title: Cross-talk between cAMP and Ca2+ signalling in cardiac pacemaker cells involves IP3-evoked Ca2+ release and stimulation of adenylyl cyclase 1

abstract: Atrial arrhythmias, such as atrial fibrillation (AF), are a major mortality risk and a leading cause of stroke. The IP3 signalling pathway has been proposed as an atrial specific target for AF therapy, and atrial IP3 signalling has been linked to the activation of calcium sensitive adenylyl cyclases AC1 and AC8. Here we investigated the involvement of AC1 in the response of intact mouse atrial tissue and isolated guinea pig atrial and sinoatrial node (SAN) cells to the -adrenoceptor agonist phenylephrine (PE) using the selective AC1 inhibitor ST034307. The maximum rate change of spontaneously beating mouse right atrial tissue exposed to PE was reduced from 14.46 % to 8.17% (P = 0.005) in the presence of 1 M ST034307, whereas the increase in tension generated in paced left atrial tissue in the presence of PE was not inhibited by ST034307 (Control = 14.20 %, ST034307 = 16.32 %; P > 0.05). Experiments were performed using isolated guinea pig atrial and SAN cells loaded with Fluo-5F-AM to record changes in calcium transient amplitude (CaT) generated by 10M PE in the presence and absence of 1M ST034307. ST034307 significantly reduced the beating rate of SAN cells (0.34-fold decrease; P = 0.004), but did not result in an inhibition of CaT amplitude increase in response to PE in atrial cells. The results presented here demonstrate the involvement of AC1 in the downstream response of atrial pacemaker activity to -adrenoreceptor stimulation and IP3R calcium release.

category: pharmacology and toxicology


title: Cytokinin signalling regulates two-stage inflorescence arrest in Arabidopsis

abstract: To maximise their reproductive success, flowering plants must correctly time their entry into and exit from the reproductive phase (flowering). While much is known about the mechanisms that regulate the initiation of flowering, the regulation of end-of-flowering remains largely uncharacterised. End-of-flowering in Arabidopsis thaliana consists of the quasi-synchronous arrest of individual inflorescences, but it is unclear how this arrest is correctly timed with respect to environmental stimuli and ongoing reproductive success. Here we show that Arabidopsis inflorescence arrest is a complex developmental phenomenon which includes a decline in size and cessation of activity in the inflorescence meristem (IM), coupled with a separable developmental arrest in all unopened floral primordia (floral arrest); these events occur well before the visible arrest of the inflorescence. We show that global removal of inflorescences can delay both IM arrest and floral arrest, but that local fruit removal only delays floral arrest, emphasising the separability of these processes. We test a role for cytokinin in regulating inflorescence arrest, and find that cytokinin treatment can delay arrest. We further show that gain-of-function cytokinin receptor hypersensitive mutants can delay floral arrest, and also IM arrest, depending on the expression pattern of the receptor; conversely, loss-of-function mutants prevent extension of flowering in response to inflorescence removal. Collectively, our data suggest that the dilution of cytokinin among an increasing number of sink organs leads to end-of-flowering in Arabidopsis by triggering IM and floral arrest, conversely meaning that a lack of reproductive success can homeostatically extend flowering in compensation.

category: plant biology


title: Dynamic changes in gas solubility of xylem sap reiterate the enigma of plant water transport under negative pressure

abstract: Despite a long research history, we do not fully understand why plants are able to transport xylem sap under negative pressure without constant failure. Microbubble formation via direct gas entry is assumed to cause hydraulic failure, while the concentration of gas dissolved in xylem sap is traditionally supposed to be constant, following Henrys law. Here, the concentration of soluble gas in xylem sap was estimated in vivo using well-watered Citrus plants under varying levels of air temperature and photoperiodic exposure, and compared to modelled data. The gas concentration in xylem sap showed non-equilibrium curves, with a minimum over- or undersaturation of 5% compared to gas solubility based on Henrys law. A similar diurnal pattern was obtained from the gas concentration in the cut-open conduits and discharge tube, and oversolubility was strongly associated with decreasing xylem water potentials during transpiration. Although our model did not explain the daily changes in gas solubility for an anisobaric situation, oversolubility characterises nanoconfined liquids, such as sap inside cell walls. Thus, plants are able to transport sap under negative pressure with relatively high amounts of dissolved gas, providing them with a buffering capacity to prevent hydraulic failure, despite diurnal changes in pressure and temperature.


title: Integrative time-scale and multi-omic analysis of host-responses to Hop stunt viroid infection

abstract: Viroids are circular RNAs of minimal complexity compelled to subvert plant-regulatory networks to accomplish their infectious process. Studies focused on the response to viroid infection have mostly addressed specific regulatory levels and considered a unique infection time. Thus, much remains to be done to understand the temporal evolution and complex nature of viroid-host interactions. Here we present an integrative analysis of the temporal evolution and intensity of the genome-wide alterations in cucumber plants infected with hop stunt viroid (HSVd) by integrating differential host transcriptome, sRNAnome and methylome. Our results support that HSVd promotes the redesign of the cucumber regulatory-pathways predominantly affecting specific regulatory layers at different infection-phases. The initial response was characterized by a reconfiguration of the host-transcriptome by differential exon usage, followed by a progressive transcriptional down-regulation modulated by epigenetic changes. Regarding endogenous small RNAs, the alterations were limited and mainly occur at the late stage. The most significant host-alterations were predominantly related to the down-regulation of transcripts involved in plant-defence mechanisms, the restriction of pathogen-movement and the systemic spreading of defence signals. Altogether our data evidence the existence of a dynamic and yet poorly known arms race between the host and the viroid. We expect that these data constituting the first comprehensive map of the plant responses to a viroid infection contribute to elucidate the molecular basis of this multifaceted defence and counter-defence layout.


title: Multiomic analisys reveals that viroid infection induces a temporal reprograming of plant-defence mechanisms at multiple regulatory levels


title: Extracellular ATP plays an important role in systemic wound response activation

abstract:
Mechanical wounding occurs in plants during biotic (e.g., herbivore or pathogen attack) or abiotic (e.g., wind damage or freezing) stresses and is associated with the activation of multiple signaling pathways. These initiate many wound responses at the wounded tissues, as well as trigger long-distance signaling pathways that activate wound responses in tissues that were not affected by the initial wounding event (termed  systemic wound response). Among the different systemic signals activated by wounding are electric signals, calcium and reactive oxygen species (ROS) waves, and different plant hormones such as jasmonic acid. The release of glutamate from cells at the wounded tissues was recently proposed to trigger several different systemic signal transduction pathways via glutamate-like receptors (GLRs). However, the role of another important compound released from cells during wounding (i.e., extracellular ATP; eATP) in triggering systemic responses is not clear. Here we show that eATP that accumulates in wounded leaves and is sensed by the purinoreceptor kinase P2K is required for the activation of the ROS wave during wounding. Application of eATP to unwounded leaves triggered the ROS wave, and the activation of the ROS wave by wounding or eATP application was suppressed in mutants deficient in P2K (i.e., p2k1-3, p2k2, and p2k1-3p2k2). In addition, the expression of several systemic wound response transcripts was suppressed in mutants deficient in P2K during wounding. Our findings reveal that in addition to sensing glutamate via GLRs, eATP sensed by P2Ks is playing a key role in the triggering of systemic wound responses in plants.

One sentence summaryExtracellular ATP plays an important role in triggering the ROS wave and systemic transcriptomics responses during wounding.


title: Validation that human microbiome phages use alternative genetic coding with TAG stop read as Q

abstract:
Metagenomic findings suggesting that bacteriophages (phages) can use genetic codes different from those of their host bacteria reveal a new dimension of phage-host interaction dynamics. Whereas reassignment of stop codons to code for amino acids has been predicted, there has been no proteomic validation of alternative coding in phages. In fact, one code where the stop codon TAG is reassigned to glutamine (code 15) has never been experimentally validated in any biological system. Here, we characterized stop codon reassignment in two crAss-like phages found in the human gut microbiome using LC-MS/MS-based metaproteomics. The proteome data from several phage structural proteins clearly demonstrates reassignment of the TAG stop codon to glutamine, establishing for the first time the expression of genetic code 15.

One-Sentence SummaryMass spectrometry confirms protein expression of predicted alternate genetic coding in phage genomes from human microbiomes.

category: systems biology


title: Examining the Neural Correlates of Error Awareness in a Large fMRI Study

abstract: Goal-directed behaviour is dependent upon the ability to detect errors and implement appropriate post-error adjustments. Accordingly, several studies have explored the neural activity underlying error-monitoring processes, identifying the insula cortex as crucial for error awareness and reporting mixed findings with respect to the anterior cingulate cortex. Variable patterns of activation have previously been attributed to insufficient statistical power. We therefore sought to clarify the neural correlates of error awareness in a large event-related functional magnetic resonance imaging (MRI) study. Four hundred and two healthy participants undertook the error awareness task, a motor Go/No-Go response inhibition paradigm in which participants were required to indicate their awareness of commission errors. Compared to unaware errors, aware errors were accompanied by significantly greater activity in a network of regions including the insula cortex, supramarginal gyrus, and midline structures such as the anterior cingulate cortex and supplementary motor area. Error awareness activity was related to indices of task performance and dimensional measures of psychopathology in selected regions including the insula, supramarginal gyrus and supplementary motor area. Taken together, we identified a robust and reliable neural network associated with error awareness.

category: neuroscience


title: Ramp-shaped neural tuning supports graded population-level representation of the object-to-scene continuum

abstract: We can easily perceive the spatial scale depicted in a picture, regardless of whether it is a small space (e.g., a close-up view of a chair) or a much larger space (e.g., an entire class room). How does the human visual system encode this continuous dimension? Here, we investigated the underlying neural coding of depicted spatial scale, by examining the voxel tuning and topographic organization of brain responses. We created naturalistic yet carefully-controlled stimuli by constructing virtual indoor environments, and rendered a series of snapshots to smoothly sample between a close-up view of the central object and far-scale view of the full environment (object-to-scene continuum). Human brain responses were measured to each position using functional magnetic resonance imaging. We did not find evidence for a smooth topographic mapping for the object-to-scene continuum on the cortex. Instead, we observed large swaths of cortex with opposing ramp-shaped profiles, with highest responses to one end of the object-to-scene continuum or the other, and a small region showing a weak tuning to intermediate scale views. Importantly, when we considered the multi-voxel patterns of the entire ventral occipito-temporal cortex, we found smooth and linear representation of the object-to-scene continuum. Thus, our results together suggest that depicted spatial scale is coded parametrically in large-scale population codes across the entire ventral occipito-temporal cortex.


title: Exploring Functional Brain Network Modularity in Educational Contexts

abstract: The brains modular functional organization facilitates adaptability. Modularity has been linked with a wide range of cognitive abilities such as intelligence, memory, and learning. However, much of this work has (1) considered modularity while a participant is at rest rather than during tasks conditions and/or (2) relied primarily on lab-based cognitive assessments. Thus, the extent to which modularity can provide information about real-word behavior remains largely unknown. Here, we investigated whether functional modularity during resting-state and task-based fMRI was associated with academic learning (measured by GPA) and ability (measured by PSAT) in a large sample of high school students. Additional questions concerned the extent to which modularity differs between rest and task conditions, and across spatial scales. Results indicated that whole-brain modularity during task conditions was significantly associated with academic learning. In contrast to prior work, no such associations were observed for resting-state modularity. We further showed that differences in modularity between task conditions and resting-state varied across spatial scales. Taken together, the present findings inform how functional brain network modularity - during task conditions and while at rest - relate to a range of cognitive abilities.


title: Receptor interacting protein kinase-3 promotes both myopathy and cardiomyopathy in dystrophin-deficient mice

abstract:
BackgroundDuchenne muscular dystrophy (DMD) is a muscle degenerative disorder that is caused by the absence of dystrophin. From early childhood, multiple rounds of myofibre necrosis and regeneration lead to fibrosis and fat deposition, irreversibly disturbing skeletal muscle function and impairing locomotion. Cell necrosis also affects respiratory muscles and cardiomyocytes, ultimately responsible for the death of DMD boys by respiratory or heart failure.

Necroptosis is a genetically programmed form of necrosis requiring the receptor-interacting serine/threonine-protein kinase (RIPK)3 and is a promising new therapeutic target for multiple degenerative disorders. We previously demonstrated that necroptosis mediates hindlimb myofibre degeneration in distinct muscular dystrophies, including in DMD. However, this pathway was recently found to be required for myogenesis. Its prevention might therefore lead to detrimental side effects on muscle repair.

Whether necroptosis also participates in the pathogenesis of respiratory and cardiac muscle dysfunction, and whether its long-term inhibition would ultimately be beneficial or detrimental to mdx mice are addressed here.

MethodsHerein, we examined the effects of RIPK3 depletion on an advanced stage of pathogenesis in mdx mice. Dystrophic mice aged 12 to 18 months were submitted to forced treadmill running to assess their locomotor function. mdx cardiomyopathy was also examined by echocardiography in 40-week-old mice. Limb skeletal muscles, diaphragm and heart were analyzed by histology and molecular biology to compare the phenotype of mdxRipk3+/+ mdxRipk3-/- mice.

ResultsIn 18-month-old mdxRipk3-/- mice, we found no sign of muscle regeneration defect compared to mdxRipk3+/+ littermates. mdxRipk3-/- mice had decreased fibrosis in limb muscles, without evidence of muscle atrophy. The size of diaphragm myofibres was slightly reduced and affected by less variability than mdx littermates. Fibrosis was also reduced in the diaphragm of RIPK3-deficient mdx mice. Notably, heart hypertrophy and left ventricle fibrosis were reduced in mdxRipk3-/- mice, and using echocardiography, we found a significant decrease of markers of cardiomyopathy by such as a reduction of the relative wall thickness and left ventricle mass.

ConclusionsOur data suggest that necroptosis is involved together in the pathogenic phenotype of locomotor, respiratory, and cardiac muscles in dystrophin-deficient mice. The long-term genetic ablation of RIPK3 does not generate evidence of sarcopenia or muscle impairment in mdx mice. Our data suggest that necroptosis may represent a new therapeutic target susceptible to improving the phenotype of myopathy and cardiomyopathy.

category: cell biology


title: A unified view of LCRs across species

abstract: Low-complexity regions (LCRs) in proteins are important for higher-order assemblies of organisms, yet we lack a unified view of their sequences, features, relationships, and functions. Here, we use dotplots and dimensionality reduction to systematically define LCR type/copy relationships and create a map of LCR sequence space capable of integrating LCR features and functions. By defining LCR relationships across the proteome, we provide insight into how LCR type and copy number contribute to higher-order assemblies, such as the importance of K-rich LCR copy number for assembly of the nucleolar protein RPA43 in vivo and in vitro. With LCR maps, we reveal the underlying structure of LCR sequence space, and relate differential occupancy in this space to the conservation and emergence of higher-order assemblies, including the metazoan extracellular matrix and plant cell wall. Together, LCR relationships and maps uncovered the distribution and prevalence of E-rich LCRs in the nucleolus, and revealed previously undescribed regions of LCR sequence space with properties of higher order assemblies, including a teleost-specific T/H-rich sequence space. Thus, this unified view of LCRs enables discovery of how LCRs encode higher-order assemblies of organisms.


title: A unified view of low complexity regions (LCRs) across species


title: Acquisition of cross-azole tolerance and aneuploidy in Candida albicans strains evolved to posaconazole

abstract: A number of in vitro studies have examined the acquisition of drug resistance to the triazole fluconazole, a first-line treatment for many Candida infections. Much less is known about posaconazole, a newer triazole. We conducted the first in vitro experimental evolution of replicates from eight diverse strains of C. albicans in a high level of the fungistatic drug posaconazole. Approximately half of the 132 evolved replicates survived 50 generations of evolution, biased towards some of the strain backgrounds. We found that although increases in drug resistance were rare, increases in drug tolerance (the slow growth of a subpopulation of cells in a level of drug above the resistance level) were common across strains. We also found that adaptation to posaconazole resulted in widespread cross-tolerance to other azole drugs. Widespread aneuploidy variation was also observed in evolved replicates from some strain backgrounds. Trisomy of chromosomes 3, 6, and R was identified in 11 of 12 whole-genome sequenced evolved SC5314 replicates. These findings document rampant evolved cross-tolerance among triazoles and highlight that increases in drug tolerance can evolve independently of drug resistance in a diversity of C. albicans strain backgrounds.

category: evolutionary biology


title: Liver-derived cell lines from cavefish Astyanax mexicanus as an in vitro model for studying metabolic adaptation

abstract: Cell lines have become an integral resource and tool for conducting biological experiments ever since the Hela cell line was first developed (1). They not only allow detailed investigation of molecular pathways but are faster and more cost-effective than most in vivo approaches. The last decade saw many emerging model systems strengthening basic science research. However, lack of genetic and molecular tools in these newer systems pose many obstacles. Astyanax mexicanus is proving to be an interesting new model system for understanding metabolic adaptation. To further enhance the utility of this system, we developed liver-derived cell lines from both surface-dwelling and cave-dwelling morphotypes. In this study, we provide detailed methodology of the derivation process along with a comprehensive biochemical and molecular characterization of the cell lines, which reflects key metabolic traits of cavefish adaptation. We anticipate these cell lines to become a useful resource for the Astyanax community as well as researchers investigating fish biology, comparative physiology, and metabolism.


title: Chromosome-scale assembly of the highly heterozygous genome of red clover (Trifolium pratense L.), an allogamous forage crop species

abstract: Red clover (Trifolium pratense L.) is used as a forage crop due to a variety of favorable traits relative to other crops. Improved varieties have been developed through conventional breeding approaches, but progress could be accelerated and gene discovery facilitated using modern genomic methods. Existing short-read based genome assemblies of the ~420 Megabase (Mb) genome are fragmented into >135,000 contigs with numerous errors in order and orientation within scaffolds, likely due to the biology of the plant which displays gametophytic self-incompatibility resulting in inherent high heterozygosity. A high-quality long-read based assembly of red clover is presented that reduces the number of contigs by more than 500-fold, improves the per-base quality, and increases the contig N50 statistic by three orders of magnitude. The 413.5 Mb assembly is nearly 20% longer than the 350 Mb short read assembly, closer to the predicted genome size. Quality measures are presented and full-length isoform sequence of RNA transcripts reported for use in assessing accuracy and for future annotation of the genome. The assembly accurately represents the seven main linkage groups present in the genome of an allogamous (outcrossing), highly heterozygous plant species.

category: genomics


title: Joint copy number and mutation phylogeny reconstruction fromsingle-cell amplicon sequencing data

abstract: Reconstructing the history of somatic DNA alterations that occurred in a tumour can help understand its evolution and predict its resistance to treatment. Single-cell DNA sequencing (scDNAseq) can be used to investigate clonal heterogeneity and to inform phylogeny reconstruction. However, existing phylogenetic methods for scDNAseq data are designed either for point mutations or for large copy number variations, but not for both types of events simultaneously. Here, we develop COMPASS, a computational method for inferring the joint phylogeny of mutations and copy number alterations from targeted scDNAseq data. We evaluate COMPASS on simulated data and show that it outperforms existing methods. We apply COMPASS to a large cohort of 123 patients with acute myeloid leukemia (AML) and detect copy number alterations, including subclonal ones, which are in agreement with and extend current knowledge of AML development. We further used bulk sequencing and SNP array data to orthogonally validate our findings.

category: bioinformatics


title: Supervised dimensionality reduction for exploration of single-cell data by Hybrid Subset Selection - Linear Discriminant Analysis

abstract: Single-cell technologies generate large, high-dimensional datasets encompassing a diversity of omics. Dimensionality reduction enables visualization of data by representing cells in two-dimensional plots that capture the structure and heterogeneity of the original dataset. Visualizations contribute to human understanding of data and are useful for guiding both quantitative and qualitative analysis of cellular relationships. Existing algorithms are typically unsupervised, utilizing only measured features to generate manifolds, disregarding known biological labels such as cell type or experimental timepoint. Here, we repurpose the classification algorithm, linear discriminant analysis (LDA), for supervised dimensionality reduction of single-cell data. LDA identifies linear combinations of predictors that optimally separate a priori classes, enabling users to tailor visualizations to separate specific aspects of cellular heterogeneity. We implement feature selection by hybrid subset selection (HSS) and demonstrate that this flexible, computationally-efficient approach generates non-stochastic, interpretable axes amenable to diverse biological processes, such as differentiation over time and cell cycle. We benchmark HSS-LDA against several popular dimensionality reduction algorithms and illustrate its utility and versatility for exploration of single-cell mass cytometry, transcriptomics and chromatin accessibility data.


title: A Computational Method to Dissect Colonization Resistance of the Gut Microbiota against Pathogens

abstract: The indigenous gut microbes have co-evolved with their hosts for millions of years. Those gut microbes play a crucial role in host health and disease. In particular, they protect the host against incursion by exogenous and often harmful microorganisms, a mechanism known as colonization resistance (CR). Yet, identifying the exact microbes responsible for the gut microbiota-mediated CR against a particular pathogen remains a fundamental challenge in microbiome research. Here, we develop a computational method --- Generalized Microbe-Phenotype Triangulation (GMPT) to systematically identify causal microbes that directly influence the microbiota-mediated CR against a pathogen. We systematically validate GMPT using a classical population dynamics model in community ecology, and then apply it to microbiome data from two mouse studies on C. difficile infection. The developed method will not only significantly advance our understanding of CR mechanisms but also pave the way for the rational design of microbiome-based therapies for preventing and treating enteric infections.


title: Stem embolism vulnerability curve depends on methods used: is there a fifth mechanism of cavitation?

abstract:
A long-established ecological paradigm predicts a functional relationship determining vulnerability to cavitation: vulnerability increases with vessel hydraulic efficiency and vessel diameter. Even within a species, big vessels cavitate before small ones.

Some centrifuge methods for measuring vulnerability are prone to artifacts due to nano-particles seeding early embolism, as the particles are drawn into vessels during measurements. Both the Sperry and Cochard rotors are prone to early cavitation due to nano-particles drawn into long and wide vessels in Robinia pseudoacacia and Quercus acutissima, whereas extraction centrifuge methods produce vulnerability curves more resistant to cavitation.

Sufficient nano-particles pass through the stems to seed early embolism in all rotor designs. For several years, people have thought that early embolism is induced by nano-particles present in laboratory water. One new hypothesis is that the origin of nano-particles is from cut-open living cells but a much bigger study including many species is required to confirm this idea. This paper confirms the hypothesis in comparisons between short-vesselled Acer, and long-vesselled Robinia, and Quercus. Our new results and a review of old results justifies bigger study.

Hypothetical nano-particles might explain why different methods for measuring vulnerability curves cause different T50 = tensions causing 50% loss of hydraulic conductivity. Hence the hypothesis for future research should be that the open-vessel artifact is consistent with  long vessels surrounded by cut open living cells.

One sentence SummaryNano-particles induced early cavitation in species with vessel lengths about [1/4] the stem length used in all centrifuge rotors, and the origin of nano-particles might be from living cells nearby vessels

category: physiology


title: Modeling Cell Biological Features of Meiotic Chromosome Pairing

abstract:
During meiosis, homologous chromosomes become associated side by side in a process known as homologous chromosome pairing. Pairing requires long range chromosome motion through a nucleus that is full of other chromosomes. It remains unclear how the cell manages to align each pair of chromosomes quickly while mitigating and resolving interlocks. Here, we use a coarse-grained molecular dynamics model to investigate how specific features of meiosis, including motor-driven telomere motion, nuclear envelope interactions, and increased nuclear size, affect the rate of pairing and the mitigation/resolution of interlocks. By creating in silico versions of three yeast strains and comparing the results of our model to experimental data, we find that a more distributed placement of pairing sites along the chromosome is necessary to replicate experimental findings. Active motion of the telomeric ends speeds up pairing only if binding sites are spread along the chromosome length. Adding a meiotic bouquet significantly speeds up pairing but does not significantly change the number of interlocks. An increase in nuclear size slows down pairing while greatly reducing the number of interlocks. Interestingly, active forces increase the number of interlocks, which raises the question: How do these interlocks resolve? Our model gives us detailed movies of interlock resolution events which we then analyze to build a step-by-step recipe for interlock resolution. In our model, interlocks must first translocate to the ends, where they are held in a quasi-stable state by a large number of paired sites on one side. To completely resolve an interlock, the telomeres of the involved chromosomes must come in close proximity so that the cooperativity of pairing coupled with random motion causes the telomeres to unwind. Together our results indicate that computational modeling of homolog pairing provides insight into the specific cell biological changes that occur during meiosis.

Author SummaryEarly in meiosis, homologous chromosomes must find each other within the crowded nuclear space and become aligned along their entire length in a process known as homologous chromosome pairing. It remains unclear how the cell manages to align each pair of chromosomes quickly while mitigating and resolving interlocks. Here, we study this process by using a computational model. Our model attempts to capture the large-scale cell biological picture of meiotic pairing including the random initial 3D search, active motion of the chromosome ends, and meiosis specific constraints such as telomere attachment to the nuclear envelope. We use our model to study how these different features of meiosis affect the rate of pairing and the mitigation/resolution of interlocks. Importantly, our model gives us detailed movies of interlock resolution events, which we then analyze to build a step-by-step recipe for interlock resolution. We believe computational modeling of homolog pairing provides valuable insight into this complex biological process.

category: biophysics


title: The CAR mRNA-Interaction Surface is a Zipper Extension of the Ribosome A Site

abstract: The ribosome CAR interaction surface behaves like an extension of the decoding center A site and has H-bond interactions with the +1 codon that is next in line to enter the A site. Through molecular dynamics simulations, we investigated the codon sequence specificity of this CAR-mRNA interaction and discovered a strong preference for GCN codons, suggesting that there may be a sequence-dependent layer of translational regulation dependent on the CAR interaction surface. Dissection of the CAR-mRNA interaction through nucleotide substitution experiments showed that the first nucleotide of the +1 codon dominates over the second nucleotide position, consistent with an energetically favorable zipper-like activity that emanates from the A site through the CAR-mRNA interface. The +1 codon/CAR interaction is also affected by the identity of nucleotide 3 of +1 GCN codons which influences the stacking of G and C. Clustering analysis suggests that the A site decoding center adopts different neighborhood substates that depend on the identity of the +1 codon.


title: Fibrin, Bone Marrow Cells and macrophages interactively modulate cardiomyoblast fate.

abstract:
Interactions between macrophages, cardiac cells and the extracellular matrix are crucial for cardiac repair following myocardial infarction (MI). The paracrine effects of cell-based treatments of MI might modulate these interactions and impact cardiac repair. The immunomodulatory capacity of the therapeutic cells is therefore of interest and could be modulated by the use of biomaterials. We first showed that bone marrow cells (BMC) associated with fibrin could treat MI. Then, we interrogated the influence of fibrin, as a biologically active scaffold, on the secretome of BMC and the impact of their association on macrophage fate and cardiomyoblast proliferation.

MethodsIn vivo, two weeks post-MI, rats were treated with epicardial implantation of BMC and fibrin or sham-operated. High-resolution echocardiography was performed to evaluate the heart function and structure changes after 4 weeeks. Histology and immunostaining were performed on harvested hearts. In vitro, BMC were first primed with fibrin. Second, non-polarized macrophages were differentiated toward either pro-inflammatory or anti-inflammatory phenotypes and stimulated with the conditioned medium of fibrin-primed BMC (F-BMC). Proteomic, cytokine levels quantification, and RT-PCR were performed. EdU incorporation and real-time cell analysis assessed cell proliferation.

ResultsThe epicardial implantation of fibrin and BMC reduced the loss of cardiac function induced by MI, increased wall thickness and prevented the fibrotic scar expansion. After 4 and 12 weeks, the infarct content of CD68+ and CD206+ was similar in control and treated animals. In vitro, we showed that fibrin profoundly influenced the gene expression and the secretome of BMC, simultaneously upregulating both pro- and anti-inflammatory mediators. Furthermore, the conditioned medium from F-BMC significantly increased the proliferation of macrophages in a subsets dependent manner and modulated their gene expression and cytokines secretion. For instance, F-BMC significantly downregulated the expression of Nos2, Il6 and Ccl2/Mcp1 while Arg1, Tgfb and IL10 were upregulated. Interestingly, macrophages educated by F-BMC increased cardiomyoblast proliferation.

In conclusion, our study provides evidence that BMC/fibrin-based treatment lowered the infarct extent and improved cardiac function. The macrophage content was unmodified when measured at a chronic stage. Nevertheless, acutely and in vitro, the F-BMC secretome promotes an anti-inflammatory response that stimulates cardiac cell growth. Finally, our study emphases the acute impact of F-BMC educated macrophages on cardiac cell fate.


title: Concurrent fMRI demonstrates propagation of TMS effects across task-related networks

abstract: Transcranial magnetic stimulation (TMS) has become an important technique in both scientific and clinical practices, and yet our understanding of how the brain responds to TMS is still limited. Concurrent neuroimaging during TMS may bridge this gap, and emerging evidence suggests widespread that modulatory effects of TMS may be best captured through changes in functional connectivity between distributed networks, rather than local changes in cortical activity. However, the relationship between TMS stimulation parameters and evoked changes in functional connectivity is unknown. In this study, 24 healthy volunteers received concurrent TMS-fMRI while performing a dot-motion direction discrimination task. An MR-compatible coil was used to apply trains of three pulses at 10 Hz rTMS over the primary visual cortex (V1) at the onset of the dot stimuli with four levels of stimulation intensity (20%, 40%, 80%, and 120% of resting motor threshold, RMT). Behavioral results demonstrated impairment of motion discrimination at 80% RMT. FMRI results yielded three findings. First, functional connectivity between visual and non-visual areas increased as a function of rTMS intensity. Second, connectivity within the visual network was positively associated with motion accuracy, while the connectivity between visual and non-visual regions was negatively associated with motion accuracy. Lastly, we found that reductions in the similarity between functional and structural connectivity associated with increasing TMS intensity were constrained to the visual network. These findings demonstrate spatially dependent nonlinear effects of TMS intensity on brain functional connectivity that proceed beyond the site of stimulation and influence associated behavior.


title: Distinct responses to rare codons in select Drosophila tissues

abstract: Codon usage bias has long been appreciated to influence protein production. Yet, relatively few studies have analyzed the impacts of codon usage on tissue-specific mRNA and protein expression. Here, we use codon-modified reporters to perform an organism-wide screen in Drosophila melanogaster for distinct tissue responses to codon usage bias. These reporters reveal a cliff-like decline of protein expression near the limit of rare codon usage in endogenously expressed Drosophila genes. Near the edge of this limit, however, we find the testis and brain are uniquely capable of expressing rare codon-enriched reporters. We define a new metric of tissue-specific codon usage, the tissue-apparent Codon Adaptation Index, to reveal a conserved enrichment for rare codon usage in the endogenously expressed genes of both Drosophila and human testis. We further demonstrate a role for rare codons in restricting protein expression of an evolutionarily young gene, RpL10Aa, to the Drosophila testis. Rare codon-mediated restriction of this testis-specific protein is critical for female fertility. Our work highlights distinct responses to rarely used codons in select tissues, revealing a critical role for codon bias in tissue biology.

category: developmental biology


title: Evaluating Human Mutation Databases for 'Treatability' Using Personalized Antisense Oligonucleotides

abstract: Genome sequencing in the clinic often allows patients to receive a molecular diagnosis. However, variants are most often evaluated for pathogenicity, neglecting potential "treatability", and thus often yielding limited clinical benefit. Several collaborative efforts now aim to provide a therapy based upon the genetic variants, even if the drug will benefit only a single patient. Antisense oligonucleotide (ASO) therapies, among others, offer attractive "programmable" and relatively safe platforms for individualized therapy. The landscape of "ASO-treatable" variants is largely uncharted, with new developments emerging for loss-of-function (LOF), haploinsufficient, and gain-of-function (GOF) variants. ASOs can access the genome to target splice-gain variants, poison exons, untranslated/regulatory regions, and naturally-occurring antisense transcripts. Many of these approaches have yet to be proven clinically beneficial, and it is unclear if disease in some patients has progressed past the point where benefit could reasonably be expected. Here we mine public variant databases to identify potential future therapeutic targets. We found that the majority of human pathogenic genetic variants have one or more approaches that could be targeted therapeutically, advantaging the many ways that ASOs can regulate gene expression. The future might see medical teams considering "treatability" when interpreting genome sequencing results, to fully realize benefits for patients.

category: genetics


title: Exploring novel fluorine rich fuberidazole derivatives as hypoxic cancer inhibitors: design, synthesis, pharmacokinetics, molecular docking and DFT evaluations

abstract: Sixteen fuberidazole derivatives as potential new anticancer bioreductive prodrugs are prepared and characterized. The in vitro anticancer potential is examined to explore their cytotoxic properties employing apoptosis, DNA damage, and proliferation tests on chosen hypoxic cancer cells. Overall, eight substances (Compound 5a, 5c, 5d, 5e, 5g, 5h, 5i, and 5m) showed good cytotoxic properties. The potential of compounds is also examined through in silico studies (against human serum albumin), including chem-informatics to understand the structure-activity relationship (SAR), pharmacochemical strength, and the mode of interactions responsible for their action. The DFT calculations revealed that only 5b compound showed the lowest {Delta}ET (2.29 eV) while 5i showed relatively highest {beta}tot (69.89 x 10-31 esu), highest ave (3.18 x 10-23 esu), and dipole moment (6.49 Debye). This study presents a novel class of fuberidazole derivatives with selectivity toward hypoxic cancer cells.

category: biochemistry


title: Machine learning-assisted identification of factors contributing to the technical variability between bulk and single-cell RNA-seq experiments

abstract:
BackgroundRecent studies in the area of transcriptomics performed on single-cell and population levels reveal noticeable variability in gene expression measurements provided by different RNA sequencing technologies. Due to increased noise and complexity of single-cell RNA-Seq (scRNA-Seq) data over the bulk experiment, there is a substantial number of variably-expressed genes and so-called dropouts, challenging the subsequent computational analysis and potentially leading to false positive discoveries. In order to investigate factors affecting technical variability between RNA sequencing experiments of different technologies, we performed a systematic assessment of single-cell and bulk RNA-Seq data, which have undergone the same pre-processing and sample preparation procedures.

ResultsOur analysis indicates that variability between gene expression measurements as well as dropout events are not exclusively caused by biological variability, low expression levels, or random variation. Furthermore, we propose FAVSeq, a machine learning-assisted pipeline for detection of factors contributing to gene expression variability in matched RNA-Seq data provided by two technologies. Based on the analysis of the matched bulk and single-cell dataset, we found the 3-UTR and transcript lengths as the most relevant effectors of the observed variation between RNA-Seq experiments, while the same factors together with cellular compartments were shown to be associated with dropouts.

ConclusionsHere, we investigated the sources of variation in RNA-Seq profiles of matched single-cell and bulk experiments. In addition, we proposed the FAVSeq pipeline for analyzing multimodal RNA sequencing data, which allowed to identify factors affecting quantitative difference in gene expression measurements as well as the presence of dropouts. Hereby, the derived knowledge can be employed further in order to improve the interpretation of RNA-Seq data and identify genes that can be affected by assay-based deviations. Source code is available under the MIT license at https://github.com/slipnitskaya/FAVSeq.


title: A Saturation-Mutagenesis Analysis of the Interplay Between Stability and Activation in Ras

abstract: Cancer mutations in Ras occur predominantly at three hotspots: Gly 12, Gly 13, and Gln 61. Previously, we reported that deep mutagenesis of H-Ras using a bacterial assay identified many other activating mutations (Bandaru et al. eLife, 2017). We now show that the results of saturation mutagenesis of H-Ras in mammalian Ba/F3 cells correlate well with results of bacterial experiments in which H-Ras or K-Ras are co-expressed with a GTPase-activating protein (GAP). The prominent cancer hotspots are not dominant in the Ba/F3 data. We used the bacterial system to mutagenize Ras constructs of different stabilities and discovered a feature that distinguishes the cancer hotspots. While mutations at the cancer hotspots activate Ras regardless of construct stability, mutations at lower-frequency sites (e.g., at Val 14 or Asp 119) can be activating or deleterious, depending on the stability of the Ras construct. We characterized the dynamics of three non-hotspot activating Ras mutants by using NMR to monitor hydrogen-deuterium exchange (HDX). These mutations result in global increases in HDX rates, consistent with the destabilization of Ras. An explanation for these observations is that mutations that destabilize Ras increase nucleotide dissociation rates, enabling activation by spontaneous nucleotide exchange. A further stability decrease can lead to insufficient levels of folded Ras - and subsequent loss of function. In contrast, the cancer hotspot mutations are mechanism-based activators of Ras that interfere directly with the action of GAPs. Our results demonstrate the importance of GAP surveillance and protein stability in determining the sensitivity of Ras to mutational activation.


title: MethylScore, a pipeline for accurate and context-aware identification of differentially methylated regions from population-scale plant WGBS data

abstract: Whole-genome bisulfite sequencing (WGBS) is the standard method for profiling DNA methylation at single-nucleotide resolution. Many WGBS-based studies aim to identify biologically relevant loci that display differential methylation between genotypes, treatment groups, tissues, or developmental stages. Over the years, different tools have been developed to extract differentially methylated regions (DMRs) from whole-genome data. Often, such tools are built upon assumptions from mammalian data and do not consider the substantially more complex and variable nature of plant DNA methylation. Here, we present MethylScore, a pipeline to analyze WGBS data and to account for plant-specific DNA methylation properties. MethylScore processes data from genomic alignments to DMR output and is designed to be usable by novice and expert users alike. It uses an unsupervised machine learning approach to segment the genome by classification into states of high and low methylation, substantially reducing the number of necessary statistical tests while increasing the signal-to-noise ratio and the statistical power. We show how MethylScore can identify DMRs from hundreds of samples and how its data-driven approach can stratify associated samples without prior information. We identify DMRs in the A. thaliana 1001 Genomes dataset to unveil known and unknown genotype-epigenotype associations. MethylScore is an accessible pipeline for plant WGBS data, with unprecedented features for DMR calling in small- and large-scale datasets; it is built as a Nextflow pipeline and its source code is available at https://github.com/Computomics/MethylScore.


title: Regulation of major bacterial survival strategies by transcript sequestration in a membraneless organelle

abstract: Liquid-liquid phase separation (LLPS) of proteins was shown in recent years to regulate spatial organization of cell content without the need for membrane encapsulation in eukaryotes and prokaryotes. Yet evidence for the relevance of LLPS for bacterial cell functionality is largely missing. Here we show that the sugar metabolism-regulating clusters, recently shown by us to assemble in the E. coli cell poles by means of the novel protein TmaR, are formed via LLPS. A mutant screen uncovered residues and motifs in TmaR that are important for its condensation. Upon overexpression, TmaR undergoes irreversible liquid-to-solid transition, similar to the transition of disease-causing proteins in human, which impairs bacterial cell morphology and proliferation. Not only does RNA contribute to TmaR phase separation, but by ensuring polar localization and stability of flagella-related transcripts, TmaR enables cell motility and biofilm formation, thus providing a linkage between LLPS and major survival strategies in bacteria.

category: microbiology


title: Reversion of Ebolavirus Disease from a Single Intramuscular Injection of a pan-Ebolavirus Immunotherapeutic

abstract: Intravenous administration (IV) of antiviral monoclonal antibodies (mAbs) is challenging due to limited resources for performing infusions during an ongoing epidemic. An ebolavirus therapeutic administered via intramuscular (IM) injection would reduce these burdens and allow rapid treatment of exposed individuals during an outbreak. Here, we demonstrate how MBP134, a two mAb pan-ebolavirus cocktail, reverses the course of Sudan ebolavirus (SUDV/Gulu) disease with a single IV or IM dose in non-human primates (NHPs) as far as five days post-exposure. Furthermore, we investigated the utility of adding half-life extension mutations to the MBP134 mAbs, ultimately creating a half-life extended cocktail designated MBP431. MBP431 demonstrated an extended serum half-life in vivo and offered complete or significant protection with a single IM dose delivered as a post-exposure prophylactic (PEP) or therapeutic in NHPs challenged with EBOV. These results support the use of MBP431 as a rapidly deployable IM medical countermeasure against every known ebolavirus.


title: STREAMING-tag system reveals spatiotemporal relationships between transcriptional regulatory factors and transcriptional activity

abstract: Transcription is a dynamic process that stochastically switches between the ON and OFF states. To detect the dynamic relationship among protein clusters of RNA polymerase II (RNAPII) and coactivators, gene loci, and transcriptional activity, we inserted an MS2 repeat, a TetO repeat, and inteins with a selection marker just downstream of the transcription start site (TSS). By optimizing the individual elements, we have developed the Spliced TetO REpeAt, MS2 repeat, and INtein sandwiched reporter Gene tag (STREAMING-tag) system. Clusters of RNAPII and BRD4 were observed proximally to the TSS of Nanog when the gene was transcribed in mouse embryonic stem cells. In contrast, clusters of MED19 and MED22 Mediator subunits were constitutively located near the TSS. Thus, the STREAMING-tag system revealed the spatiotemporal relationships between transcriptional activity and protein clusters near the gene. This powerful tool is useful for quantitatively understanding dynamic transcriptional regulation in living cells.

category: molecular biology


title: Proteomic Dissection of a Giant Cell

abstract: Many individual proteins have been identified as having defined positions relative to cell polarity axes, raising the question of what fraction of all proteins may have polarized localizations. We took advantage of the giant ciliate Stentor coeruleus to quantify the extent of polarized localization proteome-wide. This trumpet-shaped unicellular organism shows a clear morphological anterior-posterior axis defined by a circular array of cilia known as a membranellar band at one end, and a holdfast at the other end. Because individual Stentor cells are over a millimeter in length, we were able to cut the cells into three pieces along the anterior-posterior axis, followed by proteomic analysis of proteins enriched in each piece. We find that approximately 30% of all detected proteins show a polarized location relative to the anterior-posterior cell axis. Proteins with polarized enrichment include centrin-like proteins, calcium-regulated kinases, orthologs of SFI1 and GAS2, and proteases. At the organelle level, nuclear and mitochondrial proteins are enriched in the anterior half of the cell body, but not in the membranellar band itself, while ribosome related proteins are apparently uniformly distributed. RNAi of signaling proteins enriched in the membranellar band, which is the anterior-most structure in the cell, revealed a protein phosphatase 2 subunit b ortholog required for closure of the membranellar band into the ring shape characteristic of Stentor. These results suggest that a large fraction of the Stentor proteome has a polarized localization, and provide a protein-level framework for future analysis of pattern formation and regeneration in Stentor as well as defining a general strategy for subcellular spatial proteomics based on physical dissection of cells.


title: Characterization of a novel peptide mined from the Red Sea brine pools and modified to enhance its anticancer activity

abstract: Peptide-based drugs have emerged as highly selective and potent cancer therapy. Cancer is one of the leading causes of death worldwide. Multiple approaches have been developed towards cancer treatment, including chemotherapy, radiation, and hormonal therapy; however, such procedures non-specificity, toxicity, and inefficiency present a hurdle. In this study, we developed a support vector machine (SVM) model to detect the potential anticancer properties of novel peptides through scanning the American University in Cairo Red Sea metagenomics library. Further, we performed in silico studies on a novel 37-mer antimicrobial peptide mined from SVM pipeline analysis. This peptide was further modified to enhance its anticancer activity, analyzed for gene oncology, and subsequently synthesized. The anticancer properties of this 37-mer peptide were evaluated via cellular viability and cell morphology of SNU449, HepG2, SKOV3, and HeLa cells, using MTT assay. Furthermore, we assessed the migration capability of SNU449 and SKOV3 via scratch wound healing assay. Moreover, the targeted selectivity of the peptide for cancerous cells was assessed by testing its hemolytic activity on human erythrocytes. The peptide caused a significant reduction in cellular viability and critically affected the morphology of hepatocellular carcinoma (SNU449 and HepG2), ovarian cancer (SKOV3), and to a limited extent, cervical cancer cell lines (HeLa), in addition to decreasing viability of human fibroblast cell line (1Br-hTERT). Peptide treatment significantly affected the proliferation and migration ability of SNU449 and SKOV3 cells. Annexin V assay was used to evaluate induced cell death upon peptide treatment, attributing programmed cell death (Apoptosis) as the main cause of cell death in SNU449 cells. Finally, we established broad-spectrum antimicrobial properties of the peptide on both gram-positive and gram-negative bacterial strains. Thus, these findings infer the novelty of the peptide as a potential anticancer and antimicrobial agent.

category: cancer biology


title: Reconstructing Kinetic Models for Dynamical Studies of Metabolism using Generative Adversarial Networks

abstract: Kinetic models of metabolic networks relate metabolic fluxes, metabolite concentrations, and enzyme levels through well-defined mechanistic relations rendering them an essential tool for systems biology studies aiming to capture and understand the behavior of living organisms. However, due to the lack of information about the kinetic properties of enzymes and the uncertainties associated with available experimental data, traditional kinetic modeling approaches often yield only a few or no kinetic models with desirable dynamical properties making the computational analysis unreliable and computationally inefficient. We present REKINDLE (REconstruction of KINetic models using Deep LEarning), a deep-learning-based framework for efficiently generating large-scale kinetic models with dynamic properties matching the ones observed in living organisms. We showcase REKINDLEs efficiency and capabilities through three studies where we: (i) generate large populations of kinetic models that allow reliable in silico testing of hypotheses and systems biology designs, (ii) navigate the phenotypic space by leveraging the transfer learning capability of generative adversarial networks, demonstrating that the generators trained for one physiology can be fine-tuned for another physiology using a low amount of data, and (iii) expand upon existing datasets, making them amenable to thorough computational biology and data-science analyses. The results show that data-driven neural networks assimilate implicit kinetic knowledge and structure of metabolic networks and generate novel kinetic models with tailored properties and statistical diversity. We anticipate that our framework will advance our understanding of metabolism and accelerate future research in health, biotechnology, and systems and synthetic biology. REKINDLE is available as an open-access tool.


title: PhysiBoSS 2.0: a sustainable integration of stochastic Boolean and agent-based modelling frameworks

abstract:
MotivationCancer progression is a complex phenomenon that spans multiple scales from molecular to cellular and intercellular. Simulations can be used to perturb the underlying mechanisms of those systems and to generate hypotheses on novel therapies. We present a new version of PhysiBoSS, a multiscale modelling framework designed to cover multiple temporal and spatial scales, that improves its integration with PhysiCell, decoupling the cell agent simulations with the internal Boolean model in an easy-to-maintain computational framework.

ResultsPhysiBoSS 2.0 is a redesign and reimplementation of PhysiBoSS, conceived as an add-on that expands the PhysiCell agent-based functionalities with intracellular cell signalling using MaBoSS having a decoupled, maintainable and model-agnostic design. PhysiBoSS 2.0 successfully reproduces simulations reported in the former PhysiBoSS and expands its functionalities such as using user-defined models and cells specifications, having mechanistic submodels of substrate internalisation with ODEs and enabling the study of drug synergies.

AvailabilityPhysiBoSS 2.0 is open-source and publicly available on GitHub (https://github.com/PhysiBoSS/PhysiBoSS) under the BSD 3-clause license with several repositories of accompanying interoperable tools. Additionally, a nanoHUB tool has been set up to ease the use of PhysiBoSS 2.0 (http://sls_nanohub.org/tools/pba4tnf/).

Contactalfonso.valencia@bsc.es

Supplementary informationSupplementary data are available at Bioinformatics online.


title: Malformations of the sacculus and the semicircular canals in spider morph pythons

abstract: Spider morph ball pythons are a frequently bred design morph with striking alterations of the skin color pattern. We created high resolution {micro}CT-image series through the otical region of the skulls, used 3D-reconstruction software for rendering anatomical models, and compare the anatomy of the semicircular ducts, sacculus and ampullae of wildtype Python regius (ball python) with spider morph snakes. All spider morph snakes showed the wobble condition. We describe the inner ear structures in wild-type and spider-morph snakes and report a deviant morphology of semicircular canals, ampullae and sacculus in spider morph snakes. We also report about associated differences in the desmal skull bones of spider morph snakes. The spider morph snakes were characterized by wider semicircular canals, anatomically poorly defined ampulla, a deformed crus communis and a small sacculus, with a highly deviant x-ray morphology as compared to wildtype individuals. We observed considerable intra- and interindividual variability of these features. This deviant morphology of spider morph snakes can easily be associated with an impairment of sense of equilibrium and the observed neurological wobble condition. Limitations in sample size prevent statistical analyses, but the anatomical evidence is strong enough to support an association between the wobble condition in design bread spider morph snakes and a malformation of the inner ear structures. A link between artificially selected alterations in pattern and specific color design with neural-crest associated developmental malformations of the statoacoustic organ as known from other vertebrates is discussed.

category: zoology


title: High homozygosity of inversions in sunflower species largely averts accumulation of deleterious mutations

abstract: Recombination is critical both for accelerating adaptation and for the purging of deleterious mutations. Chromosomal inversions can act as recombination modifiers that suppress local recombination and, thus, are predicted to accumulate such mutations. In this study, we investigated patterns of recombination, transposable element abundance and coding sequence evolution across the genomes of 1,445 individuals from three sunflower species, as well as within nine inversions segregating within species. We also analyzed the effects of inversion genotypes on 87 phenotypic traits to test for overdominance. We found significant negative correlations of long terminal repeat retrotransposon abundance and deleterious mutations with recombination rates across the genome in all three species. However, we failed to detect an increase in these features in the inversions, except for a modest increase in the proportion of stop codon mutations in several very large or rare inversions. Moreover, there was little evidence of phenotypic overdominance in inversion heterozygotes, consistent with observations of minimal deleterious load. On the other hand, significantly greater load was observed for inversions in populations polymorphic for a given inversion compared to populations monomorphic for one of the arrangements, suggesting that the local state of inversion polymorphism affects deleterious load. These seemingly contradictory results can be explained by the geographic structuring and consequent excess homozygosity of inversions in wild sunflowers. Inversions contributing to local adaptation often exhibit geographic structure; such inversions represent ideal recombination modifiers, acting to facilitate adaptive divergence with gene flow, while largely averting the accumulation of deleterious mutations due to recombination suppression.


title: Lifetime of actin-dependent protein nanoclusters

abstract:
Protein nanoclusters (PNCs) are dynamic collections of a few proteins that spatially organize in nanometer length clusters. PNCs are one of the principal forms of spatial organization of membrane proteins and they have been shown or hypothesized to be important in various cellular processes, including cell signaling. PNCs show remarkable diversity in size, shape, and lifetime. In particular, the lifetime of PNCs can vary over a wide range of timescales. The diversity in size and shape can be explained by the interaction of the clustering proteins with the actin cytoskeleton or the lipid membrane, but very little is known about the processes that determine the lifetime of the nanoclusters. In this paper, using mathematical modelling of the cluster dynamics, we model the biophysical processes that determine the lifetime of actin-dependent PNCs. In particular, we investigated the role of actin aster fragmentation, which had been suggested to be a key determinant of the PNC lifetime, and found that it is important only for a small class of PNCs. A simple extension of our model allowed us to investigate the kinetics of protein-ligand interaction near PNCs. We found an anomalous increase in the lifetime of ligands near PNCs, which agrees remarkably well with experimental data on RAS-RAF kinetics. In particular, analysis of the RAS-RAF data through our model provides falsifiable predictions and novel hypotheses that will not only shed light on the role of RAS-RAF kinetics in various cancers, but also will be useful in studying membrane protein clustering in general.

SignificanceSpatial organization of biomolecules shapes the behavior of a cell. It is particularly important during cell-signaling, where transient, dynamic organization of the biomolecules helps cells process signals and respond to them. Nanoclusters of peripheral membrane proteins, such as KRAS, a specific form of dynamic organization of biomolecules, play a critical part in the modulation of cell signals that control various cellular behaviors including cell growth, proliferation, and differentiation. Although we have made significant progress in understanding the structure, size, and origin of the nanoclusters, very little is known about the biophysical processes that control their lifetime. In this paper, we present a mathematical framework that provides quantitative insights into these processes and explains how oncogenic mutations in KRAS may lead to cancers.


title: Transbilayer Coupling of Lipids in Cells Investigated by Imaging Fluorescence Correlation Spectroscopy

abstract: Plasma membrane hosts numerous receptors, sensors, and ion channels involved in cellular signaling. Phase separation of the plasma membrane is emerging as a key biophysical regulator of signaling reactions in multiple physiological and pathological contexts. There is much evidence that plasma membrane composition supports the co-existence liquid-ordered (Lo) and liquid-disordered (Ld) phases or domains at physiological conditions. However, this phase/domain separation is nanoscopic and transient in live cells. It is recently proposed that transbilayer coupling between the inner and outer leaflets of the plasma membrane is driven by their asymmetric lipid distribution and by dynamic cytoskeleton-lipid composites that contribute to the formation and transience of Lo/Ld phase separation in live cells. In this Perspective, we highlight new approaches to investigate how transbilayer coupling may influence phase separation. For quantitative evaluation of the impact of these interactions, we introduce an experimental strategy centered around Imaging Fluorescence Correlation Spectroscopy (ImFCS), which measures membrane diffusion with very high precision. To demonstrate this strategy we choose two well-established model systems for transbilayer interactions: crosslinking by multivalent antigen of immunoglobulin E bound to receptor Fc{varepsilon}RI, and crosslinking by cholera toxin B of GM1 gangliosides. We discuss emerging methods to systematically perturb membrane lipid composition, particularly exchange of outer leaflet lipids with exogenous lipids using methyl alpha cyclodextrin. These selective perturbations may be quantitatively evaluated with ImFCS and other high-resolution biophysical tools to discover novel principles of lipid-mediated phase separation in live cells in the context of their pathophysiological relevance.


title: Reduced mesophyll conductance by cell wall thickening and chloroplasts decreasing driven the decline of photosynthesis under sole NH4+ supply

abstract:
The relationship between nitrogen (N) sources and photosynthetic capacity of leaf differs between species. However, the leaf anatomical variabilities related to photosynthesis (A) of shrubs under different forms of N remain imperfectly known. Here, Lonicera Japonica (a shrub) was grown hydroponically in the presence of three forms of N (sole NH4+, 50%/50% NH4+/NO3- and sole NO3-). A and photosynthetic N use efficiency significantly decreased under sole NH4+ supply, in parallel with down-regulated stomatal conductance (gs), mesophyll conductance (gm), and electron transfer rate (J). Up to the total A decline of 41.28% in sole NH4+ supply (compare with sole NO3-), the gm attributed to 60.3% of the total limitations. Besides, the decreased internal air space explained the increase of gas-phase resistance, and the increased liquid-phase resistance in sole NH4+ supply was ascribed to the thicker cell wall thickness (Tcw) and decreased chloroplasts exposed surface area per unit leaf area (Sc/S). The discrepancy of Sc/S could be interpreted by the altered chloroplasts numbers and the distance between adjacent chloroplasts (Dchl-chl). These results indicate the alteration of Tcw and chloroplast numbers were the main causes of the difference in gm in coping with varied N sources.

HighlightCell wall and chloroplast variability determining the mesophyll conductance under different nitrogen forms


title: Functional oscillation of a multienzyme glucosome assembly during cell cycle progression

abstract: Glucose metabolism has been studied extensively to understand functional interplays between metabolism and a cell cycle. However, our understanding of cell cycle-dependent metabolic adaptation particularly in human cells remains largely elusive. Meanwhile, human enzymes in glucose metabolism are shown to functionally organize into three different sizes of a multienzyme metabolic assembly, the glucosome, to regulate glucose flux in a size-dependent manner. Here, using fluorescence single-cell imaging techniques, we discover that glucosomes spatiotemporally oscillate during a cell cycle in an assembly size-dependent manner. Importantly, their oscillation at single-cell levels is in accordance with functional contributions of glucose metabolism to cell cycle progression at a population level. Collectively, we demonstrate functional oscillation of glucosomes during cell cycle progression and thus their biological significance to human cell biology.


title: Orthohantavirus infection in two rodent species that inhabit wetlands in the central-east region of Argentina

abstract:
Hantavirus pulmonary syndrome (HPS) is an emerging infectious disease caused by orthohantaviruses associated to rodents of the Cricetidae family, Sigmodontinae subfamily, in the American continent. Previous research carried out in central-east region of Argentina, recorded potential orthohantavirus host rodents in diverse environments, but infected rodents were particularly present on Parana wetlands islands. The aims of this research were (1) to determine the orthohantavirus host in the rodent community focused on islands of Parana River Delta, an endemic zone of HPS, (2) to identify temporal and spatial factors associated with orthohantavirus prevalence variations, (3) to compare the individual characteristics of seropositive and seronegative rodents and, (4) to explore the association between orthohantavirus seroprevalence and rodent community characteristics in the Parana River Delta, central-east region of Argentina. Capture of small rodents was done between August 2014 and May 2018 on seven islands located in central-east region of Argentina. In this HPS endemic zone, 14.9% of Oligoryzomys flavescens and 1.5% of Oxymycterus rufus of the sampled rodents had antibodies against orthohantavirus. The individuals that were more likely to become seropositive were the reproductively active adult males. Even though O. flavescens inhabit all islands, the seropositive individuals were only present in two of these, suggesting spatial heterogeneity in the viral distribution. We found that two months later of periods with low temperature, seroprevalence increased probably due to a higher proportion of adults in the population. Additionally, higher seroprevalence was associated with greater diversity of the rodent assemblage. This association could support the idea that a rescue effect or amplification of the prevalence of orthohantavirus would be taking place by means of secondary host as O. rufus, a novelty for this species and for the region. This finding may be significant if one takes into account that O. rufus was the second most abundant species in the area of islands studied and is one of the most abundant species on the islands and riparian sectors of the study zone. In conclusion, the relative risk of HPS could be high on wetlands of Parana River Delta in the central-east region of Argentina where several favourable factors for the transmission of orthohantavirus are combined, such as the presence of several host species, two of them numerically dominant, high percentages of infection and a high degree of occupational exposure of the human population due to rural activities, the most frequently associated nationwide with HPS.

SynopsisHantavirus pulmonary syndrome (HPS) is an emerging infectious disease endemic of the American continent transmited by rodents. The aim of this research was to determine hosts species of orthohantaviruses in the rodent community on islands of Parana River Delta, an HPS endemic zone of Argentina. We recorded the 14.9% of Oligoryzomys flavescens and 1.5% of Oxymycterus rufus with antibodies against orthohantavirus, which were principally reproductively active adult males. Seroprevalence increased after periods of low temperatures, probably due to the mortality of juveniles and survival of adults in the population. Additionally, the highest percentage of seropositive rodents occurred in times with a greater diversity of the rodent assemblage. This association could support the idea of amplification of the prevalence of orthohantavirus would be taking place by means of O. rufus infected, a novelty for this species and for the region. In conclusion, HPS risk could be high on wetlands of Parana River Delta in the central-east region of Argentina where several favourable factors for the transmission of orthohantavirus are combined, such as the presence of several host species, high percentages of infection and a high degree of occupational exposure of the population due to rural activities.

category: ecology


title: Duckweed roots are dispensable and are on a trajectory toward vestigiality

abstract:
Duckweeds are morphologically simplified, free floating aquatic monocots comprising both rooted and rootless genera. This has led to the idea that roots in these species may be vestigial, but empirical evidence supporting this is lacking. Here we show that duckweed roots are no longer required for their ancestral role of nutrient uptake. Comparative analyses of nearly all rooted duckweed species revealed a highly reduced anatomy, with greater simplification in the more recently diverged genus Lemna. A series of root excision experiments demonstrated that roots are dispensable for normal growth in Spirodela polyrhiza and Lemna minor. Furthermore, ionomic analyses of fronds in these two species showed little difference in the elemental composition of plants in rooted versus root-excised samples. In comparison, another free-floating member of the Araceae, Pistia stratiotes, which colonized the aquatic environment independently of duckweeds, has retained a more complex root anatomy. Whilst Pistia roots were not absolutely required for growth, their removal inhibited plant growth and resulted in a broad change in the mineral profile of aerial tissues. Collectively, these observations suggest that duckweeds and Pistia may be different stages along a trajectory towards root vestigialization Given this, along with the striking diversity of root phenotypes, culminating in total loss in the most derived species, we propose that duckweed roots are a powerful system with which to understand organ loss and vestigiality.

One sentence summaryThrough their adaption to the aquatic environment, duckweed roots have progressively become structurally reduced making them an ideal plant model with which to study vestigiality.


title: New insights on the role of HCN in root hair elongation through single cell proteomics

abstract:
Root hairs are specialized structures involved in water and nutrient uptake by plants. They elongate from epidermal cells following a complex developmental program. {beta}-cyanoalanine synthase (CAS), which is mainly involved in hydrogen cyanide (HCN) detoxification in Arabidopsis thaliana, plays a role in root hair elongation, as evidenced by the fact that cas-c1 mutants show a severe defect in root hair shape. In addition to root hairs, CAS C1 is expressed in the quiescent center and meristem. However, the cas-c1 mutation has no visible effect on either tissue, in both control and nutrient-deprivation conditions. To identify its role in root hair formation, we conducted single cell proteomics analysis by isolating root hair cells using Fluorescence-Activated Cell Sorting (FACS) from wild type and cas-c1 mutants. We also analyzed the presence of S-cyanylation, a protein post-translational modification (PTM) mediated by HCN and affecting cysteine residues and protein activity, in proteins of wild type and cas-c1 mutants. We found that several proteins involved in root hair development, related to the receptor kinase FERONIA signaling and to DNA methylation, are modified by this new post-translational modification.

One sentence summaryArabidopsis root hair proteomics unveals that several proteins involved in root hair development are susceptible of modification by S-cyanylation.

category: plant biology


title: Natural killer (NK) cell-derived extracellular-vesicle shuttled microRNAs control T cell responses

abstract: Natural killer (NK) cells recognise and kill target cells undergoing different types of stress. NK cells are also capable of modulating immune responses. In particular, they regulate T cell functions. Small RNA next-generation sequencing of resting and activated NK cells and their secreted EVs led to the identification of a specific repertoire of NK-EV-associated microRNAs and their post-transcriptional modifications signature. Several microRNAs of NK-EVs, namely miR-10b-5p, miR-92a-3p and miR-155-5p, specifically target molecules involved in Th1 responses. NK-EVs promote the downregulation of GATA-3 mRNA in CD4+ T cells and subsequent T-bet de-repression that leads to Th1 polarization and IFN-{gamma} and IL-2 production. NK-EVs also have an effect on monocyte and moDCs function, driving their activation and increased presentation and co-stimulatory functions. Nanoparticle-delivered NK-EV microRNAs partially recapitulate NK-EV effects in vivo. Our results provide new insights on the immunomodulatory roles of NK-EVs that may help to improve their use as immunotherapeutic tools.

category: immunology


title: Barley stripe mosaic virus γb protein targets thioredoxin h-type 1 to dampen SA-mediated antiviral defenses

abstract:
Salicylic acid (SA) acts as a signaling molecule to perceive and defend against pathogen infections. Accordingly, pathogens evolve versatile strategies to disrupt the SA-mediated signal transduction. However, it is necessary to further characterize how plant viruses manipulate the SA-dependent defense responses. Here, we show that Barley stripe mosaic virus (BSMV) infection activates SA-mediated defense signaling pathway and upregulates the expression of Nicotiana benthamiana thioredoxin h-type 1 (NbTRXh1). The {gamma}b protein interacts directly with NbTRXh1 in vivo and in vitro. Overexpression of NbTRXh1, but not a reductase-defective mutant, impedes BSMV infection, whereas low NbTRXh1 expression level results in increased viral accumulation. Similar with its orthologues in Arabidopsis, NbTRXh1 also plays an essential role in SA signaling transduction in N. benthamiana. To counteract NbTRXh1-mediated defenses, the BSMV {gamma}b protein targets NbTRXh1 to dampen its reductase activity and thereby impairing downstream SA defense genes expression to optimize viral cell-to-cell movement. We also found that NbTRXh1-mediated resistance defends against Lychnis ringspot virus, Beet black scorch virus, and Beet necrotic yellow vein virus. Taken together, our results reveal a novel role for the multifunctional {gamma}b protein in counteracting plant defense responses, and broadens the broad-spectrum antibiotic role of SA signaling pathway.

One sentence summaryBSMV {gamma}b protein impairs NbTRXh1 reductase activity and dampen downstream SA-related genes expression to facilitate viral cell-to-cell movement.


title: Separate to operate: the centriole-free inner core of the centrosome regulates the assembly of the intranuclear spindle in Toxoplasma gondii

abstract: Centrosomes are the main microtubule-organizing center of the cell. They are normally formed by two centrioles, embedded in a cloud of proteins known as pericentriolar material (PCM). The PCM ascribes centrioles with their microtubule nucleation capacity. Toxoplasma gondii, the causative agent of toxoplasmosis, divides by endodyogeny. Successful cell division is critical for pathogenesis. The centrosome, one of the microtubule organizing centers of the cell, plays central roles in orchestrating the temporal and physical coordination of major organelle segregation and daughter cell formation. The Toxoplasma centrosome is constituted by two domains; an outer core, distal from the nucleus, and an inner core, proximal to the nucleus. This dual organization has been proposed to underlie T. gondiis cell division plasticity. Homeostasis of the outer core has been shown to be critical for the proper assembly of the daughter cells. However, the role of the inner core remains undeciphered. Here, we focus on understanding the function of the inner core by studying the dynamics and role of its only known molecular marker; TgCEP250L1. We show that upon conditional degradation of TgCEP250L1, parasites are unable to survive. Mutants exhibit nuclear segregation defects, whilst normally forming daughter cells. In addition, the rest of the centrosome, defined by the position of the centrioles, disconnects from the nucleus. We explore the structural defects underlying these phenotypes by high resolution microscopy. We show that TgCEP250L1s location is dynamic and encompasses the formation of the mitotic spindle. Moreover, we show that in the absence of TgCEP250L1, the microtubule binding protein TgEB1, fails to translocate from the nucleus to the mitotic spindle, while polyploid nuclei accumulate. Overall, our data supports a model in which the inner core of the T. gondii centrosome critically participates in cell division by directly impacting the formation or stability of the mitotic spindle.


title: The diversity and functional capacity of microbes associated with coastal phototrophs

abstract:
Coastal marine phototrophs exhibit some of the highest rates of primary productivity in the world. They have been found to host a diverse set of microbes, many of which may impact the biology of their phototroph hosts through metabolisms that are unique to microbial taxa. Here we characterized the metabolic functions of phototroph-associated microbial communities using metagenomes collected from 2 species of kelp (Laminaria setchellii and Nereocystis luetkeana) and 3 marine angiosperms (Phyllospadix scouleri, P. serrulatus and Zostera marina), including the rhizomes of two surfgrass species (Phyllospadix spp.) and the seagrass Zostera marina, and the sediments surrounding P. scouleri and Z. marina. Using metagenomic sequencing, we describe 72 metagenome assembled genomes (MAGs) that potentially benefit from being associated with macrophytes and may contribute to macrophyte fitness through their metabolic gene content. All host-associated metagenomes contained genes for the use of dissolved organic matter from hosts and vitamin (B1, B2, B7, B12) biosynthesis. Additionally, we found a range of nitrogen metabolism genes that transform dissolved inorganic nitrogen into forms that may be more available to the host. The rhizosphere of surfgrass and seagrass contained genes for anaerobic microbial metabolisms, including nifH genes associated with nitrogen fixation, despite residing in a well-mixed and oxygenated environment. The range of oxygen environments engineered by macrophytes likely explains the diversity of both oxidizing and reducing microbial metabolisms, and contributes to the functional capabilities of microbes and their influence on carbon and nitrogen cycling in nearshore ecosystems.

ImportanceKelps, seagrasses and surfgrasses are ecosystem engineers on rocky shorelines where they show remarkably high levels of primary production. Through analysis of their associated microbial communities, we found a variety of microbial metabolisms that may benefit the host, including nitrogen metabolisms and the production of B vitamins. In turn, these microbes have the genetic capability to assimilate the dissolved organic compounds released by their phototroph hosts. We describe a range of oxygen environments associated with surfgrass, including low-oxygen microhabitats in their rhizomes that host genes for nitrogen fixation. The tremendous productivity of coastal phototrophs is likely due in part to the activities of associated microbes and an increased understanding of these associations is needed.


title: Sulfane sulfur post-translationally modifies the global regulator AdpA to influence actinorhodin production and morphological differentiation of Streptomyces coelicolor

abstract:
The transcription factor AdpA is a key regulator controlling both secondary metabolism and morphological differentiation in Streptomyces. Due to its critical functions, its expression undergoes multi-level regulations at transcriptional, post-transcriptional, and translational levels, yet no post-translational regulation has been reported. Sulfane sulfur, such as organic polysulfide (RSnH, n[≥]2), is common inside microorganisms, but its physiological functions are largely unknown. Herein, we discovered that sulfane sulfur post-translationally modifies AdpA in S. coelicolor via specifically reacting with Cys62 of AdpA to form a persulfide (Cys62-SSH). This modification decreases the affinity of AdpA to its self-promoter PadpA, allowing increased expression of adpA, further promoting the expression of its target genes actII-4 and wblA. ActII-4 activates actinorhodin biosynthesis and WblA regulates morphological development. Bioinformatics analyses indicated that AdpA-Cys62 is highly conserved in Streptomyces, suggesting the prevalence of such modification in this genus. Thus, our study unveils a new type of regulation on the AdpA activity and sheds a light on how sulfane sulfur stimulates the production of antibiotics in Streptomyces.

IMPORTANCEStreptomyces produce myriad of polyketide compounds having (potential) clinical applications. While the database of polyketide gene clusters are quickly expanding, the regulation mechanisms of them are rarely known. Sulfane sulfur species are commonly present in microorganisms with unclear functions. Herein, we discovered that sulfane sulfur increases actinorhodin (ACT) production in S. coelicolor. The underlying mechanism is sulfane sulfur specifically reacts with AdpA, a global transcription factor controlling both ACT gene cluster and morphological differentiation related genes, to form sulfhydrated AdpA. This modification changes dynamics of AdpA-controlled gene network and leads to high expression of ACT biosynthetic genes. Given the wide prevalence of AdpA and sulfane sulfur in Streptomyces, this mechanism may represent a common regulating pattern of polyketide gene clusters. Thus, this finding provides a new strategy for mining and activating valuable polyketide gene clusters.


title: Molecular convergence by differential domain acquisition is a hallmark of chromosomal passenger complex evolution

abstract:
The chromosomal passenger complex (CPC) is a heterotetrameric regulator of eukaryotic cell division, consisting of an Aurora-type kinase and a scaffold built of INCENP, Borealin and Survivin. While most CPC components are conserved across eukaryotes, orthologs of the chromatin reader Survivin have previously only been found in animals and fungi, raising the question of how its essential role is carried out in other eukaryotes. By characterizing proteins that bind to the Arabidopsis Borealin ortholog, we identified BOREALIN RELATED INTERACTOR 1 and 2 (BORI1 and BORI2) as redundant Survivin-like proteins in the context of the CPC in plants. Loss of BORI function is lethal and a reduced expression of BORIs causes severe developmental defects. Similar to Survivin, we find that the BORIs bind to phosphorylated histone H3, relevant for correct CPC association with chromatin. However, this interaction is not mediated by a BIR domain as in previously recognized Survivin orthologs, but by an FHA domain, a widely conserved phosphate-binding module. We propose that the unifying criterion of Survivin-type proteins is a helix that facilitates complex formation with the other two scaffold components, and that the addition of a phosphate-binding domain, necessary for concentration at the inner centromere, evolved in parallel in different eukaryotic groups. Using sensitive similarity searches, we indeed find conservation of this helical domain between animals and plants, and identify the missing CPC component in most eukaryotic supergroups. Interestingly, we also detect Survivin orthologs without a defined phosphate-binding domain, possibly reflecting the situation in the last eukaryotic common ancestor.

Significance StatementThe identification of two SURVIVIN-type genes in the model plant Arabidopsis unfolded the evolutionary trajectories of this central chromosomal passenger complex component and led to the identification of SURVIVIN orthologs in almost the entire eukaryotic kingdom. Our work indicates that the central most aspect of the SURVIVIN gene family is a helix to make contact with two other core chromosomal passenger complex members whereas the addition of a phosphate-binding domain shown to bind to chromatin in animals and plants evolved in parallel at least 3 times in different eukaryotic branches.


title: Multi-omics reveals principles of gene regulation and pervasive non-productive transcription in the human cytomegalovirus genome

abstract: For decades, human cytomegalovirus (HCMV) was thought to express {approx}200 viral proteins during lytic infection. In recent years, systems biology approaches uncovered hundreds of additional viral gene products and suggested thousands of viral sites of transcription initiation. Despite all available data, the molecular mechanisms of HCMV gene regulation remain poorly understood. Here, we provide a unifying model of productive HCMV gene expression employing transcription start site profiling combined with metabolic RNA labeling as well as integrative computational analysis of previously published big data. This approach defined the expression of >2,600 high confidence viral transcripts and explained the complex kinetics of viral protein expression by cumulative effects of translation of incoming virion-associated RNA, multiple transcription start sites with distinct kinetics per viral open reading frame, and differences in viral protein stability. Most importantly, we identify pervasive transcription of transient RNAs as a common feature of this large DNA virus with its human host.


title: A kinase translocation reporter reveals real-time dynamics of ERK activity in Drosophila

abstract:
Extracellular Signal-Regulated Kinase (ERK) lies downstream of a core signalling cascade that controls all aspects of development and adult homeostasis. Recent developments have led to new tools to image and manipulate the pathway. However, visualising ERK activity in vivo with high temporal resolution remains a challenge in Drosophila. We adapted a kinase translocation reporter (KTR) for use in Drosophila, which shuttles out of the nucleus when phosphorylated by ERK. We show that ERK-KTR faithfully reports endogenous ERK signalling activity in developing and adult tissues, and that it responds to genetic perturbations upstream of ERK. Using ERK-KTR in time-lapse imaging, we made two novel observations: firstly, sustained hyperactivation of ERK by expression of dominant-active Epidermal Growth Factor Receptor raised the overall level but did not alter the kinetics of ERK activity; secondly, heterogeneity in ERK activity in retinal basal glia correlated with the direction of migration of individual cells. Our results show that KTR technology can be applied in Drosophila to monitor ERK activity in real-time and suggest that this modular tool can be further adapted to study other kinases.

Summary StatementWe describe a reporter to study the dynamics of ERK signalling in Drosophila, use it to measure signalling in individual cells over time, and monitor development.


title: In vitro and in vivo venom-inhibition assays identify metalloproteinase-inhibiting drugs as potential treatments for snakebite envenoming by Dispholidus typus

abstract: Snakebite envenoming affects more than 250,000 people annually in sub-Saharan Africa. Envenoming by Dispholidus typus (boomslang) results in venom induced consumption coagulopathy, whereby highly abundant prothrombin-activating snake venom metalloproteinases (SVMPs) consume clotting factors and deplete fibrinogen. The only available treatment for D. typus envenoming is the monovalent SAIMR Boomslang antivenom. Treatment options are urgently required because this antivenom is often difficult to source and, at $6,000/vial, typically unaffordable for most snakebite patients. We therefore investigated the in vitro and in vivo preclinical efficacy of four SVMP inhibitors to neutralise the effects of D. typus venom; the matrix metalloproteinase inhibitors marimastat and prinomastat, and the metal chelators dimercaprol and DMPS. The venom of D. typus exhibited an SVMP-driven procoagulant phenotype in vitro. Marimastat and prinomastat demonstrated equipotent inhibition of the SVMP-mediated procoagulant activity of the venom in vitro, whereas dimercaprol and DMPS showed considerably lower potency. However, when tested in preclinical murine models of envenomation, DMPS and marimastat demonstrated partial protection against venom lethality, demonstrated by prolonged survival times of experimental animals, whereas dimercaprol and prinomastat failed to confer any protection at the doses tested. The results presented here demonstrate that DMPS and marimastat show potential as novel small molecule-based therapeutics for D. typus snakebite envenomation. These two drugs have been previously shown to be effective against Echis ocellatus venom induced consumption coagulopathy (VICC) in preclinical models, and thus we conclude that marimastat and DMPS may be valuable early intervention therapeutics to broadly treat VICC following snakebite envenoming in sub-Saharan Africa.

category: pharmacology and toxicology


title: Engineering SARS-CoV-2 neutralizing antibodies for increased potency and reduced viral escape

abstract: The rapid spread of SARS-CoV-2 variants poses a constant threat of escape from monoclonal antibody and vaccine countermeasures. Mutations in the ACE2 receptor binding site on the surface S protein have been shown to disrupt antibody binding and prevent viral neutralization. Here, we use a directed evolution-based approach to engineer three neutralizing antibodies for enhanced binding to S protein. The engineered antibodies showed increased in vitro functional activity in terms of neutralization potency and/or breadth of neutralization against viral variants. Deep mutational scanning revealed that higher binding affinity reduced the total number of viral escape mutations. Studies in the Syrian hamster model showed two examples where the affinity matured antibody provided superior protection compared to the parental antibody. These data suggest that monoclonal antibodies for anti-viral indications could benefit from in vitro affinity maturation to reduce viral escape pathways and appropriate affinity maturation in vaccine immunization could help resist viral variation.

category: bioengineering


title: Heparin-derived theranostic nanoprobes overcome the blood-brain barrier and target glioma in murine model

abstract: The poor permeability of theranostic agents across the blood-brain-barrier (BBB) significantly hampers the development of new treatment modalities for neurological diseases. We have discovered a new biomimetic nanocarrier using heparin (HP) that effectively passes the BBB and targets glioblastoma. Specifically, we designed HP coated gold nanoparticles (HP-AuNPs) that were labeled with three different imaging modalities namely, fluorescein (FITC-HP-AuNP), radioisotope 68Gallium (68Ga-HP-AuNPs), and MRI active gadolinium (Gd-HP-AuNPs). The systemic infusion of FITC-HP-AuNPs in three different mouse strains (C57BL/6JRj, FVB, and NMRI-nude) displayed excellent penetration and revealed uniform distribution of fluorescent particles in the brain parenchyma (69-86%) with some accumulation in neurons (8-18%) and microglia (4-10%). Tail-vein administration of radiolabeled 68Ga-HP-AuNPs in healthy rats also showed 68Ga-HP-AuNP inside the brain parenchyma and in areas containing cerebrospinal fluid, such as the lateral ventricles, the cerebellum, and brain stem. Finally, tail-vein administration of Gd-HP-AuNPs (that display [~]3 fold higher relaxivity than that of commercial Gd-DTPA) in an orthotopic glioblastoma (U87MG xenograft) model in nude mice demonstrated enrichment of T1-contrast at the intracranial tumor with a gradual increase in the contrast in the tumor region between 1h-3h. We believe, our finding offers the untapped potential of HP-derived-NPs to deliver cargo molecules for treating neurological disorders.


title: Revised Michaelis-Menten rate law with time-varying molecular concentrations

abstract: Despite over a centurys use as a dominant paradigm in the description of biochemical rate processes, the Michaelis-Menten (MM) rate law stands on the restrictive assumption that the concentration of the complex of interacting molecules, at each moment, approaches an equilibrium much faster than the molecular concentration changes. The increasingly-appreciated, remedied form of the MM rate law is also based on this quasi-steady state assumption. Although this assumption may be valid for a range of biochemical systems, the exact extent of such systems is not clear. In this study, we relax the quasi-steady state requirement and propose the revised MM rate law for the interactions of molecules with active concentration changes over time. Our revised rate law, characterized by rigorously-derived time delay effects in molecular complex formation, improves the accuracy of models especially for protein-protein and protein-DNA interactions. Our simulation and empirical data analysis show that the improvement is not limited to the quantitatively better characterization of the dynamics, but also allows the prediction for qualitatively new patterns in the systems of interest. The latter include the oscillation condition and period patterns of the mammalian circadian clock and the spontaneous rhythmicity in the degradation rates of circadian proteins, both not properly captured by the previous approaches. Moreover, our revised rate law is capable of more accurate parameter estimation. This work offers an analytical framework for understanding rich dynamics of biomolecular systems, which goes beyond the quasi-steady state assumption.