NTHi to the host airway is not understood well. This study addressed the role of the ModA phasevarion in the regulation of adherence of NTHi to multiple substrates of the host airway. Assessment of adherence of the modA variants of four clinical isolates of NTHi showed that ModA phasevarions regulated adherence of NTHi to mucus, middle ear epithelial cells, and vitronectin in a substrate-specific manner. The adhesins Protein E and P4 were found to contribute to the ModA-regulated adherence of NTHi to distinct substrates. A better understanding of such tissue-specific regulation of NTHi adherence by the ModA phasevarion will allow identification of virulent NTHi populations at the site of disease within the host airway and facilitate more directed development of vaccines or therapeutics.


title: SARS-CoV-2 Omicron BA.1 variant infection of human colon epithelial cells

abstract: Omicron B.1.1.529 became the predominant SARS-CoV-2 variant in early 2022, causing a new wave of public anxiety. Compared to the ancestral strain, Omicron has 50 mutations, with over 30 mutations in the spike protein. These differences likely underlie the changes in Omicron biology noted in other studies, including an attenuation in the lung parenchyma, compared to the ancestral SARS-CoV-2 strain and other variants, as well as a preference for endosomal entry, in place of the TMPRSS2-mediated membrane fusion pathway. This raises questions on Omicron tropism and infectivity in various target organ systems, including the gastrointestinal (GI) tract. Up to 70% of COVID-19 patients report GI symptoms, including nausea, vomiting, and diarrhea. Here, we show that in the context of donor intrinsic genetic heterogeneity, the SARS-CoV-2 Omicron variant infects human colonoids similarly, if not less effectively, than the ancestral WT (WA1) strain or the Delta variant. Additionally, we note a higher ratio of viral RNA to infectious virus titer, which may suggest that Omicron is potentially less infectious in the intestine. This study lays the foundation for further work defining mechanisms mediating intestinal infection and pathogenesis by Omicron.


title: Local recruitment of DNA repair proteins enhances CRISPR-ssODN-HDR editing

abstract: CRISPR-Cas technologies enable precise editing of genomic sequences. One major way to introduce precise editing is through homology directed repair (HDR) of DNA double strand breaks (DSB) templated by exogenously supplied single-stranded oligodeoxyribonucleotides (ssODN). Competing pathways determine the outcome of edits. Non-homologous end-joining pathways produce destructive insertions/deletions (indels) at target sites and are dominant over the precise homology directed repair pathways. In this study, we aim to favor HDR and use two strategies to recruit DNA repair proteins (DRPs) to Cas9 cut site, the Casilio-DRP approach that recruits RNA-binding protein-tethered DRPs to target site via aptamers appended to guide RNA; and the 53BP1-DRP approach that recruits DRPs to DSBs via DSB-sensing activity of 53BP1. We conducted two screens using these approaches and identified DRPs such as FANCF and BRCA1 that when recruited to Cas9 cut site, enhance ssODN-templated HDR and increase the proportion of precise edits. This study provides not only new constructs for enhanced CRISPR-ssODN-HDR but also a collection of DRP fusions for studying DNA repair processes.


title: Gene Expression Changes in Therapeutic Ultrasound-Treated Human Chronic Wound Tissue

abstract: Low-frequency, low-intensity ultrasound has been previously shown to promote healing of chronic wounds in humans, but mechanisms behind these effects are poorly understood. The purpose of this study was to evaluate gene expression differences in debrided human venous ulcer tissue from patients treated with low-frequency (20 kHz), low-intensity (100 mW/cm2) ultrasound compared to a sham treatment in an effort to better understand the potential biological mechanisms. Debrided venous ulcer tissue was collected from 32 subjects one week after sham treatment or low-frequency, low-intensity ultrasound treatment. Of these samples, 7 samples (3 ultrasound treated and 4 sham treated) yielded sufficient quality total RNA for analysis by ultra-high multiplexed PCR (Ampliseq) and expression of more than 24,000 genes was analyzed. 477 genes were found to be significantly different between the ultrasound and sham groups using cut-off values of p<0.05 and fold change of 2. Gene set enrichment analysis identified 20 significantly enriched gene sets from upregulated genes and 4 significantly enriched gene sets from downregulated genes. Most of the enriched gene sets from upregulated genes were related to cellcell signaling pathways. The most significantly enriched gene set from downregulated genes was the inflammatory response gene set. These findings show that therapeutic ultrasound influences cellular behavior in chronic wounds as early as one week after application. Considering the well-known role of chronic inflammation in impairing wound healing in chronic wounds, these results suggest that a downregulation of inflammatory genes is a possible biological mechanism of ultrasound-mediated venous chronic wound healing. Such increased understanding may ultimately lead to the enhancement of ultrasound devices to accelerate chronic wound healing and increase patient quality of life.


title: A joint learning approach for genomic prediction in polyploid grasses

abstract: Poaceae, among the most abundant plant families, includes many economically important polyploid species, such as forage grasses and sugarcane (Saccharum spp.). These species have elevated genomic complexities and limited genetic resources, hindering the application of marker-assisted selection strategies. Currently, the most promising approach for increasing genetic gains in plant breeding is genomic selection. However, due to the polyploidy nature of these polyploid species, more accurate models for incorporating genomic selection into breeding schemes are needed. This study aims to develop a machine learning method by using a joint learning approach to predict complex traits from genotypic data. Biparental populations of sugarcane and two species of forage grasses (Urochloa decumbens, Megathyrsus maximus) were genotyped, and several quantitative traits were measured. High-quality markers were used to predict several traits in different cross-validation scenarios. By combining classification and regression strategies, we developed a predictive system with promising results. Compared with traditional genomic prediction methods, the proposed strategy achieved accuracy improvements exceeding 50%. Our results suggest that the developed methodology could be implemented in breeding programs, helping reduce breeding cycles and increase genetic gains.


title: Assignment of structural transitions during mechanical unwrapping of nucleosomes and their disassembly products

abstract:
Nucleosome DNA unwrapping and its disassembly into hexasomes and tetrasomes is necessary for genomic access and plays an important role in transcription regulation. Previous single-molecule mechanical nucleosome unwrapping revealed a low- and a high-force transitions, and force-FRET pulling experiments showed that DNA unwrapping is asymmetrical occurring always first from one side before the other. However, the assignment of DNA segments involved in these transitions remains controversial. Here, using high-resolution optical tweezers with simultaneous single-molecule FRET detection we show that the low-force transition corresponds to the undoing of the outer-wrap of one side of the nucleosome (~27 bp), a process that can occur either cooperatively or non-cooperatively, whereas the high-force transition corresponds to the simultaneous unwrapping of ~76 bp from both sides. This process may give rise stochastically to the disassembly of nucleosomes into hexasomes and tetrasomes whose unwrapping/rewrapping trajectories we establish. In contrast, nucleosome rewrapping does not exhibit asymmetry. To rationalize all previous nucleosome unwrapping experiments, it is necessary to invoke that mechanical unwrapping involves two nucleosome reorientations: one that contributes to the change in extension at the low-force transition, and another that coincides but does not contribute to the high-force transition.

Significance statementNucleosomes, the fundamental structural unit of chromatin, consists of ~147 DNA base pairs wrapped around a histone protein octamer. Determining the forces required to unwrap the DNA from the core particle and the stepwise transitions involved in the process are essential to characterize the strength of the nucleosomal barrier and its contribution as a mechanism of control of gene expression. Here, we performed combined optical tweezers and single-molecule fluorescence measurements to annotate the specific DNA segments unwrapping during the force transitions observed in mechanical unwrapping of nucleosomes. Furthermore, we characterize the mechanical signatures of subnucleosomal particles: hexasomes and tetrasomes. The characterization performed in this work is essential for the interpretation of ongoing studies of chromatin remodelers, polymerases, and histone chaperones.


title: Enhanced expression of 4-Cl-IAA and 6-Cl-IAA by touch stimulus for rapid and differential growths of the Madeira vine

abstract: Madeira vine (MV) grows 30 times faster after encountering a support. In vivo x-ray diffraction made on live MV stems revel the appearance of crystallized IAA (C10H9NO2), 4-Cl-IAA (C10H8ClNO2) and 6-Cl-IAA (C10H8ClNO2) in the stems. Small angle neutron scattering spectra of the IAA extracted from MVs stem reveal a progressive increase in the size of crystallized IAA transported downward from the apex of the shoots. High resolution X-ray diffractions made on the extracted IAA reveal significantly larger amounts of 4-Cl-IAA and 6-Cl-IAA in the climbing MVs than in the swaying around MVs. The gas chromatography-mass spectrometry spectra reveal the production of 9% more IAA and 90% more 4-Cl-IAA+6-Cl-IAA at the apexes of climbing MVs than swaying MVs. More 4-Cl-IAA+6-Cl-IAA were transported to the contact-free side than to the contact side of the vine. In vivo neutron tomography of naturally climbing MVs reveals a substantially higher H+ concentration in the contact-free parts than in the contact parts. The absorption spectra also reveal more expansin in the contact-free parts than in the contact parts. These results provide a view, at the molecular level, of what triggers the faster and differential growths in MVs in response to touching a support.

category: plant biology


title: Comparative genomics in Orobanchaceae provides insight into the origin and evolution of plant parasitism

abstract: Orobanchaceae is the largest family of plant parasites comprising autotrophic and parasitic plants with all degrees of parasitism, making it by far the best family for studying the origin and evolution of plant parasitism. Here we provide three high-quality genomes of orobanchaceous plants, the autotrophic Lindenbergia luchunensis and holoparasitic Phelipanche aegyptiaca and Orobanche cumana. Phylogenomic analysis on these three genomes and the previously published genomes and transcriptomes of other orobanchaceous species created a robust phylogenetic framework of Orobanchaceae. An ancient whole-genome duplication (WGD; about 79.29 Mya) was detected in the common ancestor of Orobanchaceae and Mimulus guttatus, and this event might have contributed to the origin of parasitism; however, except for Striga, no WGD events occurred in any lineages of orobanchaceous parasites after divergence from their autotrophic common ancestor, and the expansion of the genomes of orobanchaceous parasitic plants was mainly due to retrotransposons. We detected evident convergent gene loss in all parasites within Orobanchaceae and between Orobanchaceae and dodder Cuscuta australis. The gene families in the orobanchaceous parasites showed a clear pattern of recent gains and expansions, and the expanded gene families are enriched in functions related to development of haustorium. Thus, recent gene family expansions may have facilitated the adaptation of orobanchaceous parasites to different hosts. These data well support the previously proposed model of parasitic plant genome evolution (1). This work illustrates the trajectory of the evolution of orobanchaceous parasites, and will facilitate future studies on parasitism and the control of parasitic plants in agriculture.


title: The tissue-specific chromatin accessibility landscape of Papaver somniferum

abstract: Accessible chromatin regions (ACRs) at promoters, enhancers, and other gene regulatory regions allow transcription factors (TFs) to bind, which regulate gene transcription involved in plant development and metabolism. Papaver somniferum has been widely applied in clinical medicine as one of the most important and oldest medicinal plants due to its unique and effective active ingredients. However, the transcriptional regulatory mechanism of tissue-specific distribution of active ingredients remains unknown. In this study, transcriptome and chromatin accessibility analysis by RNA sequencing (RNA-seq) and assay for transposase-accessible chromatin sequencing (ATAC-seq) was performed to investigate these underlying molecular mechanisms. We identified tissue-specific chromatin Tn5 hypersensitive site (THS) and gene expression by examining the variation of THS and transcripts across six tissues (capsule, stem, fine root, tap root, leaf, and petal). Our results provide insight into the epigenetic mechanism of transcriptional plasticity for P. somniferum organ development. Sequence motif analysis within accessible chromatin regions for co-expressed gene modules revealed enriched binding sites of hub transcription factors that regulate tissue-specific functions. Furthermore, we identified regulatory elements for tissue-specific accumulation of morphine and noscapine in P. somniferum. This is the first tissue-specific chromatin accessibility landscape of P. somniferum providing an important resource for functional epigenetic analysis and future molecular breeding in P. somniferum for variety improvement.


title: The Computational Neuroanatomy of Predictive Dynamics of Pain Perception

abstract:
Pain perception is an active process that regulates nociceptive inputs by descending opioidergic signals, in which the brain encodes pain-related predictive and corrective terms, after having made Bayesian-like inferences about noxious amplitudes. Offset analgesia (OA), a large reduction of tonic pain after a small nociceptive termination, is typical empirical evidence of on-line pain modulation through prediction and its correction. However, the basic computational structure underlying OA is not understood. Here, we adopted a constructive approach, formulated the inference of noxious amplitudes with a Kalman filter model, i.e., a recursive Bayesian computation, and then deduced the computational structure for OA, in which an interaction between two latent state variables was implemented. Simulation results suggested that the unidirectional interaction of the two states with two dissociable roles (an integral over time and a derivative of stimulus changes) is crucial for OA. Our results, combined with previous anatomical studies, suggest a computational basis of neural connectivity for pain. The ACC and aINS interact to compute a descending prediction to the brainstem, i.e. PAG, while ascending inputs are filtered in the thalamus and delivered to the cortices as prediction errors. Thus, we suggest dissociable, computational roles of the ACC and aINS in pain processing.

Author SummaryUnderstanding the computational theory of pain perception is crucial for clarifying why some painful syndromes become chronic. Here, we propose a computational neuroanatomical model of endogenous pain modulation and we simulate a model for offset analgesia. We first demonstrate through model comparisons that the brain encodes at least two distinct states to estimate ongoing nociception: a derivative of input changes and its integral. We suggest that its neural substrate comprises hierarchical circuits composed of cortices, the thalamus, and brainstem. Second, we show that the computational basis of disrupted pain modulation in patients is pseudo-neglect of actual sensory inputs, with bias toward the internal prediction. Our results are the first to provide a neurocomputational mechanism of pain perception dynamics and a factor that determines its functionality.


title: Glossiness perception and its pupillary response

abstract: Recent studies have discovered that pupillary response changes depend on cognitive factors, such as subjective brightness caused by optical illusions and luminance. However, it remains unclear how the cognitive factor derived from the glossiness perception of object surfaces affects pupillary response. We investigated the relationship between glossiness perception and pupillary response through a gloss rating experiment that includes recording pupil diameter. For the stimuli, we prepared general object images (original) and randomized images (shuffled) that comprised of the same images with randomized small square regions. The image features were then controlled by matching the luminance histogram. The observers were asked to rate the perceived glossiness of the stimuli presented for 3,000 ms and changes in their pupil diameter were recorded. Consequently, if glossiness of the original images were rated as high, those of the shuffled were rated as low, and vice versa. High-gloss images constricted the pupil size more than the low-gloss ones near the pupillary light reflex. By contrast, the shuffled images dilated the pupil size more than the original image at a relatively later stage. These results suggest that local features comprising specular highlights involve the cognitive factor for pupil constriction, and this process is faster than pupil dilation derived from the inhibition of object recognition.


title: Tauroursodeoxycholic acid inhibits Clostridioides difficile toxin induced apoptosis

abstract: C. difficile infection (CDI) is a highly inflammatory disease mediated by the production of two large toxins that weaken the intestinal epithelium and cause extensive colonic tissue damage. Antibiotic alternative therapies for CDI are urgently needed as current antibiotic regimens prolong the perturbation of the microbiota and lead to high disease recurrence rates. Inflammation is more closely correlated with CDI severity than bacterial burden, thus therapies that target the host response represent a promising yet unexplored strategy for treating CDI. Intestinal bile acids are key regulators of gut physiology that exert cytoprotective roles in cellular stress, inflammation and barrier integrity, yet the dynamics between bile acids and host cellular processes during CDI have not been investigated. Here we show that several bile acids are protective against apoptosis caused by C. difficile toxins in Caco-2 cells and that protection is dependent on conjugation. Out of 20 tested bile acids, taurine conjugated ursodeoxycholic acid (TUDCA) was the most potent inhibitor yet unconjugated UDCA did not alter toxin-induced apoptosis. TUDCA treatment decreased expression of genes in lysosome associated and cytokine signaling pathways. TUDCA did not affect C. difficile growth or toxin activity in vitro whereas UDCA significantly reduced toxin activity in a Vero cell assay and decreased tcdA gene expression. These results demonstrate that bile acid conjugation can have profound effects on C. difficile as well as the host and that conjugated and unconjugated bile acids may exert different therapeutic mechanisms against CDI.


title: Acute appendicitis manifests as two microbiome state types with oral pathogens influencing severity

abstract:
Mounting evidence suggests that acute appendicitis (AA) is not one but two diseases: complicated appendicitis, which is associated with necrosis leading to perforation or periappendicular abscess, and uncomplicated appendicitis, which does not necessarily result in perforation. Even though AA is the most frequent cause of surgery from abdominal pain, little is known about the origins and etiopathogenesis of this disease, much less regarding the different disease types.

In this study, we investigated the microbiome of samples from the appendix, rectum and peritoneum of 60 children and adolescents with AA to assess the composition and potential function of bacteria, archaea and fungi. The analysis of the appendix microbial community revealed a shift depending on the severity of the AA. This shift was reflected by two major community state types that represented the complicated and uncomplicated cases. We could demonstrate that complicated, but not uncomplicated, appendicitis is associated with a significant local expansion of oral, bacterial pathogens in the appendix, most strongly influenced by necrotizing Fusobacterium spp., Porphyromonas and Parvimonas. Uncomplicated appendicitis, however, was characterised by gut-associated microbiomes. Our findings support the hypothesis that two disease types exist in AA, which cannot be distinguished beyond doubt using standard clinical characterization methods or by analysis of the patients rectal microbiome. An advanced microbiome diagnosis, however, could improve non-surgical treatment of uncomplicated AA.

ImportanceWith a lifetime risk of up to 17%, acute appendicitis is one of the most frequent causes of emergency abdominal surgery in westernized countries. Latest literature reports suggests that appendicitis manifests in two disease types: complicated and uncomplicated appendicitis with different, yet unknown, etiopathogenesis.

In this study, we investigated the microbial composition (bacteria, archaea and fungi) from 60 children and adolescents that were diagnosed with acute appendicitis. Appendix, rectal and peritoneal samples were analysed using amplicon and metagenomic sequencing. Our results suggest that acute appendicitis manifests in three microbial state types that reflect complicated and uncomplicated appendicitis as well as special cases that are caused by bacterial overgrowth. Strikingly, uncomplicated appendicitis appears to be caused by gut-associated pathogens while complicated appendicitis is driven by oral-associated microbes such as Fusobacterium sp. or Porphyromonas sp. The findings provided in our study are of special interest to understand the etiopathogenesis of both complicated and uncomplicated appendicitis.


title: Outer Membrane Vesicle Mediated Multidrug Resistance Gene Transfer in Avibacterium Paragallinarum

abstract: Infectious coryza is an acute upper respiratory tract infectious disease caused by Avibacterium paragallinarum, which can cause growth retardation and egg production decline of bred chickens, and bring great economic losses to poultry industry. A. Paragallinarum is a Gram-negative bacterium and can release outer membrane vesicles (OMVs). In this study, a comparative genomic analysis of A. Paragallinarum isolate P4chr1 and its OMVs were carried out, and the ability to transfer antibiotic resistance genes via the OMVs was studied. The sequencing and data analysis showed that genome size of A. paragallinarum P4chr1 is about 2.77 Mb and it has a 25 kb tolerance island covering 6 types of antibiotics and 11 resistance genes. The genome size of its OMVs is about 2.69 Mb, covering 97% genome length and almost all gene sequences of P4chr1. When purified and DNase treated A. paragallinarum P4chr1 OMVs were co-cultured with antibiotic sensitive A. paragallinarum Modesto strain on an antibiotic containing plate, the colonies grown on the plate were detected corresponding antibiotic resistance gene (ARG). However, antimicrobial susceptibility test exposed that drug resistance genes delivered by OMVs were not persistent, they only existed temporarily on the antibiotic plates. The antibiotic resistance and ARGs disappeared at second bacterial passage. Overall, this study is the first report to compare genomic characteristics of OMVs with its parent A. paragallinarum strain, and to study A. paragallinarum ARG transfer via OMVs. This work has provided useful data for further study on the issue of non-plasmid ARG transfer mediated by A. paragallinarum OMVs.

category: molecular biology


title: DAPC of genotype data only requires the first k - 1 PC axes for k populations

abstract: Multivariate methods are incredibly beneficial for population genetic analyses where the number of measured variables (genetic loci) can easily exceed the number of sampled individuals. Discriminant analysis of principal components (DAPC) has become a popular method for visualising population structure in genotype datasets due to its simplicity, its computational speed, and its freedom from demographic assumptions. Despite the popularity of DAPC in population genetic studies, there has been little discussion on best practise and parameterisation. Unappreciated, perhaps, is the fact that unlike principal component analysis (PCA), which is a hypothesis free method, discriminant analysis (DA) is a hypothesis driven method. That is, when performing a DA, a researcher is making an explicit hypothesis about how variation in a set of predictor variables is organised among pre-defined groups in a sample set. Parameter choice is critical to ensure the results produced by a DA are biologically meaningful. In a DAPC, one of the most important parameter choices is the number of PC axes, paxes, to use as predictors in a DA of among-population differences. Yet there are no clear guidelines on how researchers should choose paxes. In this work, I propose that the value of paxes is a deterministic feature of a genotype dataset based on population genetic theory. For k discrete populations, only the first k - 1 PC axes are expected to be biologically informative and capture population structure. DAs fit using more than the first k - 1 PC axes are over-parametrised and may discriminate groups using biologically uninformative predictors. Using samples drawn from simulated metapopulations, I show that DAPCs parameterised with the appropriate k - 1 PC axes are: (1) more parsimonious; (2) capture the maximal amount of among-population variation using biologically relevant predictors; (3) are less sensitive to unintended interpretations of population structure; and (4) are more generally applicable to independent sample sets.

category: genetics


title: LRT: T Cell Trajectory Inference by Integrative Analysis of Single Cell TCR-seq and RNA-seq data

abstract:
Single-cell RNA sequencing (scRNA-seq) data has been widely used for cell trajectory inference, with the assumption that cells with similar expression profiles share the same differentiation state. However, the inferred trajectory may not reflect true clonal relationships among cells. Single cell T cell receptor sequencing (scTCR-seq) data provides invaluable insights into the clonal relationship among cells, yet it lacks the functional characteristics. Therefore, scRNA-seq and scTCR-seq data complement each other in improving the trajectory inference. However, very limited computational efforts have been devoted to the integration of scRNA-seq and scTCR-seq data for cell trajectory inference. To address this gap, we developed LRT, an R package for the integrative analysis of scTCR-seq and scRNA-seq data for T cell trajectory inference. In addition, it provides two Shiny apps that allow users to interactively explore distributions of clonotypes and implement clustering of cell trajectories. We illustrated its utility using scRNA-seq and scTCR-seq data of CD4+ T cells with acute lymphocytic choriomeningitis virus infection.

AvailabilityThe R package  LRT is freely available at https://github.com/JuanXie19/LRT.

Contactchung.911@osu.edu

Supplementary informationSupplementary data are available online.


title: CanSig: Discovering de novo shared transcriptional programs in single cancer cells

abstract: Human tumors are highly heterogeneous in their cell composition; specifically, they exhibit heterogeneity in transcriptional states of malignant cells, as has been recently discovered through single-cell RNA sequencing (scRNA-seq). Distinct states of malignant cells have been linked to variability in tumorigenic properties and resistance to anti-cancer treatment. Despite the fact that scRNA-seq data contain all necessary information to uncover shared transcriptional states of malignant cells in tumors, jointly analyzing cells from multiple cancer patients comes with its set of challenges including batch correction and accounting for patient-specific genetic background driving differences between gene expression vectors. We propose CanSig, an easy-to-use approach designed to discover known and de novo shared signatures in cancer single cells. CanSig preprocesses, integrates and analyzes scRNA-seq data to provide new signatures of shared transcriptional states and links these states to known pathways. We show that CanSig successfully rediscovers ground truth pathways determining shared transcriptional states in two simulated and three experimental datasets; the latter spanning 135 patients and 72,000 cells. We then illustrate CanSigs investigative potential by discovering novel signatures in esophageal squamous cell carcinoma possibly linked to targeted patient treatment; we also point out a de novo signature in breast cancer predictive of patients survival. In the cancer types studied, we juxtapose copy number variation with discovered shared transcriptional states and uncover a genetic component predisposing cancer cells to activation of specific transcriptional programs. In sum, CanSig, specifically developed to analyze shared transcriptional heterogeneity of malignant cells of different genetic backgrounds, can greatly facilitate the exploratory analysis of scRNA-seq cancer data and efficiently identify novel transcriptional signatures linked to known biological pathways.


title: Immunogenic cell death in mice expressing caspase-resistant ROCK1 is not replicated by ROCK inhibitors

abstract: The characteristic changes in morphology during apoptosis help facilitate "immunologically-silent" cell death by limiting the release of cellular contents and enabling efficient clearance of apoptotic cell bodies. Caspase-mediated cleavage of the ROCK1 protein kinase results in its constitutive activation, which drives the rapid and forceful contraction of apoptotic cells. We previously showed in Julian et al. [1] that when ROCK1 was mutated to render it caspase-resistant, there was greater liver damage and neutrophil recruitment after acute treatment with the hepatotoxin diethylnitrosamine (DEN). We now show that acute DEN-induced liver damage resulted in greater induction of pro-inflammatory cytokines/chemokines, indicative of immunogenic cell death (ICD), in mice expressing non-cleavable ROCK1 (ROCK1nc). Hepatocellular carcinoma (HCC) tumours in ROCK1nc mice had higher grade steatosis, and more neutrophils and CD8+ T cells relative to mice expressing wild-type ROCK1 (ROCK1wt), indicating that spontaneous tumour cell death also was more immunogenic. Since the induction of ICD has been proposed to be tumour-suppressive, the effects of two structurally distinct pharmacological ROCK inhibitors on HCC tumours was examined. Both fasudil and AT13148 significantly decreased tumour numbers and area, but neither treatment resulted in greater numbers of neutrophils or CD8+ T cells to be recruited. In the context of acute DEN-induced liver damage, AT13148 reduced circulating platelet and lymphocyte numbers, and inhibited the recruitment of dendritic, natural killer and CD8+ T cells to livers. These observations indicate that there is an important role for ROCK1 cleavage to limit immunogenic cell death which was not replicated by systemic administration of pharmacological ROCK inhibitors. As a result, adjuvant administration of ROCK inhibitors with cancer therapeutics would be unlikely to result in therapeutic benefit by inducing ICD to increase anti-tumour immune responses.

category: cancer biology


title: Predictable fluctuations in excitatory synaptic strength due to natural variation in presynaptic firing rate

abstract: Many controlled, in vitro studies have demonstrated how postsynaptic responses to presynaptic spikes are not constant but depend on short-term synaptic plasticity (STP) and the detailed timing of presynaptic spikes. However, the effects of short-term plasticity (depression and facilitation) are not limited to short, sub-second timescales. The effects of STP appear on long timescales as changes in presynaptic firing rates lead to changes in steady-state synaptic transmission. Here we examine the relationship between natural variations in the presynaptic firing rates and spike transmission in vivo. Using large-scale spike recordings in awake mice from the Allen Institute Neuropixels dataset, we first detect putative excitatory synaptic connections based on cross-correlations between the spike trains of millions of pairs of neurons. For the subset of pairs where a transient, excitatory effect was detected, we use a model-based approach to track fluctuations in synaptic efficacy and find that efficacy varies substantially on slow ([~]1 minute) timescales over the course of these recordings. For many connections, the efficacy fluctuations are correlated with fluctuations in the presynaptic firing rate. To understand the potential mechanisms underlying this relationship, we then model the detailed probability of postsynaptic spiking on a millisecond timescale, including both slow changes in postsynaptic excitability and monosynaptic inputs with short-term plasticity. The detailed model reproduces the slow efficacy fluctuations observed with many putative excitatory connections, suggesting that these fluctuations can be both directly predicted based on the time-varying presynaptic firing rate and, at least partly, explained by the cumulative effects of STP.

category: neuroscience


title: Relation is an option for processing context information

abstract: Attention mechanisms are one of the most frequently used architectures in the development of artificial intelligence because they can process contextual information efficiently. Various artificial intelligence mechanisms such as transformer for processing natural language, image data, etc. include the attention mechanism. Since attention is a powerful component to realize artificial intelligence, various improvements have been made to enhance its performance. The time complexity of attention depends on the square of input sequence length. Methods to improve time complexity of attention are one of the hottest topics in various studies. In this study, we have devised a mechanism called relation that can understand the context information of sequential data without using attention. Relation is very simple to implement and its time complexity depends only on the length of the sequences; a comparison of the performance of neural networks with relation and attention mechanisms on several benchmark datasets shows that relation achieved the same context processing capability as attention with less computation time. Hence, relation is an ideal option for processing context information.


title: Acute administration of a dopamine D2/D3 receptor agonist alters behavioral and neural parameters in adult zebrafish

abstract: The dopaminergic neurotransmitter system is involved in numerous brain functions and behavioral processes. Alterations in this neurotransmitter system are associated with the pathogenesis of several human neurological disorders. Pharmacological agents that interact with the dopaminergic system allow the investigation of dopamine-mediated cellular and molecular responses and may elucidate the biological bases of such disorders. The zebrafish, a translationally relevant biomedical research organism, has been successfully employed in prior psychopharmacology studies. Here, we evaluate the effects of quinpirole (a dopamine D2/D3 receptor agonist) in adult zebrafish on behavioral parameters and neurotransmitter levels. Adult zebrafish received intraperitoneal injections of 0.5, 1.0, or 2.0 mg/kg of quinpirole or saline (control group) twice with an inter-injection interval of 48h. All tests were performed 24h after the second injection. After acute quinpirole administration, zebrafish exhibited decreased locomotor activity, increased anxiety-like behaviors and memory impairment compared to control. However, the quinpirole administration did not affect social and aggressive behavior. Quinpirole-treated fish exhibited altered swimming patterns: fish showed stereotypic swimming characterized by repetitive behavior, swimming from corner to corner at the bottom of the tank preceded and followed by episodes of immobility. Moreover, analysis of neurotransmitter levels in the brain demonstrated a significant increase in glutamate and a decrease in serotonin, while no alterations were observed in dopamine. These findings demonstrate that dopaminergic signaling altered by quinpirole administration results in significant changes in behavior and neurotransmitter levels in the central nervous system of zebrafish. Thus, we conclude that the use of quinpirole administration in adult zebrafish may be an appropriate tool for the analysis of mechanisms underlying neurological disorders related to the dopaminergic system.


title: Identification of microRNAs in the Lyme disease vector Ixodes scapularis

abstract: MicroRNAs (miRNAs) are a class of small non-coding RNAs involved in many biological processes, including the immune pathways that control bacterial, parasitic, and viral infections. Pathogens probably modify host miRNAs to facilitate successful infection, so they might be useful targets for vaccination strategies. There are little data on differentially expressed miRNAs in the black- legged tick Ixodes scapularis after infection with Borrelia burgdorferi, the causative agent of Lyme disease in the United States. Small RNA sequencing and qRT-PCR analysis were used to identify and validate differentially-expressed I. scapularis salivary miRNAs. Small RNA-seq yielded 133,465,828 ([≥]18 nucleotides) and 163,852,135 ([≥]18 nucleotides) small RNA reads from Borrelia- infected and uninfected salivary glands for downstream analysis using the miRDeep2 algorithm. Two hundred and fifty-four miRNAs were identified across all datasets, 25 of which were high confidence and 51 low confidence known miRNAs. Twenty-three miRNAs were differentially expressed in uninfected and infected salivary glands: 11 were upregulated and 12 were downregulated upon pathogen infection. This study provides new insights into the miRNAs expressed in I. scapularis salivary glands and pave the way for their functional manipulation to prevent or treat B. burgdorferi infection.


title: A mitochondrial iron-sensing pathway regulated by DELE1

abstract: The heme-regulated kinase HRI is activated under heme/iron deficient conditions; however, the underlying molecular mechanism is incompletely understood. Here, we show that iron deficiency-induced HRI activation involves a heme-independent mechanism that requires the mitochondrial protein DELE1. Notably, mitochondrial import of DELE1 and its subsequent protein stability are regulated by iron availability. Under steady state conditions, DELE1 is degraded by the mitochondrial matrix-resident protease LONP1 soon after mitochondrial import. Upon iron chelation, DELE1 import is arrested, thereby stabilizing DELE1 on the mitochondrial surface to activate the HRI-mediated integrated stress response (ISR). Moreover, depletion of the mitochondrial ABC transporter ABCB7 that is involved in iron-sulfur cluster (ISC) metabolism markedly abrogates iron deficiency-induced ISR activation, suggesting the possible involvement of ISC-related molecules in this activation. Our findings highlight mitochondrial import regulation of DELE1 as the core component of a previously unrecognized iron monitoring system that connects the mitochondria to the cytosol.

category: cell biology


title: Parallel recruitment pathways contribute to synaptonemal complex assembly during mammalian meiosis

abstract: During meiosis, the synaptonemal complex (SC) assembles between paired chromosomes, binding them together in close apposition, and facilitating recombination. SC assembly is thought to occur through the hierarchical zipper-like recruitment of axial elements, followed by transverse filaments and then central elements. However, the rapidity of SC formation in mammals has hitherto hindered investigation of its assembly mechanisms and their relationship with recombination. Using super-resolution imaging of separation-of-function mouse mutants, we show that, contrary to the hierarchical assembly model, central element protein SYCE2 is recruited to recombination sites early in SC assembly, and independently of SYCP1-containing transverse filaments. Further, SYCE2-TEX12 binds DNA in vitro, and SYCE2-containing bridges physically link paired chromosomes at recombination sites prior to transverse filament recruitment and chromosome synapsis. These data suggest that mammals integrate parallel recruitment pathways to assemble a mature SC: one recruiting central element proteins to recombination sites, and another recruiting transverse filaments to chromosomes.


title: HER2 expression defines unique requirements for flotillin and c-Src for EGFR signaling

abstract:
The epidermal growth factor receptor (EGFR) controls many cellular functions. Upon binding its ligand, the receptor undergoes dimerization, phosphorylation, and activation of signals including the phosphatidylinositol-3-kinase (PI3K)-Akt pathway. While some studies indicated that EGFR signaling may be controlled by signal enrichment within membrane raft nanodomains, others have found a limited effect of membrane raft disruption on EGFR signaling, suggesting that specific factor(s) may define context-specific control of EGFR signaling by membrane rafts. Ligand-bound EGFR can homodimerize, or instead undergo heterodimerization with the related receptor HER2 when the latter is expressed. We examined how EGFR signaling in the presence of HER2 distinctly requires membrane raft nanodomains. Induction of HER2 expression altered EGFR signaling duration consistent with EGFR/HER2 heterodimer formation. EGFR and c-Src localized within plasma membrane structures demarked by flotillin, a membrane raft protein, selectively in HER2-expressing cells. Consistently, HER2-expressing cells, but not cells lacking HER2, were dependent on flotillin and c-Src for EGFR signaling leading to Akt activation and cell proliferation. Hence, HER2 expression establishes the requirement of EGFR signaling for flotillin membrane rafts and c-Src, leading to Akt activation.

Summary statementThe role of membrane rafts in EGFR signaling may be context-specific. We find that the related receptor HER2 defines unique signaling requirements for EGFR for membrane rafts, flotillin, and c-Src.


title: A Physiology Clock for Human Aging

abstract: Why people age at different rates is a fundamental unsolved problem in biology. We created a model that predicts an individuals age, taking as input physiological traits that change with age in the large UK Biobank dataset, such as blood pressure, blood metabolites, strength, and stimulus-reaction time. The models Root Mean Square Error of age prediction (RMSE) is less than 5 years. We argue that the difference between calculated "biological" age and actual age ({Delta}Age) reflects an individuals relative youthfulness and possibly their rate of aging. Validating this interpretation, people predicted to be physiologically young for their age have a lower subsequent mortality rate and a higher parental age at death, even though no mortality data were used to calculate {Delta}Age. A Genome-Wide Association Study (GWAS) of {Delta}Age, and analysis of environmental factors associated with {Delta}Age identified known as well as new factors that may influence human aging, including genes involved in synapse biology and a tendency to play computer games. We identify 12 readily-measured physiological traits that together assess a persons biological age and may be used clinically to evaluate therapeutics designed to slow aging and extend healthy life.


title: A butterfly pan-genome reveals a large amount of structural variation underlies the evolution of chromatin accessibility

abstract: Despite insertions and deletions being the most common structural variants (SVs) found across genomes, not much is known about how much these SVs vary within populations and between closely related species, nor their significance in evolution. To address these questions, we characterized the evolution of indel SVs using genome assemblies of three closely related Heliconius butterfly species. Over the relatively short evolutionary timescales investigated, up to 18.0% of the genome was composed of indels between two haplotypes of an individual H. charithonia butterfly and up to 62.7% included lineage-specific SVs between the genomes of the most distant species (11 Mya). Lineage-specific sequences were mostly characterized as transposable elements (TEs) inserted at random throughout the genome and their overall distribution was similarly affected by linked selection as single nucleotide substitutions. Using chromatin accessibility profiles (i.e., ATAC-seq) of head tissue in caterpillars to identify sequences with potential cis-regulatory function, we found that out of the 31,066 identified differences in chromatin accessibility between species, 30.4% were within lineage-specific SVs and 9.4% were characterized as TE insertions. These TE insertions were localized closer to gene transcription start sites than expected at random and were enriched for several transcription factor binding site candidates with known function in neuron development in Drosophila. We also identified 24 TE insertions with head-specific chromatin accessibility. Our results show high rates of structural genome evolution that were previously overlooked in comparative genomic studies and suggest a high potential for structural variation to serve as raw material for adaptive evolution.