title: Shiftless Restricts Viral Gene Expression and Influences RNA Granule Formation during KSHV lytic replication.

abstract:
Herpesviral infection reflects thousands of years of co-evolution and the constant struggle between virus and host for control of cellular gene expression. During Kaposis sarcoma-associated herpesvirus (KSHV) lytic replication, the virus rapidly seizes control of host gene expression machinery by triggering a massive RNA decay event via a virally-encoded endoribonuclease, SOX. This virus takeover strategy decimates close to 80% of cellular transcripts, reallocating host resources toward viral replication. The host cell, however, is not entirely passive in this assault on RNA stability. A small pool of host transcripts that actively evade SOX cleavage has been identified over the years. One such "escapee", C19ORF66 (herein referred to as Shiftless - SHFL) encodes a potent anti-viral protein capable of restricting the replication of multiple DNA, RNA, and retroviruses including KSHV. Here, we show that SHFL restricts KSHV replication by targeting the expression of critical viral early genes, including the master transactivator protein, KSHV ORF50, and thus subsequently the entire lytic gene cascade. Consistent with previous reports, we found the SHFL interactome throughout KSHV infection is dominated by RNA-binding proteins that influence both translation and protein stability, including the viral protein ORF57, a crucial regulator of viral RNA fate. We next show that SHFL affects cytoplasmic RNA granule formation, triggering the disassembly of processing bodies. Taken together, our findings provide insights into the complex relationship between RNA stability, RNA granule formation, and the anti-viral response to KSHV infection.

SignificanceIn the past five years, SHFL has emerged as a novel and integral piece of the innate immune response to viral infection. SHFL has been reported to restrict the replication of multiple viruses including several flaviviruses and the retrovirus HIV-1. However, to date, the mechanism(s) by which SHFL restricts DNA virus infection remains largely unknown. We have previously shown that following its escape from KSHV-induced RNA decay, SHFL acts as a potent anti-viral factor, restricting nearly every stage of KSHV lytic replication. In this study, we set out to determine the mechanism by which SHFL restricts KSHV infection. We demonstrate that SHFL impacts all classes of KSHV genes and found that SHFL restricts the expression of several key early genes, including KSHV ORF50 and ORF57. We then mapped the interactome of SHFL during KSHV infection and found several host and viral RNA-binding proteins that all play crucial roles in regulating RNA stability and translation. Lastly, we found that SHFL expression influences RNA granule formation both outside of and within the context of KSHV infection, highlighting its broader impact on global gene expression. Collectively, our findings highlight a novel relationship between a critical piece of the anti-viral response to KSHV infection and the regulation of RNA-protein dynamics.


title: Babesia divergens egress from host cells is orchestrated by essential and druggable kinases and proteases

abstract:
A unique aspect of apicomplexan biology is the requirement for egress from and invasion into host red blood cells (RBCs). The cellular mechanisms and molecular mediators of RBC egress and invasion remain poorly characterized in Babesia spp., a group of parasites of veterinary importance and emerging cause of zoonotic disease. Through the use of video microscopy, transcriptomics, and chemical genetics we have implicated signaling, proteases and gliding motility in egress and/or invasion by Babesia divergens. We developed CRISPR/Cas9 and two inducible knockdown systems to perform a genetic screen of putative mediators of egress. We found that proteases ASP2 and ASP3 are required for invasion, and the latter is also required for egress. Strikingly, parasites continue to replicate intracellularly in the absence of the protein kinases, PKG or CDPK4, indicating that they are required for exit from the replication cycle and egress. These essential molecules present druggable targets for Babesia spp. All together we have established a molecular framework for the spread of infection through host RBCs, with egress of B. divergens more closely resembling T. gondii than the more evolutionarily related Plasmodium spp.

HighlightsO_LIEgress in Babesia divergens requires host cell lysis and parasite motility
C_LIO_LITranscriptomics can be used to identify egress and invasion proteins
C_LIO_LIKnockdown of the proteases, ASP2 and ASP3, inhibit egress and invasion
C_LIO_LIInhibition of PKG or CDPK4 signaling results in continued intracellular replication
C_LI

category: microbiology


title: Hinokitiol alters Gene Expression in Aspergillus fumigatus, protects against fungal keratitis by Reducing Fungal Load, LOX-1, Proinflammatory cytokines and Neutrophil Infiltration

abstract:
Hinokitiol (HK), a tropolone-related compound found in cupressaceous plants, has antifungal and anti-inflammatory properties. But its roles in Aspergillus fumigatus ( A.F. ) keratitis remains unknown. This study examined the antifungal activity of HK against A.F. and investigated its possible mechanisms at the ultrastructural and transcriptional levels. We tested the minimum inhibitory concentration (MIC) of HK against A.F.. Our data showed that the MIC50 was 2 g/ml and MIC90 was 8 g/ml, and HK could significantly inhibit the spore germination and mycelial growth of A.F.. Scanning electron microscopy (SEM) and transmission electron microscopy (TEM) observations showed that HK induced significant changes in hyphal morphology and microstructure, including cell membrane rupture and intracellular structural disorder. Adhesion assay and biofilm assay experiments showed that HK reduced the adhesion of spores to human corneal epithelial cells (HCECs) and inhibited the formation of biofilms. The genetic changes of A.F. after HK treatment were analyzed by RNA sequencing, and a total of 2487 differentially expressed genes (DEGs) were identified, including the down-regulated DEGs related to carbohydrate and various amino acid metabolism, ribosome biogenesis, asexual reproduction, and up-regulated DEGs related to steroid biosynthesis through GO and KEGG enrichment analysis. RNA-seq results suggested that HK may play an antifungal effect by destroying the structural integrity of its wall and membrane, inhibiting protein biosynthesis and the growth and reproduction of A.F..10 g/ml HK, which had no effect on proliferation and migration of HCECs, was used in the treatment of murine fungal keratitis (FK). We found that HK eyedrop treatment could reduce the severity of FK by reducing corneal fungal burden, neutrophil infiltration, and the expression of LOX-1 and pro-inflammatory factors. HK is expected to be a safe and effective new drug for FK treatment.

Author summaryFK is a serious common blind-causing eye disease. The current clinical antifungal drugs have the disadvantages of low bioavailability and high corneal toxicity, which greatly limit the clinical effectiveness. Therefore, there is an urgent need for a new, safe and effective treatment for FK. HK had shown great antifungal capacity against A.F., amazingly well anti-inflammatory effect and real improvement in murine FK in our research. These findings provide a theoretical basis for the application of HK as an antifungal drug and reveal the potential of HK to be applied in the clinical treatment of FK.


title: Aquatic long-term persistence of  Francisella tularensis  ssp.  holarctica  is driven by water temperature and transition to a viable but non-culturable state

abstract: Francisella tularensis is a highly virulent bacterium causing tularemia zoonosis. An increasing proportion of infections occur through contaminated hydro-telluric sources, especially for the subspecies holarctica (Fth). Although this bacterium has been detected in several aquatic environments, the mechanisms of its long-term persistence in water are not yet elucidated. We evaluated the culturability and the viability of a virulent Fth strain in independent microcosms filled with nutrient-poor water. At 37{degrees}C, the bacteria remained culturable for only one week, while culturability was extended to 6 weeks at 18{degrees}C and up to 11 weeks at 4{degrees}C. However, while the viability of the bacteria declined similarly to culturability at 37{degrees}C, the viability of the bacteria remained stable overtime at 18{degrees}C and 4{degrees}C for more than 24 months, long after loss of culturability. We identified water temperature as one of the major factors driving the aquatic survival of Fth through a transition of the whole Fth population in a viable but non-culturable (VBNC) state. Low temperature of water ([≤]18{degrees}C) favors the persistence of the bacteria in a VBNC state, while a temperature above 30{degrees}C kills culturable and VBNC Fth bacteria. These findings provide new insights into the environmental cycle of Francisella tularensis that suggest that the yet unidentified primary reservoir of the subspecies holarctica may be the aquatic environment itself in which the bacteria could persist for months or years without the need for a host.


title: The effect of cytoskeleton inhibitors on coccolith morphology in Coccolithus braarudii and Scyphosphaera apsteinii

abstract: The calcite platelets of coccolithophores (Haptophyta), the coccoliths, are among the most elaborate biomineral structures. How these unicellular algae accomplish the complex morphogenesis of coccoliths is still largely unknown. It has long been proposed that the cytoskeleton plays a central role in shaping the growing coccoliths. Previous studies have indicated that disruption of the microtubule network led to defects in coccolith morphogenesis in Emiliania huxleyi and Coccolithus braarudii. Disruption of the actin network also led to defects in coccolith morphology in E. huxleyi, but its impact on coccolith morphology in C. braarudii was less clear, as coccolith secretion was largely inhibited under the conditions used. A more detailed examination of the role of actin and microtubule networks is therefore required to address the wider role of the cytoskeleton in coccolith morphogenesis. In this study, we have examined coccolith morphology in C. braarudii and Scyphosphaera apsteinii following treatment with the microtubule inhibitors vinblastine and colchicine (S. apsteinii only) and the actin inhibitor cytochalasin B. We found that all cytoskeleton inhibitors induced coccolith malformations, strongly suggesting that both microtubules and actin filaments are instrumental in morphogenesis. By demonstrating the requirement for the microtubule and actin networks in coccolith morphogenesis in diverse species, our results suggest that both of these cytoskeletal elements are likely to play conserved roles in defining coccolith morphology.


title: The Chlamydia protein CpoS modulates the inclusion microenvironment and restricts the interferon response by acting on Rab35

abstract: The obligate intracellular bacterium Chlamydia trachomatis inserts into the membrane of its vacuole (the inclusion) a family of poorly characterized Inc proteins. While the Inc CpoS was recently revealed as a critical suppressor of host cellular immune surveillance, the underlying mechanism remained unknown. By complementing a cpoS mutant with modified variants of CpoS, we found that CpoS blocks distinct cellular defense responses through distinct mechanisms. Specifically, we show that the ability of CpoS to interact with Rab GTPases is not only instrumental to its ability to mediate lipid transport to the inclusion, but also key to CpoS-mediated inhibition of type I interferon responses. Indeed, depletion of Rab35 can phenocopy the respective defect of the cpoS mutant. Unexpectedly, we found that CpoS is also essential for the formation of inclusion microdomains that control the spatial organization of multiple Incs involved in signaling and modulation of the host cellular cytoskeleton. Overall, our findings highlight the modulation of membrane trafficking as a pathogenic immune evasion strategy and the role of Inc-Inc interactions in shaping the inclusion microenvironment.


title: m6a governs length-dependent enrichment of mRNAs in stress granules

abstract: Stress granules are biomolecular condensates composed of protein and mRNA. Long mRNAs are enriched in stress granules, which is thought to reflect the ability of long mRNAs to form multiple RNA-RNA interactions with other mRNAs. RNA-RNA interactions are thus thought to be critical for stress granule formation. Stress granule-enriched mRNAs also often contain multiple N6-methyladenosine (m6A) residues. YTHDF proteins bind m6A, creating mRNA-protein complexes that partition into stress granules. Here we determine the basis of length-dependent enrichment of mRNAs in stress granules. We show that depletion of m6A is sufficient to abrogate the length-dependent enrichment of mRNAs in stress granules. We show that the presence of m6A predicts which mRNAs are enriched. m6A formation is triggered by long exons, which are often found in long mRNAs, accounting for the link between m6A, length and stress granule enrichment. Thus, length-dependent enrichment of mRNAs in stress granules is driven by YTHDF-mRNA interactions.

category: molecular biology


title: Contribution of spontaneous mutations to quantitative and molecular variation at the highly repetitive rDNA locus in yeast

abstract: The ribosomal DNA array in Saccharomyces cerevisiae consists of many tandem repeats whose copy number is believed to be functionally important but highly labile. Regulatory mechanisms have evolved to maintain copy number by directed mutation, but how spontaneous variation at this locus is generated and selected has not been well characterized. We applied a mutation accumulation approach to quantify the impacts of mutation and selection on this unique genomic feature across hundreds of mutant strains. We find that mutational variance for this trait is relatively high, and that un-selected mutations throughout the genome can disrupt copy number maintenance. In consequence, copy number generally declines, consistent with a model of regulation where copy number is normally increased when low. This pattern holds across ploidy levels and strains in the standard lab environment, but differs under some stressful conditions. We identify several alleles, gene categories and genomic features that likely affect copy number, including aneuploidy for chromosome XII. Copy number change is associated with reduced growth in diploids, consistent with stabilizing selection. Levels of standing variation in copy number are well predicted by a balance between mutation and stabilizing selection, suggesting this trait is not subject to strong diversifying selection in the wild. The rate and spectrum of point mutations within the rDNA locus itself is distinct from the rest of the genome, and predictive of polymorphism locations. Our findings help differentiate the roles of mutation and selection and indicate that spontaneous mutation patterns shape several aspects of ribosomal DNA evolution.

category: genetics


title: Benchmarking Polygenic Risk Score Model Assumptions: towards more accurate risk assessment

abstract:
Polygenic risk scores represent an individuals genetic susceptibility to a phenotype. Like with any models, statistical models commonly employed to fit polygenic risk scores and assess their accuracy contain several assumptions. The effects of these assumptions on models of polygenic risk score have not been thoroughly assessed.

We assessed 26 variations of the traditional polygenic risk score model, each of which mitigate assumptions in one of five facets of disease modelling: representation of age (6 variations), censorship (3 variations), competing risks (7 variations), formation of disease labels (6 variations), and selection of covariates (4 variations). With data from the UK Biobank, each model variation included age, sex, and a polygenic risk score derived from the PGS Catalog. Each of the 26 model variations were fitted to predict 18 diseases. Compared to the plain model that contained all five facets of assumptions, the model variations often fit the data better and generated predictions that largely differed from the predictions of the plain model. The statistic Roystons R2 measured a models goodness of fit, and thereby determined if the model was an enhancement upon the plain model. For 15 of the 26 model variations Roystons R2 was greater than that of the plain model for >50% of diseases. Reclassification rates, defined as the fraction of individuals in the top five percentiles of the plain models predictions who are not in the top five percentiles of a model variations predictions, was used to determine if the variation led to significantly different predictions. For 20 of the 26 model variations the median reclassification rate calculated across the 18 diseases was greater than 10%. Comparisons of accuracy statistics further illustrated how much each model variations predictions differed from the plain models predictions.

Models containing polygenic risk scores appear to be significantly affected by many common modelling assumptions. Therefore, future investigations should consider taking some action to mitigate modelling assumptions.

Author SummaryAn individuals genetics can increase their risk of experiencing a disease. The exact magnitude of the increased risk is estimated within a statistical model. The traditional model type employed in this process is relatively plain and contains several assumptions. The predicted risk estimates from this plain model may be unnecessarily inaccurate. To test this possibility, we searched the literature for model variations that reduce the assumptions of the plain model, ultimately creating 26 distinct model variations that may improve upon the plain model. Each model variation was fit with data from the UK Biobank to predict 18 diseases. We found that 15 of the 26 models variations fit the data better than the plain model for a majority of diseases. Goodness of fit was measured with Roystons R2 statistic. Further calculations found that the predictions of the model variations were often significantly more or less accurate than the predictions of the plain model. We believe these results indicate that future investigations of polygenic risk scores should not employ the plain model, as unreliable risk predictions will likely result.

category: genomics


title: DJ-1 glyoxalase activity makes a modest contribution to cellular defense against methylglyoxal damage in neurons

abstract: Human DJ-1 is a cytoprotective protein whose absence causes Parkinsons disease and is also associated with other diseases. DJ-1 has an established role as a redox-regulated protein that defends against oxidative stress and mitochondrial dysfunction. Multiple studies have suggested that DJ-1 is also a protein/nucleic acid deglycase that plays a key role in the repair of glycation damage caused by methylglyoxal (MG), a reactive -keto aldehyde formed by central metabolism. Contradictory reports suggest that DJ-1 is a glyoxalase but not a deglycase and does not play a major role in glycation defense. Resolving this issue is important for understanding how DJ-1 protects cells against insults that can cause disease. We find that DJ-1 reduces levels of reversible adducts of MG with guanine and cysteine in vitro. The steady-state kinetics of DJ-1 acting on reversible hemithioacetal substrates are fitted adequately with a computational kinetic model that requires only a DJ-1 glyoxalase activity, supporting the conclusion that deglycation is an apparent rather than a true activity of DJ-1. Sensitive and quantitative isotope-dilution mass spectrometry shows that DJ-1 modestly reduces the levels of some irreversible guanine and lysine glycation products in primary and cultured neuronal cell lines and whole mouse brain, consistent with a small but measurable effect on total neuronal glycation burden. However, DJ-1 does not improve cultured cell viability in exogenous MG. In total, our results suggest that DJ-1 is not a deglycase and has only a minor role in protecting neurons against methylglyoxal toxicity.

category: biochemistry


title: Development of a Novel Peptide Aptamer that Interacts with the eIF4E Capped-mRNA Binding Site using Peptide Epitope Linker Evolution (PELE).

abstract: Identifying new binding sites and poses that modify biological function are an important step towards drug discovery. We have identified a novel disulphide constrained peptide that interacts with the cap-binding site of eIF4E, an attractive therapeutic target that is commonly overexpressed in many cancers and plays a significant role in initiating a cancer specific protein synthesis program though binding the 5cap (7methyl-guanoisine) moiety found on mammalian mRNAs. The use of disulphide constrained peptides to explore intracellular biological targets is limited by their lack of cell permeability and the instability of the disulphide bond in the reducing environment of the cell, loss of which results in abrogation of binding. To overcome these challenges, the cap-binding site interaction motif was placed in a hypervariable loop on an VH domain, and then selections performed to select a molecule that could recapitulate the interaction of the peptide with the target of interest in a process termed Peptide Epitope Linker Evolution (PELE). A novel VH domain was identified that interacted with the eIF4E cap binding site with a nanomolar affinity and that could be intracellularly expressed in mammalian cells. Additionally, it was demonstrated to specifically modulate eIF4E function by decreasing cap-dependent translation and cyclin D1 expression, common effects of eIF4F complex disruption.


title: A protein semisynthesis-based strategy to probe the impact of site-specific serine ADP-ribosylation on linker histone function

abstract: Recently developed chemical and enzyme-based technologies to install serine ADP-ribosylation onto synthetic peptides have enabled new approaches to study PARP biology. Here, we establish a generalizable strategy to prepare ADP-ribosylated peptides that are compatible with N-terminal, C-terminal and sequential protein ligation reactions. Two unique protein-assembly routes are employed to generate full-length linker histone constructs that are homogenously ADP-ribosylated at known DNA damage-dependent modification sites. We found that serine mono-ADP-ribosylation is sufficient to alleviate linker histone-dependent chromatin compaction, and that this effect is amplified by ADP-ribose chain elongation. Our work will greatly expand the scope of ADP-ribose-modified proteins that can be constructed via semisynthesis, which is rapidly emerging as a robust approach to elucidate the direct effects that site-specific serine mono- and poly-ADP-ribosylation have on protein function.


title: Single-particle cryo-EM analysis of the shell architecture and internal organization of an intact α-carboxysome

abstract: Carboxysomes are proteaceous bacterial microcompartments (BMCs) that sequester the key enzymes for carbon fixation in cyanobacteria and some proteobacteria. They consist of a virus-like icosahedral shell, encapsulating carbonic anhydrase and ribulose 1,5-bisphosphate carboxylase/oxygenase (RuBisCO), which catalyses the dehydration of bicarbonate into CO2, the first step of the Calvin-Benson-Bassham cycle. Despite their significance in carbon fixation and great bioengineering potentials, the structural characterization of native carboxysomes, including the shell and the internal organization, is currently limited to low-resolution tomography studies. Notably, the degree of heterogeneity of the shell, and the internal arrangement of enzymes, remain poorly understood. Here, we report the structural characterization of a native -carboxysome from a marine cyanobacterium by single-particle cryo-EM. We determine the structure of RuBisCO enzyme at 2.9 [A] resolution. In addition, we obtain low-resolution maps of the icosahedral protein shell and the concentric interior organisation. In combination with artificial intelligence (AI)-driven modelling approaches, we exploited these maps to propose a complete atomic model of an intact carboxysome. This study provides insight into carboxysome structure and protein-protein interactions involved in carboxysome assembly. Advanced knowledge about carboxysome architecture and structural plasticity is critical for not only a better understanding of biological carbon fixation mechanism but also repurposing carboxysomes in synthetic biology for biotechnological applications.

category: biophysics


title: Changing flows balance nutrient absorption and bacterial growth along the gut

abstract: Small intestine motility and its ensuing flow of luminal content impact both nutrient absorption and bacterial growth. To explore this interdependence we introduce a biophysical description of intestinal flow and absorption. Rooted in observations of mice we identify the average flow velocity as the key control of absorption efficiency and bacterial growth, independently of the exact contraction pattern. We uncover self-regulation of contraction and flow in response to nutrients and bacterial levels to promote efficient absorption while restraining detrimental bacterial overgrowth.


title: IRF4 deficiency vulnerates B cell progeny for leukemogenesis via somatically acquired Jak3 mutations conferring IL-7 hypersensitivity

abstract: The processes leading from disturbed B cell development to adult B cell progenitor acute lymphoblastic leukemia (BCP-ALL) are poorly understood. Here, we describe Irf4-/- mice as prone to developing BCP-ALL with age. Irf4-/- preB-I cells exhibited impaired differentiation but enhanced proliferation in response to IL-7, along with reduced retention in the IL-7 providing bone marrow niche due to decreased CXCL12 responsiveness. Thus selected, preB-I cells acquired Jak3 mutations, probably following irregular AID activity, resulting in malignant transformation. We demonstrate heightened IL-7 sensitivity due to Jak3 mutants, devise a model to explain it and describe structural and functional similarities to Jak2 mutations often occurring in human Ph-like ALL. Finally, targeting JAK signaling with Ruxolitinib in vivo prolonged survival of mice bearing established Irf4-/- leukemia. Intriguingly, organ infiltration including leukemic meningeosis was selectively reduced without affecting blood blast counts. In this work, we present spontaneous leukemogenesis following IRF4 deficiency with potential implications for high-risk BCP-ALL in adult humans.

category: cancer biology


title: Rapid GPR183-mediated recruitment of eosinophils to the lung after Mycobacterium tuberculosis infection

abstract:
Influx of eosinophils into the lungs is typically associated with type-II responses during allergy, fungal and parasitic infections. However, we previously reported that eosinophils accumulate in lung lesions during type-I inflammatory responses to Mycobacterium tuberculosis (Mtb) in humans, macaques, and mice where they contribute to host resistance. Here we show eosinophils migrate into the lungs of macaques and mice as early as one week after Mtb-exposure. In mice this influx was CCR3 independent and instead required cell-intrinsic expression of the oxysterol-receptor GPR183, which is highly expressed on human and macaque eosinophils. Murine eosinophils interacted directly with bacilli-laden alveolar macrophages, which upregulated the oxysterol-synthesizing enzyme Ch25h, and eosinophil recruitment was impaired in Ch25h deficient mice. Our findings show that eosinophils are among the first cells from circulation to sense and respond to Mtb infection of alveolar macrophages and reveal a novel role for GPR183 in the migration of eosinophils into lung tissue.

O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=200 SRC="FIGDIR/small/480919v1_ufig1.gif" ALT="Figure 1">
View larger version (105K):
org.highwire.dtl.DTLVardef@e8cd29org.highwire.dtl.DTLVardef@1f5769borg.highwire.dtl.DTLVardef@3dce9borg.highwire.dtl.DTLVardef@1c75587_HPS_FORMAT_FIGEXP  M_FIG C_FIG HIGHLIGHTSIn mice and macaques eosinophils accumulate early in Mtb-infected lungs preceding neutrophils Eosinophils interact with Mtb-infected cells in the alveoli in mice
Early pulmonary eosinophil migration occurs independently of CCR3 in mice
Early lung migration in mice requires Ch25h and eosinophil-intrinsic GPR183 expression

category: immunology


title: Genome-wide analyses of histone modifications and chromatin accessibility reveal the distinct genomic compartments in the Irish potato famine pathogen Phytophthora infestans

abstract:
Phytophthora infestans, the causal agent of potato late blight, is a devastating plant disease that leads to Irish potato famine and threatens world-wide food security. Despite the genome of P. infestans has provided fundamental resource for studying the aggressiveness of this pandemic pathogen, the epigenomes remain poorly understood. Here, utilizing liquid chromatography-tandem mass spectrometry (LC-MS/MS), we demonstrate post-translational modifications (PTM) at P. infestans core histone H3. The PTMs not only include these prevalent modifications in eukaryotes, and also some novel marks, such as H3K53me2 and H3K122me3. We focused on the trimethylations of H3K4, H3K9 and H3K27 and H3K36, and profiled P. infestans epigenomes employing Native Chromatin Immunoprecipitation followed by sequencing (N-ChIP-seq). In parallel, we mapped P. infestans chromomatin accessibility by Assay for Transposase-Accessible Chromatin with high-throughput sequencing (ATAC-seq). We found that adaptive genomic compartments display significantly higher levels of H3K9me3 and H3K27me3, and are generally in condense chromatin. Interestingly, we observed that genes encoding virulence factors, such as effectors, are enriched in open chromatin regions that barely have the four histone modifications. With a combination of genomic, epigenomic, transcriptomic strategies, our study illustrates the epigenetic states in P. infestans, which will help to study genomic functions and regulations in this pathogen.

Author summaryEpigenetics play an important role in various biological processes of eukaryotes, including pathogenicity of plant pathogens. However, the epigenetic landscapes are marginally known in oomycetes that are fungal-like organisms and comprise lots of destructive plant pathogens. In this study, using the Irish potato famine pathogen Phytophthora infestans as a model, we conducted genome-wide studies of histone post modifications and chromatin accessibility, and demonstrate the relationship of gene expression and evolution with the epigenetic marks. We found that one of the most important classes of virulence proteins, effectors, are enriched in open chromatin regions that barely have eu- and hetero-chromatic marks. This study provides an overview of the oomycete epigenetic atlas, and advances our understanding of the regulation of virulence factors in plant pathogens.


title: Species-Specific Formation of Paraspeckles in Intestinal Epithelium Revealed by Characterization of NEAT1 in Naked Mole-rat

abstract: Paraspeckles are mammalian-specific nuclear bodies built on the long noncoding RNA NEAT1_2. The molecular mechanisms of paraspeckle formation have been mainly studied using human or mouse cells, and it is not known if the same molecular components are involved in the formation of paraspeckles in other mammalian species. We thus investigated the expression pattern of NEAT1_2 in naked mole-rats (nNEAT1_2), which exhibit extreme longevity and lower susceptibility to cancer. In the intestine, nNEAT1_2 is widely expressed along the entire intestinal epithelium, which is different from the expression of mNeat1_2, that is restricted to the cells of the distal tip in mice. Notably, the expression of FUS, a FET family RNA binding protein, essential for the formation of paraspeckles both in humans and mice, was absent in the distal part of the intestinal epithelium in naked mole-rats. Instead, mRNAs of other FET family proteins EWSR1 and TAF15 were expressed in the distal region. Exogenous expression of these proteins in Fus-deficient murine embryonic fibroblast cells rescued the formation of paraspeckles. These observations suggest that nNEAT1_2 recruits different set of RNA binding proteins in a cell type-specific manner during the formation of paraspeckles in different organisms.


title: Population structure and inbreeding in wild house mice (Mus musculus) at different geographic scales

abstract: House mice (Mus musculus) have spread globally as a result of their commensal relationship with humans. In the form of laboratory strains, both inbred and outbred, they are also among the most widely-used model organisms in biomedical research. Although the general outlines of house mouse dispersal and population structure are well known, details have been obscured by either limited sample size or small numbers of markers. Here we examine ancestry, population structure and inbreeding using SNP microarray genotypes in a cohort of 814 wild mice spanning five continents and all major subspecies of Mus, with a focus on M. m. domesticus. We find that the major axis of genetic variation in M. m. domesticus is a south-to-north gradient within Europe and the Mediterranean. The dominant ancestry component in North America, Australia, New Zealand and various small offshore islands is of northern European origin. Next we show that inbreeding is surprisingly pervasive and highly variable, even between nearby populations. By inspecting the length distribution of homozygous segments in individual genomes, we find that inbreeding in commensal populations is mostly due to consanguinity. Our results offer new insight into the natural history of an important model organism for medicine and evolutionary biology.


title: Structural insights into Charcot-Marie-Tooth disease-linked mutations in human GDAP1

abstract: Charcot-Marie-Tooth disease (CMT) is the most common inherited peripheral polyneuropathy in humans, and its different subtypes are linked to mutations in dozens of different genes. Mutations in ganglioside-induced differentiation-associated protein 1 (GDAP1) cause two types of CMT, demyelinating CMT4A and axonal CMT2K. The GDAP1-linked CMT genotypes are mainly missense point mutations. Despite clinical profiling and in vivo studies on the mutations, the etiology of GDAP1-linked CMT is poorly understood. Here, we describe the biochemical and structural properties of the Finnish founding CMT2K mutation H123R as well as CMT2K-linked R120W, both of which are autosomal dominant mutations. The disease variant proteins retain close to normal structure and solution behaviour, but both present a large decrease in thermal stability. Using GDAP1 variant crystal structures, we identify a side chain interaction network between helices 3, 6, and 7, which is affected by CMT mutations, as well as a hinge in the long helix 6, which is linked to structural flexibility. Structural analysis of GDAP1 indicates that CMT may arise from disruption of specific intra- and intermolecular interaction networks, leading to alterations in GDAP1 structure and stability, and eventually, insufficient motor and sensory neuron function.


title: Multi-eGO: an in-silico lens to look into protein aggregation kinetics at atomic resolution

abstract:
Protein aggregation into amyloid fibrils is the archetype of aberrant biomolecular self-assembly processes, with more than 50 diseases associated that are mostly uncurable. Understanding aggregation mechanisms is thus of fundamental importance and goes in parallel with the characterization of the structures of the transient oligomers formed in the process. Oligomers have been proven elusive to high-resolution structural techniques, while the large sizes and long-time scales typical of aggregation processes have limited, so far, the use of computational methods. To surmount these limitations, we introduce here multi-eGO, an atomistic, hybrid structure-based model, which leveraging on the knowledge of monomers conformational dynamics and of fibril structures, can efficiently capture the essential structural and kinetics aspects of protein aggregation. Multi-eGO molecular dynamics simulations can describe the aggregation kinetics of thousands of monomers. The concentration dependence of the simulated kinetics, as well as the structural features of the resulting fibrils, are in qualitative agreement with in vitro experiments on an amyloidogenic peptide of Transthyretin, a protein responsible for one of the most common cardiac amyloidosis. Multi-eGO simulations allow to observe in time and at atomic resolution the formation of primary nuclei in a sea of transient lower order oligomers, to follow their growth and the subsequent secondary nucleation events, till the maturation of multiple fibrils. Multi-eGO, combined with the many experimental techniques deployed to study protein aggregation, can provide the structural basis needed to advance the design of molecules targeting amyloidogenic diseases.

Significance StatementAlzheimers and Parkinsons diseases are uncurable pathologies associated to the aberrant aggregation of specific proteins into amyloid fibrils. Understanding the mechanism leading to protein aggregation, by characterizing the structures of the oligomeric species populated in the process, would have a tremendous impact on the design of therapeutic molecules. We propose that a structure-based approach to molecular dynamics simulations can allow following at high resolution the aggregation kinetics of thousands of monomers. Having shown that simulations can describe the aggregation of a Transthyretin amyloidogenic peptide, we demonstrate how their efficiency allows acquiring a wealth of structural information. We foresee that integrating the latter with the many techniques developed to study protein aggregation will support the design of molecules to modulate amyloidogenesis.


title: ABPP-HT* - Deep meets fast for activity-based profiling of deubiquitylating enzymes using advanced DIA and DDA mass spectrometry methods

abstract: Activity-based protein profiling (ABPP) uses a combination of activity-based chemical probes with mass spectrometry (MS) to selectively characterise a particular enzyme or enzyme class. ABPP has proven invaluable for profiling enzymatic inhibitors in drug discovery. When applied to cell extracts and cells, challenging the ABP-enzyme complex formation with a small molecule can simultaneously inform on potency, selectivity, reversibility/binding affinity, permeability, and stability. ABPP can also be applied to pharmacodynamic studies to inform on cellular target engagement within specific organs when applied to in vivo models. Recently, we established separate high depth and high throughput ABPP (ABPP-HT) protocols for the profiling of deubiquitylating enzymes (DUBs). However, the combination of the two, deep and fast, in one method has been elusive. To further increase the sensitivity of the current ABPP-HT workflow we implemented state-of-the-art data-independent acquisition (DIA) and data-dependent acquisition (DDA) MS analysis tools. Hereby, we describe an improved methodology, ABPP-HT* (enhanced high-throughput-compatible activity-based protein profiling), that in combination with DIA MS methods allowed for the consistent profiling of 35-40 DUBs and provided a reduced number of missing values, whilst maintaining a throughput of 100 samples per day.


title: ABPP-HT* - Deep meets fast for activity-based profiling of deubiquitylating enzymes using advanced DIA mass spectrometry methods


title: The Effect of Lipid Composition on the Dynamics of Tau Fibrils

abstract: Knowledge of the interaction of the tau fibrils with the cell membrane is critical for the understanding of the underlying tauopathy pathogenesis. Lipid composition is found to effect the conformational ensemble of the tau fibrils. Using coarse grained and all-atom molecular dynamics simulations we have shown the effect of the lipid composition in modulating the tau structure and dynamics. Molecular dynamics simulations show that tau proteins interact differentially with the zwitterionic compared to the charged lipid membranes. The negatively charged POPG lipid membranes increase the binding affinity of the tau fibrils. The addition of cholesterol is also found to modify the tau binding to the membrane.


title: Using Mathematical Modeling to Distinguish Intrinsic and Acquired Targeted Therapeutic Resistance in Head and Neck Cancer

abstract: The promise of precision medicine has been limited by the pervasive therapeutic resistance to many targeted therapies for cancer. Inferring the timing (i.e., pre-existing or acquired) and mechanism (i.e., drug-induced) of such resistance is crucial for designing effective new therapeutics. This paper studies the mechanism and timing of cetuximab resistance in head and neck squamous cell carcinoma (HNSCC) using tumor volume data obtained from patient-derived tumor xenografts. We propose a family of mathematical models, with each member of the family assuming a different timing and mechanism of resistance. We present a method for fitting these models to individual volumetric data, and utilize model selection and parameter sensitivity analyses to ask: which member of the family of models best describes HNSCC response to cetuximab, and what does that tell us about the timing and mechanisms driving resistance? We find that along with time-course volumetric data to a single dose of cetuximab, the initial resistance fraction and, in some instances, dose escalation volumetric data are required to distinguish among the family of models and thereby infer the mechanisms of resistance. These findings can inform future experimental design so that we can best leverage the synergy of wet laboratory experimentation and mathematical modeling in the study of novel targeted cancer therapeutics.


title: C. difficile is overdiagnosed in adults and a commensal in infants

abstract: Clostridioides difficile is an urgent threat in hospital-acquired infections world-wide, yet the microbial composition associated with C. difficile, in particular in C. difficile infection (CDI) cases, remains poorly characterised. Here, we analysed 534 metagenomes from 10 publicly available CDI study populations. While we detected C. difficile in only 30% of CDI samples, multiple other toxigenic species capable of inducing CDI-like symptomatology were prevalent, raising concerns about CDI overdiagnosis. We further tracked C. difficile in 42,814 metagenomic samples from 253 public studies. We found that C. difficile prevalence, abundance and association with other bacterial species is age-dependent. In healthy adults, C. difficile is a rare taxon associated with an overall species richness reduction, while in healthy infants C. difficile is a common member of the gut microbiome and its presence is associated with a significant increase in species richness. More specifically, we identified a group of species co-occurring with C. difficile exclusively in healthy infants, enriched in obligate anaerobes and in species typically found in the gut microbiome of healthy adults. Overall, gut microbiome composition in presence of C. difficile in healthy infants is associated with multiple parameters linked to a healthy gut microbiome maturation towards an adult-like state. Our results suggest that C. difficile is a commensal in infants, and that its asymptomatic carriage is dependent on the surrounding microbial context.


title: Inhibition of the tuft cell/ILC2 axis reduces gastric tumor development in mice

abstract:
Although gastric cancer is a leading cause of cancer-related deaths, systemic treatment strategies remain scarce. Here we explore a metabolite-triggered circuit between epithelial tuft cells and innate lymphoid type 2 cells (ILC2) that is evolutionarily optimized for intestinal remodeling in response to helminth infection. We demonstrate that tuft cell-derived interleukin 25 (IL25) acts as an alarmin on ILC2s to induce the release of IL13 as a growth factor for tuft cells, and propose that this model drives early metaplastic remodeling and gastric tumor formation. Genetic ablation of tuft cells, ILC2s or antibody-mediated neutralization of IL13 or IL25 reduces the growth of established tumors. Thus, the tuft cell/ILC2 axis provides an opportunity to therapeutically inhibit preneoplastic lesions and early-stage gastric cancer through repurposing of antibody-mediated therapies.

One-Sentence SummaryTuft cells and type 2 innate lymphoid cells offer a new therapeutic target in gastric disease.


title: Density dependent environments can select for extremes of body size

abstract: Body size variation is an enigma. We do not understand why species achieve the sizes they do, and this means we also do not understand the circumstances under which gigantism or dwarfism is selected. We develop size-structured integral projection models to explore evolution of body size and life history speed. We make few assumptions and keep models simple: all functions remain constant across models except for the one that describes development of body size with age; size at sexual maturity is constant at 80% of asymptotic size across life histories; and density-dependence impacts only reproduction or juvenile survival. Carrying capacity is fitness in the models we develop and we are consequently interested in how it changes with size at sexual maturity, and how this association varies with development rate. The simple models generate complex dynamics while providing insight into the circumstances when extremes of body size evolve. We identify different areas of parameter space where gigantism and dwarfism evolve. The direction of selection depends upon emergent trade-offs among the proportion of each cohort that survives to sexual maturity, life expectancy at sexual maturity, and the per-capita reproductive rate. The specific trade-offs that emerge depend upon where density-dependence operates in the life history. Empirical application of the approach we develop has potential to help explain the enigma of body size variation across the tree of life.

category: evolutionary biology


title: Synthetic lethality between toxic amino acids, retrograde target genes and chaperones in Saccharomyces cerevisiae

abstract: The toxicity of non-proteinogenic amino acids has been known for decades. Numerous reports describe their antimicrobial/anticancer potential. However, these molecules are often toxic to the host as well, therefore a synthetic lethality approach can be beneficial. Here we investigated the potential synthetic lethality between toxic amino acids, the retrograde pathway, and molecular chaperones. In Saccharomyces cerevisiae, mitochondrial retrograde (RTG) pathway activation induces transcription of RTG-target genes, which replenishes alpha- ketoglutarate and glutamate; both metabolites are required for arginine and lysine biosynthesis. We previously reported that tolerance of canavanine, a toxic arginine derivative, requires an intact RTG pathway, and low-dose canavanine exposure reduces the expression of RTG-target genes. At higher concentrations, canavanine causes protein misfolding. Here we show that in WT, low-dose thialysine exposure, a toxic lysine analog, has a similar effect as canavanine on RTG-target gene expression. To study if single amino acid deficiency and mild protein misfolding stress elicit a similar effect on RTG-target genes, we compared expression of heat shock protein (HSP) mutants grown without arginine or lysine to WT. Arginine deprivation induces RTG-target gene expression in sse2{Delta}, hsp78{Delta}, and mdj1{Delta}, but CIT2 and DLD3 are reduced in cpr7{Delta}. Lysine deprivation has the opposite effect on RTG-target gene expression in HSP mutants. Interestingly, exposure of HSP mutants to canavanine and thialysine reversed the trend of RTG-target gene expression in several cases. The RTG-target expression pattern in HSP mutants had a predictive value in canavanine sensitivity - the mutant with the lowest expression was the most sensitive - but this was not the case for thialysine. Some, but not all, mutants in RTG-target genes are sensitive to canavanine and thialysine; additional mutation in a certain HSP can exacerbate this sensitivity. Overall, we show that inhibiting molecular chaperones, RTG-target genes, or both can sensitize cells to low doses of toxic amino acids.


title: Specific attenuation of purinergic signaling during bortezomib-induced peripheral neuropathy

abstract: Human peripheral neuropathies are poorly-understood, and the availability of experimental models limits further research. The PeriTox test uses immature dorsal root ganglia (DRG)-like neurons, derived from induced pluripotent stem cells (iPSC), to assess cell death and neurite damage. Here, we explored the suitability of matured peripheral neuron cultures for detection of sub-cytotoxic endpoints, such as altered responses of pain-related P2X receptors. A 2-step differentiation protocol, involving transient expression of ectopic neurogenin-1 (NGN1), allowed for the generation of homogeneous cultures of sensory neurons. After > 38 days-of-differentiation, they showed a robust response (Ca2+-signalling) to the P2X3 ligand ,{beta}-methylene ATP. The clinical proteasome inhibitor bortezomib abolished the P2X3 signal at [≥] 5 nM, while 50-200 nM were required in the PeriTox test to identify neurite damage and cell death. A 24 h treatment with low nM concentrations of bortezomib led to moderate increases in resting cell intracellular [Ca2+], but signalling through transient receptor potential-V1 (TRPV1) receptors or depolarization-triggered Ca2+-influx remained unaffected. We interpret the specific attenuation of purinergic signalling as functional cell stress response. A reorganization of tubulin to dense structures around the cell somata confirmed a mild, non-cytotoxic stress triggered by low concentrations of bortezomib. The proteasome inhibitors carfilzomib, delanzomib, epoxomycin and MG-132 showed similar stress responses. Thus, the model presented here may be used for profiling of new proteasome inhibitors as to their side effect (neuropathy) potential, or for pharmacological studies on the attenuation of their neurotoxicity. P2X3 signalling proved useful as endpoint to assess potential neurotoxicants in peripheral neurons.

category: pharmacology and toxicology


title: Reduced variability of bursting activity during working memory

abstract: Working memories have long been thought to be maintained by persistent spiking. However, mounting evidence from multiple-electrode recording (and single-trial analyses) shows that the underlying spiking is better characterized by intermittent bursts of activity. A counterargument suggested this intermittent activity is at odds with observations that spike-time variability reduces during task performance. However, this counterargument rests on assumptions, such as randomness in the timing of the bursts, that may not be correct. Thus, we analyzed spiking and LFPs from the prefrontal cortex (PFC) of monkeys to determine if task-related reductions in variability can co-exist with intermittent spiking. We found that it does because both spiking and associated gamma bursts were task-modulated, not random. In fact, the task-related reduction in spike variability could be explained by a related reduction in gamma burst variability. Our results provide further support for the intermittent activity models of working memory as well as novel mechanistic insights into how spike variability is reduced during cognitive tasks.

category: neuroscience


title: Self-organization of songbird neural sequences during social isolation

abstract: Behaviors emerge via a combination of experience and innate predis-positions. As the brain matures, it undergoes major changes in cellular, network and functional properties that can be due to sensory experience as well as developmental processes. In normal birdsong learning, neural sequences emerge to control song syllables learned from a tutor. Here, we disambiguate the role of experience and development in neural sequence formation by delaying exposure to a tutor. Using functional calcium imaging, we observe neural sequences in the absence of tutoring, demonstrating that experience is not necessary for the formation of sequences. However, after exposure to a tutor, pre-existing sequences can become tightly associated with new song syllables. Since we delayed tutoring, only half our birds learned new syllables following tutor exposure. The birds that failed to learn were the birds in which pre-tutoring neural sequences were most  crystallized, that is, already tightly associated with their (untutored) song.


title: Molecular characteristics and laminar distribution of prefrontal neurons projecting to the mesolimbic system

abstract: Prefrontal cortical influence over the mesolimbic system - including the nucleus accumbens (NAc) and the ventral tegmental area (VTA) - is implicated in various cognitive processes and behavioral malfunctions. The functional versatility of this system could be explained by an underlying anatomical complexity; however, the detailed characterization of the medial prefrontal cortical (mPFC) innervation of the NAc and VTA is still lacking. Therefore, combining classical retrograde and conditional viral tracing techniques with multiple fluorescent immunohistochemistry, we sought to deliver a precise, cell- and layer-specific anatomical description of the cortico-mesolimbic pathways. We demonstrated that NAc- (mPFCNAc) and VTA-projecting mPFC (mPFCVTA) populations show different laminar distribution (layers 2/3-5a and 5b-6, respectively) and express different molecular markers. Specifically, calbindin and Ntsr1 are specific to mPFCNAc neurons, while mPFCVTA neurons express high levels of Ctip2 and FoxP2, indicating that these populations are mostly separated at the cellular level. We directly tested this with double retrograde tracing and Canine adenovirus type 2-mediated viral labelling and found that there is indeed minimal overlap between the two populations. Furthermore, whole-brain analysis revealed that the projection patter of these populations is also different throughout the brain. Taken together, we demonstrated that the NAc and the VTA are innervated by two, mostly non-overlapping mPFC populations with different laminar distribution and molecular profile. These results can contribute to the advancement in our understanding of mesocorticolimbic functions and its disorders in future studies.


title: Tracer particles sense local stresses in an evolving multicellular spheroid without affecting the anomalous dynamics of the cancer cells

abstract: Measurements of local stresses on the cancer cells (CCs), inferred by embedding inert compressible tracer particles (TPs) in a growing multicellular spheroid (MCS), show that pressure decreases monotonically as the distance from the core of the MCS increases. How faithfully do the TPs report the local stresses in the CCs is an important question because pressure buildup in the MCS is dynamically generated due to CC division, which implies that the CC dynamics should be minimally altered by the TPs. Here using theory and simulations, we show that although the TP dynamics is unusual, exhibiting sub-diffusive behavior on times less than the CC division times and hyper-diffusive dynamics on in the long-time limit, they do not affect the long-time CC dynamics or the local CC stress distributions. The CC pressure profile within the MCS, which decays from a high value at the core to the periphery, is almost identical with and without the TPs. That the TPs have insignificant effect on the local stresses in the MCS implies that they are reliable reporters of the CC microenvironment.


title: Protein compactness and interaction valency define the architecture of a biomolecular condensate across scales

abstract: Formation of biomolecular condensates via liquid-liquid phase separation (LLPS) contributes to the organization and function of living cells, but the general physicochemical principles involved are not fully understood. The present study provides a quantitative, multiscale framework that connects single- and multi-copy, microsecond molecular dynamics simulations with the experimentally observed, micrometer-scale LLPS behavior of an 80-aa N-terminal fragment of yeast Lge1 (Lge11-80), a regulator of histone H2B ubiquitination. Analysis of protein self-interactions modeled at all-atom resolution elucidates the impact of key residues on interaction valency and establishes a link between configurational entropy, valency and compactness of proteins inside a model condensate. An analytical formalism derived from first principles describes condensate structure across different length scales as a function of the interaction valency and compactness of its molecular components. In analogy to fractal cluster formation seen in biological and non-biological colloids, the formalism provides an atomistically resolved model of a micrometer-size condensate starting from the simulated ensemble of individual protein conformers. Finally, the simulation-derived fractal dimensions of the condensates of Lge11-80 and its mutants are shown to be consistent with their in vitro LLPS behavior. The presented framework provides a general, experimentally testable description of the multiscale features of biomolecular condensates and embeds their study in a wider context of self-organization in colloidal systems.


title: Dilated cardiomyopathy mutation E525K in human beta-cardiac myosin stabilizes the interacting heads motif and super-relaxed state of myosin

abstract:
The auto-inhibited, super-relaxed (SRX) state of cardiac myosin is thought to be crucial for regulating contraction, relaxation, and energy conservation in the heart. We used single ATP turnover experiments to demonstrate that a dilated cardiomyopathy (DCM) mutation (E525K) in human beta-cardiac myosin increases the fraction of myosin heads in the SRX state (with slow ATP turnover), especially in physiological ionic strength conditions. We also utilized FRET between a C-terminal GFP tag on the myosin tail and Cy3ATP bound to the active site of the motor domain to estimate the fraction of heads in the closed, interacting-heads motif (IHM); we found a strong correlation between the IHM and SRX state. Negative stain EM and 2D class averaging of the construct demonstrated that the E525K mutation increased the fraction of molecules adopting the IHM. Overall, our results demonstrate that the E525K DCM mutation may reduce muscle force and power by stabilizing the auto-inhibited SRX state. Our studies also provide direct evidence for a correlation between the SRX biochemical state and the IHM structural state in cardiac muscle myosin. Furthermore, the E525 residue may be implicated in crucial electrostatic interactions that modulate this conserved, auto-inhibited conformation of myosin.

Significance StatementDilated cardiomyopathy can be caused by single point mutations in cardiac muscle myosin, the motor protein that powers contraction of the myocardium. We found that the E525K DCM mutation in the cardiac myosin heavy chain stabilizes the auto-inhibited, super-relaxed state, suggesting a mechanism by which this mutation reduces muscle force and power. The E525K mutation also highlights critical electrostatic interactions important for forming the conserved, auto-inhibited conformational state of striated muscle myosins.


title: Dyslexia linked to profound impairment in the magnocellular medial geniculate nucleus

abstract: The neurological basis of dyslexia, a common reading disorder, remains unclear but is hypothesized to be caused by either dysfunction of the magnocellular system in the brain, abnormal temporal processing, and/or deficient phonological skills. Using functional magnetic resonance imaging, we measured activity in the magnocellular portion of the medial geniculate nucleus, the auditory relay in the thalamus, and observed profoundly attenuated responses to non-linguistic transient but not sustained sounds in every subject with dyslexia we tested, compared to normal readers. Our finding unifies these three hypotheses and identifies a core deficit causing dyslexia.


title: Asymmetric requirement for α-tubulin over β-tubulin

abstract: How cells regulate the supply of - and {beta}-tubulin monomers to meet the demand for {beta}- heterodimers while avoiding consequences of monomer imbalance is not understood. We investigate the role of gene copy number in tubulin regulation and how shifting the expression of - or {beta}-tubulin genes impacts tubulin proteostasis and microtubule function. We find that - tubulin gene copy number is important for maintaining an excess -tubulin protein compared to {beta}-tubulin protein and preventing accumulation of super-stoichiometric {beta}-tubulin. Super- stoichiometric {beta}-tubulin is toxic to cells, leading to loss of microtubules, formation of non- microtubule assemblies of tubulin, and disrupted cell proliferation. In contrast, decreased {beta}- tubulin or increased -tubulin has minor effects. We provide evidence that cells rapidly equilibrate the concentration of -tubulin protein during shifts in -tubulin isotype expression to maintain a ratio in excess of {beta}-tubulin. We propose an asymmetric relationship between - and {beta}-tubulins, where -tubulins are maintained in excess to supply {beta}-heterodimers and limit the accumulation of {beta}-tubulin monomers.

category: cell biology


title: Prolonged β-Adrenergic Stimulation Disperses Ryanodine Receptor Clusters in Cardiomyocytes: Implications for Heart Failure

abstract:
Ryanodine Receptors (RyRs) exhibit dynamic arrangements in cardiomyocytes, and we previously showed that "dispersion" of RyR clusters disrupts Ca2+ homeostasis during heart failure (HF) (Kolstad et al., eLife, 2018). Here, we investigated whether prolonged {beta}-adrenergic stimulation, a hallmark of HF, promotes RyR cluster dispersion, and examined the underlying mechanisms. We observed that treatment of healthy rat cardiomyocytes with isoproterenol for 1 hour triggered progressive fragmentation of RyR clusters. Pharmacological inhibition of CaMKII reversed these effects, while cluster dispersion was reproduced by specific activation of CaMKII, and in mice with constitutively active Ser2814-RyR. A similar role of protein kinase A (PKA) in promoting RyR cluster fragmentation was established by employing PKA activation or inhibition. Progressive cluster dispersion was linked to declining Ca2+ spark fidelity and magnitude, and slowed release kinetics from Ca2+ propagation between more numerous RyR clusters. In healthy cells, this served to dampen the stimulatory actions of {beta}-adrenergic stimulation over the longer term, and protect against pro-arrhythmic Ca2+ waves. However, during HF, RyR dispersion was linked to impaired Ca2+ release. Thus, RyR localization and function are intimately linked via channel phosphorylation by both CaMKII and PKA which, while finely tuned in healthy cardiomyocytes, underlies impaired cardiac function during pathology.

Significance statementThe heartbeat is triggered by the release of Ca2+ from Ryanodine Receptors (RyRs) within cardiomyocytes. Recent data indicate RyR arrangement is highly malleable. However, mechanisms controlling RyR reorganisation and the subsequent impact on Ca2+ homeostasis remain unclear. Here, we show that prolonged {beta}-adrenergic stimulation causes RyR clusters to disperse, drastically altering the frequency and kinetics of Ca2+ release events called "Ca2+ sparks" in a process that is dependent on CaMKII and PKA. In healthy cells, these compensatory effects protect against arrhythmogenic Ca2+ over-activity. However, during heart failure, RyR hyper-phosphorylation and dispersion impairs Ca2+ release and cardiac performance. Thus, RyR localization and function are intimately linked via channel phosphorylation which, while finely tuned in health, underlies impaired cardiac function during pathology.


title: A Ferroptosis-mediated regulation of the biogenesis of the oxidative phosphorylation system

abstract: Several subunits in the matrix domain of mitochondrial complex I (CI) have been posited to be redox sensors for CI; but how elevated levels of reactive oxygen species (ROS) impinge on CI assembly is unknown. We report that when the mitochondrial NADPH-generating enzyme - Isocitrate Dehydrogenase 2 - is genetically disrupted, ROS levels are elevated and assembly of the oxidative phosphorylation system (OXPHOS) is impaired. Mechanistically, this begins with a ROS-mediated inhibition of biosynthesis of the matrix domain of CI, which progresses to a point where ferroptotic signals are induced, the mitochondrial unfolded protein response is activated and multiple OXPHOS complexes are impaired. Disruption of other enzymes that eliminate hydrogen peroxide, but not those that eliminate the superoxide radical, recapitulates the phenotype; implicating hydrogen peroxide as the signaling molecule involved. Thus, the redox status of the mitochondrion modulates the assembly of the matrix domain of CI and ultimately that of the entire OXPHOS.


title: MicroRNA-155 regulates osteogenesis and bone mass phenotype via targeting S1PR1 gene

abstract: MicroRNA-155 (miR155) is overexpressed in various inflammatory diseases and cancer, in which bone resorption and osteolysis are frequently observed. However, the role of miR155 on osteogenesis and bone mass phenotype is still unknown. Here, we report a low bone mass phenotype in the long bone of miR155-Tg mice compared with control mice. In contrast, miR155-KO mice showed a high bone mass phenotype. miR155-KO mice showed robust bone regeneration in the ectopic and orthotopic model, but miR155-Tg mice showed compromised bone regeneration compared with the control mice. Similarly, the osteogenic differentiation potential of bone marrow stromal stem cells (BMSCs) from miR155-KO mice was robust and miR155-Tg was compromised compared with that of control mice. Moreover, miR155 knockdown in BMSCs from control mice showed higher osteogenic differentiation potential, supporting the results from miR155-KO mice. TargetScan analysis predicted S1PR1 as a target gene of miR155, which was further confirmed by luciferase assay and miR155 knockdown. S1PR1 overexpression in BMSCs robustly promoted osteogenic differentiation without affecting cell viability and proliferation. Thus, miR155 showed a catabolic effect on osteogenesis and bone mass phenotype via interaction with the S1PR1 gene, suggesting inhibition of miR155 as a potential strategy for bone regeneration and bone defect healing.


title: Borrowing ecological theory to infer interactions between sensitive and resistant breast cancer cell populations

abstract:
While some forms of breast cancer are highly responsive to treatment, endocrine therapy-resistant breast cancers are disproportionately lethal. There has been significant progress in understanding how endocrine therapy-resistant strains evolve from therapy-susceptible strains of cancer, but little is understood about the proliferation of resistance through cancer cell populations, or the interactions that occur between populations of resistant and sensitive cells. In this study, we characterize the nature of the ecological interaction between populations of resistant and susceptible breast cancer cells to reveal novel methods of controlling drug resistance.

Using in-vitro data on fluorescent-tagged resistant and susceptible cells, we use an image processing algorithm to identify and count cell growth till equilibrium. We then borrow theory from population biology to infer the type of ecological interaction that occurs between populations of resistant and sensitive cells. In particular, we use a Bayesian approach to fit single culture cell populations to infer density-dependent growth parameters (growth rate, carrying capacity) and a Generalized Lotka-Volterra model to understand how susceptible and resistant co-culture populations may be depressing or supporting growth of the other.

Our results identify a net mutualistic interaction between the susceptible and resistant cancer strains, demonstrating that there are ecological dynamics to cancer resistance. Our findings also suggest that ecological dynamics change in the presence of therapy, and that an adaptive treatment protocol can induce cycling behavior suggesting that heterogeneous ecological effects contribute to empirically observed adaptive-therapeutic dynamics.


title: GPX4-associated Sedaghatian Type Spondylometaphyseal Dysplasia: A Protein Interactome Perspective

abstract: Spondylometaphyseal dysplasia, Sedaghatian type (SMDS) is a rare and lethal skeletal dysplasia inherited in an autosomal recessive manner and caused by mutations in GPX4. In order to expand the functional landscape of this poorly studied disorder and accelerate the discovery of biologically insightful and clinically actionable targets, we constructed SMDS-centric and GPX4-centric protein-protein interaction (PPI) networks, augmented with novel protein interactors predicted by our HiPPIP algorithm. The SMDS-centric networks included those that showed the interconnections of GPX4 with other putative SMDS-associated genes and genes associated with other skeletal dysplasias. The GPX4-centric network showed the interconnections of GPX4 with genes whose perturbation has been known to affect GPX4 expression. We discovered that these networks either contained or were enriched with genes associated with specific SMDS pathophenotypes, tissue-naive/fetus-specific functional modules and genes showing elevated expression in brain and/or testis similar to GPX4. We identified 7 proteins as novel interactors of GPX4 (APBA3, EGR4, FUT5, GAMT, GTF2F1, MATK and ZNF197) and showed their potential biological relevance to GPX4 or SMDS. Comparative transcriptome analysis of expression profiles associated with chondroplasia and immune-osseous dysplasia versus drug-induced profiles revealed 11 drugs that targeted the neighborhood network of GPX4 and other putative SMDS-associated genes. Additionally, resveratrol, which is currently being tested against a skeletal dysplasia in a clinical trial, was identified as another potential candidate based on the proximity of its targets to GPX4.

category: developmental biology


title: Mural norrin/β-catenin signaling regulates Lama2 expression to promote neurovascular unit assembly

abstract:
Neurovascular unit (NVU) assembly and barrier maturation rely on vascular basement membrane (vBM) composition. Laminins, a major vBM component, are critical for these processes, yet which signaling pathway(s) regulate their expression remains unknown. Here we show that mural cells have active Norrin/{beta}-catenin signaling during central nervous system development. Bulk RNA sequencing and validation using P10 and P14 wild-type versus Apcdd1-/- retinas reveal that Lama2 (Laminin-2 chain) mRNA and protein levels are increased in mutant vasculature undergoing higher Norrin/{beta}-catenin signaling. Mural cells are the main source of Lama2, and {beta}-catenin activation induces Lama2 expression in mural cells in vitro. Markers of mature astrocytes including Aquaporin-4 (a water channel in astrocyte endfeet) and Integrin-6 (a laminin receptor) are upregulated in Apcdd1-/- retinas following higher Lama2 vBM deposition. Thus, the Norrin/{beta}-catenin pathway regulates Lama2 expression in mural cells to promote NVU assembly and neurovascular barrier maturation.

SUMMARYBiswas et al., demonstrate that Norrin/{beta}-catenin signaling is active in CNS mural cells and regulates Lama2 deposition in the vascular basement membrane, promoting neurovascular unit assembly and blood-CNS barrier maturation.


title: Bespoke data augmentation and network construction enable image classification on small microscopy datasets

abstract: Deep learning is a powerful tool for image classification, yet training deep learning models often requires large datasets, which are not always available in biological research. Here we use a small dataset to train an accurate classifier by employing data augmentation regimes and Bayesian optimisation. We establish a new staging system for the Hamburger-Hamilton stage 10 chick embryo brain, based on morphology, identifying three sub-stages uncoupled from somite number, the usual metric used to stage chick embryos. Incorporating biologically informed, data-driven preprocessing, we train a deep convolutional neural network to classify our sub-stages. We find that augmenting our images with a combination of rotation, blur, shear, and cutout transformations is effective in training an accurate classifier on a small microscopy dataset. We then apply our approach to an unrelated small microscopy dataset comprising images of limb buds, finding good agreement with the results from brain classification. Through saliency analysis, we ensure that relevant features are being used by our classifier, gain insight into the efficacy of different data augmentations, and identify sub-stage specific features. In summary, we apply biological domain expertise to design effective data augmentation regimes for training a neural network-based image classifier on small, specialised datasets, classifying the developing brains and limbs with up to 90.9% and 94.4% accuracy respectively. These reliable classifiers can inform future experiments.


title: Bespoke data augmentation and network construction enable developmental morphological classification on limited microscopy datasets


title: Spatially resolved epigenomic profiling of single cells in complex tissues

abstract: The recent development of spatial omics methods enables single-cell profiling of the transcriptome and the 3D genome organization in a spatially resolved manner. Expanding the repertoire of spatial omics tools, a spatial epigenomics method will accelerate our understanding of the spatial regulation of cell and tissue functions. Here, we report a method for spatially resolved profiling of epigenomes in single cells using in-situ tagmentation and transcription followed by highly multiplexed imaging. We profiled histone modifications marking active promoters and enhancers, H3K4me3 and H3K27ac, and generated high-resolution spatial atlas of hundreds of active promoters and putative enhancers in embryonic and adult mouse brains. Our results further revealed putative promoter-enhancer pairs and enhancer hubs regulating the expression of developmentally important genes. We envision this approach will be generally applicable to spatial profiling of epigenetic modifications and DNA-binding proteins, advancing our understanding of how gene expression is spatiotemporally regulated by the epigenome.


title: Substrate stiffness impacts early biofilm formation via a modulation of twitching motility

abstract: Surface-associated lifestyles dominate in the bacterial world. Large multicellular assemblies, called biofilms, are essential to the survival of bacteria in harsh environments, and are closely linked to antibiotic resistance in pathogenic strains. Biofilms stem from surface colonization of various substrates encountered by bacteria. Here, we show that the opportunistic promiscuouspathogen Pseudomonas Aeruginosa explores substrates differently based on their rigidity, leading to striking variations in biofilm structure, surface decoration by exopolysaccharides (EPS), strain mixing during co-colonization and phenotypic expression. Using simple kinetic models, we show that these phenotypes arise through a mechanical interaction between the elasticity of the substrate and the type IV pilus (T4P) machinery, that mediates the surface-based motility called twitching. Together, our findings reveal a new role for substrate softness in the spatial organization of bacteria in complex microenvironments, with far-reaching consequences on efficient biofilm formation.


title: Regulatory mechanisms of the dynein-2 motility by post-translational modification revealed by molecular dynamic simulation

abstract: Intraflagellar transport for ciliary assembly and maintenance is driven by dynein and kinesins specific for the cilia. It has been shown that anterograde and retrograde transports run on different regions of the doublet microtubule, i.e., separate train tracks. However, little is known about the regulatory mechanism of this selective process. Since the doublet microtubule is known to display specific post-translational modifications of tubulins, i.e. "tubulin code", for molecular motor regulations, we investigated the motility of ciliary specific dynein-2 under different post-translational modification by coarse-grained molecular dynamics. Our setup allows us to simulate the stochastic stepping behaviors of dynein-2 on un-modified, detyrosinated, poly-glutamylated and poly-glycylated microtubules in silico. Our study revealed that poly-glutamylation can play an inhibitory effect on dynein-2 motility. Our result indicates that poly-glutamylation of the B-tubule of the doublet microtubule can be used as an efficient means to target retrograde intraflagellar transport onto the A-tubule.


title: Mechanisms of frustrated phagocytic spreading of human neutrophils on antibody-coated surfaces

abstract:
Complex motions of immune cells are an integral part of diapedesis, chemotaxis, phagocytosis, and other vital processes. To better understand how immune cells execute such motions, we present a detailed analysis of phagocytic spreading of human neutrophils on flat surfaces functionalized with different densities of immunoglobulin G (IgG) antibodies. We visualize the cell-substrate contact region at high resolution and without labels using reflection interference contrast microscopy (RICM) and quantify how the area, shape, and position of the contact region evolves over time. We find that the likelihood of the cell commitment to spreading strongly depends on the surface density of IgG, but the rate at which the substrate-contact area of spreading cells increases does not. Validated by a theoretical companion study, our results resolve controversial notions about the mechanisms controlling cell spreading, establishing that active forces generated by the cytoskeleton rather than cell-substrate adhesion primarily drive cellular protrusion. Adhesion, on the other hand, aids phagocytic spreading by regulating the cell commitment to spreading, the maximum cell-substrate contact area, and the directional movement of the contact region.

SummaryThe detailed analysis of immune-cell spreading on antibody-coated surfaces establishes that active cytoskeletal protrusion rather than passive substrate adhesion drives phagocytic spreading.


title: The influence of leaf anatomical traits on photosynthetic in coffee leaves in Yunnan of China

abstract: Leaf photosynthesis is largely determined by anatomical features. This work aimed to reveal the quantitative effects of Coffea arabica leaf anatomical structure on photosynthesis. Pearsons correlation and path analysis was used to explore the correlation between leaf structure and photosynthesis. The comprehensive evaluation value of the correlation between leaf anatomical traits and photosynthetic parameters is calculated by using the Criteria Importance Though Intercrieria Correlation (CRITIC) method to obtain the objective weight of each photosynthetic parameter. Most of the leafs anatomical traits significantly (P<0.05) to highly significantly (P<0.01) correlated with photosynthetic parameters, suggesting that anatomical traits greatly affected photosynthetic capacity in Coffea arabica leaf. Likewise, path coefficient analysis revealed that all the leaf anatomical traits influenced photosynthetic capacity directly and indirectly. The results of the comprehensive evaluation showed that leaf thickness (LT) and stomatal density (d) are the anatomical characteristics most closely related to photosynthesis. These results may help pinpoint anatomical features required to gain higher photosynthesis in coffee leaves.


title: Genomewide m6A mapping uncovers dynamic changes in the m6A epitranscriptome of cisplatin-treated apoptotic HeLa cells

abstract: Cisplatin, which is a traditional cancer therapeutic drug, induces apoptosis by modulating a diverse array of gene regulatory mechanisms. However, cisplatin-mediated changes in the m6A methylome is unknown. We employed m6A miCLIP-seq to investigate the effect of m6A methylation events under cisplatin-mediated apoptotic conditions in HeLa cells. Our high-resolution approach revealed numerous m6A marks on 972 target mRNAs with an enrichment on 132 apoptotic mRNAs. Following validation of site-specific m6A events on candidate RNAs, we tracked the fate of candidate mRNAs under METTL3 knockdown and cisplatin treatment conditions. We detected perturbations in the translational efficiency of PMAIP1 and PHLDA1 transcripts based on the polysome profile analyses. Congruently, PMAIP1 and p53 amounts were dependent on METTL3. Additionally, cisplatin-mediated apoptosis was sensitized by METTL3 knockdown. These results suggest that apoptotic pathways are modulated by m6A methylation events and METTL3-p53-PMAIP1 axis modulates cisplatin-mediated apoptosis in HeLa cells.


title: The AAA+ chaperone VCP disaggregates Tau fibrils and generates aggregate seeds

abstract: Amyloid-like aggregates of the microtubule-associated protein Tau are associated with several neurodegenerative disorders including Alzheimers disease. The existence of cellular machinery for the removal of such aggregates has remained unclear, as specialized disaggregase chaperones are thought to be absent in mammalian cells. Here we show in cell culture and in neurons that the AAA+ chaperone VCP is recruited to ubiquitylated Tau fibrils, resulting in their efficient disaggregation. Aggregate clearance depends on the functional cooperation of VCP with Hsp70 and the ubiquitin-proteasome machinery. Inhibition of VCP activity stabilizes large Tau aggregates, and is accompanied by a reduction in the amount of Tau species competent of prion- like aggregate seeding in recipient cells. Thus, disaggregation by VCP generates seeding-active Tau as byproduct. These findings identify VCP as a core component of the machinery for the removal of neurodegenerative disease aggregates and suggest that its activity can be associated with enhanced aggregate spreading in tauopathies.


title: Partial illustration of human sperm DNA via microscopy and quantitative analysis of nucleotides

abstract:
Backgroundgeneral structure of human sperm has not been profiled yet. Human sperm DNA characterization should progress the medical diagnostic and therapeutic methods rather than developing biological sciences. The aim of the present study was to provide biological insights into the common structure of human sperm. The value of this investigation is establishing an initial basic map of sperm head structure that leads to further advanced standardization of normality in this creature. For this purpose, analytical and microscopic methods were applied.

MethodsHigh-performance Liquid Chromatography (HPLC) and flow cytometry were hired to quantify the DNA compositions. As well fluorescent, confocal and advanced light microscopy was applied to identify the stained sperm DNA by chromomycinA3 (CMA3) and 5-methylcytosine antibody (5-mc)

ResultsHPLC demonstrated the mean values of nucleotide bases percentage in the structure of the sperm DNA regardless of the fraction that sperm was collected from gradient wash, sequenced from 27.6%, 8.92%, 27.05% and 35.36%. Also, quantitative flow cytometry of global 5-methylcytosine showed not a regular fluctuation in individuals with normal sperm while, there is a permanent increase in 50% fraction collected from percoll gradients.

CMA3-positivity levels as well, were negatively correlated with sperm quality harvest by percoll gradients (p<0.0001), and positively correlated (P<0.05) with global methylation as determined by flow cytometry. Interestingly, in this text microscopy of immunocytochemistry of sperm cells stained by CMA3, demonstrated a different view from cells heads.

Conclusionsobviously these explorations suggest some new possibilities in assessment of rough chemical level of nucleotides and cytochemistry of sperm head structure. The chromatin brightness presented with CMA3 by microscopy shows a direct relation with more extensive DNA methylation in sperms collected from low gradients of percoll wash. While, fluctuated 5-methylcytosine levels show personal presentation and even exclusive to individual sperm expression. This study induces further research on new assumptions in nuclear equilibrium in the axiom of DNA ladder in related to 5-mcytosine level in human sperm.


title: Lifespan can be extended during a specific time window early in life

abstract:
Lifespan is determined by complex and tangled mechanisms that are largely unknown. The early postnatal stage has been proposed to play a role in lifespan, but its contribution is still controversial. Here, we found that a short rapamycin treatment during early life can prolong lifespan in Mus musculus and Drosophila melanogaster. Notably, the same treatment at later time points has no evident effect on lifespan, suggesting that we found a crucial time-window involved in lifespan modulation. We discovered that sulfotransferases are upregulated during early rapamycin treatment both in newborn mice and Drosophila larvae. Furthermore, overexpression of the sulfotransferase dST1 triggers an increment in the lifespan of Drosophila melanogaster. Our findings unveil a novel link between early-life treatments and long-term effects on lifespan.

One Sentence SummaryEarly life events increase lifespan.


title: Rapamycin treatment during development extends lifespan and healthspan

abstract: The possibility that pace of development is tightly connected to aging is supported by the fact that the onset of reproduction is associated with lifespan and that many longevity interventions target growth and development. However, it has been unknown whether targeting development with pharmacological intervention can lead to a longer lifespan. To test this possibility, we subjected genetically diverse UMHET3 mice to the mTOR inhibitor rapamycin for the first 45 days of life and followed them up until death. Treated mice grew slower, with most of the deceleration occurring in the first week, and remained smaller for their entire lives. Their reproductive age was delayed but without affecting offspring numbers. The treatment was sufficient to extend the median lifespan by 10%, with the most effect in males, and to preserve better health as measured by frailty index, gait speed, and glucose and insulin tolerance tests. Mechanistically, the liver transcriptome of treated mice was younger at the completion of treatment and stayed younger into the old ages in males. Rapamycin initially reduced DNA methylation age of livers, however, that effect was lost with aging. Analogous to mice, rapamycin exposure only during development robustly extended the lifespan of Daphnia magna as well as reduced their body size, suggesting evolutionary conserved mechanisms of this early life effect. Overall, the results demonstrate that short-term rapamycin treatment during early life is a novel longevity intervention that establishes causality between pace of development and longevity in evolutionary distant organisms.


title: Dependence of diffusion in Escherichia coli cytoplasm on protein size, environmental conditions and cell growth

abstract: Inside prokaryotic cells, passive translational diffusion typically limits the rates with which cytoplasmic proteins can reach their locations and interact with partners. Diffusion is thus fundamental to most cellular processes, but the understanding of protein mobility in the highly crowded and non-homogeneous environment of a bacterial cell is still limited. Here we investigated the mobility of a large set of proteins in the cytoplasm of Escherichia coli, by employing fluorescence correlation spectroscopy (FCS) combined with simulations and theoretical modeling. We conclude that cytoplasmic protein mobility could be well described by Brownian diffusion in the confined geometry of the bacterial cell and at high viscosity imposed by macromolecular crowding. The size dependence of protein diffusion is well consistent with the Stokes-Einstein relation for small fusion proteins when taking into account their shape, but larger proteins diffuse slower than expected from this relation. Pronounced subdiffusion and hindered mobility is observed for proteins with extensive interactions within the cytoplasm. Finally, we show that cytoplasmic viscosity has a temperature dependence comparable to that of water, and that protein mobility is increased by biosynthetic activity and cell growth.


title: Spatiotemporally Mapping Thermodynamics of Lysosomes and Mitochondria using Cascade Organelle-Targeting Upconversion Nanoparticles

abstract:
The intracellular metabolism of organelles, like lysosomes and mitochondria, are highly coordinated spatiotemporally and functionally. The activities of lysosomal enzymes significantly rely on the cytoplasmic temperature, and heat is constantly released by mitochondria as the byproduct of ATP generation during active metabolism. Here, we develop temperature-sensitive LysoDots and MitoDots to monitor the in situ thermodynamics of lysosomes and mitochondria. The design is based on upconversion nanoparticles (UCNPs) with high-density surface modifications to achieve the exceptionally high sensitivity of 2.7% K-1 and accuracy of 0.8 K for nanothermometry to be used in living cells. We show the measurement is independent of the intracellular ion concentrations- and pH values. With Ca2+ ion shock, the temperatures of both lysosomes and mitochondria increased by 2[~]4 {degrees}C. Intriguingly, with Chloroquine treatment, the lysosomal temperature was observed to decrease by up to [~]3 {degrees}C, while mitochondria remained relatively stable. Lastly, with oxidative phosphorylation inhibitor treatment, we observed a 3[~]7 {degrees}C thermal increase and transition from mitochondria to lysosomes. These observations indicate different metabolic pathways and thermal transitions between lysosomes and mitochondria inside HeLa cells. The nanothermometry probes provide a powerful tool for multi-modality functional imaging of subcellular organelles and interactions with high spatial, temporal and thermal dynamics resolutions.

Graphical AbstractCascade organelle-targeted nano-thermometers based on upconversion LysoDots and MitoDots.

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title: Emergent regulation of ant foraging frequency through a computationally inexpensive forager movement rule

abstract: 1Ant colonies regulate foraging in response to their collective hunger, yet the mechanism behind this distributed regulation remains unclear. Previously, by imaging food flow within ant colonies we showed that the frequency of foraging events declines linearly with colony satiation ([1]). Our analysis implied that as a forager distributes food in the nest, two factors affect her decision to exit for another foraging trip: her current food load and its rate of change. Sensing these variables can be attributed to the foragers individual cognitive ability. Here, new analyses of the foragers trajectories within the nest imply a different way to achieve the observed regulation. Instead of an explicit decision to exit, foragers merely tend toward the depth of the nest when their food load is high and toward the nest exit when it is low. Thus, the colony shapes the foragers trajectory by controlling her unloading rate, while she senses only her current food load. Using an agent-based model and mathematical analysis, we show that this simple mechanism robustly yields emergent regulation of foraging frequency. These findings demonstrate how the embedding of individuals in physical space can reduce their cognitive demands without compromising their computational role in the group.

category: animal behavior and cognition


title: An integrated strain-level analytic pipeline utilizing longitudinal metagenomic data

abstract: The development of sequencing technology and analytic tools have advanced our insights into the complexity of microbiome. Since different strains within species may display great phenotypic variability, studying within-species variations enhances the understanding of microbial biological processes. However, most existing methods for strain-level analysis do not allow for the simultaneous interrogation of strain proportions and genome-wide variants in longitudinal metagenomic samples. In this study, we introduce LongStrain, an integrated pipeline for the analysis of metagenomic data from individuals with longitudinal or repeated samples. Our algorithm improves the efficiency and accuracy of strain identification by jointly modeling the strain proportion and genomic variants in combined multiple samples within individuals. With simulation studies of a microbial community and single species, we show that LongStrain is superior to three extensively used methods in variant calling and proportion estimation. Furthermore, we illustrate the potential applications of LongStrain in the real data analysis of The Environmental Determinants of Diabetes in the Young (TEDDY) study and a gastric intestinal metaplasia microbiome study. We investigate the association between the dynamic change of strain proportions and early life events, such as birth delivery mode, antibiotic treatment, and weaning. By joint analysis of phylogeny and strain transition, we also identify a subspecies clade of Bifidobacterium longum which is significantly correlated with breastfeeding.

category: bioinformatics


title: Proteogenomics analysis to identify acquired resistance-specific alterations in melanoma PDXs on MAPKi therapy

abstract: Therapeutic approaches to treat melanoma include small molecule drugs that target activating protein mutations in pro-growth signaling pathways like the MAPK pathway. While beneficial to the approximately 50% of patients with activating BRAFV600 mutation, mono- and combination therapy with MAPK inhibitors is ultimately associated with acquired resistance. To better characterize the mechanisms of MAPK inhibitor resistance in melanoma, we utilize patient-derived xenografts and apply proteogenomic approaches leveraging genomic, transcriptomic, and proteomic technologies that permit the identification of resistance-specific alterations and therapeutic vulnerabilities. A specific challenge for proteogenomic applications comes at the level of data curation to enable multi-omics data integration. Here, we present a proteogenomic approach that uses custom curated databases to identify unique resistance-specific alternations in melanoma PDX models of acquired MAPK inhibitor resistance. We demonstrate this approach with a NRASQ61L melanoma PDX model from which resistant tumors were developed following treatment with a MEK inhibitor. Our multi-omics strategy addresses current challenges in bioinformatics by leveraging development of custom curated proteogenomics databases derived from individual resistant melanoma that evolves following MEK inhibitor treatment and is scalable to comprehensively characterize acquired MAPK inhibitor resistance across patient-specific models and genomic subtypes of melanoma.


title: StrainPanDA: linked reconstruction of strain composition and gene content profiles via pangenome-based decomposition of metagenomic data

abstract:
BackgroundMicrobial strains of variable functional capacities co-exist in microbiomes. Current bioinformatics methods of strain analysis cannot provide the direct linkage between strain composition and their gene contents from metagenomic data.

MethodsHere we present StrainPanDA (Strain-level Pangenome Decomposition Analysis), a novel method that uses the pangenome coverage profile of multiple metagenomic samples to simultaneously reconstruct the composition and gene content variation of co-existing strains in microbial communities.

ResultsWe systematically validate the accuracy and robustness of StrainPanDA using synthetic datasets. To demonstrate the power of gene-centric strain profiling, we then apply StrainPanDA to analyze the gut microbiome samples of infants, as well as patients treated with fecal microbiota transplantation. We show that the linked reconstruction of strain composition and gene content profiles is critical for understanding the relationship between microbial adaptation and strain-specific functions (e.g., nutrient utilization, pathogenicity).

ConclusionsStrainPanDA can be applied to metagenomic datasets to detect association between molecular functions and microbial/host phenotypes to formulate testable hypotheses and gain novel biological insights at the strain or subspecies level.


title: CoDNaS-Q: a database of conformational diversity of the native state of proteins with quaternary structure

abstract:
SummaryA collection of conformers that exist in a dynamical equilibrium defines the native state of a protein. The structural differences between them describe their conformational diversity, a defining characteristic of the protein with an essential role in multiple cellular processes. Since most proteins carry out their functions by assembling into complexes, we have developed CoDNaS-Q, the first online resource to explore conformational diversity in homooligomeric proteins. It features a curated collection of redundant protein structures with known quaternary structure. CoDNaS-Q integrates relevant annotations that allow researchers to identify and explore the extent and possible reasons of conformational diversity in homooligomeric protein complexes.

Availability and implementationCoDNaS-Q is freely accessible at http://ufq.unq.edu.ar/codnasq/. The data can be retrieved from the website. The source code of the database can be downloaded from https://github.com/SfrRonaldo/codnas-q.

Contactnpalopoli@unq.edu.ar