title: A nitrogen source-regulated microprotein confers an alternative mechanism of G1/S transcriptional activation in budding yeast

abstract:
Commitment to cell division at the end of G1 phase, termed Start in the budding yeast Saccharomyces cerevisiae, is strongly influenced by nutrient availability. To identify new dominant activators of Start that might operate under different nutrient conditions, we screened a genome-wide ORF overexpression library for genes that bypass a Start arrest caused by absence of the G1 cyclin Cln3 and the transcriptional activator Bck2. We recovered a hypothetical gene YLR053c, renamed NRS1 for Nitrogen-Responsive Start regulator 1, which encodes a poorly characterized 108 amino acid microprotein. Endogenous Nrs1 was nuclear-localized, restricted to poor nitrogen conditions, induced upon mTORCl inhibition, and cell cycle-regulated with a peak at Start. NRS1 interacted genetically with SWI4 and SWI6, which encode subunits of the main G1/S transcription factor complex SBF. Correspondingly, Nrs1 physically interacted with Swi4 and Swi6 and was localized to G1/S promoter DNA. Nrs1 exhibited inherent transactivation activity and fusion of Nrs1 to the SBF inhibitor Whi5 was sufficient to suppress other Start defects. Nrs1 appears to be a recently evolved microprotein that rewires the G1/S transcriptional machinery under poor nitrogeny conditions.

Author SummarUnicellular microorganisms must adapt to ever-changing nutrient conditions and hence must adjust cell growth and proliferation to maximize fitness. In the budding yeast Saccharomyces cerevisiae, commitment to cell division, termed Start, is heavily influenced by nutrient availability. Our understanding of how Start is activated is based mainly on experiments carried out under rich nutrient conditions. To identify potential new Start regulators specific to poor nutrient environments, we screened for genes able to bypass a genetic Start arrest caused by loss of the G1 cyclin Cln3 and the transcriptional activator Bck2. This screen uncovered YLR053c, which we renamed NRS1 for Nitrogen-Responsive Start regulator. Sequence analysis across yeast species indicated that Nrs1 is a recently-evolved microprotein. We showed that NRS1 is nutrient- and cell cycle-regulated, and directly binds the main G1/S transcription factor complex SBF. We demonstrated that Nrs1 has an intrinsic trans-activation activity and provided genetic evidence to suggest that Nrs1 can bypass the requirement for normal Cln3-dependent activation of G1/S transcription. These results uncover a new mechanism of Start activation and illustrate how microproteins can rapidly emerge to rewire fundamental cellular processes.


title: Erythropoietin directly remodels the clonal composition of murine hematopoietic multipotent progenitor cells

abstract: The cytokine erythropoietin (EPO) is a potent inducer of erythrocyte development and one of the most prescribed biopharmaceuticals. The action of EPO on erythroid progenitor cells is well established, but its direct action on hematopoietic stem and progenitor cells (HSPCs) is still debated. Here, using cellular barcoding, we traced the differentiation of hundreds of single murine HSPCs, after ex vivo EPO-exposure and transplantation, in five different hematopoietic cell lineages, and observed the transient occurrence of high-output Myeloid-Erythroid-megaKaryocyte (MEK)-biased and Myeloid-B-cell-Dendritic cell (MBDC)-biased clones. Single-cell RNA sequencing (ScRNAseq) analysis of ex vivo EPO-exposed HSPCs revealed that EPO induced the upregulation of erythroid associated genes in a subset of HSPCs, overlapping with multipotent progenitor (MPP) 1 and MPP2. Transplantation of Barcoded EPO-exposed-MPP2 confirmed their enrichment in Myeloid-Erythroid-biased clones. Collectively, our data show that EPO does act directly on MPP independent of the niche, and modulates fate by remodeling the clonal composition of the MPP pool.

category: immunology


title: CDK1 controls CHMP7-dependent nuclear envelope reformation

abstract: Through membrane sealing and disassembly of spindle microtubules, the Endosomal Sorting Complex Required for Transport-III (ESCRT-III) machinery has emerged as a key player in the regeneration of a sealed nuclear envelope (NE) during mitotic exit, and in the repair of this organelle during interphase rupture. ESCRT-III assembly at the NE occurs transiently during mitotic exit and is initiated when CHMP7, an ER-localised ESCRT-II/ESCRT-III hybrid protein, interacts with the Inner Nuclear Membrane (INM) protein LEM2. Whilst classical nucleocytoplasmic transport mechanisms have been proposed to separate LEM2 and CHMP7 during interphase, it is unclear how CHMP7 assembly is suppressed in mitosis when NE and ER identities are mixed. Here, we use live cell imaging and protein biochemistry to examine the biology of these proteins during mitotic exit. Firstly, we show that CHMP7 plays an important role in the dissolution of LEM2 clusters that form at the NE during M-exit. Secondly, we show that CDK1 phosphorylates CHMP7 upon mitotic entry at Ser3 and Ser441 and that this phosphorylation suppresses CHMP7s interaction with LEM2, limiting its assembly during M-phase. We show that spatiotemporal differences in the dephosphorylation of CHMP7 license its assembly at the NE during telophase, but restrict its assembly on the ER at this time. Without CDK1 phosphorylation, CHMP7 undergoes inappropriate assembly in the peripheral ER during M-exit, capturing LEM2 and downstream ESCRT-III components. Lastly, we establish that a microtubule network is dispensable for ESCRT-III assembly at the reforming nuclear envelope. These data identify a key cell-cycle control programme allowing ESCRT-III-dependent nuclear regeneration.

category: cell biology


title: Sequence determinants and evolution of constitutive and alternative splicing in yeast species

abstract: RNA splicing is a key process in eukaryotic gene expression. Most Intron-containing genes are constitutively spliced, hence efficient splicing of an intron is crucial for efficient gene expression. Here we use a large synthetic oligo library of ~20,000 variants to explore how different intronic sequence features affect splicing efficiency and mRNA expression levels in S. cerevisiae. Using a combinatorial design of synthetic introns we demonstrate how non-consensus splice site sequences affect splicing efficiency in each of the three splice sites. We then show that S. cerevisiae splicing machinery tends to select alternative 3 splice sites downstream of the original site, and we suggest that this tendency created a selective pressure, leading to the avoidance of cryptic splice site motifs near introns 3 ends. We further use natural intronic sequences from other yeast species, whose splicing machineries have diverged to various extents, to show how intron architectures in the various species have been adapted to the organisms splicing machinery. We suggest that the observed tendency for cryptic splicing is a result of a loss of a specific splicing factor, U2AF1. Lastly, we show that synthetic sequences containing two introns give rise to alternative RNA isoforms in S. cerevisiae, exposing intronic features that control and facilitate alternative splicing. Our study reveals novel mechanisms by which introns are shaped in evolution to allow cells to regulate their transcriptome.

category: systems biology


title: Imprints of tumor mutation burden on chromosomes and relation to cancer risk in humans: A pan-cancer analysis

abstract: Cancers, resulting in uncontrolled cell proliferation, are driven by accumulation of somatic mutations. Genome-wide sequencing has produced a catalogue of millions of somatic mutations, which contain the evolutionary history of the cancers. However, the connection between the mutation accumulation and disease development and risks is poorly understood. Here, we analyzed more than 1,200,000 mutations from 5,000 cancer patients with whole-exome sequencing, and discovered two novel signatures for 16 cancer types in The Cancer Genome Atlas (TCGA) database. A strong correlation between Tumor Mutation Burden (TMB) and the Patient Age at Diagnosis (PAD) is observed for cancers with low TMB (mean value less than 3 mutations per million base pairs) but is absent in cancers with high TMB. We also validate this finding using whole-genome sequencing data from more than 2,000 patients for 24 cancer types. Surprisingly, the differences in cancer risk between the sexes are also mainly driven by the disparity in mutation burden. The TMB variations, imprinted at the chromosome level, also reflect accumulation of mutation clusters within small chromosome segments in high TMB cancers. By analyzing the characteristics of mutations based on multi-region sequencing, we found that a combination of TMB and intratumor heterogeneity could a potential biomarker for predicting the patient survival and response to treatment.

category: cancer biology


title: Cold adaptation drives population genomic divergence in the ecological specialist, Drosophila montana

abstract: Detecting signatures of ecological adaptation in comparative genomics is challenging, but analysing population samples with characterised geographic distributions, such as clinal variation, can help identify genes showing covariation with important ecological variation. Here we analysed patterns of geographic variation in the cold-adapted species Drosophila montana across phenotypes, genotypes and environmental conditions and tested for signatures of cold adaptation in population genomic divergence. We first derived the climatic variables associated with the geographic distribution of 24 populations across two continents to trace the scale of environmental variation experienced by the species, and measured variation in the cold tolerance of the flies of six populations from different geographic contexts. We then performed pooled whole genome sequencing of these six populations, and used Bayesian methods to identify SNPs where genetic differentiation is associated with both climatic variables and the population phenotypic measurements, while controlling for effects of demography and population structure. The top candidate SNPs were enriched on the X and 4th chromosomes, and they also lay near genes implicated in other studies of cold tolerance and population divergence in this species and its close relatives. We conclude that ecological adaptation has contributed to the divergence of D. montana populations throughout the genome and in particular on the X and 4th chromosomes, which also showed highest interpopulation FST. This study demonstrates that ecological selection can drive genomic divergence at different scales, from candidate genes to chromosome-wide effects.

category: evolutionary biology


title: SARS-CoV-2 Encodes a PPxY Late Domain Motif Known to Enhance Budding and Spread in Enveloped RNA Viruses

abstract: The current COVID-19 (Coronavirus Disease-2019) pandemic is affecting the health and/or socioeconomic welfare of almost everyone in the world. Finding vaccines and therapeutics is therefore urgent, but elucidation of the molecular mechanisms that allow some viruses to cross host species boundaries, becoming a threat to human health, must also be given close attention. Here, analysis of all proteins of SARS-CoV-2 revealed a unique PPxY Late (L) domain motif, 25PPAY28, in a spike (S) protein inside a predicted hot disordered loop subject to phosphorylation and binding. PPxY motifs in enveloped RNA viruses are known to recruit Nedd4 E3 ubiquitin ligases and ultimately the ESCRT complex to enhance virus budding and release, resulting in higher viral loads, hence facilitating new infections. Interestingly, proteins of SARS-CoV-1 do not feature PPxY motifs, which could explain why SARS-CoV-2 is more contagious than SARS-CoV-1. Should an experimental assessment of this hypothesis show that the PPxY motif plays the same role in SARS-CoV-2 as it does in other enveloped RNA viruses, this motif will become a promising target for the development of novel host-oriented antiviral therapeutics for preventing S proteins from recruiting Nedd4 E3 ubiquitin ligase partners.

category: bioinformatics


title: GWAS of three molecular traits highlights core genes and pathways alongside a highly polygenic background

abstract: Genome-wide association studies (GWAS) have been used to study the genetic basis of a wide variety of complex diseases and other traits. We describe UK Biobank GWAS results for three molecular traits--urate, IGF-1, and testosterone--with better-understood biology than most other complex traits. We find that many of the most significant hits are readily and surprisingly interpretable. We observe huge enrichment of associations near genes involved in the relevant biosynthesis, transport, or signaling pathways. We show how GWAS data illuminate the biology of each trait, including differences in testosterone regulation between females and males. At the same time, even these molecular traits are highly polygenic, with many thousands of variants spread across the genome contributing to trait variance. In summary, for these three molecular traits we identify strong enrichment of signal in putative core gene sets, even while most of the SNP-based heritability is driven by a massively polygenic background.

category: genetics


title: Human iPSC-derived cerebral organoids model features of Leigh Syndrome and reveal abnormal corticogenesis

abstract: Leigh syndrome (LS) is a rare, inherited neurometabolic disorder that presents with bilateral brain lesions, caused by defects in the mitochondrial respiratory chain and associated nuclear-encoded proteins. We generated iPSCs from three patient-derived LS fibroblast lines and identified, by whole-exome and mitochondrial sequencing, unreported mutations in pyruvate dehydrogenase (GM0372, PDH; GM13411, MT-ATP6/PDH) and dihydrolipoyl dehydrogenase (GM01503, DLD). LS-derived iPSC lines were viable and generally capable of differentiating into key progenitor populations, but we identified several abnormalities in three-dimensional differentiation models of brain development. LS-derived cerebral organoids showed defects in neural epithelial bud generation, size, and cortical architecture at 100 days. The double mutant MT-ATP6/PDH line produced organoid neural progenitor cells with abnormal mitochondrial morphology characterized by fragmentation and disorganization and showed an increased generation of astrocytes. These studies aim to provide a comprehensive phenotypic characterization of available patient-derived cell lines that can be used as LS model systems.


title: Negative feedback may suppress variation to improve collective foraging performance

abstract: Social insect colonies use negative as well as positive feedback signals to regulate foraging behaviour. In ants and bees individual foragers have been observed to use negative pheromones or mechano-auditory signals to indicate that forage sources are not ideal, for example being unrewarded, crowded, or dangerous. Here we propose an additional function for negative feedback signals during foraging, variance reduction. We show that while on average populations will converge to desired distributions over forage patches both with and without negative feedback signals, in small populations negative feedback reduces variation around the target distribution compared to the use of positive feedback alone. Our results are independent of the nature of the target distribution, providing it can be achieved by foragers collecting only local information. Since robustness is a key aim for biological systems, and deviation from target foraging distributions may be costly, we argue that this could be a further important and hitherto overlooked reason that negative feedback signals are used by foraging social insects.

category: ecology


title: A quantitative measure of functional redundancy in microbial ecosystems

abstract: The concept of functional redundancy has received considerable attention in both the macroecology and microbial ecology literature. As a result, multiple metrics of functional redundancy have been proposed. These vary in how they weight trait levels, species abundance, functional richness, and species richness. Here we present a new functional redundancy metric tailored for community-aggregated traits, which are traits that are quantified at the community level and can be quantitatively partitioned among species. We call this metric Contribution Evenness (CE) because it measures how evenly species contribute to a community-aggregated trait. As CE is an evenness measurement, it ranges from 0 and 1, where 0 corresponds to a single species contributing to a community-aggregated trait and 1 corresponds to all species contributing equally. Using in silico simulations of species extinctions, we demonstrate that CE reflects the stability of an ecosystem function to species extinction, a hypothesized ecological consequence of functional redundancy. As a positive control and to illustrate how CE can be used with sequence data, we analyzed the functional redundancy of eight nitrogen-transforming pathways using 2,631 metagenome-assembled genomes from 47 marine sites. CE for marine nitrogen cycle marker genes was consistent with our qualitative understanding of which nitrogen pathways are most functionally redundant in the ocean. We found that, on average, the NH4+ assimilation pathway was the most functionally redundant (0.44 {+/-} 0.08) while dissimilatory nitrate reduction was the least redundant (0.005 {+/-} 0.005). As demonstrated here, CE provides a promising framework for measuring trait stability in microbiomes.

category: microbiology


title: Contribution Evenness: A functional redundancy metric sensitive to trait stability in microbialcommunities


title: Contribution Evenness: A functional redundancy metric sensitive to trait stability in microbial communities


title: Identification of essential genes for Escherichia coli aryl polyene biosynthesis and function in biofilm formation

abstract: Aryl polyenes (APEs) are specialized polyunsaturated carboxylic acids that were identified in silico as the product of the most widespread family of bacterial biosynthetic gene clusters (BGCs). They are present in several Gram-negative host-associated bacteria, including multi-drug resistant human pathogens. Here, we characterize a biological function of APEs, focusing on the BGC from a uropathogenic Escherichia coli (UPEC) strain. We first perform a genetic deletion analysis to identify the essential genes required for APE biosynthesis. Next, we show that APEs function as fitness factors that increase protection from oxidative stress and contribute to biofilm formation. Together, our study highlights key steps in the APE biosynthesis pathway that can be explored as potential drug targets for complementary strategies to reduce fitness and prevent biofilm formation of multi-drug resistant pathogens.


title: Electrical Oscillations of Isolated Brain Microtubules

abstract:
Microtubules (MTs) are important cytoskeletal structures engaged in a number of specific cellular activities, including vesicular traffic and motility, cell division, and information transfer within neuronal processes. MTs also are highly charged polyelectrolytes. Recent in vitro electrophysiological studies indicate that different brain MT structures, including two-dimensional (2D) sheets (MT sheets) and bundles, generate highly synchronous electrical oscillations. However, no information has been heretofore available as to whether isolated MTs also engage in electrical oscillations, despite the fact that taxol-stabilized isolated MTs are capable of amplifying electrical signals. Herein we tested the effect of voltage clamping on the electrical properties of isolated non-taxol stabilized brain MTs. Electrical oscillations were observed on application of holding potentials between {+/-}200 mV that responded accordingly with changes in amplitude and polarity. Frequency domain spectral analysis of time records from isolated MTs disclosed a richer oscillatory response as compared to that observed in voltage clamped MT sheets from the same preparation. The data indicate that isolated brain MTs are electrical oscillators that behave as "ionic-based" transistors whose activity may be synchronized in higher MT structures. The ability of MTs to generate, propagate, and amplify electrical signals may have important implications in neuronal computational capabilities.

Significance StatementMicrotubules (MTs) are important cytoskeletal structures engaged in a number of specific cellular activities. Recent in vitro electrophysiological studies indicate that different brain MT structures generate highly synchronous electrical oscillations. However, no information is available as to whether isolated MTs also engage in electrical oscillations. In the present study, we provide evidence that non-taxol stabilized isolated MTs generated electrical oscillations with richer frequency spectrum as compared to MT sheets. Thus, structured MT complexes may render more coherent responses at given oscillatory frequencies, suggesting entrainment in combined MT structures. The present study provides to our knowledge the first experimental evidence for electrical oscillations of single brain MTs.

category: biophysics


title: A Substantia Innominata-midbrain Circuit Controls a General Aggressive Response

abstract:
While aggressive behaviors are universal and essential for survival,  uncontrollable and abnormal aggressive behaviors in animals or humans may have severe adverse consequences or social costs. Neural circuits regulating specific forms of aggression under defined conditions have been described, but how brain circuits govern a general aggressive response remains unknown. Here, we found that posterior substantia innominata (pSI) neurons responded to several aggression-provoking cues with the graded activity of differential dynamics, predicting the aggressive state and the topography of aggression in mice. Activation of pSI neurons projecting to the periaqueductal gray (PAG) increased aggressive arousal and robustly initiated/promoted all the types of aggressive behavior examined in an activity level-dependent manner. Inactivation of the pSI circuit largely blocked diverse aggressive behaviors but not mating. By encoding a general aggressive response, the pSI-PAG circuit universally drives multiple aggressive behaviors and may provide a potential target for alleviating human pathological aggression.

In BriefZhu et al. find that the posterior substantia innominata neurons universally drive aggressive behaviors by representing aggressive state and topography of aggression in mice.

O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=200 SRC="FIGDIR/small/047670v2_ufig1.gif" ALT="Figure 1">
View larger version (44K):
org.highwire.dtl.DTLVardef@19d72org.highwire.dtl.DTLVardef@7cc4corg.highwire.dtl.DTLVardef@1f5c3dborg.highwire.dtl.DTLVardef@d9743_HPS_FORMAT_FIGEXP  M_FIG C_FIG HighlightsO_LIpSI neuronal dynamics reflect aggressive state and the topography of aggression
C_LIO_LIThe pSI-PAG circuit promotes arousal and elicits thirteen aggressive behaviors
C_LIO_LIThe pSI controls various aggressive behaviors in an activity level-dependent manner
C_LIO_LIInactivation of the pSI circuit blocks diverse aggressive behaviors but not mating
C_LI

category: neuroscience


title: Targeted proteomics as a tool to detect SARS-CoV-2 proteins in clinical specimens.

abstract: The rapid, sensitive and specific detection of SARS-CoV-2 is critical in responding to the current COVID-19 outbreak. In this proof-of-concept study, we explored the potential of targeted mass spectrometry based (MS) proteomics for the detection of SARS-CoV-2 proteins in both research samples and clinical specimens. First, we assessed the limit of detection for several SARS-CoV-2 proteins by parallel reaction monitoring (PRM) MS in infected Vero E6 cells. For tryptic peptides of Nucleocapsid protein, the limit of detection was in the mid-attomole range (9E-13 g). Next, this PRM methodology was applied to the detection of viral proteins in various COVID-19 patient clinical specimens, such as sputum and nasopharyngeal swabs. SARS-CoV-2 proteins were detected in these samples with high sensitivity in all specimens with PCR Ct values <24 and in several samples with higher CT values. A clear relationship was observed between summed MS peak intensities for SARS-CoV-2 proteins and Ct values reflecting the abundance of viral RNA. Taken together, these results suggest that targeted MS based proteomics may have the potential to be used as an additional tool in COVID-19 diagnostics.

category: biochemistry


title: Functional and Genetic Analysis of Viral Receptor ACE2 Orthologs Reveals a Broad Potential Host Range of SARS-CoV-2

abstract: The pandemic of Coronavirus Disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is a major global health threat. Epidemiological studies suggest that bats are the natural zoonotic reservoir for SARS-CoV-2. However, the host range of SARS-CoV-2 and intermediate hosts that facilitate its transmission to humans remain unknown. The interaction of coronavirus with its host receptor is a key genetic determinant of host range and cross-species transmission. SARS-CoV-2 uses angiotensin-converting enzyme 2 (ACE2) as the receptor to enter host cells in a species-dependent manner. It has been shown that human, palm civet, pig and bat ACE2 can support virus entry, while the murine ortholog cannot. In this study, we characterized the ability of ACE2 from diverse species to support viral entry. We found that ACE2 is expressed in a wide range of species, with especially high conservation in mammals. By analyzing amino acid residues of ACE2 critical for virus entry, based on structure of SARS-CoV spike protein interaction with human, bat, palm civet, pig and ferret ACE2, we identified approximately eighty ACE2 proteins from mammals that could potentially mediate SARS-CoV-2 entry. We chose 48 representative ACE2 orthologs among eighty orthologs for functional analysis and it showed that 44 of these mammalian ACE2 orthologs, including those of domestic animals, pets, livestock, and animals commonly found in zoos and aquaria, could bind SARS-CoV-2 spike protein and support viral entry. In contrast, New World monkey ACE2 orthologs could not bind SARS-CoV-2 spike protein and support viral entry. We further identified the genetic determinant of New World monkey ACE2 that restricts viral entry using genetic and functional analyses. In summary, our study demonstrates that ACE2 from a remarkably broad range of species can facilitate SARS-CoV-2 entry. These findings highlight a potentially broad host tropism of SARS-CoV-2 and suggest that SARS-CoV-2 might be distributed much more widely than previously recognized, underscoring the necessity to monitor susceptible hosts to prevent future outbreaks.


title: SwabExpress: An end-to-end protocol for extraction-free COVID-19 testing

abstract:
Structured AbstractO_ST_ABSBackgroundC_ST_ABSThe urgent need for massively scaled clinical testing for SARS-CoV-2, along with global shortages of critical reagents and supplies, has necessitated development of streamlined laboratory testing protocols. Conventional nucleic acid testing for SARS-CoV-2 involves collection of a clinical specimen with a nasopharyngeal swab in transport medium, nucleic acid extraction, and quantitative reverse transcription PCR (RT-qPCR) (1). As testing has scaled across the world, the global supply chain has buckled, rendering testing reagents and materials scarce (2). To address shortages, we developed SwabExpress, an end-to-end protocol developed to employ mass produced anterior nares swabs and bypass the requirement for transport media and nucleic acid extraction.

MethodsWe evaluated anterior nares swabs, transported dry and eluted in low-TE buffer as a direct-to-RT-qPCR alternative to extraction-dependent viral transport media. We validated our protocol of using heat treatment for viral activation and added a proteinase K digestion step to reduce amplification interference. We tested this protocol across archived and prospectively collected swab specimens to fine-tune test performance.

ResultsAfter optimization, SwabExpress has a low limit of detection at 2-4 molecules/uL, 100% sensitivity, and 99.4% specificity when compared side-by-side with a traditional RT-qPCR protocol employing extraction. On real-world specimens, SwabExpress outperforms an automated extraction system while simultaneously reducing cost and hands-on time.

ConclusionSwabExpress is a simplified workflow that facilitates scaled testing for COVID-19 without sacrificing test performance. It may serve as a template for the simplification of PCR-based clinical laboratory tests, particularly in times of critical shortages during pandemics.

category: molecular biology


title: Mitofusins Mfn1 and Mfn2 are required in the β-cell to preserve mitochondrial architecture and insulin secretion

abstract:
Aims/hypothesisMitochondrial glucose metabolism is essential for stimulated insulin release from pancreatic beta cells. Whether mitochondrial networks may be important for glucose or incretin sensing has yet to be determined.

MethodsHere, we generated mice with beta cell-selective, adult-restricted deletion of the mitofusin genes Mfn1 and Mfn2 ({beta}Mfn1/2 dKO). Whole or dissociated pancreatic islets were used for live beta cell fluorescence imaging of cytosolic or mitochondrial Ca2+ concentration and ATP production or GSIS in response to increasing glucose concentrations or GLP-1 receptor agonists. Serum and blood samples were collected to examine oral and i.p. glucose tolerance.

Results{beta}Mfn1/2 dKO mice displayed elevated fed and fasted glycaemia (p<0.01, p<0.001) and a >five-fold decrease (p<0.0001) in plasma insulin. Mitochondrial length, glucose-induced polarisation, ATP synthesis and cytosolic Ca2+ increases were all reduced (p<0.05,p<0.01,p<0.0001) in dKO islets, and beta cell Ca2+ dynamics were suppressed in vivo (p<0.001). In contrast, oral glucose tolerance was near normal in {beta}Mfn1/2 dKO mice (p<0.05, p<0.01) and GLP-1 or GIP receptor agonists largely corrected defective GSIS from isolated islets through an EPAC-dependent signalling activation.

Conclusions/interpretationMitochondrial fusion and fission cycles are thus essential in the beta cell to maintain normal glucose, but not incretin, sensing. Defects in these cycles in some forms of diabetes might therefore provide opportunities for novel incretin-based or other therapies.

Graphical abstract

O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=180 SRC="FIGDIR/small/055384v3_ufig1.gif" ALT="Figure 1">
View larger version (38K):
org.highwire.dtl.DTLVardef@258053org.highwire.dtl.DTLVardef@c07cborg.highwire.dtl.DTLVardef@1d3bb1forg.highwire.dtl.DTLVardef@1a1f128_HPS_FORMAT_FIGEXP  M_FIG Impact of Mfn1/2 deletion on glucose and incretin stimulated-insulin secretion in beta cells. (A) In control animals, glucose is taken up by beta cells through GLUT2 and metabolised by mitochondria (elongated structure) through the citrate (TCA) cycle, leading to an increased mitochondrial proton motive force (hyperpolarised {Delta}{psi}m), accelerated ATP synthesis and O2 consumption rate (OCR). Consequently, the cytoplasmic ATP:ADP ratio rises, which causes closure of KATP channels, depolarisation of plasma membrane potential ({psi}m), opening of VDCCs and influx of cytosolic Ca2+. Elevated [Ca2+]cyt triggers a number of ATP-dependent processes including insulin secretion and improved beta-beta cell communication through connexin 36 (Cx36). (B) Following Mfn1/2 deletion (Mfn1/2 dKO), highly fragmented mitochondria were associated with reduced mitochondrial Ca2+ ([Ca2+]m) accumulation, leading to a less polarised {Delta}{psi}m, weaker OCR, lower mtDNA copy number and decreased ATP synthesis. This is expected to result in weaker {psi}m depolarisation, cytosolic Ca2+ influx and beta-beta cell connectivity due to lower expression of Cx36. Despite observing a higher number of docked insulin granules on the plasma membrane, insulin secretion was highly suppressed in these animals. This was also associated with increased beta cell death and reduced beta cell mass. (C) In response to incretins, insulin secretion is potentiated through the activation of GLP1-R and cAMP signalling involving PKA- and EPAC2-dependent pathways. Elevated [Ca2+]cyt triggers a number of ATP-dependent processes including insulin secretion and Ca2+ removal into the endoplasmic reticulum (ER).(D) In Mfn1/2 dKO cells, activation of the GLP1-R was shown to be linked with a potentiation of the EPAC2 pathway that is PKA independent, along with an increased ER Ca2+ uptake and improved beta-beta cell communication. How these amplifying signals of glucose metabolism for insulin secretion are linked with fragmented mitochondria remains unknown. Red and bold arrows represent enhanced pathways; dashed arrows represent impaired pathways. This figure was produced using illustrations from Servier Medical Art, http://smart.servier.com/

C_FIG Research in contextWhat is already known about this subject?

Mitochondrial ultrastructural variations and number are altered in beta cells of human T2D patients [1].

Mice lacking Opa1, which controls mitochondrial fusion and inner membrane cristae structure, in beta cells, develop hyperglycaemia and defects in GSIS [2].

What is the key question?

Is an interconnected mitochondrial network essential in primary mouse beta cells for normal insulin secretion and glucose homeostasis?

What are the new findings?

We generated mice with beta cell-selective, adult-restricted deletion of the mitofusin genes Mfn1 and Mfn2 and show that insulin secretion and glucose homeostasis are strongly reduced in vivo.

Cytosolic and mitochondrial Ca2+ increases, {Delta}{psi}m, ATP production and beta cell connectivity are impaired in {beta}Mfn1/2 dKO animals.

Incretins bypass the above defects through an exchange protein directly activated by cAMP (EPAC)-dependent signalling mechanism.

How might this impact on clinical practice in the foreseeable future?

The ability of incretins to bypass defects in mitochondrial function might be exploited by the design of new agonists which target this pathway.


title: Mask, the Drosophila Ankyrin Repeat and KH domain-containing protein, regulates microtubule dynamics

abstract:
Proper regulation of microtubule (MT) dynamics is vital for essential cellular processes and neuronal activities, including axonal transport as well as synaptic growth and remodeling. Here we demonstrate that Mask negatively regulates MT stability and maintains a balanced dynamics of MT length and architecture in both fly larval muscles and motor neurons. In larval muscles, loss of mask increases MT length, and genetically altering mask levels modifies the Tau-induced MT fragmentation. In motor neurons, loss of mask function reduces the number of End-Binding Protein 1 (EB1)-positive MT plus-end structures in the axons and also results in overexpansion of the presynaptic terminal at larval neuromuscular junctions (NMJs). mask shows strong genetic interaction with stathmin (stai), a neuronal modulator of MT dynamics, in regulation of axon transportation and synaptic terminal stability. Our structure/function analysis on Mask revealed that truncated Mask transgenes carrying only its N-terminal portion that contains the two Ankyrin repeats domains is able to rescue the MT-related mask loss-of-function defects in larval muscles and NMJs, suggesting an essential role of the Ankyrin repeats domains in mediating Masks MT stability-regulating function. Furthermore, we discovered that Mask negatively regulates the abundance of the microtubule-associated protein Jupiter in motor neuron axons, and that neuronal knocking down of Jupiter partially suppresses mask loss of function phenotypes at the larval NMJs. Together, our study identified Mask as a novel regulator for microtubule stability and dynamics.

Author SummaryMicrotubules (MTs) are an essential part of the cellular cytoskeleton, providing the structural basis for critical cellular processes and functionality. A series of factors are required to orchestrate the assembly and disassembly of MTs. Here, we identified Mask as a novel regulator of MT dynamics in Drosophila. Mask shows prominent interplay with two important modulators of MT, Tau and Stathmin (Stai). These findings not only support the role of Mask as a novel microtubule regulator but also provide the foundation to explore future therapeutic strategies in mitigating deficits related to dysfunction of Tau and/or Stai, both of which are linked to human neurodegenerative disorders. Further analyses on Mask demonstrated that Jupiters localization to the MTs in the axons is negatively affected by Mask, and that reducing Jupiter level is able to partially suppress synaptic defects caused by mask mutant. Together, these data imply that Masks function in regulating MT dynamics requires Jupiter.


title: Tumor secreted extracellular vesicles regulate T-cell costimulation and can be manipulated to induce tumor-specific T-cell responses

abstract: Tumor intrinsic factors negatively regulate tumor immune cell infiltration and function. Deciphering the underlying mechanisms is critical to improving immunotherapy in cancers. Our analyses of human colorectal cancer (CRC) immune profiles and tumor-immune cell interactions revealed that tumor cell secreted extracellular vesicles (TEVs) induced immunosuppression in CRC. Specifically, TEVs containing microRNA miR-424 suppressed the CD28-CD80/86 costimulatory pathway in tumor infiltrating T cells and dendritic cells. Modified TEVs with miR-424 knocked down enhanced T-cell mediated antitumor immune response in CRC tumor models and increased the response to immune checkpoint blockade therapies (ICBT). Intravenous injections of modified TEVs induced tumor antigen specific immune responses. Moreover, injections of modified TEVs boosted the ICBT efficacy in CRC models that mimic treatment refractory late-stage disease. Collectively, we demonstrate a critical role for TEVs in antitumor immune regulation and immunotherapy response, which could be developed as a novel treatment for ICBT resistant human CRC.


title: Developmental system drift in one tooth facilitates the adaptation of the other tooth

abstract:
Serial organs, such as limbs or teeth, develop with the same sets of genes and regulatory sequences. Correlated evolution is expected by default, but decoupled evolution is often achieved, as in mouse with a morphological innovation in the upper, but not the lower molar. We studied developmental evolution of hamster and mouse molars with transcriptome data. We reveal a combination of three morphogenetic changes likely causing the new morphology of the mouse upper molar. Surprisingly, most of these changes are common with the lower molar and lower molar gene expression diverged as much as, and coevolved with, the upper molar.

Hence, adaptation of the upper molar has involved changes in pleiotropic genes that also modified lower molar development but preserved its final phenotype. From the lower molar point of view, it is a case of Developmental systems drift (DSD). We think that DSD accommodates pleiotropy, explaining why in teeth and more generally in the body, the evolution of developmental gene expression is fast and correlates between organs.

HIGHLIGHTS- The evolutionary innovation of mouse upper molar involves several morphogenetic changes
- Most of the associated gene expression changes are shared with the mouse lower molar
- Lower molars phenotype is conserved, thus its developmental gene expression drifted
- Adaptation with pleiotropic genes drove developmental system drift in the other tooth


title: Genetic dissection of glutamatergic neuron subpopulations and developmental trajectories in the cerebral cortex

abstract: Diverse types of glutamatergic pyramidal neurons (PyNs) mediate the myriad processing streams and output channels of the cerebral cortex, yet all derive from neural progenitors of the embryonic dorsal telencephalon. Here, we establish genetic strategies and tools for dissecting and fate mapping PyN subpopulations based on their developmental and molecular programs. We leverage key transcription factors and effector genes to systematically target the temporal patterning programs in progenitors and differentiation programs in postmitotic neurons. We generated over a dozen temporally inducible mouse Cre and Flp knock-in driver lines to enable combinatorial targeting of major progenitor types and projection classes. Intersectional converter lines confer viral access to specific subsets defined by developmental origin, marker expression, anatomical location and projection targets. These strategies establish an experimental framework for understanding the hierarchical organization and developmental trajectory of PyN subpopulations that assemble cortical processing networks and output channels.


title: Effector membrane translocation biosensors reveal G protein and β-arrestin coupling profiles of 100 therapeutically relevant GPCRs

abstract: The recognition that individual GPCRs can activate multiple signaling pathways has raised the possibility of developing drugs selectively targeting therapeutically relevant ones. This requires tools to determine which G proteins and {beta}arrestins are activated by a given receptor. Here, we present a set of BRET sensors monitoring the activation of the 12 G protein subtypes based on the translocation of their effectors to the plasma membrane (EMTA). Unlike most of the existing detection systems, EMTA does not require modification of receptors or G proteins (except for Gs). EMTA was found to be suitable for the detection of constitutive activity, inverse agonism, biased signaling and polypharmacology. Profiling of 100 therapeutically relevant human GPCRs resulted in 1,500 pathway-specific concentration-response curves and revealed a great diversity of coupling profiles ranging from exquisite selectivity to broad promiscuity. Overall, this work describes unique resources for studying the complexities underlying GPCR signaling and pharmacology.

category: pharmacology and toxicology


title: Identification of Plitidepsin as Potent Inhibitor of SARS-CoV-2-Induced Cytopathic Effect after a Drug Repurposing Screen

abstract: There is an urgent need to identify therapeutics for the treatment of Coronavirus diseases 2019 (COVID-19). Although different antivirals are given for the clinical management of SARS-CoV-2 infection, their efficacy is still under evaluation. Here, we have screened existing drugs approved for human use in a variety of diseases, to compare how they counteract SARS-CoV-2-induced cytopathic effect and viral replication in vitro. Among the potential 72 antivirals tested herein that were previously proposed to inhibit SARS-CoV-2 infection, only 18% had an IC50 below 25 M or 102 IU/mL. These included plitidepsin, novel cathepsin inhibitors, nelfinavir mesylate hydrate, interferon 2-alpha, interferon-gamma, fenofibrate, camostat along the well-known remdesivir and chloroquine derivatives. Plitidepsin was the only clinically approved drug displaying nanomolar efficacy. Four of these families, including novel cathepsin inhibitors, blocked viral entry in a cell-type specific manner. Since the most effective antivirals usually combine therapies that tackle the virus at different steps of infection, we also assessed several drug combinations. Although no particular synergy was found, inhibitory combinations did not reduce their antiviral activity. Thus, these combinations could decrease the potential emergence of resistant viruses. Antivirals prioritized herein identify novel compounds and their mode of action, while independently replicating the activity of a reduced proportion of drugs which are mostly approved for clinical use. Combinations of these drugs should be tested in animal models to inform the design of fast track clinical trials.


title: Myomegalin regulates Hedgehog pathway by controlling PDE4D at the centrosome

abstract: Mutations in the Hedgehog (Hh) signaling are implicated in birth defects and cancers, including medulloblastoma, one of the most malignant pediatric brain tumors. Current Hh inhibitors face the challenge of drug resistance and tumor relapse, urging new insights in the Hh pathway regulation. Our previous study revealed how PDE4D controls global levels of cAMP in the cytoplasm to positively regulate Hh signaling; in the present study we found that a specific isoform PDE4D3 is tethered to the centrosome by myomegalin, a centrosome/Golgi associated protein. Myomegalin loss dislocates PDE4D3 from the centrosome, leading to local PKA over-activation and inhibition of the Hh signaling, leaving other PKA-related pathways unaffected. Myomegalin loss suppresses the proliferation of granule neuron precursors, and blocks the growth of medulloblastoma in mouse model. Our findings specify a new regulatory mechanism of the Hh pathway, and highlight an exciting therapeutic avenue for Hh-related cancers with reduced side effects.


title: MaxHiC: robust estimation of chromatin interaction frequency in Hi-C and capture Hi-C experiments

abstract:
Hi-C is a genome-wide chromosome conformation capture technology that detects interactions between pairs of genomic regions, and exploits higher order chromatin structures. Conceptually Hi-C data counts interaction frequencies between every position in the genome and every other position. Biologically functional interactions are expected to occur more frequently than random (background) interactions. To identify biologically relevant interactions, several background models that take biases such as distance, GC content and mappability into account have been proposed. Here we introduce MaxHiC, a background correction tool that deals with these complex biases and robustly identifies statistically significant interactions in both Hi-C and capture Hi-C experiments. MaxHiC uses a negative binomial distribution model and a maximum likelihood technique to correct biases in both Hi-C and capture Hi-C libraries. We systematically benchmark MaxHiC against major Hi-C background correction tools and demonstrate using published Hi-C and capture Hi-C datasets that 1) Interacting regions identified by MaxHiC have significantly greater levels of overlap with known regulatory features (e.g. active chromatin histone marks, CTCF binding sites, DNase sensitivity) and also disease-associated genome-wide association SNPs than those identified by currently existing models, and 2) the pairs of interacting regions are more likely to be linked by eQTL pairs and more likely to link known regulatory features than any of the existing methods. We also demonstrate that interactions between different genomic region types have distinct distance distribution only revealed by MaxHiC. MaxHiC is publicly available as a python package for the analysis of Hi-C and capture Hi-C data.

Author summaryMaxHiC is a robust machine learning based tool for identifying significant interacting regions from both Hi-C and capture Hi-C data. All the current existing models are designed for either Hi-C or capture Hi-C data, however we developed MaxHiC to be applicable for both Hi-C and capture Hi-C libraries (two different models have been used for Hi-C and capture Hi-C data). MaxHiC is also able to analyse very deep Hi-C libraries (e.g., MicroC) without any computational issues. MaxHiC significantly outperforms current existing tools in terms of enrichment of interactions between known regulatory regions as well as biologically relevant interactions.


title: Physiology and function of PNS axons rely on glycolic metabolism in myelinating Schwann cells

abstract: Despite the lactate shuttle theory, how glial cells support axonal metabolism and function remains unclear. Lactate production is a common occurrence following anaerobic glycolysis in muscles. However, several other cell types, including some stem cells, activatezd macrophages and tumor cells, can produce lactate in presence of oxygen and cellular respiration, using Pyruvate Kinase 2 (PKM2) to divert pyruvate to lactate dehydrogenase. We show here that PKM2 is also upregulated in mature myelinating Schwann cells (mSC) of mouse sciatic nerve. Deletion of this isoform in PLP-expressing cells in mice leads to a deficit of lactate in mSC and in peripheral nerves. This had no detectable consequences on the myelin sheath. However, mutant mice developed a peripheral neuropathy. Peripheral nerve axons of mutant mice failed to maintain lactate homeostasis upon activity, resulting in an impaired production of mitochondrial ATP. Action potential propagation was not altered but axonal mitochondria transport was slowed down, muscle axon terminals retracted and motor neurons displayed cellular stress. Additional reduction of lactate availability through dichloroacetate treatment, which diverts pyruvate to mitochondrial oxidative phosphorylation, further aggravated motor dysfunction in mutant mice. Thus, lactate production through aerobic glycolysis is essential in mSC for the long-term maintenance of peripheral nerve axon physiology and function.


title: Proliferation impairs cell viability via energy depletion

abstract:
Both proliferative and anti-proliferative pathways are induced after acute kidney injury. The consequences of proliferation on energy homeostasis and cell viability are unknown. We hypothesized that proliferation regulation is an important determinant of epithelial fate after acute kidney injury. We studied the relationship between proliferation and cell viability in kidney tubular cells. We then analyzed the effect of proliferation on the intracellular ATP/ADP ratio. Finally, we used transcriptomic data from transplanted kidneys to study the relationship between cell proliferation and energy production with different clinical evolutions. We found that proliferation is associated with decreased survival after toxic or energetic stresses in kidney proximal tubular cells. In vitro, we found that the ATP/ADP ratio oscillates reproducibly throughout the cell cycle, and that proliferation is instrumental to an overall decrease in intracellular ATP/ADP ratio. In vivo, in injured kidneys, we found that proliferation was strongly associated with a specific decrease in the expression of the mitochondria-encoded genes of the oxidative phosphorylation pathway as opposed to the nucleus-encoded ones. These observations suggest that mitochondrial function is the limiting factor for energy production in kidney cells proliferating after injury. The association of increased proliferation and decreased mitochondrial function was associated with poor renal outcomes. In summary, we show that proliferation is an energy demanding process impairing the cellular ability to cope with a toxic or ischemic injury, identifying the association of proliferative repair and metabolic recovery as indispensable and interdependent features for successful kidney repair.

One Sentence SummaryProliferation decreases energy availability in kidney epithelial cells and is associated with enhanced cell death and chronic kidney disease in case of a superimposed metabolic stress.

category: physiology


title: Degradation of Alzheimers Amyloid-beta by a Catalytically Inactive Insulin Degrading Enzyme

abstract: It is known that insulin-degrading-enzyme (IDE) plays a crucial role in the clearance of Alzheimers amyloid-{beta} (A{beta}). The cysteine-free IDE mutant (cf-E111Q-IDE) is catalytically inactive against insulin, but its effect on A{beta} degradation is unknown that would help in the allosteric modulation of the enzyme activity. Herein, the degradation of A{beta}(1-40) by cf-E111Q-IDE via a non-chaperone mechanism is demonstrated by NMR and LC-MS, and the aggregation of fragmented peptides is characterized using fluorescence and electron microscopy. cf-E111Q-IDE presented a reduced effect on the aggregation kinetics of A{beta}(1-40) when compared with the wild-type IDE. Whereas LC-MS and diffusion ordered NMR spectroscopy revealed the generation of A{beta} fragments by both wild-type and cf-E111Q-IDE. The aggregation propensities and the difference in the morphological phenotype of the full-length A{beta}(1-40) and its fragments are explained using multi-microseconds molecular dynamics simulations. Notably, our results reveal that zinc binding to A{beta}(1-40) inactivates cf-E111Q-IDEs catalytic function, whereas zinc removal restores its function as evidenced from high-speed AFM, electron microscopy, chromatography, and NMR results. These findings emphasize the catalytic role of cf-E111Q-IDE on A{beta} degradation and urge the development of zinc chelators as an alternative therapeutic strategy that switches on/off IDEs function.


title: Synchronizing vigilance or taking turns as sentinels? The importance of testing coordination

abstract:
Coordinated behavior, such as hunting in lions and coordinated vigilance as antipredator behavior, are examples of benefits of group-living. Instead of asynchronous vigilance, some social species synchronize their vigilance bouts or take turns acting as sentinels. To increase our knowledge on the evolution of vigilance behavior, we studied whether vigilance is coordinated in Barbary ground squirrels, Atlantoxerus getulus. We show that vigilance was synchronized instead of taking turns. Multiple non-mutually exclusive hypotheses could explain synchronization: Barbary ground squirrels may perch because 1) neighbors are perched (copying effect), 2) perch synchrony may be an emergent property of the ecology as all squirrels may be satiated at the same time (collective behavior), or 3) the benefits are large in terms of evading ambush predators and scanning effectiveness (watch each others back). Particularly, in habitats where the field of view is obstructed by man-made structures and multiple individuals may be necessary to watch for terrestrial predators, synchronized vigilance may have greater fitness benefits than sentinel behavior. We conclude that it is essential to test assumptions of coordination and, thus, to analyze coordination to describe sentinel systems.

Significance StatementVigilance behavior can be vital to an animals survival. Taking turns acting as sentinels or synchronizing vigilance bouts reduces the cost of the trade-off between feeding and predation risk. A sentinel system assumes that sentinels are vigilant from raised positions, warn group members of danger, and alternate vigilance bouts. However, the assumption of alternating vigilance bouts remains poorly tested. We tested this assumption in invasive Barbary ground squirrels. We found that instead of alternating, individuals synchronized their vigilance bouts. Perch synchrony may be 1) a response to perching group members (copying effect), 2) an emergent property of the species ecology, and 3) an adaptation to anthropogenically altered habitats (watch each others back).

category: animal behavior and cognition


title: Barbary ground squirrels do not have a sentinel system but instead synchronise vigilance


title: Biochemical, structural insights of newly isolated AA16 family of Lytic Polysaccharide Monooxygenase (LPMO) from Aspergillus fumigatus and investigation of its synergistic effect using biomass.

abstract:
The efficient conversion of lignocellulosic biomass into fermentable sugar is a bottleneck for the cheap production of bio-ethanol. The recently identified enzyme Lytic Polysaccharide Monooxygenase (LPMO) family has brought new hope because of its boosting capabilities of cellulose hydrolysis. In this report, we have identified and characterized a new class of auxiliary (AA16) oxidative enzyme LPMO from the genome of a locally isolated thermophilic fungus Aspergillus fumigatus (NITDGPKA3) and evaluated its boosting capacity of biomass hydrolysis. The AfLPMO16 is an intronless gene and encodes the 29kDa protein. While Sequence-wise, it is close to the C1 type of AaAA16 and cellulose-active AA10 family of LPMOs, but the predicted three-dimensional structure shows the resemblance with the AA11 family of LPMO (PDB Id: 4MAH). The gene was expressed under an inducible promoter (AOX1) with C-terminal His tag in the Pichia pastoris. The protein was purified using Ni-NTA affinity chromatography, and we studied the enzyme kinetics with 2,6-dimethoxyphenol. We observed polysaccharides depolymerization activity with Carboxymethyl cellulose (CMC) and Phosphoric acid swollen cellulose (PASC). Moreover, the simultaneous use of cellulase cocktail (commercial) and AfLPMO16 enhances lignocellulosic biomass hydrolysis by 2-fold, which is highest so far reported in the LPMO family.

ImportanceThe auxiliary enzymes, such as LPMOs, have industrial importance. These enzymes are used in cellulolytic enzyme cocktail due to their synergistic effect along with cellulases. In our study, we have biochemically and functionally characterized the new AA16 family of LPMO from Aspergillus fumigatus (NITDGPKA3). The biochemical characterization is the fundamental scientific elucidation of the newly isolated enzyme. The functional characterization, biomass degradation activity of AfLPMO16, and cellulase cocktail (commercial) combination enhancing the activity by 2-fold. This enhancement is the highest reported so far, which gives the enzyme AfLPMO16 enormous potential for industrial use.


title: Coupling spectral and resource-use complementarity in experimental grassland and forest communities

abstract: Reflectance spectra provide integrative measures of plant phenotypes by capturing chemical, morphological, anatomical and architectural trait information. Here we investigate the linkages between plant spectral variation, spectral and resource-use complementarity that contribute to ecosystem productivity. In both a prairie grassland and a forest diversity experiment, we delineated N-dimensional hypervolumes using either wavelength-bands of reflectance spectra or foliar traits. First, we compared the hypervolume fraction unique to each species in either spectral or trait space with increasing dimensionality. Then, we investigated the association between the spectral space occupied by individual plants and their growth, as well as the spectral space occupied by plant communities and ecosystem productivity. We show that species are better distinguished in spectral space than in trait space, providing a conceptual basis for identifying plant taxa spectrally. In addition, the spectral space occupied by individuals increased with plant growth, and the spectral space occupied by plant communities increased with ecosystem productivity. Furthermore, ecosystem productivity was better explained by inter-individual spectral complementarity than by the large spectral space occupied by productive individuals. Our results indicate that spectral hypervolumes of plants can reflect ecological strategies that shape community composition and ecosystem function, and that spectral complementarity can reveal resource-use complementarity.


title: Regulation of Neural Circuit Development by Cadherin-11 Provides Implications for Autism

abstract:
Autism spectrum disorder (ASD) is a neurological condition characterized by alterations in social interaction and communication, and restricted and/or repetitive behaviors. The classical type II cadherins cadherin-8 (Cdh8, CDH8) and cadherin-11 (Cdh11, CDH11) have been implicated as autism risk gene candidates. To explore the role of cadherins in the etiology of autism, we investigated their expression patterns during mouse brain development and in autism-specific human tissue. In mice, expression of cadherin-8 and cadherin-11 was developmentally regulated and enriched in the cortex, hippocampus, and thalamus/striatum during the peak of dendrite formation and synaptogenesis. Both cadherins were expressed in synaptic compartments but only cadherin-8 associated with the excitatory synaptic marker neuroligin-1. Induced pluripotent stem cell (iPSC)-derived cortical neural precursor cells (NPCs) and cortical organoids generated from individuals with autism showed upregulated CDH8 expression levels while CDH11 expression levels were downregulated. We used Cdh11 knockout mice of both sexes to analyze the function of cadherin-11, which could help explain phenotypes observed in autism. Cdh11-/- hippocampal neurons exhibited increased dendritic complexity along with altered neuronal and synaptic activity. Similar to the expression profiles in human tissue, levels of cadherin-8 were significantly elevated in Cdh11 knockout brains. Additionally, excitatory synaptic markers neuroligin-1 and PSD-95 were both increased. Together, these results strongly suggest that cadherin-11 is involved in regulating the development of neuronal circuitry and that alterations in the expression levels of cadherin-11 may contribute to the etiology of autism.

Significance StatementAutism is a neurodevelopmental condition with high genetic and phenotypic heterogeneity. Multiple genes have been implicated in autism, including the cadherin superfamily of adhesion molecules, cadherin-8 and cadherin-11. This study first characterizes the expression profiles of cadherin-8 and cadherin-11 to understand the potential roles they play in the development of neurons. The study further describes novel contributions of cadherin-11 in neural circuit formation. Loss of cadherin-11 in mice results in altered levels of several synaptic proteins, including PSD-95, neuroligin-1, and cadherin-8, and changes the morphology and activity of excitatory neurons. The levels of cadherin-8 and cadherin-11 in human cells of autistic individuals are both altered, strengthening the hypothesis that these two cadherins may involve in aspects of autism etiology.


title: Functional Annotation of Human Cognitive States using Deep Graph Convolution

abstract: A key goal in neuroscience is to understand brain mechanisms of cognitive functions. An emerging approach is "brain decoding", which consists of inferring a set of experimental conditions performed by a participant, using pattern classification of brain activity. Few works so far have attempted to train a brain decoding model that would generalize across many different cognitive tasks drawn from multiple cognitive domains. To tackle this problem, we proposed a multidomain brain decoder that automatically learns the spatiotemporal dynamics of brain response within a short time window using a deep learning approach. We evaluated the decoding model on a large population of 1200 participants, under 21 different experimental conditions spanning six different cognitive domains, acquired from the Human Connectome Project task-fMRI database. Using a 10s window of fMRI response, the 21 cognitive states were identified with a test accuracy of 90% (chance level 4.8%). Performance remained good when using a 6s window (82%). It was even feasible to decode cognitive states from a single fMRI volume (720ms), with the performance following the shape of the hemodynamic response. Moreover, a saliency map analysis demonstrated that the high decoding performance was driven by the response of biologically meaningful brain regions. Together, we provide an automated tool to annotate human brain activity with fine temporal resolution and fine cognitive granularity. Our model shows potential applications as a reference model for domain adaptation, possibly making contributions in a variety of domains, including neurological and psychiatric disorders.


title: Efficient Representations of Tumor Diversity with Paired DNA-RNA Aberrations

abstract:
Cancer cells display massive dysregulation of key regulatory pathways due to now well-catalogued mutations and other DNA-related aberrations. Moreover, enormous heterogeneity has been commonly observed in the identity, frequency and location of these aberrations across individuals with the same cancer type or subtype, and this variation naturally propagates to the transcriptome, resulting in myriad types of dysregulated gene expression programs. Many have argued that a more integrative and quantitative analysis of heterogeneity of DNA and RNA molecular profiles may be necessary for designing more systematic explorations of alternative therapies and improving predictive accuracy.

We introduce a representation of multi-omics profiles which is sufficiently rich to account for observed heterogeneity and support the construction of quantitative, integrated, metrics of variation. Starting from the network of interactions existing in Reactome, we build a library of "paired DNA-RNA aberrations" that represent prototypical and recurrent patterns of dysregulation in cancer; each two-gene "Source-Target Pair" (STP) consists of a "source" regulatory gene and a "target" gene whose expression is plausibly "controlled" by the source gene. The STP is then "aberrant" in a joint DNA-RNA profile if the source gene is DNA-aberrant (e.g., mutated, deleted, or duplicated), and the downstream target gene is "RNA-aberrant", meaning its expression level is outside the normal, baseline range. With M STPs, each sample profile has exactly one of the 2M possible configurations.

We concentrate on subsets of STPs, and the corresponding reduced configurations, by selecting tissue-dependent minimal coverings, defined as the smallest family of STPs with the property that every sample in the considered population displays at least one aberrant STP within that family. These minimal coverings can be computed with integer programming. Given such a covering, a natural measure of cross-sample diversity is the extent to which the particular aberrant STPs composing a covering vary from sample to sample; this variability is captured by the entropy of the distribution over configurations.

We apply this program to data from TCGA for six distinct tumor types (breast, prostate, lung, colon, liver, and kidney cancer). This enables an efficient simplification of the complex landscape observed in cancer populations, resulting in the identification of novel signatures of molecular alterations which are not detected with frequency-based criteria. Estimates of cancer heterogeneity across tumor phenotypes reveals a stable pattern: entropy increases with disease severity. This framework is then well-suited to accommodate the expanding complexity of cancer genomes and epigenomes emerging from large consortia projects.

Author SummaryA large variety of genomic and transcriptomic aberrations are observed in cancer cells, and their identity, location, and frequency can be highly indicative of the particular subtype or molecular phenotype, and thereby inform treatment options. However, elucidating this association between sets of aberrations and subtypes of cancer is severely impeded by considerable diversity in the set of aberrations across samples from the same population. Most attempts at analyzing tumor heterogeneity have dealt with either the genome or transcriptome in isolation. Here we present a novel, multi-omics approach for quantifying heterogeneity by determining a small set of paired DNA-RNA aberrations that incorporates potential downstream effects on gene expression. We apply integer programming to identify a small set of paired aberrations such that at least one among them is present in every sample of a given cancer population. The resulting "coverings" are analyzed for six cancer cohorts from the Cancer Genome Atlas, and facilitate introducing an information-theoretic measure of heterogeneity. Our results identify many known facets of tumorigenesis as well as suggest potential novel genes and interactions of interest.

Data Availability StatementRNA-Seq data, somatic mutation data and copy number data for The Cancer Genome Atlas were obtained through the Xena Cancer Genome Browser database (https://xenabrowser.net) from individual cancer type cohorts. Computational functionality for the optimization procedure is provided at https://github.com/wikum/lpcover and the code for the analysis in the manuscript is provided at https://github.com/wikum/CoveringAnalysis. Processed data in the form of TAB delimited files, and selected tissue-level coverings (in excel format) are provided as additional supplementary material and are also available from the Marchionni laboratory website (http://marchionnilab.org/signatures.html)

category: genomics


title: Age-dependent genetic variants associated with longitudinal changes in brain structure across the lifespan

abstract: Human brain structure changes throughout our lives. Altered brain growth or rates of decline are implicated in a vast range of psychiatric, developmental, and neurodegenerative diseases. Here, we identified common genetic variants that affect rates of brain growth or atrophy, in the first genome-wide association meta-analysis of changes in brain morphology across the lifespan. Longitudinal MRI data from 15,640 individuals were used to compute rates of change for 15 brain structures. The most robustly identified genes GPR139, DACH1 and APOE are associated with metabolic processes. We demonstrate global genetic overlap with depression, schizophrenia, cognitive functioning, insomnia, height, body mass index and smoking. Gene-set findings implicate both early brain development and neurodegenerative processes in the rates of brain changes. Identifying variants involved in structural brain changes may help to determine biological pathways underlying optimal and dysfunctional brain development and ageing.


title: Conformational Tuning of Amylin by Charged Styrene-maleic-acid Copolymers

abstract: Human amylin forms structurally heterogeneous amyloids that have been linked to type-2 diabetes. Thus, understanding the molecular interactions governing amylin aggregation can provide mechanistic insights in its pathogenic formation. Here, we demonstrate that fibril formation of amylin is altered by synthetic amphipathic copolymer derivatives of the styrene- maleic-acid (SMAQA and SMAEA). High-speed AFM is used to follow the real-time aggregation of amylin by observing the rapid formation of de novo globular oligomers and arrestment of fibrillation by the positively-charged SMAQA. We also observed an accelerated fibril formation in the presence of the negatively-charged SMAEA. These findings were further validated by fluorescence, SOFAST-HMQC, DOSY and STD NMR experiments. Conformational analysis by CD and FT-IR revealed that the SMA copolymers modulate the conformation of amylin aggregates. While the species formed with SMAQA are -helical, the ones formed with SMAEA are rich in {beta}-sheet structure. The interacting interfaces between SMAEA or SMAQA and amylin are mapped by NMR and microseconds all-atom MD simulation. SMAEA displayed {pi}-{pi} interaction with Phe23, electrostatic {pi}-cation interaction with His18 and hydrophobic packing with Ala13 and Val17; whereas SMAQA showed a selective interaction with amylins C-terminus (residues 31-37) that belongs to one of the two {beta}-sheet regions (residues 14-19 and 31-36) involved in amylin fibrillation. Toxicity analysis showed both SMA copolymers to be non-toxic in vitro and the amylin species formed with the copolymers showed minimal deformity to zebrafish embryos. Together, this study demonstrates that chemical tools, such as copolymers, can be used to modulate amylin aggregation, alter the conformation of species.


title: Spatial distribution of rice lectin protein r40g3 determines its dual regulatory role in imparting salinity tolerance while impeding seed development

abstract: While the role of R40 family of lectin proteins in osmotic stress was already reported, their mechanism of stress tolerance still remained elusive. Among them, the expression of Osr40g3 was most strongly induced in response to salinity. Here, we explored the mechanism of Osr40g3- mediated salinity tolerance in rice. The overexpression of Osr40g3 under control of a constitutive promoter significantly improved salinity tolerance but displayed pollen sterility and impaired seed development. The gene further displayed precise tissue-specific expression which was essential for proper seed development in rice. In salinity-stressed leaves, Osr40g3 interacted with OsEG45 leading to salinity tolerance. Overexpression of OsEG45 significantly improved salinity tolerance while the OsEG45 silencing lines displayed severe sensitivity thus confirming its role in imparting salinity tolerance. On the other hand, the constitutive overexpression of Osr40g3 led to its interaction with OsGF14e in stamens reducing its protein stability. This interaction further interfered with gibberellic acid (GA) metabolism thus leading to pollen sterility. The OsGF14e silencing lines also failed to set seeds and displayed diminished GA content thus supporting its involvement in regulating seed development. Surprisingly, these OsGF14e silencing lines also displayed improved salinity tolerance with higher expression of OsEG45 while the OsGF14e overexpression lines displayed opposite phenotype. This altered expression of OsEG45 was further mediated by GA levels in these transgenic lines. Together, we demonstrate that salt stress induces Osr40g3 which then positively regulates OsEG45 and negatively regulates OsGF14e. Inhibition of OsGF14e reduces GA level which further induces OsEG45 expression thus leading to salinity tolerance in rice.

category: plant biology


title: Osr40g3 imparts salinity tolerance by regulating GF14e-mediated modulation of gibberellin metabolism to activate expansin protein, EG45 in rice


title: State-selective Modulation of Heterotrimeric Gαs Signaling with Macrocyclic Peptides

abstract: The G protein-coupled receptor (GPCR) cascade leading to production of the second messenger cAMP is replete with pharmacologically targetable receptors and enzymes with the exception of the G subunit, Gs. GTPases remain largely undruggable given the difficulty of displacing high-affinity guanine nucleotides and the lack of other drug binding sites. We explored a chemical library of 1012 cyclic peptides in order to expand the chemical search for inhibitors of this enzyme class. We identified two macrocyclic peptides, GN13 and GD20, that antagonize the active and inactive states of Gs, respectively. Both macrocyclic peptides fine-tune Gs activity with high nucleotide-binding-state selectivity and G protein class-specificity. Co-crystal structures reveal that GN13 and GD20 distinguish the conformational differences within the switch II/3 pocket and block effector interactions. The Gs inhibitors showed strong activity in cellular contexts through binding to crystallographically defined pockets. The discovery of cyclic peptide inhibitors targeting Gs provides a path for further development of state-dependent GTPase inhibitors.


title: Flow-cell based technology for massively parallelcharacterization of base-modified DNA aptamers

abstract: Aptamers incorporating chemically modified bases can achieve superior affinity and specificity compared to natural aptamers, but their characterization remains a labor-intensive, low-throughput task. Here we describe the  non-natural aptamer array (N2A2) system, in which a minimally modified Illumina MiSeq instrument is used for the high-throughput generation and characterization of large libraries ([~]106) of base-modified DNA aptamer candidates on the basis of both target affinity and specificity. We first demonstrate the capability to screen multiple different base modifications to identify the optimal chemistry for high-affinity target binding. We next use N2A2 to generate aptamers that can maintain excellent specificity even in complex samples, with equally strong target affinity in both buffer and diluted human serum. Given that N2A2 requires only minor mechanical modifications to the MiSeq, we believe N2A2 offers a broadly accessible tool for generating high-quality affinity reagents for diverse applications.

category: bioengineering


title: Reverse plasticity underlies rapid evolution by clonal selection within populations of fibroblastspropagated on a novel soft substrate

abstract: Mechanical properties such as substrate stiffness are a ubiquitous feature of a cells environment. Many types of animal cells exhibit canonical phenotypic plasticity when grown on substrates of differing stiffness, in vitro and in vivo. Whether such plasticity is a multivariate optimum due to hundreds of millions of years of animal evolution, or instead is a compromise between conflicting selective demands, is unknown. We addressed these questions by means of experimental evolution of populations of mouse fibroblasts propagated for ~90 cell generations on soft or stiff substrates. The ancestral cells grow twice as fast on stiff substrate as on soft substrate and exhibit the canonical phenotypic plasticity. Soft-selected lines derived from a genetically diverse ancestral population increased growth rate on soft substrate to the ancestral level on stiff substrate and evolved the same multivariate phenotype. The pattern of plasticity in the soft-selected lines was opposite of the ancestral pattern, suggesting that reverse plasticity underlies the observed rapid evolution. Conversely, growth rate and phenotypes did not change in selected lines derived from clonal cells. Overall, our results suggest that the changes were the result of genetic evolution and not phenotypic plasticity per se. Whole-transcriptome analysis revealed consistent differentiation between ancestral and soft-selected populations, and that both emergent phenotypes and gene expression tended to revert in the soft-selected lines. However, the selected populations appear to have achieved the same phenotypic outcome by means of at least two distinct transcriptional architectures related to mechano-transduction and proliferation.


title: Cooperative stator assembly of bacterial flagellar motor mediated by rotation

abstract: Cooperativity has a central place in biological regulation, providing robust and highly-sensitive regulation. The bacterial flagellar motor (BFM) implements autonomous torque regulation based on the stators nonequilibrium structure; the stator units bind to and dissociate from the motor dynamically in response to environmental changes. However, the mechanism of this dynamic assembly is not fully understood. Here, we demonstrate the cooperativity in the stator assembly dynamics. The binding is slow at the stalled state, but the rotation in either direction boosts the stator binding. Hence, once a stator unit binds, it drives the rotor and triggers the avalanche of succeeding bindings. This cooperative mechanism based on nonequilibrium allostery accords with the recently-proposed geartype coupling between the rotor and stator.


title: Flap dynamics in pepsin-like aspartic proteases: a computational perspective using Plasmepsin-II and BACE-1 as model systems

abstract: The flexibility of a {beta} hairpin structure known as the flap plays a key role in catalytic activity and substrate intake in pepsin-like aspartic proteases. Most of these enzymes share structural and sequential similarity. In the apo form of the proteases, a conserved tyrosine residue in the flap region is in dynamic equilibrium between the normal and flipped states through rotation of the{chi} 1 and{chi} 2 angles. In this study, we have used apo Plm-II and BACE-1 as model systems. Independent MD simulations of Plm-II and BACE-1 remained stuck either in the normal or flipped state. Metadynamics simulations using side-chain torsion angles ({chi}1 and{chi} 2 of tyrosine) as collective variables sampled the transition between the normal and flipped states. Qualitatively, the two states were predicted to be equally populated. The normal and flipped states were stabilised by H-bond interactions to a tryptophan residue and to the catalytic aspartate, respectively. Further, mutation of tyrosine to an amino-acid with smaller side-chain, such as alanine, reduced the flexibility of the flap and resulted in a flap collapse (flap loses flexibility and remains stuck in a particular state). This is in accordance with previous experimental studies, which showed that mutation to alanine resulted in loss of activity in pepsin-like aspartic proteases. Our results suggest that the rotation of the tyrosine side-chain is the key movement that governs flap dynamics and opening of the binding pocket in most pepsin-like aspartic proteases.


title: Cancer-specific loss of TERT activation sensitizes glioblastoma to DNA damage

abstract: Most glioblastomas (GBMs) achieve cellular immortality by acquiring a mutation in the telomerase reverse transcriptase (TERT) promoter. TERT promoter mutations create a binding site for a GA binding protein (GABP) transcription factor complex, whose assembly at the promoter is associated with TERT reactivation and telomere maintenance. Here, we demonstrate increased binding of a specific GABPB1L isoform-containing complex to the mutant TERT promoter. Furthermore, we find that TERT promoter mutant GBM cells, unlike wild-type cells, exhibit a critical near-term dependence on GABPB1L for proliferation, both in cell culture and post-tumor establishment in vivo. Upregulation of the protein paralogue GABPB2, which is normally expressed at very low levels, can rescue this dependence. More importantly, when combined with frontline temozolomide (TMZ) chemotherapy, inducible GABPB1L knockdown and the associated TERT reduction led to an impaired DNA damage response that resulted in profoundly reduced growth of intracranial GBM tumors. Together, these findings provide new insights into the mechanism of cancer-specific TERT regulation, uncover rapid effects of GABPB1L-mediated TERT suppression in GBM maintenance, and establish GABPB1L inhibition in combination with chemotherapy as a novel therapeutic strategy for TERT promoter mutant GBM.


title: Understanding the effects of contact structures and information sharing on the FMD transmission among beef cattle farms

abstract: Moving infected animals and sharing contaminated vehicles are considered as the most potent ways for between-farm disease transmission. The objective of this study is to develop a network-based simulation model to investigate the effects of direct contact, indirect contact, and their combination on a hypothetical foot-and-mouth disease spreading between beef-cattle farms in southwest Kansas, US, and explore the effect of different types of information-sharing networks on preventing the disease spreading. Based on synthetic cattle and truck movement data in southwest Kansas, we build a farm-level contact network with three layers, a cattle movement layer (direct contact), a truck movement layer (indirect contact), and an information-sharing layer. Through scenario analyses, we compare the disease transmission dynamics, the distribution of outbreak epidemic size, and the disease breakout percentage of different contact structures - only direct contact, only indirect contact, and their combination. In addition, we evaluate different types of information sharing methods by comparing the epidemic size and the estimated economic loss. Simulation results show that neither direct contact nor indirect contact individually can result in a massive outbreak of the disease, but their combination plays a significant role. Additionally, we detect different probabilities of disease outbreaks by starting the simulations at different farms; starting at some farms with high capacity increases the probability of disease outbreaks. Three different information sharing-networks are developed and found effective in preventing the disease from spreading and reducing the economic loss. The information-sharing layer based on trading records has the best performance when compared with a random network and a geographic network.


title: Tinamou egg color displacement at ecoregion co-partitioning

abstract: The divergence of reproductive traits frequently underpins the evolution of reproductive isolation. One of the most enduring puzzles on this subject concerns the variability in egg coloration among species of tinamou (Tinamidae), endemic to neotropics. Here we investigated the hypothesis that tinamou egg coloration is a mating signal and its diversification was driven by reinforcement. For most tinamou species, the male guards the nest that is sequentially visited and laid eggs in by multiple females. The colorations of the existing eggs in the nest could signal mate quality and species identities to the upcoming females, preventing costly hybridization, thus were selected to diverge among species (Mating Signal Character Displacement Hypothesis). If so, two predictions should follow: (1) egg colors should coevolve with known mating signals as the tinamou lineages diverged; (2) species that partition similar ecoregions should display different egg colors. The tinamou songs are important mating signals and are highly divergent among species. We found that the egg luminance was significantly associated with the first principal component of the song variables, which supports prediction (1). In addition, we found support for (2): tinamou species that co-partition ecoregions tend to display different egg colors, controlling for song variation. Egg color and songs could be multimodal mating signals that are divergently selected as different tinamou species diverged. Mating signal evolution could be opportunistic and even exploit post-mating trait as premating signals that undergo character displacement at sympatry.


title: Intraflagellar transport-A deficiency attenuates ADPKD in a renal tubular- and maturation-dependent manner

abstract: Primary cilia are sensory organelles built and maintained by intraflagellar transport (IFT) multi-protein complexes. Deletion of different IFT-B genes attenuates polycystic kidney disease (PKD) severity in juvenile and adult Autosomal Dominant (AD) PKD mouse models, while deletion of an IFT-A adaptor, Tulp3, attenuates PKD severity in adult mice only. These studies indicate that dysfunction of specific cilia components has potential therapeutic value. To broaden our understanding of cilia dysfunction and its therapeutic potential, here we investigate the impact of global deletion of an IFT-A gene, Thm1, in juvenile and adult ADPKD mouse models. Both juvenile and adult models exhibited increased kidney weight:body weight (KW/BW) ratios, renal cysts, inflammation, lengthened renal cilia, and increased levels of the nutrient sensor, O-linked {beta}-N-acetylglucosamine (O-GlcNAc). Thm1 deletion in juvenile ADPKD mice reduced KW/BW ratios and cortical collecting duct cystogenesis, but increased proximal tubular and glomerular dilations and did not reduce inflammation, cilia lengths, and O-GlcNAc signaling. In contrast, Thm1 deletion in adult ADPKD mice markedly attenuated renal cystogenesis, inflammation, cilia lengths, and O-GlcNAc. Thus, unlike IFT-B genes, the role of Thm1 deletion in ADPKD mouse models is development-specific. Unlike an IFT-A adaptor gene, deleting Thm1 in juvenile ADPKD mice is partially ameliorative. Our studies suggest that different microenvironmental factors found in distinct nephron segments and between developing and mature kidneys modify ciliary homeostasis and ADPKD pathobiology. Further, elevated levels of O-GlcNAc, which regulates cellular metabolism and ciliogenesis, may be a novel feature and critical regulator of certain key ADPKD pathological processes.


title: The Genetic Basis of phage susceptibility, cross-resistance and host-range in Salmonella

abstract: Though bacteriophages (phages) are known to play a crucial role in bacterial fitness and virulence, our knowledge about the genetic basis of their interaction, cross-resistance and host-range is sparse. Here, we employed genome-wide screens in Salmonella enterica serovar Typhimurium to discover host determinants involved in resistance to eleven diverse lytic phages including 4 new phages isolated from a therapeutic phage cocktail. We uncovered 301 diverse host factors essential in phage infection, many of which are shared between multiple phages demonstrating potential cross-resistance mechanisms. We validate many of these novel findings and uncover the intricate interplay between RpoS, the virulence-associated general stress response sigma factor and RpoN, the nitrogen starvation sigma factor in phage cross-resistance. Finally, the infectivity pattern of eleven phages across a panel of 23 genome sequenced Salmonella strains indicates that additional constraints and interactions beyond the host factors uncovered here define the phage host range.


title: Flood-induced interspecific interactions in spring-fed tributary as an ecosystem function of heterogeneous river networks

abstract: Understanding the migratory community dynamics of river networks is important for maintaining lotic system integrity. River animals migrate to their preferred habitats in spatiotemporally heterogeneous river environments. Spring-fed habitats are uniquely characterized by stable temperature and flow regimes, which create suitable spawning habitats for the chum salmon Oncorhynchus keta. O. keta exhibits "run up" to its birthplace for spawning, especially during floods. Because the eggs deposited by this anadromous fish are nutritious and actively consumed by freshwater animals, the location and timing of O. keta spawning events affect the spatiotemporal accumulation of mobile consumers. In this study, we examined changes in temporal population density in spawning O. keta and a mobile consumer (juvenile O. masou masou) in a lowland, spring-fed tributary in northern Japan during a 48.5-mm autumn rainfall event. In both species, population density increased, and then decreased, after the rainfall event. In O. keta, these changes were closely associated with rainfall intensity, whereas in O. masou masou the peak was delayed until 3 days after the rainfall event. A comparison of the gut contents of O. masou masou sampled from a spring-fed tributary and an adjacent non-spring-fed tributary indicated greater consumption of O. keta eggs in the spring-fed tributary. These results suggested that preferential migration of O. keta into spring-fed tributaries for spawning induces subsequent accumulation of juvenile O. masou masou, in turn increasing O. keta egg consumption. These findings improve our understanding of community dynamics during floods in a heterogeneous river network environment.


title: LPHN2 inhibits vascular permeability by differential control of endothelial cell adhesion

abstract:
Dynamic modulation of endothelial cell-to-cell and cell-to-extracellular matrix (ECM) adhesion is essential for blood vessel patterning and functioning. Yet, the molecular mechanisms involved in this process have not been completely deciphered. We identify the adhesion G protein-coupled receptor (ADGR) Latrophilin 2 (LPHN2) as a novel determinant of endothelial cell (EC) adhesion and barrier function. In cultured ECs, endogenous LPHN2 localizes at ECM contacts, signals through cAMP/Rap1, and inhibits focal adhesion (FA) formation and nuclear localization of YAP/TAZ transcriptional regulators, while promoting tight junction (TJ) assembly. ECs also express an endogenous LPHN2 ligand, fibronectin-leucine-rich transmembrane 2 (FLRT2), that prevents ECM-elicited EC behaviors in a LPHN2-dependent manner. Vascular ECs of lphn2a knock-out zebrafish embryos become abnormally stretched, display a hyperactive YAP/TAZ pathway, and lack proper intercellular TJs. Consistently, blood vessels are hyperpermeable and intravascularly injected cancer cells extravasate more easily in lphn2a null animals. Thus, LPHN2 ligands, such as FLRT2, may be therapeutically exploited to interfere with cancer metastatic dissemination.

SUMMARYCamillo et al. show that the LPHN2 receptor, upon activation by FLRT2 ligand, inhibits focal adhesion formation and promotes tight junction assembly in endothelial cells. Blood vessels of lphn2a null animals are hyperpermeable and injected cancer cells extravasate more easily.

category: cell biology


title: Bayesian inference of kinetic schemes for ion channels by Kalman filtering

abstract: Inferring adequate kinetic schemes for ion channel gating from ensemble currents is a daunting task due to limited information in the data. We address this problem by using a parallelized Bayesian filter to specify hidden Markov models for current and fluorescence data. We demonstrate the flexibility of this algorithm by including different noise distributions. Our generalized Kalman filter outperforms both a classical Kalman filter and a rate equation approach when applied to patch-clamp data exhibiting realistic open-channel noise. The derived generalization also enables inclusion of orthogonal fluorescence data, making unidentifiable parameters identifiable and increasing the accuracy of the parameter estimates by an order of magnitude. By using Bayesian highest credibility volumes, we found that our approach, in contrast to the rate equation approach, yields a realistic quantification of uncertainty. Furthermore, the Bayesian filter delivers unbiased estimates for a wider range of data quality and identifies parameters which the rate equation approach does not identify. These results also demonstrate the power of assessing the validity of algorithms by Bayesian credibility volumes in general. Finally, we show that our Bayesian filter is more robust against errors induced by either analog filtering before analog-to-digital conversion or by limited time resolution of fluorescence data than a rate equation approach.


title: Subcortical Circuits Mediate Communication Between Primary Sensory Cortical Areas

abstract: Integration of information across the senses is critical for perception and is a common property of neurons in the cerebral cortex, where it is thought to arise primarily from corticocortical connections. Much less is known about the role of subcortical circuits in shaping the multisensory properties of cortical neurons. We show that stimulation of the whiskers causes widespread suppression of sound-evoked activity in mouse primary auditory cortex (A1). This suppression depends on the primary somatosensory cortex (S1), and is implemented through a descending circuit that links S1, via the auditory midbrain, with thalamic neurons that project to A1. Furthermore, a direct pathway from S1 has a facilitatory effect on auditory responses in higher-order thalamic nuclei that project to other brain areas. Crossmodal corticofugal projections to the auditory midbrain and thalamus therefore play a pivotal role in integrating multisensory signals and in enabling communication between different sensory cortical areas.


title: Single-cell resolution analysis of the crosstalk between chemogenically activated astrocytes and microglia

abstract: Astrocytes are the most common glial cell type in the brain, yet, it is unclear how their activation affects the transcriptome of neighboring cells. Engineered G protein-coupled receptors (GPCRs) called Designer Receptors Exclusively Activated by Designer Drugs (DREADDs) enable selective activation of specific cell types, such as astrocytes. Here, we combine activation of astrocytes in the hippocampus and cortex of healthy mice with single-cell RNA sequencing. Our data show that long-term activation of astrocytes dramatically alters the transcriptome of astrocytes and microglia. Genes that were differentially expressed in Gq-DREADD-activated astrocytes are involved in neurogenesis and low-density lipoprotein particle biology, while those in the microglia were involved in lipoprotein handling, purinergic receptor activity, and immune cell migration and chemotaxis. Furthermore, network analysis showed that Gq-DREADD-mediated activation in astrocytes resulted in an upregulation of genes involved in the GPCR signaling pathways and calcium ion homeostasis, confirming astrocyte activation. This dataset will serve as a resource for the broader neuroscience community, and our findings highlight the importance of studying transcriptomic alterations in microglia after astrocyte activation in vivo.


title: A conserved neuropeptide system links head and body motor circuits to enable adaptive behavior

abstract:
Neuromodulators promote adaptive behaviors that are often complex and involve concerted activity changes across circuits that are often not physically connected. It is not well understood how neuromodulatory systems accomplish these tasks. Here we show that the C. elegans NLP-12 neuropeptide system shapes responses to food availability by modulating the activity of head and body wall motor neurons through alternate G-protein coupled receptor (GPCR) targets, CKR-1 and CKR-2. We show ckr-2 deletion reduces body bend depth during movement under basal conditions. We demonstrate CKR-1 is a functional NLP-12 receptor and define its expression in the nervous system. In contrast to basal locomotion, biased CKR-1 GPCR stimulation of head motor neurons promotes turning during local searching. Deletion of ckr-1 reduces head neuron activity and diminishes turning while specific ckr-1 overexpression or head neuron activation promote turning. Thus, our studies suggest locomotor responses to changing food availability are regulated through conditional NLP-12 stimulation of head or body wall motor circuits.

Impact statementInvestigation of neuromodulatory control of ethologically conserved area-restricted food search behavior shows that NLP-12 stimulation of the head motor circuit promotes food searching through the previously uncharacterized CKR-1 GPCR.