title: Repeated out-of-Africa expansions of Helicobacter pylori driven by replacement of deleterious mutations

abstract: Helicobacter pylori lives in the human stomach and has a population structure which resembles that of its host. However, H. pylori from Europe and the Middle East trace a substantially higher fraction of ancestry from modern African populations than the humans that carry them. We use a collection of Afro-Eurasian genomes to show that this African ancestry is due to at least three distinct admixture events. H. pylori from East Asia, which have undergone little admixture, have accumulated many more non-synonymous mutations than African strains. European and Middle Eastern bacteria have elevated African ancestry at the sites of these mutations compared to either non-segregating or synonymous sites. We use simulations to show demographic bottlenecks can lead to long-term segregation of deleterious mutations, despite high rates of homologous recombination, but that population fitness can be restored by migration of small numbers of bacteria from non-bottlenecked populations, leading to mosaic patterns of ancestry like that seen for H. pylori. We conclude that H. pylori have been able to spread repeatedly from Africa due to deleterious mutations accumulated during the original out-of-Africa bottleneck.


title: Sustained post-developmental T-bet expression is critical for the maintenance of type 1 innate lymphoid cells in vivo

abstract: Innate lymphoid cells (ILC) play a significant role in the intestinal immune response and T-bet+ CD127+ group 1 cells (ILC1) have been linked to the pathogenesis of human inflammatory bowel disease (IBD). However, the functional importance of ILC1 in the context of an intact adaptive immune response has been controversial. In this report we demonstrate that induced depletion of T-bet using a Rosa26-Cre-ERT2 model resulted in the loss of intestinal ILC1, pointing to a post-developmental requirement of T-bet expression for these cells. In contrast, neither colonic lamina propria (cLP) ILC2 nor cLP ILC3 abundance were altered upon induced deletion of T-bet. Mechanistically, we report that STAT1 or STAT4 are not required for intestinal ILC1 development and maintenance. Mice with induced deletion of T-bet and subsequent loss of ILC1 were protected from the induction of severe colitis in vivo. Hence, this study provides support for the clinical development of an IBD treatment based on ILC1 depletion via targeting T-bet or its downstream transcriptional targets.

category: immunology


title: Learning and organization of memory for evolving patterns

abstract: Storing memory for molecular recognition is an efficient strategy for responding to external stimuli. Biological processes use different strategies to store memory. In the olfactory cortex, synaptic connections form when stimulated by an odor, and establish distributed memory that can be retrieved upon re-exposure. In contrast, the immune system encodes specialized memory by diverse receptors that recognize a multitude of evolving pathogens. Despite the mechanistic differences between the olfactory and the immune memory, these systems can still be viewed as different information encoding strategies. Here, we present a theoretical framework with artificial neural networks to characterize optimal memory strategies for both static and dynamic (evolving) patterns. Our approach is a generalization of the energy-based Hopfield model in which memory is stored as a networks energy minima. We find that while classical Hopfield networks with distributed memory can efficiently encode a memory of static patterns, they are inadequate against evolving patterns. To follow an evolving pattern, we show that a distributed network should use a higher learning rate, which in turn, can distort the energy landscape associated with the stored memory attractors. Specifically, narrow connecting paths emerge between memory attractors, leading to misclassification of evolving patterns. We demonstrate that compartmentalized networks with specialized subnetworks are the optimal solutions to memory storage for evolving patterns. We postulate that evolution of pathogens may be the reason for the immune system to encoded a focused memory, in contrast to the distributed memory used in the olfactory cortex that interacts with mixtures of static odors.

category: evolutionary biology


title: HyDrop: droplet-based scATAC-seq and scRNA-seq using dissolvable hydrogel beads

abstract: Single-cell RNA-seq and single-cell ATAC-seq technologies are being used extensively to create cell type atlases for a wide range of organisms, tissues, and disease processes. To increase the scale of these atlases, lower the cost, and allow for more specialized multi-ome assays, custom droplet microfluidics may provide complementary solutions to commercial setups. We developed HyDrop, a flexible and generic droplet microfluidic platform encompassing three protocols. The first protocol involves creating dissolvable hydrogel beads with custom oligos that can be released in the droplets. In the second protocol, we demonstrate the use of these beads for HyDrop-ATAC, a low-cost non-commercial scATAC-seq protocol in droplets. After validating HyDrop-ATAC, we applied it to flash-frozen mouse cortex and generated 8,502 high-quality single-cell chromatin accessibility profiles in a single run. In the third protocol, we adapt both the reaction chemistry and the capture sequence of the barcoded hydrogel bead to capture mRNA, and demonstrate a significant improvement in throughput and sensitivity compared to previous open-source droplet-based scRNA-seq assays (Drop-seq and inDrop). Similarly, we applied HyDrop-RNA to flash-frozen mouse cortex and generated 9,508 single-cell transcriptomes closely matching reference single-cell gene expression data. Finally, we leveraged HyDrop-RNAs high capture rate to analyse a small population of FAC-sorted neurons from the Drosophila brain, confirming the protocols applicability to low-input samples and small cells. HyDrop is currently capable of generating single-cell data in high throughput and at a reduced cost compared to commercial methods, and we envision that HyDrop can be further developed to be compatible with novel (multi-) omics protocols.

category: genomics


title: Capture of Viruses and Microorganisms in Aerosols Using A Newly Designed Collection System: A Proof-of-concept Study

abstract: Aerosols contain human pathogens that cause public health disasters such as tuberculosis (TB) and the ongoing COVID-19 pandemic. The current technologies for the collection of viruses and microorganisms in aerosols face critical limitations, necessitating the development of a new type of sampling system to advance the capture technology. Herein, we presented a new type of collection system, which exploits the affinity between carbon chains and organic molecules on the surfaces of viruses and microorganisms. We demonstrated that the physical capture efficiency of the collection system was over 99% for particle sizes from 0.3 to 10 {micro}m. We further evaluated the biochemical capture efficiency of the collection system using mass spectrometry approaches and showed that the biochemical information of viruses and microorganisms was well preserved. Coupled with well-established molecular technologies, this new type of capture technology can be used for the investigation of aerosol-related disease transmission models, as well as the development of innovative screening and monitoring tools for human diseases and public health issues.

category: biochemistry


title: Anti-allergic and anti-inflammatory activities of black cumin extracts in in vitro and in vivo model systems

abstract: Black cumin (Nigella sativa) is a widely used ingredient of traditional medicine for its broad-spectrum pharmacological actions, including anti-allergic, bronchial asthma, and anti-inflammatory properties. We sought to evaluate BC extracts efficacy for their anti-allergic and anti-inflammatory properties using a comprehensive in vitro, in vivo, and silico experimental setup. To investigate whether BC extract has anti-inflammatory, anti-allergic, and analgesic therapeutic potentials in vitro and in vivo. The activity of BC was assessed through anti-allergic activity on rat basophilic leukemia-2H3 cell line, anti-inflammatory activity on J774.1A cell line, anti-inflammatory activity by carrageenan-induced rat paw edema, analgesic activity by acetic acid-induced writhing test, and ingenuity analysis of the BC extracts in inflammation control. BC exerted potent anti-allergic activity by inhibiting antigen-induced degranulation. An anti-inflammatory effect is shown by inhibiting TNF- production. The acetic acid-induced writhing test shown a dose-dependent reduction of writhing number following BC administration. Rat paw edema test shown the dose-dependent reduction of paw edema volume following BC administration. Ingenuity Pathway Analysis (IPA) suggested BC extracts containing ferulic acid, p-coumaric acid, kaempferol, and quercetin can inhibit inflammation. This study suggests that bioactive compounds in BC extract act as an anti-allergic and anti-inflammatory agent by regulating several downstream and upstream inflammation pathways.

category: plant biology


title: Phylogenetic Analysis of Crimean-Congo Hemorrhagic Fever Virus in Inner Mongolia, China

abstract: Crimean-Congo hemorrhagic fever virus (CCHFV) is a tick-borne arbovirus that can cause bleeding and death in humans. The mortality rate in humans is between 5 to 30%. The pathogen is prevalent in more than 30 countries in the world. In China, reports of strains of CCHFV have been concentrated in Xinjiang province. However, the CCHFV strain has never been reported in Inner Mongolia, China. This study reports new CCHFV strains, HANM-18, from Hyalomma asiaticum and Hyalomma dromedarii collected in Alxa Left Banner and Alxa Right Banner in Inner Mongolia. Complete sequences of CCHFV were obtained by the nested PCR technique and used for analyzing the identity and evolutionary relationship with other CCHFV strains. Interestingly, our results showed that the S and L fragments of the HANM-18 strain had high degrees of identity with Xingjiang isolate strains, and the M fragment had significant identity with South African isolates. These analyses also indicate that the HANM-18 strain may have been prevalent in northwest Inner Mongolia for many years. This discovery will be helpful in CCHF prevention and control in Inner Mongolia, and it also adds new evidence to the epidemiology of CCHF in China.

category: microbiology


title: Site level factors that affect the rate of adaptive evolution in humans and chimpanzees; the effect of contracting population size.

abstract: It has previously been shown in other species that the rate of adaptive evolution is higher at sites that are more exposed in a protein structure and lower between amino acid pairs that are more dissimilar. We have investigated whether these patterns are found in the divergence between humans and chimpanzees using an extension of the MacDonald-Kreitman test. We confirm previous findings and find that the rate of adaptive evolution, relative to the rate of mutation, is higher for more exposed amino acids, lower for amino acid pairs that are more dissimilar in terms of their polarity, volume and lower for amino acid pairs that are subject to stronger purifying selection, as measured by the ratio of the numbers of non-synonymous to synonymous polymorphisms (pN /pS). However, the slope of this latter relationship is significantly shallower than in Drosophila species. We suggest that this is due to the population contraction that has occurred since humans and chimpanzees diverged. We demonstrate theoretically that population size reduction can generate an artefactual positive correlation between the rate of adaptive evolution and any factor that is correlated to the mean strength of selection acting against deleterious mutations, even if there has been no adaptive evolution (the converse is also expected). Our measure of selective constraint, pN /pS, is negatively correlated to the mean strength of selection, and hence we would expect the correlation between the rate of adaptive evolution to also be negatively correlated to pN /pS, if there is no adaptive evolution. The fact that our rate of adaptive evolution is positively correlated to pN /pS suggests that the correlation does genuinely exist, but that is has been attenuated by population size contraction.


title: A marginal habitat, but not a sink: Ecological genetics reveal a diversification hotspot for marine invertebrates in the brackish Baltic Sea

abstract:
AimEnvironmental gradients have emerged as important barriers structuring populations and species distributions. We set out to test whether a strong salinity gradient from marine to brackish, represented in a marginal northern European sea, should be considered a diversification hotspot or a population sink, and to identify life history traits that correlate with either evolutionary trajectory.

LocationThe Baltic Sea, the North Sea and their transition zone.

MethodsWe accumulated mitochondrial cytochrome oxidase subunit 1 sequence data and data on the distribution, salinity tolerance and life history for 28 species belonging to the Cnidaria, Crustacea, Echinodermata, Mollusca, Polychaeta and Gastrotricha, including seven non-native species. We calculated measures of genetic diversity and differentiation across the environmental gradient, coalescent times and migration rates between North and Baltic Sea populations, and analysed correlations between genetic and life history data.

ResultsThe majority of investigated species is either genetically differentiated and/or is adapted to the lower salinity conditions of the Baltic Sea. Moreover, the species exhibiting population structure have a range of patterns of genetic diversity in comparison to the North Sea, from lower in the Baltic Sea to higher in the Baltic Sea, or equally diverse in North and Baltic Sea.

Main conclusionsOur results indicate that the Baltic Sea should be considered a diversification hotspot: The diversity of genetic patterns points towards independent trajectories in the Baltic compared to the North Sea. At the same time, we found limited evidence for the traditional scenario of the Baltic Sea as a population sink with lower diversity and strong gene flow. The North Sea - Baltic Sea region provides a unique setting to study evolutionary adaptation during colonization processes at different stages by jointly considering native and non-native species.


title: Heterogeneous mutation rates and spectra within and between species of yeast and their hybrids

abstract: Mutation rates and spectra vary between species and among populations. Hybridization can contribute to this variation, but its role remains poorly understood. Estimating mutation rates requires controlled conditions where the effect of natural selection can be minimized. One way to achieve this is through mutation accumulation experiments coupled with genome sequencing. Here we investigate 400 mutation accumulation lines initiated from 11 genotypes spanning intra-lineage, inter-lineage and interspecific crosses of the yeasts Saccharomyces paradoxus and S. cerevisiae and propagated for 770 generations. We find significant differences in mutation rates and spectra among crosses, which are not related to the level of divergence of parental strains but are specific to some genotype combinations. Differences in number of generations and departures from neutrality play a minor role, whereas polyploidy and loss of heterozygosity impact mutation rates in some of the hybrid crosses in an opposite way.


title: Heterogeneous mutation rates and spectra in yeast hybrids


title: Assessing genome-wide dynamic changes in enhancer activity during early mESC differentiation by FAIRE-STARR-seq

abstract: Embryonic stem cells (ESCs) can differentiate into any given cell type and therefore represent a versatile model to study the link between gene regulation and differentiation. To quantitatively assess the dynamics of enhancer activity during the early stages of murine ESC differentiation, we analyzed accessible genomic regions using STARR-seq, a massively parallel reporter assay. This resulted in a genome-wide quantitative map of active mESC enhancers, in pluripotency and during the early stages of differentiation. We find that only a minority of accessible regions is active and that such regions are enriched near promoters, characterized by specific chromatin marks, enriched for distinct sequence motifs, and modeling shows that active regions can be predicted from sequence alone. Regions that change their activity upon retinoic acid-induced differentiation are more prevalent at distal intergenic regions when compared to constitutively active enhancers. Further, analysis of differentially active enhancers verified the contribution of individual TF motifs toward activity and inducibility as well as their role in regulating endogenous genes. Notably, the activity of retinoic acid receptor alpha (RAR) occupied regions can either increase or decrease upon the addition of its ligand, retinoic acid, with the direction of the change correlating with spacing and orientation of the RAR consensus motif and the co-occurrence of additional sequence motifs. Together, our genome-wide enhancer activity map elucidates features associated with enhancer activity levels, identifies regulatory regions disregarded by computational prediction tools, and provides a resource for future studies into regulatory elements in mESCs.


title: Whole-cell cryo-electron tomography of cultured and primary eukaryotic cells on micropatterned TEM grids

abstract: Whole-cell cryo-electron tomography (cryo-ET) is a powerful technique that can provide nanometer-level resolution of biological structures within the cellular context and in a near-native frozen-hydrated state. It remains a challenge to culture or adhere cells on TEM grids in a manner that is suitable for tomography while preserving the physiological state of the cells. Here, we demonstrate the versatility of micropatterning to direct and promote growth of both cultured and primary eukaryotic cells on TEM grids. We show that micropatterning is compatible with and can be used to enhance studies of host-pathogen interactions using respiratory syncytial virus infected BEAS-2B cells as an example. We demonstrate the ability to use whole-cell tomography of primary Drosophila neuronal cells to identify organelles and cytoskeletal stuctures in cellular axons and the potential for micropatterning to dramatically increase throughput for these studies. During micropatterning, cell growth is targeted by depositing extra-cellular matrix (ECM) proteins within specified patterns and positions on the foil of the TEM grid while the other areas remain coated with an anti-fouling layer. Flexibility in the choice of surface coating and pattern design make micropatterning broadly applicable for a wide range of cell types. Micropatterning is useful for studies of structures within individual cells as well as more complex experimental systems such as host-pathogen interactions or differentiated multi-cellular communities. Micropatterning may also be integrated into many downstream whole-cell cryo-ET workflows including correlative light and electron microscopy (cryo-CLEM) and focused-ion beam milling (FIB-SEM).

category: cell biology


title: Carboxypeptidase E is efficiently secreted and internalized via lysosomes

abstract: Carboxypeptidase E (CPE) a key factor in the biosynthesis of most peptide hormones and neuropeptides, is predominantly expressed in endocrine tissues and the nervous system. This highly conserved enzyme cleaves the C-terminal basic residues of the peptide precursors to generate their bioactive form. CPE is a secreted protein; however, the Intracellular pathways leading to its secretion are still obscure. We combined live-cell microscopy and molecular analysis to examine the intracellular distribution and secretion dynamics of fluorescently tagged CPE. CPE was found to be a soluble luminal protein as it traffics from the ER via the Golgi apparatus to lysosomes. Moreover, CPE is efficiently secreted and reinternalized to lysosomes of neighboring cells. The C-terminal amphipathic helix of CPE is essential for its efficient targeting to, and secretion from lysosomes. Fluorescence resonance energy transfer demonstrated that CPE and its substrate neuropeptide Y (NPY) interact in the Golgi apparatus and Immunoprecipitation analysis demonstrated that both CPE and NPY are co-secreted. The implications of the well-defined CPE intra and extracellular routes are discussed.


title: The ciliary gene INPP5E confers dorsal telencephalic identity to human cortical organoids by negatively regulating Sonic Hedgehog signalling

abstract: Defects in primary cilia, cellular antennas that controls multiple intracellular signalling pathways, underlie several neurodevelopmental disorders, but how cilia control essential steps in human brain formation remains elusive. Here, we show that cilia are present on the apical surface of radial glial cells in human foetal forebrain. Interfering with cilia signalling in human organoids by mutating the INPP5E gene leads to the formation of ventral telencephalic cell types instead of cortical progenitors and neurons. INPP5E mutant organoids also showed increased SHH signalling and cyclopamine treatment partially rescued this ventralisation. In addition, ciliary expression of SMO was increased and the integrity of the transition zone was compromised. Overall, these findings establish the importance of primary cilia for dorsal/ventral patterning in human corticogenesis, indicate a tissue specific role of INPP5E as a negative regulator of SHH signalling and have implications for the emerging roles of cilia in the pathogenesis of neurodevelopmental disorders.

category: developmental biology


title: Structural probing of Hsp26 activation and client binding by quantitative cross-linking mass spectrometry

abstract: Small heat-shock proteins (sHSP) are important members of the cellular stress response in all species. Their best described function is the binding of early unfolding states and the resulting prevention of protein aggregation. Most sHSPs exist as oligomers but vary in size and subunit organization. Many sHSPs exist as a polydisperse composition of oligomers which undergoes changes in subunit composition, folding status and relative distribution upon heat activation. To date only an incomplete picture of the mechanism of sHSP activation exists and in particularly the molecular basis of how sHSPs bind client proteins and mediate client specificity is not fully understood. In this study we have applied cross-linking mass spectrometry (XL-MS) to obtain detailed structural information on sHSP activation and client binding for yeast Hsp26. Our cross-linking data reveals the middle domain of Hsp26 as client-independent interface in multiple Hsp26::client complexes and indicates that client-specificity is likely mediated via additional binding sites within its CD and CTE. Our quantitative XL-MS data underpins the middle domain as the main driver of heat-induced activation and client binding but shows that global rearrangements spanning all domains of Hsp26 are taking place simultaneously. We also investigated a Hsp26::client complex in the presence of Ssa1 (Hsp70) and Ydj1(Hsp40) at the initial stage of refolding and observe that the interaction between refolding chaperones is altered by the presence of a client protein, pointing to a mechanism where interaction of Ydj1 with the HSP::client complex initiates assembly of the active refolding machinery.


title: Physical basis for distinct basal and mechanically-gated activity of the human K+ channel TRAAK

abstract: TRAAK is a mechanosensitive two-pore domain K+ (K2P) channel localized to nodes of Ranvier in myelinated neurons. TRAAK deletion in mice results in mechanical and thermal allodynia and gain-of-function mutations cause the human neurodevelopmental disorder FHEIG. TRAAK displays basal and stimulus-gated activities typical of K2Ps, but the mechanistic and structural differences between these modes are unknown. Here, we demonstrate that basal and mechanically-gated openings are distinguished by their conductance, kinetics, and structure. Basal openings are low conductance, short duration, and occur through a channel with an interior cavity exposed to the surrounding membrane. Mechanically-gated openings are high conductance, long duration, and occur through a channel that is sealed to the surrounding membrane. Our results explain how dual modes of activity are produced by a single ion channel and provide a basis for the development of state-selective pharmacology with the potential to treat disease.

category: biophysics


title: Generative replay for compositional visual understanding in the prefrontal-hippocampal circuit

abstract: Understanding the visual world is a constructive process. Whilst a frontal-hippocampal circuit is known to be essential for this task, little is known about the associated neuronal computations. Visual understanding appears superficially distinct from other known functions of this circuit, such as spatial reasoning and model-based planning, but recent models suggest deeper computational similarities. Here, using fMRI, we show that representations of a simple visual scene in these brain regions are relational and compositional - key computational properties theorised to support rapid construction of hippocampal maps. Using MEG, we show that rapid sequences of representations, akin to replay in spatial navigation and planning problems, are also engaged in visual construction. Whilst these sequences have previously been proposed as mechanisms to plan possible futures or learn from the past, here they are used to understand the present. Replay sequences form constructive hypotheses about possible scene configurations. These hypotheses play out in an optimal order for relational inference, progressing from predictable to uncertain scene elements, gradually constraining possible configurations, and converging on the correct scene configuration. Together, these results suggest a computational bridge between apparently distinct functions of hippocampal-prefrontal circuitry, and a role for generative replay in constructive inference and hypothesis testing.

category: neuroscience


title: Drug Repurposing for the SARS-CoV-2 Papain-Like Protease

abstract: As the pathogen of COVID-19, SARS-CoV-2 encodes two essential cysteine proteases that process the pathogens two large polypeptide translates ORF1a and ORF1ab in human host cells to form 15 functionally important, mature nonstructural proteins. One of the two enzymes, papain-like protease or PLpro, also possesses deubiquitination and deISGylation activities that suppresses host innate immune responses toward SARS-CoV-2 infection. Therefore, PLpro is a potential COVID-19 drug target. To repurpose drugs for PLpro, we experimentally screened 33 deubiquitinase and 37 cysteine protease inhibitors on their inhibition of PLpro. Our results showed that 15 deubiquitinase and 1 cysteine protease inhibitors exhibit potent inhibition of PLpro at 200 M. More comprehensive characterizations revealed 7 inhibitors GRL0617, SJB2-043, TCID, DUB-IN-1, DUB-IN-3, PR-619, and S130 with an IC50 value below 60 M and four inhibitors GRL0617, SJB2-043, TCID, and PR-619 with an IC50 value below 10 M. Among four inhibitors with an IC50 value below 10 M, SJB2-043 is the most unique in that it doesnt fully inhibit PLpro but has an outstanding IC50 value of 0.56 M. SJB2-043 likely binds to an allosteric site of PLpro to convene its inhibition effect, which needs to be further investigated. As a pilot study, the current work indicates that COVID-19 drug repurposing by targeting PLpro holds promises but in-depth analysis of repurposed drugs is necessary to avoid omitting allosteric inhibitors.


title: Utilizing proteomics and phosphoproteomics to predict ex vivo drug sensitivity across genetically diverse AML patients

abstract: Acute Myeloid Leukemia (AML) affects 20,000 patients in the US annually with a five-year survival rate of approximately 25%. One reason for the low survival rate is the high prevalence of clonal evolution that gives rise to heterogeneous sub-populations of leukemia. This genetic heterogeneity is difficult to treat using conventional therapies that are generally based on the detection of a single driving mutation. Thus, the use of molecular signatures, consisting of multiple functionally related transcripts or proteins, in making treatment decisions may overcome this hurdle and provide a more effective way to inform drug treatment protocols. Toward this end, the Beat AML research program prospectively collected genomic and transcriptomic data from over 1000 AML patients and carried out ex vivo drug sensitivity assays to identify signatures that could predict patient-specific drug responses. The Clinical Proteomic Tumor Analysis Consortium is in the process of extending this cohort to collect proteomic and phosphoproteomic measurements from a subset of these patient samples to evaluate the hypothesis that proteomic signatures can robustly predict drug response in AML patients. We sought to examine this hypothesis on a sub-cohort of 38 patient samples from Beat AML with proteomic and drug response data and evaluate our ability to identify proteomic signatures that predict drug response with high accuracy. For this initial analysis we built predictive models of patient drug responses across 26 drugs of interest using the proteomics and phosphproteomics data. We found that proteomics-derived signatures provide an accurate and robust signature of drug response in the AML ex vivo samples, as well as related cell lines, with better performance than those signatures derived from mutations or mRNA expression. Furthermore, we found that in specific drug-resistant cell lines, the proteins in our prognostic signatures represented dysregulated signaling pathways compared to parental cell lines, confirming the role of the proteins in the signatures in drug resistance. In conclusion, this pilot study demonstrates strong promise for proteomics-based patient stratification to predict drug sensitivity in AML.

category: bioinformatics


title: The biaxial mechanics of thermally denaturing skin - Part II: Modeling

abstract: Understanding the response of skin to superphysiological temperatures is critical to the diagnosis and prognosis of thermal injuries, and to the development of temperature-based medical therapeutics. Unfortunately, this understanding has been hindered by our incomplete knowledge about the nonlinear coupling between skin temperature and its mechanics. In Part I of this study we experimentally demonstrated a complex interdependence of time, temperature, direction, and load in skins response to superphysiological temperatures. In Part II of our study, we test two different models of skins thermo-mechanics to explain our observations. In both models we assume that skins response to superphysiological temperatures is governed by the denaturation of its highly collageneous microstructure. Thus, we capture skins native mechanics via a microstructurally-motivated strain energy function which includes probability distributions for collagen fiber orientation and waviness. In the first model, we capture skins response to superphysiological temperatures as a transition between two states that link the kinetics of collagen fiber denaturation to fiber coiling and to the transformation of each fibers constitutive behavior from purely elastic to viscoelastic. In the second model, we capture skins response to super-physiological temperatures instead via three states in which a sequence of two reactions link the kinetics of collagen fiber denaturation to fiber coiling, followed by a state of fiber damage. Given the success of both models in qualitatively capturing our observations, we expect that our work will provide guidance for future experiments that could probe each models assumptions toward a better understanding of skins coupled thermo-mechanics and that our work will be used to guide the engineering design of heat treatment therapies.


title: Cryo-EM structure of native human thyroglobulin

abstract: The thyroglobulin (Tg) protein is essential to thyroid hormone synthesis, playing a vital role in the regulation of metabolism, development and growth. Its structure is conserved among vertebrates. Tg is delivered through the secretory pathway of the thyroid follicular unit to the central colloid depository, where it is iodinated at specific tyrosine sites to form mono- or diiodotyrosine, which combine to produce triiodothyronine (T3) and thyroxine (T4), respectively. Synthesis of these hormones depends on the precise 3D structure of Tg, which has remained unknown despite decades of research. Here, we present the cryo-electron microscopy structure of human thyroglobulin (hTg) to a global resolution of 3.2 [A]. The structure provides detailed information on the location of the hTg hormonogenic sites and reveals the position as well as the role of many of its glycosylation sites. Our results offer structural insight into thyroid hormonogenesis and provide a fundamental understanding of clinically relevant hTg mutations, which can improve treatment of thyroid diseases.


title: modeling DNA opening in the eukaryotic transcription initiation complexes

abstract:
Recently, the molecular mechanisms of transcription initiation have been intensively studied. Especially, the cryo-electron microscopy revealed atomic structure details in key states in the eukaryotic transcription initiation. Yet, the dynamic processes of the promoter DNA opening in the pre-initiation complex remain obscured. In this study, based on the three cryo-electron microscopic yeast structures for the closed, open, and initially transcribing complexes, we performed multiscale molecular dynamics (MD) simulations to model structures and dynamic processes of DNA opening. Combining coarse-grained and all-atom MD simulations, we first obtained the atomic model for the DNA bubble in the open complexes. Then, in the MD simulation from the open to the initially transcribing complexes, we found a previously unidentified intermediate state which is formed by the bottleneck in the fork loop 1 of Pol II: The loop opening triggered the escape from the intermediate, serving as a gatekeeper of the promoter DNA opening. In the initially transcribing complex, the non-template DNA strand passes a groove made of the protrusion, the lobe, and the fork of Rpb2 subunit of Pol II, in which several positively charged and highly conserved residues exhibit key interactions to the non-template DNA strand.

Author SummaryTranscription is fundamental phenomenon in all species, and its regulation of the initiation process is important. In eukaryotes, multiple proteins, which is not only RNA polymerase but also transcription factors, assemble on the promotor to form the complex. After that, this complex open the part of DNA duplex, leading to forming single-stranded region for transcription. Previous study, including structural analysis and biochemical experiments, obtained the information about single-stranded region, but the structure is incomplete, so the details of the mechanism remains unclear. In this study, by the calculation using structural information about the protein-DNA complex, we obtained the structure of the complex with complete single-stranded region. As the result of the calculation, it found that the size of single-stranded region was fluctuated, which is related the sequence of the region. Furthermore, we found the intermediate state during the extended process of single-stranded region, which has not been reported in previous study. In this state, we found that the particular region of RNA polymerase is relevant to the extension of single-stranded region. These founding may contribute the understanding about the regulation of transcription initiation.


title: Combustible and electronic cigarette exposures increase ACE2 activity and SARS-CoV-2 Spike binding

abstract: The outbreak of coronavirus disease 2019 (COVID-19) has extensively impacted global health. The causative pathogen, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), binds to the angiotensin-converting enzyme 2 (ACE2) receptor, a transmembrane metallo-carboxypeptidase that is expressed in both membrane-anchored (mACE2) and soluble (sACE2) forms in the lung. Tobacco use has been speculated as a vulnerability factor for contracting SARS-CoV-2 infection and subsequent disease severity, whilst electronic cigarettes (e-cigarettes) have been shown to induce harmful proteomic and immune changes in the lungs of vapers. We therefore tested the hypothesis that combustible tobacco (e.g. cigarettes) and non-combustible e-cigarettes could affect ACE2 activity and subsequent SARS-CoV-2 infection. We observed that sACE2 activity was significantly higher in bronchoalveolar lavage fluid from both smokers and vapers compared to age-matched non-smokers. Exposure to cigarette smoke increased ACE2 levels, mACE2 activity, and sACE2 in primary bronchial epithelial cultures. Finally, treatment with either cigarette smoke condensate or JUUL e-liquid increased infections with a spike-coated SARS-CoV-2 pseudovirus. Overall, these observations suggest that tobacco product use elevates ACE2 activity and increases the potential for SARS-CoV-2 infection through enhanced spike protein binding.

category: physiology


title: Characterizing the middle-age neurophysiology using EEG/MEG

abstract:
Middle adulthood - the period of life between 40 and 60 years of age - is accompanied by important physical and emotional changes, as well as cognitive and neuronal ones. Nevertheless, middle age is often overlooked in neuroscience under the assumption that this is a time of relative stability, although cognitive decline, as well as changes in brain structure and function are well-established by the age of 60.

Here we characterized the middle-aged brain in the context of healthy younger and older adults by assessing resting-state electrophysiological and neuromagnetic activity in two different samples (N = 179, 631). Alpha and beta oscillations - two key ageing signatures - were analyzed in terms of spectral power and burst events. While posterior alpha power and burst rate features changed linearly with age, similarly to behavioral measures, sensorimotor beta power and burst rate properties varied non-linearly, with inflection points during middle age. The findings suggest that ageing is characterized by distinct spatial and temporal brain dynamics, some critically arising in middle age.


title: Spatially heterogeneous microstructural development within subcortical regions from 9-13 years

abstract: During late childhood behavioral changes, such as increased risk-taking and emotional reactivity, have been associated with the maturation of cortico-subcortical circuits. Understanding microstructural changes in subcortical regions may aid our understanding of how individual differences in these behaviors emerge. Restriction spectrum imaging (RSI) is a framework for modelling diffusion-weighted imaging that decomposes the diffusion signal from a voxel into hindered and restricted compartments. This yields greater specificity than conventional methods of characterizing intracellular diffusion. Using RSI, we modelled voxelwise restricted isotropic, N0, and anisotropic, ND, diffusion across the brain and measured cross-sectional and longitudinal age associations in a large sample (n=8,039) from the Adolescent Brain and Cognitive Development (ABCD) study aged 9-13 years. Older participants had higher N0 and ND across subcortical regions. The largest associations for N0 were within the basal ganglia and for ND within the ventral diencephalon. Importantly, age associations varied with respect to the internal cytoarchitecture within subcortical structures, for example age associations differed across thalamic nuclei. This suggests that developmental effects may map onto specific cell populations or circuits and highlights the utility of voxelwise compared to ROI-wise analyses. Future analyses will aim to understand the relevance of this subcortical microstructural developmental for behavioral outcomes.


title: Selective retinal ganglion cell loss and optic neuropathy in a humanized mouse model of familial dysautonomia

abstract: Familial dysautonomia (FD) is an autosomal recessive neurodegenerative disease caused by a splicing mutation in the gene encoding Elongator complex protein 1 (ELP1, also known as IKBKAP). This mutation results in tissue-specific skipping of exon 20 with a corresponding reduction of ELP1 protein, predominantly in the central and peripheral nervous system. Although FD patients have a complex neurological phenotype caused by continuous depletion of sensory and autonomic neurons, progressive visual decline leading to blindness is one of the most problematic aspect of the disease, as it severely affects their quality of life. To better understand the disease mechanism as well as to test the in vivo efficacy of targeted therapies for FD, we have recently generated a novel phenotypic mouse model, TgFD9; Elp1{triangleup}20/flox. This mouse exhibits most of the clinical features of the disease and accurately recapitulates the tissue-specific splicing defect observed in FD patients. Driven by the dire need to develop therapies targeting retinal degeneration in FD, herein, we comprehensively characterized the progression of the retinal phenotype in this mouse, and we demonstrated that it is possible to correct ELP1 splicing defect in the retina using the splicing modulator compound (SMC) BPN-15477.


title: Plasmodium falciparum Calcium Dependent Protein Kinase 4 is critical for male gametogenesis and transmission to the mosquito vector

abstract:
Gametocytes of the malaria parasite Plasmodium are taken up by the mosquito vector with an infectious blood meal, representing a critical stage for parasite transmission. Calcium dependent protein kinases (CDPKs) play key roles in calcium-mediated signaling across the complex life cycle of the parasite. We sought to understand their role in human parasite transmission from the host to the mosquito vector and thus investigated the role of the human-infective parasite Plasmodium falciparum CDPK4 in the parasite life cycle. P. falciparum cdpk4- parasites created by targeted gene deletion showed no effect in blood stage development or gametocyte development. However, cdpk4- parasites showed a severe defect in male gametogenesis and the emergence of flagellated male gametes. To understand the molecular underpinnings of this defect, we performed mass spectrometry-based phosphoproteomic analyses of wild type and Plasmodium falciparum cdpk4- late gametocyte stages, to identify key CDPK4-mediated phosphorylation events that may be important for the regulation of male gametogenesis. We further employed in vitro assays to identify these putative substrates of Plasmodium falciparum CDPK4. This indicated that CDPK4 regulates male gametogenesis by directly or indirectly controlling key essential events such as DNA replication, mRNA translation and cell motility. Taken together, our work demonstrates that PfCDPK4 is a central kinase that regulates exflagellation, and thereby is critical for parasite transmission to the mosquito vector.

IMPORTANCETransmission of the malaria parasite to the mosquito vector is critical for the completion of the sexual stage of the parasite life cycle and is dependent on the release of male gametes from the gametocyte body inside the mosquito midgut. In the present study, we demonstrate that PfCDPK4 is critical for male gametogenesis and is involved in phosphorylation of proteins essential for male gamete emergence. Targeting PfCDPK4 and its substrates may provide insights into achieving effective malaria transmission-blocking strategies.


title: Magnetic Bead-Based Separation (MBS) of Pneumococcal Serotypes

abstract: The separation of pneumococcal serotypes from a complex polymicrobial mixture may be required for different applications. For instance, a minority strain could be present at a low frequency in a clinical sample, making it difficult to identify and isolate by traditional culture-based methods. We therefore developed an assay to separate mixed pneumococcal samples using serotype-specific antiserum and a magnetic bead-based separation method. Using qPCR and colony counting methods, we first show that serotypes (12F, 23F, 3, 14, 19A and 15A) present at [~]0.1% of a dual serotype mixture can be enriched to between 10% and 90% of the final sample. We demonstrate two applications for this method: extraction of a known pneumococcal serotype from saliva samples and efficient purification of capsule switch variants from experimental transformation experiments. Moreover, this method may have further laboratory or clinical applications when the selection of specific serotypes is required.


title: Multi-omics profiling of Earth's biomes reveals that microbial and metabolite composition are shaped by the environment

abstract: As our understanding of the structure and diversity of the microbial world grows, interpreting how it functions is of critical interest for understanding and managing the many systems microbes influence. Despite advances in sequencing, lack of standardization challenges comparisons among studies that could provide global insight. Here, we present a multi-omics, meta-analysis of a novel, diverse set of microbial community samples collected for the Earth Microbiome Project. Standardized protocols and analytical methods for characterizing microbial communities, including assessment of function using untargeted metabolomics, facilitate identification of shared microbial and metabolite features, permitting us to explore diversity at extraordinary scale. In addition to a reference database for metagenomic and metabolomic data, we provide a framework for incorporating additional studies, enabling the expansion of existing knowledge in the form of a community resource that will become more valuable with time. To provide an example of applying this database, we tested the hypothesis that metabolic potential is not limited or enriched by the environment. Our results show that the relative abundances of microbially-related metabolites vary across habitats, and highlight the power of certain chemistry - in particular alkaloids - in distinguishing Earths environments.

category: ecology


title: Spatio-temporal point processes as meta-models for population dynamics in heterogeneous landscapes

abstract: Landscape heterogeneity affects population dynamics, which determine species persistence, diversity and interactions. These relationships can be accurately represented by advanced spatially-explicit models (SEMs) allowing for high levels of detail and precision. However, such approaches are characterised by high computational complexity, high amount of data and memory requirements, and spatio-temporal outputs may be difficult to analyse. A possibility to deal with this complexity is to aggregate outputs over time or space, but then interesting information may be masked and lost, such as local spatio-temporal relationships or patterns. An alternative solution is given by meta-models and meta-analysis, where simplified mathematical relationships are used to structure and summarise the complex transformations from inputs to outputs. Here, we propose an original approach to analyse SEM outputs. By developing a meta-modelling approach based on spatio-temporal point processes (STPPs), we characterise spatio-temporal population dynamics and landscape heterogeneity relationships in agricultural contexts. A landscape generator and a spatially-explicit population model simulate hierarchically the pest-predator dynamics of codling moth and ground beetles in apple orchards over heterogeneous agricultural landscapes. Spatio-temporally explicit outputs are simplified to marked point patterns of key events, such as local proliferation or introduction events. Then, we construct and estimate regression equations for multi-type STPPs composed of event occurrence intensity and magnitudes. Results provide local insights into spatio-temporal dynamics of pest-predator systems. We are able to differentiate the contributions of different driver categories (i.e., spatio-temporal, spatial, population dynamics). We highlight changes in the effects on occurrence intensity and magnitude when considering drivers at global or local scale. This approach leads to novel findings in agroecology where the organisation of cultivated fields and semi-natural elements are known to play a crucial role for pest regulation. It aids to formulate guidelines for biological control strategies at global and local scale.


title: Mangrove forests mitigate coral bleaching under thermal stress from climate change

abstract: Anthropogenic marine heatwaves are progressively degrading coral reef ecosystems worldwide via the process of coral bleaching (the expulsion of photosynthetic endosymbionts which reveals the coral skeleton). Corals from mangrove lagoons are hypothesised to increase resistance and resilience to coral bleaching, highlighting these areas as potential natural refuges for corals. Our study, the first conducted at a global-scale, reveals that coral reefs associated with mangrove forests are less likely to bleach under thermal stress, and thus, under scenarios of climate warming. The onset of severe bleaching occurred after 3.6 Degree Heating Weeks (DHW) in mangrove-associated reefs, compared to 2.23 DHW for non-mangrove associated reefs. These findings highlight the critical role of mangrove forests for coral reef persistence under climate change. Accordingly, conservation actions targeting the protection of mangroves are expected to contribute to the resilience and resistance of reef corals from bleaching as marine heatwaves continue to become more common.


title: Experimental depletion of gut microbiota diversity reduces host thermal tolerance and fitness under heat stress in a vertebrate ectotherm

abstract: Predicting the responses of ectotherms to climate change is a global conservation priority which requires identifying factors that influence how animals respond physiologically to changing temperature. Host-associated microbial communities impact animal physiology and have been shown to influence host thermal tolerance in invertebrate systems. However, the role of commensal microbiota in thermal tolerance of ectothermic vertebrates is unknown. Here we show that experimentally depleting the diversity of the tadpole gut microbiome through environmental water sterilization reduces the hosts acute thermal tolerance to both heat and cold, alters the thermal sensitivity of locomotor performance, and reduces animal survival under acute heat stress. We show that these tadpoles have reduced activities of mitochondrial enzymes and altered metabolic rates compared to tadpoles colonized with a diverse microbiota, which could underlie differences in thermal phenotypes. Our results demonstrate, for the first time, a link between the gut microbiome of an ectothermic vertebrate and the hosts thermal tolerance, performance, and fitness, thus highlighting the importance of considering host-associated microbial communities when predicting species responses to climate change.


title: Genome editing in animals with minimal PAM CRISPR-Cas9 enzymes

abstract:
The requirement for Cas nucleases to recognize a specific PAM is a major restriction for genome editing. SpCas9 variants SpG and SpRY, recognizing NGN and NRN PAM, respectively, have contributed to increase the number of editable genomic sites in cell cultures and plants. However, their use has not been demonstrated in animals.

We have characterized and optimized the activity of SpG and SpRY in zebrafish and C. elegans. Delivered as mRNA-gRNA or ribonucleoprotein (RNP) complexes, SpG and SpRY were able to induce mutations in vivo, albeit at a lower rate than SpCas9 in equivalent formulations. This lower activity was overcome by optimizing mRNA-gRNA or RNP concentration, leading to efficient mutagenesis at regions inaccessible to SpCas9. We also found that the CRISPRscan algorithm can predict SpG and SpRY activity in vivo. Finally, we applied SpG and SpRY to generate knock-ins by homology-directed repair. Altogether, our results expand the CRISPR-Cas targeting genomic landscape in animals.

category: genetics


title: Genome-wide reconstruction of rediploidization following autopolyploidizationacross one hundred million years of salmonid evolution

abstract: The long-term evolutionary impacts of whole genome duplication (WGD) are strongly influenced by the ensuing rediploidization process. Following autopolyploidization, rediploidization involves a transition from tetraploid to diploid meiotic pairing, allowing duplicated genes (ohnologues) to diverge genetically and functionally. Our understanding of autopolyploid rediploidization has been informed by a WGD event ancestral to salmonid fishes, where large genomic regions are characterized by temporally delayed rediploidization, allowing lineage-specific ohnologue sequence divergence in the major salmonid clades. Here, we investigate the long-term outcomes of autopolyploid rediploidization at genome-wide resolution, exploiting a recent  explosion of salmonid genome assemblies, including a new genome sequence for the huchen (Hucho hucho). We developed a genome alignment approach to capture duplicated regions across multiple species, allowing us to create 121,864 phylogenetic trees describing ohnologue divergence across salmonid evolution. Using molecular clock analysis, we show that 61% of the ancestral salmonid genome experienced an initial  wave of rediploidization in the late Cretaceous (85-106 Mya). This was followed by a period of relative genomic stasis lasting 17-39 My, where much of the genome remained in a tetraploid state. A second rediploidization wave began in the early Eocene and proceeded alongside species diversification, generating predictable patterns of lineage-specific ohnologue divergence, scaling in complexity with the number of speciation events. Finally, using gene set enrichment, gene expression, and codon-based selection analyses, we provide insights into potential functional outcomes of delayed rediploidization. Overall, this study enhances our understanding of delayed autopolyploid rediploidization and has broad implications for future studies of WGD events.


title: Microbiota and stress: a loop that impacts memory

abstract: Chronic stress and the gut microbiota appear to comprise a feed-forward loop, which contributes to the development of depressive disorders. Evidence suggests that memory can also be impaired by either chronic stress or microbiota imbalance. However, it remains to be established whether these could be a part of an integrated loop model and be responsible for memory impairments. To shed light on this, we used a two-pronged approach in Japanese quail: first stress-induced alterations in gut microbiota were characterized, then we tested whether this altered microbiota could affect brain and memory function when transferred to a germ-free host. The cecal microbiota of chronically stressed quails was found to be significantly different from that of unstressed individuals with lower  and {beta} diversities and increased Bacteroidetes abundance largely represented by the Alistipes genus, a well-known stress target in rodents and humans. The transfer of this altered microbiota into germ-free quails decreased their spatial and cue-based memory abilities as previously demonstrated in the stressed donors. The recipients also displayed increased anxiety-like behavior, reduced basal plasma corticosterone levels and differential gene expression in the brain. Furthermore, cecal microbiota transfer from a chronically stressed individual was sufficient to mimic the adverse impact of chronic stress on memory in recipient hosts and this action may be related to the Alistipes genus. Our results provide evidence of a feed-forward loop system linking the microbiota-gut-brain axis to stress and memory function and suggest that maintaining a healthy microbiota could help alleviate memory impairments linked to chronic stress.

category: animal behavior and cognition


title: Automated Generation of Cerebral Blood Flow Maps Using Deep Learning and Multiple Delay Arterial Spin-Labelled MRI

abstract: The purpose of this work was to develop and evaluate a deep learning approach for estimation of cerebral blood flow (CBF) and arterial transit time (ATT) from multiple post-label delay (PLD) arterial spin-labelled (ASL) MRI. Six-PLD ASL MRI was acquired on a 1.5T or 3T system among 99 older males and females with and without cognitive impairment. We trained and compared two network architectures: standard feed-forward convolutional neural network (CNN) and U-Net. Mean absolute error (MAE) was evaluated between model estimates and ground truth obtained through conventional processing. The best-performing model was re-trained on inputs with missing PLDs to investigate generalizability to different PLD schedules. Relative to the CNN, the U-Net yielded lower MAE on training data. On test data, the U-Net MAE was 8.4{+/-}1.4 ml/100g/min for CBF and 0.22{+/-}0.09 s for ATT. Model uncertainty, estimated with Monte Carlo dropout, was associated with model error. Network estimates remained stable when tested on inputs with up to three missing PLD images. Mean processing times were: U-Net pipeline = 10.77s; ground truth pipeline = 10min 41s. These results suggest hemodynamic parameter estimation from 1.5T and 3T multi-PLD ASL MRI is feasible and fast with a deep learning image-generation approach.

category: bioengineering


title: Accurate Virus Identification with Interpretable Raman Signatures by Machine Learning

abstract:
Rapid identification of newly emerging or circulating viruses is an important first step toward managing the public health response to potential outbreaks. A portable virus capture device coupled with label-free Raman Spectroscopy holds the promise of fast detection by rapidly obtaining the Raman signature of a virus followed by a machine learning approach applied to recognize the virus based on its Raman spectrum. In this paper, we present a machine learning analysis on Raman spectra of human and avian viruses. A Convolutional Neural Network (CNN) classifier specifically designed for spectral data achieves very high accuracy for a variety of virus type or subtype identification tasks. In particular, it achieves 99% accuracy for classifying influenza virus type A vs. type B, 96% accuracy for classifying four subtypes of influenza A, 95% accuracy for differentiating enveloped and non-enveloped viruses, and 99% for differentiating avian coronavirus (infectious bronchitis virus, IBV) from other avian viruses. Furthermore, interpretation of neural net responses in the trained CNN model using a full-gradient algorithm highlights Raman spectral ranges that are most important to virus identification. By correlating ML-selected salient Raman ranges with the signature ranges of known biomolecules and chemical functional groups (e.g. amide, amino acid, carboxylic acid) we verify that our ML model effectively recognizes the Raman signatures of proteins, lipids and other vital functional groups present in different viruses and uses a weighted combination of these signatures to identify viruses. The accurate and interpretable machine learning model developed for Raman virus identification presents promising potential in a real-time virus detection system.

Significance StatementA portable micro-fluidic platform for virus capture promises rapid enrichment and label-free optical identification of viruses by Raman spectroscopy. A large Raman dataset collected on a variety of viruses enables the training of machine learning (ML) models capable of highly accurate and sensitive virus identification. The trained ML models can then be integrated with the portable device to provide real-time virus detection and identification capability. We validate this conceptual framework by presenting highly accurate virus type and subtype identification results using a convolutional neural network to classify Raman spectra of viruses.


title: Human magnetic field registration capability using low-field magnetic sensors

abstract:
The aim of the study was to find out whether it is possible to detect the human magnetic field without shielding using sensors. For this, an experiment "the possibility of detecting the human magnetic field using sensors" was conducted. During the experiment it was found that with the help of a low-field magnetic detector it is possible to register a persons magnetic field, which is changing if there is a change in a heart rate.

During the study, a device for recording the magnetic field of a human was assembled, a methodology for obtaining data was developed, a description of the materials and equipment used was provided. In accordance with the described methods of data collection, measurements of human magnetic field with and without load were made. The data obtained during the study were processed and the results were displayed. Based on the obtained results, an analysis was carried out, conclusions were drawn and recommendations for subsequent studies were indicated. As a result, the possibility of detecting a humans magnetic field using sensors was first studied.


title: Evolutionary tracking of cancer haplotypes at single-cell resolution

abstract: Cancer genomes exhibit extensive chromosomal copy number changes and structural variation, yet how allele specific alterations drive cancer genome evolution remains unclear. Here, through application of a new computational approach we report allele specific copy number alterations in 11,097 single cell whole genomes from genetically engineered mammary epithelial cells and 21,852 cells from high grade serous ovarian and triple negative breast cancers. Resolving single cell copy number profiles to individual alleles uncovered genomic background distributions of gains, losses and loss of heterozygosity, yielding evidence of positive selection of specific chromosomal alterations. In addition specific genomic loci in maternal and paternal alleles were commonly found to be altered in parallel with convergent phenotypic transcriptional effects. Finally we show that haplotype specific alterations trace the cyclical etiology of high level amplifications and reveal clonal haplotype decomposition of complex structures. Together, our results illuminate how allele and haplotype specific alterations, here determined across thousands of single cell cancer genomes, impact the etiology and evolution of structural variations in human tumours.

category: cancer biology


title: A mathematical model for phenotypic heterogeneity in breast cancer with implications for therapeutic strategies

abstract: Inevitably, almost all cancer patients develop resistance to targeted therapy. Intratumor heterogeneity is a major cause of drug resistance. Mathematical models that explain experiments quantitatively are useful in understanding the origin of intratumor heterogeneity, which then could be used to explore scenarios for efficacious therapy. Here, we develop a mathematical model to investigate intratumor heterogeneity in breast cancer by exploiting the observation that HER2+ and HER2- cells could divide symmetrically or asymmetrically. Our predictions for the evolution of cell fractions are in quantitative agreement with single-cell experiments. Remarkably, the colony size of HER2+ cells emerging from a single HER2- cell (or vice versa), which occurs in about four cell doublings, also agrees with experimental results, without tweaking any parameter in the model. The theory quantitatively explains experimental data on the responses of breast tumors under different treatment protocols. We then used the model to predict that, not only the order of two drugs, but also the treatment period for each drug and the tumor cell plasticity could be manipulated to improve the treatment efficacy. Mathematical models, when integrated with data on patients, make possible exploration of a broad range of parameters readily, which might provide insights in devising effective therapies.


title: Quantitative examination of five stochastic cell-cycle and cell-size control models for Escherichia coli and Bacillus subtilis

abstract: We examine five quantitative models of the cell-cycle and cell-size control in Escherichia coli and Bacillus subtilis that have been proposed over the last decade to explain single-cell experimental data generated with high-throughput methods. After presenting the statistical properties of these models, we test their predictions against experimental data. Based on simple calculations of the defining correlations in each model, we first dismiss the stochastic Helmstetter-Cooper model and the Initiation Adder model, and show that both the Replication Double Adder and the Independent Double Adder model are more consistent with the data than the other models. We then apply a recently proposed statistical analysis method and obtain that the Independent Double Adder model is the most likely model of the cell cycle. By showing that the Replication Double Adder model is fundamentally inconsistent with size convergence by the adder principle, we conclude that the Independent Double Adder model is most consistent with the data and the biology of bacterial cell-cycle and cell-size control. Mechanistically, the Independent Adder Model is equivalent to two biological principles: (i) balanced biosynthesis of the cell-cycle proteins, and (ii) their accumulation to a respective threshold number to trigger initiation and division.

category: systems biology


title: Microstructural development across white matter from 9-13 years

abstract: During late childhood behavioral changes, such as increased risk-taking and emotional reactivity, have been associated with the maturation of cortico-cortico and cortico-subcortical circuits. Understanding microstructural changes in both white matter and subcortical regions may aid our understanding of how individual differences in these behaviors emerge. Restriction spectrum imaging (RSI) is a framework for modelling diffusion-weighted imaging that decomposes the diffusion signal from a voxel into hindered, restricted, and free compartments. This yields greater specificity than conventional methods of characterizing diffusion. Using RSI, we quantified voxelwise restricted diffusion across the brain and measured age associations in a large sample (n=8,086) from the Adolescent Brain and Cognitive Development (ABCD) study aged 9-14 years. Older participants showed a higher restricted signal fraction across the brain, with the largest associations in subcortical regions, particularly the basal ganglia and ventral diencephalon. Importantly, age associations varied with respect to the cytoarchitecture within white matter fiber tracts and subcortical structures, for example age associations differed across thalamic nuclei. This suggests that age-related changes may map onto specific cell populations or circuits and highlights the utility of voxelwise compared to ROI-wise analyses. Future analyses will aim to understand the relevance of this microstructural developmental for behavioral outcomes.


title: Microstructural development from 9-14 years: evidence from the ABCD Study


title: Repurposing diphenylbutylpiperidine-class antipsychotic drugs for host-directed therapy of Mycobacterium tuberculosis and Salmonella enterica infections

abstract:
The persistent increase of multidrug-resistant (MDR) Mycobacterium tuberculosis (Mtb) infections negatively impacts Tuberculosis (TB) treatment outcomes. Host-directed therapies (HDT) pose an complementing strategy, particularly since Mtb is highly successful in evading host-defense by manipulating host-signaling pathways. Here, we screened a library containing autophagy-modulating compounds for their ability to inhibit intracellular Mtb-bacteria. Several active compounds were identified, including two drugs of the diphenylbutylpiperidine-class, Fluspirilene and Pimozide, commonly used as antipsychotics. Both molecules inhibited intracellular Mtb in pro- as well as anti-inflammatory primary human macrophages in a host-directed manner and synergized with conventional anti-bacterials. Importantly, these inhibitory effects extended to MDR-Mtb strains and the unrelated intracellular pathogen, Salmonella enterica serovar Typhimurium (Stm). Mechanistically Fluspirilene and Pimozide were shown to regulate autophagy and alter the lysosomal response, partly correlating with increased bacterial localization to autophago(lyso)somes. Pimozides and Fluspirilenes efficacy was inhibited by antioxidants, suggesting involvement of the oxidative-stress response in Mtb growth control. Furthermore, Fluspirilene and especially Pimozide counteracted Mtb-induced STAT5 phosphorylation, thereby reducing Mtb phagosome-localized CISH that promotes phagosomal acidification.

In conclusion, two approved antipsychotic drugs, Pimozide and Fluspirilene, constitute highly promising and rapidly translatable candidates for HDT against Mtb and Stm and act by modulating the autophagic/lysosomal response by multiple mechanisms.

category: immunology


title: Revealing the full biosphere structure and versatile metabolic functions in the deepest ocean sediment of the Challenger Deep

abstract:
BackgroundThe full biosphere structure and functional exploration of the microbial communities of the Challenger Deep of the Mariana Trench, the deepest known hadal zone on Earth, lag far behind that of other marine realms.

ResultsWe adopt a deep metagenomics approach to investigate the microbiome in the sediment of Challenger Deep, Mariana Trench. We construct 178 metagenome-assembled genomes (MAGs) representing 26 phyla, 16 of which are reported from hadal sediment for the first time. Based on the MAGs, we find the microbial community functions are marked by enrichment and prevalence of mixotrophy and facultative anaerobic metabolism. The microeukaryotic community is found to be dominated by six fungal groups that are characterized for the first time in hadal sediment to possess the assimilatory and dissimilatory nitrate/sulfate reduction, and hydrogen sulfide oxidation pathways. By metaviromic analysis, we reveal novel hadal Caudovirales clades, distinctive virus-host interactions, and specialized auxiliary metabolic genes for modulating hosts nitrogen/sulfur metabolism. The hadal microbiome is further investigated by large-scale cultivation that cataloged 1070 bacterial and 19 fungal isolates from the Challenger Deep sediment, many of which are found to be new species specialized in the hadal habitat.

ConclusionOur hadal MAGs and isolates increase the diversity of the Challenger Deep sediment microbial genomes and isolates present in the public. The deep metagenomics approach fills the knowledge gaps in structure and diversity of the hadal microbiome, and provides novel insight into the ecology and metabolism of eukaryotic and viral components in the deepest biosphere on earth.


title: Airborne bacteria over oceans shed light on global biogeodiversity patterns

abstract: Microbes are ubiquitous in the oceans and the atmosphere, playing essential roles in biogeochemical processes. The bio-exchanges between the two environments can provide important insights into microbial distribution and diversity but are still not well understood. We simultaneously surveyed the genomic diversity of airborne and marine bacterial communities across 15 000 kilometers in the Atlantic and Pacific oceans. Higher variability of microbial community composition was observed in the atmosphere than in the ocean surface waters. In addition, a greater similarity was observed between oceans than their overlaying atmosphere, and between atmospheric samples than with the ocean beneath. We additionally detected a higher coverage rate and relative abundance of marine bacteria in the Pacific atmosphere as compared to the Atlantic, while the dominant fraction in the Atlantic atmosphere was annotated as soil-associated bacteria. This study advances our understanding of microbial dispersion in the ocean, the atmosphere, and the exchange between them, as well as their potential impact on microbial composition, ecology, and biogeochemistry.


title: A cross biomes bacterial diversity shed light on ocean-atmosphere microbial transmission.


title: Glyoxal as alternative fixative for single cell RNA sequencing

abstract: Single cell RNA sequencing (scRNA-seq) has become an important method to identify cell types, delineate the trajectories of cell differentiation in whole organisms and understand the heterogeneity in cellular responses. Nevertheless, sample collection and processing remain a severe bottleneck for scRNA-seq experiments. Cell isolation protocols often lead to significant changes in the transcriptomes of cells, requiring novel methods to preserve cell states. Here, we developed and benchmarked protocols using glyoxal as a fixative for scRNA-seq application. Using Drop-seq methodology, we detected high numbers of transcripts and genes from glyoxal-fixed Drosophila cells after scRNA-seq. The effective glyoxal fixation of transcriptomes in Drosophila and human cells was further supported by a high correlation of gene expression data between glyoxal-fixed and unfixed samples. Accordingly, we also found highly expressed genes overlapping to a large extent between experimental conditions. These results indicated that our fixation protocol did not induce considerable changes in gene expression and conserved the transcriptome for subsequent single cell isolation procedures. In conclusion, we present glyoxal as a suitable fixative for Drosophila cells and potentially cells of other species that allows high-quality scRNA-seq applications.

category: genomics


title: In-depth sequence-function characterization reveals multiple paths to enhance phenylalanine ammonia-lyase (PAL) activity.

abstract: Phenylalanine ammonia-lyases (PALs) deaminate L-phenylalanine to trans-cinnamic acid and ammonium and have idespread application in chemo-enzymatic synthesis, agriculture, and medicine. In particular, the PAL from Anabaena variabilis (Trichormus variabilis) has garnered significant attention as the active ingredient in Pegvaliase(R), the only FDA-approved drug treating classical phenylketonuria (PKU). Although an extensive body of literature exists on structure, substrate-specificity, and catalytic mechanism, protein-wide sequence determinants of function remain unknown, which limits the ability to rationally engineer these enzymes. Previously, we developed a high-throughput screen (HTS) for PAL, and here, we leverage it to create a detailed sequence-function landscape of PAL by performing deep mutational scanning (DMS). Our method revealed 79 hotspots that affected a positive change in enzyme fitness, many of which have not been reported previously. Using fitness values and structure-function analysis, we picked a subset of residues for comprehensive single- and multi-site saturation mutagenesis to improve the catalytic activity of PAL and identified combinations of mutations that led to improvement in reaction kinetics in cell-free and cellular contexts. To understand the mechanistic role of the most beneficial mutations, we performed QM/MM and MD and observed that different mutants confer improved catalytic activity via different mechanisms, including stabilizing first transition and intermediate states and improving substrate diffusion into the active site, and decreased product inhibition. Thus, this work provides a comprehensive sequence-function relationship for PAL, identifies positions that improve PAL activity when mutated and assesses their mechanisms of action.


title: Influence of the metallized coils on human leg blood circulation

abstract: The aim of the study was to find out if magnetic field generated by the human body affects a human blood flow. The idea is based on Lenzs law where the blood flow induces an opposing alternating magnetic field (OAMF). In the experiment the OAMF will be modulated by repeating heart contractions (pulses). In an experiment with metallized coils it was found that wearing metal coils affects blood flow and it differs from when coils were not worn.


title: The role of the cannabinoid system in fear memory and extinction in male and female mice

abstract: The prevalence of post-traumatic stress disorder (PTSD) is higher in women than in men. Among both humans and mice, females exhibit higher resistance to fear extinction than males, suggesting that differences between sexes in processes of fear extinction are involved in the pathophysiology of such fear-related diseases. Sex differences in molecular mechanisms for fear memory and extinction are unclear. The cannabinoid (CB) system is well known to be involved in fear memory and extinction, but this involvement is based mainly on experiments using male rodents. It has been unclear whether there are sex differences in the role of the CB system in fear memory and extinction. To explore the possibility of such differences, we investigated the effects of pharmacological manipulations of the CB system on the retrieval and extinction of contextual fear memory in male and female mice. WIN55,212-2, a CB receptor (CBR) agonist, augmented the retrieval of fear memory in both sexes, but SR141716 (a CB1R antagonist) did not affect it in either sex. An enhancement of 2-arachidonylglycerol (2-AG, one of the two major endocannabinoids) via JZL184 [an inhibitor of the 2-AG hydrolase monoacylglycerol lipase (MAGL)], augmented the retrieval of fear memory through the activation of CB1R but not CB2R in female mice. In contrast, the enhancement of N-arachidonylethanolamine (AEA, the other major endocannabinoid) via URB597, an inhibitor of an AEA hydrolase (fatty acid amide hydrolase-1) did not show any effects on the retrieval or extinction of fear memory in either sex. WIN55,212-2, SR141716, and JZL184 inhibited fear extinction irrespective of sex. These results suggest that although the role of CB1R in the retrieval and extinction of contextual fear memory is common among males and females, the effects of an increase in the 2-AG level on the retrieval of contextual fear memory differ between the sexes.


title: Meta-ecosystem dynamics drive the spatial distribution of functional groups in river networks

abstract: The meta-ecosystem concept provides a theoretical framework to study the effect of local and regional flows of resources on ecosystem dynamics. Meta-ecosystem theory has hitherto been applied to highly abstract landscapes, and meta-ecosystem dynamics in real-world landscapes remain largely unexplored. River networks constitute a prime example of meta-ecosystems, being characterized by directional resource flows from upstream to downstream communities and from the terrestrial to the aquatic realm. These flows have been thoroughly described by the River Continuum Concept (RCC), a seminal concept in freshwater ecology, stating that observed spatial variations in the relative abundances of invertebrate functional groups reflect systematic shifts in types and locations of food resources, which are in turn determined by the physical attributes of river reaches. Hence, the RCC represents a solid conceptual basis for determining how changes in landscape structure and resource flows will translate into local and regional changes in community composition. Here, we develop and analyse a riverine meta-ecosystem model inspired by the RCC, which builds upon a physically-based landscape model of dendritic river networks. We show that the spatial distributions and regional biomass of invertebrate functional groups observed in stream communities are determined by the spatial structure and scaling attributes of dendritic river networks, as well as by specific rates of resource flows. Neglecting any of these aspects in modelling river meta-ecosystems would result in unrealistic community patterns. Moreover, we observed that high rates of resource flow, for example due to river anthropization, have a negative effect on the regional biomass of all functional groups studied, and can lead to cascading extinctions at the meta-ecosystem scale. Our work paves the way for the development of physically-based meta-ecosystem models to understand the structure and functioning of real-world ecosystems.


title: Single-cell RNA-sequencing reveals widespread personalized, context-specific gene expression regulation in immune cells.

abstract: Gene expression and its regulation can be context-dependent. To dissect this, using samples from 120 individuals, we single-cell RNA-sequenced 1.3M peripheral blood mononuclear cells exposed to three different pathogens at two time points or left unexposed. This revealed thousands of cell type-specific expression changes (eQTLs) and pathogen-induced expression changes (response QTLs) that are influenced by genetic variation. In monocytes, the strongest responder to pathogen stimulations, genetics also affected co-expression of 71.4% of these eQTL genes. For example, the pathogen recognition receptor CLEC12A showed many such co-expression interactions, but only in monocytes after 3h pathogen stimulation. Further analysis linked this to interferon-regulating transcription factors, a finding that we recapitulated in an independent cohort of patients with systemic lupus erythematosus, a condition characterized by increased interferon activity. Altogether, this study highlights the importance of context for gaining a better understanding of the mechanisms of gene regulation in health and disease.


title: Mapping the sequence specificity of heterotypic amyloid interactions enables the identification of aggregation modifiers

abstract: Heterotypic amyloid interactions between related protein sequences have been observed in functional and disease amyloids. While sequence homology seems to favour heterotypic amyloid interactions, we have no systematic understanding of the structural rules determining such interactions nor whether they inhibit or facilitate amyloid assembly. Using structure-based thermodynamic calculations and extensive experimental validation, we performed a comprehensive exploration of the defining role of sequence promiscuity in amyloid interactions. Using this knowledge, we demonstrate, using tau as a model system, that predicted cross-interactions driven by sequence homology indeed can modify nucleation, fibril morphology, kinetic assembly and cellular spreading of aggregates. We also find that these heterotypic amyloid interactions can result in the mis-localisation of brain-expressed protein sequences with prevalent activities in neurodegenerative disorders. Our findings suggest a structural mechanism by which the proteomic background can modulate the aggregation propensity of amyloidogenic proteins and discuss how such sequence-specific proteostatic perturbations could contribute to the selective cellular susceptibility of amyloid disease progression.


title: How does literacy affect speech processing? Not by enhancing cortical responses to speech, but by promoting connectivity of acoustic-phonetic and graphomotor cortices.

abstract:
Previous research suggest that literacy, specifically learning alphabetic letter-to-phoneme mappings, modifies online speech processing, and enhances brain responses to speech in auditory areas associated with phonological processing (Dehaene et al., 2010). However, alphabets are not the only orthographic systems in use in the world, and hundreds of millions of individuals speak languages that are not written using alphabets. In order to make claims that literacy per se has broad and general consequences for brain responses to speech, one must seek confirmatory evidence from non-alphabetic literacy. To this end, we conducted a longitudinal fMRI study in India probing the effect of literacy in Devanagari, an abubgida, on functional connectivity and cerebral responses to speech in 91 variously literate Hindi-speaking individuals. Twenty-two completely illiterate participants underwent six months of reading and writing training. Devanagari literacy increases functional connectivity between acoustic-phonetic and graphomotor brain areas, but we find no evidence that literacy changes the way speech is processed, either in cross-sectional or longitudinal analyses. These findings shows that a radical reconfiguration of the neurofunctional substrates of online speech processing is not a universal result of learning to read, and raise the possibility that writing, not only reading, may be instrumental in moulding literate speech perception.

Significance StatementIt has come to be accepted that a consequence of being able to read is enhanced auditory processing of speech, reflected by increased cortical responses in areas associated with phonological processing. Here we find no relationship between literacy and the magnitude of brain response to speech stimuli in individuals who speak Hindi, which is written using a non-alphabetic script, Devanagari - an abugida. We propose that the exact nature of the script under examination must be considered before making sweeping claims about the consequences of literacy for the brain. Further, we find evidence that literacy enhances functional connectivity between auditory processing areas and graphomotor areas, suggesting a mechanism whereby learning to write, not only to read, might influence speech perception.


title: Single snapshot quantitative phase imaging with polarization differential interference contrast

abstract: We present quantitative phase imaging with polarization differential interference contrast (PDIC) realized on a slightly modified differential interference contrast (DIC) microscope. By recording the Stokes vector rather than the intensity of the differential interference pattern with a polarization camera, PDIC enables single snapshot quantitative phase imaging with high spatial resolution in real-time at speed limited by the camera frame rate alone. The approach applies to either absorptive or transparent samples and can integrate simply with fluorescence imaging for co-registered simultaneous measurements. Furthermore, an algorithm with total variation regularization is introduced to solve the quantitative phase map from partial derivatives. After quantifying the accuracy of PDIC phase imaging with numerical simulations and phantom measurements, we demonstrate the biomedical applications by imaging the quantitative phase of both stained and unstained histological tissue sections and visualizing the fission yeast Schizosaccharomyces pombes cytokinesis.


title: A tug of war between filament treadmilling and myosin induced contractility generates actin cortex

abstract: In most eukaryotic cells, actin filaments assemble into a shell-like actin cortex under the plasma membrane, controlling cellular morphology, mechanics, and signaling. The actin cortex is highly polymorphic, adopting diverse forms such as the ring-like structures found in podosomes, axonal rings, and immune synapses. The biophysical principles that underlie the formation of actin cortices and their structural plasticity remain unknown. Using a molecular simulation platform, called MEDYAN, we discovered that varying the filament treadmilling rate induces a finite size phase transition in actomyosin network structure. We found that actomyosin networks condense into clusters at low treadmilling rates but form ring-like or cortex-like structures at high treadmilling rates. This mechanism is supported by our corroborating experiments on live T cells, which show that disrupting filament treadmilling induces centripetal collapse of pre-existing actin rings and the formation of clusters. Our analyses suggest that the actin cortex is a preferred state of low mechanical energy, which is, importantly, only reachable at high treadmilling rates.


title: Structural insights into the modes of relaxin-binding and tethered-agonist activation of RXFP1 and RXFP2

abstract: Our poor understanding of the mechanism by which the peptide-hormone H2 relaxin activates its G protein coupled receptor, RXFP1 and the related receptor RXFP2, has hindered progress in its therapeutic development. Both receptors possess large ectodomains, which bind H2 relaxin, and contain an N-terminal LDLa module that is essential for receptor signalling and postulated to be a tethered agonist. Here, we show that a conserved motif (GDxxGWxxxF), C-terminal to the LDLa, is critical for receptor activity. Importantly, this motif adopts different structures in RXFP1 and RXFP2, suggesting distinct activation mechanisms. For RXFP1, the motif is flexible, weakly associates with the LDLa, and requires H2 relaxin binding to stabilize an active conformation. Conversely, the GDxxGWxxxF motif in RXFP2 is more closely associated with the LDLa, forming an essential binding interface for H2 relaxin. These differences in the activation mechanism will aid drug development targeting these receptors.


title: Heme oxygenase-2 (HO-2) binds and buffers labile heme, which is largely oxidized, in human embryonic kidney cells

abstract: Heme oxygenases (HO) detoxify heme by oxidatively degrading it into carbon monoxide, iron, and biliverdin, which is reduced to bilirubin and excreted. Humans express two isoforms: inducible HO-1, which is up-regulated in response to various stressors, including excess heme, and constitutive HO-2. While much is known about the regulation and physiological function of HO-1, comparatively little is known about the role of HO-2 in regulating heme homeostasis. The biochemical necessity for expressing constitutive HO-2 is largely dependent on whether heme is sufficiently abundant and accessible as a substrate under conditions in which HO-1 is not induced. By measuring labile heme, total heme, and bilirubin in human embryonic kidney HEK293 cells with silenced or over-expressed HO-2, and various HO-2 mutant alleles, we found that endogenous heme is too limiting to support HO-2 catalyzed heme degradation. Rather, we discovered that a novel role for HO-2 is to bind and buffer labile heme. Taken together, in the absence of excess heme, we propose that HO-2 regulates heme homeostasis by acting as a heme buffering factor in control of heme bioavailability. When heme is in excess, HO-1 is induced and both HO-2 and HO-1 can provide protection from heme toxicity by enzymatically degrading it. Our results explain why catalytically inactive mutants of HO-2 are cytoprotective against oxidative stress. Moreover, the change in bioavailable heme due to HO-2 overexpression, which selectively binds ferric over ferrous heme, is consistent with the labile heme pool being oxidized, thereby providing new insights into heme trafficking and signaling.


title: Expression of extracellular Hsp90 is a molecular signature of T cell activation, providing a means to image and target T Cell activation in autoimmune disease

abstract:
Heat shock protein 90 (Hsp90) maintains cellular proteostasis during stress and has been under investigation as a therapeutic target in cancer for over two decades. We and others have identified an extracellularly expressed form of Hsp90, eHsp90, that previously appeared to be restricted to rapidly proliferating cells exhibiting a metastatic phenotype. Here, we used HS-131, a fluor-tethered eHsp90 inhibitor, to quantify the effect of T cell activation on the expression of eHsp90 in human and mouse T cells. In cell based assays, stimulation of human T cells induced a 20-fold increase in eHsp90 expression at the plasma membrane, suggesting trafficking of eHsp90 is acutely regulated by TCR and inflammatory mediated signaling. Following injection of HS-131 in mouse models of human rheumatoid arthritis and inflammatory bowel disease, we detected localization of the probe at sites of active disease, consistent with immune cell invasion. Moreover, despite rapid hepatobiliary clearance, HS-131 demonstrated efficacy in delaying the onset and progression of disease in the arthritis model. Our results suggest eHsp90 expression at the plasma membrane of T cells is a molecular marker of autoimmune induced activation and potentially a therapeutic target for chronic diseases such as rheumatoid arthritis and inflammatory bowel disease.

PerspectiveT cells mediate many maladaptive disease pathologies such as autoimmune disorders. Many immunosuppressants in clinical use act by preventing the activation of T cells. However, this approach can lead to increased rates of opportunistic infection and malignancy. Here, we show for the first time that eHsp90 is upregulated during T cell activation in response to exogenous ligands. Therefore, pharmacological inhibition of eHsp90 may provide a means to target only activated T cells for immunosuppression. Selective targeting of only activated T cells could be efficacious against autoimmune disease without increasing the incidence of undesirable outcomes. Additionally, the presence of eHsp90 on the surface of activated T cells could be diagnostically useful to track the status and progression of autoimmune disease in patients.

category: pharmacology and toxicology


title: Evolution of enhanced innate immune evasion by the SARS-CoV-2 B.1.1.7 UK variant

abstract: Emergence of SARS-CoV-2 variants, including the globally successful B.1.1.7 lineage, suggests viral adaptations to host selective pressures resulting in more efficient transmission. Although much effort has focused on Spike adaptation for viral entry and adaptive immune escape, B.1.1.7 mutations outside Spike likely contribute to enhance transmission. Here we used unbiased abundance proteomics, phosphoproteomics, mRNA sequencing and viral replication assays to show that B.1.1.7 isolates more effectively suppress host innate immune responses in airway epithelial cells. We found that B.1.1.7 isolates have dramatically increased subgenomic RNA and protein levels of Orf9b and Orf6, both known innate immune antagonists. Expression of Orf9b alone suppressed the innate immune response through interaction with TOM70, a mitochondrial protein required for RNA sensing adaptor MAVS activation, and Orf9b binding and activity was regulated via phosphorylation. We conclude that B.1.1.7 has evolved beyond the Spike coding region to more effectively antagonise host innate immune responses through upregulation of specific subgenomic RNA synthesis and increased protein expression of key innate immune antagonists. We propose that more effective innate immune antagonism increases the likelihood of successful B.1.1.7 transmission, and may increase in vivo replication and duration of infection.


title: Consumers' active choice behavior promotes coevolutionary units

abstract: Individual behavior and local context are processes that can influence the structure and evolution of ecological interactions. In trophic interactions, consumers can increase their fitness by actively choosing resources that enhance their chances of exploring them successfully. Upon searching for potential resources, they are able to decide which one to choose according to their fitness benefit and maneuverability. Mathematical modeling is often employed in theoretical studies to understand the coevolutionary dynamics between these species. However, they often disregard the individual consumer behavior since the complexity of these systems usually requires simplifying assumptions about interaction details. Using an individual-based model, we model a community of several species that interact antagonistically. The trait of each individual is modeled explicitly and is subjected to the interaction pressure. In addition, consumers can actively choose the resources that guarantee greater fitness. We show that active consumer choice can generate coevolutionary units over time. It means that the traits of both consumers and resources converge into multiple groups with similar traits, exerting reciprocal selective pressure between them. We also observed that network structure has a greater dependence on the parameter that delimits active consumer choice than on the intensity of selective pressure. Consequently, this parameter can closely match empirical networks. Thus, we consider that the inclusion of consumers active choice behavior in the models plays an important role in the ecological and evolutionary processes that structure these communities.


title: The biaxial mechanics of thermally denaturing skin - Part I: Experiments

abstract: The mechanics of collageneous soft tissues, such as skin, are sensitive to heat. Thus, quantifying and modeling thermo-mechanical coupling of skin is critical to our understanding of skins physiology, pathophysiology, as well as its treatment. However, key gaps persist in our knowledge about skins coupled thermo-mechanics. Among them, we havent quantified the role of skins microstructural organization in its response to superphysiological loading. To fill this gap, we conducted a comprehensive set of experiments in which we combined biaxial mechanical testing with histology and two-photon imaging under liquid heat treatment. Among other observations, we found that unconstrained skin, when exposed to high temperatures, shrinks anisotropically with the principle direction of shrinkage being aligned with collagens principle orientation. Additionally, we found that when skin is isometrically constrained, it produces significant forces during denaturing that are also anisotropic. Finally, we found that denaturation significantly alters the mechanical behavior of skin. For short exposure times, this alteration is reflected in a reduction of stiffness at high strains. At long exposure times, the tissue softened to a point where it became untestable. We supplemented our findings with confirmation of collagen denaturation in skin via loss of birefringence and second harmonic generation. Finally, we captured all time-, temperature-, and direction-dependent experimental findings in a hypothetical model. Thus, this work fills a fundamental gap in our current understanding of skin thermo-mechanics and will support future developments in thermal injury prevention, thermal injury management, and thermal therapeutics of skin.