title: Portable framework to deploy deep learning segmentation models for medical images

abstract:
PurposeThis work presents a framework for deployment of deep learning image segmentation models for medical images across different operating systems and programming languages.

MethodsComputational Environment for Radiological Research (CERR) platform was extended for deploying deep learning-based segmentation models to leverage CERRs existing functionality for radiological data import, transformation, management, and visualization. The framework is compatible with MATLAB as well as GNU Octave and Python for license-free use. Pre and post processing configurations including parameters for pre-processing images, population of channels, and post-processing segmentations was standardized using JSON format. CPU and GPU implementations of pre-trained deep learning segmentation models were packaged using Singularity containers for use in Linux and Conda environment archives for Windows, macOS and Linux operating systems. The framework accepts images in various formats including DICOM and CERRs planC and outputs segmentation in various formats including DICOM RTSTRUCT and planC objects. The ability to access the results readily in planC format enables visualization as well as radiomics and dosimetric analysis. The framework can be readily deployed in clinical software such as MIM via their extensions.

ResultsThe open-source, GPL copyrighted framework developed in this work has been successfully used to deploy Deep Learning based segmentation models for five in-house developed and published models. These models span various treatment sites (H&N, Lung and Prostate) and modalities (CT, MR). Documentation for their usage and demo workflow is provided at https://github.com/cerr/CERR/wiki/Auto-Segmentation-models. The framework has also been used in clinical workflow for segmenting images for treatment planning and for segmenting publicly available large datasets for outcomes studies.

ConclusionsThis work presented a comprehensive, open-source framework for deploying deep learning-based medical image segmentation models. The framework was used to translate the developed models to clinic as well as reproducible and consistent image segmentation across institutions, facilitating multi-institutional outcomes modeling studies.


title: Bimodal fibrosis in a novel mouse model of bleomycin-induced usual interstitial pneumonia

abstract:
Idiopathic pulmonary fibrosis (IPF) is pathologically classified by usual interstitial pneumonia (UIP). Conventional bleomycin models used to study pathogenic mechanisms of pulmonary fibrosis display transient inflammation and fibrosis so their relevance to UIP is limited. We developed a novel chronic induced-UIP (iUIP) model, inducing fibrosis in D1CCxD1BC transgenic mice by intra-tracheal instillation of bleomycin mixed with microbubbles followed by sonoporation (BMS). A bimodal fibrotic lung disease was observed over 14 weeks, with an acute phase similar to nonspecific interstitial pneumonia (NSIP), followed by partial remission and a chronic fibrotic phase with honeycombing similar to UIP. In this secondary phase, we observed poor vascularization despite elevated PDGFR{beta} expression. {gamma}2PF- and MMP7-positive epithelial cells, consistent with an invasive phenotype, were predominantly adjacent to fibrotic areas. Most invasive cells were Scgb1a1 and/or keratin 5 positive. This iUIP mouse model displays key features of IPF and has identified potential mechanisms contributing to the onset of NSIP and progression to UIP. The model will provide a useful tool for the assessment of therapeutic interventions to oppose acute and chronic fibrosis.

Summary blurbA novel mouse model of induced-usual interstitial pneumonia shows bimodal fibrosis with honeycombing, similar to chronic lung disease seen with idiopathic pulmonary fibrosis.

category: pathology


title: Transcriptional condensates formed by phase-separated ALOG family proteins control flowering and inflorescence architecture in tomato

abstract: Plants have evolved remarkable diversity in inflorescence architecture. At the center of this diversity lies a meristem maturation program featured by transition of stem cell populations from a vegetative state into a reproductive growth, determining when, where, and how many flowers are produced on inflorescences. Here we identified a new meristem maturation regulator TMF FAMILY MEMBER3 (TFAM3) that encodes an ALOG family transcription factor. Loss of TFAM3 results in early flowering and simplified inflorescences with fewer flowers. Genetic analysis by creating high-order mutants of TFAM3 with three key regulators of tomato shoot meristem maturation, TERMINATING FLOWER (TMF), TMF FAMILY MEMBER1 (TFAM1) and TMF FAMILY MEMBER2 (TFAM2), suggested that they synergistically control flowering transition and inflorescence architecture. The four paralogous ALOG proteins share the prion-like properties and undergo liquid-liquid phase separation in vitro. Strikingly, TMF can recognize cognate TFAM proteins and selectively recruit them into phase separated condensates. Supporting this, they interact with themselves and each other to form biomolecular condensates in the nucleus. Their interaction induces formation of transcriptional condensates that directly repress expression of floral identity gene ANANTHA. Our study revealed a selective-recruitment phase separation mechanism for transcriptional condensation by which plants achieve optimal coordination of functional overlapped paralogs within a protein family to enable precise control of shoot meristem maturation for flowering and production of compound inflorescences.

category: plant biology


title: Transcriptional condensates formed by phase-separated ALOG family proteins control shoot meristem maturation for flowering


title: Ocular pigmentation in humans, great apes, and gibbons is not suggestive of communicative functions - having an eye on the 'cooperative eye hypothesis'

abstract: Pigmentation patterns of the visible part of the eyeball, encompassing the iris and portions of the sclera, have been discussed to be linked to social cognition in primates. In the context of the cooperative eye hypothesis, the white sclera of humans has been viewed as a derived adaptive trait, enhancing communication via glance cueing. Here, we provide a comparative analysis of ocular pigmentation patterns in 15 species of hominoids (humans, great apes & gibbons) representing all extant ape genera, based on photographs and literature data. Additionally, we quantify hominoid scleral exposure on the genus level during different glancing situations. Our data reveals a continuum of eye pigmentation traits among the studied taxa. Gibbons display darker, more uniformly colored eyes than great apes and expose less sclera, particularly during averted glancing. Iridoscleral contrasts in orangutans and gorillas approach the human condition but differ between congeneric species. Contrary to recent discussions, we found chimpanzee eyes to exhibit a cryptic coloration scheme that resembles gibbons more than other great apes and that does not enhance glance cueing or gaze following. We critically evaluate the evidence for links between social cognition and eye pigmentation in primates, concluding that the cooperative eye hypothesis cannot convincingly explain the patterns observed. Although the human eye exhibits unique traits that are likely linked to social communication, high iridoscleral contrast is not one of them. Differences in scleral pigmentation between great apes and humans are gradual and might have arisen via genetic drift and sexual selection.

category: zoology


title: Fiber tractography bundle segmentation depends on scanner effects, acquisition, diffusion sensitization, and bundle segmentation workflow

abstract: When investigating connectivity and microstructure of white matter pathways of the brain using diffusion tractography bundle segmentation, it is important to understand potential confounds and sources of variation in the process. While cross-scanner and cross-protocol effects on diffusion microstructure measures are well described (in particular fractional anisotropy and mean diffusivity), it is unknown how potential sources of variation effect bundle segmentation results, which features of the bundle are most affected, where variability occurs, nor how these sources of variation depend upon the method used to reconstruct and segment bundles. In this study, we investigate six potential sources of variation, or confounds, for bundle segmentation: variation (1) across scan repeats, (2) across scanners, (3) across vendors (4) across acquisition resolution, (5) across diffusion schemes, and (6) across diffusion sensitization. We employ four different bundle segmentation workflows on two benchmark multi-subject cross-scanner and cross-protocol databases, and investigate reproducibility and biases in volume overlap, shape geometry features of fiber pathways, and microstructure features within the pathways. We find that the effects of acquisition protocol, in particular acquisition resolution, result in the lowest reproducibility of tractography and largest variation of features, followed by vendor-effects, scanner-effects, and finally diffusion scheme and b-value effects which had similar reproducibility as scan-rescan variation. However, confounds varied both across pathways and across segmentation workflows, with some bundle segmentation workflows more (or less) robust to sources of variation. Despite variability, bundle dissection is consistently able to recover the same location of pathways in the deep white matter, with variation at the gray matter/ white matter interface. Next, we show that differences due to the choice of bundle segmentation workflows are larger than any other studied confound, with low-to-moderate overlap of the same intended pathway when segmented using different methods. Finally, quantifying microstructure features within a pathway, we show that tractography adds variability over-and-above that which exists due to noise, scanner effects, and acquisition effects. Overall, these confounds need to be considered when harmonizing diffusion datasets, interpreting or combining data across sites, and when attempting to understand the successes and limitations of different methodologies in the design and development of new tractography or bundle segmentation methods.

category: neuroscience


title: Fiber tractography bundle segmentation depends on scanner effects, vendor effects, acquisition resolution, diffusion sampling scheme, diffusion sensitization, and bundle segmentation workflow


title: Patterns of brain asymmetry associated with polygenic risks for autism and schizophrenia implicate language and executive functions but not brain masculinization

abstract: Autism spectrum disorder (ASD) and schizophrenia have been conceived as partly opposing disorders in terms of systemizing versus empathizing cognitive styles, with resemblances to male versus female average sex differences. Left-right asymmetry of the brain is an important aspect of its organization that shows average differences between the sexes, and can be altered in both ASD and schizophrenia. Here we mapped multivariate associations of polygenic risk scores (PRS) for ASD and schizophrenia with asymmetries of regional cerebral cortical surface area, thickness and subcortical volume measures in 32,256 participants from the UK Biobank. PRS for the two disorders were positively correlated (r=0.08, p=7.13x10-50), and both were higher in females compared to males, consistent with biased participation against higher-risk males. Each PRS was associated with multivariate brain asymmetry after adjusting for sex, ASD PRS r=0.03, p=2.17x10-9, schizophrenia PRS r=0.04, p=2.61x10-11, but the multivariate patterns were mostly distinct for the two PRS, and neither resembled average sex differences. Annotation based on meta-analyzed functional imaging data showed that both PRS were associated with asymmetries of regions important for language and executive functions, consistent with behavioural associations that arose in phenome-wide association analysis. Overall, the results indicate that distinct patterns of subtly altered brain asymmetry may be functionally relevant manifestations of polygenic risk for ASD and schizophrenia, but do not support brain masculinization or feminization in their etiologies.


title: Cross-Species Experiments Reveal Widespread Cochlear Neural Damage in Normal Hearing

abstract: Animal models suggest that cochlear afferent nerve endings may be more vulnerable than sensory hair cells to damage from acoustic overexposure and aging, but that such damage cannot be detected in standard clinical audiometry. Co-ordinated experiments in at-risk humans and a chinchilla model using two distinct physiological assays suggest that cochlear neural damage exists even in populations without clinically recognized hearing loss.


title: Rhythmic Accessibility to Sequential Working Memory in a Theta Phase-Dependent Manner

abstract: Working memory is active short-term memory storage that is easily accessible for later utilization. There is emerging evidence that memorized items are represented rhythmically on the specific phase of the theta-band (4-7 Hz) neural oscillation. However, it is still unknown how this process impacts the accessibility to the active memory storage. Here we show that simply memorizing sequential information causes theta-band fluctuation in our behaviour (i.e., reaction time, RT). We measured RTs to a visual probe that appeared at sequentially memorized locations after a random interval. Consequently, RTs to the probes fluctuated in the theta range as a function of the random interval, and the behavioural rhythmicity supported the hypothesis of the phase-dependent coding of sequential working memory. The current results demonstrate that our behaviour fluctuates unconsciously in the theta-range when recalling sequential memory, suggesting that accessibility to sequential working memory is rhythmic rather than stable, possibly reflecting theta-phase dependent coding.


title: Accessibility to sequential working memory fluctuates unconsciously in a rhythmic manner


title: Accessibility to sequential working memory fluctuates unconsciously in a theta phase-dependent manner


title: Natal and adult dispersal among four elephant seal colonies

abstract: Dispersal plays a key role fostering recovery of endangered species because reoccupying a former range can only happen via dispersal. The northern elephant seal (Mirounga angustirostris) is a large, marine predator that was nearly exterminated in the 19th century by over-hunting. Once they were afforded protection from harvest, the species spread from a single remnant colony to reoccupy its former range. As colonies in central California were reestablished during the 1960s-1990s, tagged seals documented northward dispersal from southern California. The central California colonies are now large and well-established, and tagging programs at the four northernmost colonies allowed us to quantify the extent and direction of dispersal. Natal dispersal by females was highest from the southernmost colony at Piedras Blancas, where 61% of surviving females emigrated to breed. Dispersal from the other three colonies was much lower, 5.6% from SE Farallon Island, 10.3% from Ano Nuevo, and 16.6% from Point Reyes. Adult dispersal of females, after breeding, was rare, with an annual rate < 2%. Juvenile dispersal is thus frequent in elephant seals, highest northward but also occurring southward, suggesting that continued expansion to new colonies throughout the west coast is probable.

category: ecology


title: Buried but unsafe - defoliation depletes the underground storage organ (USO) of the mesic grassland geophyte, Hypoxis hemerocallidea

abstract: Mesic grasslands in South Africa (> 650 mm a-1 MAP) are rich in herbaceous forbs, which outnumber grass species by more than 5 to 1. Many of these forbs have underground storage units (USOs), such as thickened rootstocks, rhizomes, bulbs, or corms, that provide resources (non-structural carbohydrates, minerals, and water) enabling them to resprout after dry, frosty winters, and fire. However, despite their extensive biomass and reserves ostensibly protected underground, geophytic mesic grassland forbs can be severely depleted or extirpated by chronic trampling and grazing of their aerial parts by livestock. This study examined a possible explanation for forb demise in overgrazed grassland by investigating, in a pot trial, whether the growth of forbs and the size of their USOs are negatively affected by simulated green leaf loss. In a 2x2 factorial (clipped vs. unclipped x spring regrowth in the dark vs. light), five replicate plants of Hypoxis hemerocallidea, a common mesic grassland forb that resprouts from a corm, were subject to six severe (clipped to 80 mm) defoliations during the growing season and regrown in spring under full or restricted light to measure stored reserve contribution to regrowth. Defoliated plants were resilient to defoliation during the growing season, matching the total biomass production of unclipped plants, though cutting reduced the number of leaves by {not}60% and flowers by almost 85%. Spring regrowth on stored reserves equalled that from reserves plus concurrent photosynthesis, indicating the value of USOs for regrowth. However, there was a marked carry-over effect of previous season defoliation, resulting in a one-third reduction in shoot growth and 40% fewer inflorescence in spring. Crucially, corm mass was more than halved by clipping. Above-ground spring growth was linearly related to corm mass. It was concluded that buried stored reserves are not protected by recurrent disturbance to aerial plant parts and that continued diminishment of USOs under chronic disturbance by overgrazing or frequent mowing would weaken and likely eventually kill plants, reducing forb species richness. Lenient management by infrequent summer mowing or grazing at moderate stocking rates combined with periodic rotational full season resting and dormant-season burning is recommend to maintain the USOs and vigour of forbs in mesic grassland.


title: Long-term patterns of an interconnected core marine microbiota

abstract:
BackgroundOcean microbes constitute [~]70% of the marine biomass, are responsible for [~]50% of the Earths primary production, and are crucial for global biogeochemical cycles. Marine microbiotas include core taxa that are usually key for ecosystem function. Despite their importance, core marine microbes are relatively unknown, which reflects the lack of consensus on how to identify them. So far, most core microbiotas have been defined based on species occurrence and abundance. Yet, species interactions are also important to identify core microbes, as communities include interacting species. Here, we investigate interconnected bacteria and small protists of the core pelagic microbiota populating a long-term marine-coastal observatory in the Mediterranean Sea over a decade.

ResultsCore microbes were defined as those present in >30% of the monthly samples over 10 years, with the strongest associations. The core microbiota included 259 Operational Taxonomic Units (OTUs) including 182 bacteria, 77 protists, and 1,411 strong and mostly positive ([~]95%) associations. Core bacteria tended to be associated with other bacteria, while core protists tended to be associated with bacteria. The richness and abundance of core OTUs varied annually, decreasing in stratified warmers waters and increasing in colder mixed waters. Most core OTUs had a preference for one season, mostly winter, which featured subnetworks with the highest connectivity. Groups of highly associated taxa tended to include protists and bacteria with predominance in the same season, particularly winter. A group of 13 highly-connected hub-OTUs, with potentially important ecological roles dominated in winter and spring. Similarly, 18 connector OTUs with a low degree but high centrality were mostly associated with summer or autumn and may represent transitions between seasonal communities.

ConclusionsWe found a relatively small and dynamic interconnected core microbiota in a model temperate marine-coastal site, with potential interactions being more deterministic in winter than in other seasons. These core microbes would be essential for the functioning of this ecosystem over the year. Other non-core taxa may also carry out important functions but would be redundant and non-essential. Our work contributes to the understanding of the dynamics and potential interactions of core microbes possibly sustaining ocean ecosystem function.


title: Evolutionary determinants of non-seasonal breeding in wild chacma baboons

abstract: Animal reproductive phenology varies from strongly seasonal to non-seasonal, sometimes among closely related or sympatric species. While the extent of reproductive seasonality is often attributed to environmental seasonality, this fails to explain many cases of non-seasonal breeding in seasonal environments. We investigated the evolutionary determinants of non-seasonal breeding in a wild primate, the chacma baboon (Papio ursinus), living in a seasonal environment with high climatic unpredictability. We tested three hypotheses proposing that non-seasonal breeding has evolved in response to (1) climatic unpredictability, (2) reproductive competition between females favouring birth asynchrony, and (3) individual, rank-dependent variations in optimal reproductive timing. We found strong support for an effect of reproductive asynchrony modulated by rank: (i) birth synchrony is costly to subordinate females, lengthening their interbirth intervals, and (ii) females delay their reproductive timings (fertility periods and conceptions) according to other females in the group to stagger conceptions. These results indicate that reproductive competition generates reproductive asynchrony, weakening the intensity of reproductive seasonality at the population level. This study emphasizes the importance of sociality in mediating the evolution of reproductive phenology in gregarious organisms, a result of broad significance for understanding key demographic parameters driving population responses to increasing climatic fluctuations.

category: evolutionary biology


title: A two-type branching process model of gene family evolution

abstract: Phylogenetic models of gene family evolution based on birth-death processes (BDPs) vide an awkward fit to comparative genomic data sets. A central assumption of these models is the constant per-gene loss rate in any particular family. Because of the possibility of partial functional redundancy among gene family members, gene loss dynamics are however likely to be dependent on the number of genes in a family, and different variations of commonly employed BDP models indeed suggest this is the case. We propose a simple two-type branching process model to better approximate the stochastic evolution of gene families by gene duplication and loss and perform Bayesian statistical inference of model parameters in a phylogenetic context. We evaluate the statistical methods using simulated data sets and apply the model to gene family data for Drosophila, yeasts and primates, providing new quantitative insights in the long-term maintenance of duplicated genes.


title: Cross-platform proteomics to advance genetic prioritisation strategies

abstract: Discovery of protein quantitative trait loci (pQTLs) has been enabled by affinity-based proteomic techniques and is increasingly used to guide genetically informed drug target evaluation. Large-scale proteomic data are now being created, but systematic, bidirectional assessment of platform differences is lacking, restricting clinical translation. We compared genetic, technical, and phenotypic determinants of 871 protein targets measured using both aptamer-(SomaScan(R) Platform v4) and antibody-based (Olink) assays in up to 10,708 individuals. Correlations coefficients for overlapping protein targets varied widely (median 0.38, IQR: 0.08-0.64). We found that 64% of pQTLs were shared across both platforms among all identified 608 cis- and 1,315 trans-pQTLs with sufficient power for replication, but with correlations of effect estimates being lower than previously reported (cis: 0.41, trans: 0.34). We identified technical, protein, and variant characteristics that contributed significantly to platform differences and found contradicting phenotypic associations attributable to those. We demonstrate how integrating phenomic and gene expression data improves genetic prioritisation strategies, including platform-specific pQTLs.

category: genetics


title: Comparative genomics reveals evolutionary drivers of sessile life and left-right shell asymmetry in bivalves

abstract: Bivalves are species-rich mollusks with prominent protective roles in coastal ecosystems. Across these ancient lineages, colony-founding larvae anchor themselves either by byssus production or by cemented attachment. The latter mode of sessile life is strongly molded by left-right shell asymmetry during larval development of Ostreoida oysters such as Crassostrea hongkongensis. Here, we sequenced the genome of C. hongkongensis in high resolution and compared it to reference bivalve genomes to unveil genomic determinants driving cemented attachment and shell asymmetry. Importantly, loss of the homeobox gene antennapedia (Antp) and broad expansion of lineage-specific extracellular gene families are implicated in a shift from byssal to cemented attachment in bivalves. Evidence from comparative transcriptomics shows that the left-right asymmetrical C. hongkongensis plausibly diverged from the symmetrical Pinctada fucata in expression profiles marked by elevated activities of orthologous transcription factors and lineage-specific shell-related gene families including tyrosinases, which may cooperatively govern asymmetrical shell formation in Ostreoida oysters.

category: genomics


title: BATL: Bayesian annotations for targeted lipidomics

abstract:
MotivationBioinformatic tools capable of annotating, rapidly and reproducibly, large, targeted lipidomic datasets are limited. Specifically, few programs enable high-throughput peak assessment of liquid chromatography-electrospray ionization tandem mass spectrometry (LC-ESI-MS/MS) data acquired in either selected or multiple reaction monitoring (SRM and MRM) modes.

ResultsWe present here Bayesian Annotations for Targeted Lipidomics (BATL), a Gaussian naive Bayes classifier for targeted lipidomics that annotates peak identities according to eight features related to retention time, intensity, and peak shape. Lipid identification is achieved by modelling distributions of these eight input features across biological conditions and maximizing the joint posterior probabilities of all peak identities at a given transition. When applied to sphingolipid and glycerophosphocholine SRM datasets, we demonstrate over 95% of all peaks are rapidly and correctly identified.

Availability and implementationBATL software is freely accessible online at https://complimet.ca/batl/ and is compatible with Safari, Firefox, Chrome and Edge.

Supplementary informationSupplementary data are available at Bioinformatics online.

category: bioinformatics


title: Discovery of a Novel Non-Narcotic Analgesic Derived from the CL-20 Explosive: Synthesis, Pharmacology and Target Identification of Thio-wurtzine, a Potent Inhibitor of the Opioid Receptors and the Voltage-Dependent Calcium Channels

abstract: The number of candidate molecules for new non-narcotic analgesics is extremely limited. Here we report the identification of thiowurtzine, a new potent analgesic molecule with promising application in chronic pain treatment. We describe the chemical synthesis of this unique compound derived from the hexaazaisowurtzitane (CL-20) explosive molecule. Then we use animal experiments to assess its analgesic activity in vivo upon chemical, thermal and mechanical exposures, compared to the effect of several reference drugs. Finally, we investigate the potential receptors of thiowurtzine in order to better understand its complex mechanism of action. We use docking, molecular modeling and molecular dynamics simulations to identify and characterize the potential targets of the drug and confirm the results of the animal experiments. Our findings finally indicate that thiowurtzine may have a complex mechanism of action, by targeting the mu, kappa, delta and ORL1 opioid receptors, and the voltage-gated calcium channels as well.

category: pharmacology and toxicology


title: Closed-Loop Control between Two GTPase Switches makes the Secretory Functions of the Golgi Responsive to Growth Factors

abstract:
Cancers represent complex autonomous robust systems, displaying interconnectivity with feedback control. Autonomous growth is fueled by a cancer cells ability to  secrete-and-sense growth factors: a poorly understood phenomenon. Using an integrated systems and experimental approach, here we dissect the impact of a feedback-coupled GTPase circuit within the secretory pathway that imparts secretion-coupled autonomy. The circuit is assembled when the Ras-superfamily monomeric GTPase Arf1, and the heterotrimeric GTPase Giabg and their corresponding GAPs and GEFs are coupled by GIV/Girdin, a protein that is known to fuel aggressive traits in diverse cancers. One forward and two key negative feedback loops within the circuit create closed-loop control (CLC), allow the two GTPases to coregulate each other, and convert the expected switch-like behavior of Arf1-dependent secretion into an unexpected dose response alignment behavior of sensing and secretion. Such behavior translates into cell survival that is self-sustained by stimuli-proportionate secretion. Findings highlight how enhanced coupling of two biological switches in cancer cells is critical for multiscale feedback control to achieve secretion-coupled autonomy.

GRAPHIC ABSTRACT

O_FIG O_LINKSMALLFIG WIDTH=163 HEIGHT=200 SRC="FIGDIR/small/436048v3_ufig1.gif" ALT="Figure 1">
View larger version (51K):
org.highwire.dtl.DTLVardef@183ff5corg.highwire.dtl.DTLVardef@f21de7org.highwire.dtl.DTLVardef@1893683org.highwire.dtl.DTLVardef@159d966_HPS_FORMAT_FIGEXP  M_FIG C_FIG In BriefThis work delivers an experimentally validated dynamical systems model of the cooperativity between two distinct classes of biological switches in eukaryotic cells and reveals the basis of secretion-coupled cellular autonomy in cancer.

HIGHLIGHTSO_LIModeling and experimental approaches were used to dissect a coupled GTPase circuit
C_LIO_LICoupling enables closed loop feedback and mutual control of GTPases
C_LIO_LICoupling generates dose response alignment behavior of sensing and secretion.
C_LIO_LICoupling is critical for multiscale feedback control to achieve secretion-coupled autonomy.
C_LI

category: systems biology


title: A Eukaryotic Circuit for Secrete-and-Sense Autonomy


title: A Eukaryotic Circuit for Secretion-coupled Cellular Autonomy


title: EMBED: a low dimensional reconstruction of gut microbiome dynamics based on ecological normal modes

abstract: Dimensionality reduction can offer unique insights into high dimensional microbiome dynamics by leveraging collective abundance fluctuations of multiple bacteria driven by similar ecological perturbations. However, methods providing lower-dimensional representations of microbiome dynamics both at the community and individual taxa level are not currently available. To that end, we present EMBED: Essential MicroBiomE Dynamics, a probabilistic non-linear tensor factorization approach. Similar to normal mode analysis in structural biophysics, EMBED infers ecological normal modes (ECNs), which represent the unique orthogonal modes capturing the collective behavior of microbial communities. A very small number of ECNs can accurately approximate microbiome dynamics across multiple data sets. Inferred ECNs reflect specific ecological behaviors, providing natural templates along which the dynamics of individual bacteria may be partitioned. Moreover, the multi-subject treatment in EMBED systematically identifies subject-specific and universal abundance dynamics that are not detected by traditional approaches. Collectively, these results highlight the utility of EMBED as a versatile dimensionality reduction tool for studies of microbiome dynamics.


title: EMBED: a low dimensional reconstruction of subject-specific gut microbiome dynamics based on ecological normal modes


title: EMBED: Essential Microbiome Dynamics, a dimensionality reduction approach for longitudinal microbiome studies


title: An fMRI-based brain marker predicts individual differences in delay discounting

abstract: Individual differences in impatience--how much we discount future compared to immediate rewards--are associated with general life outcomes and related to substance use, psychiatric diseases, and obesity. Here, we use machine-learning on fMRI activity during an intertemporal choice task to develop a brain marker of individual differences in delay discounting. Study 1 (N=110) was used as a training and cross-validation set, resulting in significant prediction accuracy (r = 0.49) and suggesting an interplay between brain regions associated with affect, value, and cognitive control. The validity of the brain marker was replicated in an independent data set (Study 2, N=145, r = 0.45). In both studies, responses of the marker significantly differed between overweight and lean individuals. This pattern is a first step towards a generalizable neuromarker of delay discounting and a potentially transdiagnostic phenotype, which can be used as a brain-based target measure in future studies.


title: P2X7 receptor signaling is not required but can enhance Th17 differentiation.

abstract: The purinergic receptor P2X7 (P2X7R) is important in inflammasome activation and generally considered to favor proinflammatory Th17 immune responses. However, several studies utilizing P2rx7-/- mice did not observe impaired inflammation, on the contrary, these reports demonstrate that P2rx7-/- mice can have more sever inflammation compared to WT controls. To begin to clarify this discrepancy, the impact of P2X7R signaling on primary Th17 and Th1 cell responses was examined. Initially, utilizing a global knockout approach, we found that P2rx7-/- mice develop comparable Th17 and Th1 responses to those of WT mice. However, indepth in vitro and in vivo investigations revealed differences in the immune response outcome depending on which cell type expresses P2X7R. In this regard, DC-specific P2X7R deficient chimeras demonstrate a comparable Th17 differentiation pattern with that of WT chimeras but display a significantly enhanced Th1 response. However, P2rx7-/- T cells have a suppressed Th17 differentiation profile while developing a similarly enhanced Th1 response as observed in DC-specific P2X7R deficient chimeras. Finally, P2X7R expression induces more T cell death in vivo, attributed to its cytotoxicity, which results in a similar total number of WT Th17 and P2rx7-/- Th17 cells and remarkably higher amounts of P2rx7-/- Th1 cells. Collectively, our findings establish that P2X7R expression on CD4+ T cells is necessary for Th17 differentiation while inhibiting Th1 development.

category: immunology


title: Drosophila antimicrobial peptides and lysozymes regulate gut microbiota composition and abundance

abstract:
The gut microbiota affects the physiology and metabolism of animals and its alteration can lead to diseases such as gut dysplasia or metabolic disorders. Several reports have shown that the immune system plays an important role in shaping both bacterial community composition and abundance in Drosophila, and that immune deficit, especially during aging, negatively affects microbiota richness and diversity. However, there has been little study at the effector level to demonstrate how immune pathways regulate the microbiota. A key set of Drosophila immune effectors are the antimicrobial peptides (AMPs), which confer defense upon systemic infection. AMPs and lysozymes, a group of digestive enzymes with antimicrobial properties, are expressed in the gut and are good candidates for microbiota regulation. Here, we take advantage of the model organism Drosophila melanogaster to investigate the role of AMPs and lysozymes in regulation of gut microbiota structure and diversity.

Using flies lacking AMPs and newly generated lysozyme mutants, we colonized gnotobiotic flies with a defined set of commensal bacteria and analyzed changes in microbiota composition and abundance in vertical transmission and aging contexts through 16S rRNA gene amplicon sequencing. Our study shows that AMPs and, to a lesser extent, lysozymes are necessary to regulate the total and relative abundance of bacteria in the gut microbiota. We also decouple the direct function of AMPs from the IMD signaling pathway that regulates AMPs but also many other processes, more narrowly defining the role of these effectors in the microbial dysbiosis observed in IMD-deficient flies upon aging.

ImportanceThis study advances current knowledge in the field of host-microbe interactions by demonstrating that the two families of immune effectors, antimicrobial peptides and lysozymes, actively regulate the gut microbiota composition and abundance. Consequences of the loss of these antimicrobial peptides and lysozymes are exacerbated during aging, and their loss contributes to increased microbiota abundance and shifted composition in old flies. This work shows that immune effectors, typically associated with resistance to pathogenic infections, also help shape the beneficial gut community, consistent with the idea that host-symbiont interactions use the same  language typically associated with pathogenesis.

category: microbiology


title: Transcriptomic analysis of temporal shifts in berry development between two grapevine cultivars of the Pinot family reveals potential ripening-regulative genes

abstract:
BackgroundGrapevine cultivars of the Pinot family represent clonally propagated mutants with major phenotypic and physiological differences, such as different colour or shifted ripening time, as well as changes in important viticultural traits. Specifically, the cultivars  Pinot Noir (PN) and  Pinot Noir Precoce (PNP, early ripening) flower at the same time, but vary in the beginning of berry ripening (veraison) and, consequently, harvest time. In addition to genotype, seasonal climatic conditions (i.e. high temperatures) also affect ripening times. To reveal possible regulatory genes that affect the timing of veraison onset, we investigated differences in gene expression profiles between PN and PNP throughout berry development with a closely meshed time series and over two separate years.

ResultsThe difference in the duration of berry formation between PN and PNP was quantified to be approximately two weeks under the growth conditions applied, using plant material with a proven PN and PNP clonal relationship. Clusters of co-expressed genes and differentially expressed genes (DEGs) were detected which reflect the shift in the timing of veraison onset. Functional annotation of these DEGs fit to observed phenotypic and physiological changes during berry development. In total, we observed 3,342 DEGs in 2014 and 2,745 DEGs in 2017 between PN and PNP, with 1,923 DEGs across both years. Among these, 388 DEGs were identified as veraison-specific and 12 were considered as berry ripening time regulatory candidates. The expression profiles revealed two candidate genes for ripening time control which we designated VviRTIC1 and VviRTIC2 (VIT_210s0071g01145 and VIT_200s0366g00020, respectively). These genes likely contribute the phenotypic differences observed between PN and PNP.

ConclusionsMany of the 1,923 DEGs show highly similar expression profiles in both cultivars if the patterns are aligned according to developmental stage. In our work, putative genes differentially expressed between PNP and PN which could control ripening time as well as veraison-specific genes were identified. We point out connections of these genes to molecular events during berry development and discuss potential candidate genes which may control ripening time. Two of these candidates were observed to be differentially expressed in the early berry development phase. Several down-regulated genes during berry ripening are annotated as auxin response factors / ARFs. Conceivably, general changes in auxin signaling may cause the earlier ripening phenotype of PNP.

category: developmental biology


title: Transcriptomic analysis of temporal shifts in berry development between two grapevine cultivars of the Pinot family reveals potential genes controlling ripening time


title: Agricultural pressures impair trophic link between aquatic microorganisms and invertebrates

abstract: Decadal declines in aquatic ecosystem health prompted monitoring efforts and studies on effects of human practices on aquatic biodiversity, yet a consideration of ecological processes and trophic linkages is increasingly required to develop an in-depth understanding of aquatic food webs and its vulnerability to human activities. Here, we test in laboratory incubations using natural organic matter whether agricultural practices have an effect on two interacting ecological processes (i.e., decomposition and invertebrate growth) as the relevant temporal components of the trophic linkage between aquatic microbial communities and aquatic invertebrates. We further assess whether these altered trophic interactions are visible on ecologically relevant scales. We observed clear patterns in agricultural constraints on microbial decomposition, which coincided with reduced invertebrate growth and an unexpected increase in invertebrate consumption of organic matter. Similar differences in invertebrate length depending on land use were observed in our field survey, thereby providing important clues on the relevance and vulnerability of interdependent processes that can serve to improve future forays in monitoring ecosystem health.


title: Differential responses of amphibians and reptiles to land-use change in the biodiversity hotspot of north-eastern Madagascar

abstract: Large expanses of tropical rainforest have been converted into agricultural landscapes cultivated by smallholder farmers. This is also the case in north-eastern Madagascar; a region that retains significant proportions of forest cover despite slash-and-burn hill rice cultivation and vanilla agroforestry expansion. The region is also a global hotspot for herpetofauna diversity, but how amphibians and reptiles are affected by land-use change remains largely unknown. Using a space-for-time study design, we compared species diversity and community composition across seven prevalent land uses: unburned (old-growth forest, forest fragment, and forest-derived vanilla agroforest) and burned (fallow-derived vanilla agroforest, woody fallow, and herbaceous fallow) land-use types, and rice paddy. We conducted six comprehensive, time-standardized searches across at least ten replicates of each land-use type and applied genetic barcoding to confirm species identification. We documented an exceptional diversity of herpetofauna (119 species; 91% endemic). Plot-level amphibian species richness was significantly higher in old-growth forest than in all other land-use types. Plot-level reptile species richness was significantly higher in unburned land-use types compared to burned land-use types. For both amphibians and reptiles, the less-disturbed land-use types showed more uneven communities and the species composition in old-growth forest differed significantly from all other land-use types. Amphibians had higher forest dependency (38% of species occurred exclusively in old-growth forest) than reptiles (26%). Our analyses thus revealed that the two groups respond differently to land-use change: we found less pronounced losses of reptile species richness especially in unburned agricultural habitats, suggesting that reptiles are less susceptible to land-use change than amphibians, possibly due to their ability to cope with hotter and drier microclimates. Overall, old-growth forest harboured a unique diversity, but some species also thrived in vanilla agroforestry systems, especially if these were forest-derived. This highlights the importance of conserving old-growth forests and non-burned land-use types within agricultural landscapes.


title: Ignoring errors causes inaccurate timing of single-cell phylogenies

abstract: Single-cell sequencing provides a new way to explore the evolutionary history of cells. Compared to traditional bulk sequencing, where a population of heterogeneous cells is pooled to form a single observation, single-cell sequencing isolates and amplifies genetic material from individual cells, thereby preserving the information about the origin of the sequences. However, single-cell data is more error-prone than bulk sequencing data due to the limited genomic material available per cell. Here, we present error and mutation models for evolutionary inference of single-cell data within a mature and extensible Bayesian framework, BEAST2. Our framework enables integration with biologically informative models such as relaxed molecular clocks and population dynamic models. Our simulations show that modeling errors increase the accuracy of relative divergence times and substitution parameters. We reconstruct the phylogenetic history for a colorectal cancer patient and a healthy patient from single-cell DNA sequencing data. We find that the estimated times of terminal splitting events are shifted forward in time compared to models which ignore errors. We observed that not accounting for errors can overestimate the phylogenetic diversity in single-cell DNA sequencing data. We estimate that 30-50% of the apparent diversity can be attributed to error. Our work enables a full Bayesian approach capable of accounting for errors in the data within the integrative Bayesian software framework BEAST2.


title: Accounting for errors in data improves timing in single-cell cancer evolution


title: On the genetic architecture of rapidly adapting and convergent life history traits in guppies

abstract: The genetic basis of traits can shape and constrain how adaptation proceeds in nature; rapid adaptation can be facilitated by polygenic traits, whereas polygenic traits may restrict re-use of the same genes in adaptation (genetic convergence). The rapidly evolving life histories of guppies in response to predation risk provide an opportunity to test this proposition. Guppies adapted to high- (HP) and low-predation (LP) environments in northern Trinidad evolve rapidly and convergently among natural populations. This system has been studied extensively at the phenotypic level, but little is known about the underlying genetic architecture. Here, we use an F2 QTL design to examine the genetic basis of seven (five female, two male) guppy life history phenotypes. We use RAD-sequencing data (16,539 SNPs) from 370 male and 267 female F2 individuals. We perform linkage mapping, estimates of genome-wide and per-chromosome heritability (multi-locus associations), and QTL mapping (single-locus associations). Our results are consistent with architectures of many-loci of small effect for male age and size at maturity and female interbrood period. Male trait associations are clustered on specific chromosomes, but female interbrood period exhibits a weak genome-wide signal suggesting a potentially highly polygenic component. Offspring weight and female size at maturity are also associated with a single significant QTL each. These results suggest rapid phenotypic evolution of guppies may be facilitated by polygenic trait architectures, but these may restrict gene-reuse across populations, in agreement with an absence of strong signatures of genetic convergence from recent population genomic analyses of wild HP-LP guppies.


title: Identification of a Major Locus for Flowering Pattern Sheds Light on Plant Architecture Diversification in Cultivated Peanut

abstract: Flowering pattern is a major taxonomic characteristic differentiating the two main subspecies of cultivated peanut (Arachis hypogaea L.). subsp. fastigiata possessing flowers on the mainstem (MSF) and a sequential flowering pattern, whereas subsp. hypogaea lacks flowers on the mainstem and exhibits an alternate flowering pattern. This character is considered the main contributor to plant architecture and the adaptability of each subgroup to specific growing conditions. Evidence indicates that flowering pattern differentiation occurred during the several thousand years of domestication and diversification in South America. However, the exact genetic mechanism that controls flowering pattern and the molecular changes that led to its historical diversification in peanut are unknown. We investigated the genetics of the flowering pattern in a recombinant inbred population of 259 lines (RILs), derivatives of an A. hypogaea and A. fastigiata cross. RILs segregated 1:1 in both the sequential/alternative and the MSF-plus/MSF-minus traits, indicating a single gene effect. Using the Axiom_Arachis2 SNP-array, MSF was mapped to a 1.7 Mbp segment on chromosome B02 of the cultivated A. hypogaea. Significant haplotype conservation was found for this locus in the USA peanut mini core collection, suggesting a possible selection upon hypogaea/fastigiata speciation. Furthermore, a candidate Terminal Flowering 1-like (AhTFL1) gene was identified within the MSF region, in which a 1492 bp deletion occurred in the fastigiata line that leads to a truncated protein product. Remapping MSF in the RIL population with the AhTFL1 deletion as a marker increased the LOD score from 53.3 to 158.8 with no recombination. The same deletion was also found to co-segregate with the phenotype in two EMS-mutagenized M2 families, suggesting a hotspot for large mutational deletion or gene conversion that may play a role in evolution. BLASTX analysis showed that the most similar homologous gene for TFL1-like in soybean is Det1, which previously was shown to control shoot determination. Sequence analysis of the TFL-1 in a series of domesticated lines showed that TFL1 was subjected to gain/loss events of the deletion, partly explaining the evolution of MSF in Arachis. Altogether, these results support the role of AhTFL-1 in peanut speciation during domestication and modern cultivation.


title: CONSULT: Accurate contamination removal using locality-sensitive hashing

abstract: A fundamental question appears in many bioinformatics applications: Does a sequencing read belong to a large dataset of genomes from some broad taxonomic group, even when the closest match in the set is evolutionarily divergent from the query? For example, low-coverage genome sequencing (skimming) projects either assemble the organelle genome or compute genomic distances directly from unassembled reads. Using unassembled reads needs contamination detection because samples often include reads from unintended groups of species. Similarly, assembling the organelle genome needs distinguishing organelle and nuclear reads. While k-mer-based methods have shown promise in read-matching, prior studies have shown that existing methods are insufficiently sensitive for contamination detection. Here, we introduce a new read-matching tool called CONSULT that tests whether k-mers from a query fall within a user-specified distance of the reference dataset using locality-sensitive hashing. Taking advantage of large memory machines available nowadays, CONSULT libraries accommodate tens of thousands of microbial species. Our results show that CONSULT has higher true-positive and lower false-positive rates of contamination detection than leading methods such as Kraken-II and improves distance calculation from genome skims. We also demonstrate that CONSULT can distinguish organelle reads from nuclear reads, leading to dramatic improvements in skims-based mitochondrial assemblies.


title: RENET2: High-Performance Full-text Gene-Disease Relation Extraction with Iterative Training Data Expansion

abstract:
BackgroundRelation extraction is a fundamental task for extracting gene-disease associations from biomedical text. Existing tools have limited capacity, as they can extract gene-disease associations only from single sentences or abstract texts.

ResultsIn this work, we propose RENET2, a deep learning-based relation extraction method, which implements section filtering and ambiguous relations modeling to extract gene-disease associations from full-text articles. We designed a novel iterative training data expansion strategy to build an annotated full-text dataset to resolve the scarcity of labels on full-text articles. In our experiments, RENET2 achieved an F1-score of 72.13% for extracting gene-disease associations from an annotated full-text dataset, which was 27.22%, 30.30% and 29.24% higher than the best existing tools BeFree, DTMiner and BioBERT, respectively. We applied RENET2 to (1) ~1.89M full-text articles from PMC and found ~3.72M gene-disease associations; and (2) the LitCovid articles set and ranked the top 15 proteins associated with COVID-19, supported by recent articles.

ConclusionRENET2 is an efficient and accurate method for full-text gene-disease association extraction. The source-code, manually curated abstract/full-text training data, and results of RENET2 are available at https://github.com/sujunhao/RENET2.


title: Correlation analysis of target selectivity and side effects of FDA-approved kinase inhibitors

abstract: Kinase inhibitors (KIs) represent a popular class of therapeutic agents and chemical probes but most of them tend to be polypharmacological. Receptor and non-receptor Tyrosine KIs can target more than 100 kinases simultaneously compare to other KIs. We here analyze the molecular targets of 41 U.S. Food and Drug Administration (FDA)-approved KIs. We chose 18 drugs (Tyrosine KIs) and sought out to evaluate their selectivity profile and engagement with a number of targets in vivo at clinically relevant doses. We also wanted to see whether there prevails any correlation between the target engagement profile and the reported side effects for specific KIs chosen as test cases. To explore all clinical targets of the 18 KIs, we considered the free (unbound) maximum serum concentration (Cmax) of each KI and only chose targets for which the cognate affinities lie within the reported free Cmax values, thereby allowing plausible interaction in clinical doses. We retrieved the side effects of those KIs that is reported in the FDA adverse event reporting system. We illustrate how correlation analysis of target-side effect can give a new insight into the off target of KIs and their effect on increasing the toxicity of KIs. These analyses could aid our understanding of the structural-activity relationship of KIs.


title: Facilitating the design of combination therapy in cancer using multipartite network models: Emphasis on acute myeloid leukemia

abstract: From the drug discovery perspective, combination therapy is recommended in cancer due to efficiency and safety compared to the common cytotoxic and single-targeted monotherapies. However, identifying effective drug combinations is time- and cost-consuming. Here, we offer a novel strategy of predicting potential drug combinations and patient subclasses by constructing multipartite networks using drug response data on patient samples. In the present study, we used Beat AML and GDSC, two comprehensive datasets based on patient-derived and cell line-based samples, to show the potential of multipartite network modeling in cancer combinatorial therapy. We used the median values of cell viability to compare drug potency and reconstruct a weighted bipartite network, which models the interaction of drugs and biological samples. Then, clusters of network communities were identified in two projected networks based on the topological structure of networks. Chemical structures, drug-target networks, protein-protein interactions, and signaling networks were used to corroborate the intra-cluster homogeneity. We further leveraged the community structures within the drug-based multipartite networks to discover effective multi-targeted drug combinations, and the synergy levels which were supported with more evidence using the DrugComb and the ALMANAC databases. Furthermore, we confirmed the potency of selective combinations of drugs against monotherapy in vitro experiment using three acute myeloid leukemia (AML) cell lines. Taken together, this study presents an innovative data-driven strategy based on multipartite networks to suggest potential drug combinations to improve treatment of AML.


title: Focal seizures are organized by feedback between neural activity and ion concentration changes

abstract: Human and animal EEG data demonstrate that focal seizures start with low-voltage fast activity, evolve into rhythmic burst discharges and are followed by a period of suppressed background activity. This suggests that processes with dynamics in the range of tens of seconds govern focal seizure evolution. We investigate the processes associated with seizure dynamics by complementing the Hodgkin-Huxley mathematical model with the physical laws that dictate ion movement and maintain ionic gradients. We show that the disturbance of K+ and Cl- homeostasis by the fast discharge of inhibitory interneurons is sufficient to initiate seizures, which are maintained by positive feedback between ion concentration changes and neuronal activity. Gradual Na+ accumulation increases the rate of the Na+/K+-pump, creating negative feedback which slows down and terminates ictal discharges and contributes to the postictal state. Our results emphasize ionic dynamics as elementary processes behind seizure generation and indicate targets for new therapeutic strategies.


title: Exploration-based learning of a step to step controller predicts locomotor adaptation

abstract: Humans are able to adapt their locomotion to a variety of novel circumstances, for instance, walking on diverse terrain and walking with new footwear. During locomotor adaptation, humans have been shown to exhibit stereotypical changes in their movement patterns. Here, we provide a theoretical account of such locomotor adaptation, positing that the nervous system prioritizes stability in the short timescale and improves energy expenditure over a longer timescale. The resulting mathematical model has two processes: a stabilizing controller which is gradually changed by a reinforcement learner that exploits local gradients to lower energy expenditure, estimating gradients indirectly via intentional exploratory noise. We consider this model walking and adapting under three novel circumstances: walking on a split-belt treadmill (walking with each foot on a different belt, each belt at different speeds), walking with an exoskeleton, and walking with an asymmetric leg mass. This model predicts the short and long timescale changes observed in walking symmetry on the split-belt treadmill and while walking with the asymmetric mass. The model exhibits energy reductions with exoskeletal assistance, as well as entrainment to time-periodic assistance. We show that such exploration-based learning is degraded in the presence of large sensorimotor noise, providing a potential account for some impairments in learning.


title: Chromatin architecture in addiction circuitry elucidates biological mechanisms underlying cigarette smoking and alcohol use traits.

abstract: Cigarette smoking and alcohol use are among the most prevalent substances used worldwide and account for a substantial proportion of preventable morbidity and mortality, underscoring the public health significance of understanding their etiology. Genome-wide association studies (GWAS) have successfully identified genetic variants associated with cigarette smoking and alcohol use traits. However, the vast majority of risk variants reside in non-coding regions of the genome, and their target genes and neurobiological mechanisms are unknown. Chromosomal conformation mappings can address this knowledge gap by charting the interaction profiles of risk-associated regulatory variants with target genes. To investigate the functional impact of common variants associated with cigarette smoking and alcohol use traits, we applied Hi-C coupled MAGMA (H-MAGMA) built upon cortical and midbrain dopaminergic neuronal Hi-C datasets to GWAS summary statistics of nicotine dependence, cigarettes per day, problematic alcohol use, and drinks per week. The identified risk genes mapped to key pathways associated with cigarette smoking and alcohol use traits, including drug metabolic processes and neuronal apoptosis. Risk genes were highly expressed in cortical glutamatergic, midbrain dopaminergic, GABAergic, and serotonergic neurons, suggesting them as relevant cell types in understanding the mechanisms by which genetic risk factors influence cigarette smoking and alcohol use. Lastly, we identified pleiotropic genes between cigarette smoking and alcohol use traits under the assumption that they may reveal substance-agnostic, shared neurobiological mechanisms of addiction. The number of pleiotropic genes was [~]26-fold higher in dopaminergic neurons than in cortical neurons, emphasizing the critical role of ascending dopaminergic pathways in mediating general addiction phenotypes. Collectively, brain region- and neuronal subtype-specific 3D genome architecture refines neurobiological hypotheses for smoking, alcohol, and general addiction phenotypes by linking genetic risk factors to their target genes.


title: Single-cell proteo-genomic reference maps of the hematopoietic system enable the purification and massive profiling of precisely defined cell states

abstract: Single-cell genomics has transformed our understanding of complex cellular systems. However, excessive costs and a lack of strategies for the purification of newly identified cell types impede their functional characterization and large-scale profiling. Here, we have generated high content single-cell proteo-genomic reference maps of human blood and bone marrow that quantitatively link the expression of up to 197 surface markers to cellular identities and biological processes across all major hematopoietic cell types in healthy aging and leukemia. These reference maps enable the automatic design of cost-effective high-throughput cytometry schemes that outperform state-of-the-art approaches, accurately reflect complex topologies of cellular systems, and permit the purification of precisely defined cell states. The systematic integration of cytometry and proteo-genomic data enables measuring the functional capacities of precisely mapped cell states at the single-cell level. Our study serves as an accessible resource and paves the way for a data-driven era in cytometry.


title: Understanding and predicting socioeconomic determinants of deforestation in Vietnam's Central Annamites Landscape (CAL): Pilot study implementing a spatial econometric approach

abstract: The forests of the Greater Mekong Subregion, consisting of Myanmar, Thailand, Cambodia, Laos and Vietnam, are under high pressure from economic development and exploitation of natural resources, including but not limited to land concession, smallholder plantations and commercial agriculture, agroforestry development, mining, and road infrastructure development. While these threats are well-known, the magnitude and dynamics of their individual and interacting effects on forest cover are not fully understood. This pilot study aims to apply existing, publicly available macro, micro, and socioeconomic data in addition to remote sensing forest cover data to explore economic determinants of deforestation in the Greater Mekong, using the case of the Central Annamites Landscape (CAL) ecoregion of Vietnam. A longitudinal panel was constructed for 2000-2017, containing 1,658 observations for 144 variables across 95 Tier 2 (district) administrative units in CAL from 2000-2017 for modeling macroeconomic and socioeconomic conditions against annual tree cover loss aggregated to the Tier 2 administrative unit. The first phase of the study used tiered spatial regression analysis to correlatively identify which commodities, economic development activities, and social conditions have historically had the greatest effect on forest cover by magnitude in CAL. Based on first phase results, we selected a subset of these determinants for scenario modelling to predict possible deforestation outcomes given certain economic scenarios. The results, among others, indicate that, when spatially collocated, high poverty rates and smaller scale agricultural land conversion are key immediate determinants of deforestation. This therefore provides evidence to support programs targeting rubber, acacia harvesting, artisanal mining, and land conversion for cash crop plantations. Education is also key immediate socioeconomic factor, as poverty rate is consistently associated with tree cover loss and increased educational attainment is consistently associated with reduced tree cover loss, at approximately 12 ha per percentage increase in secondary school graduation. On the macro level, economic growth in China and Vietnam are correlatively associated with tree cover loss, as are rising trade in Myanmar and Laos. This study provides a methodological contribution to the current academic literature identifying socioeconomic dimensions of deforestation through spatial econometric analysis and scenario modelling at the landscape level. For practitioner work, this pilot provides a model or tool for strategic planning of conservation interventions in light of economic conditions and factors.


title: Exploitation of the genetic variability in the genotype of Egyptian Wheat by studding Molecular Markers, Molecular Docking, and Nano Composites. Regulation of leaf and stem rust.

abstract: This manuscript has been withdrawn by the authors as it was submitted and made public without the full consent of all the authors. Therefore, the authors do not wish this work to be cited as reference for the project. If you have any questions, please contact the corresponding author.


title: In silico molecular modeling and docking studies of Nano Composites compound to Regulation, inhibition and treatment leaf and stem wheat rust


title: Exploitation of the genetic variability in the genotype of Egyptian Wheat by studding Molecular Markers, Molecular Docking and Nano Composites. Regulation of leaf and stem rust

category: molecular biology


title: scDALI: Modelling allelic heterogeneity of DNA accessibility in single-cells reveals context-specific genetic regulation

abstract:
While the functional impact of genetic variation can vary across cell types and states, capturing this diversity remains challenging. Current studies, using bulk sequencing, ignore much of this heterogeneity, reducing discovery and explanatory power. Single-cell approaches combined with F1 genetic designs provide a new opportunity to address this problem, however suitable computational methods to model these complex relationships are lacking.

Here, we developed scDALI, an analysis framework that integrates single-cell chromatin accessibility for unbiased cell state identification with allelic quantifications to assay genetic effects. scDALI builds on Gaussian process regression and can differentiate between homogeneous (pervasive) allelic imbalances and cell state-specific regulation. As a proof-of-principle, we applied scDALI to whole Drosophila embryos from F1 crosses, profiling sciATAC-seq at three embryonic stages. Even in these very complex samples, scDALI discovered hundreds of peaks with heterogeneous allelic imbalance, having effects in specific lineages and/or developmental stages. Our study provides a general strategy to identify the cellular context of allelic imbalance, a crucial step in linking genetic traits to cellular phenotypes.


title: Genomic taxonomic assignment of individual root-knot nematodes

abstract: Root-knot nematodes (RKN; genus Meloidogyne) are polyphagous plant pathogens of great economic importance to agriculturalists globally. These species are small, diverse, and can be challenging for accurate taxonomic identification. Many of the most important crop pests confound analysis with simple genetic marker loci as they are polyploids of likely hybrid origin. Here we take a low-coverage, long-read genome sequencing approach to characterisation of individual root-knot nematodes. We demonstrate library preparation for Oxford Nanopore Technologies Flongle sequencing of low input DNA from individual juveniles and immature females, multiplexing up to twelve samples per flow cell. Taxonomic identification with Kraken 2 (a k-mer-based taxonomic assignment tool) is shown to reliably identify individual nematodes to species level, even within the very closely related Meloidogyne incognita group. Our approach forms a robust, low-cost, and scalable method for accurate RKN species diagnostics.


title: Insights into single hiPSC-derived cardiomyocyte phenotypes and maturation using ConTraX, an efficient pipeline for tracking contractile dynamics

abstract:
Cardiomyocytes derived from human induced pluripotent stem cells (hiPSC-CMs) are powerful in-vitro models to study the mechanisms underlying cardiomyopathies and cardiotoxicity. To understand how cellular mechanisms affect the heart, it is crucial to quantify the contractile function in single hiPSC-CMs over time, however, such measurements remain demanding and low-throughput, and are too seldom considered.

We developed an open-access, versatile, streamlined, and highly automated pipeline to address these challenges and enable quantitative tracking of the contractile dynamics of single hiPSC- CMs over time: ConTraX. Three interlocking software modules enable: (i) parameter-based localization and selection of single hiPSC-CMs; (ii) automated video acquisition of >200 cells/hour; and (iii) streamlined measurements of the contractile parameters via traction force microscopy. Using ConTraX, we analyzed >2,753 hiPSC-CMs over time under orthogonal experimental conditions in terms of culture media and substrate stiffnesses. Using undirected high-dimensional clustering, we dissected the complex diversity of contractile phenotypes in hiPSC-CM populations and revealed converging maturation patterns.

Our modular ConTraX pipeline empowers biologists with a potent quantitative analytic tool applicable to the development of cardiac therapies.

category: bioengineering


title: ODOR IDENTITY CAN BE EXTRACTED FROM THE RECIPROCAL CONNECTIVITY BETWEEN OLFACTORY BULB AND PIRIFORM CORTEX IN HUMANS

abstract: Neuronal oscillations route external and internal information across brain regions. In the olfactory system, the two central nodes--the olfactory bulb (OB) and the piriform cortex (PC)--communicate with each other via neural oscillations to shape the olfactory percept. Communication between these nodes have been well characterized in non-human animals but less is known about their role in the human olfactory system. Using a recently developed and validated EEG-based method to extract signals from the OB and PC sources, we show in healthy human participants that there is a bottom-up information flow from the OB to the PC in the beta and gamma frequency bands, while top-down information from the PC to the OB is facilitated by delta and theta oscillations. Importantly, we demonstrate that there was enough information to decipher odor identity above chance from the low gamma in the OB-PC oscillatory circuit as early as 100ms after odor onset. These data further our understanding of the critical role of bidirectional information flow in human sensory systems to produce perception. However, future studies are needed to determine what specific odor information is extracted and communicated in the information exchange.


title: Direct induction of hemogenic endothelial progenitors from hPSCs by defined factors revealed by single-cell transcriptome analysis

abstract:
Transcription factors (TFs) play critical roles in stem cell maintenance and differentiation. Using single cell RNA sequencing, we investigated TFs expressed in hemogenic endothelial (HE) progenitors differentiated from human pluripotent stem cells (hPSCs) and identified upregulated expression of SOXF factors SOX7, SOX17, and SOX18 in the HE population. To test whether overexpression of these factors increases HE differentiation efficiency, we established inducible hPSC lines and found only SOX17 improved differentiation. Temporal expression analysis further revealed SOX17 was turned on immediately before VE-Cadherin, indicating SOX17 may be a causative factor for HE differentiation. Upon SOX17 knockdown via CRISPR-Cas13d, HE differentiation was significantly abrogated. Strikingly, we discovered SOX17 overexpression alone is sufficient to generate more than 50% CD34+VE-cadherin+CD73- cells that could be directed to hematopoietic progenitors, which emerged via an endothelial-to-hematopoietic transition and significantly upregulated definitive hematopoietic transcriptional programs. Functional assays showed that these progenitors can differentiate into blood cells from multiple lineages. Our analyses reveal an uncharacterized function of SOX17 in directing hPSCs differentiation towards HE cells.

Significance StatementHemogenic endothelial (HE) cells have been generated from human pluripotent stem cells (hPSCs) to study blood development. However, their full transcriptomic characterization and key genes involving in directing HE differentiation is unclear. Utilizing single cell RNA-seq analysis, we find that SOX17 is solely expressed in HE cells and is also required for HE differentiation. Strikingly, we find that overexpression of SOX17 alone is sufficient to program hPSCs into CD34+VE-cadherin+CD73-HE cells, which could further differentiate into blood progenitors. Our research reveals that SOX17 is sufficient to direct hPSCs differentiation to HE cells.

ClassificationPhysical Sciences/Engineering; Biological Sciences/Cell Biology.


title: Parthanatos-inducing zinc agent C010DS-Zn elicits anti-tumor immune responses involving T cells and macrophages in vivo

abstract: Immune checkpoint inhibitors opened a new horizon in cancer therapy by enabling durable and complete responses in patients, but their wider application against general solid cancers has been hampered by the lack of a broadly acting anti-cancer immune response initiating agents. Parthanatos is a previously unexplored immunogenic programmed necrosis mechanism that is triggered by the hyperactivation of PARP DNA repair and executed by an efficient DNA-fragmentation mechanism. We developed a proprietary macromolecular zinc complex agent C010DS-Zn that efficiently induced parthanatos against 4T1 murine cancer cells in vitro, which was characterized as PARP-mediated necrotic death with massive DNA damages. Ex vivo screening of its cytotoxicity against a panel of 53 low-passage human solid cancer PDX tumor fragments demonstrated its consistent delivery of characteristically DNA-damaging cell death that was unseen in the corresponding apoptosis positive controls. Further characterization of its in vivo treatment effects versus the immunosuppressive 4T1-Balb/c and immunogenic CT26-Balb/c syngeneic cancer models showed that sufficiently high intravenous C010DS-Zn treatments led to robust initiation of the tumor-suppressed antitumor immune compartments such as T cells and macrophages. At lower non-anticancer doses, C010DS-Zn treatment still led to significantly reduced macrophage content and inflammation in the 4T1 tumor, suggesting its potential utility against macrophage-mediated inflammations such as those seen in MIS-C or COVID19. Given the observation of its low serum bioavailability in a rat pharmacokinetic study, these results suggest potential development opportunities for C010DS-Zn to become a widely applicable immune initiation agent with chemo-like broad applicability upon its pharmacokinetic improvements.


title: Loss-of-function variants in the cardiac Kv11.1 channel as a genetic biomarker for SUDEP

abstract:
ObjectiveTo compare the frequency and impact on channel function of KCNH2 variants in SUDEP patients with epilepsy controls comprising patients older than 50 years, a group with low SUDEP risk, and establish loss-of-function KCNH2 variants as predictive biomarkers of SUDEP risk.

MethodsWe searched for KCNH2 variants with a minor allele frequency of < 5%. Functional analysis in Xenopus laevis oocytes was performed for all KCNH2 variants identified.

ResultsKCNH2 variants were found in 11.1% (10/90) of SUDEP individuals compared to 6.0% (20/332) of epilepsy controls (p = 0.11). Loss-of-function KCNH2 variants, defined as causing > 20% reduction in maximal amplitude, were observed in 8.9% (8/90) SUDEP patients compared to 3.3% (11/332) epilepsy controls suggesting about three-fold enrichment (nominal p = 0.04). KCNH2 variants that did not change channel function occurred at a similar frequency in SUDEP (2.2%; 2/90) and epilepsy control (2.7%; 9/332) cohorts (p > 0.99). Rare KCNH2 variants (< 1% allele frequency) associated with greater loss of function and an [~]11-fold enrichment in the SUDEP cohort (nominal p = 0.03). In silico tools were unable to predict the impact of a variant on function highlighting the need for electrophysiological analysis.

ConclusionsThese data show that loss-of-function KCNH2 variants are enriched in SUDEP patients and suggest that cardiac mechanisms contribute to SUDEP risk. We propose that genetic screening in combination with functional analysis can identify loss-of-function KCNH2 variants that could act as biomarkers of an individuals SUDEP risk.


title: Two subsets of human marginal zone B cells resolved by global analysis of lymphoid tissues and blood

abstract: B cells generate antibodies that are essential for immune protection. Major events driving B cell responses occur in lymphoid tissues, which guide antigen acquisition and support cellular interactions, yet complexities of B cell subsets in human lymphoid tissues are poorly understood. Here we perform undirected, global profiling of B cells in matched human lymphoid tissues from deceased transplant organ donors and tracked dissemination of B cell clones. In addition to identifying unanticipated features of tissue-based B cell differentiation, we resolve two clonally independent subsets of marginal zone B cells that differ in cell surface and transcriptomic profiles, tendency to disseminate, distribution bias within splenic marginal zone microenvironment and immunoglobulin repertoire diversity and hypermutation frequency. Each subset is represented in spleen, gut-associated lymphoid tissue, mesenteric lymph node, and also blood. Thus, we provide clarity and diffuse controversy surrounding human MZB - the  elephant in the room of human B cell biology.


title: Dendritic cell deficiencies persist seven months after SARS-CoV-2 infection

abstract: Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV)-2 infection induces an exacerbated inflammation driven by innate immunity components. Dendritic cells (DCs) play a key role in the defense against viral infections, for instance plasmacytoid DCs (pDCs), have the capacity to produce vast amounts of interferon-alpha (IFN-). In COVID-19 there is a deficit in DC numbers and IFN- production, which has been associated with disease severity. In this work, we described that in addition to the DC deficiency, several DC activation and homing markers were altered in acute COVID-19 patients, which were associated with multiple inflammatory markers. Remarkably, previously hospitalized and non-hospitalized patients remained with decreased numbers of CD1c+ myeloid DCs and pDCs seven months after SARS-CoV-2 infection. Moreover, the expression of DC markers as CD86 and CD4 were only restored in previously non-hospitalized patients while integrin {beta}7 and indoleamine 2,3- dyoxigenase (IDO) no restoration was observed. These findings contribute to a better understanding of the immunological sequelae of COVID-19.


title: Reduced neutralization of SARS-CoV-2 variants by convalescent plasma and hyperimmune intravenous immunoglobulins for treatment of COVID-19

abstract: Hyperimmune immunoglobulin (hCoV-2IG) preparations generated from SARS-CoV-2 convalescent plasma (CP) are under evaluation in several clinical trials of hospitalized COVID-19 patients. Here we explored the antibody epitope repertoire, antibody binding and virus neutralizing capacity of six hCoV-2IG batches as well as nine convalescent plasma (CP) lots against SARS-CoV-2 and emerging variants of concern (VOC). The Gene-Fragment Phage display library spanning the SARS-CoV-2 spike demonstrated broad recognition of multiple antigenic sites spanning the entire spike including NTD, RBD, S1/S2 cleavage site, S2-fusion peptide and S2-heptad repeat regions. Antibody binding to the immunodominant epitopes was higher for hCoV-2IG than CP, with predominant binding to the fusion peptide. In the pseudovirus neutralization assay (PsVNA) and in the wild-type SARS-CoV-2 PRNT assay, hCoV-2IG lots showed higher titers against the WA-1 strain compared with CP. Neutralization of SARS-CoV-2 VOCs from around the globe were reduced to different levels by hCoV-2IG lots. The most significant loss of neutralizing activity was seen against the B.1.351 (9-fold) followed by P.1 (3.5-fold), with minimal loss of activity against the B.1.17 and B.1.429 ([≤]2-fold). Again, the CP showed more pronounced loss of cross-neutralization against the VOCs compared with hCoV-2IG. Significant reduction of hCoV-2IG binding was observed to the RBD-E484K followed by RBD-N501Y and minimal loss of binding to RBD-K417N compared with unmutated RBD. This study suggests that post-exposure treatment with hCoV-2IG is preferable to CP. In countries with co-circulating SARS-CoV-2 variants, identifying the infecting virus strain could inform optimal treatments, but would likely require administration of higher volumes or repeated infusions of hCOV-2IG or CP, in patients infected with the emerging SARS-CoV-2 variants.


title: Autophosphorylation of the KaiC-like protein ArlH inhibits oligomerisation and interaction with ArlI, the motor ATPase of the archaellum

abstract: Motile archaea are propelled by the archaellum, whose motor complex consists of the membrane protein ArlJ, the ATPase ArlI, and the ATP-binding protein ArlH. Despite its essential function and the existence of structural and biochemical data on ArlH, the role of ArlH in archaellum assembly and function remains elusive. ArlH is a structural homolog of KaiC, the central component of the cyanobacterial circadian clock. Similar to KaiC, ArlH exhibits autophosphorylation activity, which was observed for both ArlH of the euryarchaeon Pyrococcus furiosus (PfArlH) and the crenarchaeon Sulfolobus acidocaldarius (SaArlH). Using a combination of single molecule fluorescence measurements and biochemical assays, it is shown that autophosphorylation of ArlH is closely linked to the oligomeric state of ArlH bound to ArlI. These experiments also strongly suggest that ArlH is a hexamer in its functional ArlI bound state. Mutagenesis of the putative catalytic residue Glu-57 in SaArlH results in a reduced autophosphorylation activity and abolished archaellation and motility, suggesting that optimum phosphorylation activity of ArlH is essential for both archaellation and motility.


title: Multiomics Interrogation into HBV (Hepatitis B Virus)-Host Interaction Reveals Novel Coding potential in Human Genome, and Identifies Canonical and Non-canonical Proteins as Host Restriction Factors against HBV

abstract: Hepatitis B Virus constitutes a major threat to global public health. Current understanding of HBV-host interaction is yet limited. Here, ribosome profiling, quantitative mass spectrometry and RNA-sequencing are conducted on a recently established HBV replication system. We have identified multiomic DEGs (differentially expressed genes) that HBV orchestrated to remodel host proteostasis networks. Our multiomics interrogation revealed that HBV induced significant changes in both transcription and translation of 35 canonical genes including PPP1R15A, PGAM5 and SIRT6, as well as the expression of at least 15 non-canonical ORFs including ncPON2 and ncGRWD1, thus revealing an extra coding potential of human genome. Overexpression of these five genes but not the enzymatically deficient SIRT6 mutants suppressed HBV replication while knockdown SIRT6 had opposite effect. Furthermore, the expression of SIRT6 was down-regulated in patients, cells or animal models of HBV infection. Mechanistic study further indicated that SIRT6 directly binds to mini-chromosome and deacetylates histone H3 lysine 9 (H3K9ac) and histone H3 lysine 56 (H3K56ac), and chemical activation of endogenous SIRT6 with MDL800 suppressed HBV infection in vitro and in vivo. By generating the first multiomics landscape of host-HBV interaction, our work is thus opening a new avenue to facilitate therapeutic development against HBV infection.


title: Phycobilisome breakdown effector NblD is required to maintain the cellular amino acid composition during nitrogen starvation

abstract:
Small proteins are critically involved in the acclimation response of photosynthetic cyanobacteria to nitrogen starvation. NblD is the 66-amino-acid effector of nitrogen-limitation-induced phycobilisome breakdown, which is believed to replenish the cellular amino acid pools. To address the physiological functions of NblD, the concentrations of amino acids, intermediates of the arginine catabolism pathway and several organic acids were measured during the response to nitrogen starvation in the cyanobacterium Synechocystis sp. PCC 6803 wild type and in an nblD deletion strain. A characteristic signature of metabolite pool composition was identified, which shows that NblD-mediated phycobilisome degradation is required to maintain the cellular amino acid and organic acid pools during nitrogen starvation. Specific deviations from the wild type suggest wider-reaching effects that also affect such processes as redox homeostasis via glutathione and tetrapyrrole biosynthesis, both of which are linked to the strongly decreased glutamate pool, and transcriptional reprogramming via an enhanced concentration of 2-oxoglutarate, the metabolite co-regulator of the NtcA transcription factor. The essential role played by NblD in metabolic homeostasis is consistent with the widespread occurrence of NblD throughout the cyanobacterial radiation and the previously observed strong positive selection for the nblD gene under fluctuating nitrogen supply.

ImportanceCyanobacteria play important roles in the global carbon and nitrogen cycles. In their natural environment, these organisms are exposed to fluctuating nutrient conditions. Nitrogen starvation induces a coordinated nitrogen-saving program that includes the breakdown of nitrogen-rich photosynthetic pigments, particularly phycobiliproteins. The small protein NblD was recently identified as an effector of phycobilisome breakdown in cyanobacteria. In this study, we demonstrate that the NblD-mediated degradation of phycobiliproteins is needed to sustain cellular pools of soluble amino acids and other crucial metabolites. The essential role played by NblD in metabolic homeostasis explains why genes encoding this small protein are conserved in almost all members of cyanobacterial radiation.


title: Combined computational and cellular screening identifies synergistic inhibition of SARS-CoV-2 by lenvatinib and remdesivir

abstract: Rapid repurposing of existing drugs as new therapeutics for COVID-19 has been an important strategy in the management of disease severity during the ongoing SARS-CoV-2 pandemic. Here, we used high-throughput docking to screen 6000 compounds within the DrugBank library for their potential to bind and inhibit the SARS-CoV-2 3CL main protease, a chymotrypsin-like enzyme that is essential for viral replication. For 19 candidate hits, parallel in vitro fluorescence-based protease-inhibition assays and Vero-CCL81 cell-based SARS-CoV-2 replication-inhibition assays were performed. One hit, diclazuril (an investigational anti-protozoal compound), was validated as a SARS-CoV-2 3CL main protease inhibitor in vitro (IC50 value of 29 {micro}M) and modestly inhibited SARS-CoV-2 replication in Vero-CCL81 cells. Another hit, lenvatinib (approved for use in humans as an anti-cancer treatment), could not be validated as a SARS-CoV-2 3CL main protease inhibitor in vitro, but serendipitously exhibited a striking functional synergy with the approved nucleoside analogue remdesivir to inhibit SARS-CoV-2 replication, albeit this was specific to Vero-CCL81 cells. Lenvatinib is a broadly-acting host receptor tyrosine kinase (RTK) inhibitor, but the synergistic effect with remdesivir was not observed with other approved RTK inhibitors (such as pazopanib or sunitinib), suggesting that the mechanism-of-action is independent of host RTKs. Furthermore, time-of-addition studies revealed that lenvatinib/remdesivir synergy probably targets SARS-CoV-2 replication subsequent to host-cell entry. Our work shows that combining computational and cellular screening is a means to identify existing drugs with repurposing potential as antiviral compounds. Future studies could be aimed at understanding and optimizing the lenvatinib/remdesivir synergistic mechanism as a therapeutic option.


title: Systematic in vivo quantification of microRNA affinities

abstract: The majority of mammalian genes are under regulation by microRNAs, yet predicting the extent of miRNA-mediated repression has remained elusive. Here we systematically quantified the biological impact of miRNAs conserved in vertebrates using stable mouse embryonic stem cell lines expressing sensitive fluorescent reporters. Differentiation of these 163 lines to the three germ layers revealed that the majority of conserved miRNAs have detectable changes in activity. We determined in vivo target affinity KD of 115 miRNAs by integrating activity measurements, CRISPR/Cas miRNA knockouts and miRNA sequencing. Target affinities of individual miRNAs spanned several orders of magnitude, with highly expressed miRNAs having overall higher KD. Scaling miRNA expression levels by their respective KD recapitulated the relative number of Argonaute-bound targets for individual miRNA families. Our results provide a rationale to determine the set of miRNAs with a biological activity in a given cell type, KD values setting expression thresholds for target repression.


title: The inhibitory effects of toothpaste and mouthwash ingredients on the interaction between the SARS-CoV-2 spike protein and ACE2, and the protease activity of TMPRSS2, in vitro

abstract: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) enters host cells when the viral spike protein is cleaved by transmembrane protease serine 2 (TMPRSS2) after binding to the host angiotensin-converting enzyme 2 (ACE2). Since ACE2 and TMPRSS2 are expressed in the mucosa of the tongue and gingiva, the oral cavity seems like it is an entry point for SARS-CoV-2. Daily oral care using mouthwash seems to play an important role in preventing SARS-CoV-2 infection. However, the relationship between daily oral care and the mechanisms of virus entry into host cells is unclear. In this study, we evaluated the inhibitory effects of ingredients that are generally contained in toothpaste and mouthwash on the interaction between the spike protein and ACE2 and on the serine protease activity of TMPRSS2 using an enzyme-linked immunosorbent assay and in vitro enzyme assay, respectively. Both assays detected inhibitory effects of sodium tetradecene sulfonate, sodium N-lauroyl-N-methyltaurate, sodium N-lauroylsarcosinate, sodium dodecyl sulfate, and copper gluconate. Molecular docking simulations suggested that these ingredients could bind to the inhibitor-binding site of ACE2. In addition, tranexamic acid and 6-aminohexanoic acid, which act as serine protease inhibitors, exerted inhibitory effects on TMPRSS2 protease activity. Further experimental and clinical studies are needed to further elucidate these mechanisms. Our findings support the possibility that toothpaste and mouthwash contain ingredients that inhibit SARS-CoV-2 infection.


title: Aniridia-related Keratopathy Relevant Cell Signaling Pathways in Human Fetal Corneas

abstract:
BackgroundTo study aniridia-related keratopathy (ARK) relevant cell signaling pathways (Notch1, Wnt/{beta}-catenin, Sonic hedgehog (SHH) and mTOR) in normal human fetal corneas in comparison with normal human adult corneas.

Results20 wg fetal and normal adult corneas showed similar staining patterns for Notch1, however 10-11 wg fetal corneas showed increased presence of Notch1. Numb and Dlk1 had an enhanced presence in the fetal corneas compared to the adult corneas. Fetal corneas showed stronger immunolabeling with antibodies against {beta}-catenin, Wnt5a and Wnt7a, Gli1, Hes1, p-rpS6, and mTOR when compared to the adult corneas. Gene expression of Notch1, Wnt5A, Wnt7A, {beta}-catenin, Hes1, mTOR and rps6 was higher in the 9-12 wg fetal corneas when compared to adult corneas.

ConclusionsThe cell signaling pathway differences found between human fetal and adult corneas were similar to those previously found in ARK corneas with the exception of Notch1. Analogous profiles of cell signaling pathway activation between human fetal corneas and ARK corneas suggests that there is a less differentiated host milieu in ARK.


title: Long-Term Imaging of Living Adult Zebrafish

abstract: The zebrafish has become a widely used animal model due in large part to its accessibility to and usefulness for high-resolution optical imaging. Although zebrafish research has historically focused mostly on early development, in recent years the fish has increasingly been used to study regeneration, cancer metastasis, behavior, and other processes taking place in juvenile and adult animals. However, imaging of live adult zebrafish is extremely challenging, with survival of adult fish limited to a few tens of minutes using standard imaging methods developed for zebrafish embryos and larvae. Here, we describe a new method for imaging intubated adult zebrafish using a specially designed 3D printed chamber for long-term imaging of adult zebrafish on inverted microscope systems. We demonstrate the utility of this new system by nearly day-long observation of neutrophil recruitment to a wound area in living double-transgenic adult casper zebrafish with fluorescently labeled neutrophils and lymphatic vessels.


title: Rats in the city: implications for zoonotic disease risk in an urbanizing world

abstract: Urbanization is rapidly transforming much of Southeast Asia, altering the structure and function of the landscape, as well as the frequency and intensity of the interactions between people, animals, and the environment. In this study, we began to explore the impact of urbanization on zoonotic disease risk by simultaneously characterizing changes in the abundance and diversity of reservoir hosts (rodents), ectoparasite vectors (ticks), and microbial pathogens across a gradient of urbanization in Malaysian Borneo. We found that although rodent species diversity decreased with increasing urbanization, two species appeared to thrive in anthropogenic environments: the invasive urban exploiter, Rattus rattus and the native urban adapter, Sundamys muelleri. R. rattus was strongly associated with the presence of built infrastructure across the gradient and dominated the urban rodent community where it was associated with high microbial diversity and multi-host zoonoses capable of environmental transmission, including Leptospira spp., and Toxoplasma gondii. In contrast, S. muelleri was restricted to sites with a significant vegetative component where it was found at high densities in the urban location. This species was strongly associated with the presence of ticks, including the medically important genera Ambylomma, Haemaphysalis, and Ixodes. Overall, our results demonstrate that the response to urbanization varies by species at all levels: host, ectoparasite, and microbe. This may lead to increased zoonotic disease risk in a subset of environments across urban and urbanizing landscapes that can be reduced through improved pest management and public health messaging.


title: Diet-induced changes in titer support a threshold effect of Wolbachia-associated plastic recombination in Drosophila melanogaster

abstract: Plastic recombination in Drosophila melanogaster has been associated with a variety of extrinsic and intrinsic factors such as temperature, starvation, and parasite infection. The bacterial endosymbiont Wolbachia pipientis has also been associated with plastic recombination in D. melanogaster. Wolbachia infection is pervasive in arthropods and this infection induces a variety of phenotypes in its hosts, the strength of which can depend on bacterial concentration, or titer. Here we test the hypothesis that the magnitude of Wolbachia-associated plastic recombination in D. melanogaster depends on titer. To manipulate titer, we raised Wolbachia-infected and uninfected flies on diets that have previously been shown to increase or decrease Wolbachia titer relative to controls. We measured recombination in treated and control individuals using a standard backcrossing scheme with two X-linked visible markers. Our results recapitulate previous findings that Wolbachia infection is associated with increased recombination rate across the yellow-vermillion interval of the X chromosome. Our data show no significant effect of diet or diet by Wolbachia interactions on recombination, suggesting that diet-induced changes in Wolbachia titer have no effect on the magnitude of plastic recombination. These findings represent the first step toward investigating the mechanisms behind Wolbachia-associated plastic recombination and demonstrate that the effect may be threshold-based as opposed to dose-dependent.