title: CDK8 and CDK19 act redundantly to control the CFTR pathway in the intestinal epithelium

abstract: CDK8 and CDK19 form a conserved cyclin-dependent kinase subfamily that interacts with the essential transcription complex, Mediator, and also promotes transcription by phosphorylating the C-terminal domain (CTD) of RNA polymerase II. Cells lacking either CDK8 or CDK19 are viable and have limited transcriptional alterations, but whether the two kinases redundantly control cell differentiation is unknown. Here, we find that CDK8 is dispensable for RNA polII CTD phosphorylation, regulation of gene expression, normal intestinal homeostasis and efficient tumourigenesis in mice. Furthermore, CDK8 is largely redundant with CDK19 in the control of gene expression. Yet, while their combined deletion in intestinal organoids reduces long-term proliferative capacity, it is not lethal and allows differentiation. Nevertheless, in double mutant organoids, the cystic fibrosis transmembrane conductance regulator (CFTR) pathway is transcriptionally and functionally downregulated, leading to mucus accumulation and increased secretion by goblet cells. This phenotype can be recapitulated by pharmacological inhibition of CDK8/19 kinase activity. Thus, the Mediator kinases are not essential for cell proliferation and differentiation, but they cooperate to regulate tissue-specific transcriptional programmes.

category: cell biology


title: Fgfr2b signaling is essential for the maintenance of the alveolar epithelial type 2 lineage during lung homeostasis in mice

abstract: Fibroblast growth factor receptor 2b (Fgfr2b) signaling is essential throughout lung development to form the alveolar epithelial lineage. However, its role in alveolar epithelial type 2 cells (AT2s) homeostasis was recently considered dispensable. SftpcCreERT2; tdTomatoflox/flox mice were used to delete Fgfr2b expression in cells belonging to the AT2 lineage, which contains mature AT2s and a novel SftpcLow lineage-traced population called "injury activated alveolar progenitors" or IAAPs. Upon continuous tamoxifen exposure for either one or two weeks to delete Fgfr2b, a shrinking of the AT2s is observed. Mature AT2s exit the cell cycle, undergo apoptosis and fail to form alveolospheres in vitro. However, the lung morphometry appears normal, suggesting the involvement of compensatory mechanisms. In mutant lungs, IAAPs which escaped Fgfr2b deletion expand, display enhanced alveolosphere formation in vitro and increase drastically their AT2 signature suggesting differentiation towards mature AT2s. Interestingly, a significant increase in AT2s and decrease in IAPPs occurs after a one-week tamoxifen exposure followed by an eight-week chase period. While mature AT2s partially recover their alveolosphere formation capabilities, the IAAPs no longer display this property. Single-cell RNA seq analysis confirms that AT2s and IAAPs represent stable and distinct cell populations and recapitulate some of their characteristics observed in vivo. Our results underscore the essential role played by Fgfr2b signaling in the maintenance of the AT2 lineage in the adult lung and suggest that the IAAPs could represent a new population of AT2 progenitors.

category: developmental biology


title: CyclinD2-mediated regulation of neurogenic output from the retinal ciliary margin is perturbed in albinism

abstract:
In albinism, aberrations in the ipsi-/contralateral retinal ganglion cell (RGC) ratio compromise the functional integrity of the binocular circuit. We focus here on the mouse ciliary margin zone (CMZ), a neurogenic niche at the embryonic peripheral retina, to investigate developmental processes regulating RGC neurogenesis and identity acquisition. We found that the mouse ventral CMZ has the competence to generate predominantly ipsilaterally-projecting RGCs, but this competence is altered in the albino visual system due to CyclinD2 downregulation and disturbed temporal control of the cell cycle. Consequently, albino as well as CyclinD2-deficient pigmented mice exhibit a diminished ipsilateral retinogeniculate projection and compromised depth perception. Pharmacological stimulation of calcium channels in albino mice, known to upregulate CyclinD2 in other cell types, augmented CyclinD2-dependent neurogenesis of ipsilateral RGCs, and improved stereopsis. Together, these results implicate CMZ neurogenesis and its regulators as critical for the formation and function of the mammalian binocular circuit.

HighlightsO_LIThe mouse ventral CMZ produces predominantly ipsilateral RGCs.
C_LIO_LIIn the albino visual system, CyclinD2 downregulation leads to delayed G1/S transition toward mitotic exit of CMZ progenitors.
C_LIO_LIPerturbations in the temporal control of cell cycle by CyclinD2 lead to reduced Zic2+ RGCs and consequently, a diminished ipsilateral retinogeniculate projection and compromised depth perception.
C_LIO_LICalcium channel modulation during embryogenesis normalizes the levels of CyclinD2 and restores binocular vision in albino mice.
C_LI


title: Extinction risk, reconstructed catches, and management of chondrichthyan fishes in the Western Central Atlantic Ocean

abstract: Chondrichthyan fishes are among the most threatened vertebrates on the planet because many species have slow life histories that are outpaced by intense fishing. The Western Central Atlantic Ocean, which includes the greater Caribbean, is a hotspot of chondrichthyan biodiversity and abundance, but is historically characterized by extensive shark and ray fisheries and a lack of sufficient data for effective management and conservation. To inform future research and management decisions, we analyzed patterns in chondrichthyan extinction risk, reconstructed catches, and regulations in this region. We summarized the extinction risk of 180 sharks, rays, and chimaeras using contemporary IUCN Red List assessments and found that over one-third (35.6%) were assessed as Vulnerable, Endangered, or Critically Endangered largely due to fishing. Reconstructed catches from 1950 to 2016 reached their peak in 1992, then declined by 40.2% through the end of the series. The United States, Venezuela, and Mexico were responsible for most catches and hosted large proportions of the regional distributions of threatened species; these countries therefore held the greatest responsibility for chondrichthyan management. The abundance and resolution of fisheries landings data were poor in much of the region, and national-level regulations varied widely across jurisdictions. Deepwater fisheries represent an emerging threat, although many deepwater chondrichthyans currently find refuge beyond the depths of most fisheries. Regional collaboration as well as effective and enforceable management informed by more complete fisheries data, particularly from small-scale fisheries, are required to protect and recover threatened species and ensure sustainable fisheries.

category: ecology


title: Slower organisms exhibit sudden population disappearances in a reddened world

abstract: Sudden population disappearances are a possibility in natural systems. Human-caused reddening of noise -- increasing the autocorrelation of noise -- may make sudden population disappearances more likely because red noise can enlarge the period and magnitude of perturbations, potentially overwhelming species natural compensatory responses and pushing species population dynamics away from equilibria into transient dynamics and close to extinction. Furthermore, species natural compensatory responses are related to life history along the slow-fast continuum. This interaction of slow-fast life history plus red noise may be a potent factor producing sudden population disappearances. Using a simple mathematical technique with the classic Rozenzweig-MacArthur consumer resource model, we created an experiment varying the consumers maximum population growth rate, effectively varying the consumers life history along the slow-fast continuum. Initial slowing of the consumers growth rate increased the stability of the consumer-resource model with added stochasticity. Slowing the consumers growth rate further and reddening the noise decreased the stability with population disappearances occurring frequently. Taken together, we have shown that slow life histories can both stabilize or destabilize interactions depending on the relative speeds within the interaction. Disconcertingly with a reddening world, larger and slower organisms may be especially prone to experiencing transient-driven sudden population disappearances.


title: Characterization of Cyanobacterial Communities in Lakes Requires Consideration of Diurnal and Spatial Variation

abstract:
Continental-scale increases in aquatic system eutrophication are linked with increased cyanobacteria threats to recreational water use and drinking water resources globally. While some guidance regarding monitoring is available, it is largely reactive and insufficient for proactive risk mitigation and management, which necessarily requires an understanding of the composition and dynamics of cyanobacterial communities in the aquatic system. Their distribution is impacted by several factors, including water column mixing and buoyancy regulation responses to light availability that create oscillatory diurnal migration patterns within the water column, creating challenges in the ability to accurately describe and quantify cyanobacterial densities. These dynamic fluctuations are not typically reflected in monitoring protocols, which frequently focus on surface depths and either ignore sampling time or recommend large midday timeframes (e.g., 10AM-3PM), thereby precluding accurate characterization of cyanobacterial communities. While diurnal vertical migration of cyanobacteria has been reported in marine and eutrophic freshwater systems, reports in oligotrophic freshwater lakes are scant and characterization have focused on individual 24-hour periods neglecting to consider day-to-day variability. These dynamics must be better understood and reflected in water quality monitoring guidance to advance drinking water risk management and source water protection approaches. To evaluate the impact of diurnal migrations and water column stratification on cyanobacterial abundance, communities were characterized using a multi-time point sampling series across a 48-hour period in a shallow well-mixed lake interconnected to a thermally stratified lake in the Turkey Lakes Watershed (Ontario, Canada). Amplicon sequencing of the V4 region in the 16S rRNA gene was performed to characterize microbial community composition. Cyanobacteria were significantly represented in the microbial community in the midday and afternoon sampling times in the thermally stratified lake, but not in the well-mixed lake. Although the lakes in this study are interconnected, the cyanobacterial communities within them exhibited unique composition and distribution trends, thereby underscoring the importance of developing detailed sampling guidance to maximize the utility of cyanobacteria monitoring and better characterize and mitigate risk.

Highlights{blacksquare} Water column stability impacts diurnal migrations of cyanobacteria
{blacksquare}Gas vacuolate taxa are more abundant at surface, but also present at depth
{blacksquare}Rain events can impact cyanobacteria distribution and impact detection
{blacksquare}Cyanobacteria distribution can vary significantly between interconnected lakes
{blacksquare}Cyanobacteria monitoring for risk management should incorporate time and depth


title: Soil fungal communities vary more with soil characteristics than tree diversity at a local scale

abstract: Soil fungal communities vary spatially due to factors including variations in plant diversity and soil characteristics; however, the relative influences of these factors on composition and therefore function remain unclear. Small-scale variation in fungal communities may drive local variation in nutrient cycling and decomposition and may respond more to local factors compared with large climatic variations. Clarifying the roles of these factors can improve our predictions of soil fungal community and biogeochemical cycling responses to anthropogenic changes. Therefore, we examined relationships among abiotic and biotic factors and soil fungal communities associated with Quercus rubra and Pinus resinosa saplings and mature trees in a mixed-hardwood woodland. We also compared community composition and fungal enzymatic activity. Fungal community composition was associated with spatial heterogeneity of soil characteristics, while host sapling and tree species identity were poor predictors of community composition. Further, most of the compositional variation was unexplained by measured variables, suggesting stochasticity and other environmental characteristics may drive spatial variation in these communities. Additionally, enzymatic activity did not clearly correlate with fungal community composition. Overall, soil fungal communities and enzymatic activity adjacent to saplings in this woodland are influenced primarily by soil characteristics and stochasticity and not plant identity.


title: Geographical and ecological drivers of coexistence dynamics in squamate reptiles

abstract:
AO_SCPLOWBSTRACTC_SCPLOWO_ST_ABSAimC_ST_ABSSpecies richness varies widely across space. To understand the processes behind these striking patterns, we must know what are the relevant drivers underlying species coexistence. Several factors can potentially shape species coexistence such as the speciation process, the time since divergence between lineages, environmental effects, and intrinsic properties of the organisms. For the first time, we model the coexistence dynamics of lizards and snakes across broad temporal and spatial scales, investigating the role of species interactions, dispersal ability, and geographic area.

LocationGlobal

Time periodLast 20 million years

Major taxa studiedSquamata (lizards and snakes)

MethodsWe used 448 closely related species pairs and their age since divergence across 100 dated phylogenies. We categorized each pair as sympatric or allopatric and as occurring on islands or continents. We measured morphological traits to quantify niche divergence and used range and body size as proxies for dispersal ability. We applied a model-comparison framework in lizards and snakes separately to evaluate which factors best explained their coexistence dynamics.

ResultsWe found that distinct factors drive the coexistence dynamics in lizards and snakes. In snakes, species pairs that coexist tend to occur on islands and are more different in body size, suggesting that both geographical setting and species interactions might be relevant factors. In contrast, we only found evidence that dispersal ability shaped the coexistence of lizards, where species coexist when they have higher dispersal abilities.

Main conclusionsLizards and snakes greatly differ in coexistence dynamics. Higher heterogeneity in coexistence dynamics within lizards and group-specific life-history aspects might help to explain these findings. Our results emphasize that the interaction between where organisms are and who they are, ultimately shapes biodiversity patterns. We also highlight interesting avenues for further studies on species coexistence in deep time.

category: evolutionary biology


title: Experimental disruption of social structure reveals totipotency in the orchid bee, Euglossa dilemma

abstract: Eusociality has evolved multiple times across the insect phylogeny. Social insects with greater levels of social complexity tend to exhibit specialized castes with low levels of individual phenotypic plasticity. In contrast, species with small, simple social groups may consist of totipotent individuals that can transition among behavioral and reproductive states as the social hierarchy shifts. However, recent work has shown that in some simple social groups, there can still be constraint on individual plasticity, caused by differences in maternal nourishment or initial social interaction. It is not well understood how and when these constraints arise during social evolution, ultimately leading to the evolution of nonreproductive workers. Some species of orchid bees can form social groups of a dominant and 1-2 subordinate helpers where all individuals are reproductive. Females can also disperse on emergence to start their own nest as a solitary foundress, which includes a nonreproductive nest guarding phase not typically expressed by subordinates. Little data exist to characterize the flexibility of orchid bees across these trajectories. Here, using the orchid bee Euglossa dilemma, we conduct an experiment assessing the plasticity of subordinate helpers, finding that they are highly flexible and capable of the behavioral, physiological, transcriptomic, and chemical changes seen in foundresses. Furthermore, we identify genes and gene networks associated with reproductive changes in E. dilemma that overlap with genes associated with worker physiology in eusocial species. Our results provide evidence that the lack of nonreproductive workers in E. dilemma is not due to a lack of subordinate plasticity.


title: Fitness costs and benefits in response to artificial artesunate selection in Plasmodium

abstract:
Drug resistance is a major issue in the control of malaria. Mutations linked to drug resistance often target key metabolic pathways and are therefore expected to be associated with biological costs. The spread of drug resistance depends on the balance between the benefits that these mutations provide in the drug-treated host and the costs they incur in the untreated host. The latter may therefore be expressed both in the vertebrate host and in the vector.

Current information about the costs of drug resistance mutations comes almost exclusively from vertebrate hosts. The potential for these costs to be expressed also in mosquitoes has been given only cursory attention. In this study, we aim to identify the costs and benefits of resistance against artesunate (AS), one of the main artemisinin derivatives used in malaria-endemic countries. For this purpose, we compared different AS-selected lines of the avian malaria parasite Plasmodium relictum to their ancestral (unselected) counterpart. We tested their within host dynamics and virulence both in the vertebrate host and in its natural vector, the mosquito Culex quinquefasciatus.

The within-host dynamics of the AS-selected lines in the treated birds was consistent with the phenotype of resistance described in human P. falciparum malaria: a clearance delay during the treatment followed by a recrudescence once the treatment was interrupted. In the absence of treatment, however, we found no significant costs of resistance in the bird. The results of the two experiments to establish the infectivity of the lines to mosquitoes point towards a decreased infectivity of the drug-selected lines as compared to the ancestral, reference one. We discuss the potential implication of these results on the spread of artesunate resistance in the field.


title: Extensive retargeting of plant aminoacyl tRNA synthetases correlates with mitochondrial tRNA gene loss

abstract: The number of tRNAs encoded in plant mitogenomes varies considerably, with some lineages exhibiting rapid reductions. Loss of these bacterial-like mitochondrial tRNAs necessitates the import of nuclear-encoded counterparts that share little sequence similarity, raising questions about the identity and trafficking of enzymes necessary for the maturation and function of these newly imported tRNAs. In particular, the aminoacyl tRNA synthetases (aaRSs) that charge tRNAs are usually divided into distinct classes that specialize on either organellar or cytosolic tRNAs. Here, we investigated the evolution of aaRS subcellular localization in five species from a plant lineage (Sileneae) that has experienced extensive and rapid mitochondrial tRNA loss. By analyzing full-length mRNA transcripts (PacBio Iso-Seq), we found predicted retargeting of many ancestrally cytosolic aaRSs to the mitochondrion as well as scenarios where enzyme localization does not appear to change despite functional tRNA replacement. In most cases of transit peptide acquisition, the cytosolic enzyme gained a coding extension prior to the loss of the cognate mitochondrial tRNAs - suggesting a transitional state where organellar and cytosolic aaRSs colocalize to mitochondria. The ongoing functional replacement of Sileneae mitochondrial tRNAs and subsequent evolution of tRNA-interacting enzymes present an opportunity to study the coevolutionary dynamics of plant cytonuclear genetics.


title: Genetic modifiers of Cep290-mediated retinal degeneration

abstract: Mutations in CEP290 cause up to 30% of cases of Leber congenital amaurosis (LCA), a severe childhood blindness resulting from abnormalities in the photoreceptor connecting cilia that lead to rapid retinal degeneration. Like many genetic diseases, CEP290-LCA has considerable variable expressivity, indicating the presence of other factors that influence phenotypic outcome. Here, we have undertaken a phenotype-driven approach in mice to identify genetic modifiers of CEP290-mediated retinal degeneration through backcrosses and intercrosses between BXD24-Cep290rd16 mice and the genetically distinct inbred CAST strain to introduce genetic variation. Optical coherence tomography was used to quantitatively measure retinal thickness as a surrogate indication of photoreceptor degeneration in the resulting rd16-mutant mice. It was readily apparent that CEP290-mediated retinal degeneration in the resulting mice is sensitive to genetic background, with some mice exhibiting relatively thick laminated retinas and others having thin retinas with advanced disease. Quantitative trait locus (QTL) analysis identified multiple genomic loci capable of influencing the retinal degeneration phenotype in Cep290-mutant mice that together account for 71.7% of the phenotypic variation in retinal thickness observed in our population. Following the QTL analysis, two suppressor loci were studied in detail through a combination of physical and molecular approaches to narrow the critical region for each QTL and identify the probable causative genetic variations.

category: genetics


title: A chromosome-level, fully phased genome assembly of the oat crown rust fungus Puccinia coronata f. sp. avenae: a resource to enable comparative genomics in the cereal rusts

abstract: Advances in sequencing technologies as well as development of algorithms and workflows have made it possible to generate fully phased genome references for organisms with non-haploid genomes such as dikaryotic rust fungi. To enable discovery of pathogen effectors and further our understanding of virulence evolution, we generated a chromosome-scale assembly for each of the two nuclear genomes of the oat crown rust pathogen, Puccinia coronata f. sp. avenae (Pca). This resource complements two previous released partially phased genome references of Pca, which display virulence traits absent in the isolate of historic race 203 (isolate Pca203) which was selected for this genome project. A fully phased, chromosome-level reference for Pca203 was generated using PacBio reads and Hi-C data and a recently developed pipeline named NuclearPhaser for phase assignment of contigs and phase switch correction. With 18 chromosomes in each haplotype and a total size of 208.10 Mbp, Pca203 has the same number of chromosomes as other cereal rust fungi such as Puccinia graminis f. sp. tritici and Puccinia triticina, the causal agents of wheat stem rust and wheat leaf rust, respectively. The Pca203 reference marks the third fully-phased chromosome-level assembly of a cereal rust to date. Here, we demonstrate that the chromosomes of these three Puccinia species are syntenous and that chromosomal size variations are primarily due to differences in repeat element content.

category: genomics


title: Genomic and phylogenetic analysis of the first myovirus isolated from Oceanospirillaceae, representing a novel viral cluster prevalent in polar oceans

abstract:
The marine bacterial family Oceanospirillaceae, which is abundant in the deep-seas and polar oceans, is closely associated with algal blooms and petroleum hydrocarbons degradation. However, only a few Oceanospirillaceae-infecting phages have so far been reported. Here we report on a novel Oceanospirillum phage, vB_OsaM_PD0307, which is the first myovirus to be found that infects Oceanospirillaceae. vB_OsaM_PD0307 with a 44,421 bp linear dsDNA genome. Phylogenetic analysis and average nucleotide sequence identities suggest that vB_OsaM_PD0307 is different from other phage isolates and represents a novel genus-level myoviral cluster with two high-quality uncultured viral genomes, designed as Oceanospimyovirus. Additionally, the biogeographical distribution of the vB_OsaM_PD0307 cluster suggests that they are widespread in the oceans and abundant in polar areas. In summary, our findings expand the current understanding of the phylogenetic diversity, genomic characteristic and function of Oceanospimyovirus phages, and highlight the role of the vB_OsaM_PD0307 phage as a major ecological agent that can infect certain key bacterial groups associated with polar algal blooms.

ImportanceOceanospirillumphage vB_OsaM_PD0307 is the first myovirus found to infect Oceanospirillaceae and represents a novel viral genus, Oceanospimyovirus. This study provides insights into the genomic, phylogenetic, and ecological characteristics of myoviruses infecting Oceanospirillaceae and improves our understanding of the interactions between Oceanospirillaceae and their phages in the oceans.


title: Validation of SNP markers for marker-assisted selection of genotypes with increased carotenoid and dry matter contents in cassava

abstract: Provitamin A biofortification and increased dry matter content are important breeding targets in cassava improvement programs worldwide. Biofortified varieties contribute to the alleviation of provitamin A deficiency, a leading cause of preventable blindness in developing countries. Dry matter content is a major component of dry yield and thus underlies overall variety performance and acceptability by growers, processors, and consumers. SNP markers linked to these traits have recently been discovered through several genome-wide association studies but have not been deployed for marker-assisted selection (MAS). Assessment of marker performance in diverse genetic backgrounds is an important step towards their deployment for routine MAS. In the present study, seven previously identified markers for these traits were converted to a robust set of uniplex allele-specific PCR assays and validated in two independent pre-breeding and breeding populations. These assays were efficient in discriminating marker genotypic classes and had an average call rate greater than 98%. A high correlation was observed between the predicted and observed carotenoid content as inferred by root yellowness intensity in the breeding (r = 0.92) and pre-breeding (r = 0.95) populations. On the other hand, dry matter content-markers had moderately low predictive accuracy in both populations (r < 0.40) due to the more quantitative nature of the trait. This work confirmed marker effectiveness in multiple backgrounds, therefore, further strengthening its value in cassava biofortification to ensure nutritional security as well as dry matter content productivity. Our study provides a framework to guide future marker development, thus leading to more routine use of markers in MAS in cassava improvement programs.


title: Megaviruses contain various genes encoding for eukaryotic vesicle trafficking factors

abstract:
Many intracellular pathogens, such as bacteria and large viruses, enter eukaryotic cells via phagocytosis, then replicate and proliferate inside the host. To avoid degradation in the phagosomes, they have developed strategies to modify vesicle trafficking. Although several strategies of bacteria have been characterized, it is not clear whether viruses also interfere with the vesicle trafficking of the host. Recently, we came across SNARE proteins encoded in the genomes of several bacteria of the order Legionellales. These pathogenic bacteria may use SNAREs to interfere with vesicle trafficking, since SNARE proteins are the core machinery for vesicle fusion during transport. They assemble into membrane-bridging SNARE complexes that bring membranes together. We now have also discovered SNARE proteins in the genomes of diverse giant viruses. Our biochemical experiments showed that these proteins are able to form SNARE complexes. We also found other key trafficking factors that work together with SNAREs such as NSF, SM, and Rab proteins encoded in the genomes of giant viruses, suggesting that viruses can make use of a large genetic repertoire of trafficking factors. Most giant viruses possess different collections, suggesting that these factors entered the viral genome multiple times. In the future, the molecular role of these factors during viral infection need to be studied.

O_FIG_DISPLAY_L [Figure 1] M_FIG_DISPLAY C_FIG_DISPLAY

SynopsisGiant viruses enter their eukaryotic host cells by phagocytosis. For reproduction, they hijack the host cells membranes by an unknown mechanism. Here, we found that giant viruses express several core factors of the eukaryotic vesicle fusion machinery, including SNARE, Rab, SM proteins, and the disassembly protein NSF. Very probably, these genes were transferred from different eukaryotic hosts to different viruses. Whether the viruses deploy these factors for interfering with the vesicle trafficking of the host cell needs to be investigated.


title: Bio-inspired artificial printed bioelectronic cardio-3D-cellular constructs

abstract: Bioelectronics is a growing field where novel smart materials are required to interface biology with electronic components. Conductive hydrogels have recently emerged as a promising material for biosensing/actuating applications as they can provide a wet, nanostructured and electrically conductive environment, minimising the mismatch between biological and electronic systems. In this work, we propose a strategy to develop conductive bioinks compatible with the freeform reversible embedding of suspended hydrogels (FRESH) extrusion bioprinting method. These bioinks are based on decellularized extracellular matrix (dECM), extracted from three different tissues (small intestine submucosa, liver and bone) and were characterised. 3D structures were manufactured containing human pluripotent stem cell-derived cardiomyocytes (hPSC-CMs), exhibiting cell viabilities >80%. Multi-walled carbon nanotubes (MWCNTs) were selected as an additional component of the bioinks. The addition of the MWCNTs enhanced the conductive features of the hydrogels and the morphology of the dECM fibres. Electrical stimulation (ES) through alternating currents was applied to hPSC-CMs encapsulated in 3D structures manufactured with the previous material and our results indicated two main findings: (1) in the absence of external ES, the conductive properties of the materials can improve the contractile behaviour of the hPSC-CMs and (2) this effect is significantly enhanced under the application of external ES. Genetic markers analysed showed a trend towards a more mature state of the cells evaluated by the TNNI3/TNNI1 ratio, with upregulated SERCA2 and RYR2 calcium handling proteins when compared to controls and downregulation of calcium channels involved in the generation of pacemaking currents (CACNA1H). These results demonstrate the potential of our strategy to manufacture conductive hydrogels in complex geometries for bioactuating purposes. However, further development of the 3D bioprinting techniques is required to achieve higher control over the nano- and microarchitectures of the structures to improve their biomimicry.

category: bioengineering


title: Blood flow modeling under LVAD physiology. From global circulation to local hemodynamics

abstract: This document presents the modeling strategy to address the in-silico study of different LVAD patho-physiological scenarios. The proposed approach employs a closed-loop lumped-parameter compartmental representation of the global circulation in the cardiovascular system (CVS). The CVS is coupled to a HeartMate 3 LVAD, and different cardiovascular conditions are proposed by modification of model parameters. Once the simulation for these conditions are performed, the cardiac function is analyzed in detail, and the global circulation model delivers flow rate waveforms which are employed as boundary conditions in a 3D hemodynamic simulation. This local circulation model is built using a patient-specific geometry of the aortic arch, containing 7 inlet/outlet boundaries, namely: LVAD cannula, aortic root, left and right subclavian arteries, left and right common carotid arteries and thoracic aorta. This model is exploited to investigate the impact of global cardiovascular conditions in the local hemodynamic features, particularly the wall shear stress (WSS) in different spatial regions.


title: Topology of connective tissues: a key parameter in cellular heterogeneity, beyond composition and stiffness

abstract: Cellular plasticity is essential in physiological contexts, including pathological ones. It is the basis of morphogenesis and organogenesis, as well as tumorigenesis and metastasis. The extracellular matrix (ECM) is a key player in the generation of cellular heterogeneity. Advances in our understanding of cell plasticity rely on our ability to provide relevant in vitro models. This requires to catch the characteristics of the tissues that are essential for controlling cell fate. To do this, we must consider the diversity of tissues, the diversity of physiological contexts, and the constant remodeling of ECM along these processes. To this aim, we have fabricated a library of ECM models for reproducing the scaffold of connective tissues and basement membrane with different biofabrication routes based on the electrospining and drop casting of biopolymers. Using a combination of multiphoton imaging and nanoindentation, we show that we can vary independently protein composition, topology of connective tissues and stiffness of ECM models. Reproducing the features of a tissue and physiological context in turns allows to generate the complexity of the phenotypic landscape associated with the epithelial-to-mesenchymal transition (EMT) in human ovarian cancer. We show that EMT shift cannot be directly correlated with a unique ECM feature, which reflects the multidimensionality of living environments. Very importantly, our combinatorial approach allows us to provide in vitro models, where the impact of the topological cues on cellular phenotypes can be revealed, beyond protein composition and stiffness of the ECM matrix. On this line, this work is a further step towards the development of ECM models recapitulating the constantly remodeled scaffolding environment that cells face and provides new insights for the development of cell-free matrices.


title: Generation of stable microtubule superstructures by binding of peptide-fused tetrameric proteins to inside and outside

abstract: Microtubules (MTs) play important roles in biological functions by forming superstructures, such as doublets, triplets, and branched structures, in vivo. Formation of these superstructures by exogenous molecules in vitro will be useful not only for understanding the functions of MTs but also as components of MT-based nanomaterials. Here, we developed a tetrameric fluorescent protein Azami-Green (AG) fused with a His-tag and Tau-derived peptide (TP), TP-AG, which can bind to the inside or outside of MTs depending on the polymerization conditions. The binding of TP-AG to the inside of MTs induced the formation, stabilized, and increased the rigidity of the MTs. The binding of TP-AG to the outside of MTs induced various types of MT superstructures, including doublets, multiplets, and branched structures, by recruiting tubulins to MTs. The formation of motile MT aster structures by TP-AG was also observed. The generation of MT superstructures by these exogenous proteins provides guidelines for the design of MT-based nanomaterials.


title: HydrAMP: a deep generative model for antimicrobial peptide discovery

abstract: Antimicrobial peptides (AMP) emerge as compounds that can alleviate the global health hazard of antimicrobial resistance. Since the repertoire of experimentally verified AMPs is limited, there is a need for novel computational approaches to peptide generation. For such approaches, exploring the amino-acid peptide representation space is infeasible due to its sparsity and combinatorial complexity. Thus, we propose HydrAMP, a conditional variational autoencoder that learns a lower-dimensional and continuous space of peptides representations and captures their antimicrobial properties. HydrAMP outperforms other approaches in generating peptides, either de novo, or by analogue discovery, and leverages parameter-controlled creativity. The model disentangles the latent representation of a peptide from its antimicrobial conditions, allowing for targeted generation. Wet-lab experiments and molecular dynamics simulation confirm the increased activity of a Pexiganan-based analogue produced by HydrAMP. HydrAMP proposes new promising AMP candidates, enabling progress towards a new generation of antibiotics.

category: bioinformatics


title: Comparative study of the effect of neutrons emitted from neutron source 241Am-Be and curcumin on MCF-7 breast cancer cells in 3D culture medium

abstract:
IntroductionCancer is one of the major medical problems threatening human health. Breast cancer is the most prevalent type of cancer in women. Reports indicate that treatments such as surgery, chemotherapy, biotherapy, and radiotherapy play a limited but important role in treating the disease. For more efficient treatment, new treatment strategies have been evolved based on combination therapy in which two or more different methods are exploited for this aim. In the present study, a combination therapy based on radiotherapy (using neutron radiation emitted from a 241Am-Be neutron source) and biotherapy (using curcumin) is applied to investigate the treatment efficiency of MCF-7 breast cancer in a three-dimensional culture medium.

materials and methodsThe neutron dose rate in the 241Am-Be source was measured using BF3 detection and MCNPX simulation methods, and then the results of both methods were compared. MTT, neutral red uptake assay, nitric oxide, glutathione assay, catalase, cytochrome c, comet assay, and caspase-3 were used to determine the effect and type of mortality due to neutron effect as well as the combined effect of neutron and curcumin in cancer cells.

ResultsCalculating the fast neutron flux around the source with two methods of simulation with MCNPX and detection with BF3 showed that with increasing distance from the source, the fast neutron flux decreased exponentially. The results of neutron dose rate measurement in the 241Am-Be source also showed that if the test cells in the vial are located at a distance of 22 cm from the inlet of the collimator and are exposed to neutron radiation for 5, 10, 15, and 20 hours, the neutron dose received by breast cancer cells will be 3, 6, 9, and 12 mGy/h, respectively.

The results of cytotoxicity due to neutron irradiation as well as the combined effect of neutron and curcumin (80 M concentration) showed that neutron irradiation with or without curcumin at 5, 10, 15, and 20 hours reduced the survival of tumor cells. According to the results, the rate of apoptosis due to the neutron effect at irradiation times has increased with increasing time. Statistical analysis also showed that the rate of apoptosis due to the combined effect of neutrons and curcumin was not significant compared to the effect of neutrons only. The results of studying the effect of neutrons and the combination of neutrons and curcumin on the production of nitric oxide, catalase, and GSH also showed that curcumin has an antioxidant effect by reducing the amount of nitric oxide and increasing the production of catalase and glutathione in cells. However, neutrons, alone, lacked this effect.

ConclusionOverall, this study showed that the neutron source 241Am-Be with the applied doses was able to destroy the c-o, and c-h bonds of curcumin, resulting in cell death and apoptosis induction in breast cancer cells. It was caused by neutron radiation. On the other hand, according to the results of the comet assay and caspase-3 experiments, although neutrons induced apoptosis in breast cancer cells, the death rate due to necrosis was much higher than apoptosis. Due to the significant anti-cancer effect of curcumin in 3D culture, the use of this molecule before or after neutron therapy is recommended.

HighlightsO_LIThe results of neutron dose rate measurement in the 241Am-Be source showed that if the test cells in the vial are located at a distance of 22 cm from the inlet of the collimator and are exposed to neutron radiation for 5, 10, 15, and 20 hours, the neutron dose received by breast cancer cells will be 3, 6, 9, and 12 mGy/h, respectively.
C_LIO_LIThe results of cytotoxicity due to neutron irradiation as well as the combined effect of neutron and curcumin (80 M concentration) showed that neutron irradiation with or without curcumin at 5, 10, 15, and 20 hours reduced the survival of tumor cells.
C_LIO_LIAccording to the results, the rate of apoptosis due to the neutron effect at irradiation times has increased with increasing time. The results of studying the effect of neutrons and the combination of neutrons and curcumin on the production of nitric oxide, catalase, and GSH also showed that curcumin has an antioxidant effect by reducing the amount of nitric oxide and increasing the production of catalase and glutathione in cells. However, neutrons, alone, lacked this effect.
C_LIO_LIthis study showed that the neutron source 241Am-Be with the applied doses was able to destroy the c-o, and c-h bonds of curcumin, resulting in cell death and apoptosis induction in breast cancer cells. It was caused by neutron radiation.
C_LIO_LIaccording to the results of the comet assay and caspase-3 experiments, although neutrons induced apoptosis in breast cancer cells, the death rate due to necrosis was much higher than apoptosis.
C_LI

category: biophysics


title: How to use transcriptomic data for game-theoretic modeling of treatment-induced resistance in cancer cells?A case study in patient-derived glioblastoma organoids

abstract: Game theory is a powerful theory to model strategic decision-making, but also complex biological systems, such as cancer. In the past decades, game-theoretical models have helped to understand cancer, its response to various treatments, and to design better therapies. However, to fully utilize the potential of game-theoretical modelling in designing better anti-cancer therapies, we need more information on cancer population (ecological) and strategy (evolutionary) dynamics in response to treatment. Here we explore how transcriptomics data can be utilized as inputs of game-theoretic models for predicting evolutionary response to irradiation using patient-derived glioblastoma organoids. For that purpose, we utilize both supervised and unsupervised methods to disentangle cell mixtures from publicly available datasets and identify proportions of relevant cancer cell types in patient-derived glioblastoma organoids treated with radiotherapy. We then fit these proportions to the replicator dynamics, the most classic evolutionary game dynamics, to predict both transient evolutionary dynamics and evolutionary stable cell proportions in these organoids. Hereby we demonstrate a methodology that can be utilized to design evolutionary therapies, i.e. therapies that anticipate and prevent evolution of therapy resistance in cancer cells. Our predictions in glioblastoma suggest that hypoxia is the most important factor in identifying short-term response to irradiation, while this seems much less relevant for the long-term response. Further, we conclude that supervised methods are the best way to estimate cancer evolutionary dynamics when therapy resistance is a qualitative evolutionary trait. We provide a pipeline for designing better therapies through testing evolutionary responses in patient-derived organoids, while in parallel the ecological response can be tracked through serum biomarkers and imaging in the corresponding patients.

category: cancer biology


title: Single-Cell Analysis Identifies Distinct Immune and Smooth Muscle Cell Populations that Contribute to Chronic Thromboembolic Pulmonary Hypertension

abstract: Chronic thromboembolic pulmonary hypertension (CTEPH) is a sequelae of acute pulmonary embolism (PE) in which the PE remodels into a chronic scar in the pulmonary arteries. This results in vascular obstruction, small vessel arteriopathy and pulmonary hypertension. Our current understanding of CTEPH pathobiology is primarily derived from cell-based studies limited by the use of specific cell markers or phenotypic modulation in cell culture. Here we used single cell RNA sequencing (scRNAseq) of tissue removed at the time of pulmonary thromboendarterectomy (PTE) surgery to identify the multiple cell types, including macrophages, T cells, and smooth muscle cells, that comprise CTEPH thrombus. Notably, multiple macrophage subclusters were identified but broadly split into two categories, with the larger group characterized by an upregulation of inflammatory signaling predicted to promote pulmonary vascular remodeling. Both CD4+ and CD8+ T cells were identified and likely contribute to chronic inflammation in CTEPH. Smooth muscle cells were a heterogeneous population, with a cluster of myofibroblasts that express markers of fibrosis and are predicted to arise from other smooth muscle cell clusters based on pseudotime analysis. Additionally, cultured endothelial, smooth muscle and myofibroblast cells isolated from CTEPH thrombus have distinct phenotypes from control cells with regards to angiogenic potential and rates of proliferation and apoptosis. Lastly, our analysis identified protease-activated receptor 1 (PAR1) as a potential therapeutic target that links thrombosis to chronic PE in CTEPH, with PAR1 inhibition decreasing smooth muscle cell and myofibroblast proliferation and migration. These findings suggest a model for CTEPH similar to atherosclerosis, with chronic inflammation promoted by macrophages and T cells driving vascular remodeling through smooth muscle cell modulation, and suggest new approaches for pharmacologically targeting this disease.

category: pathology


title: Lowering levels of reelin in entorhinal cortex layer II-neurons results in lowered levels of intracellular amyloid-β.

abstract:
Projection neurons in the anterolateral part of entorhinal cortex layer II (alEC LII) are the predominant cortical site for hyperphosphorylation of tau (p-tau) and formation of neurofibrillary tangles (NFTs) in brains of subjects with early-stage Alzheimers Disease (AD). A majority of alEC LII-neurons are unique among cortical excitatory neurons by expressing the protein reelin (Re+). In AD patients, and a rat model for AD overexpression mutated human APP, these Re+ excitatory projection-neurons are prone to accumulate intracellular amyloid-{beta} (iA{beta}). Biochemical pathways that involve reelin-signaling regulate levels of p-tau, and iA{beta} has been shown to impair such reelin-signaling. We therefore used the rat model and set out to assess whether accumulation of iA{beta} in Re+ alEC LII projection neurons relates to the fact that these neurons express reelin. Here we show that in Re+ alEC LII-neurons, reelin and iA{beta}42 engage in a direct protein-protein interaction, and that microRNA-mediated lowering of reelin-levels in these neurons leads to a concomitant reduction of non-fibrillar iA{beta} ranging across three levels of aggregation. Our experiments are carried out several months before plaque pathology emerges in the rat model, and the reduction of iA{beta} occurs without any substantial associated changes in human APP-levels. We propose a model positioning reelin in a sequence of changes in functional pathways in Re+ alEC LII-neurons, explaining the region and neuron-specific initiation of AD pathology.

SignificanceAnterolateral entorhinal cortex layer II (EC LII) neurons are the predominant cortical site for hyperphosphorylation of tau (p-tau) and formation of neurofibrillary tangles (NFTs) in brains of subjects with early-stage Alzheimers disease (AD). The same neurons are prone to very early accumulation of non-fibrillary forms of amyloid-{beta} in the context of AD, and are unique among cortical excitatory neurons by expressing the protein reelin. We show that in such alEC LII-neurons, reelin and iA{beta}42 engage in a direct protein-protein interaction, and that selectively lowering levels of reelin leads to a concomitant reduction of non-fibrillar A{beta}. We propose a model positioning reelin in a sequence of changes in functional pathways in reelin-expressing EC LII neurons, explaining the region and neuron specific initiation of AD.


title: Deletion of Sod1 in motor neurons exacerbates age-related changes in axons and NMJs associated with premature muscle atrophy in aging mice

abstract:
Whole body knock out of Cu, Zn superoxide dismutase1 (Sod1KO) results in accelerated, age-related loss of muscle mass and function associated with a breakdown of neuromuscular junctions (NMJ) similar to sarcopenia. In order to determine whether altered redox in motor neurons is integral to this phenotype, an inducible neuron specific deletion of Sod1 (i-mnSod1KO) was compared with wild type (WT) mice of different ages (adult, mid-age and old) and whole body Sod1KO mice. Nerve oxidative damage, motor neuron numbers and structural changes to neurons and NMJ were examined.

Deletion of neuronal Sod1 (induced by tamoxifen injection at 6 months of age) caused the exaggerated, age-associated loss of muscle mass and force generation previously reported. No effect of age or lack of neuronal Sod1 was seen on oxidation in the sciatic nerve assessed by electron paramagnetic resonance of the in vivo spin probe 1-hydroxy-3-carboxy-2,2,5,5 tetramethylpyrrolidine (CPH), analysis of protein 3-nitrotyrosines or carbonyl content. i-mnSod1KO mice showed increased numbers of denervated NMJs, a reduced number of large axons and increased number of small axons compared with age-matched old WT mice. A large proportion of the remaining innervated NMJs in i-mnSod1KO mice also displayed a much simpler structure than that seen in WT mice.

Thus, while Sod1KO mice recapitulate substantially the neuromuscular phenotypes of old WT mice, deletion of Sod1 specifically in neurons induces exaggerated loss of muscle mass and force only in old (24-29 month) mice indicating that significant muscle declines require the accumulation of age-related changes such that a threshold is reached past which maintenance of structure and function is not possible.

Significance statementSarcopenia is the age-related loss of muscle mass and function. It is a significant contributor to frailty and to increased falls in the elderly. While multifactorial, changes in redox status have been shown to have significant influence over neuromuscular aging, recent work suggests that changes in motor neurons may be the driving factor in muscle atrophy. The current study confirmed that a specific lack of Sod1 in the motor neuron causes significant alteration in axonal architecture and the neuromuscular junctions which can drive reduced muscle mass and function. Pinpointing early changes in motor neurons may provide therapeutic targets critical for maintaining muscle in the elderly.

category: physiology


title: Heterotrimeric G protein α subunit (GPA1) regulates the response to low-nitrogen stress in Arabidopsis by interacting with AtNRT1.4 and AtATG8a

abstract:
Efficient nitrogen absorption and utilization are important factors for higher plants to increase yield and reduce eutrophication (caused by excessive use of nitrogen fertilizers). Heterotrimeric G proteins, including three subunits of , {beta}, and {gamma}, participate in the pathway regulating nitrogen absorption and utilization in plants. However, the regulatory mechanism remains largely obscured. In this study, our results revealed that the G protein  subunit (AtGPA1) mutant gpa1-4 was tolerant to low-nitrogen stress in Arabidopsis. AtGPA1 was shown to directly interact with a nitrate transporter (AtNRT1.4) and a key autophagy-related protein (AtATG8a) on the plasma membrane using the yeast hybrid system and pull-down assay (in vitro) and BiFC assay (in vivo). GUS staining and subcellular localization showed that AtGPA1 and AtNRT1.4 were co-expressed in roots and leaf veins and on the plasma membrane. Under low-nitrate conditions, the single mutant gpa1-4 and NRT1.4RNAi plants (AtNRT1.4RNA interference plants) and the double mutant NRT1.4RNAi/gpa1-4 plants (AtNRT1.4RNA interference plants on a gpa1-4 background) were healthier than the wild type plants. Moreover, the phenotype of the double mutant NRT1.4RNAi/gpa1-4 plants was closer to that of the NRT1.4RNAi plants compared to that of the gpa1-4 mutants. The results of the nitrate efflux rate assay in roots were consistent with the phenotypic changes under low-nitrogen conditions. These results indicated that AtGPA1 is an upstream factor that regulated the response to low-nitrogen stress through interaction with AtNRT1.4. In addition, we found that transgenic plants overexpressing AtATG8a were more tolerant to low-nitrogen stress, and their phenotype was similar to that of gpa1-4 mutants and double mutant ATG8aOX/gpa1-4 plants (AtATG8a overexpressing plants on a gpa1-4 mutant background). Further, autophagosome observations were consistent with the phenotypes in mutant plants, indicating that AtGPA1 regulated the response to low-nitrogen stress in Arabidopsis plants by affecting the autophagosome assembly. Our findings may provide a new model for improving nitrogen-use efficiency through genetical modification to boost crop yields.

One sentence summaryAtGPA1 negative regulates low nitrogen stress response by interaction with a nitrate transporter, AtNRT1.4 and an autophagy-related protein, AtATG8a in Arabidopsis.


title: 3D Visualisation of trans-syncytial nanopores provides a pathway for paracellular diffusion across the human placental syncytiotrophoblast

abstract: The placental syncytiotrophoblast, a syncytium without cell-cell junctions, is the primary barrier between the mother and the fetus. Despite no apparent anatomical pathway for paracellular diffusion of solutes across the syncytiotrophoblast size-dependent paracellular diffusion is observed. Here we report data demonstrating that the syncytiotrophoblast is punctuated by trans-syncytial nanopores (TSNs). These membrane-bound TSNs directly connect the maternal and fetal facing sides of the syncytiotrophoblast, providing a pathway for paracellular diffusion between the mother and fetus. Mathematical modelling of TSN permeability based on their 3D geometry suggests that 10-60 million TSNs per cm3 of placental tissue could explain experimentally observed placental paracellular diffusion. TSNs may mediate physiological hydrostatic and osmotic pressure homeostasis between the maternal and fetal circulations but also expose the fetus to pharmaceuticals, environmental pollutants and nanoparticles.


title: Temperature modulates PVN pre-sympathetic neurones via transient receptor potential ion channels.

abstract:
Background and purposeThe paraventricular nucleus (PVN) of the hypothalamus plays a vital role in maintaining homeostasis and controls cardiovascular function via autonomic pre-sympathetic neurones. We have previously shown that coupling between transient receptor potential cation channel subfamily V member 4 (Trpv4) and small-conductance calcium-activated potassium channels (SK) in the PVN facilitate osmosensing. TRP channels are also thermosensitive and therefore, in this report we investigated the temperature sensitivity of PVN neurones.

Experimental approachWe identified TRP channel mRNA in mouse PVN using quantitative reverse transcription-PCR (RT-PCR). Using cell-attached patch-clamp electrophysiology, we characterised the thermosensitivity of Trpv4-like ion channels on mouse PVN neurones. Following recovery of temperature sensitive single channel kinetic schema, we constructed a novel and predictive stochastic mathematical model of these neurones. We then validated this model with electrophysiological recordings of action current frequency from mouse PVN neurones.

ResultsWe identified 7 TRP channel genes in the PVN with known thermosensitive capabilities. Trpv4 was the most abundant of these and was easily identified at the single channel level using cell-attached patch-clamp electrophysiology on PVN neurones. We investigated the thermosensitivity of these Trpv4-like channels; open probability (Po) markedly decreased when temperature was decreased, mediated by a decrease in mean open dwell times. Our neuronal model predicted that PVN spontaneous action current frequency (ACf) would increase as temperature is decreased and in our electrophysiological experiments, we found that ACf from PVN neurones was significantly higher at lower temperatures. The broad-spectrum channel blocker, gadolinium (100 M), was used to block the warm-activated Ca2+-permeable Trpv4 and Trpv3 channels. In the presence of gadolinium (100 M), the temperature effect was largely retained. Using econazole (10 M), a blocker of Trpm2, we found there were significant increases in overall ACf and the temperature effect was inhibited.

ConclusionOur work identified Trpv4 mRNA as an abundantly expressed thermosensitive TRP channel gene in the PVN and this ion channel contributes to the intrinsic thermosensitive properties of PVN neurones. At physiological temperatures (37{degrees}C), we observed relatively low ACf primarily due to the activity of Trpm2 channels, whereas at room temperature, where most of the previous characterisation of PVN neuronal activity has been performed, ACf is much higher, and appears to be predominately due to reduced Trpv4 activity. This work gives insight into the fundamental mechanisms by which the body decodes temperature signals and maintains homeostasis.


title: Arabidopsis CONSERVED BINDING OF EIF4E1 negatively regulates the NADPH oxidase RESPIRATORY BURST OXIDASE HOMOLOG D

abstract: Cell-surface pattern recognition receptors sense invading pathogens by binding microbial or endogenous elicitors to activate plant immunity. These responses are under tight control to avoid excessive or untimely activation of cellular responses, which may otherwise be detrimental to host cells. How this fine-tuning is accomplished is an area of active study. We previously described a suppressor screen that identified Arabidopsis thaliana mutants with regained immune signaling in the immunodeficient genetic background bak1-5, which we named modifier of bak1-5 (mob) mutants. Here, we report that bak1-5 mob7 restores elicitor-induced signaling. Using a combination of map-based cloning and whole-genome resequencing, we identified MOB7 as CONSERVED BINDING OF EIF4E1 (CBE1), a plant-specific protein that interacts with highly-conserved eukaryotic translation initiation factor eIF4E1. Our data demonstrate that CBE1 regulate the accumulation of RESPIRATORY BURST OXIDASE HOMOLOG D (RBOHD), the NADPH oxidase responsible for elicitor-induced apoplast reactive oxygen species (ROS) production. Furthermore, several mRNA decapping and translation initiation factors co-localize with CBE1 and similarly regulate immune signaling. This study thus identifies a novel regulator of immune signaling and provides new insights into ROS regulation, and more generally translational control during plant stress responses.

category: plant biology


title: The phloem-resident protein OCTOPUS is a novel regulator of flg22-induced responses in Arabidopsis thaliana

abstract: Phloem is a critical tissue that transports photosynthates and extracellular signals in vascular plants. Although a functional phloem is necessary for plant health, it is also an ideal environment for pathogens to access host nutrients to promote pathogenesis. Even though many vascular pathogens induce economically relevant crop damage, very little is known about the mechanism(s) by which phloem cells detect potential pathogens and signal to minimize damage. Our lab searched existing phosphoproteomic databases, mining for proteins that were phosphorylated in response to the defense-elicitor flagellin, or flg22, AND were expressed in vascular cells, and we identified Octopus (OPS). OPS is polarly associated with the plasma membrane (PM) of sieve element cells and promotes their differentiation from procambial precursor cells by inhibiting the function of BIN2 in brassinosteroid-related signaling. The observation that OPS is differentially phosphorylated in response to flg22 led us to the examine whether OPS may function in flg22-induced signaling using Arabidopsis T-DNA insertion mutants lacking a functional OPS. In wild-type (WT) seedlings, flg22 binds to the PM receptor flagellin sensing 2 (FLS2) to initiate three branches of a signaling cascade that culminates in increased expression of distinct marker genes. Ultimately these signaling pathways lead to the restriction of pathogen growth. Two independent alleles of ops were treated with 100 M flg22 and marker genes from all three branches of FLS2 signaling exhibited higher expression than WT. We also found that in the absence of any flg22, ops mutants displayed increased flg22 signaling responses. Our results indicate that OPS may function as a negative regulator of flg22-induced signaling events and is one of very few phloem-resident proteins with a documented role in flg22 signaling. These results indicate that the phloem may be able to sense and response to the threat of bacterial pathogens in a unique way.


title: Genetic basis and adaptive implications of temperature-dependent and temperature-independent effects of drought on chickpea phenology

abstract:
Water deficit often hastens flowering of pulses partially because droughted plants are hotter. Separating temperature-independent and temperature-dependent effects of drought is important to understand, model and manipulate phenology genetically and agronomically.

We define a new trait, drought effect on phenology (DEP = difference in flowering time between irrigated and rainfed crops), and use FST genome scan to probe for genomic regions under selection for this trait. Genomic regions overlapping for early- and late-sown crops would associate with temperature-independent effects and non-overlapping genomic regions would associate with temperature-dependent effects.

Time to flowering shortened with increasing water stress quantified with carbon isotope composition. Genomic regions on chromosomes 4, 5, 7 and 8 were under selection for DEP. An overlapping region for early and late sowing on chromosome 8 revealed a temperature-independent effect with four candidate genes: BAM1, BAM2, HSL2 and ANT. The non-overlapping regions included six candidate genes: EMF1, EMF2, BRC1/TCP18, BZR1, NPGR1 and ERF1.

Modelling to assess DEP adaptive value showed it reduces the likelihood of drought and heat stress at the expense of cold risk. Accounting for DEP would improve phenology models to predict adaptation to future climates and breeding against the combined risks of drought, heat, and cold stress.

HighlightPredictive and genetic models that overlook drought effects on phenology can return biased predictions of adaptation to future climates. Here we study the genetic causes and adaptive consequences of hastened flowering under drought.


title: Knockout of OsSWEET15 impaired rice embryo formation and seed-setting

abstract: we show that the knockout of a sugar transporter gene OsSWEET15 led to a significant drop in rice fertility because near half of the knockout mutant spikelets bore blighted or empty grains. The rest spikelets bore fertile grains with slightly reduced weight. Notably, the ovaries in the blighted grains of the ossweet15 mutants expanded after flowering but terminated development before the endosperm cellularization stage and aborted subsequently. GUS and GFP representing OsSWEET15 expression showed that the protein was strongly expressed in the embryo surrounding region (ESR) which was supposed to supply nutrients for the embryo development. These results joined with the proteins sucrose transport capacity and plasma membrane localization suggest that OsSWEET15 plays a prominent role during the caryopsis formation stage probably by releasing sucrose from the ESR to support the embryo development. By contrast, the empty grains were probably caused by the reduced pollen viability of the ossweet15 mutants. Investigation of the makeup of ossweet11 mutant grains revealed similar phenotypes that were observed in the ossweet15 mutants. These results indicate that both OsSWETT15 and OsSWEET11 play important and similar roles during rice pollen development, caryopsis formation, and seed-setting in addition to their function in seed-filling that was demonstrated previously.


title: A wheat kinase and immune receptor form the host-specificity barrier against the blast fungus

abstract: Since emerging in Brazil in 1985, wheat blast has spread throughout South America and recently appeared in Bangladesh and Zambia. We show that two wheat resistance genes, Rwt3 and Rwt4, acting as host-specificity barriers against non-Triticum blast pathotypes encode a nucleotide-binding leucine-rich repeat immune receptor and a tandem kinase, respectively. Molecular isolation of these genes allowed us to develop assays that will ensure the inclusion of these two genes in the wheat cultivars to forestall the recurrence of blast host jumps.


title: Compartment-specific energy requirements of photosynthetic carbon metabolism in Camelina sativa leaves

abstract:
Detailed knowledge about plant energy metabolism may aid crop improvements. Using published estimates of flux through central carbon metabolism, we phenotype energy metabolism in illuminated Camelina sativa leaves (grown at 22 {degrees}C, 500 mol photons m-2 s-1) and report several findings. First, the oxidative pentose phosphate pathway (OPPP) transfers 3.3% of the NADPH consumed in the Calvin-Benson cycle to the cytosol. NADPH supply proceeds at about 10% of the rate of net carbon assimilation. However, concomitantly respired CO2 accounts for 4.8% of total rubisco activity. Hence, 4.8% of the flux through the Calvin-Benson cycle and photorespiration is spent on supplying cytosolic NADPH, a significant investment. Associated energy requirements exceed the energy output of the OPPP. Thus, autotrophic carbon metabolism is not simply optimised for flux into carbon sinks but sacrifices carbon and energy use efficiency to support cytosolic energy metabolism. To reduce these costs, we suggest bioengineering plants with a repressed cytosolic OPPP, and an inserted cytosolic NADPH-dependent malate dehydrogenase tuned to compensate for the loss in OPPP activity (if required). Second, sucrose cycling is a minor investment in overall leaf energy metabolism but a significant investment in cytosolic energy metabolism. Third, leaf energy balancing strictly requires oxidative phosphorylation, cofactor export from chloroplasts, and peroxisomal NADH import. Fourth, mitochondria are energetically self-sufficient. Fifth, carbon metabolism has an ATP/NADPH demand ratio of 1.52 which is met if [≤]21.7% of whole electron flux is cyclic. Sixth, electron transport has a photon use efficiency of [≥]62%. Lastly, we discuss interactions between the OPPP and the cytosolic oxidation-reduction cycle in supplying leaf cytosolic NADPH.

Main ConclusionThe oxidative pentose phosphate pathway provides cytosolic NADPH yet reduces carbon and energy use efficiency. Repressing this pathway and introducing cytosolic NADPH-dependent malate dehydrogenase may increase crop yields by {approx}5%.


title: Temporal Optimization of Radiation Therapy to Heterogeneous Tumour Populations and Cancer Stem Cells

abstract:
External beam radiation therapy is a key part of modern cancer treatments which uses high doses of radiation to destroy tumour cells. Despite its widespread usage and extensive study in theoretical, experimental, and clinical works, many questions still remain about how best to administer it. Many mathematical studies have examined optimal scheduling of radiotherapy, and most come to similar conclusions. Importantly though, these studies generally assume intratumoral homogeneity. But in recent years, it has become clear that tumours are not homogeneous masses of cancerous cells, but wildly heterogeneous masses with various subpopulations which grow and respond to treatment differently. One subpopulation of particular importance is cancer stem cells (CSCs) which are known to exhibit higher radioresistence compared with non-CSCs. Knowledge of these differences between cell types could theoretically lead to changes in optimal treatment scheduling. Only a few studies have examined this question, and interestingly, they arrive at apparent conflicting results. However, an understanding of their assumptions reveals a key difference which leads to their differing conclusions.

In this paper, we generalize the problem of temporal optimization of dose distribution of radiation therapy to a two cell type model. We do so by creating a mathematical model and a numerical optimization algorithm to find the distribution of dose which leads to optimal cell kill. We then create a data set of optimization solutions and use data analysis tools to learn the relationships between model parameters and the qualitative behaviour of optimization results. Analysis of the model and discussion of biological importance are provided throughout. We find that the key factor in predicting the behaviour of the optimal distribution of radiation is the ratio between the radiosensitivities of the present cell types. These results can provide guidance for treatment in cases where clinicians have knowledge of tumour heterogeneity and of the abundance of CSCs.

category: systems biology


title: A Statistical Physics Approach for Disease Module Detection

abstract: Extensive evidence indicates that the pathobiological processes of a complex disease are associated with perturbation within specific disease neighborhoods of the human protein-protein interaction (PPI) network (a.k.a. the interactome), often referred to as the disease module. Many computational methods have been developed to integrate the interactome and omics profiles to extract context-dependent disease modules. Yet, existing methods all have fundamental limitations in terms of rigor and/or efficiency. Here, we developed a statistical physics approach based on the random-field Ising model (RFIM) for disease module detection, which is both mathematically rigorous and computationally efficient. We applied our RFIM approach with genome-wide association studies (GWAS) of six complex diseases to examine its performance for disease module detection. We found that our RFIM approach outperforms existing methods in terms of computational efficiency, connectivity of disease modules, and robustness to the interactome incompleteness.


title: Building model prototypes from time-course data

abstract: A primary challenge in building predictive models from temporal data is selecting the appropriate network and the regulatory functions that describe the data. Software packages are available for equation learning of continuous models, but not for discrete models. In this paper we introduce a method for building model prototypes that consist of a network and a set of discrete functions that can explain the time course data. The method takes as input a collection of time course data or discretized measurements over time. After model inference, we use our toolbox to simulate the prototype model as a stochastic Boolean network. Our method provides a model that can qualitatively reproduce the patterns of the original data and can further be used for model analysis, making predictions, and designing interventions. We applied our method to a time-course, gene expression data that were collected during salamander tail regeneration. The inferred model captures important regulations that were previously validated in the research literature. The toolbox for inference and simulations is freely available at github.com/alanavc/prototype-model.


title: Allatotropin in the Corpora Allata and Ovaries of Rhodnius prolixus: Probable in situ regulatory mechanisms

abstract: Originally described by Sir V. Wigglesworth in the Chagas disease vector Rhodnius prolixus, Juvenile Hormones (JHs) play critical roles during growth and reproduction. The JH described by Wigglesworth is the JH III skipped bisepoxide (JHSB3), and its titer in hemolymph varies along the 4th larval instar molting cycle. Allatotropin (AT), was originally characterized based on its ability to induce the synthesis of the JHs by the corpora allata (CA) in Lepidoptera. Beyond this function, AT has proved to be a myoregulator. Indeed, AT modulates muscle contractions in the gut, dorsal vessel and reproductive tissues. The presence of AT in the CA of 4th instar larvae of R. prolixus and the related species Triatoma infestans was previously shown, suggesting that AT might be involved in the regulation of JH synthesis in triatominae. Furthermore, the existence of allatotropic cells in this gland in T. infestans was also shown. This neuron-like cells show cytoplasmic processes projecting deeply between the cells engaged with JH synthesis. By using RT-qPCR we studied now the expression of both, AT and its receptor in the CA/CC complex along the 4th instar molting cycle, and in the ovaries of adult females. The expression of AT in the CA is highest between days 3 to 5 after meal, correlating with Mev-K and PPMev-D, two enzymes involved in the mevalonate pathway, as well as with the peak of JHSB3 on day 6. The results show that AT transcript is also present in the ovary suggesting a myoregulatory paracrine mechanism of regulation. Finally, our data suggest the existence of in situ mechanisms in the CA and ovaries of R. prolixus involving AT in both JHs synthesis and muscle contraction.

category: zoology


title: The role of preterm birth and postnatal stress in neonatal structural brain development

abstract:
Preterm birth disrupts the emerging foundations of the brains architecture, and the continuum of early-life stress-provoked alterations reaches from a healthy adaptation with resilience to severe vulnerability and maladjustment with psychopathology. The current study examined how structural brain development is affected by a stressful extra-uterine environment and whether changes in topological architecture at term-equivalent age could explain the increased vulnerability for behavioral symptoms during early childhood. Longitudinal changes in structural brain connectivity were quantified using diffusion-weighted imaging (DWI) and tractography in preterm born infants (gestational age <28 weeks), imaged at 30 and/or 40 weeks of gestation (N=145, 43.5% female). A global index of postnatal stress was based on invasive procedures during hospitalization (e.g., heel lance). Infants were classified as vulnerable and resilient based on having more or less internalizing symptoms at 2-5 years of age (n=71). Findings were replicated in an independent validation sample (N=123, 39.8% female, n=91 with follow-up). Higher stress levels impaired structural connectivity growth in the amygdala, insula, hippocampus, and posterior cingulate cortex. The hippocampus, amygdala, and subthalamic nucleus showed lower global connectivity in vulnerable relative to resilient individuals. The distinct characteristics of the resilient brain allowed for a good predictive accuracy of group membership using local network measures (80%, p<10-5, {kappa}=0.61). These findings emphasize the detrimental impact of postnatal stress and, more importantly, the relative plasticity of the preterm brain. Resilience following postnatal stress appertains to a potential compensatory or innate ability to propagate global information flow.

Significance StatementThe underdeveloped preterm brain is exposed to various external stimuli following birth. Although the importance of early adversity has been widely recognized, the essential understanding of the effects of early chronic stress on neonatal brain networks as well as the remarkable degree of resilience is not well understood. We aim to provide an increased understanding of the impact of postnatal stress on brain development between 30 and 40 weeks of gestation and describe the topological architecture of a resilient brain. We observed global alteration in neonatal brain networks following postnatal stress and identified key contributive regions conferring resilience to the development of future internalizing symptoms.

category: neuroscience


title: Inter-animal variability in activity phase is constrained by synaptic dynamics in an oscillatory network

abstract: The levels of voltage-gated and synaptic currents in the same neuron type can vary substantially across individuals. Yet, the phase relationships between neurons in oscillatory circuits are often maintained, even in the face of varying oscillation frequencies. We examined whether synaptic and intrinsic currents are matched to maintain constant activity phases across preparations, using the lateral pyloric (LP) neuron of the stomatogastric ganglion of the crab, Cancer borealis. LP produces stable oscillatory bursts upon release from inhibition, with an onset phase that is independent of oscillation frequency. We quantified the parameters that define the shape of the synaptic current inputs across preparations and found no linear correlations with voltage-gated currents. However, several synaptic parameters were correlated with oscillation period and burst onset phase, suggesting they may play a role in phase maintenance. We used the dynamic clamp to apply artificial synaptic inputs and found that those synaptic parameters correlated with phase and period were ineffective in influencing burst onset. Instead, parameters that showed the least variability across preparations had the greatest influence. Thus, parameters that influence circuit phasing are constrained across individuals, while those that have little effect simply co-vary with phase and frequency.


title: Multisensory information about changing object properties can be used to quickly correct predictive force scaling for object lifting

abstract: Sensory information about object properties, such as size or material, can be used to make an estimate of object weight and to generate an accurate motor plan to lift the object. When object properties change, the motor plan needs to be corrected based on the new information. The current study investigated whether such corrections could be made quickly, after the movement was initiated. Participants had to grasp and lift objects of different weights that could be indicated with different cues. During the reaching phase, the cue could change to indicate a different weight and participants had to quickly adjust their planned forces in order to lift the object skilfully. The object weight was cued with different object sizes (Experiment 1) or materials (Experiment 2) and the cue was presented in different sensory modality conditions: visually, haptically or both (visuohaptic). Results showed that participants could adjust their planned forces based on both size and material and in all sensory modality conditions. Furthermore, the findings indicate that visual and haptic information were integrated in the visuohaptic condition, although the multisensory condition did not outperform the conditions with one sensory modality. These results suggest that motor plans can be quickly corrected based on sensory information about object properties from different sensory modalities. These findings provide insights into the information that can be shared between brain areas for the online control of hand-object interactions.


title: Changes in cellular ferritin distribution of human brain tissue during autolysis revealed using analytical electron microscopy

abstract: Iron in the human brain is stored in the cores of ferritin proteins. Excess iron has been implicated in neurological disorders, so a careful balance of the iron concentration is thought to be essential for human health. Though it is known that oligodendrocytes contain most of the brain ferritin, followed by other glial cells and neurons, little is known about changes in the cellular ferritin distribution when total iron load changes. Moreover, changes in the number of filled ferritins or in their cellular distribution during autolysis have not been revealed yet. To reveal these changes, we examined brain samples taken from six deceased humans at different post mortem times. To compare samples with different ferritin content, the samples included the frontal gray and frontal white matter, which store a low amount of iron, and the putamen and globus pallidus, which store a high amount of iron. We quantified the number of loaded ferritin cores from iron L - elemental maps obtained with energy filtered transmission electron microscopy and compared this number to the iron concentrations determined using inductively coupled plasma mass spectrometry and quantitative magnetic resonance imaging. The more loaded ferritin cores we found in the tissues, the higher the proportion of ferritins found in neurons instead of glial cells, indicating that total ferritin load scales with the proportion of ferritin that is located in neurons. Second, we found a statistically significant correlation between the post mortem interval and the amount/ concentration of loaded ferritins and found that this concentration is highly dependent on the post mortem interval (PMI): the longer the PMI, the lower the ferritin concentration found in a sample. Third, the longer the post mortem interval, the higher the proportion of ferritins found in neurons instead of glial cells, indicating that ferritin loss during autolysis affects neurons and glial cells at different rates.


title: RNase L-mediated RNA decay alters 3' end formation and splicing of host mRNAs

abstract: The antiviral endoribonuclease, RNase L, is a vital component of the mammalian innate immune response that destroys host and viral RNA to reduce viral gene expression. Herein, we show that a consequence of RNase L-mediated decay of cytoplasmic host RNAs is the widespread re-localization of RNA-binding proteins (RBPs) from the cytoplasm to the nucleus, due to the presence of nuclear RNA. Concurrently, we observe global alterations to host RNA processing in the nucleus, including alterations of splicing and 3 end formation, with the latter leading to downstream of gene (DoG) transcripts. While affecting many host mRNAs, these alterations are pronounced in mRNAs encoding type I and type III interferons and coincide with the retention of their mRNAs in the nucleus. Similar RNA processing defects also occur during infection with either dengue virus or SARS-CoV-2 when RNase L is activated. These findings reveal that the distribution of RBPs between the nucleus and cytosol is fundamentally dictated by the availability of RNA in each compartment and thus viral infections that trigger cytoplasmic RNA degradation alter RNA processing due to the nuclear influx of RNA binding proteins.

category: immunology


title: Preclinical stage abundance and nuclear antigen reactivity of fecal Immunoglobulin A (IgA) varies among males and females of lupus-prone mouse models

abstract: Systemic lupus erythematosus (SLE) is characterized by the production of pathogenic autoantibodies with nuclear antigen (nAg) specificity. Using (SWRxNZB)F1 (SNF1) mice, we showed higher levels of IgA production in the intestine and the nAg reactivity of fecal IgA under lupus susceptibility. Here, we determined if the fecal IgA abundance and nAg reactivity are higher in, different among, various lupus-prone preclinical models (MRL/lpr, NZBxNZW-F1, SNF1, NZM2410 and NZM2328). We also determined if the fecal IgA nAg reactivity at pre-seropositive ages correlates with the eventual serum autoantibody levels in males and females of these mouse models. We show that age dependent increase in the abundance and nAg reactivity of fecal IgA can vary among different lupus-prone mouse models. Importantly, fecal IgA in these mice show significant levels of nAg reactivity, starting as early as at juvenile age. Furthermore, the pre-seropositive stage nAg reactivity of fecal IgA in most lupus-prone strains correlates well with that of eventual, seropositive stage systemic autoantibody levels. Gender differences in serum autoantibody levels were preceded by similar differences in the fecal IgA abundance and nAg reactivity. These observations suggest that fecal IgA features, nAg reactivity particularly, could serve as a biomarker for early prediction of the eventual systemic autoimmunity in lupus-prone subjects.


title: Spatial and molecular anatomy of germ layers in the gastrulating primate embryo

abstract:
During mammalian embryogenesis, spatial regulation of gene expression and cell signaling are functionally coupled with lineage specification, patterning of tissue progenitors and germ layer morphogenesis. While the mouse model has been instrumental for our understanding of mammalian development, comparatively little is known about human and non-human primate gastrulation due to the restriction of both technical and ethical issues. Here, we present a morphological and molecular survey of spatiotemporal dynamics of cell types populating the non-human primate embryos during gastrulation. We performed serial sections of Cynomolgus monkeys (Macaca fascicularis) gastrulating embryos at 1-day temporal resolution from E17 to E21, and reconstructed three-dimensional digital models based on high-resolution anatomical atlas that revealed the dynamic changes in the geography of the mesoderm and primitive streaks. Spatial transcriptomics identified unique gene profiles that correspond to distinct germ layers and cross-species spatiotemporal transcriptome analysis revealed a developmental coordinate of germ layer segregation between mouse and primate. Furthermore, we identified species-specific transcription programs during gastrulation. These results offer important insights into evolutionarily conserved and divergent processes during mammalian gastrulation.

O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=196 SRC="FIGDIR/small/474719v2_ufig1.gif" ALT="Figure 1">
View larger version (41K):
org.highwire.dtl.DTLVardef@1058f45org.highwire.dtl.DTLVardef@105cborg.highwire.dtl.DTLVardef@12362d7org.highwire.dtl.DTLVardef@2e2346_HPS_FORMAT_FIGEXP  M_FIG C_FIG HighlightO_LIA high-resolution anatomical atlas of Cynomolgus gastrulation embryos
C_LIO_LICreated a three-dimensional digital template from serial sections of five developmental stages
C_LIO_LIA two-dimensional spatiotemporal transcriptome of the germ layers of gastrulating embryos
C_LIO_LICross-species comparison infers conservation of functional attributes of regulome and signaling activity in germ layer formation
C_LI


title: The limits of metabolic heredity in protocells

abstract: The universal core of metabolism could have emerged from thermodynamically favoured prebiotic pathways at the origin of life. Starting with H2 and CO2, the synthesis of amino acids and mixed fatty acids, which self-assemble into protocells, is favoured under warm anoxic conditions. Here we address whether it is possible for protocells to evolve greater metabolic complexity, through positive feedbacks involving nucleotide catalysis. Using mathematical simulations to model metabolic heredity in protocells, based on branch points in proto-metabolic flux, we show that nucleotide catalysis can indeed promote protocell growth. This outcome only occurs when nucleotides directly catalyse CO2 fixation. Strong nucleotide catalysis of other pathways (e.g. fatty acids, amino acids) generally unbalances metabolism and slows down protocell growth, and when there is competition between catalytic functions cell growth collapses. Autocatalysis of nucleotide synthesis can promote growth but only if nucleotides also catalyse CO2 fixation; autocatalysis alone leads to the accumulation of nucleotides at the expense of CO2 fixation and protocell growth rate. Our findings offer a new framework for the emergence of greater metabolic complexity, in which nucleotides catalyse broad-spectrum processes such as CO2 fixation, hydrogenation and phosphorylation important to the emergence of genetic heredity at the origin of life.


title: Did Caenorhabditis nematodes recycle transposons to fight pathogens?

abstract:
Animal genomes consist largely of sequences derived from transposons which were previously considered as junk DNA and active transposons can even be deleterious for organismal fitness. Nevertheless, the huge pool of transposon-derived sequences also forms the raw material for molecular innovations. Here, we follow up on the incidental finding of a transposon-derived DNA binding domain in a subset of F-box genes in Caenorhabditis elegans. Based on phylogenetic analysis, we show that a single gene fusion followed by individual losses explains most members of this novel gene family. Phylogenomic data of available Caenorhabditis genomes allowed us to trace this fusion event to the ancestor of the Elegans group. Additional homology searches suggest endogenous Mariner transposons as the likely source of the coopted sequence. Further bioinformatic characterization of different F-box families by Gene Ontology analysis, gene module comparisons, and literature research identified first evidence that some F-box genes might be involved in innate immunity, as it had been proposed previously based on adaptive signatures of molecular evolution. Specifically, the F-box gene fbxa-158 contains one of the transposon-derived domains and was shown to interact with the components of the intracellular pathogen response machinery targeting Microsporidia and viruses. Thus, cooption of transposon-derived sequences likely contributed to the adaptive evolution of the F-box superfamily in Caenorhabditis nematodes.

Significance statementWhen considering transposons as genomic junk or selfish elements that are detrimental for organismal fitness, we often neglect the potential of transposon-derived sequences as a source of molecular innovation. Here, we characterize a case where a transposon-derived sequence has been coopted by one of the largest and fastest evolving gene superfamilies in Caenorhabditis nematodes which include the model organism C. elegans. The resulting chimeric gene family has been stably maintained for about 20 million years and bioinformatic analysis reveals first evidence for potential functions in innate immunity. Thus, strong evolutionary pressure might have forced Caenorhabditis nematodes to recycle transposons in order to fight pathogens.


title: Genetic characterization of ABC pesticide transporters establishes Drosophila as an in vivo model for toxicogenetics

abstract: Pesticides remain one of the most effective ways of controlling agricultural and public health insects, but much is still unknown regarding how these compounds reach their targets. Specifically, the role of ABC transporters in pesticide absorption and excretion is poorly understood, especially compared to the detailed knowledge in mammalian systems. Here, we present a comprehensive characterization of pesticide transporters in the model insect D. melanogaster. An RNAi screen was performed, which knocked down individual ABCs in targeted epithelial tissue, examining the subsequent changes in sensitivity to the pesticides spinosad and fipronil. This simultaneously implicated a novel ABC drug transporter CG4562 but also highlighted a predominant role for the P-glycoprotein orthologue Mdr65. Further characterization of the P-glycoprotein family was performed via transgenic overexpression and immunolocalization, finding that Mdr49 and Mdr50 play enigmatic roles in pesticide toxicology perhaps determined by their different subcellular localizations within the midgut. Lastly, heterologous expression of the Mdr65 orthologue from the major malaria vector Anopheles gambiae was used to establish an in vivo characterization system for the characterization of P-glycoproteins from non-model insects in D. melanogaster. This study provides the basis for establishing Drosophila as a model for toxicology research regarding drug transporters.


title: Inducible degradation of dosage compensation protein DPY-27 facilitates isolation of Caenorhabditis elegans males for molecular and biochemical analyses

abstract: Biological sex affects numerous aspects of biology, yet how sex influences different biological processes has not been extensively studied at the molecular level. Caenorhabditis elegans, with both hermaphrodites (functionally females as adults) and males, is an excellent system to uncover how sex influences physiology. Here, we describe a method to isolate large quantities of C. elegans males by conditionally degrading DPY-27, a component of the dosage compensation complex essential for hermaphrodite, but not male, development. We show that germ cells from males isolated following DPY-27 degradation undergo meiosis and spermiogenesis like wild type and are competent to mate and produce viable offspring. We demonstrate the efficacy of this system by analyzing gene expression and performing affinity pull-downs from male worm extracts.


title: Structures of the Type IX Secretion/gliding motility motor from across the phylum Bacteroidetes

abstract:
Gliding motility using cell surface adhesins and export of proteins by the Type IX Secretion System (T9SS) are two phylum-specific features of the Bacteroidetes. Both of these processes are energized by the GldLM motor complex which transduces the protonmotive force at the inner membrane into mechanical work at the outer membrane. We previously used cryo-electron microscopy to solve the structure of the GldLM motor core from Flavobacterium johnsoniae at 3.9 [A] resolution (Nat Microbiol (2021) 6: 221-233). Here we present structures of homologous complexes from a range of pathogenic and environmental Bacteroidetes species at up to 3.0 [A] resolution. These structures show that the architecture of the GldLM motor core is conserved across the Bacteroidetes phylum although there are species-specific differences at the N-terminus of GldL. The resolution improvements reveal a cage-like structure that ties together the membrane-proximal cytoplasmic region of GldL and influences gliding function. These findings add detail to our structural understanding of bacterial ion-driven motors that drive the T9SS and gliding motility.

ImportanceMany bacteria in the Bacteroidetes phylum use the Type IX Secretion System to secrete proteins across their outer membrane. Most of these bacteria can also glide across surfaces using adhesin proteins that are propelled across the cell surface. Both secretion and gliding motility are driven by the GldLM protein complex which forms a nanoscale electrochemical motor. We used cryo-electron microscopy to study the structure of the GldLM protein complex from different species including the human pathogens Porphyromonas gingivalis and Capnocytophaga canimorsus. The organisation of the motor is conserved across species, but we find species-specific structural differences and resolve motor features at higher resolution. This work improves our understanding of the Type IX Secretion System, which is a virulence determinant in human and animal diseases.

category: biochemistry


title: Self-assembled DNA nanostructures promote cell migration & differentiation of human umbilical vein endothelial cells

abstract: DNA nanostructures have been explored for capabilities to influence cellular behavior and its functions. Recent times have seen the development of new emergent functionalities of DNA nanodevices as class of biomaterials with immense capacity to interface with biological systems and having vast potential in disease diagnosis and therapeutics. Being chemically robust and biocompatible in nature, DNA nanostructures have been surface modified and structurally fine-tuned to find emerging applications in the field of stem cell therapy and tissue regeneration. DNA nanostructures can be utilized for therapeutic angiogenesis that involves induction of blood vessel formation and can be used to treat ischemic diseases like stroke or heart failure. This work addresses the effect of DNA nanostructures structural topology in their capacity to stimulate endothelial cells angiogenesis. We tested a panel of four geometries of DNA nanostructure and checked their potential on the differentiation of human umbilical vein endothelial cells (HUVECs). While different DNA nanostructure geometries showed successful angiogenesis induction and cell migration in HUVECs, tetrahedral DNA cages showed the maximum uptake and angiogenesis potential indicating that not only the composition of materials, but also the 3D arrangement of ligands might also play role in stimulating the angiogenesis process.