title: Megakaryocyte Progenitor Cell Function is Enhanced Upon Aging Despite the Functional Decline of Aged Hematopoietic Stem Cells

abstract:
Age-related morbidity is associated with a decline in hematopoietic stem cell (HSC) function, but the mechanisms of HSC aging remain unclear. We performed heterochronic HSC transplants followed by quantitative analysis of cell reconstitution. While young HSCs outperformed old HSCs in young recipients, young HSCs unexpectedly failed to outcompete the old HSCs of aged recipients. Interestingly, despite substantial enrichment of megakaryocyte progenitors (MkPs) in old mice in situ and reported platelet (Plt) priming with age, transplanted old HSCs were deficient in reconstitution of all lineages, including MkPs and Plts. We therefore performed functional analysis of young and old MkPs. Surprisingly, old MkPs displayed unmistakably greater regenerative capacity compared to young MkPs. Transcriptome analysis revealed putative molecular regulators of old MkP expansion. Collectively, these data demonstrated that aging affects HSCs and megakaryopoiesis in fundamentally different ways: whereas old HSCs functionally decline, MkPs gain expansion capacity upon aging.

HIGHLIGHTSO_LIFrequencies and total cell numbers of HSCs and MkPs were increased upon aging
C_LIO_LIReconstitution deficit by old HSCs was observed by chimerism and absolute cell numbers
C_LIO_LIYoung HSCs did not have competitive advantage over old HSCs in aged recipient mice
C_LIO_LIOld MkPs display remarkable capacity to engraft, expand, and reconstitute platelets
C_LIO_LIAging is associated with changes in MkP genome-wide expression signatures
C_LI


title: Nodal modulator is required to sustain endoplasmic reticulum morphology

abstract: Nodal Modulator (NOMO) is a widely conserved type I transmembrane protein of unknown function, with three nearly identical orthologs specified in the human genome. We identified NOMO1 in a proteomics approach aimed at the identification of proteins that support the structural integrity of the endoplasmic reticulum (ER). Overexpression of NOMO1 imposes a sheet morphology on the ER, while depletion of NOMO1 and its orthologs causes a collapse of ER morphology concomitant with the formation of membrane-delineated holes in the ER network. These structures are positive for the autophagy marker LAMP1, and LC3 is profoundly upregulated upon NOMO depletion. In vitro reconstitution of NOMO1 revealed a dimeric state that is mediated by the cytosolic tail domain, with each monomer featuring a "beads on a string" structure likely representing bacterial Ig-like folds. Based on these observations and a genetic epistasis analysis including the known ER-shaping proteins Atlastin2 and Climp63, we propose a role for NOMO1 in the functional network of ER-shaping proteins.

category: cell biology


title: Fish primary embryonic stem cells self-assemble into retinal tissue mirroring in vivo early eye development

abstract: Organoids derived from pluripotent stem cells promise the solution to current challenges in basic and biomedical research. Further progress and widespread applications are however limited by long developmental time, variable success, and lack of direct comparison to an in vivo reference. To overcome those limitations, we derived organoids from rapidly developing teleosts. We demonstrate how primary embryonic stem cells from zebrafish and medaka efficiently self-organize into anterior neural structures, particularly retina. Within four days, blastula-stage cell aggregates reproducibly execute key steps of eye development: retinal specification, morphogenesis and differentiation. The number of aggregated cells as well as genetic factors crucially impacted upon the concomitant morphological changes that were intriguingly reflecting the in vivo situation. High reproducibility and rapid development of fish-derived organoids in combination with advanced genome editing techniques immediately allow addressing aspects of development and disease, and systematically probing the impact of the physical environment on morphogenesis and differentiation.

category: developmental biology


title: Characterization in mice of the stromal niche maintaining AT2 stem cell self-renewal in homeostasis and disease

abstract:
Resident mesenchymal cells (rMCs defined as Cd31NegCd45NegEpcamNeg) control the self-renewal and differentiation of alveolar epithelial type 2 (AT2) stem cells in vitro. The identity of these rMCs is still elusive. Among them, Axin2Pos mesenchymal alveolar niche cells (MANCs), which are expressing Fgf7, have been previously described. We propose that an additional population of rMCs, expressing Fgf10 (called rMC-Sca1PosFgf10Pos) are equally important to maintain AT2 stem cell self-renewal.

The alveolosphere model, based on the AT2-rMC co-culture in growth factor reduced Matrigel, was used to test the efficiency of different rMC subpopulations isolated by FACS from adult murine lung to sustain the self-renewal and differentiation of AT2 stem cells.

We demonstrate that rMC-Sca1PosFgf10Pos cells are efficient to promote the self-renewal and differentiation of AT2 stem cells. Co-staining of adult lung for Fgf10 mRNA and Sftpc protein respectively, indicate that 28% of Fgf10Pos cells are located close to AT2 cells. Co-ISH for Fgf7 and Fgf10 indicate that these two populations do not significantly overlap. Gene arrays comparing rMC-Sca1PosAxin2Pos and rMC-Sca1PosFgf10Pos support that these two cell subsets express differential markers. In addition, rMC function is decreased in diabetic and obese ob/ob mutant compared to WT mice with a much stronger loss of function in males compared to females.

In conclusion, rMC-Sca1PosFgf10Pos cells play important role in supporting AT2 stem cells self-renewal and differentiation. This result sheds a new light on the subpopulations of rMCs contributing to the AT2 stem cell niche in homeostasis and in the context of COVID-19 pathogenesis.

Key messageO_ST_ABSWhat is already known about the subject?C_ST_ABSResident mesenchymal cells (rMCs defined as Cd31NegCd45NegEpcamNeg) control the self-renewal and differentiation of alveolar epithelial type 2 (AT2) stem cells in vitro. The identity of these rMCs is still elusive. Among them, Axin2Pos mesenchymal alveolar niche cells (MANCs), which are expressing Fgf7, have been previously described.

What does this study add?Our study shows that an additional population of rMCs, expressing Fgf10 (called rMC-Sca1PosFgf10Pos) is equally important to maintain AT2 stem cell self-renewal. rMC-Sca1PosFgf10Pos are LipidToxHigh and are located close to AT2s. In addition, rMC-Sca1PosFgf10Pos cells support AT2 stem cell self-renewal and differentiation thereby identifying these cells as bone fide functional lipofibroblasts (LIFs). We have previously reported that LIF can transdifferentiate into activated MYF in the context of bleomycin-induced fibrosis in mice [1] and that activated MYF isolated from the lungs of end stage idiopathic fibrosis human patients can respond to Metformin to undergo transdifferentiation back to the LIF phenotype [2]. We also show that the function of rMCs-Sca1Pos is negatively impacted by gender and obesity, which represent two major aggravating factors for COVID-19 pathogenesis, leading to either death or major complications after infection recovery such as lung fibrosis.

How might this impact on clinical practice and future development?By establishing that rMC-Sca1PosFgf10Pos are different from the MANCs, our study opens the way for a new key mesenchymal cell population that should be targeted to either prevent or reverse fibrosis. In addition, as this population maintains the AT2 stem cells self-renewal and differentiation, such targeting will also allow to progressively recover the loss in respiratory function.


title: Genome-wide DNA methylation predicts environmentally-driven life history variation in a marine fish

abstract: The molecular mechanisms underlying intraspecific variation in life history strategies are still poorly understood, despite the importance of this question for understanding of organisms responses to environmental variability. Theoretical work proposed that epigenetic mechanisms such as DNA methylation might regulate intraspecific variation in life history strategies, however this assumption has rarely been verified empirically in wild populations. We examined associations between genome-wide methylation changes and environmentally-driven life history variation in two lineages of a marine fish that diverged approximatively 2.5 Mya, the capelin (Mallotus villosus), from North America and Europe. In both lineages, capelin harbour two contrasted life history strategies: some are strictly semelparous, experience fast actuarial senescence, but benefit from high hatching success by spawning on demersal sites where water temperature is low and relatively stable. In contrast, others are facultative iteroparous, have slower actuarial senescence, and suffer from lower hatching success by breeding in the intertidal zone where temperature is warmer, thermohaline parameters are less stable, and egg desiccation risk is high. Performing whole genome and epigenome sequencing, we showed that these contrasted life history strategies are more likely governed by epigenetic changes than by differences in DNA sequence. While genetic differentiation between the capelin harbouring different life history strategies was negligible, we detected parallel genome-wide methylation changes across lineages. We identified 1,067 differentially methylated regions (DMRs) comprising 15,818 CpGs, with 22% of them located within 5-kb around genes comprising promotor regions. We found that all DMRs were hypermethylated in demersal-spawning individuals. This striking result suggests that lower water temperature at demersal sites leads to an overall hypermethylation of the genome determined during the epigenetic reprogramming occurring over embryonic development. Our study emphasizes that parallel epigenetics changes in lineages with divergent genetic background could have a functional role in the regulation of intraspecific life history variation.

category: evolutionary biology


title: Interpretable prioritization of splice variants in diagnostic next-generation sequencing

abstract: A critical challenge in genetic diagnostics is the computational assessment of candidate splice variants, specifically the interpretation of nucleotide changes located outside of the highly conserved dinucleotide sequences at the 5' and 3' ends of introns. To address this gap, we developed the Super Quick Informationcontent Random-forest Learning of Splice variants (SQUIRLS) algorithm. SQUIRLS generates a small set of interpretable features for machine learning by calculating the information-content (IC) of wildtype and variant sequences of canonical and cryptic splice sites, assessing changes in candidate splicing regulatory sequences, and incorporating characteristics of the sequence such as exon length, disruptions of the AG exclusion zone, and conservation. We curated a comprehensive collection of disease-associated splicealtering variants at positions outside of the highly conserved AG/GT dinucleotides at the termini of introns. SQUIRLS trains two random-forest classifiers for the donor and for the acceptor and combines their outputs by logistic regression to yield a final score. We show that SQUIRLS transcends previous state of the art accuracy in classifying splice variants as assessed by rank analysis in simulated exomes and is significantly faster than competing methods. SQUIRLS provides tabular output files for incorporation into diagnostic pipelines for exome and genome analysis, as well as visualizations that contextualize predicted effects of variants on splicing to make it easier to interpret splice variants in diagnostic settings

category: bioinformatics


title: VeloViz: RNA-velocity informed 2D embeddings for visualizing cellular trajectories

abstract: 0Single cell transcriptomic technologies enable genome-wide gene expression measurements in individual cells but can only provide a static snapshot of cell states. RNA velocity analysis can infer cell state changes from single cell transcriptomics data. To interpret these cell state changes as part of underlying cellular trajectories, current approaches rely on visualization with principal components, t-distributed stochastic neighbor embedding, and other 2D embeddings derived from the observed single cell transcriptional states. However, these 2D embeddings can yield different representations of the underlying cellular trajectories, hindering the interpretation of cell state changes. We developed VeloViz to create RNA-velocity-informed 2D and 3D embeddings from single cell transcriptomics data. Using both real and simulated data, we demonstrate that VeloViz embeddings are able to consistently capture underlying cellular trajectories across diverse trajectory topologies, even when intermediate cell states may be missing. By taking into consideration the predicted future transcriptional states from RNA velocity analysis, VeloViz can help visualize a more reliable representation of underlying cellular trajectories. VeloViz is available as an R package on GitHub (https://github.com/JEFworks-Lab/veloviz) with additional tutorials at https://JEF.works/veloviz/.


title: VeloViz: RNA-velocity informed embeddings for visualizing cellular trajectories


title: Coronavirus associated molecular mimicry common to SARS-CoV-2 peptide

abstract: This study aims to predict autoimmunity-related pathological mechanisms that possess risk for individuals with specific human leukocyte antigen (HLA) serotypes and shared by certain coronaviruses including SARS-CoV-2, based on homology to a SARS-CoV-2 peptide. With the given aim, 1-) coronavirus-associated sequences, which are homologous to the 15mer SARS-CoV-2 peptide CFLGYFCTCYFGLFC, are obtained. 2-) Human peptides that have at least 7 residue matches with those coronavirus sequences, and the SARS-CoV-2 15mer, are found. 3-) Epitope pairs, which are sourced by those aligned coronavirus and human sequences are identified. 4-) Epitope pairs that are predicted to bind strongly not only to the same HLA allele with each other but also to the same HLA allele as those of the respective alignment of the SARS-CoV-2 peptide are selected. Following are the identified proteins or peptides (with HLA-A*02:01 or HLA-A*24:02 epitopes), as described in 1-to-4: Immunoglobulin heavy chain junction regions, CRB1 isoform I precursor, slit homolog 2 protein, hCG1995581, hCG2028737, phospholipid phosphatase-related protein type 2. Among those, CRB1 isoform I precursor sequence with the predicted HLA-A*24:02 epitope aligns with the highest number of different sequences. Results imply autoimmunity risk in COVID-19 patients with HLA-A*02:01 and HLA-A*24:02 serotypes, through molecular mimicry, as a shared pathogenicity risk that can be prevalent upon getting infected with certain coronaviruses. These can pave way to improved risk groups assessment and autoimmunity treatment options, for COVID-19 and its associated diseases. Also, the approach in this study can be used to predict prospective pathologies of the transmissible variants in susceptible humans.

category: immunology


title: Coronavirus-associated molecular mimicry through homology to a SARS-CoV-2 peptide could be leading to susceptibility in patients with HLA-A*02:01 and HLA-A*24:02 serotypes


title: Genetic and structural basis for recognition of SARS-CoV-2 spike protein by a two-antibody cocktail

abstract: The SARS-CoV-2 pandemic has led to an urgent need to understand the molecular basis for immune recognition of SARS-CoV-2 spike (S) glycoprotein antigenic sites. To define the genetic and structural basis for SARS-CoV-2 neutralization, we determined the structures of two human monoclonal antibodies COV2-2196 and COV2-21301, which form the basis of the investigational antibody cocktail AZD7442, in complex with the receptor binding domain (RBD) of SARS-CoV-2. COV2-2196 forms an "aromatic cage" at the heavy/light chain interface using germline-encoded residues in complementarity determining regions (CDRs) 2 and 3 of the heavy chain and CDRs 1 and 3 of the light chain. These structural features explain why highly similar antibodies (public clonotypes) have been isolated from multiple individuals1-4. The structure of COV2-2130 reveals that an unusually long LCDR1 and HCDR3 make interactions with the opposite face of the RBD from that of COV2-2196. Using deep mutational scanning and neutralization escape selection experiments, we comprehensively mapped the critical residues of both antibodies and identified positions of concern for possible viral escape. Nonetheless, both COV2-2196 and COV2-2130 showed strong neutralizing activity against SARS-CoV-2 strain with recent variations of concern including E484K, N501Y, and D614G substitutions. These studies reveal germline-encoded antibody features enabling recognition of the RBD and demonstrate the activity of a cocktail like AZD7442 in preventing escape from emerging variant viruses.


title: High current production of Shewanella oneidensis with electrospun carbon nanofiber anodes is directly linked to biofilm formation

abstract: 1We study the current production of Shewanella oneidensis MR-1 with electro-spun carbon fiber anode materials and analyze the effect of the anode morphology on the micro-, meso-and macroscale. The materials feature fiber diameters in the range between 108 nm and 623 nm, resulting in distinct macropore sizes and surface roughness factors. A maximum current density of (255{+/-} 71) {micro}A cm-2 was obtained with 286 nm fiber diameter material. Additionally, micro-and mesoporosity were introduced by CO2 and steam activation which did not improve the current production significantly. The current production is directly linked to the biofilm dry mass under anaerobic and micro-aerobic conditions. Our findings suggest that either the surface area or the pore size related to the fiber diameter determines the attractiveness of the anodes as habitat and there-fore biofilm formation and current production. Reanalysis of previous works supports these findings.

category: microbiology


title: Spike mutations decrease SARS-CoV-2 sensitivity to neutralizing antibodies but not ACE2-Ig in vitro

abstract: The emergence of SARS-CoV-2 variants poses greater challenges to the control of COVID-19 pandemic. Here, we parallelly investigated three important characteristics of seven SARS-CoV-2 variants, including two mink-associated variants, the B.1.617.1 variant, and the four WHO-designated variants of concerns (B.1.1.7, B.1.351, P.1, and B.1.617.2). We first investigated the ability of these variants to bind and use animal ACE2 orthologs as entry receptor. We found that, in contrast to a prototype variant, the B.1.1.7, B.1.351, and P.1 variants had significantly enhanced affinities to cattle, pig, and mouse ACE2 proteins, suggesting increased susceptibility of these species to these SARS-CoV-2 variants. We then evaluated in vitro neutralization sensitivity of these variants to four monoclonal antibodies in clinical use. We observed that all the variants were partially or completely resistant against at least one of the four tested antibodies, with B.1.351 and P.1 showing significant resistance to three of them. As ACE2-Ig is a broad-spectrum anti-SARS-CoV-2 drug candidate, we then evaluated in vitro neutralization sensitivity of these variants to eight ACE2-Ig constructs previously described in three different studies. All the SARS-CoV-2 variants were efficiently neutralized by these ACE2-Ig constructs. Interestingly, compared to the prototype variant, most tested variants including the variants of concern B.1.1.7, B.1.351, P.1, and B.1.617.2 showed significantly increased (up to [~]15-fold) neutralization sensitivity to ACE2-Ig constructs that are not heavily mutated in the spike-binding interface of the soluble ACE2 domain, suggesting that SARS-CoV-2 evolves toward better utilizing ACE2, and that ACE2-Ig is an attractive drug candidate for coping with SARS-CoV-2 mutations.


title: Circulating SARS-CoV-2 variants B.1.1.7, 501Y.V2, and P.1 have gained ability to utilize rat and mouse Ace2 and altered in vitro sensitivity to neutralizing antibodies and ACE2-Ig


title: Effect of SARS-CoV-2 spike mutations on animal ACE2 usage and in vitro neutralization sensitivity


title: RSC primes the quiescent genome for hypertranscription upon cell cycle re-entry

abstract: Quiescence is a reversible G0 state essential for differentiation, regeneration, stem cell renewal, and immune cell activation. Necessary for long-term survival, quiescent chromatin is compact, hypoacetylated, and transcriptionally inactive. How transcription activates upon cell-cycle re-entry is undefined. Here we report robust, widespread transcription within the first minutes of quiescence exit. During quiescence, the chromatin-remodeling enzyme RSC was already bound to the genes induced upon quiescence exit. RSC depletion caused severe quiescence exit defects: a global decrease in RNA polymerase II (Pol II) loading, Pol II accumulation at transcription start sites, initiation from ectopic upstream loci, and aberrant antisense transcription. These phenomena were due to a combination of highly robust Pol II transcription and severe chromatin defects in the promoter regions and gene bodies. Together, these results uncovered multiple mechanisms by which RSC facilitates initiation and maintenance of large-scale, rapid gene expression despite a globally repressive chromatin state.

category: molecular biology


title: Two step PCR method to exchange the resistance cassette of a vector

abstract:
For co-transformation of two plasmids, both have to possess different antibiotic selection markers. If that is not the case, normally the gene of interest (GOI) is subcloned into another vector. Here we introduce a fast and easy method to exchange the antibiotic resistance cassette (ARC) in only two PCR steps.

Method SummaryTo shuttle the antibiotic resistance cassette (ARC) from one vector to another, one can amplify the ARC of interest and use the resulting PCR-product as a primer pair for the next amplification step. Simply remove parental DNA template by DpnI digestion, transform PCR product directly in E. coli cells, select transformants on an appropriate agar plate and isolate target vector by plasmid preparation.


title: Female immunity protects from cutaneous squamous cell carcinoma

abstract:
PurposeCancer susceptibility and mortality are higher in males, and the mutational and transcriptomic landscape of cancer differs by sex. The current assumption is that men are at higher risk of epithelial cancers as they expose more to carcinogens and accumulate more damage than women. We present data showing women are more protected from aggressive cutaneous squamous cell carcinoma (cSCC) due to strong immune activation.

MethodsWe explored clinical and molecular sexual disparity in immunocompetent and immunosuppressed patients (N= 738, N=160) with carcinoma cSCC, in FVB/N mice exposed to equal doses of DMBA, and in human keratinocytes by whole exome sequencing, bulk and single cell RNA sequencing.

ResultsWe show cSCC is more aggressive in men, and immunocompetent women develop mild cSCC, later in life. To test if sex drives disparity, we exposed male and female mice to equal doses of carcinogen, and found males present more aggressive, metastatic cSCC than females. Critically, females activate cancer immune-related expression pathways and CD4 and CD8 T cell infiltration independently of mutations. In contrast, males increase the rate of mitoses and proliferation in response to carcinogen. Human female skin and keratinocytes also activate immune-cancer fighting pathways and immune cells at ultraviolet radiation-damaged sites. Critically, a compromised immune system leads to high-risk, aggressive cSCC specifically in women.

ConclusionsThis work shows the immune response is sex biased in cSCC, and highlights female immunity offers greater protection than male immunity.

category: cancer biology


title: Lesion Shedding Model: unraveling site-specific contributions to ctDNA.

abstract:
MotivationSampling circulating tumor DNA, ctDNA, using liquid biopsies offers clinically important benefits for monitoring of cancer progression. A single ctDNA sample represents a mixture of shed tumor DNA from all known and unknown lesions within a patient. Although shedding levels have been suggested to hold the key to identifying targetable lesions and uncovering treatment resistance mechanisms, the amount of DNA shed by any one specific lesion is still not well characterized. We designed the LSM (Lesion Shedding Model) to order lesions from the strongest to the poorest shedding for a given patient. Our framework intrinsically models for missing/hidden lesions and operates on blood ctDNA and lesion assays to estimate the potential relative shedding levels of lesions into the blood. By characterizing the lesion-specific ctDNA shedding levels, we can better understand the mechanisms of shedding as well as more accurately contextualize and interpret ctDNA assays to improve their clinical impact.

ResultsWe verified the accuracy of the LSM under controlled conditions using a simulation approach as well as testing on two gastrointestinal cancer patients. In the simulation we created a synthetic blood ctDNA sample per patient, where specific lesions are assigned predefined shedding levels. The simulated data mirrors real data lesion genomic similarities. The LSM correctly obtains a partial order of the lesions, i.e. accurately stratifies the lesions by their assigned shedding levels for simulations on two patients with strikingly different numbers of biopsied lesions, 4 and 17. The LSMs accuracy in identifying the top shedding lesion was not impacted by the higher number of lesions considered. We then applied LSM to two gastrointestinal cancer patients with available ctDNA blood samples and multiple biopsied lesions and found that indeed there were lesions that were consistently shedding more than other lesions into the patients blood. We also found that in both patients the top shedding lesion was one of the only clinically progressing lesions at the time of biopsy suggesting a connection between high ctDNA shedding and clinical progression. The LSM provides a much needed framework with which to understand ctDNA shedding and how to apply ctDNA assays.

AvailabilityBinary is available at https://github.com/ComputationalGenomics/LSM


title: Exploring the prognostic value of SCARF1 in non-small cell lung cancers

abstract: Scavenger receptor class F member 1 (SCARF1) has previously been shown to be highly expressed within the human liver, hold prognostic value in hepatocellular carcinoma and mediate the specific recruitment of leukocytes to liver sinusoidal endothelial cells; however, to date, the liver remains the only major organ in which SCARF1 has been explored in any detail. Here, we utilised publically-available RNA-sequencing data from The Cancer Genome Atlas (TGCA) to identify the lungs as a site of significant SCARF1 expression and attribute the majority of its expression to endothelial cell populations. Next, we show that SCARF1 expression is significantly reduced in two histologically distinct types of non-small cell lung carcinoma cancers (NSCLCs), lung adenocarcinoma (LUAD) and lung squamous cell carcinoma (LUSC), compared to non-tumoural tissues. Interestingly, loss of SCARF1 expression was associated with aggressive tumour biology in LUAD tissues, but not in LUSC. Furthermore, increased SCARF1 expression was highly prognostic of better overall survival in LUAD tumour tissues, but this was again in contrast to LUSC tumours, in which SCARF1 held no prognostic value. Finally, we showed that SCARF1 is widely expressed in tumour endothelial cells of non-small cell lung cancers and that its total expression in LUAD tumour tissues correlated with immune score and CD4+ T cell infiltration. This study represents the first detailed exploration of SCARF1 expression in normal and diseased human lung tissues and further highlights the prognostic value and therapeutic potential of SCARF1 in immunologically active cancers.


title: Pre-existing cell subpopulations in primary prostate cancers display surface fingerprint of docetaxel-resistant cells

abstract:
BackgroundDocetaxel resistance represents a leading obstacle in the therapy of prostate cancer (PCa), resulting in lethal disease. Intratumoral heterogeneity, which is frequently driven by epithelial-mesenchymal plasticity significantly contributes to the limited treatment response, chemoresistance, and subsequent poor prognosis of patients with lethal PCa.

MethodsWe employed a high-throughput flow cytometry screening to identify cell surface fingerprint that associates with docetaxel resistance in PCa cells. Using patient-derived xenografts, we validated protein expression of the most robustly changed antigens in vivo and further assessed this 6-molecule surface fingerprint in primary PCa tumors.

ResultsWe revealed the overexpression of SSEA-4 antigen in both in vitro and in vivo docetaxel-resistant models and confirmed the SSEA-4 enrichment in a subpopulation of freshly isolated primary PCa tumors. The level of ST3GAL2, an enzyme that is critically involved in the SSEA-4 synthesis, correlated with increased expression of CD44, CD59, and CD95 and reduced expression of EpCAM and CD9. SSEA-4 was further directly linked to the antimicrotubule agent resistance and poor prognosis in PCa patients.

ConclusionsWe propose that the 6-molecule surface fingerprint associates with docetaxel resistance and pre-exists in a cell subpopulation of primary PCa tumors even before docetaxel treatment.


title: A novel allele in the Arabidopsis thaliana MACPF protein CAD1 results in deregulated immune signaling

abstract: Immune recognition in plants is governed by two major classes of receptors: pattern recognition receptors (PRRs) and nucleotide-binding leucine-rich repeat receptors (NLRs). Located at the cell surface, PRRs bind extracellular ligands originating from microbes (indicative of  non-self) or damaged plant cells (indicative of  infected-self), and trigger signaling cascades to protect against infection. Located intracellularly, NLRs sense pathogen-induced physiological changes and trigger localized cell death and systemic resistance. Immune responses are under tight regulation in order to maintain homeostasis and promote plant health. In a forward-genetic screen to identify regulators of PRR-mediated immune signaling, we identified a novel allele of the membrane-attack complex and perforin (MACPF)-motif containing protein CONSTITUTIVE ACTIVE DEFENSE 1 (CAD1) resulting from a missense mutation in a conserved N-terminal cysteine. We show that cad1-5 mutants display deregulated immune signaling and symptoms of autoimmunity dependent on the lipase-like protein ENHANCED DISEASE SUSCEPTIBILITY1 (EDS1), suggesting that CAD1 integrity is monitored by the plant immune system. We further demonstrate that CAD1 localizes to both the cytosol and plasma membrane using confocal microscopy and subcellular fractionation. Our results offer new insights into immune homeostasis and provide tools to further decipher the intriguing role of MACPF proteins in plants.

category: plant biology


title: Contribution of climate models and APSIM phenological parameters to uncertainties in spring wheat simulations: application of SUFI-2 algorithm in northeast Australia

abstract: We used SUFI-2 for the first time to calibrate the phenology module of the APSIM-wheat model for 10 spring wheat cultivars cultivated in northeast Australia (south-eastern Queensland). Calibration resulted in an average RMSE of 5.5 d for developmental stages from stem elongation up to flowering. Projections from 33 climate models under the representative concentration pathway 8.5 were used for simulations at 17 sites. Using adapted sowing times, we simulated significantly shorter crop cycles and grain yield improvements for the period 2036-2065 relative to 1990-2019 for three selected cultivars (Hartog, Scout and Gregory). Photoperiod and vernalisation sensitivities were shown to be the largest and smallest contributors to total uncertainties in the simulated flowering day and grain yield. Uncertainties in climate models had a relatively minor contribution to the total uncertainties in the simulated values of target traits. This contribution significantly increased when climate change impact on the target traits was estimated.


title: Two softwood GUX clades are responsible for distinct glucuronic acid patterns on xylan.

abstract: Wood of coniferous (softwood) trees, is a globally significant carbon sink and an important source of biomass for industrial applications. Despite its importance, very little is known about the genetic basis of softwood biosynthesis. Glucomannan and xylan are the main hemicelluloses in softwood secondary cell walls. Xylan interacts with the cellulose fibrils in a two-fold screw configuration. Moreover, we have shown that xylan GUX (GlucUronic acid substitution of Xylan)-dependent branching with glucuronic acid is critical for biomass recalcitrance. Here, we investigated the decoration patterns of xylan by softwood GUX enzymes. Using in vitro and in planta assays we demonstrate that two distinct clades of conifer GUX enzymes are active glucuronyltransferases. Interestingly, these enzymes have different specific activities, with one adding evenly spaced GlcA branches and the other one being also capable of glucuronidating two consecutive xyloses. Since xylan patterning might modulate xylan-cellulose and xylan-lignin interactions, our result further the understanding of softwood biosynthesis and can contribute to strategies aimed at modifying softwood cell wall properties.


title: A quick and versatile protocol for the 3D visualization of transgene expression across the whole body of larval Drosophila

abstract: Larval Drosophila are used as a genetically accessible study case in many areas of biological research. Here we report a fast, robust and user-friendly procedure for the whole-body multifluorescence imaging of Drosophila larvae; the protocol has been optimized specifically for larvae by systematically tackling the pitfalls associated with clearing this small but cuticularized organism. Tests on various fluorescent proteins reveal that the recently introduced monomeric infrared fluorescent protein (mIFP) is particularly suitable for our approach. This approach comprises an effective, low-cost clearing protocol with minimal handling time and reduced toxicity in the reagents employed. It combines a success rate high enough to allow for small-scale screening approaches and a resolution sufficient for cellular-resolution analyses with light sheet and confocal microscopy. Given that publications and database documentations typically specify expression patterns of transgenic driver lines only within a given organ system of interest, the present procedure should be versatile enough to extend such documentation systematically to the whole body. As examples, the expression patterns of transgenic driver lines covering the majority of neurons, or subsets of chemosensory, central brain or motor neurons, are documented in the context of whole larval body volumes (using nsyb-Gal4, IR76b-Gal4, APL-Gal4 and mushroom body Kenyon cells, or OK371-Gal4, respectively). Notably, the presented protocol allows for triple-color fluorescence imaging with near-infrared, red and yellow fluorescent proteins.

category: neuroscience


title: Fluoxetine acts concomitantly on dorsal and ventral hippocampus to Trk-dependently modulate the extinction of fear memory

abstract:
BackgroundHippocampus can be divided along its longitudinal axis into dorsal and ventral parts. Both are usually committed to modulate different aspects of behavior and stress response. However, it is not clear whether the hippocampal subregions could differently modulate the effect of antidepressant drugs. Since fluoxetine (FLX) effect on extinction of aversive memory is well known to depend on hippocampal BDNF levels, we hypothesized that the hippocampal subregions might play different roles in fluoxetine efficacy in decreasing fear response.

MethodWistar rats were fear-cued conditioned and treated chronically with fluoxetine to enhance their subsequent extinction memory. First, FLX effect on BDNF levels was assessed considering the dorsal (dHC) and ventral (vHC) hippocampus apart. Then, K252a (a functional Trk blocker) was infused either into the dHC or vHC to assay its interaction with FLX treatment over the fear response. Next, BDNF was directly infused into either the dHC or vHC to compare its behavioral effects with FLX. Finally, FLX effect on c-Fos expression was evaluated also considering the dHC and vHC apart, along with subareas of amygdala and medial prefrontal cortex.

ResultsChronic FLX treatment increased BDNF in the dHC, whereas BDNF was increased in the vHC after acute treatment only. K252a infused after the extinction protocol into either dHC or vHC was able to prevent FLX effect on fear response. BDNF directly infused into the dHC increased fear response, however its administration into the vHC induced an opposite effect. Besides, a negative correlation between the fear response and c-Fos expression was observed after chronic FLX treatment specifically in the dHC CA3/CA1 and vHC CA1/DG.

ConclusionBoth dHC and vHC are important for the Trk-dependent FLX effect on extinction memory, although a discrepancy on the fear response was observed with the direct infusion of BDNF into the dHC or vHC.


title: Altered cleavage of Caspase-1 in hepatocytes limits control of malaria in the liver

abstract: Malaria, caused by Plasmodium parasites, is a devastating disease that kills over half a million people each year1. Plasmodium sporozoites inoculated by mosquitoes into mammalian hosts undergo a clinically silent phase of obligatory development and replication in hepatocytes before initiating the life-threatening blood-stage of malaria2. Thus, understanding the immune responses elicited by Plasmodium infection in the liver is key to controlling clinical malaria and transmission3,4. Here, we show that Plasmodium DNA can be detected by AIM2 (absent in melanoma 2) sensors in the infected hepatocytes, resulting in Caspase-1 activation and pyroptotic cell-death. However, Caspase-1 was observed to undergo only partial cleavage in hepatocytes, limiting pyroptosis, and the maturation of pro-inflammatory cytokines classically associated with Caspase-1 activation. We discovered that the extent of Caspase-1 cleavage in cells is determined by the expression of ASC (apoptosis-associated speck-like protein containing a CARD). ASC expression is inherently low in hepatocytes, and transgenically enhancing it in the hepatocytes induced complete processing of Caspase-1, efficient secretion of pro-inflammatory cytokines, enhanced pyroptotic cell-death, and markedly improved control of malaria infection in the liver. In addition to describing a novel pathway of natural immunity to malaria, our findings uncover a key aspect of liver biology that may have been exploited during evolution by successful hepatotropic pathogens.


title: Polyclonal antibody responses to HIV Env immunogens resolved using cryoEM

abstract:
In BriefHerein, we evaluated the immunogenicity of several BG505 SOSIP-based HIV Env immunogens in the rhesus macaque animal model using a combination of serology and biophysical approaches. We applied electron cryo-microscopy for high-resolution mapping of elicited polyclonal antibody responses, which provided detailed insights into the binding modes of the most common classes of antibodies elicited by BG505 SOSIP immunogens as well as the critical differences in immunogenicity that can occur as a consequence of engineered stabilizing mutations and partial glycan occupancy at different sites.

SummaryEngineered ectodomain trimer immunogens based on BG505 envelope glycoprotein are widely utilized as components of HIV vaccine development platforms. In this study, we used rhesus macaques to evaluate the immunogenicity of several stabilized BG505 SOSIP constructs both as free trimers and presented on a nanoparticle. We applied a cryoEM-based method for high-resolution mapping of polyclonal antibody responses elicited in immunized animals (cryoEMPEM). Mutational analysis coupled with neutralization assays were used to probe the neutralization potential at each epitope. We demonstrate that cryoEMPEM data can be used for rapid, high-resolution analysis of polyclonal antibody responses without the need for monoclonal antibody isolation. This approach allowed to resolve structurally distinct classes of antibodies that bind overlapping sites. In addition to comprehensive mapping of commonly targeted neutralizing and non-neutralizing epitopes in BG505 SOSIP immunogens, our analysis revealed that epitopes comprising engineered stabilizing mutations and of partially occupied glycosylation sites can be immunogenic.

Graphical abstract O_FIG_DISPLAY_L [Figure 1] M_FIG_DISPLAY C_FIG_DISPLAY


title: Identifying drivers of spatio-temporal variation in survival in four blue tit populations

abstract: In a context of rapid climate change, the influence of large-scale and local climate on population demography is increasingly scrutinized, yet studies are usually focused on one population. Demographic parameters, including survival, can vary significantly across populations of a given species, depending on global or local climatic fluctuations but also on many other population-specific parameters such as breeding density, habitat naturalness, predation or parasitism. Such ecological differences between populations could lead to different paces-of-life (POL), whereby populations where individuals display higher reproductive investment and bolder behaviours would have lower survival probabilities. We use here long-term (19 to 38 years) monitoring datasets from four Mediterranean populations of blue tits (Cyanistes caeruleus) to investigate the effects of sex, age class, large-scale and local climate temporal variation and population breeding density, on adult survival, using Capture-Mark-Recapture modelling. Environment heterogeneity in these four populations (two in evergreen and two in deciduous forests) has been linked to strong multi-trait phenotypic variation, suggesting blue tits in deciduous forests display faster POL compared to their conspecifics in evergreen habitats. The present results show heterogeneity in average survival probabilities across the four populations, with, as predicted, lower survival in the  fast blue tits occupying deciduous habitats. Interestingly, the year-to-year variation in survival probabilities was synchronous among populations. This suggests that regional environmental conditions could drive survival fluctuations across populations. However, breeding densities were not correlated across populations, and we found no evidence that adult survival is correlated with either large-scale or local, climate temporal variation in these four blue tit populations. Finally, two of the focal populations displayed a linear temporal decrease in adult survival over the study period, calling for further investigation to explain this decline. Overall, this multi-site study shows that blue tit parental survival from one spring to the next can vary substantially across years, in a synchronous way across populations, yet the climate indices we used are not correlated with the temporal variation. This calls for further investigations in other potential drivers such as resource (in particular insect) abundance, predation or parasitism.

category: ecology


title: Physiology and ecology combine to determine host and vector importance for Ross River virus and other vector-borne diseases

abstract: Identifying the key vector and host species driving transmission is notoriously difficult for vector-borne zoonoses, but critical for disease control. Here, we present a general approach for quantifying the role hosts and vectors play in transmission that integrates species physiological competence with their ecological traits. We apply this model to the medically important arbovirus Ross River virus (RRV), in Brisbane, Australia. We found that vertebrate species with high physiological competence werent the most important for community transmission. Instead, we estimated that humans (previously overlooked as epidemiologically important hosts) potentially play an important role in RRV transmission, in part, because highly competent vectors readily feed on them and are highly abundant. By contrast, vectors with high physiological competence were also important for community transmission. Finally, we uncovered two potential transmission cycles: an enzootic cycle involving birds and an urban cycle involving humans. This modelling approach has direct application to other zoonotic arboviruses.


title: Physiology and ecology together regulate host and vector importance for Ross River virus and other vector-borne diseases


title: Organelle bottlenecks facilitate evolvability by traversing heteroplasmic fitness valleys

abstract: Bioenergetic organelles - mitochondria and plastids - retain their own genomes, and these organelle DNA (oDNA) molecules are vital for eukaryotic life. Like all genomes, oDNA must be able to evolve to suit new environmental challenges. However, mixed oDNA populations can challenge cellular bioenergetics, providing a penalty to the appearance and adaptation of new mutations. Here we show that organelle  bottlenecks, mechanisms increasing cell-to-cell oDNA variability during development, can overcome this mixture penalty and facilitate the adaptation of beneficial mutations. We show that oDNA heteroplasmy and bottlenecks naturally emerge in evolutionary simulations subjected to fluctuating environments, demonstrating that this evolvability is itself evolvable. Usually thought of as a mechanism to clear damaging mutations, organelle bottlenecks therefore also resolve the tension between intracellular selection for pure oDNA populations and the  bet-hedging need for evolvability and adaptation to new environments. This general theory suggests a reason for the maintenance of organelle heteroplasmy in cells, and may explain some of the observed diversity in organelle maintenance and inheritance across taxa.

category: genetics


title: PredicTF: a tool to predict bacterial transcription factors in complex microbial communities.

abstract: Transcription Factors (TFs) are proteins that control the flow of genetic information by regulating cellular gene expression. Here we describe PredicTF, a first platform supporting the prediction and classification of novel bacterial TF in complex microbial communities. We evaluated PredicTF using a two-step approach. First, we tested PredictTFs ability to predict TFs for the genome of an environmental isolate. In the second evaluation step, PredicTF was used to predict TFs in a metagenome and 11 metatranscriptomes recovered from a community performing anaerobic ammonium oxidation (anammox) in a bioreactor. PredicTF is open source pipeline available at https://github.com/mdsufz/PredicTF.


title: Correlated dipolar and dihedral fluctuations in a protein

abstract: Correlation between dihedral fluctuations is a possible way to understand coordination between various amino acid residues of the protein. The nanosecond timescales of correlated fluctuations of dihedral angle do not allow direct probing by experimental methods. However, NMR experiments probe dipolar fluctuations given in terms of cross correlated relaxation (CCR) rates, expressed as zero frequency spectral density function (J) of the fluctuations of the mutual orientation of two spatially separated dipole vectors. Here we illustrate the correlation of protein dipolar and dihedral angle using molecular dynamics simulation of protein Ubiquitin (Ub) and GB3. We calculate CCR rates between protein bond vector from simulation and compare with CCR data obtained from NMR experiments. A good correlation between theoretical and experimental values is found. We further show that the zero frequency spectral functions of backbone dihedral{psi} auto-correlation function and dipole orientation fluctuations show strong correlations. These correlations are not sensitive to protein and forcefield parameters. Hence, CCR may act as a marker for protein backbone dihedral fluctuations.

category: biophysics


title: Identification and characterization of a biphasic/bidirectional wound-inducible RHA3B gene promoter from Arabidopsis thaliana

abstract:
Conditional promoters such as wound inducible are important tools for plant biotechnology to selectively express agronomically important genes. From a set of Enhancer trap (DsE-uidA) transposant lines we identified wound inducible ET1075 line by injuring leaf blade and screening for Ds linked GUS gene expression. Earliest GUS stain detected at petiolar region at 2hrs post injury with a progressive attainment of maximum visual intensity between 12 and 24hrs wherein, the transcript expression induced in a bidirectional manner. DsE was found to be inserted in the intergenic region between AT4G35480 and AT4G35490. To find the essential transcriptional regulatory region, deletion constructs comprising upstream sequences of pRHA3B fused to GUS reporter gene were functionally tested in Arabidopsis plants by generating stable transgenics. A 481 bp of upstream sequence from ATG is found to be sufficient to promote wound inducible gene expression. Sequence analysis revealed the presence of several regulatory elements implicated in wound inducible gene expression. Comparative analysis with similar wound inducible promoters revealed the presence of common cis-regulatory elements. This promoter can essentially be used in pest control and in molecular pharming to conditionally express agronomically/commercially important genes in plants.

HighlightsO_LIDsE enhancer trap transposant lines were generated.
C_LIO_LIIdentified a novel wound inducible promoter line ET1075.
C_LIO_LIWound inducible promoter pRHA3B is bidirectional and induces the expression of RHA3B and MRPL11 genes.
C_LIO_LIWound responsive key cis-elements WRKY, W-box, FORCA are present in the pRHA3B promoter.
C_LI


title: ssDNA recombineering boosts in vivo evolution of nanobodies displayed on bacterial surfaces

abstract: In vivo evolution of antibodies facilitates emergence of novel target specificities from pre-existing clones. In this work we show how mutagenic ssDNA recombineering of camel-derived nanobodies encoded in a bacterial genome enables clonal hyper-diversification and the rise of new properties. As a proof-of-principle we used a nanobody recognizing the antigen TirM from enterohaemorrhagic E. coli (EHEC) and evolved it towards the otherwise not recognized TirM antigen from enteropathogenic E. coli (EPEC). To this end, E. coli cells displaying on their surface this nanobody fused to the intimin outer membrane anchor domain were subjected to multiple rounds of mutagenic ssDNA recombineering targeted to the CDR1, CDR2 and CDR3 regions of its genomically encoded VHH sequence. Binders to the new antigen (EPEC TirM) were then selected upon immunomagnetic capture of bacteria bearing the corresponding nanobody variants. As a result, several modified nanobodies were identified which maintained recognition of EHEC TirM but acquired the ability to bind the new antigen with high affinity (Kd ~20 nM). The results highlight the power of combining evolutionary properties of bacteria in vivo with oligonucleotide synthesis in vitro for the sake of focusing diversification to specific segments of a gene (or protein thereof) of interest. Our experimental workflow empowers the evolution of nanobodies displayed on the surface of bacterial cells for a large number of potential applications in medical and industrial biotechnology.

category: synthetic biology


title: Th17 immunity in the colon is controlled by two novel subsets of colon-specific mononuclear phagocytes

abstract: Intestinal immunity is coordinated by specialized mononuclear phagocyte populations, constituted by a diversity of cell subsets. Although the cell subsets constituting the mononuclear phagocyte network are thought to be similar in both small and large intestine, these organs have distinct anatomy, microbial composition, and immunological demands. Whether these distinctions demand organ-specific mononuclear phagocyte populations with dedicated organ-specific roles in immunity are unknown. Here we implement a new strategy to subset murine intestinal mononuclear phagocytes and identify two novel subsets which are colon-specific: a macrophage subset and a Th17-inducing dendritic cell (DC) subset. Colon-specific DCs and macrophages co-expressed CD24 and CD14, and surprisingly, both were dependent on the transcription factor IRF4. Novel IRF4-dependent CD14+CD24+ macrophages were markedly distinct from conventional macrophages and failed to express classical markers including CX3CR1, CD64 and CD88, and surprisingly expressed little IL-10, which was otherwise robustly expressed by all other intestinal macrophages. We further found that colon-specific CD14+CD24+ mononuclear phagocytes were essential for Th17 immunity in the colon, and provide definitive evidence that colon and small intestine have distinct antigen presenting cell requirements for Th17 immunity. Our findings reveal unappreciated organ-specific diversity of intestine-resident mononuclear phagocytes and organ-specific requirements for Th17 immunity.


title: Differential contribution of two organelles of endosymbiotic origin to iron-sulfur cluster synthesis in Toxoplasma

abstract:
Iron-sulfur (Fe-S) clusters are one of the most ancient and ubiquitous prosthetic groups, and they are required by a variety of proteins involved in important metabolic processes. Apicomplexan parasites have inherited different plastidic and mitochondrial Fe-S clusters biosynthesis pathways through endosymbiosis. We have investigated the relative contributions of these pathways to the fitness of Toxoplasma gondii, an apicomplexan parasite causing disease in humans, by generating specific mutants. Phenotypic analysis and quantitative proteomics allowed us to highlight notable differences in these mutants. Both Fe-S cluster synthesis pathways are necessary for optimal parasite growth in vitro, but their disruption leads to markedly different fates: impairment of the plastidic pathway leads to a loss of the organelle and to parasite death, while disruption of the mitochondrial pathway trigger differentiation into a stress resistance stage. This highlights that otherwise similar biochemical pathways hosted by different sub-cellular compartments can have very different contributions to the biology of the parasites, which is something to consider when exploring novel strategies for therapeutic intervention.

Author summaryToxoplasma gondii is a ubiquitous unicellular parasite that harbours two organelles of endosymbiotic origin: the mitochondrion, and a relict plastid named the apicoplast. Each one of these organelles contains its own machinery for synthesizing iron-sulfur clusters, which are important protein co- factors. In this study, we show that interfering with either the mitochondrial or the plastidic iron- sulfur cluster synthesizing machinery has a profound impact on parasite growth. However, while disrupting the plastidic pathway led to an irreversible loss of the organelle and subsequent death of the parasite, disrupting the mitochondrial pathway led to conversion of the parasites into a stress resistance form. We used a comparative quantitative proteomic analysis of the mutants, combined with experimental validation, to provide mechanistic clues into these different phenotypic outcomes. Although the consequences of disrupting each pathway were manifold, our data highlighted distinct changes at the metabolic level. For instance, the plastidic iron-sulfur cluster synthesis pathway is likely important for maintaining the lipid homeostasis of the parasites, while the mitochondrial pathway is clearly crucial for maintaining their respiratory capacity. Interestingly, we have discovered that other mutants severely impacted for mitochondrial function, in particular the respiratory chain, are able to survive and initiate conversion to the stress resistance form. This illustrates a different capacity for T. gondii to adapt for survival in response to distinct metabolic dysregulations.


title: Differential contribution of two organelles of endosymbiotic origin to iron-sulfur cluster synthesis and overall fitness in Toxoplasma


title: Targeting cellular metabolism to inhibit synergistic biofilm formation of multi-species isolated from a cooling water system

abstract: Biofilm is ubiquitous in natural environments, causing biofouling in industrial water systems and leading to liquidity and heat transfer efficiency decreases. In particular, multi-species coexistence in biofilms can provide the synergy needed to boost biomass production and enhance treatment resistance. In this study, a total of 37 bacterial strains were isolated from a cooling tower where acetic acid and propionic acid were used as the primary carbon sources. These isolates mainly belonged to Proteobacteria and Firmicutes, which occupied more than 80% of the total strains according to the 16S rRNA gene amplicon sequencing. Four species (Acinetobacter sp. CTS3, Corynebacterium sp. CTS5, Providencia sp. CTS12, and Pseudomonas sp. CTS17) were observed to co-exist in the synthetic medium, showing a synergistic effect towards biofilm formation. Three metabolic inhibitors (sulfathiazole, 3-Bromopyruvic acid, and 3-Nitropropionic acid) were employed as possible treatments against biofilm formation due to their inhibition effect on c-di-GMP biosynthesis or assimilation of volatile fatty acids. All of them displayed evident inhibition profiles to biofilm formation. Notably, the combination of these three inhibitors possessed a remarkable ability to block the development of a multi-species biofilm with lower concentrations, suggesting an enhanced effect with their simultaneous use. This study demonstrates that targeting cellular metabolism is an effective way to inhibit biofilm formation derived from multi-species.


title: Streptococcus pneumoniae, S. pyogenes, and S. agalactiae membrane phospholipid remodeling in response to human serum

abstract: Streptococcus pneumoniae, S. pyogenes (Group A Streptococcus; GAS), and S. agalactiae (Group B Streptococcus; GBS) are major etiological agents of diseases in humans. The cellular membrane, a crucial site in host-pathogen interactions, is poorly characterized in streptococci. Moreover, little is known about whether or how environmental conditions influence their lipid compositions. Using normal phase liquid chromatography coupled with electrospray ionization mass spectrometry, we characterized the phospholipids and glycolipids of S. pneumoniae, GAS, and GBS in routine undefined laboratory medium, streptococcal defined medium, and, in order to mimic the host environment, defined medium supplemented with human serum. In human serum-supplemented medium, all three streptococcal species synthesize phosphatidylcholine (PC), a zwitterionic phospholipid commonly found in eukaryotes but relatively rare in bacteria. We previously reported that S. pneumoniae utilizes the glycerophosphocholine (GPC) biosynthetic pathway to synthesize PC. Through substrate tracing experiments, we confirm that GAS and GBS scavenge lysoPC, a major metabolite in human serum, thereby using an abbreviated GPC pathway for PC biosynthesis. Furthermore, we found that plasmanyl-PC is uniquely present in the GBS membrane during growth with human serum, suggesting GBS possesses unusual membrane biochemical or biophysical properties. In summary, we report cellular lipid remodeling by the major pathogenic streptococci in response to metabolites present in human serum.


title: Umibato: estimation of time-varying microbial interaction using continuous-time regression hidden Markov model

abstract:
MotivationAccumulating evidence has highlighted the importance of microbial interaction networks. Methods have been developed for estimating microbial interaction networks, of which the generalized Lotka-Volterra equation (gLVE)-based method can estimate a directed interaction network. The previous gLVE-based method for estimating microbial interaction networks did not consider time-varying interactions.

ResultsIn this study, we developed unsupervised learning based microbial interaction inference method using Bayesian estimation (Umibato), a method for estimating time-varying microbial interactions. The Umibato algorithm comprises Gaussian process regression (GPR) and a new Bayesian probabilistic model, the continuous-time regression hidden Markov model (CTRHMM). Growth rates are estimated by GPR, and interaction networks are estimated by CTRHMM. CTRHMM can estimate time-varying interaction networks using interaction states, which are defined as hidden variables. Umibato outperformed the existing methods on synthetic datasets. In addition, it yielded reasonable estimations in experiments on a mouse gut microbiota dataset, thus providing novel insights into the relationship between consumed diets and the gut microbiota.

AvailabilityThe C++ and python source codes of the Umibato software are available at https://github.com/shion-h/Umibato

Contactshion_hosoda@asagi.waseda.jp, mhamada@waseda.jp


title: Differential susceptibility of neuronal neurotransmitter phenotypes to HHV6 infection

abstract: Within the family Herpesviridae, sub-family {beta}-herpesvirinae, and genus Roseolovirus, there are only three human herpesviruses that have been discovered and described: HHV-6A, HHV-6B, and HHV-7. Initially, HHV-6A and HHV-6B were considered to be simply two variants of the same virus (i.e., HHV6). Despite high overall genetic sequence identity (~90%), HHV-6A and HHV-6B are now recognized as two distinct viruses of the genus. Limited sequence identity (e.g., <70%) in key coding regions as well as significant differences in physiological and biochemical profiles (e.g., preferential use of different receptors for viral entry into susceptible hosts) underscore the conclusion that HHV-6A and HHV-6B are distinct virus species. Likewise, each virus appears to differentially contribute as putative etiologic agents to a variety of neurological disorders, including: multiple sclerosis, epilepsy, and chronic fatigue syndrome. Despite being implicated as causative agents in nervous system dysfunction, mechanisms of action and relative contributions of each virus to neural disorders remain elusive. Unresolved questions regarding: cell receptor use and binding affinity (i.e., CD49 versus CD134); cell tropism; the role of HHV-7 superinfection; and, relative virulence between HHV-6A versus HHV-6B - prevent a complete characterization. Although it has been demonstrated that both HHV-6A and HHV-6B can infect glia and, more recently, cerebellar Purkinje cells, cell tropism of HHV-6A versus HHV-6B for different nerve cell types remains vague. In this study, we demonstrate that both HHV-6A and HHV-6B can infect different nerve cell types (i.e., glia versus neurons) and different neuronal neurotransmitter phenotypes derived from the differentiation of human neural stem cells. We further show that both HHV-6A and HHV-6B induce cytopathic effects (CPEs) in susceptible nerve cells. However, the time-course and severity of CPEs appear to differ between HHV-6A versus HHV-6B infections and are dependent upon multiplicity of infection (MOI). As demonstrated by immunofluorescence, although both the HHV-6A and HHV-6B viruses productively infected VGluT1-containing cells (i.e., glutamatergic neurons) and dopamine-containing cells (i.e., dopaminergic neurons), neither HHV-6A nor HHV-6B challenge resulted in the productive infection of GAD67-containing cells (i.e., GABAergic cells). The reason underlying the apparent resistance of GABAergic cells to HHV-6A and HHV-6B infection remains unclear. Morphometric and image analyses of neurite extension and retraction dynamics as well as the time-course of cell aggregation phenomena (e.g., syncytia formation) during infection also indicate that HHV-6A induces more severe CPEs than HHV-6B at the same time-point and MOI. These data suggest that HHV-6A is more virulent than HHV-6B on susceptible human neural stem cells (HNSCs) differentiated into neuronal phenotypes, while neither virus is able to infect GABAergic cells. If these in vitro data hold in vivo, the inhibitory interneuron dysfunction hypothesis for HHV6-driven seizures may be ruled out as a potential mechanism for HHV6-induced epileptogenesis.


title: Regulation of blood-brain barrier integrity and cognition by the microbiome-associated methylamines trimethylamine N-oxide and trimethylamine

abstract:
BackgroundCommunication between the gut microbiota and the brain is primarily mediated via soluble microbe-derived metabolites, but the details of this pathway remain poorly defined. Methylamines produced by microbial metabolism of dietary choline and L-carnitine have received attention due to their proposed association with vascular disease, but their effects upon the cerebrovascular circulation have hitherto not been studied.

ResultsHere we use an integrated in vitro/in vivo approach to show that physiologically relevant concentrations of the dietary methylamine trimethylamine N-oxide (TMAO) enhanced blood-brain barrier (BBB) integrity and protected it from inflammatory insult, acting through the tight junction regulator annexin A1. In contrast, the TMAO precursor trimethylamine (TMA) impaired BBB function and disrupted tight junction integrity. Moreover, we show that long-term exposure to TMAO protects murine cognitive function from inflammatory challenge, acting to limit astrocyte and microglial reactivity in a brain region-specific manner.

ConclusionOur findings demonstrate the mechanisms through which microbiome-associated methylamines directly interact with the mammalian BBB, with consequences for cerebrovascular and cognitive function.

category: systems biology


title: Regulation of blood-brain barrier integrity by microbiome-associated methylamines and cognition by trimethylamine N-oxide


title: Amplicon sequencing of variable 16S rRNA and ITS2 regions reveal honeybee susceptibility to diseases resulted of their dietary preferences under anthropogenic landforms

abstract: European Apis mellifera and Asian Apis cerana honeybees, are essential crop pollinators. Microbiome studies can provide complex information on health and fitness of these insects in relation to environmental changes, and plant availability. Amplicon sequencing of variable regions of 16S rRNA and internally transcribed spacers (ITSs) allow identification of the metabiome. These methods provide a tool for monitoring otherwise uncultured microbes isolated from the gut of the honeybees. They also help monitor the composition of the gut fungi and, intriguingly, pollens collected by the insect. Here, we present data from amplicon sequencing of the 16S rRNA and ITS2 regions from honeybees collected at various time points from anthropogenic landforms as urban areas in Poland, UK, Spain, Greece, and Thailand. We have analysed microbial composition of honeybee intestine as well as fungi and pollens. We conclude that differences between samples were mainly influenced by the bacteria, plant pollens and fungi, respectively. Moreover, honeybees feeding on a honeydew diet, mainly based on sugars, were more prone to fungal pathogens (Nosema ceranae) and neogregarines. Finally, the period when honeybees switch to the winter generation (longer-lived forager honeybees) is the most sensitive to diet perturbations and hence pathogens attack, for the whole beekeeping season. It is possible that evolutionary adaptation of bees fails to benefit them in the modern anthropomorphised environment.

category: zoology


title: Intrinsic network activity in human brain organoids

abstract: Human brain organoids replicate much of the cellular diversity and developmental anatomy of the human brain. However, the physiological behavior of neuronal circuits within organoids remains relatively under-explored. With high-density CMOS microelectrode arrays (26,400 electrodes) and shank electrodes (960 electrodes), we probed broadband and three-dimensional extracellular field recordings generated by spontaneous activity of human brain organoids. These recordings simultaneously captured local field potentials (LFPs) and single-unit activity extracted through spike sorting. From spiking activity, we estimated a directed functional connectivity graph of synchronous neural network activity, which showed a large number of weak functional connections enmeshed within a network skeleton of significantly fewer strong connections. Treatment of the organoid with a benzodiazepine induced a reproducible signature response that shortened the inter-burst intervals, increased the uniformity of the firing pattern within each burst and decreased the population of weakly connected edges. Simultaneously examining the spontaneous LFPs and their phase alignment to spiking showed that spike bursts were coherent with theta oscillations in the LFPs. Our results demonstrate that human brain organoids have self-organized neuronal assemblies of sufficient size, cellular orientation, and functional connectivity to co-activate and generate field potentials from their collective transmembrane currents that phase-lock to spiking activity. These results point to the potential of brain organoids for the study of neuropsychiatric diseases, drug mechanisms, and the effects of external stimuli upon neuronal networks.


title: Human brain organoid networks


title: A unified mechanism to support innate and learned use of visual landmark guidance in insects

abstract:
Insects can navigate efficiently in both novel and familiar environments, and this requires flexiblity in how they are guided by sensory cues. A prominent landmark, for example, can ellicit strong innate behaviours (attraction or menotaxis) but can also be used, after learning, as a specific directional cue as part of a navigation memory. However, the mechanisms that allow both pathways to co-exist, interact or override each other are largely unknown. Here we propose a model for the behavioural integration of innate and learned guidance based on the neuroanatomy of the central complex (CX), adapted to control landmark guided behaviours. We consider a reward signal provided either by an innate attraction to landmarks or a long-term visual memory in the mushroom bodies (MB) that modulates the formation of a local vector memory in the CX. Using an operant strategy for a simulated agent exploring a simple world containing a single visual cue, we show how the generated short-term memory can support both innate and learned steering behaviour. In addition, we show how this architecture is consistent with the observed effects of unilateral MB lesions in ants that cause a reversion to innate behaviour. We suggest the formation of a directional memory in the CX can be interpreted as transforming rewarding (positive or negative) sensory signals into a mapping of the environment that describes the geometrical attractiveness (or repulsion). We discuss how this scheme might represent an ideal way to combine multisensory information gathered during the exploration of an environment and support optimized cue integration.

1 Author summaryIn this paper, we modeled the neural pathway allowing insects to perform landmark guided behaviours using their internal compass. First, we observed the intrinsic property of the connectome, extracted from drosophila online database, between the internal compass neurons and the steering neurons to support an oriented behaviour towards a single landmark. Then, we proposed and evaluated an adaptation of the bees path integration neural circuit, to sustain flexible landmark guidance behaviours such as attraction or menotaxis. We showed the model ability to form a memory during the exploration of the local environment to support both innate or learned navigation behaviour using a single landmark in the environment. In addtion, we demonstrated the transformation of a simple goodness/badness signal, from innate or long-term memory pathways, into an oriented steering signal that could be applied to other sensory pathways. Furthermore, by reproducing lesion experiments in the mushroom bodies of wood ants we highlight the consistency of the model with biological observation. We then discuss the different emergent properties and the potential outcome that this local, and operant, memory supports.

category: animal behavior and cognition


title: A unified mechanism for innate and learned visual landmark guidance in the insect central complex


title: Network Pharmacology Analysis of the active components and anticancer targets of Rhubarb

abstract: To investigate the mechanisms and active components governing the anticancer activity of rhubarb.The TCMSP database was screened to identify the active components of rhubarb and Swiss target predictions were generated to predict their cellular targets. TTD and OMIM databases were used to predict tumor-related target genes. "Cytoscape" was used to construct drug targets. PPI network analysis, GO enrichment analysis and KEGG pathway analysis of the key targets were investigated using String and David databases. A total of 33 components and 116 corresponding targets were screened. Amongst them, the key active compounds in rhubarb included emodin, aloe emodin, {beta}-sitosterol, emodin methyl ether and rhein, which were predicted to target TP53, AKT1, STAT3, PIK3CA, HRAS, and VEGFA. GO analysis revealed that the cellular targets clustered into 159 biological processes, including those involved in cellular composition (n=24) and molecular functions (n=42, P<0.01). KEGG pathway analysis revealed 85 (P < 0.01) pathways related to cancer. The active compounds in rhubarb target TP53, AKT1 and PIK3CA. Rhubarb therefore regulates cancer development through an array of biological pathways.


title: Estimating the societal disease burden of East Coast fever among rural cattle keeping households of Namwala District, Zambia

abstract:
The study aimed to estimate the disease burden of East Coast fever (ECF) among rural cattle keeping households of Namwala District of Zambia using Productivity Adjusted Life Years (PALYs). We modified Disability Adjusted Life Year (DALY) equations for humans to PALYs to estimate the societal burden of animal diseases. We used a structured questionnaire to collect data on parameters that feed into PALY equations. We coded and entered data from questionnaires directly into Statistical Package of Social Sciences (IBM SPSS Version 20), and entered the estimated values of PALY parameters into Mathematical Calculus Software called Integral Calculator (https://www.integral-calculator.com/). We then used the integral calculator to calculate PALY equations, which we used to estimate the societal disease burden of ECF in cattle. PALYs calculations were done in three categories; PALYs without discounting and age weighting, PALYs with only discounting, and PALYs with discounting and age weighting.

Results revealed that the years of productivity lost by a cow, bull, and ox that suffered from ECF were estimated at 15, 10, and 15 years, respectively. In the second category, the years of productivity lost by a cow, bull, and ox were seven, six, and seven years, respectively. In the final category, the years of productivity lost by a cow, bull, and ox were five years.

ECF caused a total of 517,165 PALYs in Namwala District. The quality of life reduced in years due to disability (YLD) caused by ECF per cow, bull, and ox was 0.07, 0.07, and 0.02 percent of their life expectancy, respectively. The estimated values for the years of a lifetime lost due to mortality (YLL) caused by ECF were 35, 49, and 35 percent of the life expectancy per cow, bull, and ox. These results are important for measuring outcomes of animal health problems in terms of PALYs. The findings are helpful in future projections for the future burden of any disease and can be used as a basis in policy-making and decision-making, particularly on priorities in animal health research. We recommend that a classification of animal diseases of national economic importance should consider both the societal burden and economic impact instead of the common practice of only considering the economic impact.

category: scientific communication and education


title: Statistical learning as reinforcement learning phenomena

abstract: Statistical learning (SL) is the ability to extract regularities from the environment. In the domain of language, this ability is fundamental in the learning of words and structural rules. In lack of reliable online measures, statistical word and rule learning have been primarily investigated using offline (post-familiarization) tests, which gives limited insights into the dynamics of SL and its neural basis. Here, we capitalize on a novel task that tracks the online statistical learning of language rules combined with computational modelling to show that online SL responds to reinforcement learning principles rooted in striatal function. Specifically, we demonstrate - on two different cohorts - that a Temporal Difference model, which relies on prediction errors, accounts for participants online learning behavior. We then show that the trial-by-trial development of predictions through learning strongly correlates with activity in both ventral and dorsal striatum. Our results thus provide a detailed mechanistic account of language-related SL and an explanation for the oft-cited implication of the striatum in SL tasks. This work, therefore, bridges the longstanding gap between language learning and reinforcement learning phenomena.


title: Encephalitis patient derived monoclonal GABAA receptor antibodies cause catatonia and epileptic seizures

abstract: Autoantibodies targeting the GABAA receptor (GABAAR) hallmark an autoimmune encephalitis presenting with frequent seizures and psychomotor abnormalities. Their pathogenic role is still not well-defined, given the common overlap with further autoantibodies and the lack of patient derived monoclonal antibodies (mAbs). We cloned and recombinantly produced five affinity-maturated GABAAR IgG1 mAbs from cerebrospinal fluid cells, which bound to various epitopes involving 1 and {gamma}2 receptor subunits, with variable binding strength and partial competition. mAbs selectively reduced GABAergic currents in neuronal cultures without causing receptor internalization. Cerebroventricular infusion of GABAAR mAbs and Fab fragments into rodents induced a severe phenotype with catatonia, seizures and increased mortality, reminiscent of encephalitis patients symptoms. Our results prove direct functional effects of autoantibodies on GABAARs and provide an animal model for GABAAR encephalitis. They further provide the scientific rationale for clinical treatments using antibody depletion and pave the way for future antibody-selective immunotherapies.


title: AP2 regulates Thickveins trafficking through Rab11 to attenuate NMJ growth signaling in Drosophila

abstract: Compromised endocytosis in neurons leads to synapse overgrowth and altered organization of synaptic proteins. However, the molecular players and the signaling pathways which regulate the process remains poorly understood. Here we show that {sigma}2-adaptin, one of the subunits of the AP2-complex, genetically interacts with BMP type I receptor, Thickveins (Tkv), and Daughter against decapentaplegic (Dad), two of the components of BMP signaling. We found that mutations in {sigma}2-adaptin lead to an accumulation of Tkv receptors at the NMJ and results in a significant reduction in Tkv-positive early endosomes in the presynaptic terminals. Interestingly, the level of small GTPase Rab11 was significantly reduced in the {sigma}2-adaptin mutant synapses. Consistent with the role of {sigma}2-adaptin and Rab11 in the regulation of the same signaling pathway, a mutation in Rab11 or overexpression of a GDP-locked form of Rab11 (Rab11S25N) phenocopies the morphological and signaling defects of the {sigma}2-adaptin mutants. Finally, we demonstrate that{sigma} 2-adaptin mutants show an accumulation of large vesicles and massive membranous structures, akin to endosomes at the synapse. Thus, we propose a model in which AP2 regulates Tkv internalization and recycling through a process that requires Rab11 activity to control the synaptic growth.


title: A comparative baseline of coral disease across the central Red Sea

abstract: The Red Sea is a unique environment for corals with a strong environmental gradient characterized by temperature extremes and high salinities, but minimal terrestrial runoff or riverine input and their associated pollution. Disease surveys were conducted along 22 reefs in the central Red Sea along the Saudi Arabian coast in October 2015, which coincided with a bleaching event. Our objectives were to 1) document types, prevalence, and distribution of coral diseases in a region with minimal terrestrial input, 2) compare regional differences in diseases and bleaching along a latitudinal gradient of environmental conditions, and 3) use histopathology to characterize disease lesions at the cellular level. Coral reefs of the central Red Sea had a widespread but a surprisingly low prevalence of disease (<0.5%), based on the examination of >75,750 colonies. Twenty diseases were recorded affecting 16 coral taxa and included black band disease, white syndromes, endolithic hypermycosis, skeletal eroding band, growth anomalies and focal bleached patches. The three most common diseases were Acropora white syndrome (59.1% of the survey sites), Porites growth anomalies (40.9%), and Porites white syndrome (31.8%). Over half of the coral genera within transects had lesions and corals from the genera Acropora, Millepora and Lobophyllia were the most commonly affected. Cell-associated microbial aggregates were found in four coral genera resembling patterns found in the Indo-Pacific. Differences in disease prevalence, coral cover, amount of heat stress as measured by degree heating weeks (DHW) and extent of bleaching was evident among sites. Disease prevalence was not explained by coral cover or DHW, and a negative relationship between coral bleaching and disease prevalence was found. The northern-most sites off the coast of Yanbu had the highest average DHW values but absence of bleaching and the highest average disease prevalence was recorded. Our study provides a foundation and baseline data for coral disease prevalence in the Red Sea, which is projected to increase as a consequence of increased frequency and severity of ocean warming.


title: Occasional paternal inheritance of the germline-restricted chromosome in songbirds

abstract: All songbirds have one special accessory chromosome1-4, the so-called germline-restricted chromosome (GRC)4-7, which is only present in germline cells and absent from all somatic tissues. Earlier work on the zebra finch (Taeniopygia guttata castanotis) showed that the GRC is inherited only through the female line4,6,8,9 - like mitochondrial DNA7,9-12 - and is eliminated from the sperm during spermatogenesis5,7,9-11. Here we show that the GRC can also be paternally inherited. Confocal microscopy using GRC-specific FISH probes indicated that a considerable fraction of sperm heads (1-19%) in zebra finch ejaculates still contained the GRC. In line with these cytogenetic data, sequencing of ejaculates revealed that individual males from two families differed strongly and consistently in the number of GRCs in their ejaculates. Examining a captive-bred population of hybrids of the two zebra finch subspecies (T. g. guttata and T. g. castanotis) revealed that the descendants inherited their mitochondria from a castanotis mother but their GRC from a guttata father. Moreover, GRC haplotypes across nine different castanotis matrilines showed at best a weak tendency to be co-inherited with mtDNA haplotypes. Within castanotis, the GRC showed little variability, while the mtDNA of matrilines was highly divergent. This suggests that a single GRC haplotype has recently spread across the entire castanotis population, crossing the matriline boundaries via paternal spillover. Our findings raise the possibility that certain GRC haplotypes could selfishly spread through the population, via additional paternal transmission, thereby outcompeting other GRC haplotypes that were limited to strict maternal inheritance, even if this was partly detrimental to organismal fitness.

category: genomics


title: Immune elicitation by sensing the conserved signature from phytocytokines and microbes via the Arabidopsis MIK2 receptor

abstract: Sessile plants encode a large number of small peptides and cell surface-resident receptor kinases, most of which have unknown functions. Here, we report that the Arabidopsis receptor kinase MALE DISCOVERER 1-INTERACTING RECEPTOR-LIKE KINASE 2 (MIK2) recognizes the conserved signature motif of SERINE RICH ENDOGENOUS PEPTIDEs (SCOOPs) from plants as well as proteins present in fungal Fusarium spp. and bacterial Comamonadaceae, and elicits potent immune responses. SCOOP signature peptides trigger diverse immune and physiological responses in a MIK2-dependent manner with a sub-nanomolar sensitivity and directly bind to the extracellular leucine rich-repeat domain of MIK2 in vivo and in vitro, indicating that MIK2 is the receptor of SCOOP peptides. Perception of SCOOP peptides induces the association of MIK2 and the coreceptors SOMATIC EMBRYOGENESIS RECEPTOR KINASE 3 (SERK3) and SERK4 and relays the signaling through the cytosolic receptor-like kinases BOTRYTIS-INDUCED KINASE 1 (BIK1) and AVRPPHB SUSCEPTIBLE1 (PBS1)-LIKE 1 (PBL1). Our study identified a unique plant receptor that bears a dual recognition capability sensing the conserved peptide motif from phytocytokines and microbial proteins via a convergent signaling relay to ensure a robust immune response.


title: A hetero-oligomeric remorin-receptor complex regulates plant development

abstract: Plant growth and development are modulated by both biotic and abiotic stress. Increasing evidence suggests that cellular integration of the corresponding signals occurs within preformed hubs at the plasma membrane called nanodomains. These membrane sub-compartments are organized by multivalent molecular scaffold proteins, such as remorins. Here, we demonstrate that Group 1 remorins form a hetero-oligomeric complex at the plasma membrane. While these remorins are functionally redundant for some pathways their multivalency also allows the recruitment of specific interaction partners. One of them, the receptor-like kinase REMORIN-INTERACTING RECEPTOR 1 (RIR1), that acts redundantly with the closely related receptor NILR2, is specifically recruited by REM1.2 in a phosphorylation-dependent manner. Overlapping developmental phenotypes suggest that the REM/RIR complex regulates key developmental pathways.


title: TRIPLE-NEGATIVE BREAST CANCER CELLS RECRUIT NEUTROPHILS BY SECRETING TGF-β AND CXCR2 LIGANDS

abstract: Tumor associated neutrophils (TANs) are frequently detected in triple-negative breast cancer (TNBC). Recent studies also reveal the importance of neutrophils in promoting tumor progression and metastasis during breast cancer. However, the mechanisms regulating neutrophil trafficking to breast tumors are less clear. We sought to determine whether neutrophil trafficking to breast tumors is determined directly by the malignant potential of cancer cells. We found that tumor conditioned media (TCM) harvested from highly aggressive, metastatic TNBC cells induced a polarized morphology and robust neutrophil migration, while TCM derived from poorly aggressive estrogen receptor positive (ER+) breast cancer cells had no activity. In a three-dimensional (3D) type-I collagen matrix, neutrophils migrated toward TCM from aggressive breast cancer cells with increased velocity and directionality. Moreover, in a neutrophil-tumor spheroid co-culture system, neutrophils migrated with increased directionality towards spheroids generated from TNBC cells compared to ER+ cells. Based on these findings, we next sought to characterize the active factors secreted by TNBC cell lines. We found that TCM-induced neutrophil migration is dependent on tumor-derived chemokines, and screening TCM elution fractions based on their ability to induce polarized neutrophil morphology revealed the molecular weight of the active factors to be around 12 kDa. TCM from TNBC cell lines contained copious amounts of GRO (CXCL1/2/3) chemokines and TGF-{beta} cytokines compared to ER+ cell-derived TCM. TCM activity was inhibited by simultaneously blocking receptors specific to GRO chemokines and TGF-{beta}, while the activity remained intact in the presence of either single receptor inhibitor. Together, our findings establish a direct link between the malignant potential of breast cancer cells and their ability to induce neutrophil migration. Our study also uncovers a novel coordinated function of TGF-{beta} and GRO chemokines responsible for guiding neutrophil trafficking to the breast tumor.


title: The coral symbiont Candidatus Aquarickettsia is variably abundant in threatened Caribbean acroporids and transmitted horizontally.

abstract: The aquatic symbiont "Candidatus Aquarickettsia rohweri" infects a diversity of non-bilaterian metazoan phyla. In the threatened coral Acropora cervicornis, Aquarickettsia proliferates in response to increased nutrient exposure, resulting in suppressed growth and increased disease susceptibility and mortality. This study evaluated the extent, as well as the ecology and evolution of Aquarickettsia infecting the Caribbean corals: Ac. cervicornis and Ac. palmata and their hybrid ( Ac. prolifera). The bacterial parasite Aquarickettsia was found in all acroporids, with host and sampling location impacting infection magnitude. Phylogenomic and genome-wide single nucleotide variant analysis found Aquarickettsia clustering by region, not by coral taxon. Fixation analysis suggested within coral colonies, Aquarickettsia are genetically isolated to the extent that reinfection is unlikely. Relative to other Rickettsiales, Aquarickettsia is undergoing positive selection, with Florida populations experiencing greater positive selection relative to the other Caribbean locations. This may be due to Aquarickettsia response to increased nutrient stress in Florida, as indicated by greater in situ replication rates in these corals. Aquarickettsia did not significantly codiversify with either coral animal nor algal symbiont, and qPCR analysis of gametes and juveniles from susceptible coral genotypes indicated absence in early life stages. Thus, despite being an obligate parasite, Aquarickettsia must be horizontally transmitted via coral mucocytes, an unidentified secondary host, or a yet unexplored environmentally mediated mechanism. Importantly, the prevalence of Aquarickettsia in Ac. cervicornis and high abundance in Florida populations suggests that disease mitigation efforts in the US and Caribbean should focus on preventing early infection via horizontal transmission.


title: BnaA03.WRKY28, interacting with BnaA09.VQ12, acts as a brake factor of activated BnWRKY33-mediated resistance outburst against Sclerotinia sclerotiorum in Brassica napus

abstract:
Sclerotinia sclerotiorum causes substantial damage to the growth of Brassica napus (rapeseed) and makes a significant loss of crop yield. The plant innate immune system may be the primary solution to defense against S. sclerotiorum for rapeseed. Here, we identify that BnWRKY33, a transcription factor in the innate immune pathway, can be rapidly phosphorylated and activated by the MAPK cascade after rapeseed is infected with S. sclerotiorum. In the MAPK cascade, activated BnaA03.MKK4 phosphorylates and activates BnaA06.MPK3 and BnaC03.MPK3. The activated BnMPK3 acts on the substrate BnWRKY33 to enhance its transcriptional activity and trigger a transcriptional burst of BnWRKY33, which helps plants effectively resist the pathogenic fungi by enhancing the expression of phytoalexin synthesis-related genes. With constant infection, BnaA03.WRKY28 and BnaA09.VQ12 are induced, and BnaA03.WRKY28 physically interacts with BnaA09.VQ12 to form a protein complex. BnaA03.WRKY28 preferentially binds to the promoter of BnWRKY33 with the help of BnaA09.VQ12. Compared with activated BnWRKY33, BnaA03.WRKY28 has a lower transcriptional activity on downstream BnWRKY33, which leads to weaker resistance against S. sclerotiorum for rapeseed in the later stage of infection. Furthermore, the induced BnaA03.WRKY28 may promote axillary bud activity and axillary meristem initiation by regulating the expression of branching-related genes (such as BnBRC1), thus promoting the formation of branches in the leaf axils.

One-sentence summaryUnder constant infection by Sclerotinia sclerotiorum, BnaA03.WRKY28 interacts with BnaA09.VQ12 and takes precedence over phosphorylated BnWRKY33 to bind to the BnWRKY33 promoter, thereby weakening resistance but promoting branching.


title: Adaptations and responses of the common dandelion to low atmospheric pressure in high altitude environments

abstract: Atmospheric pressure is an important, yet understudied factor that may shape plant ecology and evolution. By growing plants under controlled conditions at different experimental stations in the Swiss alps, we evaluated the impact of ecologically realistic atmospheric pressures between 660 and 950 hPa on the growth and defence of different dandelion populations. Low atmospheric pressure was associated with reduced root growth and defensive sesquiterpene lactone production. Defense suppression only occurred in populations originating from lower altitudes. Populations from higher altitudes constitutively produced less sesquiterpene lactones and did not suffer from suppression under low atmospheric pressure. We conclude that atmospheric pressure modulates root growth and defence traits, and that evolutionary history shapes plant phenotypic responses to atmospheric pressure. Our findings have important implications for our understanding of altitudinal gradients and the future use of plants as a source of food and bioactive metabolites in extraterrestrial habitats.


title: Another mystery snail in the Adirondacks: DNA barcoding reveals the first record of Sinotaia cf. quadrata (Caenogastropoda: Viviparidae) from North America

abstract: Alien molluscs pose a serious threat to global freshwater diversity and have been implicated in many ecosystem-altering invasion events over the past few decades. Biomonitoring surveys are therefore a key tool for ensuring biosecurity in diversity hotspots and vulnerable habitats. In this study, we use DNA barcoding to provide the first record of the viviparid, Sinotaia cf. quadrata from North America. Reciprocal monophyly and low genetic divergence (uncorrected p-distance: 0.004) with a Bellamya quadrata individual from the type region (China) provides strong support for this identification. The species was recovered as part of a routine biomonitoring survey of the Adirondack region of northern New York. Only three adults were recovered (no populations or juveniles) indicating that the discovery represents a very recent arrival. Considering the proximity of the sampling site from the massive St. Lawrence River, it is likely that S. cf. quadrata was introduced into the St. Lawrence, probably via the aquarium plant trade, and was able to spread into smaller river system in northern New York and possibly other border states. This record represents the fourth alien viviparid, the third of which is of Asian origin, that have made its way to New York waters. Future biomonitoring efforts for the upcoming summer period will involve targeted searches for S. cf. quadrata to determine the extent of its spread in the region.


title: mTOR repression in response to amino acid starvation promotes ECM degradation through MT1-MMP endocytosis arrest

abstract: Under conditions of starvation, normal and tumor epithelial cells can rewire their metabolism towards the consumption of extracellular matrix-derived components as nutrient sources. The mechanism of pericellular matrix degradation by starved cells has been largely overlooked. Here we show that matrix degradation by breast and pancreatic tumor cells and patient-derived xenograft explants increases by one order of magnitude upon amino acid and growth factor deprivation. In addition, we found that collagenolysis requires the invadopodia components, TKS5 and the transmembrane metalloproteinase, MT1-MMP, which are key to the tumor invasion program. Increased collagenolysis is controlled by mTOR repression upon nutrient depletion or pharmacological inhibition by rapamycin. Our results reveal that starvation hampers clathrin-mediated endocytosis, resulting in MT1-MMP accumulation in arrested clathrin-coated pits. Our study uncovers a new mechanism whereby mTOR repression in starved cells leads to the repurposing of abundant plasma membrane clathrin-coated pits into robust ECM-degradative assemblies.