title: Detecting change in interconnected ecosystem assets to inform indicators of condition in environmental economic accounts

abstract:
Environmental Economic Accounts track the condition of interconnected ecosystem assets, to inform environmental decision makers about its influence on the past and current status of ecosystem services. Indicators of condition need to be analysed to determine if they lead, are coincident with or lag environmental change, so that indicators are interpreted appropriately by decision makers. Here we conduct performance testing of ecological condition indicators developed with the United Nations System of Environmental-Economic Accounting - Ecosystem Accounting (SEEA-EA) framework. We chose a case-study of a catchment-to-coast system with strongly interconnected assets and high natural variability, which likely confounds our ability to track long-term change. We first quantified covariation among ecological indicators for pasture biomass, vegetation greenness and barramundi catch per unit effort. Covariation in the indicators was driven by river flow, with higher values of all indicators occurring in years with greater river flow. Barramundi catch per unit effort was most sensitive to changes in river flow, followed by a vegetation greenness and pasture biomass. We then defined reference bounds for each indicator that accounted for natural variation in river flow. We predicted the emergence times for each indicator, the time taken for each indicator to emerge from the background of natural variation. Emergence times were >10 years in all cases. Detecting change was more difficult where there were gaps in data. Ecosystem accounts can be used to compare ecological condition against performance objectives, but should consider natural variation in the system. National accounts are often used by decision makers to directly inform near-term actions, because economic indicators respond rapidly to new policies and the prevailing economic conditions. We found that ecological condition indicators in highly variable ecosystems are lagging indicators of change, and as such should be used to assess historical performance, not as leading indicators of future change.

Article impact statementEcological condition is a lagging indicator of environmental change and should only be used to inform on historical management performance.


title: Phylo-taxonogenomics of 182 strains of genus Leuconostoc elucidates its robust taxonomy and biotechnological importance

abstract: Genus Leuconostoc is a group of a diverse range of lactic acid bacteria (LAB) majorly found in dairy, food and environmental ecology. These microbes are commercially important for several industries due to their intrinsic genomic attributes such as bacteriocins, carbohydrate-active enzymes, plasmids etc. Even though the species of Leuconostoc are commercially significant, their taxonomy is largely based on old, low resolution traditional methods. There have been several taxonomic reclassifications in the past which are inadequate for microbiologist and food industry professionals to truly demarcate any new strain of genus Leuconostoc. The current taxonomy of the genus is largely based on classical approaches, which are in utmost need of reinvestigation by whole genome-based approaches. In the present study, the taxono-phylogenomic analysis clearly depicted sixteen species including three novel genomospecies in addition to several reshufflings across the species namely, L. mesenteroides, L. pseudomesenteroides, L. gelidum and L. lactis. The presence of a wide range of carbohydrate-active enzymes, type III polyketide synthase and vector plasmids suggested the biotechnological potential of constituent strains of the genera. Further, the absence of antibiotic gene clusters reaffirms their utility in industries such as food and dairy. Such large-scale in-depth genome-based study can shed light on the nature of the genome dynamics of the species and help to obtain a more robust taxonomic classification.

category: genomics


title: Strategies of tolerance reflected in two North American maple genomes

abstract:
Maples (the genus Acer) represent important and beloved forest, urban, and ornamental trees distributed throughout the Northern hemisphere. They exist in a diverse array of native ranges and distributions, across spectrums of tolerance or decline, and have varying levels of susceptibility to biotic and abiotic stress. Among Acer species, several stand out in their importance to economic interest. Here we report the first two chromosome-scale genomes for North American species, Acer negundo and Acer saccharum. Both assembled genomes contain scaffolds corresponding to 13 chromosomes, with A. negundo at a length of 442 Mb, N50 of 32 Mb and 30,491 genes, and A. saccharum at 626 Mb, N50 of 46 Mb, and 40,074 genes. No recent whole genome duplications were detected, though A. saccharum has local gene duplication and more recent bursts of transposable elements, as well as a large-scale translocation between two chromosomes. Genomic comparison revealed that A. negundo has a smaller genome with recent gene family evolution that is predominantly contracted and expansions that are potentially related to invasive tendencies and tolerance to abiotic stress. Examination of expression from RNA-Seq obtained from A. saccharum grown in long-term aluminum and calcium soil treatments at the Hubbard Brook Experimental Forest, provided insights into genes involved in aluminum stress response at the systemic level, as well as signs of compromised processes upon calcium deficiency, a condition contributing to maple decline.

Significance statementThe first chromosome-scale assemblies for North American members of the Acer genus, sugar maple (Acer saccharum) and boxelder (Acer negundo), as well as transcriptomic evaluation of abiotic stress response in A. saccharum. This integrated study describes in-depth aspects contributing to each species approach to tolerance and applies current knowledge in many areas of plant genome biology with Acer physiology to help convey the genomic complexities underlying tolerance in broadleaf tree species.


title: Machine learning models based on molecular descriptors to predict human and environmental toxicological factors in continental freshwater

abstract:
AO_SCPLOWBSTRACTC_SCPLOWIt is a real challenge for life cycle assessment practitioners to identify all relevant substances contributing to the ecotoxicity. Once this identification has been made, the lack of corresponding ecotoxicity factors can make the results partial and difficult to interpret. So, it is a real and important challenge to provide ecotoxicity factors for a wide range of compounds. Nevertheless, obtaining such factors using experiments is tedious, time-consuming, and made at a high cost. A modeling method that could predict these factors from easy-to-obtain information on each chemical would be of great value. Here, we present such a method, based on machine learning algorithms, that used molecular descriptors to predict two specific endpoints in continental freshwater for ecotoxicological and human impacts. The different tested machine learning algorithms show good performances on a learning database and the non-linear methods tend to outperform the linear ones. The cluster-then-predict approaches usually show the best performances which suggests that these predicted models must be derived for somewhat similar compounds. Finally, predictions were derived from the validated model for compounds with missing toxicity/ecotoxicity factors.

HighlightsO_LICharacterization factors (for human health and ecotoxicological impacts) were predicted using molecular descriptors.
C_LIO_LISeveral linear or non-linear machine learning methods were compared.
C_LIO_LIThe non-linear methods tend to outperform the linear ones using a train and test procedure. Cluster-then-predict approaches often show the best performances, highlighting their usefulness.
C_LIO_LIThis methodology was then used to derive characterization factors that were missing for more than a hundred chemicals in USEtox(R).
C_LI

Graphical abstract

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category: biochemistry


title: Task-Assisted GAN for Resolution Enhancement and Modality Translation in Fluorescence Microscopy

abstract: We introduce a deep learning model for resolution enhancement and prediction of super-resolved biological structures, which is based on a Generative Adversarial Network (GAN) assisted by a complementary segmentation task. It is applied to predict biological nanostructures from diffraction-limited images and to guide microscopists for quantitative fixed- and live-cell STimulated Emission Depletion (STED) microscopy. More specifically, we show that the use of a complementary segmentation task improves the accuracy of the predicted nanostructures over state-of-the art resolution enhancement generative approaches, allowing quantitative analysis of the sub-diffraction structures in the resulting generated images.

category: bioinformatics


title: FISH-quant v2: a scalable and modular analysis tool for smFISH image analysis

abstract: Regulation of RNA abundance and localization is a key step in gene expression control. Single-molecule RNA fluorescence in-situ hybridization (smFISH) is a widely used single-cell-single-molecule imaging technique enabling a quantitative understanding of gene expression and its regulatory mechanisms. Recent progress in experimental techniques provides larger data-sets, requiring adequate tools for data analysis and exploration. Here, we present FISH-quant v2, a highly modular analysis tool accessible both for non-experts and experts, which we validated and applied on large-scale smFISH image datasets. Our package allows the user to detect isolated and clustered mRNA spots, segment nuclei and cells, quantify RNA localization patterns and visualize these results at the single-cell level.


title: PSINDB: A comprehensive database of postsynaptic protein-protein interactions

abstract: The postsynaptic region is the receiving part of the synapse comprising thousands of proteins forming an elaborate and dynamically changing network indispensable for the molecular mechanisms behind fundamental phenomena such as learning and memory. Despite the growing amount of information about individual protein-protein interactions in this network, these data are mostly scattered in the literature or are stored in generic databases that are not designed to display aspects which are fundamental to understanding postsynaptic functions. To overcome these limitations we collected postsynaptic protein-protein interactions (PPIs) together with a high amount of detailed structural and biological information and launched a freely available resource, the Postsynaptic Interaction Database (PSINDB) to make these data and annotations accessible. PSINDB includes tens of thousands of binding regions together with structural features mediating and regulating the formation of PPIs, annotated with detailed experimental information about each interaction. PSINDB is expected to be useful for numerous aspects of molecular neurobiology research, from experiment design to network and systems biology-based modeling and analysis of changes in the protein network upon various stimuli. PSINDB is available at http://psindb.itk.ppke.hu/.


title: The mitotic spindle protein CKAP2 potently increases formation and stability of microtubules

abstract: Cells increase microtubule dynamics to make large rearrangements to their microtubule cytoskeleton during cell division. Changes in microtubule dynamics are essential for the formation and function of the mitotic spindle, and misregulation can lead to aneuploidy and cancer. Using in vitro reconstitution assays we show that the mitotic spindle protein Cytoskeleton-Associated Protein 2 (CKAP2) has a strong effect on nucleation of microtubules by lowering the critical tubulin concentration 100-fold. CKAP2 increases the apparent rate constant ka of microtubule growth by 50-fold and increases microtubule growth rates. In addition, CKAP2 strongly suppresses catastrophes. Our results identify CKAP2 as the most potent microtubule growth factor to date. These finding help explain CKAP2s role as an important spindle protein, proliferation marker, and oncogene.

category: biophysics


title: Imaging biological samples by integrated differential phase contrast (iDPC) STEM technique

abstract: Scanning transmission electron microscopy (STEM) is a powerful imaging technique and has been widely used in current material science research. The attempts of applying STEM into biological research have been going on for decades while applications have still been limited because of the existing bottlenecks in dose efficiency and non-linearity in contrast. Recently, integrated differential phase contrast (iDPC) STEM technique emerged and achieved a linear phase contrast imaging condition, while resolving signals of light elements next to heavy ones even at low electron dose. This enables successful investigation of beam sensitive materials. Here, we investigate iDPC-STEM advantages in biology, in particular, chemically fixed and resin embedded biological tissues. By comparing results to the conventional TEM, we have found that iDPC-STEM not only shows better contrast but also resolves more structural details at molecular level, including conditions of extremely low dose and minimal heavy-atom staining. For thick sample sections, iDPC-STEM is particularly advantageous. Unlike TEM, it avoids contrast inversion canceling effects, and by adjusting the depth of focus, fully preserves the contrast of relevant features along with the sample. In addition, using depth-sectioning, iDPC-STEM enables resolving in-depth structural variation. Our work suggests that promising, wide and attractive applications of iDPC-STEM in biological research are opening.


title: Somatic point mutations are enriched in long non-coding RNAs with possible regulatory function in breast cancer

abstract: De novo somatic point mutations identified in breast cancer are predominantly non-coding and typically attributed to altered regulatory elements such as enhancers and promoters. However, while the non-coding RNAs (ncRNAs) form a large portion of the mammalian genome, their biological functions are mostly poorly characterized in cancers. In this study, using a newly developed tool, SomaGene, we reanalyze de novo somatic point mutations from the International Cancer Genome Consortium (ICGC) whole-genome sequencing data of 1,855 breast cancers. We identify 929 candidates of ncRNAs that are significantly and explicitly mutated in breast cancer samples. By integrating data from the ENCODE regulatory features and FANTOM5 expression atlas, we show that the candidate ncRNAs in breast cancer samples significantly enrich for active chromatin histone marks (1.9 times), CTCF binding sites (2.45 times), DNase accessibility (1.76 times), HMM predicted enhancers (2.26 times) and eQTL polymorphisms (1.77 times). Importantly, we show that the 929 ncRNAs contain a much higher level (3.64 times) of breast cancer-associated genome-wide association (GWAS) single nucleotide polymorphisms (SNPs) than genome-wide expectation. Such enrichment has not been seen with GWAS SNPs from other diseases. Using breast tissue related Hi-C data we then show that 82% of our candidate ncRNAs (1.9 times) significantly interact with the promoter of protein-coding genes, including previously known cancer-associated genes, suggesting the critical role for candidate ncRNA genes in activation of essential regulators of development and differentiation in breast cancer. We provide an extensive web-based resource (http://ncrna.ictic.sharif.edu), to communicate our results with the research community. Our list of breast cancer-specific ncRNA genes has the potential to provide a better understanding of the underlying genetic causes of breast cancer. Lastly, the tool developed in this study can be used in the analysis of somatic mutations in all cancers.

category: cancer biology


title: Facilitation of TRKB activation by the angiotensin II receptor type-2 (AT2R) agonist C21

abstract:
Blockers of angiotensin II type-1 receptor (AT1R) exert antidepressant-like effects by indirectly facilitating the activation of the angiotensin II type-2 receptor (AT2R), which leads to increased surface expression and transactivation of tropomyosin-related kinase B receptors (TRKB). Compound 21 (C21) is a non-peptide AT2R agonist that produces neuroprotective effects. However, the behavioral effects of C21 and its involvement with the brain-derived neurotrophic factor (BDNF)-TRKB system still need further investigation.

The aim of the present study was to assess the effect of C21 on the activation of TRKB and its consequences on conditioned fear. The administration of C21 (0.1-10M/15min) increased the surface levels of TRKB but was not sufficient to increase the levels of phosphorylated TRKB (pTKB) in cultured cortical neurons from rat embryos. Consistent with increased TRKB surface expression, C21 (10M/15min or 3 days) facilitated the effect of BDNF (0.1ng/ml/15min) on pTRKB in these cells. In contextual fear conditioning, the freezing time of C21-treated (administered intranasally) wild-type mice was decreased compared to the vehicle-treated group, but no effect of C21 was observed in BDNF.het animals. We observed no effect of C21 in the elevated plus-maze test for anxiety.

Taken together, our results indicate that C21 facilitated BDNF effect by increasing the levels of TRKB on the cell surface and reduced the freezing time of mice in a BDNF-dependent manner, but not through a general anxiolytic-like effect.

category: pharmacology and toxicology


title: Spectral estimation of in-vivo wheat chlorophyll a/b ratio under contrasting water availabilities

abstract: To meet the ever-growing global population necessities, it is needed to identify climate change-relevant plant traits to integrate into breeding programs. Developing new tools for fast and accurate estimation of chlorophyll parameters, chlorophyll a (Chl-a), chlorophyll b (Chl-b) content, and their ratio (Chl-a/b), can promote breeding programs of wheat with enhanced climate adaptively. Spectral reflectance of leaves is affected by changes in pigments concentration and can be used to estimate chlorophyll parameters. The current study identified and validated the top spectral indices known and developed new vegetation indices (VIs) for Chl-a and Chl-b content estimation and used them to non-destructively estimate Chl-a/b values and compare them to hyperspectral estimations. Three wild emmer introgression lines, with contrasting drought stress responsiveness dynamics, were selected. Well and limited irrigation irrigation regimes were applied. The wheat leaves were spectrally measured with a handheld spectrometer to acquire their reflectance at the 330 to 790 nm range. Regression models based on calculated VIs as well as all hyperspectral curves were calibrated and validated against chlorophyll extracted values. The developed VIs resulted in high accuracy of Chl-a and Chl-b estimation allowing indirect non-destructive estimation of Chl-a/b with root mean square error (RMSE) values that could fit 6 to 10 times in the range of the measured values. They also performed similarly to the hyperspectral models. Altogether, we present here a new tool for a non-destructive estimation of Chl-a/b which can serve as a basis for future breeding efforts of climate-resilience wheat as well as other crops.

category: physiology


title: Dynamics of synthetic yeast chromosome evolution shaped by hierarchical chromatin organization

abstract: Synthetic genomics provides a distinct approach to systematically explore the process of genome evolution in a dynamic manner. SCRaMbLE is an evolutionary system intrinsic to the synthetic yeast genome that can rapidly drive structural variations. Here, we detected over 260,000 rearrangement events after SCRaMbLEing of a synthetic strain harboring 6 synthetic yeast chromosomes. Remarkably, it was found that the rearrangement events exhibited a specific landscape of rearrangement frequency. We further revealed that the landscape was shaped by coordinated effects of chromatin accessibility and spatial contact probability. The rearrangements tend to occur in 3D spatially proximal and chromatin-accessible regions. Enormous numbers of rearrangements by SCRaMbLE provide a driving force to potentiate directed genome evolution and investigation of the population genomic resource offer mechanistic insights into the dynamic genome evolution.

category: synthetic biology


title: Protein kinase Cδ is essential for the IgG response against T cell-independent type 2 antigens and commensal bacteria

abstract: Antigens (Ags) with multivalent and repetitive structure elicit IgG production in a T cell-independent manner. However, the mechanisms by which such T cell-independent type-2 (TI-2) Ags induce IgG responses remain obscure. Here we report that BCR engagement with a TI-2 Ag but not with a T cell-dependent (TD) Ag was able to induce the transcription of activation-induced cytidine deaminase (AID) and efficient class switching to IgG3 upon co-stimulation with IL-1 or IFN-. TI-2 Ags strongly induced the phosphorylation of protein kinase C (PKC){delta} and PKC{delta} mediated the AID transcription through the induction of BATF, the key transcriptional regulator of AID expression. In PKC{delta}-deficient mice, production of IgG was intact against TD Ag but abrogated against typical TI-2 Ags as well as commensal bacteria, and experimental disruption of the gut epithelial barrier resulted in fatal bacteremia. Thus, our results revealed novel molecular requirements for class-switching in the TI-2 response and highlighted its importance in homeostatic commensal-specific IgG production.

category: immunology


title: Integration of the cyanophage-encoded phosphate binding protein into the cyanobacterial phosphate uptake system

abstract: To acquire phosphorus, cyanobacteria use the typical bacterial ABC-type phosphate transporter, which is composed of a periplasmic high-affinity phosphate-binding protein PstS and a channel formed by two transmembrane proteins PstC and PstA. The pstS gene has been identified in the genomes of cyanophages that infect the unicellular cyanobacteria Prochlorococcus and Synechococcus. However, it is unknown how the cyanophage PstS interplays with the host PstC and PstA to function as a chimeric ABC transporter. Here we showed that the cyanophage P-SSM2 PstS protein was abundant in the infected Prochlorococcus NATL2A cells and the host phosphate uptake rate was enhanced after infection. This is consistent with our biochemical and structural analyses showing that the phage PstS protein is indeed a high-affinity phosphate-binding protein. We further modeled the complex structure of phage PstS with host PstCA and revealed three putative interfaces that may facilitate the formation of the chimeric ABC transporter. Our results provide insights into the molecular mechanism by which cyanophages enhance the phosphate uptake rate of cyanobacteria. Phosphate acquisition by infected bacteria can increase the phosphorus contents of released cellular debris and virus particles, which together constitute a significant proportion of the marine dissolved organic phosphorus pool.

category: microbiology


title: MCPH1 inhibits condensin II during interphase by regulating its SMC2-kleisin interface.

abstract: The dramatic change in morphology of chromosomal DNAs between interphase and mitosis is one of the defining features of the eukaryotic cell cycle. Two types of enzymes, namely cohesin and condensin confer the topology of chromosomal DNA by extruding DNA loops. While condensin normally configures chromosomes exclusively during mitosis, cohesin does so during interphase. The processivity of cohesins LE during interphase is limited by a regulatory factor called WAPL, which induces cohesin to dissociate from chromosomes via a mechanism that requires dissociation of its kleisin from the neck of SMC3. We show here that a related mechanism may be responsible for blocking condensin II from acting during interphase. Cells from patients carrying mutations in the Mcph1 gene undergo premature chromosome condensation but it has never been established for certain whether MCPH1 regulates condensin II directly. We show that deletion of Mcph1 in mouse embryonic stem cells unleashes an activity of condensin II that triggers formation of compact chromosomes in G1 and G2 phases, which is accompanied by enhanced mixing of A and B chromatin compartments, and that this occurs even in the absence of CDK1 activity. Crucially, inhibition of condensin II by MCPH1 depends on the binding of a short linear motif within MCPH1 to condensin IIs NCAPG2 subunit. We show that the activities of both Cohesin and Condensin II may be restricted during interphase by similar types of mechanisms as MCPH1s ability to block condensin IIs association with chromatin is abrogated by the fusion of SMC2 with NCAPH2. Remarkably, in the absence of both WAPL and MCPH1, cohesin and condensin II transform chromosomal DNAs of G2 cells into chromosomes with a solenoidal axis showing that both SMC complexes must be tightly regulated to adjust both the chromatids structure and their segregation.

category: cell biology


title: Patterns of mesozooplankton community composition and vertical fluxes in the global ocean

abstract: Vertical variations in physical and chemical conditions drive changes in marine zooplankton community diversity and composition. In turn, zooplankton communities play a critical role in regulating the transfer of organic matter produced in the surface ocean to deeper layers. Yet, the links between zooplankton community composition and the strength of vertical fluxes of particles remain elusive, especially on a global scale. Here, we provide a comprehensive analysis of variations in zooplankton community composition and vertical particle flux in the upper kilometer of the global ocean. Zooplankton samples were collected across five depth layers and vertical particle fluxes were assessed using continuous profiles of the Underwater Vision Profiler (UVP5) at 57 stations covering seven ocean basins. Zooplankton samples were analysed using a Zooscan and individual organisms were classified into 19 groups for the quantitative analyses. Zooplankton abundance, biomass and vertical particle flux decreased from the surface to 1000m depth at all latitudes. The zooplankton abundance decrease rate was stronger at sites characterised by oxygen minima (< 5{micro}mol O2.kg-1) where most zooplankton groups showed a marked decline in abundance, except the jellyfishes, molluscs, annelids, large protists and a few copepod families. The attenuation rate of vertical particle fluxes was weaker at such oxygen-depleted sites. Canonical redundancy analyses showed that the epipelagic zooplankton community composition depended on the community structure of surface phytoplankton and the quantity and the quality of the produced particulate organic matter. We provide a consistent baseline of plankton community structure together with estimates of vertical flux and a contribution to our understanding of global zooplankton dynamics in the upper kilometer of the global ocean. Our results further suggest that future changes in surface phytoplankton composition and mesopelagic oxygen loss might lead to profound changes in zooplankton abundance and community structure in both the euphotic and mesopelagic ocean. These changes may affect the vertical export and hereby the strength of the biological carbon pump

category: ecology


title: Tissue-engineered collagenous fibrous cap models to systematically elucidate atherosclerotic plaque rupture.

abstract:
A significant amount of vascular thrombotic events is associated with rupture of the fibrous cap that overlie atherosclerotic plaques. Cap rupture is however difficult to predict due to the heterogenous composition of the plaque, unknown material properties, and the stochastic nature of the event. Here, we aim to create tissue engineered human fibrous cap models with a variable but controllable collagen composition, suitable for mechanical testing, to scrutinize the reciprocal relationships between composition and mechanical properties.

Myofibroblasts were cultured in 1 x 1.5 cm-sized fibrin-based constrained gels for 21 days according to established (dynamic) culture protocols (i.e. static, intermittent or continuous loading) to vary collagen composition (e.g. amount, type and organization). At day 7, a soft 2 mm O fibrin inclusion was introduced in the centre of each tissue to mimic the soft lipid core, simulating the heterogeneity of a plaque.

Results demonstrate reproducible collagenous tissues, that mimic the bulk mechanical properties of human caps and vary in collagen composition due to the presence of an successfully integrated soft inclusion and the culture protocol applied. The models can be deployed to assess tissue mechanics, evolution and failure of fibrous caps or complex heterogeneous tissues in general.

category: bioengineering


title: Multi-omics analysis identifies essential regulators of mitochondrial stress response in two wild-type C. elegans strains

abstract: The mitochondrial unfolded protein response (UPRmt) is a promising pharmacological target for aging and age-related diseases. However, the integrative analysis of the impact of UPRmt activation on different layers of signaling in animals with a different genetic background is lacking. In this study, we applied systems approaches to investigate the effect of UPRmt induced by administering doxycycline (Dox) on transcriptome, proteome, lipidome, and metabolome in two genetically divergent C. elegans strains. We found that Dox prolongs lifespan of both worm strains through pathways in both shared and strain-specific manners. From the integrated omics datasets, we observed a strong impact of Dox on mitochondrial functions, detected upregulated defense response and lipid metabolism, identified decreased triglycerides and lowered metabolome profiles in both strains. This conserved phenomic footprint has great translational value as it indicates that the beneficial effects of Dox-induced UPRmt on health and lifespan are consistent across different genetic backgrounds.

category: systems biology


title: Phylogenomic analyses of echinoid diversification prompt a re-evaluation of their fossil record

abstract: Echinoids are key components of modern marine ecosystems. Despite a remarkable fossil record, the emergence of their crown group is documented by few specimens of unclear affinities, rendering much of their early history uncertain. The origin of sand dollars, one of its most distinctive clades, is also unclear due to an unstable phylogenetic context and discrepancies between molecular divergence times and fossil evidence. We employ seventeen novel genomes and transcriptomes to build a phylogenomic dataset with a near-complete sampling of major lineages. With it, we revise the phylogeny and divergence times of echinoids, and place their history within the broader context of echinoderm evolution. We also introduce the concept of a chronospace--a multidimensional representation of node ages--and use it to explore the effects of using alternative gene samples, models of molecular evolution, and clock priors. We find the choice of clock model to have the strongest impact on divergence times, while the use of site-heterogeneous models shows little effects. The choice of loci shows an intermediate impact, affecting mostly deep Paleozoic nodes, for which clock-like genes recover dates more congruent with fossil evidence. Our results reveal that crown group echinoids originated in the Permian and diversified rapidly in the Triassic, despite the relative lack of fossil evidence for this early diversification. We also clarify the relationships among sand dollars and their close relatives, showing that the genus Apatopygus represents a relict lineage with a deep Jurassic origin. Surprisingly, the origin of sand dollars is confidently dated to the Cretaceous, implying ghost ranges spanning approximately 50 million years, a remarkable discrepancy with their rich fossil record.

category: evolutionary biology


title: CRISPR screens for host factors critical for infection by SARS-CoV-2 variants of concern identify GATA6 as a central modulator of ACE2.

abstract: The global spread of SARS-CoV-2 led to the most challenging pandemic in this century, posing major economic and health challenges worldwide. Revealing host genes essential for infection by multiple variants of SASR-CoV-2 can provide insights into the virus pathogenesis, and facilitates the development of novel broad-spectrum host-directed therapeutics. Here, employing genome-scale CRISPR screens, we provide a comprehensive data-set of cellular factors that are exploited by WT-SARS-CoV-2 as well as two additional recently emerged variants of concerns (VOCs), Alpha and Beta. These screens identified known and novel host factors critical for SARS-CoV-2 infection, including various components belonging to the Clathrin-dependent transport pathway, ubiquitination and Heparan sulfate biogenesis. In addition, the host phosphatidylglycerol biosynthesis processes appeared to have major anti-viral functions. Comparative analysis of the different VOCs revealed the host factors KREMEN2 and SETDB1 as potential unique candidates required only to the Alpha variant, providing a possible explanation for the increased infectivity of this variant. Furthermore, the analysis identified GATA6, a zinc finger transcription factor, as an essential pro-viral gene for all variants inspected. We revealed that GATA6 directly regulates ACE2 transcription and accordingly, is critical for SARS-CoV-2 cell entry. Analysis of clinical samples collected from SARS-CoV-2 infected individuals showed an elevated level of GATA6, indicating the important role GATA6 may be playing in COVID-19 pathogenesis. Finally, pharmacological inhibition of GATA6 resulted in down-modulation of ACE2 and consequently to inhibition of the viral infectivity. Overall, we show GATA6 represents a target for the development of anti-SARS-CoV-2 therapeutic strategies and reaffirm the value of the CRISPR loss-of-function screens in providing a list of potential new targets for therapeutic interventions.


title: The SARS-CoV-2 reproduction number R0 in cats

abstract: Domestic cats are susceptible to SARS-CoV-2 virus infection and given that they are in close contact with people, assessing the potential risk cats represent for the transmission and maintenance of SARS-CoV-2 is important. Assessing this risk implies quantifying transmission from humans-to-cats, from cats-to-cats and from cats-to-humans. Here we quantified the risk of cat-to-cat transmission by reviewing published literature describing transmission either experimentally or under natural conditions in infected households. Data from these studies were collated to quantify the SARS-CoV-2 reproduction number R0 among cats. The estimated R0 was significantly higher than 1, hence cats could play a role in the transmission and maintenance of SARS-CoV-2. Questions that remain to be addressed are the risk of transmission from humans-to-cats and cats-to-humans. Further data on household transmission and data on virus levels in both the environment around infected cats and their exhaled air could be a step towards assessing these risks.


title: HLA-dependent variation in SARS-CoV-2 CD8+ T cell cross-reactivity with human coronaviruses

abstract: Pre-existing T cell immunity to SARS-CoV-2 in individuals without prior exposure to SARS-CoV-2 has been reported in several studies. While emerging evidence hints toward prior exposure to common-cold human coronaviruses (HCoV), the extent of- and conditions for-cross-protective immunity between SARS-CoV-2 and HCoVs remain open. Here, by leveraging a comprehensive pool of publicly available functionally evaluated SARS-CoV-2 peptides, we report 126 immunogenic SARS-CoV-2 peptides with high sequence similarity to 285 MHC-presented target peptides from at least one of four HCoV, thus providing a map describing the landscape of SARS-CoV-2 shared and private immunogenic peptides with functionally validated T cell responses. Using this map, we show that while SARS-CoV-2 immunogenic peptides in general exhibit higher level of dissimilarity to both self-proteome and -microbiomes, there exist several SARS-CoV-2 immunogenic peptides with high similarity to various human protein coding genes, some of which have been reported to have elevated expression in severe COVID-19 patients. We then combine our map with a SARS-CoV-2-specific TCR repertoire data from COVID-19 patients and healthy controls and show that whereas the public repertoire for the majority of convalescent patients are dominated by TCRs cognate to private SARS-CoV-2 peptides, for a subset of patients, more than 50% of their public repertoires that show reactivity to SARS-CoV-2, consist of TCRs cognate to shared SARS-CoV-2-HCoV peptides. Further analyses suggest that the skewed distribution of TCRs cognate to shared and private peptides in COVID-19 patients is likely to be HLA-dependent. Finally, by utilising the global prevalence of HLA alleles, we provide 10 peptides with known cognate TCRs that are conserved across SARS-CoV-2 and multiple human coronaviruses and are predicted to be recognised by a high proportion of the global population. Overall, our work indicates the potential for HCoV-SARS-CoV-2 reactive CD8+ T cells, which is likely dependent on differences in HLA-coding genes among individuals. These findings may have important implications for COVID-19 heterogeneity and vaccine-induced immune responses as well as robustness of immunity to SARS-CoV-2 and its variants.


title: Previously unrecognized non-reproducible antibody-antigen interactions and their implications for diagnosis of viral infections including COVID-19

abstract: Antibody-antigen (Ab-Ag) interactions are canonically described by a model which exclusively accommodates non-interaction (0) or reproducible-interaction (RI) states, yet this model is inadequate to explain often-encountered non-reproducible signals. Here, by monitoring diverse experimental systems and confirmed COVID-19 clinical sera using a peptide microarray, we observed that non-specific interactions (NSI) comprise a substantial proportion of non-reproducible antibody-based results. This enabled our discovery and capacity to reliably identify non-reproducible Ab-Ag interactions (NRI), as well as our development of a powerful explanatory model ("0-RI-NRI-Hook four-state model") that is [mAb]-dependent, regardless of specificity, which ultimately shows that both NSI and NRI are not predictable yet certain-to-happen. In experiments using seven FDA-approved mAb drugs, we demonstrated the use of NSI counts in predicting epitope type. Beyond challenging the centrality of Ab-Ag interaction specificity data in serology and immunology, our discoveries also facilitated the rapid development of a serological test with uniquely informative COVID-19 diagnosis performance.


title: The Tabula Sapiens: a single cell transcriptomic atlas of multiple organs from individual human donors

abstract: Molecular characterization of cell types using single cell transcriptome sequencing is revolutionizing cell biology and enabling new insights into the physiology of human organs. We created a human reference atlas comprising nearly 500,000 cells from 24 different tissues and organs, many from the same donor. This atlas enabled molecular characterization of more than 400 cell types, their distribution across tissues and tissue specific variation in gene expression. Using multiple tissues from a single donor enabled identification of the clonal distribution of T cells between tissues, the tissue specific mutation rate in B cells, and analysis of the cell cycle state and proliferative potential of shared cell types across tissues. Cell type specific RNA splicing was discovered and analyzed across tissues within an individual.


title: The Tabula Sapiens: a multiple organ single cell transcriptomic atlas of humans


title: Regulation of a bacterial histidine kinase by a phase separating scaffolding protein

abstract: Scaffolding proteins customize the response of signaling networks to support cell development and behaviors. We investigated how the bacterial scaffolding protein PodJ regulates the histidine kinase PleC involved in the asymmetric cell division of Caulobacter crescentus. We reconstituted the PleC-PodJ signaling complex through both heterologous expression in E. coli and in vitro studies. In vitro PodJ phase separates as a biomolecular condensate that recruits and inhibits PleC kinase activity. By constructing an in vivo PleC-CcaS chimeric histidine kinase reporter assay, we have demonstrated how PodJ leverages its intrinsically disordered region (IDR) to bind and regulate PleC-CcaS signaling. Moreover, we observed that full-length PodJL regulates PleC-CcaS signaling, while a truncated PodJs could not regulate signaling activity. These results support a model where PodJ biomolecular condensate formation regulates the localization and activity of the cell fate determining kinase PleC.


title: Co-transcriptional RNA strand displacement circuits

abstract: Engineered molecular circuits that process information in biological systems could address emerging human health and biomanufacturing needs. However, such circuits can be difficult to rationally design and scale. DNA-based strand displacement reactions have demonstrated the largest and most computationally powerful molecular circuits to date but are limited in biological systems due to the difficulty in genetically encoding components. Here, we develop scalable co-transcriptional RNA strand displacement (ctRSD) circuits that are rationally programmed via base pairing interactions. ctRSD addresses the limitations of DNA-based strand displacement circuits by isothermally producing circuit components via transcription. We demonstrate the programmability of ctRSD in vitro by implementing logic and amplification elements, and multi-layer signaling cascades. Further, we show ctRSD kinetics are accurately predicted by a simple model of coupled transcription and strand displacement, enabling model-driven design. We envision ctRSD will enable rational design of powerful molecular circuits that operate in biological systems, including living cells.


title: Myotubularin-related phosphatase 5 is a critical determinant of autophagy in neurons

abstract: Autophagy is a conserved, multi-step process of capturing proteolytic cargo in autophagosomes for lysosome degradation. The capacity to remove toxic proteins that accumulate in neurodegenerative disorders attests to the disease-modifying potential of the autophagy pathway. However, neurons respond only marginally to conventional methods for inducing autophagy, limiting efforts to develop therapeutic autophagy modulators for neurodegenerative diseases. The determinants underlying poor autophagy induction in neurons and the degree to which neurons and other cell types are differentially sensitive to autophagy stimuli are incompletely defined. Accordingly, we sampled nascent transcript synthesis and stabilities in fibroblasts, induced pluripotent stem cells (iPSCs) and iPSC-derived neurons (iNeurons), thereby uncovering a neuron-specific stability of transcripts encoding myotubularin-related phosphatase 5 (MTMR5). MTMR5 is an autophagy suppressor that acts with its binding partner, MTMR2, to dephosphorylate phosphoinositides critical for autophagy initiation and autophagosome maturation. We found that MTMR5 is necessary and sufficient to suppress autophagy in iNeurons and undifferentiated iPSCs. Using optical pulse labeling to visualize the turnover of endogenously-encoded proteins in live cells, we observed that knockdown of MTMR5 or MTMR2, but not MTMR9, significantly enhances neuronal degradation of TDP-43, an autophagy substrate implicated in several neurodegenerative diseases. Accordingly, our findings establish a regulatory mechanism of autophagy intrinsic to neurons and targetable for clearing disease-related proteins in a cell type-specific manner. In so doing, our results not only unravel novel aspects of neuronal biology and proteostasis, but also elucidate a strategy for modulating neuronal autophagy that could be of high therapeutic potential for multiple neurodegenerative diseases.

category: neuroscience


title: Single-cell genomics reveals region-specific developmental trajectories underlying neuronal diversity in the prenatal human hypothalamus

abstract: The hypothalamus is critically important for regulating most autonomic, metabolic, and behavioral functions essential for life and species propagation, yet a comprehensive understanding of neuronal subtypes and their development in the human brain is lacking. Here, we characterized the prenatal human hypothalamus by sequencing the transcriptomes of 45,574 single-cells from 12 embryos, spanning gestational weeks 4 through 25. These cells describe a temporal trajectory from proliferative stem cell populations to maturing neurons and glia, including 38 distinct excitatory and inhibitory neuronal subtypes. Merging these data with paired samples from the cortex and ganglionic eminences (GE) revealed two distinct neurogenesis pathways, one shared between GE and hypothalamus and a second unique to cortex. Gene regulatory network modeling predicted that these distinct maturation trajectories involve the activation of region- and cell type-specific transcription factor networks. These results provide the first comprehensive transcriptomic view of human hypothalamus development at cellular resolution.


title: Structural snapshots of La Crosse virus polymerase reveal the mechanisms underlying Peribunyaviridae replication and transcription

abstract: Segmented negative-strand RNA bunyaviruses encode a multi-functional polymerase that performs genome replication and transcription. Here, we establish conditions for in vitro activity of La Crosse virus polymerase and visualize by cryo-electron microscopy its conformational dynamics, unveiling the precise molecular mechanics underlying its essential activities. Replication initiation is coupled to distal duplex promoter formation, endonuclease movement, prime-and-realign loop extension and closure of the polymerase core that direct the template towards the active site. Transcription initiation depends on C-terminal region closure and endonuclease movements that firstly prompt primer cleavage and secondly promote primer entry in the active site. Product realignment after priming, observed in replication and transcription, is triggered by the prime-and-realign loop. Switch to elongation results in polymerase reorganization and core region opening to facilitate template-product duplex formation in the active site cavity. The detailed uncovered mechanics will be crucial for future design of antivirals counteracting bunyaviral life-threatening pathogens.


title: The efficacy of antimicrobial agents is decreased in a polymicrobial environment

abstract: The airways of people with cystic fibrosis (CF) often harbour diverse polymicrobial communities. These airway infections can be impossible to resolve though antibiotic intervention, even though isolates of the individual species present are susceptible to the treatment when tested in vitro. This suggests that susceptibility to antimicrobial agents may be altered in the presence of other microbial species. In this work, we investigate how polymicrobial cultures of key CF-associated species respond to challenge with species-specific antimicrobial agents; colistin (targets Pseudomonas aeruginosa), fusidic acid (targets Staphylococcus aureus) and fluconazole (targets Candida albicans). We found that, compared with growth in axenic cultures, the target organism was protected (sometimes by several orders of magnitude) from the effect(s) of the antimicrobial agent when grown in a polymicrobial culture. This decreased antimicrobial efficacy in polymicrobial cultures was found to have both phenotypic and inherited components. Whole genome sequencing of the colistin-resistant P. aeruginosa isolates revealed single nucleotide polymorphisms and indels in genes encoding lipopolysaccharide (LPS) biosynthesis or pilus biogenesis. Colistin resistance associated with loss-of-function mutations in the LPS biosynthetic gene, wzy, could be complemented by expression of the wild-type wzy gene in trans. Our findings indicate that the polymicrobial nature of the CF airways is likely to have a significant impact on the clinical response to antimicrobial therapy.


title: Genotype of Human Papilloma virus in Male Genital Warts In Korean Men and Review of Literature

abstract:
PurposeGenital warts are one of the most common sexually transmitted infections and are known to develop due to human papillomavirus (HPV) infection, especially HPV types 6 and 11. However, their prevalence and subtypes in male genital warts remains poorly defined. HPV vaccine is administered to men in part to prevent anogenital warts and it is important to investigate their expected impact in male anogenital warts.

Materials and MethodsWe have herein conducted a multicenter, prospective study to analyze HPV type distribution in genital warts of 1000 Korean men by using DNA microarray that can detect 40 types of genital HPV.

Results1000 out of 1015 genital warts showed HPV DNA. Out of 1000 HPV-positive samples, 18.8% showed mixed infection and 81.2% showed single infection. Of 18 high-risk (16.2%) and 14 low-risk (94.3%) HPV types detected, the most common type of HPV types were HPV6 (59.5%), followed by HPV11 (24.3%), HPV16 (5.8%), HPV91 (5.3%), HPV40 (3.3%). 85.9% showed the 9 HPV types covered by the vaccine. Sixteen of the 200 HPV specimens submitted for sequencing showed discrepant results compared to the DNA sequencing.

ConclusionsMale genital warts predominantly show low-risk type HPV (HPV 6 and 11). However, high-risk HPV is not uncommon and the role of high-risk HPV in genital warts may be considered. The Gardasil 9 HPV vaccine is expected to provide protection against about >80% of male genital warts. Further HPV typing studies in male genital warts are necessary in other races and geographical areas to define the role and management of high-risk type HPV in male genital warts.


title: Plant-associated Pseudomonas aeruginosa harbor multiple virulence traits essential for mammalian infection

abstract: Pseudomonas aeruginosa is a leading opportunistic pathogen capable of causing fatal infections in immunocompromised individuals and patients with degenerative lung diseases. Agricultural soil and plants are the vast reservoirs of this dreaded pathogen. However, there have been limited attempts to analyze the pathogenicity of P. aeruginosa strains associated with edible vegetable plants. This study aims to elucidate the virulence attributes of P. aeruginosa strains isolated from the rhizosphere and endophytic niches of cucumber, tomato, eggplant, and chili collected from agricultural fields. Virulence of the agricultural strains was compared to three previously characterized clinical isolates. Our results showed that 50% of the plant-associated strains formed significant levels of biofilm and exhibited swarming motility. Nearly 80% of these strains produced considerable levels of rhamnolipid and exhibited at least one type of lytic activity (hemolysis, proteolysis, and lipolysis). Their virulence was also assessed based on their ability to suppress the growth of plant pathogens (Xanthomonas oryzae, Pythium aphanidermatum, Rhizoctonia solani, and Fusarium oxysporum) and kill a select nematode (Caenorhabditis elegans). The plant-associated strains showed significantly higher virulence against the bacterial phytopathogen whereas the clinical strains had significantly higher antagonism against the fungal pathogens. In C. elegans slow-killing assay, the clinical strains caused 50-100% death while a maximum of 40% mortality was induced by the agricultural strains. This study demonstrates that some of the P. aeruginosa strains associated with edible plants harbor multiple virulence traits. Upon infection of humans or animals, these strains may evolve to be more pathogenic and pose a significant health hazard.


title: Growth and immunolocalisation of the brown alga Ectocarpus in a microfluidic environment

abstract: PDMS chips have proven to be suitable environments for the growth of several filamentous organisms. However, depending on the specimen, the pattern of growth and cell differentiation has been rarely investigated. We monitored the developmental pattern of the brown alga Ectocarpus inside a PDMS lab-on-chip. Two main methods of inoculation of the lab-on-chip were tested, i.e. by injection of spores or by insertion of sporophyte filaments into the chamber. Growth rate, growth trajectory, cell differentiation, and branching were the main development steps that were monitored for 20 days inside 25 m or 40 m parallel channels under standard light and temperature conditions. They were shown to be similar to those observed in non-constrained in-vitro conditions. Labelling of Ectocarpus cell wall polysaccharides - both with calcofluor for cellulose, and by immunolocalisation for alginates with monoclonal antibodies-showed expected patterns when compared to open space growth using either epifluorescence or confocal microscopy. Overall this article describes the experimental conditions for observing and studying the basic unaltered processes of brown algal growth using microfluidic technology, which provides the basis for future biochemical and biological research.


title: Lipid-induced polymorphic amyloid fibrils formation by α-synuclein.

abstract: Many proteins that self-assemble into amyloid and amyloid-like fibres can adopt polymorphic forms. These forms have been observed both in vitro and in vivo and can arise through variations in the steric-zipper interactions between {beta}-sheets, variations in the arrangements between protofilaments, and differences in the number of protofilaments that make up a given fibre class. Different polymorphs which arise from the same precursor molecule not only exhibit different levels of toxicity, but importantly can contribute to different disease conditions. In this work, we show that in the presence of 1,2-dimyristoyl-sn-glycero-3-phospho-L-serine, a highly abundant lipid in the plasma membrane of neurons, the aggregation of -synuclein is markedly accelerated and yields a diversity of polymorphic forms under identical experimental conditions. This morphological diversity includes thin and curly amyloid fibrils, helical and twisted ribbons, nanotubes and flat sheets. TEM analysis of fibrils sampled from the early stage of the growth phase shows the presence of helical and twisted ribbons, indicating that these morphological variants form at the early stages of aggregation. Total internal reflection fluorescence microscopy (TIRFM) indicated the presence of lipids collocated with the mature fibrils. This finding has important implication as the presence of -synuclein with co-localized high lipid content has been reported in Lewy bodies, the pathological hallmark of Parkinsons disease and other synucleinopathies. Thus, the present study demonstrates that an interface, such as that provided by a lipid membrane, can not only modulate the kinetics of -synuclein amyloid aggregation but also plays an important role in the formation of morphological variants by incorporating lipid molecules in the process of amyloid fibril formation.


title: Deficient thalamo-cortical networks dynamics and sleep homeostatic processes in a redox dysregulation model relevant to schizophrenia.

abstract: A growing body of evidence implicates thalamo-cortical oscillations with the neuropathophysiology of schizophrenia (SZ) in both mice and humans. Yet, the precise mechanisms underlying sleep perturbations in SZ remain unclear. Here, we characterised the dynamics of thalamo-cortical networks across sleep-wake states in a mouse model carrying a mutation in the enzyme glutathione synthetase gene (Gclm-/-) associated with SZ in humans. We hypothesised that deficits in parvalbumin immunoreactive cells in the thalamic reticular nucleus (TRN) and the anterior cingulate cortex (ACC) - caused by oxidative stress - impact thalamocortical dynamics, thus affecting non-rapid eye movement (NREM) sleep and sleep homeostasis. Using polysomnographic recordings in mice, we showed that KO mice exhibited a fragmented sleep architecture, similar to SZ patients and altered sleep homeostasis responses revealed by an increase in NREM latency and slow wave activities during the recovery period (SR). Although NREM sleep spindle rate during spontaneous sleep was similar in Gclm-/- and Gcml +/+, KO mice lacked a proper homeostatic response during SR. Interestingly, using multisite electrophysiological recordings in freely-moving mice, we found that high order thalamic network dynamics showed increased synchronisation, that was exacerbated during the sleep recovery period subsequent to SD, possibly due to lower bursting activity in TRN-antero dorsal thalamus circuit in KO compared to WT littermates. Collectively, these findings provide a mechanism for SZ associated deficits of thalamo-cortical neuron dynamics and perturbations of sleep architecture.


title: Engineered Bacteriophage T4 Nanoparticle as a Potential Targeted Activator of HIV-1 Latency in CD4+ Human T cells

abstract: The latent HIV-1 reservoir containing stably integrated and transcriptionally silent proviruses in CD4+ T cells is a major barrier for virus eradication. Targeted reactivation of the latent reservoir remains a major challenge in establishing a path for an HIV-1 cure. Here, we investigated the possibility of reactivating the HIV-1 reservoir by targeting engineered bacteriophage T4 capsid nanoparticles to reservoir cells. The surface lattice of the 120 x 86 nm phage capsid was arrayed with CD4 binding ligands such as recombinant CD4DARPin or the HIV-1 gp140 envelope protein. When exposed to either PBMCs or the resting CD4+ T cells in vitro, these nanoparticles caused T cells activation without inducing global T cell activation. Furthermore, the nanoparticles reactivated HIV-1 proviral transcription that led to virus assembly and release in the J-Lat cells, a cell line model of HIV-1 latency. Intriguingly, the observed T cell activation and HIV-1 latency reversal did not occur through the classic PKC or NFAT pathways suggesting the involvement of a yet unknown pathway. These studies demonstrate that engineered non-infectious bacteriophages could be potentially exploited for HIV-1 cure and other targeted T cell therapies.


title: Engineering well-expressed, V2-immunofocusing HIV-1 envelope glycoprotein membrane trimers for use in heterologous prime-boost vaccine regimens

abstract:
HIV-1 vaccine immunofocusing strategies have the potential to induce broadly reactive nAbs. Here, we engineered a panel of diverse, membrane-resident native HIV-1 trimers vulnerable to two broad targets of neutralizing antibodies (NAbs), the V2 apex and fusion peptide (FP). Selection criteria included i) high expression and ii) infectious function, so that trimer neutralization sensitivity can be profiled in pseudovirus assays. Initially, we boosted the expression of 17 candidate trimers by truncating gp41 and introducing a gp120-gp41 SOS disulfide to prevent gp120 shedding. "Repairs" were made to fill glycan holes and other strain-specific aberrations. A new neutralization assay allowed PV infection when our standard assay was insufficient. Trimers with exposed V3 loops, a target of non-neutralizing antibodies, were discarded. To try to increase V2-sensitivity, we removed clashing glycans and modified the V2 loops C-strand. Notably, a 167N mutation improved V2-sensitivity. Glycopeptide analysis of JR-FL trimers revealed near complete sequon occupation and that filling the N197 glycan hole was well-tolerated. In contrast, sequon optimization and inserting/removing other glycans in some cases had local and global "ripple" effects on glycan maturation and sequon occupation in the gp120 outer domain and gp41. V2 mAb CH01 selectively bound trimers with small high mannose glycans near the base of the V1 loop, thereby avoiding clashes. Knocking in a N49 glycan perturbs gp41 glycans via a distal glycan network effect, increasing FP NAb sensitivity - and sometimes improving expression. Finally, a biophysical analysis of VLPs revealed that i) [~]25% of particles bear Env spikes, ii) spontaneous particle budding is high and only increases 4-fold upon Gag transfection, and iii) Env+ particles express [~]30-40 spikes. Overall, we identified 7 diverse trimers with a range of sensitivities to two targets that should enable rigorous testing of immunofocusing vaccine concepts.

Author SummaryDespite almost 40 years of innovation, an HIV vaccine to induce antibodies that block virus infection remains elusive. Challenges include the unparalleled sequence diversity of HIVs surface spikes and its dense sugar coat that limits antibody access. However, a growing number of monoclonal antibodies from HIV infected donors provide vaccine blueprints. To date, these kinds of antibodies have been difficult to induce by vaccination. However, two antibody targets, one at the spike apex and another at the side of the spikes are more forgiving in their  demands for unusual antibodies. Here, we made a diverse panel of HIV spikes vulnerable at these two sites for later use as vaccines to try to focus antibodies on these targets. Our selection criteria for these spikes were: i) that the spikes, when expressed on particles, are infectious, allowing us to appraise our vaccine designs in an ideal manner; ii) that spikes are easy to produce by cells in quantities sufficient for vaccine use. Ultimately, we selected 7 trimers that will allow us to explore concepts that could bring us closer to an HIV vaccine.


title: Immunodominant surface epitopes power immune evasion in the African trypanosome

abstract:
The African trypanosome survives the immune response of its mammalian host by antigenic variation of its major surface antigen (the Variable Surface Glycoprotein, or VSG). Here we describe the antibody repertoires elicited by different VSGs. We show that the repertoires are highly restricted, directed predominantly to epitopes on the surface of the VSGs. They are also highly discriminatory: minor alterations within these exposed epitopes confer antigenically-distinct properties to these VSGs and elicit different repertoires. We propose that the patterned and repetitive nature of the VSG coat focuses host immunity to a restricted set of immunodominant epitopes per VSG, eliciting a highly stereotyped response, minimizing cross reactivity between different VSGs and facilitating prolonged immune evasion through epitope variation.

One Sentence SummaryHyper-focused antibody responses to variable antigenic coats allow pathogens to escape immune recognition.


title: Discovery of genes that modulate flavivirus replication in an interferon-dependent manner

abstract: Establishment of the interferon (IFN)-mediated antiviral state provides a crucial initial line of defense against viral infection. Numerous genes that contribute to this antiviral state remain to be identified. Using a loss-of-function strategy, we screened an original library of 1156 siRNAs targeting 386 individual curated human genes in stimulated microglial cells infected with Zika virus (ZIKV), an emerging RNA virus that belongs to the flavivirus genus. The screen recovered twenty-one potential host proteins that modulate ZIKV replication in an IFN-dependent manner, including the previously known IFITM3 and LY6E. Further characterization contributed to delineate the spectrum of action of these genes towards other pathogenic RNA viruses, including Hepatitis C virus and SARS-CoV-2. Our data revealed that APOL3 acts as a proviral factor for ZIKV and several other related and unrelated RNA viruses. In addition, we showed that MTA2, a chromatin remodeling factor, possesses potent flavivirus-specific antiviral functions. Our work identified previously unrecognized genes that modulate the replication of RNA viruses in an IFN-dependent way, opening new perspectives to target weakness points in the life cycle of these viruses.


title: ENGINEERING, DECODING AND SYSTEMS-LEVEL CHARACTERIZATION OF CHIMPANZEE CYTOMEGALOVIRUS

abstract: The chimpanzee cytomegalovirus (CCMV) is the closest relative of human CMV (HCMV). Because of the high conservation between these two species and the ability of human cells to fully support CCMV replication, CCMV holds great potential as a model system for HCMV. To make the CCMV genome available for precise and rapid gene manipulation techniques, we captured the genomic DNA of CCMV strain Heberling as a bacterial artificial chromosome (BAC). Selected BAC clones were reconstituted to infectious viruses, growing to similar high titers as parental CCMV. DNA sequencing confirmed the integrity of our clones and led to the identification of two polymorphic loci within the CCMV genome. To re-evaluate the CCMV coding potential, we analyzed the transcriptome and proteome of infected cells and identified several novel ORFs, splice variants, and regulatory RNAs. We further characterized the dynamics of CCMV gene expression and found that viral proteins cluster into five distinct temporal classes. In addition, our datasets revealed that the host response to CCMV infection and the de-regulation of cellular pathways are in line with known hallmarks of HCMV infection. In a first functional experiment, we investigated a proposed frameshift mutation in UL128 that was suspected to restrict CCMVs cell tropism. In fact, repair of this frameshift re-established productive CCMV infection in endothelial and epithelial cells, expanding the options of CCMV as an infection model. Thus, BAC-cloned CCMV can serve as a powerful tool for systematic approaches in comparative functional genomics, exploiting the close phylogenetic relationship between CCMV and HCMV.


title: ChAdOx1 NiV vaccination protects against lethal Nipah Bangladesh virus infection in African green monkeys

abstract:
Nipah virus (NiV) is a highly pathogenic and re-emerging virus which causes sporadic but severe infections in humans. Currently, no vaccines against NiV have been approved. We previously showed that ChAdOx1 NiV provides full protection against a lethal challenge with NiV Bangladesh (NiV-B) in hamsters. Here, we investigated the efficacy of ChAdOx1 NiV in the lethal African green monkeys (AGMs) NiV challenge model. AGMs were vaccinated either 4 weeks before challenge (prime vaccination), or 8 and 4 weeks before challenge with ChAdOx1 NiV (prime-boost vaccination). A robust humoral and cellular response was detected starting 14 days post initial vaccination. Upon challenge, control animals displayed a variety of signs and had to be euthanized between 5- and 7-days post inoculation. In contrast, vaccinated animals showed no signs of disease, and we were unable to detect infectious virus in all but one swab and all tissues. Importantly, no to limited antibodies against fusion protein or nucleoprotein IgG could be detected 42 days post challenge, suggesting that vaccination induced a very robust protective immune response preventing extensive virus replication.

One Sentence SummaryA single vaccination with ChAdOx1 NiV protects African green monkeys against lethal disease induced by Nipah virus inoculation.


title: ENKD1 is a centrosomal and ciliary microtubule-associated protein important for primary cilium assembly and Hedgehog signaling

abstract: Centrioles and cilia are conserved, microtubule-based structures critical for cell function and development. Their structural and functional defects cause cancer and developmental disorders. How microtubules are organized into ordered structures by microtubule-associated proteins (MAPs) and tubulin modifications is best understood during mitosis but is largely unexplored for the centrioles and the ciliary axoneme, which are composed of remarkably stable microtubules that maintain their length at steady state. In particular, we know little about the identity of the centriolar and ciliary MAPs and how they work together during the assembly and maintenance of the cilium and centriole. Here, we identified Enkurin domain containing 1 (ENKD1) as a component of the centriole wall and the axoneme in mammalian cells, and showed that it has extensive proximity interactions with these compartments and MAPs. Using in vitro and cellular assays, we found that ENKD1 is a new MAP that promotes microtubule polymerization and regulates microtubule organization and stability. Consistently, overexpression of ENKD1 increased tubulin polymerization and acetylation and disrupted microtubule organization. Cells depleted for ENKD1 were defective in ciliary length and content regulation and failed to respond to Hedgehog pathway activation. Together, our results establish ENKD1 as a new centriolar and ciliary MAP that regulate primary cilium structure and function, and advances our understanding of the functional and regulatory relationship between MAPs and the primary cilium.


title: Mechanisms of translation inhibition and suppression of Stress Granule formation by cisplatin

abstract: Platinum-based antineoplastic drugs, such as cisplatin, are commonly used to induce tumor cell death. Cisplatin is believed to induce apoptosis as a result of cisplatin-DNA adducts that inhibit DNA and RNA synthesis. Although idea that DNA damage underlines anti-proliferative effects of cisplatin is dominant in cancer research, there is a poor correlation between the degree of the cell sensitivity to cisplatin and the extent of DNA platination. Here, we propose a novel mechanism of cisplatin-mediated cytotoxicity. We show that cisplatin suppresses formation of Stress Granules (SGs), pro-survival RNA granules with multiple roles in cellular metabolism. Mechanistically, cisplatin inhibits cellular translation to promote disassembly of polysomes and aggregation of ribosomal subunits. As SGs are in equilibrium with polysomes, cisplatin-induced shift towards ribosomal aggregation suppresses SG formation and promotes cellular death. Our data also explain nephrotoxic, neurotoxic and ototoxic effects of cisplatin treatment.


title: A comparative network approach to assess the social-ecological underpinnings of zoonotic outbreaks at human-wildlife interfaces

abstract:
O_LIPandemics caused by wildlife-origin pathogens, like COVID-19, highlight the importance of understanding the ecology of zoonotic transmission and outbreaks among wildlife populations at human-wildlife interfaces. To-date, the relative effects of human-wildlife and wildlife-wildlife interactions on the likelihood of such outbreaks remain unclear.
C_LIO_LIIn this study, we used social network analysis and epidemiological Susceptible Infected Recovered (SIR) models, to track zoonotic outbreaks through wild animals joint propensities to engage in social-ecological co-interactions with humans, and their social grooming interactions with conspecifics.
C_LIO_LIWe collected behavioral and demographic data on 10 groups of macaques (Macaca spp.) living in (peri)urban environments across Asia. Outbreak sizes predicted by the SIR models were related to structural features of the social networks, and particular properties of individual animals connectivity within those networks.
C_LIO_LIOutbreak sizes were larger when the first-infected animal was highly central, in both types of networks. Across host-species, particularly for rhesus and bonnet macaques, the effects of network centrality on outbreak sizes were stronger through macaques human co-interaction networks compared to grooming networks.
C_LIO_LIOur findings, independent of pathogen-transmissibility, suggest that wildlife populations in the Anthropocene are vulnerable to zoonosis more so due to their propensities to aggregate around anthropogenic factors than their gregariousness with conspecifics. Thus, the costs of zoonotic outbreaks may outweigh the potential/perceived benefits of jointly interacting with humans to procure anthropogenic food. From One Health perspectives, animals that consistently interact with both humans and conspecifics across time and space are useful targets for disease spillover assessments and control.
C_LI


title: Joint interactions with humans may pose a higher risk of zoonotic outbreaks than interactions with conspecifics among wildlife populations at human-wildlife interfaces


title: Transcription factor regulation of eQTL activity across individuals and tissues

abstract:
Tens of thousands of genetic variants associated with gene expression (cis-eQTLs) have been discovered in the human population. These eQTLs are active in various tissues and contexts, but the molecular mechanisms of eQTL variability are poorly understood, hindering our understanding of genetic regulation across biological contexts. Since many eQTLs are believed to act by altering transcription factor (TF) binding affinity, we hypothesized that analyzing eQTL effect size as a function of TF level may allow discovery of mechanisms of eQTL variability. Using GTEx Consortium eQTL data from 49 tissues, we analyzed the interaction between eQTL effect size and TF level across tissues and across individuals within specific tissues and generated a list of 6,262 TF-eQTL interactions across 1,598 genes that are supported by at least two lines of evidence. These TF-eQTLs were enriched for various TF binding measures, supporting with orthogonal evidence that these eQTLs are regulated by the implicated TFs. We also found that our TF-eQTLs tend to overlap genes with gene-by-environment regulatory effects and to colocalize with GWAS loci, implying that our approach can help to elucidate mechanisms of context-specificity and trait associations. Finally, we highlight an interesting example of IKZF1 TF regulation of an APBB1IP gene eQTL that colocalizes with a GWAS signal for blood cell traits. Together, our findings provide candidate TF mechanisms for a large number of eQTLs and offer a generalizable approach for researchers to discover TF regulators of genetic variant effects in additional QTL datasets.

Author SummaryGene expression is regulated by local genomic sequence and can be affected by genetic variants. In the human population, tens of thousands of cis-regulatory variants have been discovered that are associated with altered gene expression across tissues, cell types, or environmental conditions. Understanding the molecular mechanisms of how these small changes in the genome sequence affect genome function would offer insight to the genetic regulatory code and how gene expression is controlled across tissues and environments. Current research efforts suggest that many regulatory variants effects on gene expression are mediated by them altering the binding of transcription factors, which are proteins that bind to DNA to regulate gene expression. Here, we exploit the natural variation of TF activity among 49 tissues and between 838 individuals to elucidate which TFs regulate which regulatory variants. We find 6,262 TF-eQTL interactions across 1,598 genes that are supported by at least two lines of evidence. We validate these interactions using functional genomic and experimental approaches, and we find indication that they may pinpoint mechanisms of environment-specific genetic regulatory effects and genetic variants associated to diseases and traits.


title: Hierarchical clustering optimizes the tradeoff between compositionality and expressivity of task structures in reinforcement learning

abstract: A hallmark of human intelligence, but challenging for reinforcement learning (RL) agents, is the ability to compositionally generalise, that is, to recompose familiar knowledge components in novel ways to solve new problems. For instance, when navigating in a city, one needs to know the location of the destination and how to operate a vehicle to get there, whether it be pedalling a bike or operating a car. In RL, these correspond to the reward function and transition function, respectively. To compositionally generalize, these two components need to be transferable independently of each other: multiple modes of transport can reach the same goal, and any given mode can be used to reach multiple destinations. Yet there are also instances where it can be helpful to learn and transfer entire structures, jointly representing goals and transitions, particularly whenever these recur in natural tasks (e.g., given a suggestion to get ice cream, one might prefer to bike, even in new towns). Prior theoretical work has explored how, in model-based RL, agents can learn and generalize task components (transition and reward functions). But a satisfactory account for how a single agent can simultaneously satisfy the two competing demands is still lacking. Here, we propose a hierarchical RL agent that learns and transfers individual task components as well as entire structures (particular compositions of components) by inferring both through a non-parametric Bayesian model of the task. It maintains a factorised representation of task components through a hierarchical Dirichlet process, but it also represents different possible covariances between these components through a standard Dirichlet process. We validate our approach on a variety of navigation tasks covering a wide range of statistical correlations between task components and show that it can also improve generalisation and transfer in more complex, hierarchical tasks with goal/subgoal structures. Finally, we end with a discussion of our work including how this clustering algorithm could conceivably be implemented by cortico-striatal gating circuits in the brain.

category: animal behavior and cognition


title: Hierarchical clustering optimizes the tradeoff between compositionality and expressivity of task structures for flexible reinforcement learning


title: Solid state NMR reveals a parallel in register architecture for an infectious recombinant prion

abstract:
Two alternative architectures have been proposed for PrPSc, the most notorious prion: a parallel in register {beta} stack (PIRIBS) and a 4-rung {beta}-solenoid (4R{beta}S). We challenged these two models by measuring intermolecular 13C-13C dipole-dipole couplings of 13CO-labelled Phe residues in a fully infectious sample of recombinant bank vole PrPSc (recBVPrPSc) using a PITHIRDS-CT solid state NMR (ssNMR) experiment. To our surprise, data strongly support a PIRIBS architecture. However, the mean distance measured ([~]6.5 [A]) suggests that a minimum of two of the three Phe residues are not perfectly stacked at the canonical [~]5 [A] cross-{beta} distance. Additional ssNMR experiments show some local conformational variability of the Phe residues within limits of a relatively high rigidity. The most parsimonious interpretation of our data is that recBVPrPSc is arranged as a PIRIBS, although additional conformers with alternative architectures cannot be excluded, including a mixture of PIRIBS and 4R{beta}S.

Author summaryPrPSc is the most notorious prion. It is an infectious protein that cuases fatal neurodegenerative diseases in humans and animals. PrPSc is the aberrant version of a brain protein, PrPC. PrPSc and PrPC have the same prinary structure, but different secondary, tertiaty and quaternary structures. PrPSc is capable of templating PrPC to convert to the PrPSc conformation, which is the basis of its capacity to propagate. Two plausible structural models of PrPSc have been proposed, the four-rung {beta}-solenoid (4R{beta}S) and the parallel in-register {beta} stack (PIRIBS) model. In both cases the driving force of the templating mechanism consists of "sticky" surface {beta}-strands; however, in the PIRIBS model all the {beta}-strands that conform a PrPSc monomer lie flat on a surface whereas in the 4R{beta}S model they wind in a corkscrew fashion. Here, we analyzed fully infectious recombinant PrPSc using a solid state NMR technique, PITHIRDS, that allows probing distances between specific labelled amino acid residues. To our surprise (as we have defended the 4R{beta}S model in the past), results clearly show the presence of a PIRIBS structure in our sample.


title: Differences in the dynamics of the tandem-SH2 modules of the Syk and ZAP-70 tyrosine kinases

abstract: The catalytic activity of Syk-family tyrosine kinases is regulated by a tandem-SH2 module (tSH2 module). In the autoinhibited state, this module adopts a conformation which stabilizes an inactive conformation of the kinase domain. The binding of the tSH2 module to doubly-phosphorylated tyrosine-containing motifs necessitates a conformational change, thereby relieving kinase inhibition and promoting activation. We determined the crystal structure of the isolated tSH2 module of Syk and find, in contrast to ZAP-70, that its conformation more closely resembles that of the peptide-bound state, rather than the autoinhibited state. Hydrogen-deuterium exchange by mass spectrometry, as well as molecular dynamics simulations, reveal that the dynamics of the tSH2 modules of Syk and ZAP-70 differ, with most of these differences occurring in the C-terminal SH2 domain. Our data suggest that the conformational landscapes of the tSH2 modules in Syk and ZAP-70 have been tuned differently, such that the auto-inhibited conformation of the Syk tSH2 module is less stable. This feature of Syk likely contributes to its ability to more readily escape autoinhibition when compared to ZAP-70, consistent with tighter control of downstream signaling pathways in T cells.


title: Metabolic turnover and dynamics of modified ribonucleosides by 13C labeling

abstract: Tandem mass spectrometry (MS/MS) is an accurate tool to assess modified ribonucleosides and their dynamics in mammalian cells. Yet, MS/MS quantification of lowly abundant modifications in non-ribosomal RNAs is unreliable, and the dynamic features of various modifications poorly understood. We developed a 13C labeling approach, 13C-dynamods, to quantify the turnover of base modifications in newly transcribed RNA. This turnover-based approach helped to resolve mRNA from ncRNA modifications in purified RNA or free ribonucleosides, and showed the distinct kinetics of N6-methyladenosine (m62A) versus 7-methylguanosine (m7G) in polyA+-purified RNA. We uncovered that N6,N6-dimethyladenosine (m62A) exhibits a distinct turnover in small RNAs and free ribonucleosides when compared to the known m6 A-modified large rRNAs. Finally, combined measurements of turnover and abundance informed on the transcriptional versus posttranscriptional sensitivity of modified ncRNAs and mRNAs, respectively, to stress conditions. Thus, 13C-dynamods enables studies of origin of modified RNAs at steady-state and their dynamics under non-stationary conditions.


title: Diverse human astrocyte and microglial transcriptional responses to Alzheimer's pathology

abstract: To better define roles that astrocytes and microglia play in Alzheimers disease (AD), we used single-nuclei RNA sequencing to comprehensively characterize transcriptomes in astrocyte and microglia nuclei isolated post mortem from neuropathologically-defined AD and control brains with a range of amyloid-beta and phospho-tau (pTau) pathology. Significant differences in glial gene expression (including AD risk genes expressed in astrocytes [CLU, MEF2C, IQCK] and microglia [APOE, MS4A6A, PILRA]) were correlated with tissue amyloid and pTau expression. Astrocytes were enriched for proteostatic, inflammatory and metal ion homeostasis pathways. Pathways for phagocytosis, proteostasis and autophagy were highly enriched in microglia and perivascular macrophages. Gene co-expression analyses revealed potential functional associations of soluble biomarkers of AD in astrocytes (CLU) and microglia (GPNMB). Our work highlights responses of both astrocytes and microglia for pathological protein clearance and inflammation, as well as glial transcriptional diversity in AD.


title: ASXL3 controls cortical neuron fate specification through extrinsic self-renewal pathways

abstract: During corticogenesis, transcription plasticity is fundamental to the restriction of neural progenitor cell (NPC) multipotency and production of cortical neuron heterogeneity. Human and mouse genetic studies have highlighted the role of Polycomb transcriptional regulation in this process. ASXL3, which encodes a component of the Polycomb repressive deubiquitination (PR-DUB) complex, has been identified as a high confidence autism spectrum disorder (ASD) risk gene. Genetic inactivation of Asxl3, in a mouse model that carries a clinically relevant ASXL3 frameshift (Asxl3fs) variant, disrupts lateral expansion of NPCs and delays cortical neuron differentiation. Single-cell RNA sequencing analysis implicates Notch signaling, which alters the composition of excitatory neurons and fidelity of cortical layer deposition. Our data provides a new link between extrinsic signaling cues and intrinsic epigenetic regulation that together control the timing of cell fate programs. Furthermore, transcriptomic analysis revealed dysregulation of other known ASD risk genes indicating that a convergent developmental pathway is affected. Collectively our work provides important insights about developmental mechanisms that contribute to ASD neuropathology.


title: Regulation of stem cell identity by miR-200a during spinal cord regeneration

abstract:
Axolotls are an important model organism for multiple types of regeneration, including functional spinal cord regeneration. Remarkably, axolotls can repair their spinal cord after a small lesion injury and can also regenerate their entire tail following amputation. Several classical signaling pathways that are used during development are reactivated during regeneration, but how this is regulated remains a mystery. We have previously identified miR-200a as a key factor that promotes successful spinal cord regeneration. Here, using RNA-seq analysis, we discovered that the inhibition of miR-200a results in an upregulation of the classical mesodermal marker brachyury in spinal cord cells after injury. However, these cells still express the neural stem cell marker sox2. In vivo lineage tracing allowed us to determine that these cells can give rise to cells of both the neural and mesoderm lineage. Additionally, we found that miR-200a can directly regulate brachyury via a seed sequence in the 3UTR of the gene. Our data indicate that miR-200a represses mesodermal cell fate after a small lesion injury in the spinal cord when only glial cells and neurons need to be replaced.

Summary StatementAfter spinal cord injury, miR-200 fine-tunes expression levels brachyury and {beta}-catenin to direct spinal cord stem into cells of the mesodermal or ectodermal lineage.

category: developmental biology


title: Drosophila beta-Heavy-Spectrin is required in polarized ensheathing glia that forma diffusion-barrier around the neuropil

abstract: In the central nervous system (CNS), functional tasks are often allocated to distinct compartments. This is also evident in the insect CNS where synapses and dendrites are clustered in distinct neuropil regions. The neuropil is separated from neuronal cell bodies by ensheathing glia, which as we show using dye injection experiments forms an internal diffusion barrier. We find that ensheathing glial cells are polarized with a basolateral plasma membrane rich in phosphatidylinositol-(3,4,5)-triphosphate (PIP3) and the Na+/K+-ATPase Nervana2 (Nrv2) that abuts an extracellular matrix formed at neuropil-cortex interface. The apical plasma membrane is facing the neuropil and is rich in phosphatidylinositol-(4,5)-bisphosphate (PIP2) that is supported by a sub-membranous {beta}Heavy-Spectrin cytoskeleton. {beta}Heavy-spectrin mutant larvae affect ensheathing glial cell polarity with delocalized PIP2 and Nrv2 and exhibit an abnormal locomotion which is similarly shown by ensheathing glia ablated larvae. Thus, polarized glia compartmentalizes the brain and is essential for proper nervous system function.


title: CryoEM structure of the outer membrane secretin channel pIV from the f1 filamentous bacteriophage

abstract: The Ff family of filamentous bacteriophages infect gram-negative bacteria, but do not cause lysis of their host cell. Instead, new virions are extruded via the phage-encoded pIV protein, which has homology with bacterial secretins. Here, we determine the structure of pIV from the f1 filamentous bacteriophage at 2.7 [A] resolution by cryo-electron microscopy, the first near-atomic structure of a phage secretin. Fifteen f1 pIV subunits assemble to form a gated channel in the bacterial outer membrane, with associated soluble domains projecting into the periplasm. We model channel opening and propose a mechanism for phage egress. By single-cell microfluidics experiments, we demonstrate the potential for secretins such as pIV to be used as adjuvants to increase the uptake and efficacy of antibiotics in bacteria. Finally, we compare the f1 pIV structure to its homologues to reveal similarities and differences between phage and bacterial secretins.


title: Crystal structures of taxane-tubulin complexes: Implications for the mechanism of microtubule stabilization by Taxol

abstract: Paclitaxel (Taxol(R)) is a first-line chemotherapeutic drug that promotes the curved-to-straight conformational transition of tubulin, an activation step that is necessary for microtubule formation. Crystallization of Taxol bound to tubulin has been long elusive. We found that baccatin III, the core structure of paclitaxel which lacks the C13 side chain, readily co-crystallizes with curved tubulin. Tailor-made taxanes with alternative side chains also co-crystallized, allowing us to investigate their binding modes. Interestingly, these Taxol derived compounds lost their microtubule stabilizing activity and cytotoxicity but kept their full microtubule binding affinity, and all induced lattice expansion upon binding. Additional nuclear magnetic resonance studies propose that Taxol binds to a small fraction of straight tubulin present in solution. Our results suggest a mode of action of Taxol, where the core structure is responsible for the interacting energy while the bulky hydrophobic C13 side chain enables binding selectively to straight tubulin and promotes stabilization.


title: From the Modern Synthesis to the Molecular Synthesis: updating how we teach and assess evolution by natural selection

abstract: Evolution by natural selection is recognized as both the most important concept in undergraduate biology and the most difficult to teach. Unfortunately, teaching and assessment of evolution have been impaired by legacy approaches that focus on Darwins original insights and the Modern Synthesis integration of Mendelian genetics, but ignore or downplay advances from what we term the Molecular Synthesis. To create better alignment between instructional approaches and contemporary research in the biosciences, we propose that the primary learning goal in teaching evolution should be for students to connect genotypes, phenotypes, and fitness. To support this approach, we developed and tested assessment questions and scoring rubrics called the Extended Assessing Conceptual Reasoning of Natural Selection (E-ACORNS) instrument. Initial E-ACORNS data suggest that after traditional instruction, few students recognize the molecular synthesis--prompting us to propose that introductory course sequences be re-organized with the molecular synthesis as their central theme.

category: scientific communication and education


title: Measuring fingerpad deformation during active object manipulation

abstract: AO_SCPLOWBSTRACTC_SCPLOWDuring active object manipulation, the finger-object interactions give rise to complex fingertip skin deformations. These deformations are in turn encoded by the local tactile afferents and provide rich and behaviorally relevant information to the central nervous system. Most of the work studying the mechanical response of the finger to dynamic loading has been performed under a passive setup, thereby precisely controlling the kinematics or the dynamics of the loading. However, to identify aspects of the deformations that are relevant to online control during object manipulation, it is desirable to measure the skin response in an active setup. To that end, we developed a device that allows us to monitor finger forces, skin deformations, and kinematics during fine manipulation. We describe the device in detail and test it to precisely describe how the fingertip skin in contact with the object deforms during a simple vertical oscillation task. We show that the level of grip force directly influences the fingerpad skin strains and that the strain rates are substantial during active manipulation (norm up to 100%/s). The developed setup will enable us to causally relate sensory information, i.e. skin deformation, to online control, i.e. grip force adjustment, in future studies.


title: Neural Collision Detection: an open source library to study the three-dimensional interactions of neurons and other tree-like structures

abstract: AO_SCPLOWBSTRACTC_SCPLOWThe analysis of neuronal structure and its relation to function has become a fundamental pillar in neuroscience since its earliest days, with the underlying premise that morphological properties can modulate neuronal computations. It is often the case that the rich three-dimensional structure of neurons is quantified by tools developed in other fields, such as graph theory and computational geometry; nevertheless, some of the more advanced tools developed in these fields have not yet been made accessible to the neuroscience community. Here we present Neural Collision Detection, a library providing high-level interfaces to collision-detection routines and alpha shape calculations, as well as statistical analysis and visualizations for 3D objects, with the aim to lower the entry gap for neuroscientists into these worlds. Our work here also demonstrates a variety of use cases for the library and exemplary analysis and visualizations that were carried out with it on real neuronal and vascular data.


title: Viral receptor profiles of masked palm civet revealed by single-cell transcriptomics

abstract: Civets are small mammals belonging to the family Viverridae. The masked palm civets (Paguma larvata) served as an intermediate host in the bat-to-human transmission of severe acute respiratory syndrome coronavirus (SARS-CoV) in 20031. Because of their unique role in the SARS outbreak, civets were suspected as a potential intermediate host of SARS-CoV-2, the etiological pathogen of the COVID-19 pandemic. Besides their susceptibility to coronaviruses, civets can also be infected by other viruses, such as canine distemper viruses2, parvoviruses3, influenza viruses4, etc. Regarding the ecological and economical role of civets, it is vital to evaluate the potential threats from different pathogens to these animals. Receptor binding is a necessary step for virus entry into host cells. Understanding the distribution of receptors of various viruses provides hints to their potential tissue tropisms. Herein, we characterized the cell atlas of five important organs (the frontal lobe, lung, liver, spleen and kidney) of masked palm civets (Paguma larvata) and described the expression profiles of receptor associated genes of 132 viruses from 25 families, including 16 viruses from 10 families reported before that can attack civets and 116 viruses with little infection record.


title: Immunogenic SARS-CoV2 Epitopes Defined by Mass Spectrometry

abstract:
SARS-CoV-2 infections elicit both humoral and cellular immune responses. For the prevention and treatment of COVID19, the disease caused by SARS-CoV-2, T cell responses are important in mediating recovery and immune-protection. The identification of immunogenic epitopes that can elicit a meaningful T cell response can be elusive. Traditionally, this has been achieved using sophisticated in silico methods to predict putative epitopes; however, our previous studies find that  immunodominant SARS-CoV-2 peptides defined by such in silico methods often fail to elicit T cell responses recognizing SARS-CoV-2. We postulated that immunogenic epitopes for SARS-CoV-2 are best defined by directly analyzing peptides eluted from the peptide-MHC complex and then validating immunogenicity empirically by determining if such peptides can elicit T cells recognizing SARS-CoV-2 antigen-expressing cells. Using a tandem mass spectrometry approach, we identified epitopes of SARS-CoV-2 derived not only from structural but also non-structural genes in regions highly conserved among SARS-CoV-2 strains including recently recognized variants. We report here, for the first time, several novel SARS-CoV-2 epitopes from membrane glycol-protein (MGP) and non-structure protein-13 (NSP13) defined by mass-spectrometric analysis of MHC-eluted peptides, provide empiric evidence for their immunogenicity to induce T cell response.

Significance StatementCurrent state of the art uses putative epitope peptides based on in silico prediction algorithms to evaluate the T cell response among COVID-19 patients. However, none of these peptides have been tested for immunogenicity, i.e. the ability to elicit a T cell response capable of recognizing endogenously presented peptide. In this study, we used MHC immune-precipitation, acid elution and tandem mass spectrometry to define the SARS-CoV-2 immunopeptidome for membrane glycol-protein and the non-structural protein. Furthermore, taking advantage of a highly robust endogenous T cell (ETC) workflow, we verify the immunogenicity of these MS-defined peptides by in vitro generation of MGP and NSP13 peptide-specific T cells and confirm T cell recognition of MGP or NSP13 endogenously expressing cell lines.