title: Maternal effects on early-life gut microbiome maturation in a wild nonhuman primate

abstract: Early-life gut microbial colonization is an important process shaping host physiology, immunity and long-term health outcomes in humans and other animals. However, our understanding of this dynamic process remains poorly investigated in wild animals, where developmental mechanisms can be better understood within ecological and evolutionary relevant contexts. Using 16s rRNA amplicon sequencing on 525 fecal samples from a large cohort of infant and juvenile geladas (Theropithecus gelada), we characterized gut microbiome maturation during the first three years of life and assessed the role of maternal effects in shaping offspring microbiome assembly. Microbial diversity increased rapidly in the first months of life, followed by more gradual changes until weaning. As expected, changes in gut microbiome composition and function with increasing age reflected progressive dietary transitions: in early infancy when infants rely heavily on their mothers milk, microbes that facilitate milk glycans and lactose utilization dominated, while later in development as graminoids are progressively introduced into the diet, microbes that metabolize plant complex polysaccharides became dominant. Furthermore, the microbial community of nursing infants born to first-time (primiparous) mothers was more "milk-oriented" compared to similarly-aged infants born to experienced (multiparous) mothers. Comparisons of matched mother-offspring fecal samples to random dyads did not support vertical transmission as a conduit for these maternal effects, which instead could be explained by slower phenotypic development (and associated slower gut microbiome maturation) in infants born to first-time mothers. Together, our findings highlight the dynamic nature of gut colonization in early life and the role of maternal effects in modulating this trajectory in a wild primate.


title: specificity	: an R package for generalized specificity analysis, with example analyses of Hawaiian foliar endophytic Fungi, human gut microbiome bacteria, and Antarctic glacier bacteria.

abstract: Understanding the factors that influence microbes environmental distributions is important for determining drivers of microbial community composition. Species distributions are governed by parameters that influence their dispersal or survival. These include environmental variables like temperature and pH, and higher-dimensional variables like geographic distance and host species phylogenies. In microbial ecology, "specificity" is often described in the context of symbiotic or host parasitic interactions, but specificity can be more broadly used to describe the extent to which a species occupies a narrower range of an environmental variable than expected by chance. Using a standardization we describe here, Raos (1982, 2010) Quadratic Entropy can be conveniently applied to calculate specificity of a focal species to many different environmental variables, including 1-dimensional variables (vectors), dissimilarity matrices, phylogenies, and ontologies. We present our R package specificity for performing the above analyses, and apply it to four real-life microbial datasets to demonstrate its application: fungi living within the leaves of native Hawaiian plants, bacteria from the human gut microbiome, bacteria living within Antarctic glacier ice, and the Earth Microbiome Project data set. Finally, we present an interactive visualization and data exploration tool for these analyses, available as a companion R-package called specificity.shiny.

category: microbiology


title: Lipopolysaccharide induces placental mitochondrial dysfunction by reducing MNRR1 levels via a TLR4-independent pathway

abstract: Mitochondria play a key role in the growth and development of the placenta, an organ essential for pregnancy in eutherian mammals. Mitochondrial dysfunction has been associated with pregnancy pathologies. However, the mechanisms whereby placental mitochondria sense inflammatory signals at a cellular and mechanistic level are unknown. Mitochondrial Nuclear Retrograde Regulator 1 (MNRR1) is a bi-organellar protein responsible for optimal mitochondrial function to achieve energy and redox homeostasis. In addition, MNRR1 also is required for optimal induction of cellular stress-responsive signaling pathways such as the mitochondrial unfolded protein response (UPRmt). Here, in a lipopolysaccharide-induced model of placental inflammation, we show that MNRR1 levels are reduced in placental tissues and cell lines. Reduction in MNRR1 is associated with mitochondrial dysfunction and enhanced oxidative stress along with activation of pro-inflammatory signaling. Mechanistically, we uncover a non-conventional pathway independent of Toll-like receptor 4 (TLR4) that results in a specific ATM kinase-dependent threonine phosphorylation and activation of a mitochondrial protease, YME1L1, degrading MNRR1. Furthermore, enhancing MNRR1 levels in placental cells either genetically or with specific activators abrogates the bioenergetic defect and induces an anti-inflammatory phenotype, suggesting that MNRR1 is upstream of the mitochondrial dysfunction observed in our model. Reduction in MNRR1 levels is a generalized phenomenon observed in cells under an inflammatory stimulus. We therefore propose MNRR1 as a novel anti-inflammatory therapeutic target in pathologies associated with placental inflammation.

category: molecular biology


title: Integrated analyses of the single-cell ATAC-seq and RNA-seq reveal the epigenetic landscape of human ovarian aging

abstract: Studying the molecular mechanisms of ovarian aging is crucial for understanding the age-related fertility issues in females. Recently, a single-cell transcriptomic roadmap of ovarian aging based on non-human primates revealed the molecular signatures of the oocytes at different developmental stages. Herein, we present the first epigenetic landscape of human ovarian aging, through an integrated analysis of the single-cell assay for transposase-accessible chromatin using sequencing (scATAC-seq) and single-cell RNA-seq. We depicted the transcriptional profiles and chromatin accessibility of the ovarian tissues isolated from old (n=4) and young (n=2) donors. The unsupervised clustering of data revealed seven distinct cell populations in the ovarian tissues and six subtypes of oocytes, which could be distinguished by age difference. Further analysis of the scATAC-seq data from the young and old oocytes revealed that the interaction between the Notch signaling pathway and AP-1 family transcription factors may crucially determine oocyte aging. Finally, a machine-learning algorithm was applied to calculate the optimal model based on the single-cell dataset for predicting oocyte aging, which exhibited excellent accuracy with a cross-validated area under the receiver operating characteristics score of 0.99. In summary, this study provides a comprehensive understanding of human ovarian aging at both the transcriptomic and epigenetic levels, based on an integrated analysis of large-scale single-cell datasets. We believe our results will shed light on the discovery of potential therapeutic targets or diagnostic markers for age-related ovarian disorders.

category: genetics


title: Molecular recording of sequential cellular events into DNA

abstract: Genetically encoded DNA recorders noninvasively convert transient biological events into durable mutations in a cells genome, allowing for the later reconstruction of cellular experiences using high-throughput DNA sequencing1. Existing DNA recorders have achieved high-information recording2-14, durable recording3,5-10,13,15-18, prolonged recording over multiple timescales3,5,8,10, multiplexed recording of several user-selected signals5-8,18, and temporally resolved signal recording5-8,18, but not all at the same time. We present a DNA recorder called peCHYRON (prime editing19 Cell HistorY Recording by Ordered iNsertion) that does. In peCHYRON, prime editor guide RNAs19 (pegRNAs) insert a variable triplet DNA sequence alongside a constant propagation sequence that deactivates the previous and activates the next step of insertion. This process results in the sequential accumulation of regularly spaced insertion mutations at a synthetic locus. Accumulated insertions are permanent throughout editing because peCHYRON uses a prime editor that avoids cutting both DNA strands, which risks deletions. Editing continues indefinitely because each insertion adds the complete sequence needed to initiate the next step. Constitutively expressed pegRNAs generate insertion patterns that support straightforward reconstruction of cell lineage relationships. Pulsed expression of different pegRNAs enables the reconstruction of pulse sequences, which may be coupled to biological stimuli for temporally-resolved multiplexed event recording.


title: Active DNA demethylation of developmental cis-regulatory regions predates vertebrate origins

abstract: DNA methylation (5-methylcytosine; 5mC) is a repressive gene-regulatory mark required for vertebrate embryogenesis. Genomic 5mC is tightly regulated through the coordinated action of DNA methyltransferases, which deposit 5mC, and TET enzymes, which participate in its active removal through the formation of 5-hydroxymethylcytosine (5hmC). TET enzymes are essential for mammalian gastrulation and activation of vertebrate developmental enhancers, however, to date, a clear picture of 5hmC function, abundance, and genomic distribution in non-vertebrate lineages is lacking. By employing base-resolution 5mC and 5hmC quantification during sea urchin and lancelet embryogenesis, we shed light on the roles of non-vertebrate 5hmC and TET enzymes. We find that these invertebrate deuterostomes employ TET enzymes for targeted demethylation of regulatory regions associated with developmental genes and show that the complement of identified 5hmC-regulated genes is conserved to vertebrates. This work thus demonstrates that active 5mC removal from regulatory regions is a common feature of deuterostome embryogenesis suggestive of unexpected deep conservation of a major gene-regulatory module.

category: genomics


title: Intrinsically disordered regions of Tristetraprolin and DCP2 directly interact to mediate decay of ARE-mRNA

abstract: The RNA binding protein Tristetraprolin (TTP) is a potent activator of mRNA decay, specifically for transcripts bearing AU-rich elements (AREs) in their 3'-untranslated regions. TTP functions as a mediator for mRNA decay by interacting with the decay machinery and recruiting it to the target ARE-mRNA. In this study, we report a weak, but direct interaction between TTP and the human decapping enzyme DCP2, which impacts the stability of ARE-transcripts. The TTP-DCP2 interaction is unusual as it involves intrinsically disordered regions (IDRs) of both binding partners. We show that the IDR of DCP2 has a propensity for oligomerization and liquid-liquid phase separation (LLPS) in vitro. Binding of TTP to DCP2 leads to its partitioning into phase-separated droplets formed by DCP2, suggesting that molecular crowding might facilitate the weak interaction between the two proteins and enable assembly of a decapping-competent mRNA-protein complex on TTP-bound transcripts in cells. Our studies underline the role of weak interactions in the cellular interaction network and their contribution towards cellular functionality.

category: biochemistry


title: Mesowestern Blot: Simultaneous Analysis of Hundreds of Sub-Microliter Lysates

abstract: Western blotting is a widely-used technique for molecular-weight-resolved analysis of proteins and their post-translational modifications, but has been refractory to affordable scale-up. Here, we report the Mesowestern blot, which uses a 3D-printable gel-casting mold to enable affordable, high-throughput Western blotting with standard sample preparation and small (<1 uL) sample sizes. The casted polyacrylamide gel contains 336, 0.5 uL micropipette-loadable sample wells arranged within a standard microplate footprint. Polyacrylamide % can be altered to change molecular weight resolution range. Proof-of-concept experiments using both infrared-fluorescent molecular weight protein ladder as well as cell lysate (RIPA buffer) demonstrate protein loaded in Mesowestern gels is amenable to the standard Western blotting steps. The main difference between Mesowestern and traditional Western is that semi-dry horizontal instead of immersed vertical gel electrophoresis is used. The linear range of detection is approximately 2 orders of magnitude, with a limit of detection (for {beta}-actin) of around 30 ng of total protein from mammalian cell lysates (~30-3000 cells). Because the gel mold is 3D-printable, users have significant design freedom for custom layouts, and there are few barriers to adoption by the typical cell and molecular biology laboratory already performing Western blots.


title: Cell cycle stage classification using phase imaging with computational specificity

abstract:
Traditional methods for cell cycle stage classification rely heavily on fluorescence microscopy to monitor nuclear dynamics. These methods inevitably face the typical phototoxicity and photobleaching limitations of fluorescence imaging. Here, we present a cell cycle detection workflow using the principle of phase imaging with computational specificity (PICS). The proposed method uses neural networks to extract cell cycle-dependent features from quantitative phase imaging (QPI) measurements directly. Our results indicate that this approach attains very good accuracy in classifying live cells into G1, S, and G2/M stages, respectively. We also demonstrate that the proposed method can be applied to study single-cell dynamics within the cell cycle as well as cell population distribution across different stages of the cell cycle. We envision that the proposed method can become a nondestructive tool to analyze cell cycle progression in fields ranging from cell biology to biopharma applications.

TeaserWe present a non-destructive, high-throughput method for cell cycle detection combining label-free imaging and deep learning.

category: bioengineering


title: ANKLE1 cleaves mitochondrial DNA and contributes to cancer risk by driving the Warburg effect and apoptosis resistance

abstract: Alleles within the chr19p13.1 locus are associated with increased risk of both ovarian and breast cancer and increased expression of the ANKLE1 gene. ANKLE1 is molecularly characterized as an endonuclease that efficiently cuts branched DNA and shuttles between the nucleus and cytoplasm. However, the role of ANKLE1 in mammalian development and homeostasis remains unknown. In normal development ANKLE1 expression is limited to the erythroblast lineage and we found that ANKLE1s role is to cleave the mitochondrial genome during erythropoiesis. We show that ectopic expression of ANKLE1 in breast epithelial-derived cells leads to genome instability and mitochondrial DNA (mtDNA) cleavage. mtDNA degradation then leads to mitophagy and causes a shift from oxidative phosphorylation to glycolysis (Warburg effect). Moreover, mtDNA degradation activates STAT1 and expression of epithelial-mesenchymal transition (EMT) genes. Reduction in mitochondrial content contributes to apoptosis resistance, which may allow precancerous cells to avoid apoptotic checkpoints and proliferate. These findings provide evidence that ANKLE1 is the causal cancer susceptibility gene in the chr19p13.1 locus and describe mechanisms by which higher ANKLE1 expression promotes cancer risk.

category: cancer biology


title: Bacteria modulate tamoxifen-induced death via host fatty acid metabolism

abstract: Tamoxifen is a selective estrogen receptor (ER) modulator that is used to treat ER-positive breast cancer, but that at high doses kills both ER-positive and ER-negative breast cancer cells. We recapitulate this off-target effect in Caenorhabditis elegans, which does not have an ER ortholog. We find that different bacteria dramatically modulate tamoxifen toxicity in C. elegans, with a three-order of magnitude difference between animals fed Escherichia coli, Comamonas aquatica, and Bacillus subtilis. Remarkably, host fatty acid (FA) biosynthesis mitigates tamoxifen toxicity, and different bacteria provide the animal with different FAs, resulting in distinct FA profiles. Surprisingly these bacteria modulate tamoxifen toxicity by different death mechanisms, some of which are modulated by FA supplementation and others by antioxidants. Together, this work reveals a complex interplay between microbiota, FA metabolism and tamoxifen toxicity that may provide a blueprint for similar studies in more complex mammals.

category: systems biology


title: Common resistance mechanisms are deployed by plants against sap-feeding herbivorous insects: insights from a meta-analysis and systematic review

abstract: Sap-feeding insects cause significant yield losses to the worlds crops, these insects feed using syringe-like mouthparts and electrophysiology can be used to compare feeding behaviour on susceptible and resistant plants to identify the mechanistic processes behind resistant phenotypes. Data extracted from 129 studies, comprising 41 insect species across eight insect taxa and 12 host-plant families representing over 30 species, demonstrates that mechanisms deployed by resistant plants have common consequences on the feeding behaviour of diverse insect groups. We show that insects feeding on resistant plants take longer to establish a feeding site and have their feeding duration suppressed two-fold compared with insects feeding on susceptible plants. Our results reveal that the underlying traits contributing towards resistant phenotypes are conserved across plant families, deployed against taxonomically diverse insect groups, and that the underlying resistance mechanisms are conserved. These findings provide new insight that will be beneficial when developing future crop varieties.

category: zoology


title: Opposing roles of Granzymes A and B in the immune response to intestinal infection

abstract: The cytotoxic proteases Granzymes A (GzmA) and B (GzmB) are important components of the arsenal used by cytotoxic immune cells to kill virally infected/damaged cells. Until now, there has been limited evidence that GzmA/B proteins contribute to combating intracellular bacterial pathogens in mammals. Here, we find that the route of infection of the intracellular bacterial pathogen Salmonella enterica serovar Typhimurium reveals the distinct roles that Granzymes play in defending against bacterial infection. We used Gzma-/-Gzmb-/- mice to discover that Granzymes are required to protect mice against oral infection with Salmonella. However, Granzymes do not play a role in systemic infection. We investigated the tissue-specific expression of Granzymes and determined that intestinal intraepithelial lymphocytes (IEL) are the only cell types that express Granzymes in healthy non-infected mice. In fact, IEL are sufficient to mediate the protective effects of Granzymes against Salmonella infection. Intriguingly, we found that GzmA and GzmB play opposing roles in Salmonella control, with GzmA being protective against infection whilst GzmB promoted infection. Both GzmA and GzmB proteins functioned independently of the pore-forming molecule Perforin, suggesting extracellular action. Our study reveals that IEL-expressed Granzymes play significant and distinct functions in host defense from oral bacterial infection.

category: immunology


title: Obesity and adiposity have opposing genetic impacts on human blood traits

abstract: Obesity, hyperlipidemia, and truncal adiposity concordantly elevate cardiovascular disease risks, but have unknown genetic effects on blood trait variation. Using Mendelian randomization, we define unexpectedly opposing roles for generalized obesity and truncal adiposity on blood traits. Elevated genetically determined body mass index (BMI) and lipid levels decreased hemoglobin and hematocrit levels, explaining consistent with clinical observations associating obesity and anemia. However, lipid-related effects were confined to erythroid traits, whereas BMI affected multiple blood lineages, indicating broad effects on hematopoiesis. BMI-related effects were unexpectedly opposed by truncal adipose distribution, which increased hemoglobin and blood cell counts across lineages. Conditional analyses indicated genes, pathways, and cell types responsible for these effects, including Leptin Receptor and other blood cell-extrinsic factors in adipocytes and endothelium, which regulate hematopoietic stem and progenitor cell biology. Our findings identify novel roles for obesity and adipose distribution on hematopoiesis and show that genetically determined adiposity plays a previously underappreciated role in determining blood cell formation and function.


title: Tumour mutations in long noncoding RNAs that enhance cell fitness

abstract: Tumour DNA contains thousands of single nucleotide variants (SNVs) in non-protein-coding elements, yet their functional significance remains poorly understood. Amongst the most highly mutated elements are long noncoding RNAs (lncRNAs), functional transcripts known to play key roles in carcinogenesis. Here, we investigate whether mutations in lncRNAs can act as "drivers" that promote cancer cell fitness. We develop an integrative driver lncRNA discovery algorithm and apply it to single nucleotide variants (SNVs) from 2583 primary tumours and 3527 metastases to reveal 54 potential "driver lncRNAs". Their relevance is supported by enrichment for previously-reported cancer genes, and by clinical and genomic features. Using knockdown and transgene overexpression experiments, we find that tumour SNVs in two novel lncRNAs can boost cell fitness. Driver analysis confirms a particularly high mutation rate in the iconic cancer lncRNA, NEAT1, whose functional significance has been debated in previous studies. We apply in cellulo mutagenesis to identify discrete regions of NEAT1 where SNVs reproducibly increase cell proliferation in both cancerous and normal backgrounds. We show that mutations in the 5 region of NEAT1 alter ribonucleoprotein assembly and boost the population of subnuclear paraspeckles, thus linking genetic mutations to cellular fitness. In summary, this work establishes function-altering somatic mutations in vulnerable lncRNA sites as a route by which cells acquire fitness during tumorigenesis. Such mutations may act by altering the composition of lncRNA-containing ribonucleoproteins.


title: Tumour mutations in long noncoding RNAs enhance cell fitness


title: Core and rod structures of a thermophilic cyanobacterial light-harvesting phycobilisome

abstract: Cyanobacteria, glaucophytes, and rhodophytes utilize giant, light-harvesting phycobilisomes (PBSs) for capturing solar energy and conveying it to photosynthetic reaction centers. PBSs are compositionally and structurally diverse, and exceedingly complex, all of which pose a challenge for a comprehensive understanding of their function. To date, three detailed architectures of PBSs by cryo-electron microscopy (cryo-EM) have been described: a hemiellipsoidal type, a block-type from rhodophytes, and a cyanobacterial hemidiscoidal-type. Here, we report cryo-EM structures of a pentacylindrical allophycocyanin core and phycocyanin-containing rod of a thermophilic cyanobacterial hemidiscoidal PBS. The structures define the spatial arrangement of protein subunits and chromophores, crucial for deciphering the energy transfer mechanism. They reveal how the pentacylindrical core is formed, identify key interactions between linker proteins and the bilin chromophores, and indicate pathways for unidirectional energy transfer.


title: Identification of Low Population States in Cryo-EM Using Deep Learning

abstract: Cryo-EM has made extraordinary headway towards becoming a semi-automated, high-throughput structure determination technique. In the general workflow, high-to-medium population states are grouped into two- and three-dimensional classes, from which structures can be obtained with near-atomic resolution and subsequently analyzed to interpret function. However, low population states, which are also functionally important, are often discarded. Here, we describe a technique whereby low population states can be efficiently identified with minimal human effort via a deep convolutional neural network classifier. We use this deep learning classifier to describe a transient, low population state of bacteriophage A511 in the midst of infecting its bacterial host. This method can be used to further automate data collection and identify other functionally important low population states.

category: biophysics


title: Emergence and maintenance of different sized actin filaments in a common pool of building blocks

abstract:
Actin is one of the key structural components of the eukaryotic cytoskeleton that regulates cellular architecture and mechanical properties. Dynamic regulation of actin filament length and organization is essential for the control of many physiological processes including cell adhesion, motility and division. While previous studies have mostly focused on the mechanisms controlling the mean length of individual actin filaments, it remains poorly understood how distinct actin filament populations in cells maintain different size using the same set of molecular building blocks. Here we develop a theoretical model for the length regulation of multiple actin filaments by nucleation and growth rate modulation by actin binding proteins in a limiting pool of monomers. We first show that spontaneous nucleation of actin filaments naturally leads to heterogeneities in filament length distribution. We then investigate the effects of filament growth inhibition by capping proteins and growth promotion by formin proteins on filament length distribution. We find that filament length heterogeneity can be increased by growth inhibition, whereas growth promoters do not significantly affect length heterogeneities. Interestingly, a competition between filament growth inhibitors and growth promoters can give rise to bimodal filament length distribution as well as a highly heterogeneous length distribution with large statistical dispersion. We quantitatively predict how heterogeneity in actin filament length can be modulated by tuning F-actin nucleation and growth rates in order to create distinct filament subpopulations with different lengths.

SIGNIFICANCEActin filaments organize into different functional network architectures within eukaryotic cells. To maintain different actin network architectures, actin filaments of different lengths are often required. How cells regulate the length heterogeneity in actin filaments is not well understood. Here we show that the modulation of filament growth rates and nucleation rate by binding partners like formin and capping proteins can regulate the emergent length heterogeneity in the filament population and can create distinct sub-populations with different lengths. Our study sheds light into how actin binding proteins can control various aspects of filament size distribution by tuning their concentration or expression levels in the cell.


title: Modelling the coupling of the M-clock and C-clock in lymphatic muscle cells

abstract: Lymphoedema develops due to chronic dysfunction of the lymphatic vascular system which results in fluid accumulation between cells. The condition is commonly acquired secondary to diseases such as cancer or the therapies associated with it. The primary driving force for fluid return through the lymphatic vasculature is provided by contractions of the muscularized lymphatic collecting vessels, driven by electrical oscillations. However, there is an incomplete understanding of the molecular and bioelectric mechanisms involved in lymphatic muscle cell excitation, hampering the development and use of pharmacological therapies. Modelling in silico has contributed greatly to understanding the contributions of specific ion channels to the cardiac action potential, but modelling of these processes in lymphatic muscle remains limited. Here, we propose a model of oscillations in the membrane voltage (M-clock) and intracellular calcium concentrations (C-clock) of lymphatic muscle cells. We modify a model by Imtiaz and colleagues to enable the M-clock to drive the C-clock oscillations. This approach differs from typical models of calcium oscillators in lymphatic and related cell types, but is required to fit recent experimental data. We include an additional voltage dependence in the gating variable control for the L-type calcium channel, enabling the M-clock to oscillate independently of the C-clock. We use phase-plane analysis to show that these M-clock oscillations are qualitatively similar to those of a generalised FitzHugh-Nagumo model. We also provide phase plane analysis to understand the interaction of the M-clock and C-clock oscillations. The model and methods have the potential to help determine mechanisms and find targets for pharmacological treatment of lymphoedema.


title: NMDA receptor-targeted enrichment of CaMKIIα improves fear memory

abstract: Calcium/calmodulin-dependent protein kinase II alpha (CaMKII) is an essential player in long-term potentiation and memory formation. However, the establishment of effective molecular interventions with CaMKII to improve memory remains a long-standing challenge. Here we report a novel intrabody targeting GluN1, a subunit of N-methyl-D-aspartate receptors (NMDARs). We identify this anti-GluN1 intrabody (termed VHH Anti-GluN1; VHHAN1) by a synthetic phage display library selection and yeast-two-hybrid screenings. We validate specific targeting of VHHAN1 to GluN1 in heterologous cells and the mouse hippocampus. We further show that adeno-associated virus (AAV)-mediated expression of CaMKII fused with VHHAN1 is locally enriched at excitatory postsynaptic regions of the mouse hippocampus. We also find that the AAV- and VHHAN1-mediated postsynaptic enrichment of CaMKII in the hippocampus improves contextual fear memory in mice. This novel approach opens a new avenue to enhance memory ability in health and diseases.

category: neuroscience


title: Dopamine neuron morphology and output are differentially controlled by mTORC1 and mTORC2

abstract: The mTOR pathway is an essential regulator of cell growth and metabolism. Midbrain dopamine neurons are particularly sensitive to mTOR signaling status as activation or inhibition of mTOR alters their morphology and physiology. mTOR exists in two distinct multiprotein complexes termed mTORC1 and mTORC2. How each of these complexes affect dopamine neuron properties and whether they act together or independently is unknown. Here we investigated this in mice with dopamine neuron-specific deletion of Rptor or Rictor, which encode obligatory components of mTORC1 or mTORC2, respectively. We find that inhibition of mTORC1 strongly and broadly impacts dopamine neuron structure and function causing somatodendritic and axonal hypotrophy, increased intrinsic excitability, decreased dopamine production, and impaired dopamine release. In contrast, inhibition of mTORC2 has more subtle effects, with selective alterations to the output of ventral tegmental area dopamine neurons. As mTOR is involved in several brain disorders caused by dopaminergic dysregulation including Parkinsons disease and addiction, our results have implications for understanding the pathophysiology and potential therapeutic strategies for these diseases.


title: An extended amygdala-midbrain circuit controlling cocaine withdrawal-induced anxiety and reinstatement

abstract: While midbrain dopamine (DA) neuronal circuits are central to motivated behaviors, much remains unknown about our knowledge of how these circuits are modified over time by experience to facilitate selective aspects of experience-dependent plasticity. Most studies of the DA system in drug addiction focus on the role of the mesolimbic DA pathway from the ventral tegmental area (VTA) to the nucleus accumbens (NAc) in facilitating drug-associated reward. In contrast, less is known about how midbrain DA cells and associated circuits contribute to negative affective states including anxiety that emerge during protracted withdrawal from drug administration. Here, we demonstrate the selective role of a midbrain DA projection to the amygdala (VTADA[->]Amygdala) for anxiety that develops during protracted withdrawal from cocaine administration but does not participate in cocaine reward or sensitization. Our rabies virus-mediated circuit mapping approach revealed a persistent elevation in spontaneous and task-related activity of GABAergic cells from the bed nucleus of the stria terminals (BNST) and downstream VTADA[->]Amygdala cells that could be detected even after a single cocaine exposure. Activity in BNSTGABA cells was related to cocaine-induced anxiety but not reward or sensitization, and silencing the projection from these cells to the midbrain was sufficient to prevent the development of anxiety during protracted withdrawal following cocaine administration. We observed that VTADA[->]Amygdala cells, but not other midbrain DA cells, were strongly activated after a challenge exposure to cocaine, and found that activity in these cells was necessary for the expression of reinstatement of cocaine place preference. Lastly, the importance of activity in VTADA[->]Amygdala cells extends beyond cocaine, as these cells mediate the development of anxiety states triggered by morphine and a predator odor. Our results provide an exemplar for how to identify key circuit substrates that contribute to behavioral adaptations and reveal a critical role for BNSTGABA[->]VTADA[->]Amygdala pathway in anxiety states induced by drugs of abuse or natural experiences as well as cocaine-primed reinstatement of conditioned place preference.


title: Sleep promoting neurons remodel their response properties to calibrate sleep drive with environmental demands.

abstract: Falling asleep at the wrong time can place an individual at risk of immediate physical harm. However, not sleeping degrades cognition and adaptive behavior. To understand how animals match sleep need with environmental demands, we used live-brain imaging to examine the physiological response properties of the Drosophila sleep homeostat (dFB) following interventions that modify sleep (sleep deprivation, starvation, time-restricted feeding, memory consolidation). We report that dFB neurons can distinguish between different types of waking and can change their physiological response-properties accordingly. That is, dFB neurons are not simply passive components of a hard-wired circuit. Rather, the dFB neurons themselves can determine their response to the activity from upstream circuits. Finally, we show that the dFB appears to contain a memory trace of prior exposure to metabolic challenges induced by starvation or time-restricted feeding. Together these data highlight that the sleep homeostat is plastic and suggests an underlying mechanism.


title: Mushroom body input connections form independently of sensory activity in Drosophila melanogaster

abstract: Associative brain centers, such as the insect mushroom body, need to represent sensory information in an efficient manner. In Drosophila melanogaster, the Kenyon cells of the mushroom body integrate inputs from a random set of olfactory projection neurons, but some projection neurons -- namely those activated by a few ethologically meaningful odors -- connect to Kenyon cells more frequently than others. This biased and random connectivity pattern is conceivably advantageous, as it enables the mushroom body to represent a large number of odors as unique activity patterns while prioritizing the representation of a few specific odors. How this connectivity pattern is established remains largely unknown. Here, we test whether the mechanisms patterning the connections between Kenyon cells and projection neurons depend on sensory activity or whether they are hardwired. We mapped a large number of mushroom body input connections in anosmic flies -- flies lacking the obligate odorant co-receptor Orco -- and in wildtype flies. Statistical analyses of these datasets reveal that the random and biased connectivity pattern observed between Kenyon cells and projection neurons forms normally in the absence of most olfactory sensory activity. This finding supports the idea that even comparatively subtle, population-level patterns of neuronal connectivity can be encoded by fixed genetic programs and are likely to be the result of evolved prioritization of ecologically and ethologically salient stimuli.


title: MAP4K3 inhibits Sirtuin-1 to repress LKB1-AMPK to promote amino acid dependent activation of mTORC1

abstract: mTORC1 is the key rheostat controlling cellular metabolic state. Of the various inputs to mTORC1, the most potent effector of intracellular nutrient status is amino acid supply. Despite an established role for MAP4K3 in promoting mTORC1 activation in the presence of amino acids, the signaling pathway by which MAP4K3 controls mTORC1 activation remains unknown. Here we examined the process of MAP4K3 activation of mTORC1 and found that MAP4K3 represses the LKB1-AMPK pathway to prevent TSC1/2 complex inactivation of Rheb. When we sought the regulatory link between MAP4K3 and LKB1 inhibition, we discovered that MAP4K3 physically interacts with the master nutrient regulatory factor Sirtuin-1 and phosphorylates Sirtuin-1 to repress LKB1 activation. Our results reveal the existence of a novel signaling pathway linking amino acid satiety with MAP4K3-dependent suppression of SIRT1 to inactivate the repressive LKB1-AMPK pathway and thereby potently activate the mTORC1 complex to dictate the metabolic disposition of the cell.

category: cell biology


title: The Ecology of Palm Genomes: Repeat-associated genome size expansion is constrained by aridity

abstract:
O_LIGenome size varies 2,400-fold across plants, influencing their evolution through changes in cell size and cell division rates which impact plants environmental stress tolerance. Repetitive element expansion explains much genome size diversity, and the processes structuring repeat  communities are analogous to those structuring ecological communities. However, which environmental stressors influence repeat community dynamics has not yet been examined from an ecological perspective.
C_LIO_LIWe measured genome size and leveraged climatic data for 91% of genera within the ecologically diverse palm family (Arecaceae). We then generated genomic repeat profiles for 141 palm species, and analysed repeats using phylogenetically-informed linear models to explore relationships between repeat dynamics and environmental factors.
C_LIO_LIWe show that palm genome size and repeat  community composition are best explained by aridity. Specifically, EnSpm CACTA repeats were more abundant in palm species from wetter environments, which generally had larger genomes (>2.15Gbp/1C), suggesting amplification. In contrast, Ty1-copia Angela elements were more abundant in drier environments.
C_LIO_LIOur results suggest water stress inhibits the expansion of repeats through selection on upper genome size limits. However, Ty1-copia Angela elements, which may associate with stress-response genes, have amplified in arid-adapted palm species. Overall, we provide novel evidence of climate influencing the assembly of repeat  communities.
C_LI

category: evolutionary biology


title: Multiview Graph Learning for single-cell RNA sequencing data

abstract: Characterizing the underlying topology of gene regulatory networks is one of the fundamental problems of systems biology. Ongoing developments in high throughput sequencing technologies has made it possible to capture the expression of thousands of genes at the single cell resolution. However, inherent cellular heterogeneity and high sparsity of the single cell datasets render void the application of regular Gaussian assumptions for constructing gene regulatory networks. Additionally, most algorithms aimed at single cell gene regulatory network reconstruction, estimate a single network ignoring group-level (cell-type) information present within the datasets. To better characterize single cell gene regulatory networks under different but related conditions we propose the joint estimation of multiple networks using multiview graph learning (mvGL). The proposed method is developed based on recent works in graph signal processing (GSP) for graph learning, where graph signals are assumed to be smooth over the unknown graph structure. Graphs corresponding to the different datasets are regularized to be similar to each other through a learned consensus graph. We further kernelize mvGL with the kernel selected to suit the structure of single cell data. An efficient algorithm based on prox-linear block coordinate descent is used to optimize mvGL. We study the performance of mvGL using synthetic data generated with a diverse set of parameters. We further show that mvGL successfully identifies well-established regulators in a mouse embryonic stem cell differentiation study and a cancer clinical study of medulloblastoma.


title: Nucleobase clustering contributes to the formation and hollowing of repeat-expansion RNA condensate

abstract: RNA molecules with repeat expansion sequences can phase separate into gel-like condensate, and this process may lead to neurodegenerative diseases. Here we report that in the presence of Mg2+ ion, RNA molecules containing 20xCAG repeats coacervate into filled droplets or hollowed condensate. Using hyperspectral stimulated Raman spectroscopy, we show that RNA coacervation is accompanied by the stacking and clustering of nucleobases, while forfeiting the canonical base-paired structure. At an increasing RNA/Mg2+ ratio, the RNA droplets first expand in sizes, and then shrink and adopt hollow vesicle-like structures. Significantly, for both large and vesicle-like droplets, the nucleobase-clustered structure is more prominent at the rim than at the center, accounting for the rigidification of RNA droplets. Thus, our finding has broad implications for the general aging processes of RNA-containing membrane-less organelles.


title: Three-dimensional in vitro model of the device-tissue interface reveals innate neuroinflammation can be mitigated by antioxidant ceria nanoparticles

abstract: The recording instability of neural implants due to neuroinflammation at the device-tissue interface (DTI) is a primary roadblock to broad adoption of brain-machine interfaces. While a multiphasic immune response, marked by glial scaring, oxidative stress (OS), and neurodegeneration, is well-characterized, the independent contributions of systemic and local "innate" immune responses are not well-understood. Three-dimensional primary neural cultures provide a unique environment for studying the drivers of neuroinflammation by decoupling the innate and systemic immune systems, while conserving an endogenous extracellular matrix and structural and functional network complexity. We created a three-dimensional in vitro model of the DTI by seeding primary cortical cells around microwires. Live imaging of microtissues over time revealed independent innate neuroinflammation, marked by increased OS, decreased neuronal density, and increased functional connectivity. We demonstrated the use of this model for therapeutic screening by directly applying drugs to neural tissue, bypassing low bioavailability through the in vivo blood brain barrier. As there is growing interest in long-acting antioxidant therapies, we tested efficacy of "perpetual" antioxidant ceria nanoparticles, which reduced OS, increased neuronal density, and protected functional connectivity. Overall, our avascular in vitro model of the DTI exhibited symptoms of OS-mediated innate neuroinflammation which were mitigated by antioxidant intervention.


title: CPTAC Pancancer Phosphoproteomics Kinase Enrichment Analysis with ProKAP Provides Insights into Immunogenic Signaling Pathways

abstract: The National Cancer Institute (NCI) Clinical Proteomic Tumor Analysis Consortium (CPTAC) initiative has generated extensive phosphoproteomics and proteomics data for tumor and tumor-adjacent normal tissue across multiple cancer types. This dataset provides an unprecedented opportunity to systematically characterize pan-cancer kinase activities, which is essential for coupling tumor subtypes with kinase inhibitors as potential treatment. In this work, we performed Kinase Enrichment Analysis (KEA) using a CPTAC phosphoproteomics dataset to identify putative differences in kinase state between tumor and normal tissues within and across five types of cancer. We then implemented an interactive web-portal, the ProTrack Kinase Activity Portal (ProKAP), for querying, visualizing, and downloading the derived pan-cancer kinase activity scores together with the corresponding sample metadata, and protein and phosphoprotein expression profiles. To illustrate the usage of this digital resource, we analyzed the association between kinase activity scores and immune subtypes of clear cell renal cell carcinoma (ccRCC) derived from the CPTAC ccRCC study. We found multiple kinases, whose inhibition has been suggested to have therapeutic effect in other tumor types, are highly active in CD8+-enriched ccRCC tumors. The ProTrack Kinase Activity Portal (ProKAP) is available at: https://pancan-kea3.cptac-data-view.org.

category: bioinformatics


title: Fast and Optimal Sequence-to-Graph Alignment Guided by Seeds

abstract:
We present a novel A[*] seed heuristic that enables fast and optimal sequence-to-graph alignment, guaranteed to minimize the edit distance of the alignment assuming non-negative edit costs.

We phrase optimal alignment as a shortest path problem and solve it by instantiating the A[*] algorithm with our seed heuristic. The seed heuristic first extracts non-overlapping substrings (seeds) from the read, finds exact seed matches in the reference, marks preceding reference positions by crumbs, and uses the crumbs to direct the A[*] search. The key idea is to punish paths for the absence of foreseeable seed matches. We prove admissibility of the seed heuristic, thus guaranteeing alignment optimality.

Our implementation extends the free and open source aligner and demonstrates that the seed heuristic outperforms all state-of-the-art optimal aligners including GO_SCPLOWRAPHC_SCPLOWAO_SCPLOWLIGNERC_SCPLOW, VO_SCPLOWARGASC_SCPLOW, PO_SCPLOWAC_SCPLOWSGAL, and the prefix heuristic previously employed by ASO_SCPLOWTARIXC_SCPLOW. Specifically, we achieve a consistent speedup of >60x on both short Illumina reads and long HiFi reads (up to 25kbp), on both the E. coli linear reference genome (1Mbp) and the MHC variant graph (5Mbp). Our speedup is enabled by the seed heuristic consistently skipping >99.99% of the table cells that optimal aligners based on dynamic programming compute.

ASO_SCPLOWTARIXC_SCPLOW aligner and evaluations: https://github.com/eth-sri/astarix Full paper: https://www.biorxiv.org/content/10.1101/2021.11.05.467453


title: A switch in the development: microRNA arm usage screening in zebrafish suggests an important role of arm switching events in ontogenesis

abstract: In metazoan, regulatory molecules tightly control gene expression. Among them, microRNAs (miRNAs) are key regulators of several important features, like cell proliferation, differentiation, and homeostasis. During miRNA biogenesis, the canonical strand that loads onto RISC can be switched, in a process called "arm switching." Due to the miRNA-to-target pairing peculiarities, switching events can lead to changes on the gene-targeted repertoire, promoting the modulation of a distinct set of biological routes. To understand how these events affect cell regulation, we conducted an extensive and detailed in silico analysis of RNA-seq datasets from several tissues and key developmental stages of zebrafish. We identified interesting patterns of miRNA arm switching occurrence, mainly associated with the control of protein coding genes during embryonic development. Additionally, our data show that miRNA isoforms (isomiRs) play an important role in differential arm usage. Our findings provide new insights on how such events emerge and coordinate gene expression regulation, opening perspectives for novel investigations in the area.


title: AN ECONOMIC, SQUARE-SHAPED FLAT-FIELD ILLUMINATION MODULE FOR TIRF-BASED SUPER-RESOLUTION MICROSCOPY

abstract: Super-resolution (SR) microscopy allows complex biological assemblies to be observed with remarkable resolution. However, the presence of uneven Gaussian-shaped illumination hinders its use in quantitative imaging or high-throughput assays. Methods developed to circumvent this problem are often expensive, hard-to-implement, or not applicable to total internal reflection fluorescence (TIRF) imaging. We herein demonstrate a cost-effective method to overcome these challenges using a small square-core multimodal optical fibre as the coupler. We characterise our method with synthetic, recombinant and cellular systems imaged under TIRF and highly inclined and laminated optical sheet (HILO) illuminations to demonstrate its ability to produce highly uniform images under all conditions.


title: Identifiability of pharmacological models for online individualization

abstract: There is a large variability between individuals in the response to anesthetic drugs, that seriously limits the achievable performance of closed-loop controlled drug dosing. Full individualization of patient models based on early clinical response data has been suggested as a means to improve performance with maintained robustness (safety). We use estimation theoretic analysis and realization theory to characterize practical identifiability of the standard pharmacological model structure from anesthetic induction phase data and conclude that such approaches are not practically feasible.

category: pharmacology and toxicology


title: Single-cell metabolomics reveals the metabolic heterogeneity among microbial cells

abstract: In microbial research, the heterogeneity phenomenon is closely associated with microbial physiology in multiple dimensions. For now, A few studies were proposed in transcriptome and proteome analysis to discover the heterogeneity among single cells. However, microbial single cell metabolomics has not been possible yet. Herein, we developed a method, RespectM, based on discontinuous mass spectrometry imaging, which can detect more than 700 metabolites at a rate of 500 cells per hour. While ensuring the high throughput of RespectM, it integrates matrix sublimation, QC-based peak filtering, and batch correction strategies to improve accuracy. The results show that RespectM can distinguish single microbial cells from the blank matrix with an accuracy of 98.4%, depending on classification algorithms. Furthermore, to verify the accuracy of RespectM for distinguishing different single cells, we performed a classification test on Chlamydomonas reinhardtii single cells among allelic strains. The results showed an accuracy of 93.1%, which provides RespectM with enough confidence to perform microbial single cell metabolomics analysis. As we expected, untreated microbial cells will spontaneously undergo metabolic grouping coherence with genetic and biochemical similarities. Interestingly, the pseudo-time analysis also provided intuitive evidence on the metabolic dimension, indicating the cell grouping is based on microbial population heterogeneity. We believe that the RespectM can offer a powerful tool in the microbial study. Researchers can now directly analyze the changes in microbial metabolism at a single-cell level with high efficiency.


title: The effect of the preceding masking noise on monaural and binaural release from masking

abstract: The auditory system uses various signal properties to separate a target signal from background noise. When a target tone is preceded by a noise, the threshold for target detection can be increased or decreased depending on the type of a preceding masker. The effect of the preceding masker on the following sound can be interpreted as stream formation. The effect of stream formation is assumed to be either the result of adaptation at a low-level or high-level auditory processing. In an attempt to disentangle these, we investigated the time constant of the underlying process of adaptation by varying the length of the preceding masker. We designed stimuli consisting of the preceding masker and the following masked tone. Each stimulus induces various stream formation, affecting following target detection or masking release. Target tone was presented in comodulated masking noise and with interaural phase difference (IPD), inducing comodulation masking release (CMR) and binaural masking level difference (BMLD), respectively. We measured CMR and BMLD when the length of preceding maskers varied from 0 (no preceding masker) to 500 ms. We postulate that if the adaptation is dominated by high-level auditory processing, both CMR and BMLD will be affected by an increase in the length of the preceding masker. Results showed that CMR was more affected with longer preceding maskers from 100 ms to 500 ms compared to shorter maskers. On the contrary, the preceding masker did not affect the BMLD. Based on the results, we suggest that the adaptation to a preceding masking sound may arise from a low-level (e.g., cochlear nucleus, CN) rather than the temporal integration by the high-level auditory processing.


title: Three-dimensional spike localization and improved motion correction for Neuropixels recordings

abstract: Neuropixels (NP) probes are dense linear multi-electrode arrays that have rapidly become essential tools for studying the electrophysiology of large neural populations. Unfortunately, a number of challenges remain in analyzing the large datasets output by these probes. Here we introduce several new methods for extracting useful spiking information from NP probes. First, we use a simple point neuron model, together with a neural-network denoiser, to efficiently map single spikes detected on the probe into three-dimensional localizations. Previous methods localized individual spikes in two dimensions only; we show that the new localization approach is significantly more robust and provides an improved feature set for clustering spikes according to neural identity ("spike sorting"). Next, we denoise the resulting three-dimensional point-cloud representation of the data, and show that the resulting 3D images can be accurately registered over time, leading to improved tracking of time-varying neural activity over the probe, and in turn, crisper estimates of neural clusters over time. Open source code is available at https://github.com/int-brain-lab/spikes_localization_registration.git.


title: Neural correlates of masked and unmasked tones: psychoacoustics and late auditory evoked potentials (LAEPs)

abstract: Hearing thresholds are commonly used to quantify a listeners ability to detect sound. In the presence of masking sounds, hearing thresholds can vary depending on the signal properties of the target and the masker, commonly referred to as auditory cues. Target detection can be facilitated with comodulated masking noise and interaural phase disparity (IPD). This can be quantified with a decrease in detection thresholds or masking release: comodulation masking release (CMR, for comodulation) and binaural masking level difference (BMLD, for IPD). As these measures only reflect the low limit of levels for target detection, the relevance of masking release at supra-threshold levels is still unclear. Here, we used psychoacoustic and electrophysiological measures to investigate the effect of masking release for a masked tone at supra-threshold levels. Behaviorally, we investigated how the amount of masking release affects the salience at supra-threshold levels. We used intensity just-noticeable difference (JND) to quantify level-dependent changes in the salience of the tonal signal. As a physiological correlate, we investigated late auditory evoked potentials (LAEPs) with electroencephalography (EEG). The results showed that the intensity JNDs were equal at the same physical target tone level, regardless of the presence or absence of masking release. Estimated salience was correlated with the amount of masking release. However, salience measures across conditions converged with the target tone level above 70 dB SPL. For the LAEPs, the P2 amplitudes were more closely linked to behavioral measures than the N1 amplitudes. Both behavioral and electrophysiological measures suggest that the salience of a masked tone at supra-threshold levels is correlated with the amount of masking release.


title: Embryonic valproate exposure alters mesencephalic dopaminergic neurons distribution and septal dopaminergic gene expression in domestic chicks

abstract: In recent years, the role of the dopaminergic system in the regulation of social behavior is being progressively outlined, and dysfunctions of the dopaminergic system are increasingly associated with neurodevelopmental disorders, including ASD. To further elucidate the role of the dopaminergic system in ASD, we investigated the effects of embryonic exposure to valproic acid (VPA) on the postnatal development of the mesencephalic DA system in the domestic chick. We found that VPA affected the rostro-caudal distribution of DA neurons, without changing the expression levels of several dopaminergic markers in the mesencephalon. We also investigated a potential consequence of this altered DA neuronal distribution in the septum, a social brain area previously associated to social behaviour in several vertebrate species, describing alterations in the expression of genes linked to DA neurotransmission. These findings support the emerging hypothesis of a role of DA dysfunction in ASD pathogenesis. Together with previous studies showing impairments of early social orienting behaviour, these data also support the use of the domestic chick model to investigate the neurobiological mechanisms involved in early ASD symptoms.


title: TRIM24 controls induction of latent HIV-1 by stimulating transcriptional elongation

abstract: The conserved HIV-1 LTR cis elements RBE1/3 bind the factor RBF2, consisting of USF1/2 and TFII-I, and are essential for reactivation of HIV-1 by T cell signaling. We determined that TFII-I recruits the tripartite motif protein TRIM24 to the LTR, and this interaction is required for efficient reactivation of HIV-1 expression in response to T cell signaling, similar to the effect of TFII-I depletion. Knockout of TRIM24 did not affect recruitment of RNA Pol II to the LTR promoter, but inhibited transcriptional elongation, an effect that was associated with decreased RNA Pol II CTD S2 phosphorylation and impaired recruitment of CDK9 to the LTR. These results demonstrate that TFII-I promotes transcriptional elongation in response to T cell activation through recruitment of the co-factor TRIM24, which is necessary for efficient recruitment of the elongation factor P-TEFb.


title: Developmental regulation and functional prediction of microRNAs in an expanded Fasciola hepatica miRNome

abstract:
1The liver fluke, Fasciola hepatica, is a global burden on the wellbeing and productivity of farmed ruminants, and a zoonotic threat to human health. Despite the clear need for accelerated discovery of new drug and vaccine treatments for this pathogen, we still have a relatively limited understanding of liver fluke biology and host interactions. Noncoding RNAs, including micro (mi)RNAs, are key to transcriptional regulation in all eukaryotes, such that an understanding of miRNA biology can shed light on organismal function at a systems level. Four previous publications have reported up to 89 mature miRNA sequences from F. hepatica, but our data show that this does not represent a full account of this species miRNome. We have expanded on previous studies by sequencing, for the first time, miRNAs from multiple life stages (adult, newly excysted juvenile (NEJ), metacercariae and adult-derived extracellular vesicles (EVs)). These experiments detected an additional 61 high-confidence miRNAs, most of which have not been described in any other species, expanding the F. hepatica miRNome to 150 mature sequences. We used quantitative (q)PCR assays to provide the first developmental profile of miRNA expression across metacercariae, NEJ, adult and adult-derived Evs. The majority of miRNAs were expressed most highly in metacercariae, with at least six distinct expression clusters apparent across life stages. Intracellular miRNAs were functionally analysed to identify target mRNAs with inversely correlated expression in F. hepatica tissue transcriptomes, highlighting regulatory interactions with key virulence transcripts including cathepsin proteases, and neuromuscular genes that control parasite growth, development and motility. We also linked 28 adult-derived EV miRNAs with downregulation of 397 host genes in F. hepatica-infected transcriptomes from ruminant lymph node, peripheral blood mononuclear cell (PBMC) and liver tissue transcriptomes. These included genes involved in signal transduction, immune and metabolic pathways, adding to the evidence for miRNA-based immunosuppression during fasciolosis. These data expand our understanding of the F. hepatica miRNome, provide the first data on developmental miRNA regulation in this species, and provide a set of testable hypotheses for functional genomics interrogations of liver fluke miRNA biology.

CONTRIBUTION TO THE FIELDPrevious studies identified 89 micro (mi)RNAs (non-coding RNAs responsible for regulating gene expression) in the trematode parasite, Fasciola hepatica, and attached functional annotations to the miRNAs that are secreted by liver fluke in vitro. This study expands the known miRNA complement of F. hepatica by 40%, adding an additional 61 miRNAs, many of which appear Fasciola-specific. We used this expanded dataset to perform the first analysis of developmental miRNA expression across intra-mammalian parasites, showing clear developmentally regulated expression profiles across infectious metacercariae, juvenile and adult parasites, and extracellular vesicles secreted by adult parasites. We performed rigorous functional annotation of cellular miRNAs, correlating their expression with mRNA transcriptomes to identify potential roles for specific miRNAs in regulating expression of important proteases and nerve/muscle transcripts, all of which are important for parasite virulence. We also functionally analysed miRNAs secreted by adult parasites in terms of interactions with host transcripts; for the first time this analysis was supported by host transcriptome data, linking secreted miRNAs with mRNAs that are downregulated by fluke infection in sheep and cattle. This work contributes new data, insights and analyses to the field, providing a rich source of hypotheses for future experimental validation.


title: Control of Neutrophil activation through Semaphorin 7A-Plexin C1 is essential for immune defense during pulmonary sepsis.

abstract:
Pulmonary defense mechanisms are critical for host integrity during the early phase of pneumonia and sepsis. These processes are fundamentally dependent on the activation of neutrophils during the early phase of the innate immune response. Recent work has shown that semaphorin 7A (Sema7A) holds significant impact on platelet activation, yet its role in neutrophil migration and function is not well known. We report here that Sema7A binds to neutrophil PlexinC1, increasing integrins and L-selectin on the neutrophil surface. Sema7A-induced neutrophil activation also prompted neutrophil chemotaxis in vitro and the formation of platelet-neutrophil complexes in vivo. We also observed altered adhesion and transmigration of neutrophils in Sema7A-/- animals in the lung. Sema7A-/- animals also showed altered crawling properties of neutrophils. This resulted in increased number of neutrophils in the interstitial space of Sema7A-/- animals but reduced numbers of neutrophils in the alveolar space during pneumonia-induced pulmonary sepsis. This was associated with significantly worse outcome of Sema7A-/- animals in a model of Klebsiella pneumoniae. Furthermore, we were able to show a correlation between serum levels of Sema7A in patients with ARDS and oxygenation levels. Thus, we show here that Sema7A has an immunomodulatory effect though which might influence patient outcome during pulmonary sepsis.

SummarySema7A controls pulmonary immune defense


title: Biogeographic multi-species occupancy models for large-scale survey data

abstract:
O_LIEcologists often seek to infer patterns of species occurrence or community structure from survey data. Hierarchical models, including multi-species occupancy models (MSOMs), can improve inference by pooling information across multiple species via random effects. Originally developed for local-scale survey data, MSOMs are increasingly applied to larger spatial scales that transcend major abiotic gradients and dispersal barriers. At biogeographic scales, the benefits of partial pooling in MSOMs trade off against the difficulty of incorporating sufficiently complex spatial effects to account for biogeographic variation in occupancy across multiple species simultaneously.
C_LIO_LIWe show how this challenge can be overcome by incorporating pre-existing range information into MSOMs, yielding a  biogeographic multi-species occupancy model (bMSOM). We illustrate the bMSOM using two published datasets: Parulid warblers in the United States Breeding Bird Survey, and entire avian communities in forests and pastures of Colombias West Andes.
C_LIO_LICompared to traditional MSOMs, the bMSOM provides dramatically better predictive performance at lower computational cost. The bMSOM avoids severe spatial biases in predictions of the traditional MSOM and provides principled species-specific inference even for never-observed species.
C_LIO_LIIncorporating pre-existing range data enables principled partial pooling of information across species in large-scale MSOMs. Our biogeographic framework for multi-species modeling should be broadly applicable in hierarchical models that predict species occurrences, whether or not false-absences are modeled in an occupancy framework.
C_LI

category: ecology


title: Fossils Do Not Substantially Improve, and May Even Harm, Estimates of Diversification Rate Heterogeneity

abstract: The fossilized birth-death (FBD) model is a naturally appealing way of directly incorporating fossil information when estimating diversification rates. However, an important yet often overlooked property of the original FBD derivation is that it distinguishes between two types of sampled lineages. Here we first discuss and demonstrate the impact of severely undersampling, and even not including fossils that represent samples of lineages that also had sampled descendants. We then explore the benefits of including fossils, generally, by implementing and then testing two-types of FBD models, including one that converts a fossil set into stratigraphic ranges, in more complex likelihood-based models that assume multiple rate classes across the tree. Under various simulation scenarios, including a scenario that exists far outside the set of models we evaluated, including fossils rarely outperforms analyses that exclude them altogether. At best, the inclusion of fossils improves precision but does not influence bias. Similarly, we found that converting the fossil set to stratigraphic ranges, which is one way to remedy the effects of undercounting the number of k-type fossils, results in turnover rates and extinction fraction estimates that are generally underestimated. While fossils remain essential for understanding diversification through time, in the specific case of understanding diversification given an existing, largely modern tree, they are not especially beneficial.


title: On the Effect of Intralocus Recombination on Triplet-Based Species Tree Estimation

abstract: We consider species tree estimation from multiple loci subject to intralocus recombination. We focus on R*, a summary coalescent-based methods using rooted triplets. We demonstrate analytically that intralocus recombination gives rise to an inconsistency zone, in which correct inference is not assured even in the limit of infinite amount of data. In addition, we validate and characterize this inconsistency zone through a simulation study that suggests that differential rates of recombination between closely related taxa can amplify the effect of incomplete lineage sorting and contribute to inconsistency.


title: A framework for detecting noncoding rare variant associations of large-scale whole-genome sequencing studies

abstract: Large-scale whole-genome sequencing studies have enabled analysis of noncoding rare variants (RVs) associations with complex human traits. Variant set analysis is a powerful approach to study RV association, and a key component of it is constructing RV sets for analysis. However, existing methods have limited ability to define analysis units in the noncoding genome. Furthermore, there is a lack of robust pipelines for comprehensive and scalable noncoding RV association analysis. Here we propose a computationally-efficient noncoding RV association-detection framework that uses STAAR (variant-set test for association using annotation information) to group noncoding variants in gene-centric analysis based on functional categories. We also propose SCANG (scan the genome)-STAAR, which uses dynamic window sizes and incorporates multiple functional annotations, in a non-gene-centric analysis. We furthermore develop STAARpipeline to perform flexible noncoding RV association analysis, including gene-centric analysis as well as fixed-window-based and dynamic-window-based non-gene-centric analysis. We apply STAARpipeline to identify noncoding RV sets associated with four quantitative lipid traits in 21,015 discovery samples from the Trans-Omics for Precision Medicine (TOPMed) program and replicate several noncoding RV associations in an additional 9,123 TOPMed samples.


title: RUV-III-NB: Normalization of single cell RNA-seq Data

abstract: Despite numerous methodological advances, the normalization of single cell RNA-seq (scRNA-seq) data remains a challenging task and the performance of different methods can vary greatly across datasets. Part of the reason for this is the different kinds of unwanted variation, including library size, batch and cell cycle effects, and the association of these with the biology embodied in the cells. A normalization method that does not explicitly take into account cell biology risks removing some of the signal of interest. Furthermore, most normalization methods remove the effects of unwanted variation for the cell embedding used for clustering-based analysis but not from gene-level data typically used for differential expression (DE) analysis to identify marker genes. Here we propose RUV-III-NB, a statistical method that can be used to remove unwanted variation from both the cell embedding and gene-level counts. RUV-III-NB explicitly takes into account its potential association with biology when removing unwanted variation via the use of pseudo-replicates. The method can be used for both UMI or sequence read counts and returns adjusted counts that can be used for downstream analyses such as clustering, DE and pseudotime analyses. Using five publicly available datasets that encompass different technological platforms, kinds of biology and levels of association between biology and unwanted variation, we show that RUV-III-NB manages to remove library size and batch effects, strengthen biological signals, improve differential expression analyses, and lead to results exhibiting greater concordance with independent datasets of the same kind. The performance of RUV-III-NB is consistent across the five datasets and is not sensitive to the number of factors assumed to contribute to the unwanted variation. It also shows promise for removing other kinds of unwanted variation such as platform effects. The method is implemented as a publicly available R package available from https://github.com/limfuxing/ruvIIInb.


title: LMPred: Predicting Antimicrobial Peptides Using Pre-Trained Language Models and Deep Learning

abstract: Antimicrobial peptides (AMPs) are increasingly being used in the development of new therapeutic drugs, in areas such as cancer therapy and hypertension. Additionally, they are seen as an alternative to antibiotics due to the increasing occurrence of bacterial resistance. Wet-laboratory experimental identification, however, is both time consuming and costly, so in-silico models are now commonly used in order to screen new AMP candidates. This paper proposes a novel approach of creating model inputs; using pre-trained language models to produce contextualized embeddings representing the amino acids within each peptide sequence, before a convolutional neural network is then trained as the classifier. The optimal model was validated on two datasets, being one previously used in AMP prediction research, and an independent dataset, created by this paper. Predictive accuracies of 93.33% and 88.26% were achieved respectively, outperforming all previous state-of-the-art classification models.


title: Making Common Fund data more Findable: Catalyzing a Data Ecosystem

abstract: The Common Fund Data Ecosystem (CFDE) has created a flexible system of data federation that enables users to discover datasets from across the U.S. National Institutes of Health Common Fund without requiring that data owners move, reformat, or rehost those data. The CFDEs federation system is centered on a catalog that ingests metadata from individual Common Fund Programs Data Coordination Centers (DCCs) into a uniform metadata model that can then be indexed and searched from a centralized portal. This uniform Crosscut Metadata Model (C2M2) supports the wide variety of data types and metadata terms used by the individual DCCs and is designed to enable easy expansion to accommodate new data types. We describe its use to ingest and index data from ten DCCs.


title: PacRAT: A program to improve barcode-variant mapping from PacBio long reads using multiple sequence alignment

abstract:
MotivationUse of PacBio sequencing for characterizing barcoded libraries of genetic variants is on the rise. PacBio sequencing is useful in linking variant alleles in a library with their associated barcode tag. However, current approaches in resolving PacBio sequencing artifacts can result in a high number of incorrectly identified or unusable reads.

ResultsWe developed a PacBio Read Alignment Tool (PacRAT) that improves the accuracy of barcode-variant mapping through several steps of read alignment and consensus calling. To quantify the performance of our approach, we simulated PacBio reads from eight variant libraries of various lengths and showed that PacRAT improves the accuracy in pairing barcodes and variants across these libraries. Analysis of real (non-simulated) libraries also showed an increase in the number of reads that can be used for downstream analyses when using PacRAT.

AvailabilityPacRAT is written in Python and is freely available on GitHub (https://github.com/dunhamlab/PacRAT).


title: Temporal saliency for motion direction may arise from visual stimulus-specific adaptation in avian midbrain inhibitory nucleus

abstract: Food and predators are the most noteworthy objects for the basic survival of wild animals. In nature, both of these are often rare or deviant in both spatial and temporal domains and would soon attract an animals attention. Although stimulus-specific adaptation (SSA) is considered to be one neural basis of salient sound detection in the temporal domain, related research on visual SSA is lacking. The avian nucleus isthmi pars magnocellularis (Imc), which plays an extremely important role in the selective attention network, is one of the best models for investigating the neural correlate of visual stimulus-specific adaptation (SSA) and detection of salient stimulus in the temporal domain. Here, we used a constant order paradigm to test the existence of SSA in the pigeons Imc. We found that the strength of response of Imc neurons significantly decreased after repetitive motion stimuli, but recovered when the motion was switched to a novel direction, leading to the saliency detection of the novel motion direction. These results suggest that the inhibitory nucleus Imc shows visual SSA to motion direction, allowing the Imc to implement temporal saliency mapping and to determine the spatial-temporal saliency of the current stimulus. This also implies that pigeons may detect novel spatial-temporal stimuli during the early stage of sensory processing.


title: Hippocampus-sensitive and striatum-sensitive learning one month after morphine or cocaine exposure in male rats

abstract: These experiments examined whether exposure to drugs of abuse altered the balance between hippocampal and striatal memory systems as measured long after drug treatments. Male rats received injections of morphine (5 mg/kg), cocaine (20 mg/kg), or saline for five consecutive days. One month later, rats were then trained to find food on a hippocampus-sensitive place task or a striatum-sensitive response task. Relative to saline controls, morphine-treated rats exhibited impaired place learning but enhanced response learning; prior cocaine exposure did not significantly alter learning on either task. Another set of rats was trained on a dual-solution T-maze that can be solved with either place or response strategies. While a majority (67%) of control rats used place solutions in this task, morphine treatment one month prior resulted in a shift to response solutions exclusively (100%). Prior cocaine treatment did not significantly alter strategy selection. Molecular markers related to learning and drug abuse were measured in the hippocampus and striatum one month after drug exposure in behaviorally untested rats. Protein levels of glial-fibrillary acidic protein (GFAP), an intermediate filament specific to astrocytes, increased significantly in the hippocampus after morphine, but not after cocaine exposure. Exposure to morphine or cocaine did not significantly change levels of brain-derived neurotrophic factor (BDNF) or a downstream target of BDNF signaling, glycogen synthase kinase 3{beta} (GSK3{beta}), in the hippocampus or striatum. Thus, exposure to morphine results in a long-lasting shift from hippocampal toward striatal dominance during learning. The effects of prior morphine injections on GFAP suggest that long-lasting alterations in hippocampal astrocytes may be associated with these behavioral strategy shifts.


title: Neuronal origins of biases in economic choices under sequential offers

abstract: Economic choices are characterized by a variety of biases. Understanding their origins is a long-term goal for neuroeconomics, but progress on this front has been limited. Here we examined choice biases observed when two goods are offered sequentially. In the experiments, rhesus monkeys chose between different juices offered simultaneously or in sequence. Choices under sequential offers were less accurate (higher variability). They were also biased in favor of the second offer (order bias) and in favor of the preferred juice (preference bias). Analysis of neuronal activity recorded in orbitofrontal cortex revealed that these phenomena emerged at different computational stages. The lower choice accuracy reflected weaker offer value signals (valuation stage), the order bias emerged during value comparison (decision stage), and the preference bias emerged late in the trial (post-comparison). Our approach, leveraging recent notions on the neural mechanisms of economic decisions, may shed light on other aspects of choice behavior.


title: Oxytocinergic modulation of stress-associated amygdala-hippocampus pathways in humans is specially mediated by serotonergic mechanisms

abstract:
BackgroundThe hypothalamic neuropeptide oxytocin (OXT) may exert anxiolytic and stress-reducing actions via modulatory effects on amygdala circuits. Animal models and initial findings in humans suggest that some of these effects are mediated by interactions with other neurotransmitter systems, in particular the serotonin (5-HT) system. Against this background, the present pharmacological resting state fMRI study aimed at determining whether effects of OXT on stress-associated amygdala intrinsic networks are mediated by 5-HT.

MethodsWe employed a randomized placebo-controlled double-blind parallel-group pharmacological fMRI resting state experiment during which n = 112 healthy male participants underwent a transient decrease in 5-HT signaling via acute tryptophan depletion (ATD) or the corresponding placebo-control protocols (ATDc) before the administration of intranasal OXT or placebo intranasal spray, respectively.

ResultsOXT and 5-HT modulation exerted interactive effects on the coupling of the left amygdala with the ipsilateral hippocampus and adjacent midbrain. OXT increased intrinsic coupling in this pathway, while this effect of OXT was significantly attenuated during transiently decreased central serotonergic signaling induced via ATD. In the absence of OXT or 5-HT modulation this pathway showed a trend for an association with self-reported stress perception in everyday life. No interactive effects were observed for the right amygdala.

ConclusionsTogether, the findings provide first evidence that effects of OXT on stress-associated amygdala-hippocampal-midbrain pathways are critically mediated by the 5-HT system in men.


title: Oxytocinergic modulation of stress-associated amygdala-hippocampus pathways in humans is mediated by serotonergic mechanisms


title: Robust transcriptional profiling and identification of differentially expressed genes with low input RNA sequencing of adult hippocampal neural stem and progenitor populations

abstract: Multipotent neural stem cells (NSCs) are found in several isolated niches of the adult mammalian brain where they have unique potential to assist in tissue repair. Modern transcriptomics offer high-throughput methods for identifying disease or injury associated gene expression signatures in endogenous adult NSCs, but they require adaptation to accommodate the rarity of NSCs. Bulk RNA sequencing (RNAseq) of NSCs requires pooling several mice, which impedes application to labor-intensive injury models. Alternatively, single cell RNAseq can profile hundreds to thousands of cells from a single mouse and is increasingly used to study NSCs. The consequences of the low RNA input from a single NSC on downstream identification of differentially expressed genes (DEGs) remains largely unexplored. Here, to clarify the role that low RNA input plays in NSC DEG identification, we directly compared DEGs in an oxidative stress model of cultured NSCs by bulk and single cell sequencing. While both methods yielded DEGs that were replicable, single cell sequencing DEGs derived from genes with higher relative transcript counts compared to all detected genes and exhibited smaller fold changes than DEGs identified by bulk RNAseq. The loss of high fold-change DEGs in the single cell platform presents an important limitation for identifying disease-relevant genes. To facilitate identification of such genes, we determined an RNA-input threshold that enables transcriptional profiling of NSCs comparable to standard bulk sequencing and used it to establish a workflow for in vivo profiling of endogenous NSCs. We then applied this workflow to identify DEGs after lateral fluid percussion injury, a labor-intensive animal model of traumatic brain injury. Our work suggests that single cell RNA sequencing may underestimate the diversity of pathologic DEGs but population level transcriptomic analysis can be adapted to capture more of these DEGs with similar efficacy and diversity as standard bulk sequencing. Together, our data and workflow will be useful for investigators interested in understanding and manipulating adult hippocampal NSC responses to various stimuli.


title: Cold protection allows local cryotherapy in a clinical-relevant model of traumatic optic neuropathy

abstract: Therapeutic hypothermia (TH) is potentially an important therapy for central nervous system (CNS) trauma. However, its clinical application remains controversial, hampered by two major factors: 1) Many of the CNS injury sites, such as the optic nerve (ON), are deeply buried, preventing access for local TH. The alternative is to apply TH systemically, which significantly limits the applicable temperature range. 2) Even with possible access for "local refrigeration", cold-induced cellular damage offsets the benefit of TH. Here we present a clinically translatable model of traumatic optic neuropathy (TON) by applying clinical trans-nasal endoscopic surgery to goats and non-human primates. This model faithfully recapitulates clinical features of TON such as the injury site (pre-chiasmatic ON), the spatiotemporal pattern of neural degeneration, and the accessibility of local treatments with large operating space. We also developed a computer program to simplify the endoscopic procedure and expand this model to other large animal species. Moreover, applying a cold-protective treatment, inspired by our previous hibernation research, enables us to deliver deep hypothermia (4{degrees}C) locally to mitigate inflammation and metabolic stress (indicated by the transcriptomic changes after injury) without cold-induced cellular damage, and confers prominent neuroprotection both structurally and functionally. Intriguingly, neither treatment alone was effective, demonstrating that in situ deep hypothermia combined with hibernation-mimicking cold protection constitutes a breakthrough for TH as a therapy for TON and other CNS traumas.


title: Circuit-specific sonogenetic stimulation of the deep brain elicits distinct signaling and behaviors in freely moving mice

abstract: Sonogenetics uses heterologously-expressed proteins to sensitize neurons to ultrasound, enabling selective, non-invasive, and deep brain stimulation. However, its ability to modulate specific circuits or induce behavioral changes remains to be studied and characterized. Here, we demonstrate that sonogenetics enables efficient activation of well-defined neural circuits by transcranial low-intensity, low-frequency ultrasonic stimulation with high spatiotemporal resolution. Targeted neurons in subcortical regions were made to express a mechanosensitive ion channel (MscL-G22S). Ultrasound could trigger activity in MscL-expressing neurons in the dorsal striatum without increased activation in neighboring regions, and increase locomotion in freely-moving mice. Ultrasound stimulation of MscL-expressing neurons in the ventral tegmental area could activate the mesolimbic pathway to trigger dopamine release in the nucleus accumbens and modulate appetitive conditioning. In MscL-expressing cells, neuronal responses to ultrasound pulses were rapid, reversible and repeatable. Altogether, we show that sonogenetics can selectively manipulate targeted cells to activate defined neural pathways and affect behaviors.


title: Sonogenetic stimulation of the brain at a spatiotemporal resolution suitable for vision restoration

abstract: Remote, precisely controlled activation of the brain is a fundamental challenge in the development of brain-machine interfaces providing feasible rehabilitation strategies for neurological disorders. Low-frequency ultrasound stimulation can be used to modulate neuronal activity deep in the brain1-7, but this approach lacks spatial resolution and cellular selectivity and loads the brain with high levels of acoustic energy. The combination of the expression of ultrasound-sensitive proteins with ultrasound stimulation ( sonogenetic stimulation) can provide cellular selectivity and higher sensitivity, but such strategies have been subject to severe limitations in terms of spatiotemporal resolution in vivo8-10, precluding their use for real-life applications. We used the expression of large-conductance mechanosensitive ion channels (MscL) with high-frequency ultrasonic stimulation for a duration of milliseconds to activate neurons selectively at a relatively high spatiotemporal resolution in the rat retina ex vivo and the primary visual cortex of rodents in vivo. This spatiotemporal resolution was achieved at low energy levels associated with negligible tissue heating and far below those leading to complications in ultrasound neuromodulation6,11. We showed, in an associative learning test, that sonogenetic stimulation of the visual cortex generated light perception. Our findings demonstrate that sonogenetic stimulation is compatible with millisecond pattern presentation for visual restoration at the cortical level. They represent a step towards the precise transfer of information over large distances to the cortical and subcortical regions of the brain via an approach less invasive than that associated with current brain-machine interfaces and with a wide range of applications in neurological disorders.


title: Beyond Fixation: detailed characterization of neural selectivity in free-viewing primates

abstract:
Virtually all vision studies use a fixation point to stabilize gaze, rendering stimuli on video screens fixed to retinal coordinates. This approach requires trained subjects, is limited by the accuracy of fixational eye movements, and ignores the role of eye movements in shaping visual input. To overcome these limitations, we developed a suite of hardware and software tools to study vision during natural behavior in untrained subjects. We show this approach recovers receptive fields and tuning properties of visual neurons from multiple cortical areas of marmoset monkeys. Combined with high-precision eye-tracking, it achieves sufficient resolution to recover the receptive fields of foveal V1 neurons. These findings demonstrate the power of free viewing to characterize neural response while simultaneously studying the dynamics of natural behavior.

HighlightsO_LIWe introduce a free-viewing paradigm for studying neural mechanisms of visual processing during active vision
C_LIO_LIReceptive fields (RFs) and neural selectivity in primary visual cortex (V1) and area MT can be extracted during free-viewing in minimally-trained subjects
C_LIO_LINovel high-resolution eye tracking in this context supports detailed measurements of receptive fields in foveal V1
C_LI


title: Weak Coupling Between Spontaneous Local Cortical Activity State Switches Under Anesthesia Leads to Strongly Correlated Global Cortical States

abstract: Under anesthesia, neural dynamics deviate dramatically from those seen during wakefulness. During recovery from this perturbation, thalamocortical activity abruptly switches among a small set of metastable intermediate states. These metastable states and structured transitions among them form a scaffold that guides the brain back to the waking state. Here, we investigate the mechanisms that constrain cortical activity to discrete states and give rise to abrupt transitions among them. If state transitions were imposed onto the thalamocortical system by changes in the subcortical modulation, different cortical sites should exhibit near-synchronous state transitions. To test this hypothesis, we quantified state synchrony at different cortical sites in anesthetized rats. States were defined by compressing spectra of layer-specific local field potentials (LFPs) in visual and motor cortices. Transition synchrony, mutual information, and canonical correlations all demonstrate that most state transitions in the cortex are local and that coupling between sites is weak. Fluctuations in the LFP in the thalamic input layer 4 were particularly dissimilar from those in supra- and infra-granular layers. Thus, our results suggest that the discrete global cortical states are not imposed by the ascending modulatory pathways but emerge from the multitude of weak pairwise interactions within the cortex.


title: Normalization by orientation anisotropy in human V1-V3

abstract: An influential account of neuronal responses in primary visual cortex is the normalized energy model. This model is often implemented as a two-stage computation. The first stage is the extraction of contrast energy, whereby a complex cell computes the squared and summed outputs of a pair of linear filters in quadrature phase. The second stage is normalization, in which a local population of complex cells mutually inhibit one another. Because the population includes cells tuned to a range of orientations and spatial frequencies, the result is that the responses are effectively normalized by the local stimulus contrast. Here, using evidence from human functional MRI, we show that the classical model fails to account for the relative responses to two classes of stimuli: straight, parallel, band-passed contours (gratings), and curved, band-passed contours (snakes). The snakes elicit fMRI responses that are about twice as large as the gratings, yet traditional energy models, including normalized energy models, predict responses that are about the same. Here, we propose a computational model, in which responses are normalized not by the sum of the contrast energy, but by the orientation anisotropy, computed as the variance in contrast energy across orientation channels. We first show that this model accounts for differential responses to these two classes of stimuli. We then show that the model successfully generalizes to other band-pass textures, both in V1 and in extrastriate cortex (V2 and V3). We speculate that high anisotropy in the orientation responses leads to larger outputs in downstream areas, which in turn normalizes responses in these later visual areas, as well as in V1 via feedback.


title: Telomere length regulation by Rif1 protein from Hansenula polymorpha

abstract: Rif1 is a large multifaceted protein involved in various processes of DNA metabolism - from telomere length regulation and replication to double-strand break repair. The mechanistic details of its action, however, are often poorly understood. Here, we report functional characterization of the Rif1 homologue from methylotrophic thermotolerant budding yeast Hansenula polymorpha DL-1. We show that, similar to other yeast species, H. polymorpha Rif1 suppresses telomerase-dependent telomere elongation. We uncover two novel modes of Rif1 recruitment at H. polymorpha telomeres: via direct DNA binding and through the association with the Ku heterodimer. Both of these modes (at least partially) require the intrinsically disordered N-terminal extension - a region of the protein present exclusively in yeast species. We also demonstrate that Rif1 binds Stn1 and promotes its accumulation at telomeres in H. polymorpha.


title: Nuclear mRNA metabolism drives selective basket assembly on a subset of nuclear pores in budding yeast

abstract: To determine which transcripts should reach the cytoplasm for translation, eukaryotic cells have established mechanisms to regulate selective mRNA export through the nuclear pore complex (NPC). The nuclear basket, a substructure of the NPC protruding into the nucleoplasm, is thought to function as a stable platform where mRNA-protein complexes (mRNPs) are rearranged and undergo quality control (QC) prior to export, ensuring that only mature mRNAs reach the cytoplasm. Here, we use proteomic, genetic, live-cell, and single-molecule resolution microscopy approaches in budding yeast to demonstrate that baskets assemble only on a subset of NPCs and that basket formation is dependent on RNA polymerase II (Pol II) transcription and subsequent mRNP processing. Specifically, we observe that the cleavage and polyadenylation machinery, the poly(A)-binding protein Pab1, and pre-mRNA-leakage factor Pml39 are required for basket assembly. We further show that while all nuclear pores can bind Mlp1, baskets assemble only on a subset of nucleoplasmic NPCs, and these basket-containing pores associate a distinct protein and RNA interactome. Taken together, our data points towards nuclear pore heterogeneity and an RNA-dependent mechanism for functionalization of nuclear pores in budding yeast through nuclear basket assembly.


title: Optogenetic dissection of the roles of actomyosin in the mechanics underlying tissue fluidity

abstract: Rapid epithelial tissue flows are essential to building and shaping developing embryos. However, it is not well understood how the mechanical properties of tissues and the forces driving them to flow are jointly regulated to accommodate rapid tissue remodeling. To dissect the roles of actomyosin in the mechanics of epithelial tissue flows, here we use two optogenetic tools, optoGEF and optoGAP, to manipulate Rho/Rho-kinase signaling and actomyosin contractility in the germband epithelium, which flows via convergent extension movements during Drosophila body axis elongation. The ability to perturb actomyosin in the tissue allows us to analyze the effects of actomyosin on cell rearrangements, tissue tensions, and tissue mechanical properties. We find that either optogenetic activation or deactivation of Rho1 signaling and actomyosin contractility at the apical surface of the germband disrupts cell rearrangements and tissue-level flows. Rho1 activation leads to poorly oriented rearrangements that are associated with a redistribution of myosin II from the junctional to the medial-apical domain, whereas Rho1 deactivation leads to fewer, slower cell rearrangements that are associated with decreased junctional and medial myosin. By probing mechanical tensions in the tissue using laser ablation and inferring tissue mechanical properties from cell packings, we find that actomyosin influences both the anisotropic forces that drive tissue flow and the mechanical properties of the tissue that resist flow, leading to complex relationships between actomyosin activity and tissue fluidity. Moreover, our results link the subcellular distribution of myosin II to tissue tension and cell packings, revealing how junctional and medial myosin have differential roles in promoting and orienting cell rearrangements during tissue flow.

category: developmental biology


title: Optogenetic dissection of actomyosin-dependent mechanics underlying tissue fluidity