title: hNOP2/NSUN1 Regulates Ribosome Biogenesis through Stabilization of snoRNP Complexes and Cytosine-5 Methylation of 28S rRNA.

abstract: 5-Methylcytosine (m5C) is a base modification broadly found on a variety of RNAs in the human transcriptome. In eukaryotes m5C is catalyzed by enzymes of the NSUN family, which is composed of seven members in humans (NSUN1-7). NOP2/NSUN1 has been mostly characterized in budding yeast as an essential ribosome biogenesis factor required for the deposition of m5C on the 25S rRNA. Although human NOP2/NSUN1 has been known to be an oncogene overexpressed in several types of cancer, its functions remain poorly characterized. To define the roles of human NOP2/NSUN1, we used an miCLIP-seq approach to identify its RNA substrates. Our analysis reveals that vault RNA 1.2 and rRNA are NOP2/NSUN1-specific methylated targets and we further confirm by bisulfite sequencing that NOP2/NSUN1 is responsible for the deposition of m5C at residue 4447 on the 28S rRNA. Depletion of NOP2/NSUN1 impairs cell proliferation, rRNA processing and 60S ribosome biogenesis. Additionally, we find that NOP2/NSUN1 binds to the 5ETS region of the pre-rRNA transcript and regulates pre-rRNA processing in part through non-catalytic complex formation with box C/D snoRNAs. Our study identifies for the first time the RNA substrates of human NOP2/NSUN1 and reveals additional functions in rRNA processing beyond catalyzing m5C base modification.

category: molecular biology


title: Molecular basis for the regulation of human glycogen synthase by phosphorylation and glucose-6-phosphate

abstract: Glycogen synthase (GYS1), in complex with glycogenin (GYG1), is the central enzyme of muscle glycogen biosynthesis, and its inhibition has been proposed as a therapeutic avenue for various glycogen storage diseases (GSDs). GYS1 activity is inhibited by phosphorylation of its N- and C-termini, which can be relieved by allosteric activation of glucose-6-phosphate. However, the structural basis of GYS1 regulation is unclear. Here, we present the first cryo-EM structures of phosphorylated human GYS1 complexed with a minimal interacting region of GYG1 in the inhibited, activated, and catalytically competent states at resolutions of 3.0-4.0 [A]. These structures reveal how phosphorylations of specific N- and C- terminal residues are sensed by different arginine clusters that lock the GYS1 tetramer complex in an inhibited state via inter-subunit interactions. The allosteric activator, glucose-6-phopshate, promotes a conformational change by disrupting these interactions and increases flexibility of GYS1 allowing for a catalytically competent state to occur when bound to the sugar donor UDP-glucose. We also identify an inhibited-like conformation that has not transitioned into the activated state, whereby the locking interaction of phosphorylation with the arginine cluster impedes the subsequent conformational changes due to glucose-6-phosphate binding. Finally, we show that the PP1 phosphatase regulatory subunit PPP1R3C (PTG) is recruited to the GYS1:GYG1 complex through direct interaction with glycogen. Our results address long-standing questions into the mechanism of human glycogen synthase regulation.

category: biochemistry


title: Site-Specific Synthesis of N4-Acetylcytidine in RNA Reveals Physiological Duplex Stabilization

abstract: N4-acetylcytidine (ac4C) is a post-transcriptional modification of RNA that is conserved across all domains of life. All characterized sites of ac4C in eukaryotic RNA occur in the central nucleotide of a 5-CCG-3 consensus sequence. However, the thermodynamic consequences of cytidine acetylation in this context have never been assessed due to its challenging synthesis. Here we report the synthesis and biophysical characterization of ac4C in its endogenous eukaryotic sequence context. First, we develop a synthetic route to homogenous RNAs containing electrophilic acetyl groups. Next, we use thermal denaturation to interrogate the effects of ac4C on duplex stability and mismatch discrimination in a native sequence found in human ribosomal RNA. Finally, we demonstrate the ability of this chemistry to incorporate ac4C into the complex modification landscape of human tRNA, and use duplex melting combined with sequence analysis to highlight a potentially unique enforcing role for ac4C in this setting. By enabling the analysis of nucleic acid acetylation in its physiological sequence context, these studies establish a chemical foundation for understanding the function of a universally-conserved nucleobase in biology and disease.


title: A New Approach to Testing Mediation of the Microbiome using the LDM

abstract:
BackgroundUnderstanding whether and which microbes played a mediating role between an exposure and a disease outcome are essential for researchers to develop clinical interventions to treat the disease by modulating the microbes. Existing methods for mediation analysis of the microbiome are often limited to a global test of community-level mediation or selection of mediating microbes without control of the false discovery rate (FDR). Further, while the null hypothesis of no mediation at each microbe is a composite null that consists of three types of null (no exposure-microbe association, no microbe-outcome association given the exposure, or neither), most existing methods for the global test such as MedTest and MODIMA treat the microbes as if they are all under the same type of null.

MethodsWe propose a new approach based on inverse regression that regresses the (possibly transformed) relative abundance of each taxon on the exposure and the exposure-adjusted outcome to assess the exposure-taxon and taxon-outcome associations simultaneously. Then the association p-values are used to test mediation at both the community and individual taxon levels. This approach fits nicely into our Linear Decomposition Model (LDM) frame-work, so our new method is implemented in the LDM and enjoys all the features of the LDM, i.e., allowing an arbitrary number of taxa to be tested, supporting continuous, discrete, or multivariate exposures and outcomes as well as adjustment of confounding covariates, accom-modating clustered data, and offering analysis at the relative abundance or presence-absence scale. We refer to this new method as LDM-med.

ResultsUsing extensive simulations, we showed that LDM-med always controlled the type I error of the global test and had compelling power over existing methods; LDM-med always preserved the FDR of testing individual taxa and had much better sensitivity than alternative approaches. In contrast, MedTest and MODIMA had severely inflated type I error when different taxa were under different types of null. The flexibility of LDM-med for a variety of mediation analyses is illustrated by the application to a murine microbiome dataset.

Availability and ImplementationOur new method has been added to our R package LDM, which is available on GitHub at https://github.com/yijuanhu/LDM.

category: bioinformatics


title: Precision size and refractive index analysis of weakly scattering nanoparticles in polydispersions.

abstract: Characterization of the size and material properties of particles in liquid suspensions is in very high demand, e.g., for the analysis of colloidal samples or of bodily fluids such as urine or blood plasma. However, the existing methods are limited in deciphering the constituents of realistic samples. Here, we introduce iNTA as a new method, which combines interferometric detection of scattering with nanoparticle tracking analysis, to reach an unprecedented sensitivity and precision in determining the size and refractive index distributions of nanoparticles in suspensions. After benchmarking iNTA with samples of colloidal gold, we present its remarkable ability to resolve the constituents of various multi-component and polydisperse samples of known origin. Furthermore, we showcase the method by elucidating the refractive index and size distributions of extracellular vesicles from Leishmania parasites and nanoparticles in human urine. The current performance of iNTA already enables advances in several important applications, but we also discuss possible improvements.

category: biophysics


title: Uncovering natural variation in root system architecture and growth dynamics using a robotics-assisted phenomics platform

abstract: The plant kingdom contains a stunning array of complex morphologies easily observed above ground, but largely unexplored below-ground. Understanding the magnitude of diversity in root distribution within the soil, termed root system architecture (RSA), is fundamental to determining how this trait contributes to species adaptation in local environments. Roots are the interface between the soil environment and the shoot system and therefore play a key role in anchorage, resource uptake, and stress resilience. Previously, we presented the GLO-Roots (Growth and Luminescence Observatory for Roots) system to study the RSA of soil-grown Arabidopsis thaliana plants from germination to maturity (Rellan-Alvarez et al. 2015). In this study, we present the automation of GLO-Roots using robotics and the development of image analysis pipelines in order to examine the natural variation of RSA in Arabidopsis over time. This dataset describes the developmental dynamics of 93 accessions and reveals highly complex and polygenic RSA traits that show significant correlation with climate variables.

category: plant biology


title: Protection of mice against experimental cryptococcosis by synthesized peptides delivered in glucan particles

abstract:
The high global burden of cryptococcosis has made development of a protective vaccine a public health priority. We previously demonstrated that a vaccine composed of recombinant Cryptococcus neoformans chitin deacetylase 2 (Cda2) delivered in glucan particles (GPs) protects BALB/c and C57BL/6 mice from an otherwise lethal challenge with a highly virulent C. neoformans strain. An immunoinformatic analysis of Cda2 revealed a peptide sequence predicted to have strong binding to the MHC Class II (MHC II) H2-IAd allele found in BALB/c mice. BALB/c mice vaccinated with GPs containing a 32 amino acid peptide (Cda2-Pep1) that included this strong binding region were protected from cryptococcosis. Protection was lost with GP-based vaccines containing versions of recombinant Cda2 protein and Cda2-Pep1 with mutations predicted to greatly diminish MHC II binding. Cda2 has homology to the three other C. neoformans chitin deacetylases, Cda1, Cda3 and Fpd1, in the high MHC II binding region. GPs loaded with homologous peptides of Cda1, Cda3 and Fpd1 protected BALB/c mice from experimental cryptococcosis, albeit not as robustly as the Cda2-Pep1 vaccine. Finally, seven other peptides were synthesized based on regions in Cda2 predicted to contain promising CD4+ T cell epitopes in BALB/c or C57BL/6 mice. While five peptide vaccines significantly protected BALB/c mice, only one protected C57BL/6 mice. Thus, GP-based vaccines containing a single peptide can protect mice against cryptococcosis. However, given the diversity of human MHC II alleles, a peptide-based Cryptococcus vaccine for use in humans would be challenging and likely need to contain multiple peptide sequences.

ImportanceCryptococcosis, due to infection by fungi of the Cryptococcus neoformans species complex, is responsible for substantial morbidity and mortality in immunocompromised persons, particularly those with AIDS. Cryptococcal vaccines are a public health priority yet are not available for human use. We previously demonstrated mice could be protected from experimental cryptococcosis with vaccines composed of recombinant cryptococcal proteins encased in hollow highly purified yeast cell walls (glucan particles). Here, we examined one such protective protein, Cda2, and using bioinformatics, identified a region predicted to stimulate strong T cell responses. A peptide containing this region formulated in glucan particle-based vaccines protected mice as well as the recombinant protein. Other peptide vaccines also protected, including peptides containing sequences from proteins homologous to Cda2. These preclinical mouse studies provide a proof of principle that peptides can be effective as vaccines to protect against cryptococcosis and that bioinformatic approaches can guide peptide selection.

category: immunology


title: FoxP3 associates with enhancer-promoter loopsto regulate Treg-specific gene expression

abstract:
Gene expression programs are specified by higher-order chromatin structure and enhancer-promoter loops (EPL). T regulatory cells (Treg) identity is dominantly specified by the transcription factor FoxP3, whose mechanism of action is unclear. We applied proximity-ligation with chromatin immunoprecipitation (HiChIP) in Treg and closely related conventional CD4+ T cells (Tconv). EPL identified by H3K27Ac HiChIP showed a range of connection intensity, with some super-connected genes. TF-specific HiChIP showed that FoxP3 interacts with EPLs at a large number of genes, including some not differentially expressed in Treg vs Tconv, but enriched at the core Treg signature loci that it upregulates. FoxP3 association correlates with heightened H3H27Ac looping, as ascertained by analysis of FoxP3-deficient Treg-like cells. There was marked asymmetry in the loci where FoxP3 associated at the enhancer- or the promoter-side of EPLs, with enrichment for different transcriptional cofactors. FoxP3 EPL intensity distinguished gene clusters identified by single-cell ATAC-seq as co-varying between individual Tregs, supporting a direct transactivation model for FoxP3 in determining Treg identity.

One Sentence SummaryFoxP3 is associated with enhancer-promoter loops in Treg cells, and correlates with heightened enhancer-promoter cross-talk


title: Ferric Citrate Uptake is a Virulence Factor in Uropathogenic Escherichia coli

abstract:
More than half of women will experience a urinary tract infection (UTI) with uropathogenic Escherichia coli (UPEC) causing [~]80% of uncomplicated cases. Iron acquisition systems are essential for uropathogenesis, and UPEC encode functionally redundant iron acquisition systems, underlining their importance. However, a recent UPEC clinical isolate, HM7 lacks this functional redundancy and instead encodes a sole siderophore, enterobactin. To determine if E. coli HM7 possesses unidentified iron acquisition systems, we performed RNA-sequencing under iron-limiting conditions and demonstrated that the ferric citrate uptake system (fecABCDE and fecIR) was highly upregulated. Importantly, there are high levels of citrate within urine, some of which is bound to iron, and the fec system is highly enriched in UPEC isolates compared to environmental or fecal strains. Therefore, we hypothesized that HM7 and other similar strains use the fec system to acquire iron in the host. Deletion of both enterobactin biosynthesis and ferric citrate uptake ({Delta}entB/{Delta}fecA) abrogates use of ferric citrate as an iron source and fecA provides an advantage in human urine in absence of enterobactin. However, in a UTI mouse model, fecA is a fitness factor independent of enterobactin production, likely due to the action of host Lipocalin-2 chelating ferrienterobactin. These findings indicate that ferric citrate uptake is used as an iron source when siderophore efficacy is limited, such as in the host during UTI. Defining these novel compensatory mechanisms and understanding the nutritional hierarchy of preferred iron sources within the urinary tract are important in the search for new approaches to combat UTI.

ImportanceUPEC, the primary causative agent of uncomplicated UTI is responsible for five billion dollars in healthcare costs in the US each year. Rates of antibiotic resistance are on the rise therefore it is vital to understand the mechanisms of UPEC pathogenesis to uncover potential targets for novel therapeutics. Iron acquisition systems used to obtain iron from sequestered host sources are essential for UPEC survival during UTI and have been used as vaccine targets to prevent infection. This study reveals the ferric citrate uptake system is another important iron acquisition system that is highly enriched in UPEC strains. Ferric citrate uptake has not previously been associated with these pathogenic isolates, underlining the importance of the continued study of these strains to fully understand their mechanisms of pathogenesis.

category: microbiology


title: Recombinant Group A Carbohydrate backbone embedded into Outer Membrane Vesicles is a potent vaccine candidate targeting Group A Streptococcus from Streptococcus pyogenes and Streptococcus dysgalactiae subsp. equisimilis

abstract:
BackgroundGroup A Streptococcus (GAS) are responsible for a wide range of human-exclusive infections, annually killing more than 500,000 people. Antibiotic resistance incidence of invasive GAS tripled in the past decade and emphasises the need to develop a universal GAS vaccine. We have produced, for the first time, a recombinant polyrhamnose backbone (pRha), a validated universal GAS vaccine candidate. E. coli outer membrane vesicles (OMVs) carrying pRha were investigated for their immunogenicity and efficacy in an animal model.

MethodsOMVs decorated with pRha were administered to C57BL/6J mouse and rabbit models. Flow cytometry, ELISA, Luminex, immunofluorescence microscopy and serum bactericidal assay assays were conducted to investigate the ability of pRha-specific antibodies to recognise and kill clinical (hypervirulent) GAS strains.

ResultsOur results suggest that pRha-OMVs induce specific antibodies which recognise Group A Carbohydrate (GAC) from S pyogenes and S. dysgalactiae subsp. equisimilis. Increased IgG levels correlate with increased bactericidal killing of the hypervirulent GAS M89 strain. Elevated IL-17a from pRha-OMV-immunised splenocytes indicates possible stimulation of long-term memory immune cells.

ConclusionWe are the first to report efficacy and potency of this unique, exogenously produced polysaccharide, pRha, in the induction of humoral-mediated immune responses to GAS.

TopicStreptococcus pyogenes, immunoglobulins, polysaccharides, opsonophagocytosis, acute rheumatic fever, M protein, invasive Group A Streptococcus, hyaluronic acid


title: Three-dimensional structure of the kinetochore-fibers in human mitotic spindles

abstract: During cell division, kinetochore microtubules (KMTs) provide a physical linkage between the spindle poles and the chromosomes. KMTs in mammalian cells are organized into bundles, so-called kinetochore-fibers (k-fibers), but the ultrastructure of these fibers is currently not well characterized. Here we show by large-scale electron tomography that each k-fiber in HeLa cells in metaphase is composed of approximately nine KMTs, only half of which reach the spindle pole. Our comprehensive reconstructions allowed us to analyze the three-dimensional (3D) morphology of k-fibers in detail, and we find that they exhibit remarkable variation. K-fibers display differences in circumference and KMT density along their length, with the pole-facing side showing a splayed-out appearance. We further observed that the association of KMTs with non-KMTs predominantly occurs in the spindle pole regions. Our 3D reconstructions have implications for models of KMT behavior and k-fiber self-organization as covered in a parallel publication applying complementary live-cell imaging in combination with biophysical modeling (Conway et al., 2021). The presented data will also serve as a resource for further studies on mitosis in human cells.

category: cell biology


title: A novel mechanism of bulk cytoplasmic transport by cortical dynein in Drosophila ovary

abstract: Cytoplasmic dynein, a major minus-end directed microtubule motor, plays essential roles in eukaryotic cells. Drosophila oocyte growth is mainly dependent on the contribution of cytoplasmic contents from the interconnected sister cells, nurse cells. We have previously shown that cytoplasmic dynein is required for Drosophila oocyte growth, and assumed that it transports cargoes along microtubule tracks from nurse cells to the oocyte. Here we report that instead transporting cargoes along microtubules into the oocyte, cortical dynein actively moves microtubules in nurse cells and from nurse cells to the oocyte via the cytoplasmic bridges, the ring canals. We demonstrate this microtubule movement is sufficient to drag even inert cytoplasmic particles through the ring canals to the oocyte. Furthermore, replacing dynein with a minus-end directed plant kinesin linked to the actin cortex is sufficient for transporting organelles and cytoplasm to the oocyte and driving its growth. These experiments show that cortical dynein can perform bulk cytoplasmic transport by gliding microtubules along the cell cortex and through the ring canals to the oocyte. We propose that the dynein-driven microtubule flow could serve as a novel mode of cargo transport for fast cytoplasmic transfer to support rapid oocyte growth.


title: A Multi-Omics and Bioenergetics Longitudinal Aging Dataset in Primary Human Fibroblasts with Mitochondrial Perturbations

abstract: Aging is a process of progressive change. In order to develop biological models of aging, longitudinal datasets with high temporal resolution are needed. Here we report a multi-omic longitudinal dataset for cultured primary human fibroblasts measured across their replicative lifespans. Based on the accelerated nature of epigenetic aging in vitro, these longitudinal data are equivalent to [~]40 years of follow-up sampling at a frequency of every [~]3 years. Fibroblasts were sourced from both healthy donors (n=6) and individuals with lifespan-shortening mitochondrial disease (n=3). The dataset includes cytological (cell size, morphology), bioenergetic (energy expenditure, derived ATP synthesis rates), epigenetic (DNA methylation), gene expression (RNA sequencing), secreted proteins, mitochondrial DNA (mtDNA) copy number and mutations, cell-free DNA, telomere length, and whole-genome sequencing data. This dataset enables the bridging of mechanistic processes of aging as outlined by the "hallmarks of aging", with the descriptive characterization of aging provided by epigenetic clocks and other metrics. Here we focus on bridging the gap for the hallmark mitochondrial metabolism. Our dataset includes measurement of healthy cells replicating through senescence without intervention, as well as cells subjected to over a dozen experimental manipulations targeting oxidative phosphorylation (OxPhos), glycolysis, and glucocorticoid signaling, among others. These experiments provide opportunities to test how cellular energetics affect the biology of cellular aging. All data are publicly available at our webtool: https://columbia-picard.shinyapps.io/shinyapp-Lifespan_Study/


title: A quantitative synthesis of soil microbial effects on plant species coexistence

abstract: Soil microorganisms play a major role in shaping plant diversity, not only through their direct effects as pathogens, mutualists, and decomposers, but also by altering interactions between plants. In particular, previous research has shown that the soil community often generates frequency-dependent feedback loops among plants that can either destabilize species interactions, or generate stabilizing niche differences that promote species coexistence. However, recent insights from modern coexistence theory have shown that microbial effects on plant coexistence depend not only on these stabilizing or destabilizing effects, but also on the degree to which they generate competitive fitness differences. While many previous experiments have generated the data necessary for evaluating microbially mediated fitness differences, these effects have rarely been quantified in the literature. Here we present a meta-analysis of data from 50 studies, which we used to quantify the microbially mediated (de)stabilization and fitness differences derived from a classic plant-soil feedback model. Across 518 pairwise comparisons, we found that soil microbes generated both stabilization (or destabilization) and fitness differences, but also that the microbially mediated fitness differences dominated. As a consequence, if plants are otherwise equivalent competitors, the balance of soil microbe-generated (de)stabilization and fitness differences drives species exclusion much more frequently than coexistence or priority effects. Our work shows that microbially mediated fitness differences are an important but overlooked effect of soil microbes on plant coexistence. This finding paves the way for a more complete understanding of the processes that maintain plant biodiversity.

category: ecology


title: Stage-specific disruption of X chromosome expression during spermatogenesis in sterile house mouse hybrids

abstract: Hybrid sterility is a complex phenotype that can result from the breakdown of spermatogenesis at multiple developmental stages. Here, we disentangle two proposed hybrid male sterility mechanisms in the house mice, Mus musculus domesticus and M. m. musculus, by comparing patterns of gene expression in sterile F1 hybrids from a reciprocal cross. We found that hybrid males from both cross directions showed disrupted X chromosome expression during prophase of meiosis I consistent with a loss of Meiotic Sex Chromosome Inactivation (MSCI) and Prdm9-associated sterility, but that the degree of disruption was greater in mice with an M. m. musculus X chromosome consistent with previous studies. During postmeiotic development, gene expression on the X chromosome was only disrupted in one cross direction, suggesting that misexpression at this later stage was genotype-specific and not a simple downstream consequence of MSCI disruption which was observed in both reciprocal crosses. Instead, disrupted postmeiotic expression may depend on the magnitude of earlier disrupted MSCI, or the disruption of particular X-linked genes or gene networks. Alternatively, only hybrids with a potential deficit of Sly copies, a Y-linked ampliconic gene family, showed overexpression in postmeiotic cells, consistent with a previously proposed model of antagonistic coevolution between the X and Y-linked ampliconic genes contributing to disrupted expression late in spermatogenesis. The relative contributions of these two regulatory mechanisms and their impact on sterility phenotypes awaits further study. Our results further support the hypothesis that X-linked hybrid sterility in house mice has a variable genetic basis, and that genotype-specific disruption of gene regulation contributes to overexpression of the X chromosome at different stages of development. Overall, these findings underscore the critical role of epigenetic regulation of the X chromosome during spermatogenesis and suggest that these processes are prone to disruption in hybrids.

category: evolutionary biology


title: Persistent parental RNAi in the beetle Tribolium castaneum involves maternal transmission of long double-stranded RNA

abstract: Parental RNA interference (pRNAi) is a powerful and widely used method for gene-specific knockdown. Yet in insects its efficacy varies between species, and how the systemic RNAi response is transmitted from mother to offspring remains elusive. Using the flour beetle Tribolium castaneum, we report an RT-qPCR strategy to unmask the presence of double-stranded RNA (dsRNA) distinct from endogenous mRNA. We find that the injected dsRNA is directly transmitted into the egg and persists throughout embryogenesis. Despite this depletion of dsRNA from the mother, we show that strong pRNAi can persist for months before waning at strain-specific rates. In seeking the receptor proteins for cellular uptake of long dsRNA into the egg, we lastly present a phylogenomics profiling approach to ascertain macroevolutionary distributions of candidate proteins. We demonstrate a visualization strategy based on taxonomically hierarchical assessment of orthology clustering data to rapidly assess gene age and copy number changes, refined by several lines of sequence-based evidence. We use this approach to document repeated losses of SID-1-like channel proteins in the arthropods, including wholesale loss in the Heteroptera (true bugs), which are nonetheless highly sensitive to pRNAi. Overall, we elucidate practical considerations for insect pRNAi against a backdrop of outstanding questions on the molecular mechanism of dsRNA transmission to achieve long-term, systemic knockdown.

category: genetics


title: Timelapse viability assay to detect division and death of primary multiple myeloma cells in response to drug treatments with single cell resolution

abstract:
Heterogeneity among cancer cells and in the tumor microenvironment (TME) is thought to be a significant contributor to the heterogeneity of clinical therapy response observed between patients and can evolve over time. A primary example of this is multiple myeloma (MM), a generally incurable cancer where such heterogeneity contributes to the persistent evolution of drug resistance. However, there is a paucity of functional assays for studying this heterogeneity in patient samples or for assessing the influence of the patient TME on therapy response. Indeed, the population-averaged data provided by traditional drug response assays and the large number of cells required for screening remain significant hurdles to advancement. To address these hurdles, we developed a suite of accessible technologies for quantifying functional drug response to a panel of therapies in ex vivo three-dimensional culture using small quantities of a patients own cancer and TME components. This suite includes tools for label-free single-cell identification and quantification of both cell division and death events with a standard brightfield microscope, an open-source software package for objective image analysis and feasible data management of multi-day timelapse experiments, and a new approach to fluorescent detection of cell death that is compatible with long-term imaging of primary cells. These new tools and capabilities are used to enable sensitive, objective, functional characterization of primary MM cell therapy response in the presence of TME components, laying the foundation for future studies and efforts to enable predictive assessment drug efficacy for individual patients.

Insight BoxThe new tools and capabilities described here allow new insights into functional primary cell therapy response by (i) enabling more drugs to be tested on precious and limited numbers of patient cells ex vivo (ii) providing the ability to discriminate both cell division and death events over multiple days with single-cell resolution, and (iii) by incorporating the influences of a patients own cancer cells and TME components on drug response.

category: bioengineering


title: Inhibition of Interactions Between NDPK-B and NDPK-C in Presence of Graphene Oxide

abstract: During a heart failure, higher amount of nucleoside diphosphate kinase (NDPK) enzyme in the sarcolemma membrane inhibits the synthesis of second messenger cyclic adenosine monophosphate (cAMP), which is required for the regulation of the calcium ion balance for normal functioning of the heart. In a dependent pathway, NDPK normally phosphorylates the stimulatory guanosine diphosphate, GDP(s), to a guanosine triphosphate, GTP(s), on the heterotrimeric (, {beta} and {gamma} subunits) guanine nucleotide binding protein (G protein), resulting in the stimulation of the cAMP formation. In case of a heart failure, an increased quantity of NDPK also reacts with the inhibitory GDP(i), which is converted to a GTP(i), resulting in the inhibition of the cAMP formation. Typically, the {beta}{gamma} dimer of the G protein binds with hexameric NDPK-B/C complex and receives the phosphate at the residue His266 from residue His118 of NDPK-B. It is known that NDPK-C is required for NDPK-B to phosphorylate the G protein. In this work, the interactions between NDPK-B and NDPK-C are quantified in the presence and absence of graphene oxide (GO) as well as those between NDPK-B and GO through stability analysis involving hydrogen bonds, center of mass (COM), root mean square deviation (RMSD), and salt bridges, and energetics analysis involving van der Waals (VDW) and electrostatic energies. Furthermore, the role of water molecules at the interface of NDPK-B and NDPK-C as well as between NDPK-B and GO is investigated to understand the nature of interactions. It is found that the adsorption of NDPK-B on GO triggers a potential conformational change in the structure of NDPK-B, resulting in a diminished interaction with NDPK-C. This is confirmed through a reduced center of mass (COM) distance between NDPK-B and GO (from 40 [A] to 30 [A]) and an increased COM distance between NDPK-B and NDPK-C (from 50 [A] to 60 [A]). Furthermore, this is also supported by fewer salt bridges between NDPK-B and NDPK-C, and an increased number of hydrogen bonds formed by the interfacial water molecules. As NDPK-C is crucial to be complexed with NDPK-B for successful interaction of NDPK-B with the G protein, this finding shows that GO can suppress the interactions between NDPK-B/C and G proteins, thereby providing an additional insight into the role of GO in the heart failure mechanism.


title: A new approach to the determination of tubular membrane capacitance: passive membrane electrical properties under reduced electrical conductivity of the extracellular solution

abstract:
The tubular system of cardiomyocytes plays a key role in excitation-contraction coupling. To determine the area of the tubular membrane in relation to the area of the surface membrane, indirect measurements through the determination of membrane capacitances by electrophysiological measurements are currently used in addition to microscopic methods. Unlike existing electrophysiological methods based on an irreversible procedure (osmotic shock), the proposed approach uses a reversible short-term intermittent increase in the electrical resistance of the extracellular medium. The resulting increase in the lumen resistance of the tubular system makes it possible to determine separately capacitances of the tubular and surface membranes from altered capacitive current responses to subthreshold voltage-clamped rectangular pulses. Based on the analysis of the time course of capacitive current, computational relations were derived which allow to quantify elements of the electrical equivalent circuit of the measured cardiomyocyte including both capacitances. The exposition to isotonic low-conductivity sucrose solution is reversible which is the main advantage of the proposed approach allowing repetitive measurements on the same cell under control and sucrose solutions. In addition, it might be possible to identify changes in both surface and tubular membrane capacitances caused by various interventions. Preliminary experiments in rat ventricular cardiomyocytes (n = 10) resulted in values of the surface and tubular capacitances 72.3 {+/-} 16.4 and 42.1 {+/-} 14.7 pF, respectively, implying the fraction of tubular capacitance/area of 0.36 {+/-} 0.08. We conclude that the newly proposed method provides results comparable to those reported in literature and, in contrast to the currently used methods, enables repetitive evaluation of parameters describing the surface and tubular membranes. It may be used to study alterations of the tubular system resulting from various interventions including associated cardiac pathologies.

Author summaryThe cell membrane of cardiomyocytes is invaginated forming a net of tubules through the whole cell (the tubular system). These invaginations are essential for the coordinated contraction of cardiomyocytes. Various cardiac diseases may lead to an alteration of the tubular system and vice versa alteration of the tubular system may result in cardiac dysfunction. Therefore, it is desirable to investigate the tubular membrane separately. Unfortunately, it is not easy and methods currently used for this purpose provide diverse results. The widely used detubulation methods (separating the tubular and surface membrane by an osmotic shock) are irreversible. It makes impossible repeated measurements on the same cell, thus, disabling evaluation of parameters describing the surface and tubular membranes and particularly testing changes in the tubular system. We developed an alternative approach based on the electrical separation of the tubular and surface membranes induced by exposition of the cardiomyocyte to an isotonic sucrose solution with low electrical conductivity. It allows to quantify the approximate area of the surface and tubular membrane using evaluation of electrical capacitance of both membrane areas. Measurements can be repeated several times on the same cell.


title: Cryo-EM structure of the Inner Ring from Xenopus laevis Nuclear Pore Complex

abstract: Nuclear pore complex (NPC) mediates nucleocytoplasmic shuttling. Here we present single-particle cryo-electron microscopy (cryo-EM) structure of the inner ring (IR) subunit from Xenopus laevis NPC at an average resolution of 4.4 [A]. The symmetric IR subunit comprises a cytoplasmic half and a nuclear half. A homo-dimer of Nup205 resides at the center of the IR subunit, flanked by two molecules of Nup188. Four molecules of Nup93 each places an extended helix into the axial groove of Nup205 or Nup188, together constituting the central scaffold. The channel nucleoporin heterotrimer (CNT) of Nup54/58/62 is anchored on the central scaffold. Six Nup155 molecules interact with the central scaffold and together with the NDC1-ALADIN hetero-dimers anchor the IR subunit to the nuclear envelope and to outer rings. The scarce inter-subunit contacts may allow sufficient latitude in conformation and diameter of the IR. Our structure of vertebrate IR reveals key insights that are functionally important.


title: Progressive enhancement of kinetic proofreading in T cell antigen discrimination from receptor activation to DAG generation

abstract: T cells use kinetic proofreading to discriminate antigens by converting small changes in antigen binding lifetime into large differences in cell activation, but where in the signaling cascade this computation is performed is unknown. Previously, we developed a light-gated immune receptor to probe the role of ligand kinetics in T cell antigen signaling. We found significant kinetic proofreading at the level of the signaling lipid diacylglycerol (DAG) but lacked the ability to determine where the multiple signaling steps required for kinetic discrimination originate in the upstream signaling cascade (Tischer and Weiner, 2019). Here we uncover where kinetic proofreading is executed by adapting our optogenetic system for robust activation of early signaling events. We find the strength of kinetic proofreading progressively increases from Zap70 recruitment to LAT clustering to downstream DAG generation. These data suggest a distributed kinetic proofreading mechanism, with proofreading steps both at the receptor and at downstream signaling events. Leveraging the ability of our system to rapidly disengage ligand binding, we measure slower reset rates for downstream signaling events. Our observations of distributed kinetic proofreading and slowed resetting of downstream steps suggest a basis of cooperativity between multiple active receptors with implications in tissue homeostasis, autoimmunity, and immunotherapy off-target effects.


title: The Transcriptome Architecture of Polyomaviruses

abstract: Polyomaviruses (PyV) are ubiquitous pathogens that can cause devastating human diseases. Due to the small size of their genomes, PyV utilize complex patterns of RNA splicing to maximize their coding capacity. Despite the importance of PyV to human disease, their transcriptome architecture is poorly characterized. Here, we compare short- and long-read RNA sequencing data from eight human and non-human PyV. We provide a detailed transcriptome atlas for BK polyomavirus (BKPyV), an important human pathogen, and the prototype PyV, simian virus 40 (SV40). We identify pervasive wraparound transcription in PyV, wherein transcription runs through the polyA site and circles the genome multiple times. Comparative analyses identify novel, conserved transcripts that increase PyV coding capacity. One of these conserved transcripts encodes superT, a T antigen containing two RB-binding LxCxE motifs. We find that superT-encoding transcripts are abundant in PyV-associated human cancers. Together, we show that comparative transcriptomic approaches can greatly expand known transcript and coding capacity in one of the simplest and most well-studied viral families.


title: Poly ADP-ribosylation of SET8 leads to aberrant H4K20me1 domains in mammalian cells

abstract: In mammalian cells, SET8 mediated Histone H4 Lys 20 monomethylation (H4K20me1) has been implicated in regulating mitotic condensation, DNA replication, DNA damage response, and gene expression. Here we show SET8, the only known enzyme for H4K20me1 is post-translationally poly ADP-ribosylated by PARP1 on lysine residues. PARP1 interacts with SET8 in a cell cycle-dependent manner. Poly ADP-ribosylation on SET8 renders it catalytically compromised, and degradation via ubiquitylation pathway. Knockdown of PARP1 led to an increase of SET8 protein levels, leading to aberrant H4K20me1 and H4K20me3 domains genome-wide. H4K20me1 is associated with higher gene transcription levels while the increase of H4K20me3 levels was predominant in DNA repeat elements correlating with modulation of chromatin states. Hence, SET8 mediated chromatin remodeling in mammalian cells are modulated by poly ADP-ribosylation by PARP1.


title: Poly ADP-ribosylation of SET8 leads to aberrant H4K20 methylation domains in mammalian cells


title: Siderophores as an iron source for Prochlorococcus in deep chlorophyll maximum layers of the oligotrophic ocean

abstract: Prochlorococcus is one of the most abundant photosynthesizing organisms in the oligotrophic oceans. Gene content variation among Prochlorococcus populations in separate ocean basins often mirrors the selective pressures imposed by the regions distinct biogeochemistry. By pairing genomic datasets with trace metal concentrations from across the global ocean, we show that the genomic capacity for siderophore-mediated iron uptake is widespread in low-light adapted Prochlorococcus populations from iron-depleted regions of the oligotrophic Pacific and S. Atlantic oceans: Prochlorococcus siderophore consumers were absent in the N. Atlantic ocean (higher iron flux) but constituted up to half of all Prochlorococcus genomes from metagenomes in the N. Pacific (lower iron flux). Prochlorococcus siderophore consumers, like many other bacteria with this trait, also lack siderophore biosynthesis genes indicating that they scavenge exogenous siderophores from seawater. Statistical modeling suggests that the capacity for siderophore uptake is endemic to remote ocean regions where atmospheric iron fluxes are the smallest, particularly at deep chlorophyll maximum and primary nitrite maximum layers. We argue that abundant siderophore consumers at these two common oceanographic features could be a symptom of wider community iron stress, consistent with prior hypotheses. Our results provide a clear example of iron as a selective force driving the evolution of Prochlorococcus.


title: Homology mediated end joining enables efficient non-viral targeted integration of large DNA templates in primary human T cells

abstract: Adoptive cellular therapy using genetically engineered immune cells holds tremendous promise for the treatment of advanced cancers. While the number of available receptors targeting tumor specific antigens continues to grow, the current reliance on viral vectors for clinical production of engineered immune cells remains a significant bottleneck limiting translation of promising new therapies. Here, we describe an optimized methodology for efficient CRISPR-Cas9 based, non-viral engineering of primary human T cells that overcomes key limitations of previous approaches. By synergizing temporal optimization of reagent delivery, reagent composition, and integration mechanism, we achieve targeted integration of large DNA cargo at efficiencies nearing those of viral vector platforms with minimal toxicity. CAR-T cells generated using our approach are highly functional and elicit potent anti-tumor cytotoxicity in vitro and in vivo. Importantly, our method is readily adaptable to cGMP compliant manufacturing and clinical scale-up, offering a near-term alternative to the use of viral vectors for production of genetically engineered T cells for cancer immunotherapy.


title: Age-linked suppression of lipoxin A4 mediates cognitive deficits in mice and humans

abstract: Age increases the risk for cognitive impairment and is the single major risk factor for Alzheimers disease (AD), the most prevalent form of dementia in the elderly. The pathophysiological processes triggered by aging that render the brain vulnerable to dementia involve, at least in part, changes in inflammatory mediators. Here we show that lipoxin A4 (LXA4), a lipid mediator of inflammation resolution known to stimulate endocannabinoid signaling in the brain, is reduced in the aging central nervous system. We demonstrate that genetic suppression of 5-lipoxygenase (5-LOX), the enzyme mediating LXA4 synthesis, promotes learning impairment in mice. Conversely, administration of exogenous LXA4 attenuated cytokine production and memory loss induced by inflammation in mice. We further show that cerebrospinal fluid LXA4 is reduced in patients with dementia and positively associates with memory performance, brain-derived neurotrophic factor (BDNF), and AD-linked amyloid-. Our findings suggest that reduced LXA4 levels may lead to vulnerability to age-related cognitive disorders and that promoting LXA4 signaling may comprise an effective strategy to prevent early cognitive decline in AD.

category: neuroscience


title: Vγ usage distinguishes pro- and anti-tumor intestinal γδ T cell subsets

abstract: {gamma}{delta} T cells physiologically scan the intestinal epithelium, representing a substantial fraction of infiltrating lymphocytes in colorectal cancer (CRC), albeit their role in CRC remains unclear. Using murine CRC models, we found that most {gamma}{delta} T cells in pre- or non-tumor colon express V{gamma}1+ or V{gamma}7+ and exhibit a cytotoxic profile. Targeting these {gamma}{delta} T cell subsets, as well as conditionally interfering with {gamma}{delta} T cell function at early stages of tumorigenesis led to heightened tumor development, suggesting anti-CRC functions for V{gamma}1+ and V{gamma}7+ subsets. In contrast, ROR{gamma}t+ {gamma}{delta} T cell subsets, including V{gamma}4+ and microbiotadependent V{gamma}6+, accumulated during CRC progression. Conditional deletion of ROR{gamma}t or V{gamma} chains revealed redundant roles for IL-17-producing V{gamma}4+ and V{gamma}6+ {gamma}{delta} T cells in promoting tumor growth. Our results uncover pro- and anti-tumor roles for {gamma}{delta} T cell subsets.


title: A deep learning framework for quantitative analysis of actin microridges

abstract: Microridges are evolutionarily conserved actin-rich protrusions present on the apical surface of the squamous epithelial cells. In zebrafish epidermal cells, microridges form self-evolving patterns due to the underlying actomyosin network dynamics. However, their morphological and dynamic characteristics have remained poorly understood owing to lack of automated segmentation methods. We achieved ~97% pixel-level accuracy with the deep learning microridge segmentation strategy enabling quantitative insights into their bio-physical-mechanical characteristics. From the segmented images, we estimated an effective microridge persistence length as ~0.61m. We discovered the presence of mechanical fluctuations and found relatively greater stresses stored within patterns of yolk than flank, indicating distinct regulation of their actomyosin networks. Furthermore, spontaneous formations and positional fluctuations of actin clusters within microridge influenced pattern rearrangements over short length/time-scales. Our framework allows large-scale spatiotemporal analysis of microridges during epithelial development and probing of their responses to chemical and genetic perturbations to unravel the underlying patterning mechanisms.

category: developmental biology


title: F0-F1 coupling and symmetry mismatch in ATP synthase resolved in every F0 rotation step

abstract: The F0F1 ATP synthase, essential for cellular energy production, is composed of the F0 and F1 rotary motors. While both F0 and F1 have pseudo-symmetric structures, their symmetries do not match. How the symmetry mismatch is solved remains elusive due to missing intermediate structures of rotational steps. Here, for ATP synthases with 3- and 10-fold symmetries in F1 and F0, respectively, we uncovered the mechanical couplings between F0 and F1 at every 36{degrees} rotation step via molecular dynamics simulations and comparison of cryo-electron microscopy structures from three species. We found that the frustration is shared by several elements. The F1 stator partially rotates relative to the F0 stator via elastic distortion of the b-subunits. The rotor can be distorted. The c-ring rotary angles can be deviated from symmetric ones. Additionally, the F1 motor may take non-canonical structures relieving stronger frustration. Together, we provide comprehensive understanding to solve the symmetry mismatch.


title: Modeling Macroscopic Currents of Ion Channels

abstract: Ion-channel functions are often studied by the current-voltage relation, which is commonly fitted by the Boltzmann equation, a powerful model widely used nowadays. However, the Boltzmann model is restricted to a two-state ion-permeation process. Here we present an improved model that comprises a flexible number of states and incorporates both the single-channel conductance and the open-channel probability. Employing the channel properties derived from the single-channel recording experiments, the proposed model is able to describe various current-voltage relations, especially the reversal ion-permeation curves showing the inward- and outward-rectifications. We demonstrate the applicability of the proposed model using the published patch-clamp data of BK and MthK potassium channels, and discuss the similarity of the two channels based on the model studies.

category: physiology


title: Mechanism of glycogen synthase inactivation and interaction with glycogenin

abstract: Glycogen is the major glucose reserve in eukaryotes, and defects in glycogen metabolism and structure lead to disease. Glycogenesis involves interaction of glycogenin (GN) with glycogen synthase (GS), where GS is activated by glucose-6-phosphate (G6P) and inactivated by phosphorylation. We describe the 2.6 [A] resolution cryo-EM structure of phosphorylated human GS revealing an autoinhibited GS tetramer flanked by two GN dimers. Phosphorylated N- and C-termini from two GS protomers converge near the G6P-binding pocket and buttress against GS regulatory helices. This keeps GS in an inactive conformation mediated by phospho-Ser641 interactions with a composite "arginine cradle". Structure-guided mutagenesis perturbing interactions with phosphorylated tails led to increased basal/unstimulated GS activity. We propose that multivalent phosphorylation supports GS autoinhibition through interactions from a dynamic "spike" region, allowing a tuneable rheostat for regulating GS activity. This work therefore provides new insights into glycogen synthesis regulation and facilitates studies of glycogen-related diseases.


title: Initiation of organ maturation and fruit ripening in grapevine is controlled by the CARPO-NAC transcription factor

abstract:
Grapevine is a woody temperate perennial plant and one of the most important fruit crops with global relevance in both the fresh fruit and winemaking industries. Unfortunately, global warming is affecting viticulture by altering developmental transitions and fruit maturation processes. In this context, uncovering the molecular mechanisms controlling the onset and progression of ripening could prove essential to maintain high-quality grapes and wines. Through a deep inspection of previously published transcriptomic data we identified the NAC family member VviCARPO (Controlled Adjustment of Ripening and maturation of Plant Organs) as a key regulator of grapevine maturation whose induction precedes the expression of well-known ripening associated genes. We explored VviCARPO binding landscapes through DAP-seq and overlapped its bound genes with transcriptomics datasets from stable and transient VviCARPO overexpressing grapevine plants to define a set of high-confidence targets. Among these, we identified key molecular ripening markers. Physiological, metabolic and promoter activation analyses showed that VviCARPO induces chlorophyll degradation and anthocyanin accumulation through the up-regulation of VviSGR1 and VviMYBA1, respectively, with the latter being up-regulated through a VviCARPO-VviNAC03 regulatory complex. Despite showing a closer phylogenetic relationship to senescent-related AtNAP homologues, VviCARPO complemented the nor mutant phenotype in tomato, suggesting it may have acquired a dual role as an orchestrator of both ripening- and senescence-related processes. Our data supports CARPO as a master regulator of the grapevine vegetative-to-mature phase organ transition and therefore an essential target for insuring fruit quality and environmental resilience.

SIGNIFICANT STATEMENTCARPO is a grape NAC transcription factor central to fruit ripening and tissue senescence. This regulator influences multiple biological pathways common to both processes including cell wall metabolism, chlorophyll degradation, pigment production and hormone synthesis/signaling through regulation of their key genes. As various external stresses and changing climatic conditions influence vegetative growth and berry ripening, CARPO could prove a useful genetic and breeding target towards maintaining necessary crop performance and fruit-quality characteristics.


title: Batch-Mask: An automated Mask R-CNN workflow to isolate non-standard biological specimens for color pattern analysis

abstract:
O_LIEfficient comparisons of biological color patterns are critical for understanding the mechanisms by which organisms evolve in ecosystems, including sexual selection, predator-prey interactions, and thermoregulation. However, elongate or spiral-shaped organisms do not conform to the standard orientation and photographic techniques required for automated analysis. Currently, large-scale color analysis of elongate animals requires time-consuming manual landmarking, which reduces their representation in coloration research despite their ecological importance.
C_LIO_LIWe present Batch-Mask: an automated and customizable workflow to facilitate the analysis of large photographic data sets of non-standard biological subjects. First, we present a user guide to run an open-source region-based convolutional neural network with fine-tuned weights for identifying and isolating a biological subject from a background (masking). Then, we demonstrate how to combine masking with existing manual visual analysis tools into a single streamlined, automated workflow for comparing color patterns across images.
C_LIO_LIBatch-Mask was 60x faster than manual landmarking, produced masks that correctly identified 96% of all snake pixels, and produced pattern energy results that were not significantly different from the manually landmarked data set.
C_LIO_LIThe fine-tuned weights for the masking neural network, user guide, and automated workflow substantially decrease the amount of time and attention required to quantitatively analyze non-standard biological subjects. By using these tools, biologists will be able to compare color, pattern, and shape differences in large data sets that include significant morphological variation in elongate body forms. This advance will be especially valuable for comparative analyses of natural history collections, and through automation can greatly expand the scale of space, time, or taxonomic breadth across which color variation can be quantitatively examined.
C_LI

category: zoology


title: Polymer skulls with integrated transparent electrode arrays for cortex-wide opto-electrophysiological recordings

abstract: Electrophysiological and optical imaging provide complementary neural sensing capabilities - electrophysiological recordings have the highest temporal resolution, while optical imaging allows recording the activities of genetically defined populations at high spatial resolution. Combining these complementary, yet orthogonal modalities to perform simultaneous large-scale, multimodal sensing of neural activity across multiple brain regions would be very powerful. Here we show that transparent, inkjet-printed electrocorticography (ECoG) electrode arrays can be seamlessly integrated with morphologically conformant transparent polymer skulls for multimodal recordings across the cortex. These  eSee-Shells were implanted on transgenic mice expressing the Ca2+ indicator GCaMP6f in cortical excitatory cells and provided a robust opto-electrophysiological interface for over 100 days. eSee-Shells enable simultaneous mesoscale Ca2+ imaging and ECoG acquisition under anesthesia as well as in awake animals presented with sensory stimuli. eSee-Shells further show sufficient clarity and transparency to observe single-cell Ca2+ signals directly below the electrodes and interconnects. Simultaneous multimodal measurement of cortical dynamics reveals changes in both ECoG and Ca2+ signals that depend on the behavioral state.


title: Exploring the kinetic selectivity of antipsychotics for dopamine D2 and 5-HT2A receptors: implications for the prevalence of EPS and receptor occupancy

abstract:
Certain atypical antipsychotic drugs (APDs) used in the treatment of schizophrenia have been hypothesized to show reduced extrapyramidal side effects (EPS), due to their ability to promote nigrostriatal dopamine release through 5-HT2A receptor (5-HT2AR) blockade. The strength of this hypothesis is currently limited to a consideration of the relative receptor affinities of APDs for the 5-HT2AR and dopamine D2 receptor (D2R). Here we measure the 5-HT2AR kinetic binding properties of a series of typical and atypical APDs in a novel time-resolved fluorescence resonance energy transfer assay and correlate these properties with their observed EPS at therapeutic doses. For compounds with negligible affinity for 5-HT2AR, EPS is robustly predicted by a D2R specific rebinding model that integrates D2R association and dissociation rates to calculate the net rate of reversal of receptor blockade (kr). However, we show that for compounds with significant affinity for the 5-HT2AR, such as sertindole, higher relative 5-HT2A occupancy over time is an indicator for a reduced propensity to cause EPS.

This study suggests that there is room for the development of novel kinetically optimised antipsychotic agents that modulate both serotonergic and dopamine function in a manner beneficial in the treatment of this chronic and debilitating disease.


title: ORYX-MRSI: A Fully-Automated Open-Source Software for Three-Dimensional Proton Magnetic Resonance Spectroscopic Imaging Data Analysis

abstract: Proton magnetic resonance spectroscopic imaging (1H-MRSI) provides noninvasive evaluation of brain metabolism. However, there are some limitations of 1H-MRSI preventing its wider use in the clinics, including the spectral quality issues, partial volume effect and chemical shift artifact. Additionally, it is necessary to create metabolite maps for analyzing spectral data along with other MRI modalities. In this study, a MATLAB-based open-source data analysis software for 3D 1H-MRSI, called Oryx-MRSI, which includes modules for visualization of raw 1H-MRSI data and LCModel outputs, chemical shift correction, tissue fraction calculation, metabolite map production, and registration onto standard MNI152 brain atlas while providing automatic spectral quality control, is presented. Oryx-MRSI implements region of interest analysis at brain parcellations defined on MNI152 brain atlas. All generated metabolite maps are stored in NIfTI format. Oryx-MRSI is publicly available at https://github.com/sevimcengiz/Oryx-MRSI along with six example datasets.


title: Fluorescent and bioluminescent calcium indicators with tuneable colors and affinities

abstract:
We introduce a family of bright, rhodamine-based calcium indicators with tuneable affinities and colors. The indicators can be specifically localized to different cellular compartments and are compatible with both fluorescence and bioluminescence readouts through conjugation to HaloTag fusion proteins. Importantly, their increase in fluorescence upon localization enables no-wash live-cell imaging, which greatly facilitates their use in biological assays. Applications as fluorescent indicators in rat hippocampal neurons include the detection of single action potentials and of calcium fluxes in the endoplasmic reticulum (ER). Applications as bioluminescent indicators include the recording of the pharmacological modulation of nuclear calcium in high-throughput-compatible assays. The versatility and remarkable ease of use of these indicators make them powerful tools for bioimaging and bioassays.

Graphical abstract

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title: Defining Innate Immune Responses to the Human Gut Microbiota from Phylum to Strain

abstract: The functional potential of the gut microbiota remains largely uncharacterized. Efforts to understand how the immune system responds to commensal organisms have been hindered by the large number of strains that comprise the human gut microbiota. We develop a screening platform to measure innate immune responses towards 277 bacterial strains isolated from the human gut microbiota. We find that innate immune responses to gut derived bacteria are as strong as responses towards pathogenic bacteria, and vary from phylum to strain. Myeloid cells differentially rely upon TLR2 or TLR4 to sense particular taxa, an observation that predicts in vivo function. These innate immune responses can be modeled using combinations of up to 8 TLR agonists. Furthermore, the immunogenicity of strains is stable over time and following transplantation into new humans. Collectively, we demonstrate a powerful high-throughput approach to determine how commensal microorganisms shape innate immune phenotypes.


title: CXCR4+ Treg cells control serum IgM levels and natural IgM autoantibody production by B1 cells in the bone marrow

abstract: Regulatory T (Treg) cells represent a specialized lineage of suppressive CD4+ T cells, whose functionality is critically dependent on their ability to migrate to, and dwell in the proximity of cells they control. Here we show that continuous expression of the chemokine receptor CXCR4 in Treg cells is required for their ability to accumulate in the bone marrow (BM). Induced CXCR4 ablation in Treg cells led to their rapid depletion and consequent increase in mature B cells, foremost B-1 subset, observed exclusively in the BM without detectable changes in plasma cells or hematopoietic stem cells or any signs of systemic or local immune activation elsewhere. Dysregulation of BM B-1 B cells was associated with a highly specific increase in IgM autoantibodies and the total serum IgM levels. Thus, Treg cells control autoreactive B-1 B cells in a CXCR4-dependent manner. These findings have significant implications for understanding of regulation of B cell autoreactivity and malignancies.


title: Aerobic Bacteria Produce Nitric Oxide via Denitrification and Trigger Algal Population Collapse

abstract:
Microbial interactions govern marine biogeochemistry. These interactions are generally considered to rely on exchange of organic molecules. Here we report on a novel inorganic route of microbial communication, showing that algal-bacterial interactions are mediated through inorganic nitrogen exchange. Under oxygen-rich conditions, aerobic bacteria reduce algal-secreted nitrite to nitric oxide (NO) through denitrification, a well-studied anaerobic respiration mechanism. Bacteria secrete NO, triggering a cascade in algae akin to programmed cell death. During death, algae further generate NO, thereby propagating the signal in the algal population. Eventually, the algal population collapses, similar to the sudden demise of oceanic algal blooms. Our study suggests that the exchange of denitrification intermediates, particularly in oxygenated environments, is an overlooked yet ecologically significant route of microbial communication within and across kingdoms.

One Sentence SummaryAerobic bacteria activate denitrification in oxygenated conditions and produce nitric oxide that kills their algal partners


title: Investigating Increased CO2 concentration on the pH of various plant species

abstract: The concept of bioremediation is quickly becoming the norm in the resolution of environmental issues. The steady increase in carbon dioxide (CO2) levels, as documented by NASA, inspired scientists to engineer plants to absorb excess CO2 from the atmosphere. Here, we have explored the consequences of the uptake of excess CO2 by select plants. Carbon dioxide dissolves in H2O to produce H2CO3, which dissociates to yield H+ ions. We hypothesized that increased CO2 absorption results in decrease in pH of plant sap. Three plants (Byophyllum pinnatum, Romaine Lettuce and Nevada Lettuce), exposed to increased CO2 concentrations (15%), demonstrated a consistent increase in pH towards alkalinity compared to control plants. Based on the outcome being opposite of what we have hypothesized, our results suggest Byophyllum pinnatum, Romaine lettuce and Nevada lettuce, all have a unique homeostatic system to prevent over-absorption of CO2 in a CO2-rich environment.


title: Causation without correlation: parasite-mediated frequency-dependent selection and infection prevalence

abstract:
Parasite-mediated selection is thought to maintain host genetic diversity for resistance. We might thus expect to find a strong positive correlation between host genetic diversity and infection prevalence across natural populations. Here we used computer simulations to examine host-parasite coevolution in 20 simi-isolated clonal populations across a broad range of values for both parasite virulence and parasite fecundity. We found that the correlation between host genetic diversity and infection prevalence can be significantly positive for intermediate values of parasite virulence and fecundity. But the correlation can also be weak and statistically non-significant, even when parasite-mediated frequency-dependent selection is the sole force maintaining host diversity. Hence correlational analyses of field populations, while useful, might underestimate the role of parasites in maintaining host diversity.

Subject Area. Evolution


title: Allochronic isolation on a latitudinal gradient in the polyphagous moth Hyphantria cunea

abstract: Allochronic speciation, where reproductive isolation between populations of a species is facilitated by a difference in reproductive timing, depends on the existence of seasonality. Seasonality is strongly driven by latitude, so there may be a relationship between latitude and divergence among populations separated by life history timing. Here we explore the relationship between allochronic speciation and latitude using Hyphantria cunea (the fall webworm), a Lepidopteran defoliator with red and black colour morphs that may be undergoing an incipient allochronic speciation. We annotated >9000 community science observations of fall webworm to model colour morph phenology and differences in phenotype across North America. We also examined the physiology of two sympatric populations to determine differences in diapause intensity. We found the fall webworm is multivoltine with differing numbers of generations between colour morphs at lower latitudes, and univoltine at latitudes higher than 41{degrees}. This shift to univoltism correlated with a decline in morphological differentiation. This shows that conditions at lower latitudes facilitate greater divergence in an incipient allochronic speciation potentially due to longer reproductive seasons allowing for greater mismatches in generations. Our results demonstrate how latitude affects allochronic speciation, and how sympatric speciation along latitudinal gradients contributes to trends in global biodiversity.


title: Formal meta-analysis of hypoxic gene expression profiles reveals a universal gene signature and cell type-specific effects

abstract:
BackgroundIntegrating transcriptional profiles results in the identification of gene expression signatures that are more robust than those obtained for individual datasets. However, direct comparison of datasets derived from heterogeneous experimental conditions is not possible and their integration requires the application of specific meta-analysis techniques. The transcriptional response to hypoxia has been the focus of intense research due to its central role in tissue homeostasis and in prevalent diseases. Accordingly, a large number of studies have determined the gene expression profile of hypoxic cells. Yet, in spite of this wealth of information, little effort have been done to integrate these dataset to produce a robust hypoxic signature.

ResultsWe applied a formal meta-analysis procedure to a dataset comprising 425 RNAseq samples derived from 42 individual studies including 33 different cell types, to derive a pooled estimate of the effect of hypoxia on gene expression. This approach revealed that a large proportion of the transcriptome (8556 genes out of 20888) is significantly regulated by hypoxia. However, only a small fraction of the differentially expressed genes (1265 genes, 15%) show an effect size that, according to comparisons to gene pathways known to be regulated by hypoxia, is likely to be biologically relevant. By focusing on genes ubiquitously expressed we identified a signature of 291 genes robustly and consistently regulated by hypoxia. Finally, by a applying a moderator analysis we found that endothelial cells show a characteristic gene expression pattern that is significantly different from other cell types.

ConclusionBy the application of a formal meta-analysis to hypoxic gene profiles, we have developed a robust gene signature that characterizes the transcriptomic response to low oxygen. In addition to identifying a universal set of hypoxia-responsive genes, we found a set of genes whose regulation is cell-type specific and suggest a unique metabolic response of endothelial cells to reduced oxygen tension.

category: genomics


title: Cellular and transcriptional diversity over the course of human lactation

abstract: Human breast milk is a dynamic fluid that contains millions of cells, but their identities and phenotypic properties are poorly understood. We used single-cell RNA-seq (scRNA-seq) to characterize the transcriptomes of cells from human breast milk (hBM) across lactational time from 3 to 632 days postpartum in 15 donors. We find that the majority of cells in human breast milk are lactocytes, a specialized epithelial subset, and cell type frequencies shift over the course of lactation yielding greater epithelial diversity at later points. Analysis of lactocytes reveals a continuum of cell states characterized by transcriptional changes in hormone, growth factor, and milk production related pathways. Generalized additive models suggest that one sub-cluster, LALBAlow epithelial cells, increase as a function of time postpartum, daycare attendance, and the use of hormonal birth control. We identify several sub-clusters of macrophages in hBM that are enriched for tolerogenic functions, possibly playing a role in protecting the mammary gland during lactation. Our description of the cellular components of breast milk, their association with maternal-infant dyad metadata and quantification of alterations at the gene and pathways levels provides the first detailed longitudinal picture of human breast milk cells across lactational time. This work paves the way for future investigations of how a potential division of cellular labor and differential hormone regulation might be leveraged therapeutically to support healthy lactation and potentially aid in milk production.


title: Genomic evidence of paternal genome elimination in globular springtails

abstract: Paternal genome elimination (PGE) - a type of reproduction in which males inherit but fail to pass on their fathers genome - evolved independently in six to eight arthropod clades. Thousands of species, including several important for agriculture, reproduce via this mode of reproduction. While PGE is well established in some of the clades, the evidence in globular springtails (Symphypleona) remains elusive, even though they represent the oldest and most species rich clade putatively reproducing via PGE. We sequenced genomic DNA from whole bodies of Allacma fusca males with high fractions (>27.5%) of sperm to conclusively confirm that all the sperm carry one parental haplotype only. Although it is suggestive that the single haplotype present in sperm is maternally inherited, definitive genetic proof of the parent of origin is still needed. The genomic approach we developed allows for detection of genotypic differences between germline and soma in all species with sufficiently high fraction of germline in their bodies. This opens new opportunities for scans of reproductive modes in small organisms.


title: Genomic evidence of paternal genome elimination in the globular springtail Allacma fusca


title: The impact of rare germline variants on human somatic mutation processes

abstract: Somatic mutations are an inevitable component of ageing and the most important cause of cancer. The rates and types of somatic mutation vary across individuals, but relatively few inherited influences on mutation processes are known. We performed a comprehensive gene-based rare variant association study with diverse mutational processes, using human cancer genomes from over 11,000 individuals of European ancestry. By combining burden and variance tests, we identify 207 associations involving 15 somatic mutational phenotypes and 42 genes that replicated in an independent data set at a FDR of 1%. We associated rare inherited deleterious variants in novel genes such as MSH3, EXO1, SETD2, and MTOR with two different forms of DNA mismatch repair deficiency, and variants in genes such as EXO1, PAXIP1, and WRN with deficiency in homologous recombination repair. In addition, we identified associations with other mutational processes, such as APEX1 with APOBEC-signature mutagenesis. Many of the novel genes interact with each other and with known mutator genes within cellular sub-networks. Considered collectively, damaging variants in the newly-identified genes are prevalent in the population. We suggest that rare germline variation in diverse genes commonly impacts mutational processes in somatic cells.


title: Transmembrane helices mediate the formation of a stable ternary complex of cyt b5 reductase, cyt b5, and SCD1

abstract: Mammalian cytochrome b5 (cyt b5) and cytochrome b5 reductase (b5R) are electron carrier proteins required for many membrane-embedded oxidoreductases. Both cyt b5 and b5R have a cytosolic domain anchored to the membrane by a single transmembrane helix (TM). It is not clear if b5R, cyt b5 and their partner oxidoreductases assemble as binary or ternary complexes. Here we show that b5R and cyt b5 form a stable binary complex, and that b5R, cyt b5 and a membrane-embedded oxidoreductase, stearoyl-CoA desaturase 1 (SCD1) form a stable ternary complex. The formation of the complexes significantly enhances electron transfer rates, and that the single TM of cyt b5 and b5R mediated assembly of the complexes. These results reveal a novel functional role of TMs in cyt b5 and b5R and suggest that an electron transport chain composed of a stable ternary complex may be a general feature in oxidoreductases that require the participation of cyt b5 and b5R.


title: An Integrated Process Analytical Platform for Automated Monitoring of Monoclonal Antibody N-linked Glycosylation

abstract:
The biopharmaceutical industry is transitioning towards adoption of continuous biomanufacturing practices that are often more flexible and efficient than traditional batch processes. Regulatory agencies such as the Food and Drug Administration (FDA) are further urging use of advanced PAT to analyze the design space to increase process knowledge and enable high quality biologics production. Post-translational modification of proteins, such as N-linked glycosylation are often critical quality attributes known to affect biologics safety and efficacy hence requiring close monitoring during manufacturing. Here, we developed an online sequential-injection based PAT system, called N-GLYcanyzer, that can rapidly monitor mAb glycosylation during upstream biomanufacturing. The key innovation includes design of an integrated mAb sampling and derivation system for antibody titer and glycoform analysis in under 2 hours. The N-GLYcanyzer process includes mAb capture, deglycosylation, fluorescent glycan labeling, and glycan enrichment for direct injection and analysis on an integrated high performance liquid chromatography (HPLC) system. Different fluorescent tags and reductants were tested to maximize glycan labeling efficiency under aqueous conditions, while porous graphitized carbon (PGC) was studied for optimum glycan recovery and enrichment. We find that 2-AB labeling of glycans with 2-picoline borane as a reducing agent, using the N-GLYcanyzer workflow, gives higher glycan labeling efficiency under aqueous conditions leading to upwards of a 5-fold increase in fluorescent products intensity. Finally, we showcase how the N-GLYcanyzer platform can be implemented at/on-line to an upstream bioreactor for automated and near real-time glycosylation monitoring of a Trastuzumab biosimilar produced by Chinese Hamster Ovary (CHO) cells.

Graphical Abstract

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title: Automated Parallel Pattern Search Optimisation of Microfluidic Geometry for Extracellular Vesicle Liquid Biopsies

abstract: Microfluidic liquid biopsies using affinity-based capture of extracellular vesicles (EVs) have demonstrated great potential for providing rapid disease diagnosis and monitoring. However, little effort has been devoted to optimising the geometry of the microfluidic channels for maximum EV capture due to the inherent challenges of physically testing many geometric designs. To address this, we developed an automated parallel pattern search (PPS) optimiser by combining a Python optimiser, COMSOL Multiphysics, and high performance computing. This unique approach was applied to a triangular micropillar array geometry by parameterising repeating unit cells, making several assumptions, and optimising for maximum particle capture efficiency. We successfully optimised the triangular pillar arrays and surprisingly found that simply maximising the total number of pillars and effective surface area did not result in maximum EV capture, as devices with slightly larger pillars and more spacing between pillars allowed contact with slower moving EVs that followed the pillar contours more closely. We then experimentally validated this finding using bioreactor-produced EVs in the best and worst channel designs that were functionalised with an antibody against CD63. Captured EVs were quantified using a fluorescent plate reader, followed by an established elution method and nanoparticle tracking analysis. These results demonstrate the power of automated microfluidic geometry optimisations for EV liquid biopsies and will support further development of this rapidly growing field.


title: Chromosome 1q amplification perturbs a ceRNA network to promote melanoma metastasis

abstract: Somatic copy number alterations (CNAs) promote cancer, but the underlying driver genes are often not obvious when only the functions of the encoded proteins are considered. mRNAs can act as competitive endogenous miRNA sponges (ceRNAs) to post-transcriptionally regulate gene expression in a protein coding-independent manner. However, whether ceRNAs contribute to the oncogenic effects of CNAs is unknown. We report that chromosome 1q gains promote melanoma progression and metastasis at least in part through overexpression of three mRNAs with ceRNA activity: CEP170, NUCKS1, and ZC3H11A. Genetic studies reveal that these ceRNAs enhance melanoma metastasis by sequestering tumor suppressor miRNAs, thereby alleviating the repression of several pro-metastatic target genes. This regulatory RNA network is evident in other cancer types, suggesting that chromosome 1q ceRNA deregulation is a common driver of cancer progression. Taken together, our work demonstrates that ceRNAs mediate the oncogenicity of somatic CNAs.

category: cancer biology


title: Microfluidic system-based time-course tracking of physical proximity between cells and its effect on gene expression for elucidating live single cancer-immune cell interactions

abstract: Cell-cell communication and physical interactions play a vital role in cancer initiation, homeostasis, progression, and immune response. Here, we report a system that combines live capture of different cell types, co-incubation, time-lapse imaging, and gene expression profiling of doublets using a microfluidic integrated fluidic circuit (IFC) that enables measurement of physical distances between cells and the associated transcriptional profiles due to cell-cell interactions. The temporal variations in natural killer (NK) - triple-negative breast cancer (TNBC) cell distances were tracked and compared with terminally profiled cellular transcriptomes. The results showed the time-bound activities of regulatory modules and alluded to the existence of transcriptional memory. Our experimental and bioinformatic approaches serve as a proof of concept for interrogating live cell interactions at doublet resolution, which can be applied across different cancers and cell types.


title: Ethylene signaling increases reactive oxygen species accumulation to drive root hair initiation in Arabidopsis thaliana

abstract:
Root hair initiation is a highly regulated aspect of root development. The plant hormone, ethylene, and its precursor, 1-amino-cyclopropane-1-carboxylic acid (ACC), induce formation and elongation of root hairs. Using confocal microscopy paired with redox biosensors and dyes, we demonstrated that treatments that elevate ethylene levels led to increased hydrogen peroxide accumulation in hair cells prior to root hair formation. In two ethylene-insensitive mutants, etr1-3 and ein3/eil1, there was no increase in root hair number or ROS accumulation. Conversely, etr1-7, a constitutive ethylene signaling receptor mutant, has increased root hair formation and ROS accumulation like ethylene-treated Col-0 seedlings. The caprice and werewolf transcription factor mutants have decreased and elevated ROS levels, which are correlated with levels of root hair initiation. The rhd2-6 mutant, with a defect in the gene encoding a ROS synthesizing Respiratory Burst Oxidase Homolog C (RBOHC) and the prx44-2 mutant defective in a class III peroxidase, showed impaired ethylene-dependent ROS synthesis and root hair formation and EIN3/EIL1 dependent transcriptional regulation. Together, these results indicate that ethylene increases ROS accumulation through RBOHC and PRX44 to drive root hair formation.

SUMMARY STATEMENTThe gaseous hormone ethylene increases root hair initiation by elevating reactive oxygen species (ROS) in trichoblast cells. Genetic and biochemical approaches identified ethylene-regulated ROS producing enzymes that drive root hair initiation.


title: Semaphorin signaling restricts neuronal regeneration in C. elegans

abstract: Extracellular signaling proteins serve as neuronal growth cone guidance molecules during development and are well positioned to be involved in neuronal regeneration and recovery from injury. Semaphorins and their receptors, the plexins, are a family of conserved proteins involved in development that, in the nervous system, are axonal guidance cues mediating axon pathfinding and synapse formation. The Caenorhabditis elegans genome encodes for three semaphorins and two plexin receptors: the transmembrane semaphorins, SMP-1 and SMP-2, signal through their receptor, PLX-1, while the secreted semaphorin, MAB-20, signals through PLX-2. Here, we determined the neuronal morphology and locomotion behavior of knockout animals missing each of the semaphorins and plexins; we described the expression pattern of all plexins in the nervous system of C. elegans; and we evaluated their effect on the regeneration of motoneuron neurites and the recovery of locomotion behavior following precise laser microsurgery.


title: Functional ultrasound imaging of recent and remote memory recall in the associative fear neural network in mice

abstract:
Scientific AbstractEmotional learning and memory are affected in numerous psychiatric disorders. At a systems level, however, the underlying neural circuitry is not well defined. Rodent fear conditioning (FC) provides a translational model to study the networks underlying associative memory retrieval. In the current study, functional connectivity among regions related to the cue associative fear network were investigated using functional ultrasound (fUS), a novel imaging technique with great potential for detecting regional neural activity through cerebral blood flow. Behavioral fear expression and fUS imaging were performed one and thirty-one days after FC to assess recent and remote memory recall. Cue-evoked increases in functional connectivity were detected throughout the amygdala, with the lateral (LA) and central (CeA) amygdalar nuclei emerging as major hubs of connectivity, though CeA connectivity was reduced during remote recall. The hippocampus and sensory cortical regions displayed heightened connectivity with the LA during remote recall, whereas interconnectivity between the primary auditory cortex and temporal association areas was reduced. Subregions of the prefrontal cortex exhibited variable connectivity changes, where prelimbic connectivity with the amygdala was refined while specific connections between the infralimbic cortex and amygdalar subregions emerged during remote memory retrieval. Moreover, freezing behavior positively correlated with functional connectivity between hubs of the associative fear network, suggesting that emotional response intensity reflected the strength of the cue-evoked functional network. Overall, our data provide evidence of the functionality of fUS imaging to investigate the neural dynamics of memory encoding and retrieval, applicable in the development of innovative treatments for affective disorders.

HighlightsFunctional ultrasound imaging can elucidate fear associated neural networks

Freezing behavior correlates with cue-evoked functional connectivity changes

The lateral and central amygdalar nuclei are major hubs in the fear network

The hippocampus is active during recent and remote cued fear memory retrieval

Connectivity profiles of the prelimbic and infralimbic areas vary in remote recall


title: Global landscape of replicative DNA polymerase usage in the human genome

abstract: The division of labour among DNA polymerase underlies the accuracy and efficiency of replication. However, the roles of replicative polymerases have not been directly established in human cells. We developed polymerase usage sequence (Pu-seq) in HCT116 cells and mapped Pol{varepsilon} and Pol usage genome wide. The polymerase usage profiles show Pol{varepsilon} synthesises the leading strand and Pol contributes mainly to lagging strand synthesis. Combining the Pol{varepsilon} and Pol profiles, we accurately predict the genome-wide pattern of fork directionality plus zones of replication initiation and termination. We confirm that transcriptional activity contributes to the pattern of initiation and termination and, by separately analysing the effect of transcription on both co-directional and converging forks, demonstrate that coupled DNA synthesis of leading and lagging strands in both co- directional and convergent forks is compromised by transcription. Polymerase uncoupling is particularly evident in the vicinity of large genes, including the two most unstable common fragile sites, FRA3B and FRA3D, thus linking transcription-induced polymerase uncoupling to chromosomal instability.

category: molecular biology


title: Detection, not mortality, constrains the evolution of virulence

abstract: Why would a pathogen evolve to kill its hosts when killing a host ends a pathogens own opportunity for transmission? A vast body of scientific literature has attempted to answer this question using "trade-off theory," which posits that host mortality persists due to its cost being balanced by benefits of other traits that correlate with host mortality. The most commonly invoked trade-off is the mortality-transmission trade-off, where increasingly harmful pathogens are assumed to transmit at higher rates from hosts while the hosts are alive, but the pathogens truncate their infectious period by killing their hosts. Here I show that costs of mortality are too small to plausibly constrain the evolution of disease severity except in systems where survival is rare. I alternatively propose that disease severity can be much more readily constrained by a cost of behavioral change due to the detection of infection, whereby increasingly harmful pathogens have increasing likelihood of detection and behavioral change following detection, thereby limiting opportunities for transmission. Using a mathematical model, I show the conditions under which detection can limit disease severity. Ultimately, this argument may explain why empirical support for trade-off theory has been limited and mixed.


abstract:
Subspace clustering identifies multiple feature subspaces embedded in a dataset together with the underlying sample clusters. When applied to omic data, subspace clustering is a challenging task, as additional problems have to be addressed: the curse of dimensionality, the imperfect data quality and cluster separation, the presence of multiple subspaces representative of divergent views of the dataset, and the lack of consensus on the best clustering method.

First, we propose a computational method (discover) to perform subspace clustering on tabular high dimensional data by maximizing the internal clustering score (i.e. cluster compactness) of feature subspaces. Our algorithm can be used in both unsupervised and semi-supervised settings. Secondly, by applying our method to a large set of omic datasets (i.e. microarray, bulk RNA-seq, scRNA-seq), we show that the subspace corresponding to the provided ground truth annotations is rarely the most compact one, as assumed by the methods maximizing the internal quality of clusters. Our results highlight the difficulty of fully validating subspace clusters (justified by the lack of feature annotations). Tested on identifying the ground-truth subspace, our method compared favorably with competing techniques on all datasets. Finally, we propose a suite of techniques to interpret the clustering results biologically in the absence of annotations. We demonstrate that subspace clustering can provide biologically meaningful sample-wise and feature-wise information, typically missed by traditional methods.

CCS Concepts: * Computing methodologies [->] Genetic algorithms; Mixture models; Cluster analysis.

ACM Reference FormatMadalina Ciortan and Matthieu Defrance. 2021. Optimization algorithm for omic data subspace clustering. 1, 1 (September 2021), 40 pages. https://doi.org/10.1145/nnnnnnn.nnnnnnn

category: bioinformatics


title: Pathological characteristics of pulmonary toxicity in F344 rats exposed by inhalation to cross-linked water-soluble acrylic acid polymers

abstract:
BackgroundRecently in Japan, six workers at a chemical plant that manufactures resins developed interstitial lung diseases after being involved in loading and packing cross-linked water-soluble acrylic acid polymers (CWAAPs). Since CWAAPs are not on the list of occupational diseases, the present study examined the lung damage potential of two CWAAPs (CWAAP-A and CWAAP-B) in rats, investigated pathological mechanisms, and established a method to rapidly evaluate the harmfulness of CWAAPs.

MethodsUsing a whole-body inhalation exposure system, male F344 rats were exposed once to 40 or 100 mg/m3 of CWAAP-A for 4 hours or to 15 or 40 mg/m3 of CWAAP-A for 4 hours per day once per week for 2 months (a total of 9 exposures). In a separate set of experiments, male F344 rats were administered 1 mg/kg CWAAP-A or CWAAP-B by intratracheal instillation once every two weeks for 2 months (a total of five doses). Lung tissues, mediastinal lymph nodes, and bronchoalveolar lavage fluid were collected and subjected to biological and histopathological analyses.

ResultsA single 4-hour exposure to CWAAP caused alveolar injury, and repeated exposures resulted in regenerative changes in the alveolar epithelium with activation of TGF{beta} signaling. During the recovery period after the last exposure, some alveolar lesions were partially healed, but other lesions developed into alveolitis with fibrous thickening of the alveolar septum. Rats administered CWAAP-A by intratracheal instillation developed qualitatively similar pulmonary pathology as rats exposed to CWAAP-A by inhalation. At 2 weeks after intratracheal instillation, rats administered CWAAP-B appeared to have a slightly higher degree of lung lesions compared to rats administered CWAAP-A, however, there was no difference in these lesions of CWAAP-A and CWAAP-B in rats examined 18 weeks after administration of these materials.

ConclusionsThe present study provides evidence of rat lung pathogenesis after inhalation exposure to CWAAP-A. This study also demonstrates that the lung pathology of rats exposed to CWAAP-A by systemic inhalation was qualitatively similar to that of rats administered CWAAP-A by intratracheal instillation. The use of intratracheal instillation as an adjunct to systemic inhalation is expected to significantly accelerate the risk assessment for a variety of CWAAPs.

category: pharmacology and toxicology


title: Sensory processing sensitivity and axonal microarchitecture: Identifying brain structural characteristics for behavior

abstract: Previously, researchers used functional MRI to identify regional brain activations associated with sensory processing sensitivity (SPS), a proposed normal phenotype trait. To further validate SPS as a behavioral entity, to characterize it anatomically, and to test the usefulness in psychology of methodologies that assess axonal properties, the present study correlated SPS proxy questionnaire scores (adjusted for neuroticism) with diffusion tensor imaging measures. Participants (n=408) from the Young Adult Human Connectome Project that are free of neurologic and psychiatric disorders were investigated. We computed mean diffusivity (MD), radial diffusivity (RD), axial diffusivity (AD) and fractional anisotropy (FA). A voxelwise, exploratory analysis showed that MD and RD correlated positively with SPS proxy scores in the right and left subcallosal and anterior ventral cingulum bundle, and the right forceps minor of the corpus callosum (peak Cohens D effect size = 0.269). Further analyses showed correlations throughout the entire right and left ventromedial prefrontal cortex, including the superior longitudinal fasciculus, inferior fronto-occipital fasciculus, uncinate and arcuate fasciculus. These prefrontal regions are generally involved in emotion, reward and social processing. FA was negatively correlated with SPS proxy scores in white matter of the right premotor/motor/somatosensory/supramarginal gyrus regions, which are associated with empathy, theory of mind, primary and secondary somatosensory processing. Region of interest (ROI) analysis, based-on previous fMRI results and Freesurfer atlas-defined areas, showed small effect sizes, (+0.151 to -0.165) in white matter of the precuneus and inferior frontal gyrus. Other ROI effects were found in regions of the dorsal and ventral visual pathways and primary auditory cortex. The results reveal that in a large, diverse group of participants axonal microarchitectural differences can be identified with SPS traits that are subtle and in the range of typical behavior. The results suggest that the heightened sensory processing in people who show SPS may be influenced by the microstructure of white matter in specific neocortical regions. Although previous fMRI studies had identified most of these general neocortical regions, the DTI results put a new focus on brain areas related to attention and cognitive flexibility, empathy, emotion and low-level sensory processing, as in the primary sensory cortex. Psychological trait characterization may benefit from diffusion tensor imaging methodology by identifying influential brain systems for traits.