title: Regulatory role of sphingolipid metabolites, sphingosine-1-phosphate and C16:0 ceramide, in immunogenic cell death of colon cancer cells induced by Bak/Bax-activation.

abstract: We have previously identified sphingolipid metabolism as a key intracellular process associated with immunogenic cell death (ICD) induced by mitoxantrone in colon cancer cells. Specifically, we have demonstrated that inhibition of the sphingosine kinases (SphKs) synergistically enhanced production of hallmarks of ICD including ectoCRT production. To better understand the mechanism associated with ICD enhanced by SphK1-inhibition, we focused on the ER stress-associated intracellular signaling pathways leading to ectoCRT production. It is known that ABT-263 and AZD-5991 (ABT/AZD) are inhibitors of Bcl-2/Bcl-XL and MCL-1, respectively, leading to activation of Bak/Bax. Herein, we now provide evidence that treatment of DLD-1 colon cancer cells with ABT/AZD results in the production of ectoCRT indicative of ICD. Additionally, our data show that ABT/AZD-induced ectoCRT production is significantly enhanced by combination treatment with the SphK1 inhibitor, PF-543. Mechanistically, we demonstrate that combined treatment of ABT/AZD+PF-543 induces ectoCRT exposure in a caspase 8-dependent manner. Accordingly, we have identified a Bak/Bax activation-dependent pathway that leads to activation of a pro-survival SphK1/sphingosine-1-phosphate (S1P) signaling that attenuates ectoCRT production. Additionally, we have identified a regulatory role of ceramide synthase 6 (CerS6)- C16:0 Cer in transporting of dimeric CRT to the cell surface (ectoCRT). Together, these results indicate that sphingolipid metabolites, such as S1P and C16:0 Cer, have a key regulatory role for survival/death decisions of cancer cells in response to ICD-inducing chemotherapeutic agents such as mitoxantrone and ABT/AZD. Hence, targeting SphKs may be an innovative means to enhance the efficacy of ICD-inducing chemotherapeutic agents promoting anti-tumor innate/adaptive immune response since SphK inhibition blocks the anti-ICD effects of S1P while simultaneously accumulating sphingosine (Sph) leading to pro-ICD C16:0 Cer synthesis.


title: Sister chromatid exchanges induced by perturbed replication are formed independently of homologous recombination factors

abstract: Sister chromatid exchanges (SCEs) are products of joint DNA molecule resolution, and are considered to form through homologous recombination (HR). Indeed, upon generation of irradiation-induced DNA breaks, SCE induction was compromised in cells deficient for canonical HR factors BRCA1, BRCA2 and RAD51. Contrarily, replication-blocking agents, including PARP inhibitors, induced SCEs independently of BRCA1, BRCA2 and RAD51. PARP inhibitor-induced SCEs were enriched at common fragile sites (CFSs), and were accompanied by post-replicative single-stranded DNA (ssDNA) gaps. Moreover, PARP inhibitor-induced replication lesions were transmitted into mitosis, suggesting that SCEs originate from mitotic processing of under-replicated DNA. We found that DNA polymerase theta (POLQ) was recruited to mitotic DNA lesions, and loss of POLQ resulted in reduced SCE numbers and severe chromosome fragmentation upon PARP inhibition in HR-deficient cells. Combined, our data show that PARP inhibition generates under-replicated DNA, which is transferred into mitosis and processed into SCEs, independently of canonical HR factors.

category: cancer biology


title: CanIsoNet: A Database to Study the Functional Impact of Isoform Switching Events in Cancer

abstract:
MotivationAlternative splicing, as an essential regulatory mechanism in normal mammalian cells, is frequently disturbed in cancer. Switches in the expression of alternative isoforms can alter protein interaction networks of associated genes giving rise to cancer progression and metastases. We have recently analyzed the pathogenic impact of switching events in 1209 cancer samples covering 24 different cancer types. Here, we are presenting CanIsoNet (Cancer Isoform specific interaction Network), a database to view, browse and search these isoform switching events. CanIsoNet is the first webserver that incorporates isoform expression data with STRING interaction networks and COSMIC annotations to predict the pathogenic impact of isoform switching events in various cancer types.

ResultsData in CanIsoNet can be browsed by cancer types or searched by genes or isoforms in annotation rich data tables. Various annotations for 11,041 isoforms and 31,748 unique isoform switching events are provided across 24 cancer types, including proximity information to COSMIC cancer census genes, network density data for each cancer-specific isoform, PFAM domain IDs of disrupted interactions, domain structure visualization of transcripts and expression data of switched isoforms for each sample.

AvailabilityCanIsoNet is freely available at https://caniso.net under a Creative Common License. The source codes can be found at https://github.com/KarakulakTulay/CanIsoNet_Web


title: Data Representation in the DARPA SD2 Program

abstract:
1Modern scientific enterprises are often highly complex and multidisciplinary, particularly in areas like synthetic biology where the subject at hand is itself inherently complex and multidisciplinary. Collaboration across many organizations is necessary to efficiently tackle such problems [6, 15], but remains difficult. The challenge is further amplified by automation that increases the pace at which new information can be produced, and particularly so for matters of fundamental research, where concepts and definitions are inherently fluid and may rapidly change as an investigation evolves [7].

The DARPA program Synergistic Discovery and Design (SD2) aimed to address these challenges by organizing the development of data-driven methods to accelerate discovery and improve design robustness, with one of the key domains under study being synthetic biology. The program was specifically organized such that teams provided complementary types of expertise and resources, and without any team being in a dominant organizational position, such that subject-matter investigations would necessarily require peer-level collaboration across multiple team boundaries. With more than 100 researchers across more than 20 organizations, several of which ran experimental facilities with high-throughput automation, participants were forced to confront challenges around effective data sharing.

The default architecture for scientific collaboration is essentially one of anarchy, with ad-hoc bilateral relations between pairs of collaborators or experimental phases (Figure 1(a)). This was by necessity the case during early phases of the SD2 program as well, in which incorporating new tools into pipelines was ad-hoc and time-consuming, and data was generally disconnected from genetic designs and experimental plans. The other typical approach for collaboration is one of "command and control", in which a dominant organization determines the data sharing content and format for all participants (Figure 1(b)). This can be efficient, but tends to be limited in flexibility and extensibility, rendering it unsuitable for research collaboration, as indeed was found when we attempted this approach during the first year of the SD2 program. We addressed these problems with the application of distributed standards to create a "flexible rendezvous" model of collaboration (Figure 1(c)), enabling information flow to track evolving collaborative relationships, improving the sharing and utility of information across the community and supporting accelerated rates of experimentation.

O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=71 SRC="FIGDIR/small/460644v1_fig1.gif" ALT="Figure 1">
View larger version (15K):
org.highwire.dtl.DTLVardef@fc7371org.highwire.dtl.DTLVardef@1ff2733org.highwire.dtl.DTLVardef@66af53org.highwire.dtl.DTLVardef@1809640_HPS_FORMAT_FIGEXP  M_FIG O_FLOATNOFigure 1:C_FLOATNO Architectures for data sharing: bilateral relations (a), command and control (b), and flexible rendezvous (c).

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category: synthetic biology


title: Mu-opioid receptor system modulates responses to vocal bonding and distress signals in humans

abstract: Laughter is a contagious prosocial signal that conveys bonding motivation; adult crying conversely communicates desire for social proximity by signalling distress. Endogenous mu-opioid receptors (MORs) modulate sociability in humans and non-human primates. In this combined PET-fMRI study (n=17) we tested whether central MOR tone is associated with regional brain responses to social signals of laughter and crying sounds. MOR availability was measured with positron emission tomography using high-affinity agonist radioligand [11C]carfentanil. Haemodynamic responses to social laughter and crying sounds were measured using functional magnetic resonance imaging (fMRI). Social laughter evoked activation in the auditory cortex, insula, cingulate cortex, amygdala, primary and secondary somatosensory cortex, primary and secondary motor cortex; crying sounds led to more restricted activation in auditory cortex and nearby areas. MOR availability was negatively correlated with the haemodynamic responses to social laughter in primary and secondary somatosensory cortex, primary and secondary motor cortex, posterior insula, posterior cingulate cortex, precuneus, cuneus, temporal gyri, and lingual gyrus. For crying-evoked activations, MOR availability was negatively correlated with medial and lateral prefrontal haemodynamic responses. Altogether our findings highlight the role of MOR system in modulating acute brain responses to both positive and negative social signals.

category: neuroscience


title: A CLN6-CRMP2-KLC4 complex regulates anterograde ER-derived vesicle trafficking in cortical neurites

abstract: As neurons establish extensive connections throughout the central nervous system, the transport of cargo along the microtubule network of the axon is crucial for differentiation and homeostasis. Specifically, building blocks such as membrane and cytoskeletal components, organelles, transmembrane receptors, adhesion molecules, and peptide neurotransmitters all require proper transport to the presynaptic compartment. Here, we identify a novel complex regulating vesicular endoplasmic reticulum transport in neurites, composed of CLN6: an ER-associated protein of relatively unknown function implicated in CLN6-Batten disease; CRMP2: a tubulin binding protein important in regulating neurite microtubule dynamics; and KLC4: a classic transport motor protein. We show that this "CCK" complex allows ER-derived vesicles to migrate to the distal end of the axon, aiding in proper neurite outgrowth and arborization. In the absence of CLN6, the CCK complex does not function effectively, leading to reduced vesicular transport, stunted neurite outgrowth, and deficits in CRMP2 binding to other protein partners. Treatment with a CRMP2 modulating compound, lanthionine ketimine ester, partially restores these deficits in CLN6-deficient mouse neurons, indicating that stabilization of CRMP2 interacting partners may prove beneficial in lieu of complete restoration of the CCK complex. Taken together, these findings reveal a novel mechanism of ER-derived vesicle transport in the axon and provide new insights into therapeutic targets for neurodegenerative disease.


title: Transmembrane Batten disease proteins interact with a shared network of vesicle sorting proteins to regulate synaptic composition and function.

abstract: Batten disease is unique among lysosomal storage disorders for the early and profound manifestation in the central nervous system, but little is known regarding potential neuron-specific roles for the disease-associated proteins. We demonstrate substantial overlap in the protein interactomes of three transmembrane Batten proteins (CLN3, CLN6, and CLN8), and that their absence leads to synaptic depletion of key partners (i.e. SNAREs and tethers) and aberrant synaptic SNARE dynamics in vivo, demonstrating a novel shared etiology.


title: Transcriptional and translational regulation of pathogenesis in Alzheimer's disease model mice

abstract:
BackgroundDefining the cellular mechanisms that drive Alzheimers disease (AD) pathogenesis and progression will be aided by studies defining how gene expression patterns change during pre-symptomatic AD and the ensuing periods of steadily declining cognition. Previous studies have emphasized changes in transcriptional regulation, but not translational regulation, leaving the ultimate results of gene expression alterations relatively unexplored in the context of AD.

ObjectiveTo identify genes whose expression might be regulated at the transcriptional, and especially at the translational levels in AD, we analyzed gene expression in cerebral cortex of two AD model mouse strains, CVN (APPSwDI;NOS2-/-) and Tg2576 (APPSw), and their companion wild type (WT) strains at 6 months of age by tandem RNA-Seq and Ribo-Seq (ribosome profiling).

MethodsIdentical starting pools of bulk RNA were used for RNA-Seq and Ribo-Seq. Differential gene expression analysis was performed at the transcriptional and translational levels separately, and also at the translational efficiency level. Regulated genes were functionally evaluated by gene ontology tools.

ResultsCompared to WT mice, AD model mice had similar levels of transcriptional regulation, but displayed differences in translational regulation. A specific microglial signature associated with early stages of A{beta} accumulation was up-regulated at both transcriptome and translatome levels in CVN mice. Although the two mice strains did not share many regulated genes, they showed common regulated pathways related to APP metabolism associated with neurotoxicity and neuroprotection.

ConclusionThis work represents the first genome-wide study of brain translational regulation in animal models of AD, and provides evidence of a tight and early translational regulation of gene expression controlling the balance between neuroprotective and neurodegenerative processes in brain.


title: Genetically engineered microglia-like cells have therapeutic potential for neurodegenerative disease

abstract: Hematopoietic stem/progenitor cell gene therapy (HSPC-GT) results in the engraftment of genetically modified microglia-like cells (MLCs) in the brain. While HSPC-GT has shown a clear neurological benefit in the clinic for specific rare diseases, the nature of MLC engraftment in the brain and the functional characteristics of MLCs remain contentious. Here we comprehensively characterized how different routes of administration affect the engraftment and biodistribution of genetically engineered HSPC-derivatives in mice. Using high-throughput single-cell profiling, we show that MLCs bear a transcriptional signature similar to resident microglia rather than invading macrophages. However, MLCs could clearly be distinguished from resident microglia by expression of a specific set of genes. Finally, in murine models of Parkinsons disease and frontotemporal dementia, we demonstrate that MLCs can provide therapeutically relevant levels of protein to the brain, thereby potentially opening avenues of HSPC-GT to address the underlying disease etiology of these and other similar disorders.


title: Nanoscale organization of the endogenous ASC speck

abstract:
The NLRP3 inflammasome is a central component of the innate immune system. Its activation leads to the formation of a supramolecular assembly of the inflammasome adaptor protein ASC, commonly referred to as the "ASC speck". Different models of the overall structure of the ASC speck, as well as the entire NLRP3 inflammasome, have been reported in the literature. While many experiments involve overexpression or in vitro reconstitution of recombinant ASC, the cytoplasmic endogenous ASC speck remains difficult to study due to its relatively small size and structural variability.

Here, we use a combination of fluorescence imaging techniques including dual-color 3D super-resolution imaging (dSTORM and DNA-PAINT) to visualize the endogenous ASC speck following NLRP3 inflammasome activation. We observe that the complex varies in diameter between [~]800 and 1000 nm and is composed of a dense core from which filaments extend into the periphery. We used a combination of anti-ASC antibodies as well as much smaller nanobodies for labeling, and find that the larger antibodies reliably label the lower-density periphery whereas the nanobody, which has a lower binding affinity, is more efficient in labeling the dense core. Imaging whole cells using dSTORM, furthermore, allowed us to sort the imaged structures into a pseudo-time sequence suggesting that the endogenous ASC speck becomes denser but not much larger during its formation. The reported results add an important piece of information towards a comprehensive understanding of the supramolecular structure of the endogenous inflammasome complex.

SignificanceThe assembly of ASC into a supramolecular complex referred to as the ASC speck is a critical step in the NLRP3 inflammasome response. Despite significance research, the organization and formation of the endogenous ASC speck remain elusive. We used a combination of differently sized ASC labels with super-resolution microscopy to address the organization of the ASC speck at the nanoscale. Our results allow inference of the supramolecular structure of the unperturbed, endogenous speck and characterize how it changes during ASC recruitment. We find that the complex varies in size and is composed of a dense core from which filaments extend into the periphery. Notably, our results further indicate that during inflammasome formation, ASC specks become denser but only slightly larger.

category: immunology


title: Accumulation of the GSK3 target protein β-catenin is lethal for B cell precursors and malignant B cells

abstract: Glycogen synthase kinase 3 (GSK3) is a ubiquitously expressed kinase involved in a myriad of biological processes. Although GSK3 mediated phosphorylation has been shown to induce the degradation of many pro-survival and pro-proliferation factors, cancer cells of different origin show reduced proliferation or survival after GSK3 inhibition. Our current understanding of the role GSK3 plays in normal mature B cells, B cell precursors and transformed B cells is incomplete and does not allow to assess whether GSK3 inhibitors can be used to treat B cell derived malignancies. Here we identify {beta}-catenin as the major factor driving GSK3-inhibition induced changes in B cells. We show that {beta}-catenin accumulation has opposing effects on cell metabolism and survival in mature B cells and B cell precursors. Moreover, we demonstrate that {beta}-catenin destabilizes the commitment to the B cell lineage. In summary, our study identifies {beta}-catenin induced signaling as a factor that can be exploited to limit the survival of malignant B cells.


title: Lactobacillus rhamnosus reduces the cytotoxic effects of Group B Streptococcus on HeLa cells

abstract: Group B Streptococcus (GBS) is an opportunistic pathogen found in the vaginal tract and is a leading cause of preterm birth and neonatal illness. Aside from GBS, the vaginal tract is predominantly colonized by commensal Lactobacillus species that are thought to protect the vaginal tract from pathogens, including GBS. Studies that examined if, and how Lactobacilli modulate GBS pathogenicity remain limited. This study sought to investigate the potential protective role of Lactobacillus rhamnosus against GBS, using an in vitro model system. Immunofluorescence microscopy and Scanning Electron Microscopy (SEM) captured images of infected HeLa cells and were analyzed using the image analysis program ImageJ. Results indicate that GBS causes HeLa cell detachment unless L. rhamnosus is present. SEM images show that GBS reduces length and number of microvilli on HeLa cell surface, as well as size of secreted vesicles. L. rhamnosus partially inhibits GBS-dependent microvilli and vesicle disruption. GBS also disrupts HeLa cell F-actin fibers unless L. rhamnosus is present. These results reveal effects of GBS infection on the host cell cytoskeleton and implies a protective role of L. rhamnosus against GBS colonization.

category: microbiology


title: Deconstructing Gastrulation at the Single Cell Level

abstract: Gastrulation movements in all animal embryos start with regulated deformations of patterned epithelial sheets. Current studies of gastrulation use a wide range of model organisms and emphasize either large-scale tissue processes or dynamics of individual cells and cell groups 1,2,11-13,3-10. Here we take a step towards bridging these complementary strategies and deconstruct early stages of gastrulation in the entire Drosophila embryo, where transcriptional patterns in the blastoderm give rise to region-specific cell behaviors. Our approach relies on an integrated computational framework for cell segmentation and tracking and on efficient algorithms for event detection. Our results reveal how thousands of cell shape changes, divisions, and intercalations drive large-scale deformations of the patterned blastoderm, setting the stage for systems-level dissection of a pivotal step in animal development.

category: developmental biology


title: Thymocyte regulatory variant alters transcription factor binding and protects from type 1 diabetes in infants

abstract: We recently mapped a genetic susceptibility locus on chromosome 6q22.33 for type 1 diabetes diagnosed below age of 7 years near the gene Protein tyrosine phosphatase receptor type K (PTPRK) and the thymocyte selection associated gene (THEMIS). As the thymus plays a central role in shaping the T cell repertoire, we aimed to identify the most likely causal genetic factors behind the association using thymocyte genomic data. In four thymocyte populations we identified 253 DNA sequence motifs underlying histone modifications. The G insertion allele of rs138300818, associated with protection from diabetes, created thymocyte motifs for multiple histone modifications and thymocyte types. The insertion also disrupted a predicted RFX5/7 transcription factor binding site. RFX7 is abundantly expressed in thymus. Chromatin state and RNA sequencing data suggested strong transcription overlapping rs138300818 in fetal thymus, while eQTL and chromatin conformation data indicated that the rs138300818 insertion is associated with lower THEMIS expression. Taken together, our results support a role for thymic THEMIS gene expression and the rs138300818 variant in promoting the development and diagnosis of type 1 diabetes at an earlier age.

category: genetics


title: Chromosome level genome assembly and annotation of highly invasive Japanese stiltgrass (Microstegium vimineum)

abstract:
The invasive Japanese stiltgrass (Microstegium vimineum) affects a wide range of ecosystems and threatens biodiversity across the eastern USA. However, the mechanisms underlying rapid adaptation, plasticity, and epigenetics in the invasive range are largely unknown. We present a chromosome-level assembly for M. vimineum to investigate genome dynamics, evolution, adaptation, and the genomics of phenotypic plasticity. We generated a 1.12 Gb genome with scaffold N50 length of 53.44 Mb respectively, taking a de novo assembly approach that combined PacBio and Dovetail Genomics Omni-C sequencing. The assembly contains 23 pseudochromosomes, representing 99.96% of the genome. BUSCO assessment indicated that 80.3% of Poales gene groups are present in the assembly. The genome is predicted to contain 39,604 protein-coding genes, of which 26,288 are functionally annotated. Furthermore, 66.68% of the genome is repetitive, of which unclassified (35.63%) and long terminal repeat (LTR) retrotransposons (26.90%) are predominant. Similar to other grasses, Gypsy (41.07%) and Copia (32%) are the most abundant LTR-retrotransposon families. The majority of LTR-retrotransposons are derived from a significant expansion in the past 1-2 million years, suggesting the presence of relatively young LTR-retrotransposon lineages. We find corroborating evidence from Ks plots for a stiltgrass-specific duplication event, distinct from the more ancient grass-specific duplication event. The assembly and annotation of M. vimineum will serve as an essential genomic resource facilitating studies of the invasion process, the history and consequences of polyploidy in grasses, and provides a crucial tool for natural resource managers.

SignificanceThe current lack of genomic resources for the invasive Japanese stiltgrass--and thousands of other invasive species globally--severely limits our understanding of the invasion process and hinders decision-making for effective management and control. In this study, we present a chromosome-level genome assembly and annotation of Japanese stiltgrass, a problematic weed in eastern North America, identifying a clear history of polyploidy and recent activity of transposable elements. The ultimate goal is to advance genomic studies to better understand the dynamics of non-native species during the various invasion phases, thereby providing insights into effective control strategies to manage current and future invasions.

category: genomics


title: Structural analysis and construction of thermostable antifungal chitinase

abstract:
Chitin is a biopolymer of N-acetyl-D-glucosamine with {beta}-1,4-bond and is the main component of arthropod exoskeletons and the cell walls of many fungi. Chitinase (EC 3.2.1.14) is an enzyme that hydrolyzes the {beta}-1,4-bond in chitin and degrades chitin into oligomers. It has been found in a wide range of organisms. Chitinase from Gazyumaru (Ficus microcarpa) latex exhibits antifungal activity by degrading chitin in the cell wall of fungi and is expected to be used in medical and agricultural fields. However, the enzymes thermostability is an important factor; chitinase is not thermostable enough to maintain its activity under the actual applicable conditions. We solved the crystal structure of chitinase to explore the target sites to improve its thermostability. Based on the crystal structure and sequence alignment among other chitinases, we rationally introduced proline residues, a disulfide bond, and salt bridge in the chitinase using protein engineering methods. As a result, we successfully constructed the thermostable mutant chitinases rationally with high antifungal and specific activities. The results provide a useful strategy to enhance the thermostability of this enzyme family.

IMPORTANCEWe solved the crystal structure of the chitinase from Gazyumaru (Ficus microcarpa) latex exhibiting antifungal activity. Furthermore, we demonstrated that the thermostable mutant enzyme with a melting temperature (Tm) 6.9 {degrees}C higher than wild type (WT) and a half-life at 60{degrees}C that is 15 times longer than WT was constructed through 10 amino acid substitutions, including five proline residues substitutions, making disulfide bonding, and building a salt bridge network in the enzyme. These mutations do not affect its high antifungal activity and chitinase activity, and the principle for the construction of the thermostable chitinase was well explained by its crystal structure. Our results provide a useful strategy to enhance the thermostability of this enzyme family and to use the thermostable mutant as a seed for antifungal agents for practical use.

category: biochemistry


title: A flexible electronic strain sensor for the real-time monitoring of tumor progression

abstract: Assessing the efficacy of cancer therapeutics in mouse models is a critical step in treatment development. However, low resolution measurement tools and small sample sizes make determining drug efficacy in vivo a difficult and time-intensive task. Here we present a commercially scalable wearable electronic sensor that automates the in vivo testing of cancer therapeutics by continuously monitoring micrometer-scale tumor volume progression or regression in real-time. Histology, caliper measurements, and bioluminescence imaging over a one-week treatment period validated the sensors recordings, but the sensors higher time and length scale resolutions provided the only measurement technique capable of continuously monitoring the immediate hour-scale pharmacodynamic response of a given drug. In mice with two subcutaneously implanted tumor models our sensors recorded significant volume reductions in tumors just 5 hours after small molecule or immunotherapy treatment initiation. We anticipate that real-time tumor regression datasets could help expedite and automate the process of screening cancer therapies in vivo.

category: bioengineering


title: A flexible electronic strain sensor for the real-time monitoring of tumor regression


title: CUX2 mutations in temporal lobe epilepsy; increased kainate susceptibility and excitatory input to hippocampus in deficient mice

abstract: CUX2 gene encodes a transcription factor that controls neuronal proliferation, dendrite branching and synapse formation, locating at the epilepsy-associated chromosomal region 12q24 that we previously identified by a genome-wide association study (GWAS) in Japanese population. A CUX2 recurrent de novo variant p.E590K has been described in patients with rare epileptic encephalopathies and the gene is a candidate for the locus, however the mutation may not be enough to generate the genome-wide significance in the GWAS and whether CUX2 variants appear in other types of epilepsies and physiopathological mechanisms are remained to be investigated. Here in this study, we conducted targeted sequencings of CUX2, a paralog CUX1 and its short isoform CASP harboring a unique C-terminus on 271 Japanese patients with a variety of epilepsies, and found that multiple CUX2 missense variants, other than the p.E590K, and some CASP variants including a deletion, predominantly appeared in patients with temporal lobe epilepsy (TLE). The CUX2 variants showed abnormal localization in human cell culture analysis. While wild-type CUX2 enhances dendritic arborization in fly neurons, the effect was compromised by some of the variants. Cux2- and Casp-specific knockout mice both showed high susceptibility to kainate, increased excitatory cell number in the entorhinal cortex, and significant enhancement in glutamatergic synaptic transmission to the hippocampus. CASP and CUX2 proteins physiologically bound to each other and co-expressed in excitatory neurons in brain regions including the entorhinal cortex. These results suggest that CUX2 and CASP variants contribute to the TLE pathology through a facilitation of excitatory synaptic transmission from entorhinal cortex to hippocampus.


title: CUX2 deficiency causes facilitation of excitatory synaptic transmission onto hippocampus and increased seizure susceptibility to kainate


title: Robust effects of working memory demand during naturalistic language comprehension in language-selective cortex

abstract:
A standard view of human language processing is that comprehenders build richly structured mental representations of natural language utterances, word by word, using computationally costly memory operations supported by domain-general working memory resources. However, three core claims of this view have been questioned, with some prior work arguing that (1) rich word-by-word structure building is not a core function of the language comprehension system, (2) apparent working memory costs are underlyingly driven by word predictability (surprisal), and/or (3) language comprehension relies primarily on domain-general rather than domain-specific working memory resources. In this work, we simultaneously evaluate all three of these claims using naturalistic comprehension in fMRI. In each participant, we functionally localize (a) a language-selective network and (b) a  multiple-demand network that supports working memory across domains, and we analyze the responses in these two networks of interest during naturalistic story listening with respect to a range of theory-driven predictors of working memory demand under rigorous surprisal controls. Results show robust surprisal-independent effects of word-by-word memory demand in the language network and no effect of working memory demand in the multiple demand network. Our findings thus support the view that language comprehension (1) entails word-by-word structure building using (2) computationally intensive memory operations that are not explained by surprisal. However, these results challenge (3) the domain-generality of the resources that support these operations, instead indicating that working memory operations for language comprehension are carried out by the same neural resources that store linguistic knowledge.

Significance StatementThis study uses fMRI to investigate signatures of working memory (WM) demand during naturalistic story listening, using a broad range of theoretically motivated estimates of WM demand. Results support a strong effect of WM demand in language-selective brain regions but no effect of WM demand in "multiple demand" regions that have previously been associated with WM in non-linguistic domains. We further show evidence that WM effects in language regions are distinct from effects of word predictability. Our findings support a core role for WM in incremental language processing, using WM resources that are specialized for language.


title: Reversing chemorefraction in colorectal cancer cells by controlling mucin secretion

abstract: 15% of colorectal cancers (CRC) cells exhibit a mucin hypersecretory phenotype, which is suggested to provide resistance to immune surveillance and chemotherapy. We now formally show that colorectal cancer cells build a barrier to chemotherapeutics by increasing mucins secretion. We show that low levels of KChIP3, a negative regulator of mucin secretion (Cantero-Recasens et al., 2018), is a risk factor for CRC patients relapse in subset of untreated tumours. Our results also reveal that cells depleted of KChIP3 are four times more resistant (measured as cell viability and DNA damage) to chemotherapeutics 5-Fluorouracil plus Irinotecan (5-FU+iri.) compared to control cells, whereas KChIP3 overexpressing cells are 10 times more sensitive to killing by chemotherapeutics. Similar increase in tumour cell death is observed upon chemical inhibition of mucin secretion by the sodium/calcium exchanger (NCX) blockers (Mitrovic et al., 2013). Finally, sensitivity of CRC patient-derived organoids to 5-FU+iri increases 40-fold upon mucin secretion inhibition. Reducing mucin secretion thus provides a means to control chemoresistance of mucinous colorectal cancer cells and other mucinous tumours.

category: cell biology


title: WDR60-mediated dynein-2 loading into cilia powers retrograde IFT and transition zone crossing

abstract: The dynein-2 motor complex drives retrograde intraflagellar transport (IFT), playing a pivotal role in the assembly and functions of cilia. However, the mechanisms that regulate dynein-2 motility remain poorly understood. Here, we identify the Caenorhabditis elegans WDR60 homolog (WDR-60) and dissect the roles of this intermediate chain using genome editing and live imaging of endogenous dynein-2/IFT components. We find that loss of WDR-60 impairs dynein-2 recruitment to cilia and its incorporation onto anterograde IFT trains, reducing the availability of the retrograde motor at the ciliary tip. Consistently, we show that less dynein-2 motors power WDR-60-deficient retrograde IFT trains, which move at reduced velocities and fail to exit cilia, accumulating on the distal side of the transition zone. Remarkably, disrupting the transition zones NPHP module almost fully restores ciliary exit of underpowered retrograde trains in wdr-60 mutants. This work establishes WDR-60 as a major contributor to IFT and the NPHP module as a roadblock to dynein-2 passage through the transition zone.


title: A condensate dynamic instability orchestrates oocyte actomyosin cortex activation

abstract: A key event at the onset of development is the activation of a contractile actomyosin cortex during the oocyte-to-embryo transition. We here report on the discovery that in C. elegans oocytes, actomyosin cortex activation is supported by the emergence of thousands of short-lived protein condensates rich in F-actin, N-WASP, and ARP2/3 that form an active micro-emulsion. A phase portrait analysis of the dynamics of individual cortical condensates reveals that condensates initially grow, and then switch to disassembly before dissolving completely. We find that in contrast to condensate growth via diffusion, the growth dynamics of cortical condensates are chemically driven. Remarkably, the associated chemical reactions obey mass action kinetics despite governing both composition and size. We suggest that the resultant condensate dynamic instability suppresses coarsening of the active micro-emulsion, ensures reaction kinetics that are independent of condensate size, and prevents runaway F-actin nucleation during the formation of the first cortical actin meshwork.

category: biophysics


title: Spatial working memory representations in human cortex are robust to a task-irrelevant interrupting stimulus

abstract: Visual working memory (WM) enables the maintenance and manipulation of information no longer accessible in the visual world. Previous research has identified spatial WM representations in activation patterns in visual, parietal, and frontal cortex. In natural vision, the period between the encoding of information into WM and the time when it is used to guide behavior (the delay period) is rarely "empty", as is the case in most of the above laboratory experiments. In naturalistic conditions, eye movements, movement of the individual, and events in the environment result in visual signals which may overwrite or impair the fidelity of WM representations, especially in early sensory cortices. Here, we evaluated the extent to which a brief, irrelevant interrupting visual stimulus presented during a spatial WM delay period impaired behavioral performance and WM representation fidelity assayed using an image reconstruction technique (inverted encoding model). On each trial, participants (both sexes) viewed two target dots and were immediately post-cued to remember the precise spatial position of one dot. On 50% of trials, a brief interrupter stimulus appeared. While we observed strong transient univariate visual responses to the distracter stimulus, we saw no change in reconstructed neural WM representations under distraction, nor a change in behavioral performance on a continuous recall task. This suggests that spatial WM representations may be particularly robust to interference from incoming task-irrelevant visual information, perhaps related to their role in guiding movements.


title: Epilepsy-causing KCNT1 variants increase KNa1.1 channel activity by disrupting the activation gate.

abstract: Gain-of-function pathogenic missense KCNT1 variants are associated with several developmental and epileptic encephalopathies (DEE). With few exceptions, patients are heterozygous and there is a paucity of mechanistic information about how pathogenic variants increase KNa1.1 channel activity and the behaviour of heterotetrameric channels comprising both wild-type (WT) and variant subunits. To better understand these, we selected a range of variants across the DEE spectrum, involving mutations in different protein domains and studied their functional properties. Whole-cell electrophysiology was used to characterise homomeric and heteromeric KNa1.1 channel assemblies carrying DEE-causing variants in the presence and absence of 10 mM intracellular sodium. Voltage-dependent activation of homomeric variant KNa1.1 assemblies were more hyperpolarised than WT KNa1.1 and, unlike WT KNa1.1, exhibited voltage-dependent activation in the absence of intracellular sodium. Heteromeric channels formed by co-expression of WT and variant KNa1.1 had activation kinetics intermediate of homomeric WT and variant KNa1.1 channels, with residual sodium-independent activity. In general, WT and variant KNa1.1 activation followed a single exponential, with time constants unaffected by voltage or sodium. Mutating the threonine in the KNa1.1 selectivity filter disrupted voltage-dependent activation, but sodium-dependence remained intact. Our findings suggest that KNa1.1 gating involves a sodium-dependent activation gate that modulates a voltage-dependent selectivity filter gate. Collectively, all DEE-associated KNa1.1 mutations lowered the energetic barrier for sodium-dependent activation, but some also had direct effects on selectivity filter gating. Destabilisation of the inactivated unliganded channel conformation can explain how DEE-causing amino acid substitutions in diverse regions of the channel structure all cause gain-of-function.


title: High-throughput super-resolution single particle trajectory analysis reconstructs organelle dynamics and membrane re-organization

abstract: Super-resolution imaging can generate thousands of single-particle trajectories. These data can potentially reconstruct subcellular organization and dynamics, as well as measure disease-linked changes. However, computational methods that can derive quantitative information from such massive datasets are currently lacking. Here we present data analysis and algorithms that are broadly applicable to reveal local binding and trafficking interactions and organization of dynamic sub-cellular sites. We applied this analysis to the endoplasmic reticulum and neuronal membrane. The method is based on spatio-temporal time window segmentation that explores data at multiple levels and detects the architecture and boundaries of high density regions in areas that are hundreds of nanometers. By statistical analysis of a large number of datapoints, the present method allows measurements of nano-region stability. By connecting highly dense regions, we reconstructed the network topology of the ER, as well as molecular flow redistribution, and the local space explored by trajectories. Segmenting trajectories at appropriate scales extracts confined trajectories, allowing quantification of dynamic interactions between lysosomes and the ER. A final step of the method reveals the motion of trajectories relative to the ensemble, allowing reconstruction of dynamics in normal ER and the atlastin-null mutant. Our approach allows users to track previously inaccessible large scale dynamics at high resolution from massive datasets. The SPtsAnalysis algorithm is available as an ImageJ plugin that can be applied by users to large datasets of overlapping trajectories and offer a standard of SPTs metrics.


title: Cochlear organoids reveal epigenetic and transcriptional programs of postnatal hair cell differentiation from supporting cells

abstract: We explored the transcriptional and epigenetic programs underlying the differentiation of hair cells from postnatal progenitor cells in cochlear organoids. Heterogeneity in the cells including cells with the transcriptional signatures of mature hair cells allowed a full picture of possible cell fates. Construction of trajectories identified Lgr5+ cells as progenitors for hair cells and the genomic data revealed gene regulatory networks leading to hair cells. We validated these networks, demonstrating dynamic changes both in expression and predicted binding sites of these transcription factors during organoid differentiation. We identified known regulators of hair cell development, Atoh1, Pou4f3, and Gfi1, and predicted novel regulatory factors, Tcf4, an E-protein and heterodimerization partner of Atoh1, and Ddit3, a CCAAT/enhancer-binding protein (C/EBP) that represses Hes1 and activates transcription of Wnt signaling-related genes. Deciphering the signals for hair cell regeneration from mammalian cochlear supporting cells reveals candidates for HC regeneration which is limited in the adult.


title: Symmetry breaking of hPSCs in micropattern generates a polarized spinal cord-like organoid (pSCO) with dorsoventral organization

abstract: Brain organoid research is advancing, but generation of organoids with proper axis formation, which could lead to spatially ordered structures for complex brain structure and function, still remains a challenge. Axis formation and related spatial cell organization in the CNS are initiated by the symmetry breaking during the early embryo development. It has been demonstrated that the geometrically confined culture of human pluripotent stem cells (hPSCs) can be used to induce symmetry breaking and regionalized cell differentiation. In this study, we generated a polarized spinal cord organoid with a self-organized dorsoventral (DV) organization, using 2D cell patterning by geometric confinement. Initially, the application of caudalization signals to hPSCs promoted the regionalized cell differentiation along the radial axis and sprouting-like protrusion morphogenesis in cell colonies confined to ECM protein micropatterns. Detachment of colonies turned them into extended spinal cord-like organoids which maintained center- and edge-derived two poles. Further analyses including single cell RNA sequencing and spatial transcriptome analysis unveiled that these organoids contained rich repertoire of developing spinal cord cells and exhibited the spatially ordered DV domain formation along the long axis without external organizing signals. Modulation of BMP and Shh signaling can control the extent of DV coverage in organoids following the principles of embryo patterning. Our study provides a simple, and precisely controllable method to generate spatially-ordered organoids for understanding of biological principles of cell patterning and axis formation during neural development.


title: Lysosome-related organelles contain an expansion compartment that mediates delivery of zinc transporters to promote homeostasis

abstract: Lysosome-related organelles play evolutionarily conserved roles in zinc storage, but mechanisms that control zinc flow in and out are not well understood. In C. elegans intestinal cells, the CDF-2 transporter stores zinc in these organelles during excess. Here we identify ZIPT-2.3 as the transporter that releases zinc during deficiency. The expression levels of CDF-2 and ZIPT-2.3 are reciprocally regulated in zinc excess and deficiency, establishing a fundamental mechanism of homeostasis. Super-resolution microscopy demonstrated these organelles are composed of a spherical acidified compartment and a hemispherical expansion compartment. The expansion compartment inflates during zinc excess and deficiency by vesicle fusion delivering zinc transporters. These results identify an unexpected structural feature of lysosome-related organelles that facilitates rapid transitions in the composition of zinc transporters to mediate homeostasis.


title: DNA dynamics dictates p53 functional outcome

abstract: The tumor suppressor protein p53 is activated in response to cellular stress. An unresolved question in the field is how p53 is able to parse its myriad functions in a timely manner in accordance with the severity of the stress signal. Here we show across the genome that p53 target genes belonging to pathways acting early in the stress response have REs that are significantly more flexible than REs of genes involved in pathways that need to be more strictly regulated, or whose functional outcome occurs later in the response to stress. We validated these findings by several complementary experimental approaches, for six p53 REs belonging to pathways that operate at different times post p53 induction. Our results demonstrate that the flexibility of p53 REs contributes significantly to the temporal expression of p53 target genes and thereby to life versus death decisions in the p53 system.


title: Multi-functional feedforward inhibitory circuits for cortical odor processing

abstract: Feedforward inhibitory circuits are key contributors to the complex interplay between excitation and inhibition in the brain. Little is known about the function of feedforward inhibition in the primary olfactory (piriform) cortex. Using in vivo two-photon targeted patch clamping and calcium imaging in mice, we find that odors evoke strong excitation in two classes of interneurons - neurogliaform (NG) cells and horizontal (HZ) cells - that provide feedforward inhibition in layer 1 of the piriform cortex. NG cells fire much earlier than HZ cells following odor onset, a difference that can be attributed to the faster odor-driven excitatory synaptic drive that NG cells receive from the olfactory bulb. As a consequence, NG cells strongly but transiently inhibit odor-evoked excitation in layer 2 principal cells, whereas HZ cells provide more diffuse and prolonged feedforward inhibition. Our findings reveal unexpected complexity in the operation of inhibition in the piriform cortex.


title: Long term nasopharyngeal colonization by Staphylococcus aureus  determinants of adaptation

abstract: Staphylococcus aureus nasal colonization is a risk factor for infection. A large proportion of the population are identified as potential S. aureus carriers yet we only partially understand the repertoire of genetic factors that promote long-term nasal colonization. Here we present a novel murine model of nasopharyngeal colonization that requires a low S. aureus inoculum and is amenable to experimental evolution approaches. We used this model to experimentally evolve S. aureus using successive passages in the nasopharynx to identify those genetic loci under selection. After 3 cycles of colonization, mutations were identified in mannitol, sorbitol, arginine, nitrite and lactate metabolism genes promoting key pathways in nasal colonization. Stress responses were identified as being under selective pressure, with mutations in DNA repair genes including dnaJ and recF and key stress response genes clpL, rpoB and ahpF. Peptidoglycan synthesis pathway genes also revealed mutations indicating potential selection for alteration of the cell surface. The infection model used here is versatile to assist decolonization and persistence studies.


title: Multiplexed transcriptional repression identifies a network of bactericidal interactions between mycobacterial respiratory complexes

abstract: Mycobacterium tuberculosis remains a leading cause of infectious disease morbidity and mortality for which new drug combination therapies are needed. Combinations of respiratory inhibitors can have synergistic or synthetic lethal interactions suggesting that regimens with multiple bioenergetic inhibitors will drastically shorten treatment times. However, realizing this potential is hampered by a lack of on-target inhibitors and a poor understanding of which inhibitor combinations have the strongest interactions. To overcome these limitations, we have used CRISPR interference (CRISPRi) to characterize the consequences of transcriptionally inhibiting individual respiratory complexes and identify bioenergetic complexes that when simultaneously inhibited result in cell death. In this study, we identified known and novel synthetic lethal interactions and demonstrate how the engineering of CRISPRi-guide sequences can be used to further explore networks of interacting gene pairs. These results provide fundamental insights into the functions of and interactions between bioenergetic complexes and the utility of CRISPRi in designing drug combinations.


title: Identification of Serum Bridging Molecules that Mediate Human Endothelial Cell Invasion by Candida species

abstract:
During hematogenously disseminated candidiasis, blood borne fungi must invade the endothelial cells that line the blood vessels to infect the deep tissues. Although Candida albicans, which forms hyphae, readily invades endothelial cells, other medically important species of Candida are poorly invasive in standard in vitro assays. Here, we show that Candida glabrata, Candida tropicalis, Candida parapsilosis, and Candida krusei can bind to vitronectin and high molecular weight kininogen present in human serum. Acting as bridging molecules, vitronectin and kininogen bind to v integrins and the globular C1q receptor (gC1qR), inducing human endothelial cells to endocytose the fungus. This mechanism of endothelial cell invasion is poorly supported by mouse endothelial cells, but can be restored when mouse endothelial cells are engineered to express human gC1qR or v integrin. Overall, these data indicate that bridging molecule-mediated endocytosis is a common pathogenic strategy used by many medically important Candida spp. to invade human vascular endothelial cells.

SignificanceThe invasion of vascular endothelial cells is a key step in the pathogenesis of hematogenously disseminated candidiasis. How species of Candida other than C. albicans invade endothelial cells is poorly understood because these fungi are weakly invasive in serum-free media. Here, we demonstrate that C. glabrata and other Candida spp. bind to the serum proteins kininogen and vitronectin, which act as bridging molecules and mediate the adherence and endocytosis of the organisms by endothelial cells. These serum proteins induce endocytosis when they interact with the globular C1q receptor and v integrins on human, but not mouse endothelial cells. Thus, bridging molecule-mediated endocytosis is a common mechanism by which medically important Candida spp. invade human endothelial cells.


title: The master energy homeostasis regulator PGC-1alpha couples transcriptional co-activation and mRNA nuclear export

abstract: PGC-1 plays a central role in maintaining the mitochondrial and energy metabolism homeostasis, linking external stimuli to the transcriptional co-activation of genes involved in adaptive and age-related pathways. The carboxyl-terminus encodes a serine/arginine-rich (RS) region and a putative RNA recognition motif, however potential RNA-processing role(s) have remained elusive for the past 20 years. Here, we show that the RS domain of human PGC-1 directly interacts with RNA and the nuclear RNA export factor NXF1. Inducible depletion of endogenous PGC-1 and expression of RNAi-resistant RS-deleted PGC-1 further demonstrate that the RNA-binding activity is required for nuclear export of co-activated transcripts and mitochondrial homeostasis. Moreover, a quantitative proteomics approach confirmed PGC-1-dependent RNA transport and mitochondrial-related functions, identifying also novel mRNA nuclear export targets in age-related telomere maintenance. Discovering a novel function for a major cellular homeostasis regulator provides new directions to further elucidate the roles of PGC-1 in gene expression, metabolic disorders, ageing and neurodegenerative diseases.

category: molecular biology


title: A specific eIF4A paralog facilitates LARP1-mediated translation repression during mTORC1 inhibition

abstract: Eukaryotic translation initiation factor (eIF) 4A -- a DEAD-box RNA-binding protein -- plays an essential role in translation initiation. Two mammalian eIF4A paralogs, eIF4A1 and eIF4A2, have been assumed to be redundant because of their high homology, and the difference in their functions has been poorly understood. Here, we show that eIF4A1, but not eIF4A2, enhances translational repression during the inhibition of mechanistic target of rapamycin complex 1 (mTORC1), an essential kinase complex controlling cell proliferation. RNA-immunoprecipitation sequencing (RIP-Seq) of the two eIF4A paralogs revealed that eIF4A1 preferentially binds to mRNAs containing terminal oligopyrimidine (TOP) motifs, whose translation is rapidly repressed upon mTOR inhibition. This biased interaction depends on a La-related RNA-binding protein, LARP1. Ribosome profiling revealed that the deletion of EIF4A1, but not EIF4A2, rendered the translation of TOP mRNAs resistant to mTOR inactivation. Moreover, eIF4A1 enhances the affinity between TOP mRNAs and LARP1 and thus ensures stronger translation repression upon mTORC1 inhibition. Our data show that the distinct protein interactions of these highly homologous translation factor paralogs shape protein synthesis during mTORC1 inhibition and provide a unique example of the repressive role of a universal translation activator.


title: Targeted biallelic integration of an inducible Caspase 9 suicide gene for safer iPSC-based cellular therapies

abstract:
Drug-inducible suicide systems may help to minimize risks of cellular therapies due to the tumor forming potential of human induced pluripotent stem cells (hiPSCs). Recent research challenged the usefulness of such systems since rare drug-resistant subclones were observed that showed elimination or silencing of the transgene.

We have introduced a drug-inducible Caspase9 suicide system (iCASP9) into the AAVS1 safe harbor locus of hiPSCs. In these cells, apoptosis could be efficiently induced in vitro. In mice, drug treatment generally led to rapid elimination of teratomas, but individual animals subsequently formed tumor tissue from monoallelic iCASP9 hiPSCs. Very rare drug-resistant subclones of monoallelic iCASP9 hiPSCs appeared in vitro with frequencies of ~ 3x10-8. Transgene elimination, presumably via Loss of Heterozygosity (LoH), or methylation of the CAG promoter but not methylation of the O_SCPLOWPPPC_SCPLOWO_SCPCAP1C_SCPCAPO_SCPLOWRC_SCPLOWO_SCPCAP12C_SCPCAPO_SCPLOWCC_SCPLOW locus were identified as underlying mechanisms. In contrast, we never observed any escapees from biallelic iCASP9 hiPSCs, even after treatment of up to 0.8 billion hiPSCs.

In conclusion, biallelic integration of an iCASP9 system in the AAVS1 locus may substantially contribute to the safety level of iPSC-based therapies, which should be calculated by relating clonal escapee frequencies to the cell number in tumors of a size that is readily detectable during routine screening procedures.


title: Targeted biallelic integration of an inducible Caspase 9 suicide gene for safer cellular therapies prevents development of drug-resistant escapees in human iPSCs


title: Shedding light on biosilica morphogenesis by comparative analysis of the silica-associated proteomes from three diatom species

abstract:
O_LIMorphogenesis of the intricate patterns of diatom silica cell walls is a protein-guided process, yet to date only very few such silica morphogenetic proteins have been identified. Therefore, it is unknown whether all diatoms share conserved proteins of a basal silica forming machinery, and whether unique proteins are responsible for the morphogenesis of species specific silica patterns.
C_LIO_LITo answer these questions, we extracted proteins from the silica of three diatom species (Thalassiosira pseudonana, Thalassiosira oceanica and Cyclotella cryptica) by complete demineralization of the cell walls. LC-MS/MS analysis of the extracts identified 92 proteins that we name  Soluble Silicome Proteins (SSPs).
C_LIO_LISurprisingly, no SSPs are common to all three species, and most SSPs showed very low similarity to one another in sequence alignments. In depth bioinformatics analyses revealed that SSPs can be grouped into distinct classes bases on short unconventional sequence motifs whose functions are yet unknown. The results from in vivo localization of selected SSPs indicates that proteins, which lack sequence homology but share unconventional sequence motifs may exert similar functions in the morphogenesis of the diatom silica cell wall.
C_LI


title: Large herbivore impact on plant biomass along multiple resource gradients in the Serengeti

abstract: Herbivores form an important link in the transfer of energy within a food web and are strongly influenced by bottom-up trophic cascades. Current hypotheses suggest that herbivore consumption and impact on plants should scale positively with plant resource availability. However, depending on the effect of resources on plant quantity and quality, herbivore impact may vary with different types of resources. We test four alternative hypotheses for the relationship between plant biomass, herbivore impact on plant biomass, and plant resource gradients, each based on how resources might affect plant abundance and quality to herbivores. We measured plant biomass for four non-consecutive years in a long-term grazing exclosure experiment in the Serengeti National Park that includes seven sites that vary substantially in rainfall and soil and plant nitrogen (N) and phosphorus (P). Our data supported the hypothesis that herbivore impact is controlled by plant quality, in this case driven by plant P, as herbivore effects on biomass decreased with higher rainfall but increased with greater plant P, but not N content. To our knowledge, this is the first experimental study to indicate that wild mammalian herbivory is associated with P availability rather than N. Our results suggest that P, in addition to water and N, may play a more important role in driving trophic interactions in terrestrial systems than previously realized.

category: ecology


title: Necroptosis contributes to chronic inflammation and fibrosis in aging liver

abstract:
Inflammaging, characterized by an increase in low-grade chronic inflammation with age, is a hallmark of aging and is strongly associated with various age-related diseases, including chronic liver disease (CLD) and hepatocellular carcinoma (HCC). Because necroptosis is a cell death pathway that induces inflammation through the release of DAMPs, we tested the hypothesis that age-associated increase in necroptosis contributes to chronic inflammation in aging liver. Phosphorylation of MLKL and MLKL-oligomers, markers of necroptosis, as well as phosphorylation of RIPK3 and RIPK1 were significantly upregulated in the livers of old mice relative to young mice and this increase occurred in the later half of life (i.e., after 18 months of age). Markers of M1 macrophages, expression of proinflammatory cytokines (TNF, IL6 and IL-1{beta}), and markers of fibrosis were significantly upregulated in the liver with age and the change in necroptosis paralleled the changes in inflammation and fibrosis. Hepatocytes and liver macrophages isolated from old mice showed elevated levels of necroptosis markers as well as increased expression of proinflammatory cytokines relative to young mice. Short term treatment with the necroptosis inhibitor, necrostatin-1s (Nec-1s), reduced necroptosis, markers of M1 macrophages, expression of proinflammatory cytokines, and markers of fibrosis in the livers of old mice. Thus, our data show for the first time that liver aging is associated with increased necroptosis and necroptosis contributes to chronic inflammation in the liver, which in turn appears to contribute to liver fibrosis and possibly CLD.

Graphical abstract

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title: Structural and biochemical analyses of selectivity determinants in chimeric Streptococcus Class A sortase enzymes

abstract: Sequence variation in related proteins is an important characteristic that modulates activity and selectivity. An example of a protein family with a large degree of sequence variation is that of bacterial sortases, which are cysteine transpeptidases on the surface of gram-positive bacteria. Class A sortases are responsible for attachment of diverse proteins to the cell wall to facilitate environmental adaption and interaction. These enzymes are also used in protein engineering applications for sortase-mediated ligations (SML) or sortagging of protein targets. We previously investigated SrtA from Streptococcus pneumoniae, identifying a number of putative {beta}7-{beta}8 loop-mediated interactions that affected in vitro enzyme function. We identified residues that contributed to the ability of S. pneumoniae SrtA to recognize several amino acids at the P1 position of the substrate motif, underlined in LPXTG, in contrast to the strict P1 Gly recognition of SrtA from Staphylococcus aureus. However, motivated by the lack of a structural model for the active, monomeric form of S. pneumoniae SrtA, here, we expanded our studies to other Streptococcus SrtA proteins. We solved the first monomeric structure of S. agalactiae SrtA which includes the C-terminus, and three others of {beta}7-{beta}8 loop chimeras from S. pyogenes and S. agalactiae SrtA. These structures and accompanying biochemical data support our previously identified {beta}7-{beta}8 loop-mediated interactions and provide additional insight into their role in Class A sortase substrate selectivity. We argue that a greater understanding of individual SrtA sequence and structural determinants of target selectivity can facilitate the design or discovery of improved sortagging tools.


title: Colony-like Protocell Superstructures

abstract: We report the formation, growth, and dynamics of model protocell superstructures on solid surfaces, resembling single cell colonies. These structures, consisting of several layers of lipidic compartments enveloped in a dome-shaped outer lipid bilayer, emerged as a result of spontaneous shape transformation of lipid agglomerates deposited on thin film aluminum surfaces. Collective protocell structures were observed to be mechanically more stable compared to isolated spherical compartments. We show that the model colonies encapsulate DNA and accommodate non-enzymatic, strand displacement DNA reactions. The membrane envelope is able to disassemble and expose individual daughter protocells, which can migrate and attach via nano-tethers to distant surface locations, while maintaining their encapsulated contents. Some colonies feature  exo-compartments, which spontaneously extend out of the enveloping bilayer, internalize DNA, and merge again with the superstructure. A continuum elastohydrodynamic theory that we developed reveals that the subcompartment formation must be governed by attractive van der Waals (vdW) interactions between the membrane and surface. The balance between membrane bending and vdW interactions yields a critical length scale of 273 nm, above which the membrane invaginations can form subcompartments. The findings support our hypotheses that in extension of the  lipid world hypothesis, protocells may have existed in the form of colonies, potentially benefiting from the increased mechanical stability provided by a superstructure.


title: A Taphrina strain infecting the model plant Arabidopsis thaliana.

abstract: Yeasts are important plant-associated organisms that can modulate host immunity to either promote or prevent disease. Mechanisms of plant-yeast interactions, specifically of yeast perception by the plant innate immune system, remain unknown. Progress has been hindered by the scarcity of yeast species associated with the model plant Arabidopsis thaliana (Arabidopsis). We have previously isolated Taphrina strain M11 from wild Arabidopsis in the field. Taphrina are poorly studied dimorphic yeast-like fungi that are plant pathogens, often producing plant hormones and causing tumour-like and leaf deformation symptoms on their hosts. Here we characterize the interaction of M11 with Arabidopsis. Infection of Arabidopsis with the birch pathogen T. betulina, used as a non-host control, shows early HR, enhanced ROS accumulation, and limitation of growth, demonstrating that Arabidopsis had immunity against non-adapted yeasts. M11 triggered limited cell death, an attenuated ROS response, and grew in planta, as well as subtle but clear leaf deformation symptoms, demonstrating it is pathogenic. Hormone responsive promoter-reporter analysis demonstrated activation of cytokinin signalling during infection. Mutant infection assays indicate jasmonate and ethylene were required for immunity against M11. Analysis of the Taphrina M11 genome was used to mine evidence for yeast specific PAMPs which may underlie host immune responses against yeast-like fungi.

category: plant biology


title: Network-based prediction and functional validation of metformin for potential treatment of atrial Fibrillation using human inducible pluripotent stem cell-derived atrial-like cardiomyocytes

abstract: Atrial fibrillation (AF) is a significant cause of morbidity and mortality, and effective therapeutic interventions are lacking. Here, we harness an integrative, network medicine approach to repurpose FDA-approved drugs for AF. We hypothesize that the use of an unbiased method for prioritizing AF drugs using patient transcriptomics data can help to identify alternative therapeutic strategies and mechanism-of-action for these drugs. To achieve this, we first characterized the molecular networks specific to AF by incorporating transcriptomic data of left atrial tissue. We quantified the network proximity of genes differentially expressed in AF to drug targets to identify putative drugs for repurposing. We identified nine high-confidence drug candidates that were validated using enrichment analysis of drug-gene signatures in human cell lines. We identified metformin for the potential treatment of AF and validated its use in human inducible pluripotent stem cell-derived atrial-like cardiomyocytes. We identified AF-specific dysregulated networks enriched in cardiac metabolism, ion transport, and immune pathways that were improved following metformin treatment. In summary, this study utilized network-based approaches for rapid identification of drugs that may be repurposed for AF treatment and validated metformin as a candidate drug using a robust human atrial cell model.

category: systems biology


title: Experimental and computational analysis of calcium dynamics in 22q11.2 deletion model astrocytes

abstract: Intracellular calcium dynamics in spontaneously active cells such as neurons or astrocytes is an information-rich readout of the physiological state of the cell. Methods for deriving mechanistic information from biological time courses, as well as for algorithmically extracting cellular activity time courses from imaging data, have significantly advanced in recent years but been mostly applied to neuronal data. At the same time, the role for astrocytes, a type of glial brain cells, in cognition and psychiatric diseases remains poorly understood. Using calcium imaging, computer vision, and Bayesian kinetic inference, we analyze calcium dynamics in primary astrocytes derived from control or Df1/+ mice, a model of 22q11.2 deletion syndrome (DiGeorge syndrome). Inference of highest-likelihood molecular kinetic characteristics from the intracellular calcium time courses pinpoints a significant change in the activity of the sarcoendoplasmic reticulum calcium ATPase (SERCA). Applying a SERCA inhibitor to the control cells reproduces the differences detected in the deletion-bearing cells. Our work identifies for the first time the molecular changes driving the calcium kinetics in 22q11.2 deletion model astrocytes. We conclude that Bayesian kinetic inference is a useful tool for mechanistic dissection of a complex cellular phenotype, calcium dynamics, in glial cells. This method has the potential to facilitate formulation of specific hypotheses concerning the underlying molecular mechanisms, prioritization of experiments testing such hypotheses, and, in the future, individualized functional molecular diagnostics.


title: Temporal filters in response to presynaptic spike trains: Interplay of cellular, synaptic and short-term plasticity time scales

abstract: Temporal filters, the ability of postsynaptic neurons to preferentially select certain presynaptic input patterns over others, have been shown to be associated with the notion of information filtering and coding of sensory inputs. Short-term plasticity (depression and facilitation; STP) has been proposed to be an important player in the generation of temporal filters. We carry out a systematic modeling, analysis and computational study to understand how characteristic postsynaptic (low-, high- and band-pass) temporal filters are generated in response to periodic presynaptic spike trains in the presence STP. We investi-gate how the dynamic properties of these filters depend on the interplay of a hierarchy of processes, including the arrival of the presynaptic spikes, the activation of STP, its effect on the excitatory synaptic connection efficacy, and the response of the postsynaptic cell. These mechanisms involve the inter-play of a collection of time scales that operate at the single-event level (roughly, during each presynaptic interspike-interval) and control the long-term development of the temporal filters over multiple presynaptic events. These time scales are generated at the levels of the presynaptic cell (captured by the presynaptic interspike-intervals), short-term depression and facilitation, synaptic dynamics and the post-synaptic cellular currents. We develop mathematical tools to link the single-event time scales with the time scales governing the long-term dynamics of the resulting temporal filters for a relatively simple model where depression and facilitation interact at the level of the synaptic efficacy change. We extend our results and tools to account for more complex models. These include multiple STP time scales and non-periodic presynaptic inputs. The results and ideas we develop have implications for the understanding of the generation of temporal filters in complex networks for which the simple feedforward network we investigate here is a building block.


title: Ribosomal RNA 2'-O-methylations regulate translation by impacting ribosome dynamics

abstract: Protein synthesis by ribosomes is critically important for gene expression in all cells. The ribosomal RNAs (rRNAs) are marked by numerous chemical modifications. An abundant group of rRNA modifications, present in all domains of life, is 2-O-methylation guided by box C/D small nucleolar RNAs (snoRNAs) which are part of small ribonucleoprotein complexes (snoRNPs). Although 2-O-methylations are required for proper production of ribosomes, the mechanisms by which these modifications contribute to translation have remained elusive. Here, we show that a change in box C/D snoRNP biogenesis in actively growing yeast cells results in the production of hypo 2-O-methylated ribosomes with distinct translational properties. Using RiboMeth-Seq for the quantitative analysis of 2-O methylations, we identify site-specific perturbations of the rRNA 2-O-methylation pattern and uncover sites that are not required for ribosome production under normal conditions. Characterization of the hypo 2-O-methylated ribosomes reveals significant translational fidelity defects including frameshifting and near-cognate start codon selection. Using rRNA structural probing, we show that hypo 2-O-methylation affects the inherent dynamics of the ribosomal subunits and impacts the binding of translation factor eIF1 thereby causing translational defects. Our data reveal an unforeseen spectrum of 2-O-methylation heterogeneity in yeast rRNA and suggest a significant role for rRNA 2-O-methylation in regulating cellular translation by controlling ribosome dynamics and ligand binding.


title: A machine learning model that emulates experts decision making in vancomycin initial dose planning

abstract:
Vancomycin is a glycopeptide antibiotic that has been used primarily in the treatment of methicillin-resistant Staphylococcus aureus infections. To enhance its clinical effectiveness and prevent nephrotoxicity, therapeutic drug monitoring (TDM) of trough concentrations is recommended.

Initial vancomycin dosing regimens are determined based on patient characteristics such as age, body weight, and renal function, and dosing strategies to achieve therapeutic concentration windows at initial TDM have been extensively studied. Although numerous dosing nomograms for specific populations have been developed, no comprehensive strategy exists for individually tailoring initial dosing regimens; therefore, decision making regarding initial dosing largely depends on each clinicians experience and expertise.

In this study, we applied a machine-learning (ML) approach to integrate clinician knowledge into a predictive model for initial vancomycin dosing. A dataset of vancomycin initial dose plans defined by pharmacists experienced in vancomycin TDM (i.e., experts) was used to build the ML model. The target trough concentration was attained at comparable rates with the model- and expert-recommended dosing regimens, suggesting that the ML model successfully incorporated the experts knowledge. The predictive model developed here will contribute to improved decision making for initial vancomycin dosing and early attainment of therapeutic windows.

category: pharmacology and toxicology


title: Serotonin regulates hepcidin expression via a gut-liver axis

abstract: Liver hepcidin, is well recognized as the central hormone of systemic iron regulation. Although serotonin is most recognized as a brain neurotransmitter, prodigious quantities are synthesized in gut enterochromaffin cells and several lines of evidence, also identified the gut as an essential sensor and regulator of iron homeostasis. Using a mouse model deficient for peripheral serotonin (Tph1 KO), we identified gut-derived serotonin as a key physiological factor in hepcidin regulation. Serotonin represses hepcidins through a 5HT2B receptor-dependent pathway, independently of any other known hepcidin regulators, including bone marrow signals. This regulation is conserved in humans and shows physiological significance as a negative correlation between serotonin and hepcidin levels was observed in a cohort of healthy individuals. Moreover, in pathological situation such as acute heart failure, where iron deficiency has a negative prognostic impact, we provide evidence that an increase in serotonin level seems necessary to repress hepcidin level, to increase iron availability.

category: physiology


title: Behavioral prioritization enhances working memory precision and neural population gain

abstract: Humans allocate visual working memory (WM) resource according to behavioral relevance, resulting in more precise memories for more important items. Theoretically, items may be maintained by feature-tuned neural populations, where the relative gain of the populations encoding each item determines precision. To test this hypothesis, we compared the amplitudes of delay-period activity in the different parts of retinotopic maps representing each of several WM items, predicting amplitude would track with behavioral priority. Using fMRI, we scanned participants while they remembered the location of multiple items over a WM delay, then reported the location of one probed item using a memory-guided saccade. Importantly, items were not equally probable to be probed (0.6, 0.3, 0.1, 0.0), which was indicated with a pre-cue. We analyzed fMRI activity in ten visual field maps in occipital, parietal, and frontal cortex known to be important for visual WM. In early visual cortex, but not association cortex, the amplitude of BOLD activation within voxels corresponding to the retinotopic location of visual WM items increased with the priority of the item. Interestingly, these results were contrasted with a common finding that higher-level brain regions had greater delay-period activity, demonstrating a dissociation between the absolute amount of activity in a brain area, and the activity of different spatially-selective populations within it. These results suggest that the distribution of WM resources according to priority sculpts the relative gains of neural populations that encode items, offering a neural mechanism for how prioritization impacts memory precision.


title: Intergenerational effects of a paternal Western diet during adolescence on offspring gut microbiota, stress reactivity and social behavior

abstract: The global consumption of highly processed, calorie-dense foods has contributed to an epidemic of overweight and obesity, along with negative consequences for metabolic dysfunction and disease susceptibility. As it becomes apparent that overweight and obesity have ripple effects through generations, understanding of the processes involved is required, in both maternal and paternal epigenetic inheritance. We focused on the patrilineal effects of a Western-style high-fat (21%) and high-sugar (34%) diet (WD) compared to control diet (CD) during adolescence and investigated F0 and F1 mice for physiological and behavioral changes. F0 males (fathers) showed increased body weight, impaired glycemic control, and decreased attractiveness to females. Paternal WD caused significant phenotypic changes in F1 offspring, including higher body weights of pups, increased Actinobacteria abundance in the gut microbiota (ascertained using 16S microbiome profiling), a food preference for WD pellets, increased male dominance and attractiveness to females, as well as decreased behavioral despair. These results collectively demonstrate the long-term intergenerational effects of a Western-style diet during paternal adolescence. The behavioral and physiological alterations in F1 offspring provide evidence of adaptive paternal programming via epigenetic inheritance. These findings have important implications for understanding paternally mediated intergenerational inheritance, and its relevance to offspring health and disease susceptibility.


title: Evolution of antigen-specific follicular helper T cell transcriptional programs across effector function and through to memory

abstract:
Understanding how follicular helper T cells (TFH) regulate the specialization, maturation, and differentiation of adaptive B cell immunity is crucial for developing durable high-affinity immune protection. Using indexed-single cell molecular strategies, we reveal a skewed intra-clonal assortment of higher affinity TCR and the distinct molecular programming of the localized TFH compartment compared to emigrant conventional effector TH (ETH) cells. We find a temporal shift in BCR class switch which permits identification of inflammatory and anti-inflammatory modules of transcriptional programming that subspecialize TFH function before and during the germinal center (GC) reaction. Late collapse of this local primary GC reaction reveals a persistent post-GC TFH population which discloses a putative memory TFH program. These studies define specialized antigen-specific TFH transcriptional programs that progressively direct class-specific evolution of high-affinity B cell immunity and uncover the transcriptional program of a memory TFH population as the regulators of antigen recall.

Graphical Abstract

O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=149 SRC="FIGDIR/small/460841v1_ufig1.gif" ALT="Figure 1">
View larger version (48K):
org.highwire.dtl.DTLVardef@17413c2org.highwire.dtl.DTLVardef@1bd505borg.highwire.dtl.DTLVardef@1e6bc99org.highwire.dtl.DTLVardef@167e6e9_HPS_FORMAT_FIGEXP  M_FIG C_FIG SummaryDistinct inflammatory and anti-inflammatory antigen-specific TFH transcriptional programs regulate class-specific B cell maturation.

Highlights- Skewed intra-clonal assortment of high affinity TCR into the TFH compartment
- Significant temporal delay in anti-inflammatory IgG1 production
- Inflammatory and anti-inflammatory transcriptional modules subspecialize TFH
- Late GC collapse reveals a persisting post-GC putative memory TFH compartment


title: Green spotted puffer can detect an almost nontoxic TTX analog odor using crypt olfactory sensory neurons

abstract:
Tetrodotoxin (TTX) is a well-known neurotoxin that functions as a defense substance for toxic puffers. Several behavioral studies reported that TTX attracts toxic puffers belonging to the genus Takifugu. Although our electrophysiological and behavioral studies showed that a TTX analog, 5,6,11-trideoxyTTX, acts as an olfactory chemoattractant for grass puffers (T. alboplumbeus), it is unclear whether toxic puffers are commonly attracted to 5,6,11-trideoxyTTX, and which types of olfactory sensory neurons (OSNs) detect 5,6,11-trideoxyTTX.

Here we investigated whether the green spotted puffer (Dichotomyctere nigroviridis), a phylogenetically different species from the grass puffer, is attracted to 5,6,11-trideoxyTTX. Administration of 5,6,11-trideoxyTTX attracted green spotted puffers, but TTX or vehicle did not. Furthermore, immunohistochemistry of the olfactory epithelium exposed to 5,6,11-trideoxyTTX with an antibody against phosphorylated ribosomal protein S6 (pS6), a neuronal activity marker, labeled oval cells with apical invagination. These oval cells were also labeled by the antibody against S100, a specific marker of crypt OSNs. Thus, our results suggest that 5,6,11-trideoxyTTX acts as an olfactory chemoattractant that is detected by crypt-type OSNs in the olfactory epithelium of green spotted puffers. Toxic puffers may use 5,6,11-trideoxyTTX as an olfactory chemoattractant involved in reproduction and parental care or as an olfactory cue of TTX-bearing organisms for effective toxification.

Summary statementBehavioral and immunohistochemical experiments suggest that an almost nontoxic TTX analog, 5,6,11-trideoxyTTX, acts as an olfactory chemoattractant for green spotted puffers, and crypt-type olfactory sensory neurons detect it.

category: zoology


title: Synchronous spiking of cerebellar Purkinje cells during control of movements

abstract: The information that the brain transmits from one region to another is often viewed through the lens of firing rates. However, if the output neurons could vary the timing of their spikes with respect to each other, then through synchronization they could highlight information that may be critical for control of behavior. In the cerebellum, the computations that are performed by the cerebellar cortex are conveyed to the nuclei via inhibition. Yet, synchronous activity entrains nucleus neurons, making them fire. Does the cerebellar cortex rely on spike synchrony within populations of Purkinje cells (P-cells) to convey information to the nucleus? We recorded from multiple P-cells while marmosets performed saccadic eye movements and organized them into populations that shared a complex spike response to error. Before movement onset, P-cells transmitted information via a rate code: the simple spike firing rates predicted the direction and velocity of the impending saccade. However, during the saccade, the spikes became temporally aligned within the population, signaling when to stop the movement. Thus, the cerebellar cortex relies on spike synchronization within a population of P-cells, not individual firing rates, to convey to the nucleus when to stop a movement.

category: neuroscience


title: RECIPROCALLY INHIBITORY CIRCUITS OPERATING WITH DISTINCT MECHANISMS ARE DIFFERENTLY ROBUST TO PERTURBATION AND MODULATION

abstract: What features are important for circuit robustness? Reciprocal inhibition is a building block in many circuits. We used dynamic clamp to create reciprocally inhibitory circuits from pharmacologically isolated neurons of the crab stomatogastric ganglion by injecting artificial synaptic (ISyn) and hyperpolarization-activated inward (IH) currents. There are two mechanisms of antiphase oscillations in these circuits: "escape" and "release". In release, the active neuron primarily controls the off/on transitions. In escape, the inhibited neuron controls the transitions. We characterized the robustness of escape and release circuits to alterations in circuit parameters, temperature, and neuromodulation. We found that escape circuits rely on tight correlations between synaptic and H conductances to generate bursting but are resilient to temperature increase. Release circuits are robust to variations in synaptic and H conductances but fragile to temperature increase. The modulatory current (IMI) restores oscillations in release circuits but has little effect in escape circuits. Thus, the same perturbation can have dramatically different effects depending on the circuits mechanism of operation that may not be observable from basal circuit activity.


title: Progenitor cell integration into a barrier epithelium during adult organ turnover

abstract: Barrier epithelial organs face the constant challenge of sealing the interior body from the external environment while simultaneously replacing the cells that contact this environment. These replacement cells--the progeny of basal stem cells--are born without apical, barrier-forming structures such as a protective, lumen-facing membrane and occluding junctions. How stem cell progeny acquire these structures to become part of the barrier is unknown. Here we use Focused Ion Beam-Scanning Electron Microscopy (FIB-SEM), Correlative Light-Electron Microscopy (CLEM), and volumetric imaging of live and fixed organs to investigate progenitor integration in the intestinal epithelium of adult Drosophila. We find that stem cell daughters gestate their future lumenal-apical membrane beneath a transient, basal niche formed by an umbrella-shaped occluding junction that shelters the growing cell and adheres it to mature neighbor cells. The umbrella junction both targets formation of a deep, microvilli-lined, apical invagination and closes it off from the contents of the gut lumen. When the growing cell is sufficiently mature, the umbrella junction retracts to expose this Pre-Assembled Apical Compartment (PAAC) to the gut lumen, thus incorporating the new cell into the intestinal barrier. When we block umbrella junctions, stem cell daughters grow and attempt to differentiate but fail to integrate; when we block cell growth, no umbrella junctions form and daughters arrest in early differentiation. Thus, stem cell progeny build new barrier structures in the shelter of a transient niche, where they are protected from lumenal insults until they are prepared to withstand them. By coordinating this dynamic junctional niche with progenitor cell differentiation, a physiologically active epithelial organ incorporates new cells while upholding integrity of its barrier.


title: Spatio-temporal analysis of remote sensing images provides early warning signals of forest mortality

abstract: Ecosystems are under unprecedented pressures, reflected in rapid changes in the regime of disturbances that may cause negative impacts on them. This highlights the importance of characterizing the state of an ecosystem and its response to disturbances, which is known as a notoriously difficult task. The state-of-the-art knowledge has been tested rarely in real ecosystems for a number of reasons such as mismatches between the time scale of ecosystem processes and data accessibility as well as weaknesses in the performance of available methods. This study aims to use remotely sensed spatio-temporal data to identify early warning signals of forest mortality using satellite images. For this purpose, I propose a new approach that measures local spatial autocorrelation (using local Morans I and local Gearys c method) at each time, which proved to produce robust results in multiple different study sites examined in this article. This new approach successfully generates early warning signals from time series of local spatial autocorrelation values in unhealthy study sites 2 years prior to forest mortality occurrence. Furthermore, I develop a new R package, called "stew", that enables users to explore spatio-temporal analysis of ecosystem state changes. This work corroborates the suggestion that spatio-temporal indicators have the potential to diagnose early warning signals to identify upcoming climate-induced forest mortality, up to two years before its occurrence.


title: Context, competition, and symbiont-induced bet-hedging between Dictyostelium discoideum and Paraburkholderia

abstract:
Symbiotic interactions change with environmental context. Measuring these context-dependent effects in hosts and symbionts is critical to determining the nature of symbiotic interactions. We investigated context-dependence in the symbiosis between social amoeba hosts and their inedible Paraburkholderia bacterial symbionts, where the context is the abundance of host food bacteria. Paraburkholderia have been shown to harm hosts dispersed to food-rich environments, but aid hosts dispersed to food-poor environments by allowing hosts to carry food bacteria. Through measuring symbiont density and host spore production, we show that this food context matters in three other ways. First, it matters for symbionts, who suffer a greater cost from competition with food bacteria in the food-rich context. Second, it matters for host-symbiont conflict, changing how symbiont density negatively impacts host spore production. Third, data-based simulations show that symbiosis often provides a long-term fitness advantage for hosts after rounds of growth and dispersal in variable food-contexts, especially when conditions are harsh with little food. These results show how food context can have many consequences for the Dictyostelium-Paraburkholderia symbiosis and that both sides can frequently benefit.

Impact StatementMany organisms form symbiotic relationships with other species. These symbioses often exhibit context-dependence, where the sign or magnitude of one partners effect on the other will change in different environments. Context-dependent effects make it difficult to assign interactions to categories like mutualisms or antagonisms because they involve both benefits and costs depending on the environment. However, in some cases, accounting for context-dependence can clarify an interaction so that it more easily fits a mutualism or antagonism. We investigated context-dependence using the symbiosis between Dictyostelium discoideum and two symbiotic Paraburkholderia species. In this symbiosis, Paraburkholderia bacteria allow hosts to carry food bacteria to food-poor contexts, where hosts rarely survive without food, but reduce host fitness in the more hospitable food-rich contexts. The effect of food context on Paraburkholderia symbionts is unknown. We show that Paraburkholderia symbionts are also affected by this context, through facing reduced competition after being dispersed by hosts to food-poor contexts. We also identify a new way that symbionts affect hosts, where symbiont density reduces host fitness, but less so in food-poor contexts. Finally, we use simulations to show that infected hosts benefit in the long-term across variable food contexts, especially in the harshest environments with little food. These results show that context-dependence in symbiosis can have many consequences for hosts and symbionts, though in general for D. discoideum and Paraburkholderia, both are likely to benefit.


title: Context-dependence in the symbiosis between Dictyostelium discoideum and Paraburkholderia

category: evolutionary biology


title: Haplotype-level metabarcoding of freshwater macroinvertebrate species: a prospective tool for population genetic analysis

abstract: The development and evaluation of DNA metabarcoding protocols for haplotype-level resolution require attention, specifically for population genetic analysis, i.e., parallel estimation of genetic diversity and dispersal patterns among multiple species present in a bulk sample. Further exploration and assessment of the laboratory and bioinformatics strategies are warranted to unlock the potential of metabarcoding-inferred population genetic analysis. Here, we assessed the inference of freshwater macroinvertebrate haplotypes from DNA metabarcoding data using mock samples with known Sanger-sequenced haplotypes. We also examined the influence of different DNA template concentrations and PCR cycles on detecting true haplotypes and the reduction of spurious haplotypes obtained from DNA metabarcoding. We tested our haplotyping strategy on a mock sample containing 20 specimens from four species with known haplotypes based on the 658-bp Folmer region of the mitochondrial cytochrome c oxidase gene. The read processing and denoising step resulted in 14 zero-radius operational taxonomic units (ZOTUs) of 421-bp length, with 12 ZOTUs having 100% match with 12 of the Sanger haplotype sequences. Quality passing reads relatively increased with increasing PCR cycles, and the relative abundance of each ZOTUs was consistent for each cycle number. This suggests that increasing the cycle number from 24 to 64 did not affect the relative abundance of quality passing filter reads of each ZOTUs. Our study demonstrated the ability of DNA metabarcoding to infer intraspecific variability while highlighting the challenges that need to be addressed before its possible applications to population genetic studies.


title: Global distribution of the rooting zone water storage capacity reflects plant adaptation to the environment

abstract: The rooting zone water storage capacity (S0) extends from the soil surface to the weathered bedrock (the Critical Zone) and determines land-atmosphere exchange during dry periods. Despite its importance to land-surface modeling, variations of S0 across space are largely unknown as they cannot be observed directly. We developed a method to diagnose global variations of S0 from the relationship between vegetation activity (measured by sun-induced fluorescence and by the evaporative fraction) and the cumulative water deficit (CWD). We then show that spatial variations in S0 can be predicted from the assumption that plants are adapted to sustain CWD extremes occurring with a return period that is related to the life form of dominant plants and the large-scale topographical setting. Predicted biome-level S0 distributions, translated to an apparent rooting depth (zr) by accounting for soil texture, are consistent with observations from a comprehensive zr dataset. Large spatial variations in S0 across the globe reflect adaptation of zr to the hydroclimate and topography and implies large heterogeneity in the sensitivity of vegetation activity to drought. The magnitude of S0 inferred for most of the Earths vegetated regions and particularly for those with a large seasonality in their hydroclimate indicates an important role for plant access to water stored at depth - beyond the soil layers commonly considered in land-surface models.