title: An all-solid-state heterojunction oxide transistor for the rapid detection of biomolecules and SARS-CoV-2 spike S1 protein

abstract: Solid-state transistor sensors that can detect biomolecules in real time are highly attractive for emerging bioanalytical applications. However, combining cost-effective manufacturing with high sensitivity, specificity and fast sensing response, remains challenging. Here we develop low-temperature solution-processed In2O3/ZnO heterojunction transistors featuring a geometrically engineered tri-channel architecture for rapid real-time detection of different biomolecules. The sensor combines a high electron mobility channel, attributed to the quasi-two-dimensional electron gas (q2DEG) at the buried In2O3/ZnO heterointerface, in close proximity to a sensing surface featuring tethered analyte receptors. The unusual tri-channel design enables strong coupling between the buried q2DEG and the minute electronic perturbations occurring during receptor-analyte interactions allowing for robust, real-time detection of biomolecules down to attomolar (aM) concentrations. By functionalizing the tri-channel surface with SARS-CoV-2 (Severe Acute Respiratory Syndrome Coronavirus 2) antibody receptors, we demonstrate real-time detection of the SARS-CoV-2 spike S1 protein down to attomolar concentrations in under two minutes.


title: Accounting for fragments of unexpectedorigin improves transcript quantification inRNA-seq simulations focused on increased realism

abstract:
Transcript and gene quantification is the first step in many RNA-seq analyses. While many factors and properties of experimental RNA-seq data likely contribute to differences in accuracy between various approaches to quantification, it has been demonstrated (1) that quantification accuracy generally benefits from considering, during alignment, potential genomic origins for sequenced fragments that reside outside of the annotated transcriptome.

Recently, Varabyou et al. (2) demonstrated that the presence of transcriptional noise leads to systematic errors in the ability of tools -- particularly annotation-based ones -- to accurately estimate transcript expression. Here, we confirm the findings of Varabyou et al. (2) using the simulation framework they have provided. Using the same data, we also examine the methodology of Srivastava et al.(1) as implemented in recent versions of salmon (3), and show that it substantially enhances the accuracy of annotation-based transcript quantification in these data.

category: bioinformatics


title: Somatic Mutations in Collagens are Associated with a Distinct Tumor Environment and Overall Survival in Gastric Cancer

abstract:
BackgroundGastric cancer is a heterogeneous disease with poorly understood genetic and microenvironmental factors. Mutations in collagen genes are associated with genetic diseases that compromise tissue integrity, but their role in tumor progression has not been extensively reported. Aberrant collagen expression has been long associated with malignant tumor growth, invasion, chemoresistance, and patient outcomes. We hypothesized that somatic mutations in collagens could functionally alter the tumor extracellular matrix.

MethodsWe used publicly available datasets including The Tumor Cancer Genome Atlas (TCGA) to interrogate somatic mutations in collagens in stomach adenocarcinomas. To demonstrate that collagens were significantly mutated above background mutation rates, we used a moderated Kolmogorov-Smirnov test along with combination analysis with a bootstrap approach to define the background accounting for mutation rates. Association between mutations and clinicopathological features was evaluated by Fisher or chi-squared tests. Association with overall survival was assessed by Kaplan-Meier and the Cox-Proportional Hazards Model. Gene Set Enrichment Analysis was used to interrogate pathways. Immunohistochemistry and in situ hybridization tested expression of COL7A1 in stomach tumors.

ResultsIn stomach adenocarcinomas, we identified individual collagen genes and sets of collagen genes harboring somatic mutations at a high frequency compared to background in both microsatellite stable, and microsatellite instable tumors in TCGA. Many of the missense mutations resemble the same types of loss of function mutations in collagenopathies that disrupt tissue formation and destabilize cells providing guidance to interpret the somatic mutations. We identified combinations of somatic mutations in collagens associated with overall survival, with a distinctive tumor microenvironment marked by lower matrisome expression and immune cell signatures. Truncation mutations were strongly associated with improved outcomes suggesting that loss of expression of secreted collagens impact tumor progression and treatment response. Germline collagenopathy variants guided interpretation of impactful somatic mutations on tumors.

ConclusionsThese observations highlight that many collagens, expressed in non-physiologically relevant conditions in tumors, harbor impactful somatic mutations in tumors, suggesting new approaches for classification and therapy development in stomach cancer. In sum, these findings demonstrate how classification of tumors by collagen mutations identified strong links between specific genotypes and the tumor environment.

Research HighlightsCollagen mutations are prevalent in stomach cancer

Collagen somatic missense mutations resemble collagenopathy mutations

Collagen mutations associate with overall survival in stomach cancer

Tumors with collagen mutations have distinct molecular pathways and tumor microenvironments

category: cancer biology


title: Predicting genotype-specific gene regulatory networks

abstract:
Understanding how each persons unique genotype influences their individual patterns of gene regulation has the potential to improve our understanding of human health and development and to refine genotype-specific disease risk assessments and treatments. However, the effects of genetic variants are not typically considered when constructing gene regulatory networks, despite the fact that many disease-associated genetic variants are thought to have regulatory effects, including the disruption of transcription factor (TF) binding. We developed EGRET (Estimating the Genetic Regulatory Effect on TFs), which infers a genotype-specific gene regulatory network (GRN) for each individual in a study population. EGRET begins by constructing a genotype-informed TF-gene prior network derived using TF motif predictions, eQTL data, individual genotypes, and the predicted effects of genetic variants on TF binding. It then uses message passing to integrate this prior network with gene expression and TF protein-protein interaction data to produce a refined, genotype-specific regulatory network. We used EGRET to infer GRNs for two blood-derived cell lines and identified genotype-associated, cell-line specific regulatory differences that we subsequently validated using allele-specific expression, chromatin accessibility QTLs, and differential ChIP-seq TF binding. We also inferred EGRET GRNs for three cell types from each of 119 individuals and identified cell type-specific regulatory differences associated with diseases related to those cell types. EGRET is, to our knowledge, the first method that infers networks that reflect individual genetic variation in a way that provides insight into genetic regulatory associations that drive complex phenotypes.

EGRET is available through the Network Zoo R package (netZooR v0.9; netzoo.github.io).

category: systems biology


title: The variability in potential biomarkers for cochlear synaptopathy after recreational noise exposure

abstract:
PurposeSpeech-in-noise tests and suprathreshold auditory evoked potentials are promising biomarkers to diagnose cochlear synaptopathy (CS) in humans. This study investigated whether these biomarkers changed after recreational noise exposure.

MethodThe baseline auditory status of 19 normal hearing young adults was analyzed using questionnaires, pure-tone audiometry, speech audiometry and auditory evoked potentials. Nineteen subjects attended a music festival and completed the same tests again at day one, day three and day five after the music festival.

ResultsNo significant relations were found between lifetime noise-exposure history and the hearing tests. Changes in biomarkers from the first session to the follow-up sessions were non-significant, except for speech audiometry, that showed a significant learning effect (performance improvement).

ConclusionsDespite the individual variability in pre-festival biomarkers, we did not observe changes related to the noise-exposure dose caused by the attended event. This can indicate the absence of noise-exposure-driven cochlear synaptopathy in the study cohort, or reflect that biomarkers were not sensitive enough to detect mild CS. Future research should include a more diverse study cohort, dosimetry and results from test-retest reliability studies to provide more insight into the relationship between recreational noise-exposure and cochlear synaptopathy.

category: neuroscience


title: All-optical electrophysiology in hiPSC-derived neurons with synthetic voltage sensors

abstract: Voltage imaging and "all-optical electrophysiology" in human induced pluripotent stem cell (hiPSC)-derived neurons have opened unprecedented opportunities for high-throughput phenotyping of activity in neurons possessing unique genetic backgrounds of individual patients. While prior all-optical electrophysiology studies relied on genetically encoded voltage indicators, viral transduction of human neurons with large or multiple expression vectors can impact cell function and often lead to massive cell death. Here, we demonstrate an alternative protocol using a synthetic voltage sensor and genetically encoded optogenetic actuator that generate robust and reproducible results. We demonstrate the functionality of this method by measuring spontaneous and evoked activity in three independent hiPSC-derived neuronal cell lines with distinct genetic backgrounds.


title: Representation learning for neural population activity with Neural Data Transformers

abstract:
Neural population activity is theorized to reflect an underlying dynamical structure. This structure can be accurately captured using state space models with explicit dynamics, such as those based on recurrent neural networks (RNNs). However, using recurrence to explicitly model dynamics necessitates sequential processing of data, slowing real-time applications such as brain-computer interfaces. Here we introduce the Neural Data Transformer (NDT), a non-recurrent alternative. We test the NDTs ability to capture autonomous dynamical systems by applying it to synthetic datasets with known dynamics and data from monkey motor cortex during a reaching task well-modeled by RNNs. The NDT models these datasets as well as state-of-the-art recurrent models. Further, its non-recurrence enables 3.9ms inference, well within the loop time of real-time applications and more than 6 times faster than recurrent baselines on the monkey reaching dataset. These results suggest that an explicit dynamics model is not necessary to model autonomous neural population dynamics.

Codegithub.com/snel-repo/neural-data-transformers.


title: Individual-Specific Areal-Level Parcellations Improve Functional Connectivity Prediction of Behavior

abstract: Resting-state functional MRI (rs-fMRI) allows estimation of individual-specific cortical parcellations. We have previously developed a multi-session hierarchical Bayesian model (MS-HBM) for estimating high-quality individual-specific network-level parcellations. Here, we extend the model to estimate individual-specific areal-level parcellations. While network-level parcellations comprise spatially distributed networks spanning the cortex, the consensus is that areal-level parcels should be spatially localized, i.e., should not span multiple lobes. There is disagreement about whether areal-level parcels should be strictly contiguous or comprise multiple non-contiguous components, therefore we considered three areal-level MS-HBM variants spanning these range of possibilities. Individual-specific MS-HBM parcellations estimated using 10min of data generalized better than other approaches using 150min of data to out-of-sample rs-fMRI and task-fMRI from the same individuals. Resting-state functional connectivity (RSFC) derived from MS-HBM parcellations also achieved the best behavioral prediction performance. Among the three MS-HBM variants, the strictly contiguous MS-HBM (cMS-HBM) exhibited the best resting-state homogeneity and most uniform within-parcel task activation. In terms of behavioral prediction, the gradient-infused MS-HBM (gMS-HBM) was numerically the best, but differences among MS-HBM variants were not statistically significant. Overall, these results suggest that areal-level MS-HBMs can capture behaviorally meaningful individual-specific parcellation features beyond group-level parcellations. Multi-resolution trained models and parcellations are publicly available (https://github.com/ThomasYeoLab/CBIG/tree/master/stable_projects/brain_parcellation/Kong2022_ArealMSHBM).


title: Kinetic analysis of ASIC1a delineates conformational signaling from proton sensing domains to the channel gate

abstract: Acid-sensing ion channels (ASICs) are neuronal Na+ channels that are activated by a drop in pH. Their established physiological and pathological roles, involving fear behaviors, learning, pain sensation and neurodegeneration after stroke, make them promising targets for future drugs. Currently, the ASIC activation mechanism is not understood. Here we used voltage-clamp fluorometry (VCF) combined with fluorophore-quencher pairing to determine the kinetics and direction of movements. Molecular dynamics simulations were used to further evaluate VCF-predicted movements. We show that conformational changes with the speed of channel activation occur close to the gate and in more distant extracellular sites, where they may be driven by local protonation events. Further, we provide evidence for fast conformational changes in a pathway linking protonation sites to the channel pore, in which an extracellular interdomain loop interacts via aromatic residue interactions with the upper end of a transmembrane helix and would thereby open the gate.


title: Saccades along spatial neural circuit discontinuities

abstract:
Saccades are realized by six extraocular muscles that define the final reference frame for eyeball rotations. However, upstream of the nuclei innervating the eye muscles, eye movement commands are represented in two-dimensional retinocentric coordinates, as is the case in the superior colliculus (SC). In such spatial coordinates, the horizontal and vertical visual field meridians, relative to the line of sight, are associated with neural tissue discontinuities due to routing of binocular retinal outputs when forming retinotopic sensory-motor maps. At the level of the SC, a functional discontinuity along the horizontal meridian was additionally discovered, beyond the structural vertical discontinuity associated with hemifield lateralization. How do such neural circuit discontinuities influence purely cardinal saccades? Using thousands of saccades from 3 rhesus macaque monkeys and 14 human subjects, we show how the likelihood of purely horizontal or vertical saccades is infinitesimally small, nulling a discontinuity problem. This does not mean that saccades are sloppy. On the contrary, saccades exhibit remarkable direction and amplitude corrections to account for small initial eye position deviations due to fixational variability: "purely" cardinal saccades can deviate, with an orthogonal component of as little as 0.03 deg, to correct for tiny target position deviations from initial eye position. In humans, probing perceptual target localization additionally revealed that saccades show different biases from perception when targets deviate slightly from purely cardinal directions. These results demonstrate a new functional role for fixational eye movements in visually-guided behavior, and they motivate further neurophysiological investigations of saccade trajectory control in the brainstem.

New and NoteworthyPurely cardinal saccades are often characterized as being straight. We show how a small amount of curvature is inevitable, alleviating an implementational problem of dealing with neural circuit discontinuities in the representations of the visual meridians. The small curvature functionally corrects for minute variability in initial eye position due to fixational eye movements. Saccades are far from sloppy; they deviate by as little as <1% of the total vector size to adjust their landing position.


title: Hinge Influences in Murine IgG Binding to Cryptococcus neoformans Capsule

abstract:
Decades of studies on antibody structure led to the tenet that the V region binds antigens while the C region interacts with immune effectors. In some antibodies, however, the C region affects affinity and/or specificity for the antigen. One such case is that of the 3E5 antibodies, a family of monoclonal murine IgGs in which the mIgG3 isotype has different fine specificity to the Cryptococcus neoformans capsule polysaccharide than the other mIgG isotypes. Our group serendipitously found another pair of mIgG1/mIgG3 antibodies based on the 2H1 hybridoma to the C. neoformans capsule that recapitulated the differences observed with 3E5. In this work, we report the molecular basis of the constant domain effects on antigen binding using recombinant antibodies. As with 3E5, immunofluorescence experiments show a punctate pattern for 2H1-mIgG3 and an annular pattern for 2H1-mIgG1. Also as observed with 3E5, 2H1-mIgG3 bound on ELISA to both acetylated and non-acetylated capsular polysaccharide, whereas 2H1-mIgG1 only bound well to the acetylated form, consistent with differences in fine specificity. In engineering hybrid mIgG1/mIgG3 antibodies, we found that switching the 2H1-mIgG3 hinge for its mIgG1 counterpart changed the immunofluorescence pattern to annular, but a 2H1-mIgG1 antibody with a mIgG3 hinge still had an annular pattern. The hinge is thus necessary but not sufficient for these changes in binding to the antigen. This important role for the constant region in binding of antibodies to the antigen could affect the design of therapeutic antibodies and our understanding of their function in immunity.

Key pointsO_LIKey point 1- 2H1 antibodies recapitulate differences between mIgG isotypes observed with 3E5.
C_LIO_LIKey point 2 - The hinge region is necessary but not sufficient for these differences.
C_LIO_LIKey point 3 - The antibody constant region can also play a role in mIgG binding to antigen.
C_LI

category: immunology


title: Metabolic control of type 2 innate lymphoid cells plasticity toward protective type 1-like cells during Mycobacterium tuberculosis infection

abstract: Tissue-resident innate lymphoid cells (ILCs) regulate tissue homeostasis, protect against pathogens at mucosal surfaces and are key players at the interface of innate and adaptive immunity. How ILCs adapt their phenotype and function to environmental cues within tissues remains to be fully understood. Here, we show that Mycobacterium tuberculosis infection alters the phenotype and function of immature lung ILC2 toward a protective interferon-{gamma}-producing ILC1-like population. This differentiation is controlled by type 1 cytokines and is associated with a glycolytic program involving the transcription factor HIF1. Collectively, our data reveal how tissue-resident ILCs adapt to type 1 inflammation toward a pathogen tailored immune response.


title: Metabolic regulation of ILC2 differentiation into ILC1-like cells during Mycobacterium tuberculosis infection


title: Mitochondrial oxidative stress drives IL-12/IL-18-induced IFN-gamma production by CD4+ T cells and is controlled by Fas

abstract: Mitochondrial activation and mROS production are crucial for CD4+ T cell responses and have a role in naive cell signaling after TCR activation. However, little is known about their role in recall responses driven by cytokine signaling. Here, we found that mROS are required for IL-12 plus IL-18-driven production of IFN-{gamma}, an essential cytokine in inflammatory and autoimmune disease development. In particular, memory-like cells obtained after activation-induced differentiation showed faster and augmented mROS accumulation and increased IFN-{gamma} production in response to IL-12 plus IL-18 compared to naive T cells. In contrast, mROS induction was similar in naive and memory-like cells after TCR-dependent signaling. Taken together these results suggested that memory-like CD4+ T cells treated by IL-12 plus IL-18 attained conditions for an extraordinary mROS-producing potential. mROS inhibition significantly downregulated the production of IFN-{gamma} and the expression of CD44 activation marker, suggesting a direct mROS effect on the activation of memory-like T cells. Mechanistically, mROS was required for optimal activation of key signaling pathways that drive IFN-{gamma} production after IL-12 plus IL-18 T cell stimulation, such as PKC-{theta}, AKT and STAT4 phosphorylation, and NF-{kappa}B activation. Notably, we identified increased mROS as key promoters of hyperactivation and IFN-{gamma} overproduction in Fas-deficient lpr memory-like CD4+ T cells compared to WT cells, following IL-12 plus IL-18 stimulation. mROS inhibition significantly reduced the population of disease-associated CD44hiCD62Llo lpr CD4+ T cells and their IFN-{gamma} production. These findings uncover a previously unidentified role for Fas in regulating mitochondrial ROS production by memory-like T cells. This apoptosis-independent Fas activity might contribute to the accumulation of CD44hiCD62Llo CD4+ T cells that produce increased IFN-{gamma} levels in lpr mice. Overall, our findings pinpoint mROS as central regulators of TCR-independent signaling, and support mROS pharmacological targeting to control aberrant immune responses in autoimmune-like disease.


title: The impact of Spike mutations on SARS-CoV-2 neutralization

abstract: Multiple SARS-CoV-2 vaccines have shown protective efficacy, which is most likely mediated by neutralizing antibodies recognizing the viral entry protein, Spike. Antibodies from SARS-CoV-2 infection neutralize the virus by focused targeting of Spike and there is limited serum cross-neutralization of the closely-related SARS-CoV. As new SARS-CoV-2 variants are rapidly emerging, exemplified by the B.1.1.7, 501Y.V2 and P.1 lineages, it is critical to understand if antibody responses induced by infection with the original SARS-CoV-2 virus or the current vaccines will remain effective against virus variants. In this study we evaluate neutralization of a series of mutated Spike pseudotypes including a B.1.1.7 Spike pseudotype. The analyses of a panel of Spike-specific monoclonal antibodies revealed that the neutralizing activity of some antibodies was dramatically reduced by Spike mutations. In contrast, polyclonal antibodies in the serum of patients infected in early 2020 remained active against most mutated Spike pseudotypes. The majority of serum samples were equally able to neutralize the B.1.1.7 Spike pseudotype, however potency was reduced in a small number of samples (3 of 36) by 5-10-fold. This work highlights that changes in the SARS-CoV-2 Spike can alter neutralization sensitivity and underlines the need for effective real-time monitoring of emerging mutations and their impact on vaccine efficacy.


title: Antifungal activity of Propranolol against Fusarium keratitis isolates from the Mycotic Ulcer Treatment Trial (MUTT) and the United States.

abstract:
SYNOPSISO_ST_ABSBackgroundC_ST_ABSFusarium keratitis is an infection of the cornea that often results in corneal perforation requiring corneal transplantation even with topical ocular antifungal therapy. The polyene natamycin remains the current antifungal of choice for Fusarium keratitis, but prompt sterilization of the cornea is often not achieved with contemporary therapy. Recently, natamycin synergy with the beta-adrenergic antagonist timolol against Fusarium species was reported.

ObjectiveOur objective in this study was to characterize the in vitro antifungal effects of additional beta-adrenergic antagonists alone or in combination with natamycin on Fusarium keratitis isolates from the Mycotic Ulcer Treatment Trial (MUTT) and USA.

MethodsMicrobroth dilution assays were used to determine the minimal inhibitory concentration (MIC) of beta-adrenergic antagonists against 18 Fusarium spp. keratitis (10 from MUTT, 8 from USA) and 3 Aspergillus fumigatus isolates. The fractional inhibitory concentration index (FICI) was calculated to assess interactions with natamycin.

ResultsMost beta-blockers did not show antifungal activity or synergy with natamycin with the exception of propranolol. A racemic mix of propranolol had fungicidal activity with MIC between 31 and 83 g/mL for the Fusarium isolates. The MIC of the less cardioactive R enantiomer was lower (27-83 g/mL) than the MIC of the S enantiomer (42-104 g/mL). The MICs of both propranolol and natamycin were lower in combination but were not synergistic. The MIC of propranolol was 156 g/mL for the A. fumigatus isolates.

ConclusionsPropranolol has intrinsic in vitro fungicidal activity and lowers the MIC of natamycin. Both the R and S enantiomers of propranolol had antifungal activity with the MIC modestly but significantly lower for R-propranolol. These findings have relevance both for the treatment of fungal keratitis and of glaucoma in the setting of fungal keratitis. Further study of propranolols antifungal activity may lead to a novel treatment for fungal keratitis and possibly other fungal infections.

Trial RegistrationClinicalTrials.gov Identifier: NCT00997035 (MUTT Trial)

category: microbiology


title: Experimental re-infected cats do not transmit SARS-CoV-2

abstract: SARS-CoV-2 is the causative agent of COVID-19 and responsible for the current global pandemic. We and others have previously demonstrated that cats are susceptible to SARS-CoV-2 infection and can efficiently transmit the virus to naive cats. Here, we address whether cats previously exposed to SARS-CoV-2 can be re-infected with SARS-CoV-2. In two independent studies, SARS-CoV-2-infected cats were re-challenged with SARS-CoV-2 at 21 days post primary challenge (DPC) and necropsies performed at 4, 7 and 14 days post-secondary challenge (DP2C). Sentinels were co-mingled with the re-challenged cats at 1 DP2C. Clinical signs were recorded, and nasal, oropharyngeal, and rectal swabs, blood, and serum were collected and tissues examined for histologic lesions. Viral RNA was transiently shed via the nasal, oropharyngeal and rectal cavities of the re-challenged cats. Viral RNA was detected in various tissues of re-challenged cats euthanized at 4 DP2C, mainly in the upper respiratory tract and lymphoid tissues, but less frequently and at lower levels in the lower respiratory tract when compared to primary SARS-CoV-2 challenged cats at 4 DPC. Histologic lesions that characterized primary SARS-CoV-2 infected cats at 4 DPC were absent in the re-challenged cats. Naive sentinels co-housed with the re-challenged cats did not shed virus or seroconvert. Together, our results indicate that cats previously infected with SARS-CoV-2 can be experimentally re-infected with SARS-CoV-2; however, the levels of virus shed was insufficient for transmission to co-housed naive sentinels. We conclude that SARS-CoV-2 infection in cats induces immune responses that provide partial, non-sterilizing immune protection against reinfection.


title: A trans-complementation system for SARS-CoV-2

abstract: The biosafety level-3 (BSL-3) requirement to culture severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a bottleneck for research and countermeasure development. Here we report a trans-complementation system that produces single-round infectious SARS-CoV-2 that recapitulates authentic viral replication. We demonstrate that the single-round infectious SARS-CoV-2 can be used at BSL-2 laboratories for high-throughput neutralization and antiviral testing. The trans-complementation system consists of two components: a genomic viral RNA containing a deletion of ORF3 and envelope gene, and a producer cell line expressing the two deleted genes. Trans-complementation of the two components generates virions that can infect naive cells for only one round, but does not produce wild-type SARS-CoV-2. Hamsters and K18-hACE2 transgenic mice inoculated with the complementation-derived virions exhibited no detectable disease, even after intracranial inoculation with the highest possible dose. The results suggest that the trans-complementation platform can be safely used at BSL-2 laboratories for research and countermeasure development.


title: Azithromycin Plus Zinc Sulfate Rapidly and Synergistically Suppresses IκBα-Mediated In Vitro Human Airway Cell ACE2 Expression for SARS-CoV-2 Entry

abstract: Large-scale efforts have been persistently undertaken for medical prophylaxis and treatment of COVID-19 disasters worldwide. A variety of novel viral spike protein-targeted vaccine preparations have recently been clinically distributed based on accelerated approval. We revisited the early but inconclusive clinical interest in the combination of azithromycin and zinc sulfate repurposing with safety advantages. In vitro proof of concept was provided for rapid and synergistic suppression of ACE2 expression following treatments in human airway cells, Calu-3 and H322M. The two representative ACE2-expressing human airway cells indicate the upper and lower respiratory tracts. Prophylactic and early therapeutic roles of azithromycin combined with zinc are proposed for virus cellular entry prevention potential bridging to effective antibody production.

category: molecular biology


title: BRD2 inhibition blocks SARS-CoV-2 infection in vitro by reducing transcription of the host cell receptor ACE2

abstract: SARS-CoV-2 infection of human cells is initiated by the binding of the viral Spike protein to its cell-surface receptor ACE2. We conducted a targeted CRISPRi screen to uncover druggable pathways controlling Spike protein binding to human cells. We found that the protein BRD2 is required for ACE2 transcription in human lung epithelial cells and cardiomyocytes, and BRD2 inhibitors currently evaluated in clinical trials potently block endogenous ACE2 expression and SARS-CoV-2 infection of human cells, including those of human nasal epithelia. Moreover, pharmacological BRD2 inhibition with the drug ABBV-744 inhibited SARS-CoV-2 replication in Syrian hamsters. We also found that BRD2 controls transcription of several other genes induced upon SARS-CoV-2 infection, including the interferon response, which in turn regulates the antiviral response. Together, our results pinpoint BRD2 as a potent and essential regulator of the host response to SARS-CoV-2 infection and highlight the potential of BRD2 as a novel therapeutic target for COVID-19.

category: cell biology


title: BRD2 inhibition blocks SARS-CoV-2 infection by reducing transcription of the host cell receptor ACE2


title: Global analysis of cell behavior and protein localization dynamics reveals region-specific functions for Shroom3 and N-cadherin during neural tube closure.

abstract: Failures of neural tube closure are common and serious birth defects, yet we have a poor understanding of the interaction of genetics and cell biology during neural tube closure. Additionally, mutations that cause neural tube defects (NTDs) tend to affect anterior or posterior regions of the neural tube but rarely both, indicating a regional specificity to NTD genetics. To better understand the regional specificity of cell behaviors during neural tube closure, we analyzed the dynamic localization of actin and N-cadherin via high-resolution tissue-level time-lapse microscopy during Xenopus neural tube closure. To investigate the regionality of gene function, we generated mosaic mutations in shroom3, a key regulator or neural tube closure This approach elucidates new differences between cell behaviors during cranial/anterior and spinal/posterior neural tube closure, provides mechanistic insight into the function of shroom3 and demonstrates the ability of tissue-level imaging and analysis to generate cell-biological mechanistic insights into neural tube closure.

category: developmental biology


title: In vivo proximity labeling identifies cardiomyocyte protein networks during zebrafish heart regeneration

abstract: Strategies have not been available until recently to uncover interacting protein networks specific to key cell types, their subcellular compartments, and their major regulators during complex in vivo events. Here we apply BioID2 proximity labeling to capture protein networks acting within cardiomyocytes during a key model of innate heart regeneration in zebrafish. Transgenic zebrafish expressing a promiscuous BirA2 localized to the entire myocardial cell or membrane compartment were generated, each identifying unique proteomes in adult cardiomyocytes that became altered during regeneration. BioID2 profiling for interactors with ErbB2, a co-receptor for the cardiomyocyte mitogen Nrg1, implicated Rho A as a target of ErbB2 signaling in cardiomyocytes. Blockade of Rho A during heart regeneration, or during cardiogenic stimulation by the mitogenic influences Nrg1, Vegfaa or Vitamin D, disrupted muscle creation. Our findings reveal proximity labeling as a useful resource to interrogate cell proteomes and signaling networks during tissue regeneration in zebrafish.


title: Empirical abundance distributions are more uneven than expected given their statistical baseline

abstract: Exploring and accounting for the emergent properties of ecosystems as complex systems is a promising horizon in the search for general processes to explain common ecological patterns. For example, the ubiquitous hollow-curve form of the species abundance distribution is frequently assumed to reflect ecological processes structuring communities, but can also emerge as a statistical phenomenon from the mathematical definition of an abundance distribution. Although the hollow curve may be a statistical artefact, ecological processes may induce subtle deviations between empirical species abundance distributions and their statistically most probable forms. These deviations may reflect biological processes operating on top of mathematical constraints and provide new avenues for advancing ecological theory. Examining [~]22,000 communities, we found that empirical SADs are highly uneven and dominated by rare species compared to their statistical baselines. Efforts to detect deviations may be less informative in small communities - those with few species or individuals - because these communities have poorly-resolved statistical baselines. The uneven nature of many empirical SADs demonstrates a path forward for leveraging complexity to understand ecological processes governing the distribution of abundance, while the issues posed by small communities illustrate the limitations of using this approach to study ecological patterns in small samples.

category: ecology


title: Variant Library Annotation Tool (VaLiAnT): an oligonucleotide library design and annotation tool for Saturation Genome Editing and other Deep Mutational Scanning experiments

abstract:
MotivationRecent advances in CRISPR/Cas9 technology allow for the functional analysis of genetic variants at single nucleotide resolution whilst maintaining genomic context (Findlay et al., 2018). This approach, known as saturation genome editing (SGE), is a distinct type of deep mutational scanning (DMS) that systematically alters each position in a target region to explore its function. SGE experiments require the design and synthesis of oligonucleotide variant libraries which are introduced into the genome by homology-directed repair (HDR). This technology is broadly applicable to diverse research fields such as disease variant identification, drug development, structure-function studies, synthetic biology, evolutionary genetics and the study of host-pathogen interactions. Here we present the Variant Library Annotation Tool (VaLiAnT) which can be used to generate saturation mutagenesis oligonucleotide libraries from user-defined genomic coordinates and standardised input files. This software package is intentionally versatile to accommodate diverse operability, with species, genomic reference sequences and transcriptomic annotations specified by the user. Genomic ranges, directionality and frame information are considered to allow perturbations at both the nucleotide and amino acid level.

ResultsCoordinates for a genomic range, that may include exonic and/or intronic sequence, are provided by the user in order to retrieve a corresponding oligonucleotide reference sequence. A user-specified range within this sequence is then subject to systematic, nucleotide and/or amino acid saturating mutator functions, with each discrete mutation returned to the user as a separate sequence, building up the final oligo library. If desired, variant accessions from genetic information repositories, such as ClinVar and gnomAD, that fall within the user-specified ranges, will also be incorporated into the library.

For SGE library generation, base reference sequences can be modified to include PAM (Protospacer Adjacent Motif) and protospacer  protection edits that prevent Cas9 from cutting incorporated oligonucleotide tracts. Mutator functions modify this protected reference sequence to generate variant sequences. Constant regions are designated for non-editing to allow specific adapter annealing for downstream cloning and amplification from the library pool.

A metadata file is generated, delineating annotation information for each variant sequence to aid computational analysis. In addition, a library file is generated, which contains unique sequences (any exact duplicate sequences are removed) ready for submission to commercial synthesis platforms. A VCF file listing all variants is also generated for analysis and quality control processes.

The VaLiAnT software package provides a novel means to systemically retrieve, mutate and annotate genomic sequences for oligonucleotide library generation. Specific features for SGE library generation can be employed, with other diverse applications possible.

Availability and ImplementationVaLiAnT is a command line tool written in Python. Source code, testing data, example library input and output files, and executables are available at https://github.com/cancerit/VaLiAnT. A user manual details step by step instructions for software use, available at https://github.com/cancerit/VaLiAnT/wiki. The software is freely available for non-commercial use (see Licence for more details, https://github.com/cancerit/VaLiAnT/blob/develop/LICENSE).

category: genomics


title: H2AFB1 is a cancer/testis gene involved in hyperactivation of ribosome biogenesis in Hodgkin Lymphoma

abstract: Testis-specific regulators of chromatin function are commonly ectopically expressed in human cancers, but their roles are poorly understood. Examination of 81 primary Hodgkin Lymphoma (HL) samples showed that the ectopic expression of the eutherian testis-specific histone variant H2A.B is an inherent feature of HL. In experiments using two HL-derived cell lines derived from different subtypes of HL, H2A.B knockdown inhibited cell proliferation. H2A.B was enriched in both the nucleoli of these HL cell lines and primary HL samples. We found that H2A.B enhanced ribosomal DNA (rDNA) transcription, was enriched at the rDNA promoter and transcribed regions, and interacted with RNA Pol I. Depletion of H2A.B caused the loss of RNA Pol I from rDNA chromatin. Remarkably, H2A.B was also required for high levels of ribosomal protein gene expression being located at the transcriptional start site and within the gene body. H2A.B knockdown reduced gene body chromatin accessibility of active RNA Pol II genes concurrent with a decrease in transcription. Taken together, our data show that in HL H2A.B has acquired a new function, the ability to increase ribosome biogenesis.


title: H2A.B is a cancer/testis factor involved in activation of ribosome biogenesis in Hodgkin Lymphoma


title: Maximum likelihood inference of pathogen population size history from a phylogeny

abstract: Inference of effective population size from genomic data can provide unique information about demographic history, and when applied to pathogen genetic data can also provide insights into epidemiological dynamics. The combination of non-parametric models for population dynamics with molecular clock models which relate genetic data to time has enabled phylodynamic inference based on large sets of time-stamped genetic sequence data. The methodology for non-parametric inference of effective population size is well-developed in the Bayesian setting, but here we develop a frequentist approach based on non-parametric latent process models of population size dynamics. We appeal to statistical principles based on out-of-sample prediction accuracy in order to optimize parameters that control shape and smoothness of the population size over time. We demonstrate the flexibility and speed of this approach in a series of simulation experiments, and apply the methodology to reconstruct the previously described waves in the seventh pandemic of cholera. We also estimate the impact of non-pharmaceutical interventions for COVID-19 in England using thousands of SARS-CoV-2 sequences. By incorporating a measure of the strength of these interventions over time within the phylodynamic model, we estimate the impact of the first national lockdown in the UK on the epidemic reproduction number.


title: Model design for non-parametric phylodynamic inference and applications to pathogen surveillance


title: Learning to see colours: generating biologically relevant fluorescent labels from bright-field images

abstract: Fluorescence microscopy, which visualizes cellular components with fluorescent stains, is an invaluable method in image cytometry. From these images various cellular features can be extracted. Together these features form phenotypes that can be used to determine effective drug therapies, such as those based on nanomedicines. Unfortunately, fluorescence microscopy is time-consuming, expensive, labour intensive, and toxic to the cells. Bright-field images lack these downsides but also lack the clear contrast of the cellular components and hence are difficult to use for downstream analysis. Generating the fluorescence images directly from bright-field images would get the best of both worlds, but can be very challenging to do for poorly visible cellular structures in the bright-field images. To tackle this problem deep learning models were explored to learn the mapping between bright-field and fluorescence images to enable virtual staining for adipocyte cell images. The models were tailored for each imaging channel, paying particular attention to the various challenges in each case, and those with the highest fidelity in extracted cell-level features were selected. The solutions included utilizing privileged information for the nuclear channel, and using image gradient information and adversarial training for the lipids channel. The former resulted in better morphological and count features and the latter resulted in more faithfully captured defects in the lipids, which are key features required for downstream analysis of these channels.


title: Sterically-Confined Rearrangements of SARS-CoV-2 Spike Protein Control Cell Invasion

abstract: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is highly contagious, and transmission involves a series of processes that may be targeted by vaccines and therapeutics. During transmission, host cell invasion is controlled by a large-scale conformational change of the Spike protein. This conformational rearrangement leads to membrane fusion, which creates transmembrane pores through which the viral genome is passed to the host. During Spike-protein-mediated fusion, the fusion peptides must be released from the core of the protein and associate with the host membrane. Interestingly, the Spike protein possesses many post-translational modifications, in the form of branched glycans that flank the surface of the assembly. Despite the large number of glycosylation sites, until now, the specific role of glycans during cell invasion has been unclear. Here, we propose that glycosylation is needed to provide sufficient time for the fusion peptides to reach the host membrane, otherwise the viral particle would fail to enter the host. To understand this process, an all-atom model with simplified energetics was used to perform thousands of simulations in which the protein transitions between the prefusion and postfusion conformations. These simulations indicate that the steric composition of the glycans induces a pause during the Spike protein conformational change. We additionally show that this glycan-induced delay provides a critical opportunity for the fusion peptides to capture the host cell. This previously-unrecognized role of glycans reveals how the glycosylation state can regulate infectivity of this pervasive pathogen.

category: biophysics


title: Txikispora philomaios n. sp., n. g., a Micro-Eukaryotic Pathogen of Amphipods, Reveals Parasitism and Hidden Diversity in Class Filasterea

abstract: This study provides a morphological, ultrastructural, and phylogenetic characterization of a novel micro-eukaryotic parasite (2.3-2.6 {micro}m) infecting genera Echinogammarus and Orchestia. Longitudinal studies across two years revealed that infection prevalence peaked in late April and May, reaching 64% in Echinogammarus sp. and 15% in Orchestia sp., but was seldom detected during the rest of the year. The parasite infected predominantly haemolymph, connective tissue, tegument, and gonad, although hepatopancreas and nervous tissue were affected in heavier infections, eliciting melanization and granuloma formation. Cell division occurred inside walled parasitic cysts, often within host haemocytes, resulting in haemolymph congestion. Small subunit (18S) rRNA gene phylogenies including related environmental sequences placed the novel parasite as a highly divergent lineage within Class Filasterea, which together with Choanoflagellatea represent the closest protistan relatives of Metazoa. We describe the new parasite as Txikispora philomaios n. sp. n. g., the first confirmed parasitic filasterean lineage, which otherwise comprises four free-living flagellates and a rarely observed endosymbiont of snails. Lineage-specific PCR probing of other hosts and surrounding environments only detected T. philomaios in the platyhelminth Procerodes sp. We expand the known diversity of Filasterea by targeted searches of metagenomic datasets, resulting in 13 previously unknown lineages from environmental samples.

category: pathology


title: Attenuation of Hyperalgesia and Allodynia by some Phenolic Acids in Paclitaxel Induced Neuropathy

abstract:
Paclitaxel, an anticancer drug induced neuropathy is widely used animal model to evaluate new drugs in neuropathy. As oxidative stress is key contributor in pathogenesis of neuropathy, many phenolic acids with antioxidant potential are proven as neuroprotective. So,present work undertaken to evaluate effect of syringic acid and sinapic acid in paclitaxel induced neuropathy. We evaluated effect on mechanical and thermal hyperalgesia and allodynia which are vital signs of neuropathy. 4 weeks treatment by different doses of syringic acid and sinapic acid shown significant protective effect on hyperalgesia and allodynia in dose dependant manner assessed by Randello Selitto, hot plate, cold plate and Von Frey filament test. As these phenolic acids attenuates hyperalgesia and allodynia in neuropathy, can be therapeutically used in combination with current treatment of neuropathy.

Summary statementHyperlagesia and allodynia are major signs of neuropathy and this article focus on reduction of hyperalgesia and allodynia by syringic and sinapic acid in neuropathy induced by paclitaxel.

category: pharmacology and toxicology


title: METHYLOME DYNAMIC UPON PROTEASOME INHIBITION BY THE PSEUDOMONAS VIRULENCE FACTOR SYRINGOLIN A

abstract: DNA methylation is an important epigenetic mark required for proper gene expression and silencing of transposable elements. DNA methylation patterns can be modified by environmental factors such as pathogen infection, where modification of DNA methylation can be associated with plant resistance. To counter the plant defense pathways, pathogens produce effectors molecule, several of which act as proteasome inhibitors. Here we investigated the effect of proteasome inhibition by the bacterial virulence factor Syringolin A on genome-wide DNA methylation. We show that Syringolin A treatment results in an increase of DNA methylation at centromeric and pericentromeric regions of Arabidopsis chromosomes. We identify several CHH DMRs that are enriched in the proximity of transcriptional start sites. Syringolin A treatment does not result in significant changes in small RNA composition. However, significant changes in genome transcriptional activity can be observed, including a strong upregulation of resistance genes that are located on chromosomal arms. We hypothesize that DNA methylation changes could be linked to the upregulation of some atypical members of the de novo DNA methylation pathway: AGO3, AGO9 and DRM1. Our data suggests that modification of genome-wide DNA methylation resulting from an inhibition of the proteasome by bacterial effectors could be part of a epi-genomic arms race against pathogens.

category: plant biology


title: METHYLOME DYNAMICS UPON PROTEASOME INHIBITION BY THE PSEUDOMONAS VIRULENCE FACTOR SYRINGOLIN A


title: Methylome dynamic upon proteasome inhibition by the Pseudomonas syringae virulence factor Syringolin A


title: Surface GluA1 and glutamate transmission are increased in VPS35 D620N neurons and altered by LRRK2 kinase inhibition

abstract: Vacuolar protein sorting 35 (VPS35) regulates receptor recycling from endosomes. A missense mutation in VPS35 (D620N) leads to autosomal-dominant, late-onset Parkinsons disease. Here, we use a VPS35 D620N knock-in mouse to study the neurobiology of this mutation. In brain tissue, we confirm previous findings that the mutation results in reduced binding of VPS35 with WASH-complex member FAM21, and robustly elevated phosphorylation of the LRRK2 kinase substrate Rab10. In cultured cortical neurons, the mutation results in increased endosomal recycling protein density (VPS35-FAM21 co-clusters and Rab11 clusters), glutamate release, and GluA1 surface expression. LRRK2 kinase inhibition exerted genotype-specific effects on GluA1 surface expression, but did not impact glutamate release phenotypes. These results improve our understanding of the early effects of the D620N mutation on cellular functions that are specific to neurons. These observations provide candidate pathophysiological pathways that may drive eventual transition to late-stage parkinsonism in VPS35 families, and support a synaptopathy model of neurodegeneration.


title: Autism Spectrum Disorder is a Risk Factor for PTSD-like Memory Formation

abstract: The predisposition of Autism Spectrum Disorder (ASD) to Post-Traumatic Stress Disorder (PTSD) remained to be established. Here, we show that exposure to a single mild stressful event induces maladaptive memory, which recapitulates all features of PTSD, and is associated with the broad dysfunction of the prefrontal-hippocampo-amygdalar network. Using optogenetics, we demonstrate that prefrontal cortex hyperactivation triggers this PTSD-like memory. Finally, we show that recontextualization of the traumatic event normalizes maladaptive memory in ASD conditions. Overall, this study provides the first direct demonstration that ASD represents a risk factor for PTSD and uncovers new mechanisms that underlie pathological memory formation.


title: Differential investment in visual and olfactory brain regions mirrors the sensory needs of a paper wasp social parasite and its host

abstract: Obligate social parasites evolve traits to effectively locate and then exploit their hosts, whereas hosts have complex social behavioral repertoires, which include sensory recognition to reject potential conspecific intruders and heterospecific parasites. While social parasite and host behaviors have been studied extensively, less is known about how their sensory systems function to meet their specific selective pressures. Here, we compare investment in visual and olfactory brain regions in the paper wasp Polistes dominula, and its obligate social parasite P. sulcifer, to explore the link between sensory systems and brain plasticity. Our results show opposite and significant differences, consistent with their very different life-histories, in the sensory investments between these two closely-related species. Social parasites initially invest in the optic lobes to likely locate their hosts. After host colony usurpation, the parasite increases its brain volume, with specific investment in antennal lobes, which mirrors the behavioral switch from a usurping parasite to an integrated parasitic queen of the host colony. Contrastingly, hosts initially invest in the antennal lobes and sensory processing compared to social parasites, as predicted by their need to maintain social cohesion, allocate colony tasks, and recognize con- and heterospecific intruders. Host queens show a trend of higher investment in all sensory brain regions compared to workers, paralleling differences in task allocations. Our work provides novel insights into how intraspecific brain plasticity can facilitate the unique sensory adaptations needed to perform specific tasks by the host or to transition from searching to successful host exploitation by the social parasite.


title: SARS-CoV-2 infection of circulating immune cells is not responsible for virus dissemination in severe COVID-19 patients

abstract: In late 2019 a novel coronavirus (SARS-CoV-2) emerged, and has since caused a global pandemic. Understanding the pathogenesis of COVID-19 disease is necessary to inform development of therapeutics, and management of infected patients. Using scRNAseq of blood drawn from SARS-CoV-2 patients, we asked whether SARS-CoV-2 may exploit immune cells as a  Trojan Horse to disseminate and access multiple organ systems. Our data suggests that circulating cells are not actively infected with SARS-CoV-2, and do not appear to be a source of viral dissemination.


title: Reference genes for mesangial cell and podocyte qPCR gene expression studies under high-glucose and renin-angiotensin-system blocker conditions

abstract:
BackgroundReal-time PCR remains currently the gold standard method for gene expression studies. Identification of the best reference gene is a key point in performing high quality qPCR, providing strong support for results, as well as performing as a source of bias when inappropriately chosen. Mesangial cells and podocytes, as essential cell lines to study diabetic kidney disease (DKD) physiopathology, demand accurate analysis of the reference genes used so far to enhance validity of gene expression studies, especially regarding high glucose (HG) and DKD treatments, with angiotensin II receptor blockers (e.g. Losartan) being the most commonly used. This study aimed to evaluate the suitability and define the most stable reference gene for mesangial cells and podocytes studies of an in vitro DKD model of disease and its treatment.

MethodsFive software packages (RefFinder, NormFinder, GeNorm, Bestkeeper, and DataAssist) and the comparative {Delta}Ct method were selected to analyze six different candidate genes: HPRT, ACTB, PGAM-1, GAPDH, PPIA, and B2M. RNA was extracted and cDNA was synthesized from immortalized mouse mesangial cells and podocytes cultured in 4 groups: control (n=5; 5mM glucose), mannitol (n=5; 30mM, as osmotic control), HG (n=5; 30mM glucose), and HG + losartan (n=5; 30mM glucose and 10-4 mM of losartan). Real-time PCR was performed according to MIQE guidelines.

ResultsWe identified that the use of 2 genes is the best combination for qPCR normalization for both mesangial cell and podocytes. For mesangial cells, the combination of HPRT and ACTB presented higher stability values. For podocytes, HPRT and GAPDH showed the best results.

ConclusionThis analysis provides support for the use of HPRT and ACTB as reference genes in mouse mesangial cell studies of gene expression via real-time PCR technique, while for podocytes, HPRT and GAPDH should be chosen.


title: Individuality, as well as genotype, affects characteristics and temporal consistency of courtship songs in male mice

abstract:
Courtship songs in mice have been investigated to understand the mechanisms and ecological relevance of vocal communication. There is evidence that courtship song characteristics vary between different genotypes, but little is known on whether individuals, even within the same genotype, differ from each other in the composition, complexity, and temporal consistency of their songs. In a first study, we aimed to systematically identify song features typical of different genotypes, by assessing the composition and complexity (i.e., entropy) of the syllabic sequences of male laboratory mice from four different strains (Mus musculus f. domestica: C57BL/6J, BALB/c, DBA/2 and B6D2F1). Mice were individually presented with a swab containing fresh female urine for 5 minutes to elicit courtship songs. The four strains differed not only in the composition but also in the complexity of their syllabic sequences. In a second study, we investigated within-strain individual differences in temporal consistency and recurring motifs (i.e., identical sets of syllables that are repeated within a song), using BALB/c and DBA/2 mice. The same procedure as in the first study was followed, but in addition testing was repeated weekly over three weeks. Both strains showed some level of individual temporal consistency; BALB/c in the overall amount of emitted vocalisations and DBA/2 in the expression of specific syllable types. However, hierarchical cluster analysis revealed remarkable individual variability in how consistent song characteristics were over time. Furthermore, recurring motifs were expressed at varying levels depending on the individual. Taken together, not only genotype but also individuality can affect variability in courtship songs in mice, suggesting the existence of different courtship strategies (e.g., higher song consistency to facilitate individual identification) related to varying levels of behavioural plasticity.

HIGHLIGHTSO_LICourtship songs in mice can serve as a model to study vocal communication
C_LIO_LIWe explore how genotype and individuality affect courtship songs characteristics
C_LIO_LIGenotypes differ in composition and also in complexity of syllabic sequences
C_LIO_LIWe find remarkable individual variability in how consistent songs are over time
C_LIO_LIResults suggest the existence of variation in male courting behaviour
C_LI

category: animal behavior and cognition


title: COVID-19 Knowledge, Attitudes, and Practices of United Arab Emirates Medical and Health Sciences Students: A Cross Sectional Study

abstract: COVID-19 pandemic is the largest unprecedented viral pandemic of the 21st century. We aimed to study the COVID-19 knowledge, attitudes, and practices (KAP) among medical and health sciences students in the United Arab Emirates (UAE). We performed a cross-sectional study between 2nd June and 19th August 2020. The survey was developed using online Survey Monkey. The link was distributed via UAE University to all students and via WhatsApp(C) groups. The self-administered questionnaire was conducted in English and comprised of two parts: socio-demographic characteristics and KAP towards COVID-19. A total of 712 responses to the questionnaire were collected. 90% (n=695) were under-graduate, while 10% (n=81) were post-graduate students. Majority (87%, n=647) stated that they obtained COVID-19 information from multiple reliable sources. They were highly knowledgeable about COVID-19 pandemic but 76% (n=539) did not recognize its routes of transmission. 63% (n=431) were worried of getting COVID-19, while 92% (n=633)) were worried that a family member could get infected with the virus. 97% (n=655) took precautions when accepting home deliveries, 94% (n=637) had been washing their hands more frequently, and 95% (n=643) had been wearing face masks. In conclusion, participants showed high levels of knowledge and awareness about COVID-19. They were worried about getting infected themselves or their family members, and had good practices against COVID-19.

category: scientific communication and education


title: Evaluation and resolution of many challenges of neural spike-sorting: a new sorter

abstract: We evaluate existing spike sorters and present a new one that resolves many sorting challenges. The new sorter, called "full binary pursuit" or FBP, comprises multiple steps. First, it thresholds and clusters to identify the waveforms of all unique neurons in the recording. Second, it uses greedy binary pursuit to optimally recognize the spike events in the original voltages. Third, it resolves spike events that are described more accurately as the superposition of spikes from two other neurons. Fourth, it resolves situations where the recorded neurons drift in amplitude or across electrode contacts during a long recording session. Comparison with other sorters on real and simulated ground-truth datasets reveals many of the failure modes of spike sorters. We suggest a set of post-sorting analyses that can improve the veracity of neural recordings by minimizing the intrusion of those failure modes into analysis and interpretation of neural data.


title: NF-kB c-Rel is dispensable for the development but is required for the cytotoxic function of NK cells

abstract: Natural Killer (NK) cells are cytotoxic lymphocytes critical to the innate immune system. We found that germline deficiency of NF-kB c-Rel results in a marked decrease in cytotoxic function of NK cells, both in vitro and in vivo, with no significant differences in the stages of NK cell development. We found that c-Rel binds to the promoters of perforin and granzyme B, two key proteins required for NK cytotoxicity, and controls their transactivation. We generated a NK cell specific c-Rel conditional knockout to study NK cell intrinsic role of c-Rel and found that both global and conditional c-Rel deficiency leads to decreased perforin and granzyme B expression and thereby cytotoxic function. We also confirmed the role of c-Rel in perforin and granzyme B expression in human NK cells. c-Rel reconstitution rescued perforin and granzyme B expressions in c-Rel deficient NK cells and restored their cytotoxic function. Our results show a previously unknown role of c-Rel in transcriptional regulation of perforin and granzyme B expressions and control of NK cell cytotoxic function.


title: In Vivo Subcellular Mass Spectrometry Enables Proteo-Metabolomic Single-cell Systems Biology in a Chordate Embryo Developing to a Normally Behaving Tadpole (X. laevis)

abstract: We present the first example of in vivo high-resolution mass spectrometry (HRMS) for subcellular molecular systems biology of proteins and metabolites. With light microscopy, we identified the left-dorsal and left-ventral animal cells in cleavage-stage non-sentient Xenopus laevis embryos. Using precision-translated fabricated microcapillaries, the subcellular content of each cell was double-probed, each time collecting <5% of cell volume (~10 nL) swiftly (<5 s/event). The proteins and metabolites were analyzed by custom-built ultrasensitive capillary electrophoresis electrospray ionization employing Orbitrap and time-of-flight HRMS. Label-free detection of ~150 metabolites (57 identified) and 738 proteins found proteo-metabolomic networks with differential quantitative activities between the cell types. Spatially and temporally scalable sampling the technology preserved the integrity of the analyzed cells, the neighboring cells, and the embryo. 95% of the analyzed embryos developed into sentient tadpoles that were indistinguishable from their wild-type siblings based on anatomy and visual function in a background color preference assay.


title: VISUAL network analysis reveals the role of BEH3 as a stabilizer in the secondary vascular development in Arabidopsis

abstract: During secondary growth in plants, vascular stem cells located in the cambium continuously undergo self-renewal and differentiation throughout the lifetime. Recent cell-sorting technique enables to uncover transcriptional regulatory framework for cambial cells. However, the mechanisms underlying the robust control of vascular stem cells have not been understood yet. By coexpression network analysis using multiple transcriptome datasets of an ectopic vascular cell transdifferentiation system using Arabidopsis cotyledons, VISUAL, we newly identified a cambium-specific gene module from an alternative approach. The cambium gene list included a transcription factor BES1/BZR1 homolog 3 (BEH3), whose homolog BES1 is known to control vascular stem cell maintenance negatively. Interestingly, the vascular size of the beh3 mutants showed a large variation, implying the role of BEH3 as a stabilizer. BEH3 almost lost the transcriptional repressor activity and functioned antagonistically with other BES/BZR members via competitive binding to the same motif BRRE. Indeed, mathematical modeling suggests that the competitive relationship among BES/BZRs leads to the robust regulation of vascular stem cells.


title: Sahul's megafauna were vulnerable to extinction due to their position in the trophic network

abstract: Extinctions stemming from environmental change often trigger trophic cascades and coextinctions. However, it remains unclear whether trophic cascades were a large contributor to the megafauna extinctions that swept across several continents in the Late Pleistocene. The pathways to megafauna extinctions are particularly unclear for Sahul (landmass comprising Australia and New Guinea), where extinctions happened earlier than on other continents. We investigated the role of bottom-up trophic cascades in Late Pleistocene Sahul by constructing pre-extinction (~ 80 ka) trophic network models of the vertebrate community of Naracoorte, south-eastern Australia. These models allowed us to predict vertebrate species vulnerability to cascading extinctions based on their position in the network. We tested whether the observed extinctions could be explained by bottom-up cascades, or if they should be attributed to other external causes. Species that disappeared from the community were more vulnerable, overall, to bottom-up cascades than were species that survived. The position of extinct species in the network - having few or no predators - also suggests they might have been particularly vulnerable to a new predator. These results provide quantitative evidence that trophic cascades and naivety to predators could have contributed to the megafauna extinction event in Sahul.


title: Sahul's megafauna were vulnerable to plant-community changes due to their position in the trophic network


title: Close-kin methods to estimate census size and effective population size

abstract: The last two decades have witnessed rapid developments and increasing interest in use of (1) genetic methods to estimate effective population size (Ne) and (2) close-kin mark-recapture (CKMR) methods to estimate abundance based on the incidence of close relatives. Whereas Ne estimation methods have been applied to a wide range of taxa, all CKMR applications to date have been for aquatic species. These two fields of inquiry have developed largely independently, and this is unfortunate because deeper insights can be gained by joint evaluation of eco-evolutionary processes. In this synthesis, we use simple analytical models and simulated pedigree data to illustrate how various factors (life-history traits; patterns of variation in individual reproductive success; experimental design; stochasticity; marker type) can affect performance of the estimators. We show that the Ne/N ratio and the probability of a close-kin match both depend on a vector of parental weights that specify relative probabilities that different individuals will produce offspring. Although age-specific vital rates are central to both methodologies, for CKMR they can potentially bias abundance estimates unless properly accounted for, whereas they represent the signals of genetic drift that Ne estimation methods depend upon. Coordinating Ne and CKMR estimation methods using the same or overlapping datasets would facilitate joint evaluation of both the ecological and evolutionary consequences of abundance.

category: evolutionary biology


title: Evolution of gene expression variance during adaptation to high temperature in Drosophila

abstract: Shifts in trait means are widely considered as evidence for adaptive responses, but the impact on phenotypic variance remains largely unexplored. Classic quantitative genetics provides a theoretical framework to predict how selection on phenotypic mean affects the variance. In addition to this indirect effect, it is also possible that the variance of the trait is the direct target of selection, but experimentally characterized cases are rare. Here, we studied gene expression variance of Drosophila simulans males before and after 100 generations of adaptation to a novel hot laboratory environment. In each of the two independently evolved populations, the variance of 125 and 97 genes was significantly reduced. We propose that the drastic loss in environmental complexity from nature to the lab may have triggered selection for reduced variance. Our observation that selection could drive changes in the variance of gene expression could have important implications for studies of adaptation processes in natural and experimental populations.


title: Evolution of phenotypic variance during adaptation to high temperature in Drosophila


title: Universal markers support a long inter-domain branch between Archaea and Bacteria

abstract: Core gene phylogenies provide a window into early evolution, but different gene sets and analytical methods have yielded substantially different views of the tree of life. Trees inferred from a small set of universal core genes have typically supported a long branch separating the archaeal and bacterial domains. By contrast, recent analyses of a broader set of non-ribosomal genes have suggested that Archaea may be less divergent from Bacteria, and that estimates of inter-domain distance are inflated due to accelerated evolution of ribosomal proteins along the inter-domain branch. Resolving this debate is key to determining the diversity of the archaeal and bacterial domains, the shape of the tree of life, and our understanding of the early course of cellular evolution. Here, we investigate the evolutionary history of the marker genes key to the debate. We show that estimates of a reduced Archaea-Bacteria (AB) branch length result from inter-domain gene transfers and hidden paralogy in the expanded marker gene set. By contrast, analysis of a broad range of manually curated marker gene datasets from an evenly sampled set of 700 Archaea and Bacteria reveal that current methods likely underestimate the AB branch length due to substitutional saturation and poor model fit; that the best-performing phylogenetic markers tend to support longer inter-domain branch lengths; and that the AB branch lengths of ribosomal and non-ribosomal marker genes are statistically indistinguishable. Furthermore, our phylogeny inferred from the 27 highest-ranked marker genes recovers a clade of DPANN at the base of the Archaea, and places CPR within Bacteria as the sister group to the Chloroflexota.


title: An estimate of the deepest branches of the tree of life from ancient vertically-evolving genes


title: Protein-coding repeat polymorphisms strongly shape diverse human phenotypes

abstract: Hundreds of the proteins encoded in human genomes contain domains that vary in size or copy number due to variable numbers of tandem repeats (VNTRs) in proteincoding exons. VNTRs have eluded analysis by the molecular methods--SNP arrays and high-throughput sequencing--used in large-scale human genetic studies to date; thus, the relationships of VNTRs to most human phenotypes are unknown. We developed ways to estimate VNTR lengths from whole-exome sequencing data, identify the SNP haplotypes on which VNTR alleles reside, and use imputation to project these haplotypes into abundant SNP data. We analyzed 118 protein-altering VNTRs in 415,280 UK Biobank participants for association with 791 phenotypes. Analysis revealed some of the strongest associations of common variants with human phenotypes including height, hair morphology, and biomarkers of human health; for example, a VNTR encoding 13-44 copies of a 19-amino-acid repeat in the chondroitin sulfate domain of aggrecan (ACAN) associated with height variation of 3.4 centimeters (s.e. 0.3 cm). Incorporating large-effect VNTRs into analysis also made it possible to map many additional effects at the same loci: for the blood biomarker lipoprotein(a), for example, analysis of the kringle IV-2 VNTR within the LPA gene revealed that 18 coding SNPs and the VNTR in LPA explained 90% of lipoprotein(a) heritability in Europeans, enabling insights about population differences and epidemiological significance of this clinical biomarker. These results point to strong, cryptic effects of highly polymorphic common structural variants that have largely eluded molecular analyses to date.

category: genetics


title: Significance of linkage disequilibrium and epistasis on the genetic variances and covariance between relatives in non-inbred and inbred populations

abstract: Because no feasible theoretical model can depict the complexity of phenotype development from a genotype, the joint significance of linkage disequilibrium (LD), epistasis, and inbreeding on the genetic variances remains unclear. The objective of this investigation was to assess the impact of LD and epistasis on the genetic variances and covariances between relatives in non-inbred and inbred populations using simulated data. We provided the theoretical background and simulated grain yield assuming 400 genes in 10 chromosomes of 200 and 50 cM. We generated five populations with low to high LD levels, assuming 10 generations of random cross and selfing. The analysis of the parametric LD in the populations shows that the LD level depends mainly on the gene density. The significance of the LD level is impressive on the magnitude of the genotypic and additive variances, which is the most important component of the genotypic variance, regardless of the LD level and the degree of inbreeding. Regardless of the type of epistasis, the ratio epistatic variance/genotypic variance is proportional to the percentage of the epistatic genes. For the epistatic variances, except for duplicate epistasis and dominant and recessive epistasis, with 100% of epistatic genes, their magnitudes are much lower than the magnitude of the additive variance. The additive x additive variance is the most important epistatic variance. Our results explain why LD for genes and relationship information are key factors affecting the genomic prediction accuracy of complex traits and the efficacy of association studies.


title: Genetic diversity, population structure and selection signature in Ethiopian Sorghum (Sorghum bicolor L. ) germplasm

abstract: Ethiopia, the probable center of origin and diversity for sorghum (Sorghum bicolor L. [Moench]) and with unique eco-geographic features, possesses a large number of sorghum landraces that have not been well studied. Increased knowledge of this diverse germplasm through large-scale genomic characterization may contribute for understanding of evolutionary biology, and adequate use of these valuable resources from the center of origin. In this study, we characterized genetic diversity, population structure and selection signature in 304 sorghum accessions collected from diverse sorghum growing regions of Ethiopia using genotyping-by-sequencing (GBS). We identified a total of 108,107 high-quality single nucleotide polymorphism (SNPs) markers that were evenly distributed across the sorghum genome. The average gene diversity among accessions was high (He = 0.29). We detected a relatively low frequency of rare alleles (26%), highlighting the potential of this germplasm for subsequent allele mining studies through genome wide association studies (GWAS). While we found no evidence of genetic differentiation among administrative regions (FST = 0.02, p = 0.12), population structure and cluster analyses showed clear differentiation among six Ethiopian sorghum populations (FST = 0.28, p = 0.01) adapting to different environments. Analysis of SNP differentiation between the identified genetic groups revealed a total of 40 genomic regions carrying signatures of selection. These regions harbored candidate genes potentially involved in a variety of biological processes, including abiotic stress tolerance, pathogen defense and reproduction. Overall, a high level of untapped diversity for sorghum improvement remains available in Ethiopia, with patterns of diversity consistent with divergent selection on a range of adaptive characteristics.


title: A scalable pipeline for local ancestry inference using tens of thousands of reference haplotypes

abstract:
Ancestry deconvolution is the task of identifying the ancestral origins of chromosomal segments of admixed individuals. It has important applications, from mapping disease genes to identifying loci potentially under natural selection. However, most existing methods are limited to a small number of ancestral populations and are unsuitable for large-scale applications.

In this article, we describe Ancestry Composition, a modular pipeline for accurate and efficient ancestry deconvolution. In the first stage, a string-kernel support-vector-machines classifier assigns provisional ancestry labels to short statistically phased genomic segments. In the second stage, an autoregressive pair hidden Markov model corrects phasing errors, smooths local ancestry estimates, and computes confidence scores.

Using publicly available datasets and more than 12,000 individuals from the customer database of the personal genetics company, 23andMe, Inc., we have constructed a reference panel containing more than 14,000 unrelated individuals of unadmixed ancestry. We used principal components analysis (PCA) and uniform manifold approximation and projection (UMAP) to identify genetic clusters and define 45 distinct reference populations upon which to train our method. In cross-validation experiments, Ancestry Composition achieves high precision and recall.


title: Impact of sterilization on a conjugated polymer based bioelectronic patch

abstract: Translation into the clinic of organic bioelectronic devices having conjugated polymers as the active material will hinge on their long-term operation in vivo. This will require the device to be subject to clinically approved sterilization techniques without a deterioration in its physical and electronic properties. To date, there remains a gap in the literature addressing the impact of this critical pre-operative procedure on the properties of conjugated polymers. This study aims to address this gap by assessing the physical and electronic properties of a sterilized porous bioelectronic patch having polyaniline as the conjugated polymer. The patch was sterilized by autoclave, ethylene oxide and gamma ({gamma}-) irradiation at 15, 25, and 50 kGy doses. Autoclaving resulted in cracking and macroscopic degradation of the patch, while patches sterilized by {gamma}-irradiation at 50 kGy exhibited reduced mechanical and electronic properties, attributed to chain scission and non-uniform crosslinking caused by the high dose irradiation. Ethylene oxide and {gamma}-irradiation at 15 and 25 kGy sterilization appeared to be the most effective at maintaining the mechanical and electronic properties of the patch, as well as inducing a minimal immune response as revealed by a receding fibrotic capsule after 4 weeks implantation. Our findings pave the way towards closing the gap for the translation of organic bioelectronic devices from acute to long-term in vivo models.

category: bioengineering


title: LINE-1 Retrotransposon expression in cancerous, epithelial and neuronal cells revealed by 5'-single cell RNA-Seq

abstract: LINE-1 retrotransposons are sequences capable of copying themselves to new genomic loci via an RNA intermediate. New studies implicate LINE-1 in a range of diseases, especially in the context of aging, but without an accurate understanding of where and when LINE-1 is expressed, a full accounting of its role in health and disease is not possible. We therefore developed a method - 5 scL1seq - that makes use of a widely available library preparation method (10x Genomics 5 single cell RNA-seq) to measure LINE-1 expression in tens of thousands of single cells. We recapitulated the known pattern of LINE-1 expression in tumors - present in cancer cells, absent from immune cells - and identified hitherto undescribed LINE-1 expression in human epithelial cells and mouse hippocampal neurons. In both cases, we saw a modest increase with age, supporting recent research connecting LINE-1 to age related diseases.

category: bioinformatics


title: Scalpel: Information-based Dimensionality Reduction for Rare Cell Type Discovery

abstract: Dimensionality reduction is crucial to summarizing the complex transcriptomic landscape of single cell datasets for downstream analyses. However, current dimensionality reduction approaches favor large cellular populations defined by many genes, at the expense of smaller and more subtly-defined populations. Here, we present surprisal component analysis (SCA), a technique that leverages the information-theoretic notion of surprisal for dimensionality reduction, and demonstrate its ability to improve the representation of clinically important populations that are indistinguishable using existing pipelines. For example, in cytotoxic T-cell data, SCA cleanly separates the gamma-delta and MAIT cell subpopulations, which are not detectable via PCA, ICA, scVI, or a wide array of specialized rare cell recovery tools. We also show that, when used instead of PCA, SCA improves downstream imputation to more accurately restore mRNA dropouts and recover important gene-gene relationships. SCAs information-theoretic paradigm opens the door to more meaningful signal extraction, with broad applications to the study of complex biological tissues in health and disease.


title: Discovering Rare Cell Types through Information-based Dimensionality Reduction


title: Recovering Single-cell Heterogeneity through Information-based Dimensionality Reduction


title: Validation of binary non-targeted approaches: mathematical framework and experimental designs

abstract: Non-targeted methods (NTMs) are being increasingly developed and adopted to detect food fraud and identify the authenticity of the food. Method validation is a critical step before bringing the NTMs to the routine to be assured of method performance and trust that its outcomes are reliable. However, the paucity of well structured and harmonized validation strategies has been one of the hurdles, withholding the exploitation of NTMs. This report aims to describe a validation framework for methods that involve binary classification, which are prevalent in non-targeted workflows. We foresee this work to contribute to filling the current gap in the provisions for NTM method validation; perhaps also push the dialogue further to collectively resolve existing challenges.


title: Integration of spatial transcriptomic and single cell sequencing identifies expression patterns underlying immune and epithelial cell cross-talk in acute kidney injury

abstract: Despite important advances in studying experimental and clinical acute kidney injury (AKI), the pathogenesis of this disease remains incompletely understood. Single cell sequencing studies have closed this knowledge gap by characterizing the transcriptomic signature of different cell types within the kidney. However, the spatial distribution of injury can be regional and affect cells heterogeneously. We first optimized coordination of spatial transcriptomics and single nuclear sequencing datasets, mapping 30 dominant cell types to a human nephrectomy sample. The predicted cell type spots corresponded with the underlying hematoxylin and eosin histopathology. To study the implications of acute kidney injury on the distribution of transcript expression, we then characterized the spatial transcriptomic signature of two murine AKI models: ischemia reperfusion injury (IRI) and cecal ligation puncture (CLP). Localized regions of reduced overall expression were found associated with tissue injury pathways. Using single cell sequencing, we deconvoluted the signature of each spatial transcriptomic spot, identifying patterns of colocalization between immune and epithelial cells. As expected, neutrophils infiltrated the renal medullary outer stripe in the ischemia model. Atf3 was identified as a chemotactic factor in S3 proximal tubule cells. In the CLP model, infiltrating macrophages dominated the outer cortical signature and Mdk was identified as a corresponding chemotactic factor. The regional distribution of these immune cells was validated with multiplexed CO-Detection by inDEXing (CODEX) immunofluorescence. Spatial transcriptomic sequencing can aid in uncovering the mechanisms driving immune cell infiltration and allow detection of relevant subpopulations in single cell sequencing. The complementarity of these technologies facilitates the development of a transcriptomic kidney atlas in health and disease.


title: AutoSmarTrace: Automated Chain Tracing and Flexibility Analysis of Biological Filaments

abstract:
Single-molecule imaging is widely used to determine statistical distributions of molecular properties. One such characteristic is the bending flexibility of biological filaments, which can be parameterized via the persistence length. Quantitative extraction of persistence length from images of individual filaments requires both the ability to trace the backbone of the chains in the images and sufficient chain statistics to accurately assess the persistence length. Chain tracing can be a tedious task, performed manually or using algorithms that require user input and/or supervision. Such interventions have the potential to introduce user-dependent bias into the chain selection and tracing. Here, we introduce a fully automated algorithm for chain tracing and determination of persistence lengths. Dubbed "AutoSmarTrace", the algorithm is built off a neural network, trained via machine learning to identify filaments within images recorded using atomic force microscopy (AFM). We validate the performance of AutoSmarTrace on simulated images with widely varying levels of noise, demonstrating its ability to return persistence lengths in agreement with the ground truth. Persistence lengths returned from analysis of experimental images of collagen and DNA agree with previous values obtained from these images with different chain-tracing approaches. While trained on AFM-like images, the algorithm also shows promise to identify chains in other single-molecule imaging approaches, such as rotary shadowing electron microscopy and fluorescence imaging.

Statement of SignificanceMachine learning presents powerful capabilities to the analysis of large data sets. Here, we apply this approach to the determination of bending flexibility - described through persistence length - from single-molecule images of biological filaments. We present AutoSmarTrace, a tool for automated tracing and analysis of chain flexibility. Built on a neural network trained via machine learning, we show that AutoSmarTrace can determine persistence lengths from AFM images of a variety of biological macromolecules including collagen and DNA. While trained on AFM-like images, the algorithm works well to identify filaments in other types of images. This technique can free researchers from tedious tracing of chains in images, removing user bias and standardizing determination of chain mechanical parameters from single-molecule conformational images.


title: Identification and characterization of a G-quadruplex structure in the pre-core promoter region of hepatitis B virus

abstract: Worldwide, [~]250 million people are chronically infected with the hepatitis B virus (HBV) and are at increased risk of cirrhosis and hepatocellular carcinoma. The HBV persists as covalently closed circular DNA (cccDNA), which acts as the template for all HBV mRNA transcripts. Nucleos(t)ide analogs do not directly target the HBV cccDNA and cannot eradicate the HBV. We have discovered a unique structural motif, a G-quadruplex in HBVs pre-core promoter region that is conserved amongst nearly all genotypes, and is central to critical steps in the viral life-cycle including the production of pre-genomic RNA, core and polymerase proteins, and encapsidation. Thus, an increased understanding of the HBV pre-core may lead to the development of novel anti-HBV cccDNA targets. We utilized biophysical methods to characterize the presence of the G-quadruplex, employed assays using a known quadruplex- binding protein (DHX36) to pull-down HBV cccDNA, and compared HBV infection in HepG2 cells transfected with wild-type and mutant HBV plasmids. This study provides insights into the presence of a G-quadruplex in the HBV pre-core promoter region essential for HBV replication. The evaluation of this critical host-protein interaction site in the HBV cccDNA may ultimately facilitate the development of novel anti-HBV therapeutics against the resilient cccDNA template.


title: Mechanosensitive remodeling of the bacterial flagellar motor is independent of direction of rotation

abstract:
Motility is critical for the survival and dispersal of bacteria, and it plays an important role during infection. How bacteria regulate motility is thus a question of broad interest. Regulation of bacterial motility by chemical stimuli is well studied, but recent work has added a new dimension to the problem of motility control. The bidirectional flagellar motor of the bacterium Escherichia coli recruits or releases torque-generating units (stator units) in response to changes in load. Here, we show that this mechanosensitive remodeling of the flagellar motor is independent of direction of rotation. Remodeling rate constants in clockwise rotating motors and in counterclockwise rotating motors, measured previously, fall on the same curve if plotted against torque. Increased torque decreases the off rate of stator units from the motor, thereby increasing the number of active stator units at steady state. A simple mathematical model based on observed dynamics provides quantitative insight into the underlying molecular interactions. The torque-dependent remodeling mechanism represents a robust strategy to quickly regulate output (torque) in response to changes in demand (load).

SignificanceMacromolecular machines carry out most of the biological functions in living organisms. Despite their significance, we do not yet understand the rules that govern the self-assembly of large multi-protein complexes. The bacterial flagellar motor tunes the assembly of its torque-generating stator complex with changes in external load. Here, we report that clockwise and counterclockwise rotating motors have identical remodeling response to changes in the external load, suggesting a purely mechanical mechanism for this regulation. Autonomous control of self-assembly may be a general strategy for tuning the functional output of protein complexes. The flagellar motor is a prime example of a macromolecular machine in which the functional regulation of assembly can be rigorously studied.


title: Thermodynamic and Kinetic Characterization of Protein Conformational Dynamics within a Riemannian Framework

abstract: We have formulated a Riemannian framework for describing the geometry of collective variable spaces of biomolecules within the context of molecular dynamics (MD) simulations. The formalism provides a theoretical framework to develop enhanced sampling techniques, path-finding algorithms, and transition rate estimators consistent with a Riemannian treatment of the collective variable space, where the quantities of interest such as the potential of mean force (PMF) and minimum free energy path (MFEP) remain invariant under coordinate transformation. Specific algorithms within this framework are discussed such as the Riemannian umbrella sampling, the Riemannian string method, and a Riemannian-Bayesian estimator of free energy and diffusion constant, which can be used to estimate the transition rate along an MFEP.


title: Single particle combinatorial multiplexed liposome fusion mediated by DNA

abstract: Combinatorial high throughput methodologies are central for both screening and discovery in synthetic biochemistry and biomedical sciences. They are, however, often reliant on large scale analyses and thus limited by long running time and excessive materials cost. We herein present Single PARticle Combinatorial multiplexed Liposome fusion mediated by DNA (SPARCLD), for the parallelized, multi-step and non-deterministic fusion of individual zeptoliter nanocontainers. We observed directly the efficient (>93%), and leakage free stochastic fusion sequences for arrays of surface tethered target liposomes with six freely diffusing populations of cargo liposomes, each functionalized with individual lipidated ssDNA (LiNA) and fluorescent barcoded by distinct ratio of chromophores. The stochastic fusion results in distinct permutation of fusion sequences for each autonomous nanocontainer. Real-time TIRF imaging allowed the direct observation of >16000 fusions and 566 distinct fusion sequences accurately classified using machine learning. The high-density arrays of surface tethered target nanocontainers [~]42,000 containers per mm2 offers entire combinatorial multiplex screens using only picograms of material.


title: Silencing of lncRNA NEAT1 inhibits esophageal squamous cell carcinoma proliferation, migration, and invasion via regulation of the miR-1299/MMP2 axis

abstract: Esophageal squamous cell carcinoma (ESCC) is the most prevalent form of esophageal cancer worldwide. Considerable evidence has verified that abnormal expression of lncRNAs can effectively influence the progression of various malignant tumors. However, the regulatory mechanisms of lncRNAs underlying ESCC development and progression remain poorly defined. Here, we investigated the role of lncRNA nuclear-enriched abundant transcript 1 (NEAT1) in ESCC via regulating microRNA 1299 (miR-1299) and matrix metalloproteinase 2 (MMP2). A total of 32 ESCC tissue samples were obtained from the First Affiliated Hospital of Zhengzhou University. The mRNA levels of lncRNA NEAT1, miR-1299, and MMP2 mRNA were measured via quantitative real-time PCR. Interactions among miR-1299, lncRNA NEAT1, and MMP2 mRNA in EC9706 cells were confirmed by dual-luciferase reporter assays and RNA immunoprecipitation (RIP) assays. The proliferation and migration/invasion of ESCC cells were verified by CCK-8 and transwell assays, respectively. lncRNA NEAT1 was up-regulated in ESCC tissues and cells. lncRNA NEAT1 silencing inhibited migration, invasion, and proliferation of ESCC cells. Furthermore, lncRNA NEAT1 sponged and negatively regulated miR-1299, thus giving rise to increased expression of MMP2. Moreover, miR-1299 inhibitors and MMP2 rescued the invasion of ESCC cells following silencing of lncRNA NEAT1. lncRNA NEAT1 was overexpressed in ESCC tissues and cells. Silencing of lncRNA NEAT1 inhibited ESCC proliferation, migration, and invasion via reducing competitive binding of lncRNA NEAT1 with miR-1299 and enhancing miR-1299-targeted suppression of MMP2. Taken together, our findings suggest that lncRNA NEAT1 is a potential target for ESCC therapy and rehabilitation.

category: cancer biology


title: Convergent evolution of resistance pathways during early stage breast cancer treatment with combination cell cycle (CDK) and endocrine inhibitors

abstract: Combining cyclin-dependent kinase (CDK) inhibitors with endocrine therapy improves outcomes for metastatic estrogen receptor positive (ER+), HER2 negative, breast cancer patients. However, the value of this combination in potentially curable earlier stage patients is not clear. Using single cell transcriptomic profiling, we examined the evolutionary trajectories of early stage breast cancer tumors using serial tumor biopsies from a clinical trial of preoperative endocrine therapy (letrozole) alone or in combination with the cell cycle inhibitor ribociclib. Applying hierarchical regression and Gaussian process mathematical modelling, we classified each tumor by whether it shrinks or persists with therapy and determined cancer phenotypes related to evolution of resistance and cell cycle transcriptional rewiring. We found that all patients tumors undergo subclonal evolution during therapy, irrespective of the clinical response. However, tumors subjected to endocrine therapy alone showed reduced diversity over time, while those facing combination therapy exhibited increased diversity. Despite different subclonal diversity, single nuclei RNA sequencing uncovered common phenotypic changes in tumor cells that persist following treatment. In these tumors, cancer cells with accelerated loss of estrogen signaling have convergent up-regulation of the JNK pathway, while cells that maintain estrogen signaling during therapy show potentiation of CDK4/6 activation consistent with ERBB4 and ERK signaling up-regulation. These convergent phenotypes were associated with growing tumors resistant to combination therapy. Cell cycle reconstruction identified that these tumors can rebound during combination therapy treatment, indicating stronger selection and promotion of a proliferative state. These results indicate that combination therapy in early stage ER+ breast cancers with ER and CDK inhibition drives rapid evolution of resistance via a shift from estrogen signaling to alternative growth factor receptor mediated proliferation and JNK signaling activation, concordant with a bypass in the G1 checkpoint.