title: A chemical biology toolbox to investigate in-cell target engagement and specificity of PRMT5-inhibitors

abstract:
Increasing evidence suggests the protein arginine methyltransferase PRMT5 as a contributor to tumorigenesis in various cancer types and several inhibitors have entered clinical trials. Robust assays to determine cellular target engagement and selectivity are an important asset for the optimisation of inhibitors and the design of relevant in vivo studies. Here we report a suite of chemical biology assays enabling quantitative assessment of PRMT5 inhibitor in-cell target engagement and global selectivity profiling using a representative set of inhibitors. With the help of a bespoke cellular probe, we assess inhibitor target occupancy in cells in relation to biochemical and functional cellular assays. Investigating the influence of SAM, the natural cofactor of PRMT5, our results support the hypothesis that SAM positively contributes to the engagement of substrate-competitive inhibitors via a PRMT5:SAM:inhibitor ternary complex. Extensive proteomic profiling studies by drug affinity chromatography and thermal profiling further indicate high specificity of the clinical PRMT5 inhibitor GSK3326595 (pemrametostat).

Graphical abstract

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category: systems biology


title: Microglia integration into human midbrain organoids leads to increased neuronal maturation and functionality.

abstract:
The human brain is a complex, three-dimensional structure. To better recapitulate brain complexity, recent efforts have focused on the development of human specific midbrain organoids. Human iPSC-derived midbrain organoids consist of differentiated and functional neurons, which contain active synapses, as well as astrocytes and oligodendrocytes. However, the absence of microglia, with their ability to remodel neuronal networks and phagocytose apoptotic cells and debris, represents a major disadvantage for the current midbrain organoid systems. Additionally, neuro-inflammation related disease modeling is not possible in the absence of microglia. So far, no studies about the effects of human iPSC-derived microglia on midbrain organoid neural cells have been published. Here we describe an approach to derive microglia from human iPSCs and integrate them into iPSC-derived midbrain organoids. Using single nuclear RNA Sequencing, we provide a detailed characterization of microglia in midbrain organoids as well as the influence of their presence on the other cells of the organoids. Furthermore, we describe the effects that microglia have on cell death and oxidative stress- related gene expression. Finally, we show that microglia in midbrain organoids affect synaptic remodeling and increase neuronal excitability. Altogether, we show a more suitable system to further investigate brain development, as well as neurodegenerative diseases and neuro- inflammation.

Main Points- Macrophage precursors can be efficiently co-cultured with midbrain organoids, they integrate into the tissue and differentiate into microglia in 3D.
- Organoids containing microglia have a smaller size and show a down-regulation of oxidative stress-related genes.
- Organoids co-cultured with microglia show differences in genes related to synaptic remodeling and action potential, as well as a more spontaneous action potential firing.

category: neuroscience


title: Mast cell-mediated inflammation relies on insulin-regulated aminopeptidase controlling cytokine export from the Golgi

abstract:
Mast cells are tissue-resident immune cells known best for their role in allergic reactions and inflammation. Upon activation, mast cells rapidly release histamine, lysosomal proteases and inflammatory mediators from large cytoplasmic granules via regulated exocytosis. This acute anaphylactic degranulation is followed by a late activation phase involving synthesis and secretion of cytokines, growth factors and other inflammatory mediators via the constitutive pathway that remains mechanistically ill-defined. Here we describe a role for an inflammation-induced endosomal compartment, marked by insulin-regulated aminopeptidase (IRAP), in constitutive exocytosis in mast cells and macrophages. We show that IRAP endosomes are required for efficient secretion of the pro-inflammatory cytokines TNF- and IL-6 in vitro and in vivo, but not for the regulatory cytokine IL-10. In line with this data, we find that IRAP-deficient mice are protected from TNF-dependent cisplatin-induced kidney injury and inflammatory arthritis. In the absence of IRAP, TNF fails to be efficiently exported from the Golgi. Subsequently, reduced co-localization of VAMP3+ endosomes with Stx4 was observed, while VAMP8-dependent exocytosis of secretory granules was facilitated.

Chemical targeting of IRAP+ endosomes reduced cytokine secretion thereby highlighting this compartment as a promising target for the therapeutic control of inflammation.

category: immunology


title: Heterosis counteracts hybrid breakdown to forestall speciation by parallel natural selection

abstract: In contrast to ecological speciation, where reproductive isolation evolves as a consequence of divergent natural selection, speciation by parallel natural selection has been less thoroughly studied. To test whether parallel evolution drives speciation, we leveraged the repeated evolution of benthic and limnetic ecotypes of threespine stickleback fish and estimated fitness for pure crosses and within-ecotype hybrids in semi-natural ponds and in laboratory aquaria. In ponds, we detected hybrid breakdown in both ecotypes but this was counterbalanced by heterosis and the strength of post-zygotic isolation was nil. In aquaria, we detected heterosis only in limnetic crosses and breakdown in neither ecotype, suggesting that hybrid incompatibilities are environment-dependent for both ecotypes and that heterosis is environment-dependent in benthic crosses. Heterosis and breakdown were 3x greater in limnetic crosses than in benthic crosses, contrasting the prediction that the fitness consequences of hybridization should be greater in crosses among more derived ecotypes. Consistent with a primary role for stochastic processes, patterns differed among crosses between populations from different lakes. Yet, we observed qualitatively similar patterns of heterosis and hybrid breakdown in benthic crosses and limnetic crosses when averaging the lake pairs, suggesting that the outcome of hybridization is repeatable in a general sense.

category: evolutionary biology


title: Pharmacological inhibition of HDAC6 downregulates TGF-β via Smad2/3 acetylation and improves dystrophin-deficient muscles.

abstract: Abstract / SummaryThe absence of dystrophin in Duchenne muscular dystrophy (DMD) disrupts the dystrophin dystroglycan glycoprotein complex (DGC) resulting in fibers fragility and atrophy, associated with fibrosis and microtubules and neuromuscular junction (NMJ) disorganization. The specific non-conventional cytoplasmic histone deacetylase 6 (HDAC6) was previously shown to regulate acetylcholine receptor distribution and muscle atrophy. Here we show that administration of the HDAC6 specific inhibitor tubastatin A to the DMD mouse model mdx improves muscle strength, restores microtubules, NMJ and DGC organization, and reduces muscle atrophy and fibrosis. These effects involve the known action of HDAC6 on microtubules acetylation and muscle atrophy but also involve a yet undiscovered action of HDAC6 on transforming growth factor beta (TGF-{beta}) signaling. Conversely, to inhibitors of nuclear HDACs that regulate TGF-{beta} signaling via the activation of Follistatin expression, HDAC6 inhibition acts downstream of TGF-{beta} ligands and receptors by increasing Smad2/3 acetylation in the cytoplasm which in turn inhibits its phosphorylation and transcriptional activity.

category: physiology


title: Structure and function of BcpE2, the most promiscuous GH3-family beta-glucosidase for scavenging glucose from heterosides

abstract: Cellulose being the most abundant polysaccharide on earth, beta-glucosidases hydrolyzing cello-oligosaccharides are key enzymes to fuel glycolysis in microorganisms developing on plant material. In Streptomyces scabiei, the causative agent of common scab in root and tuber crops, a genetic compensation phenomenon safeguards the loss of the gene encoding the cello-oligosaccharide hydrolase BglC by awakening the expression of alternative beta-glucosidases. Here we reveal that the BglC compensating enzyme BcpE2 is the GH3-family beta-glucosidase that displays the highest reported substrate promiscuity able to release the glucose moiety of all tested types of plant-derived heterosides (aryl {beta}-glucosides, monolignol glucosides, cyanogenic glucosides, anthocyanosides, and coumarin heterosides). BcpE2 structure analysis highlighted a large cavity in the PA14 domain that covers the active site, and the high flexibility of this domain would allow proper adjustment of this cavity for disparate heterosides. The exceptional substrate promiscuity of BcpE2 provides microorganisms a versatile tool for scavenging glucose from plant-derived nutrients that widely vary in size and structure. Importantly, scopolin is the only substrate commonly hydrolyzed by both BglC and BcpE2 thereby generating the potent virulence inhibitor scopoletin. Next to fueling glycolysis, both enzymes thus also interfere with the plant defense mechanisms to fine-tune the strength of virulence.

category: biochemistry


title: Dissociation protocols used for sarcoma tissues bias the transcriptome observed in single-cell and single-nucleus RNA sequencing

abstract:
BackgroundSingle-cell RNA-seq has emerged as an innovative technology used to study complex tissues and characterize cell types, states, and lineages at a single-cell level. Classification of bulk tumors by their individual cellular constituents has also created new opportunities to generate single-cell atlases for many organs, cancers, and developmental models. Despite the tremendous promise of this technology, recent evidence studying epithelial tissues and diverse carcinomas suggests the methods used for tissue processing, cell disaggregation, and preservation can significantly bias gene expression and alter the observed cell types. To determine whether sarcomas - tumors of mesenchymal origin - are subject to the same technical artifacts, we profiled patient-derived tumor explants (PDXs) propagated from three aggressive subtypes: osteosarcoma, Ewing sarcoma (ES), desmoplastic small round cell tumor (DSRCT). Given the rarity of these sarcoma subtypes, we explored whether single-nuclei RNA-seq from more widely available archival frozen specimens could accurately be identified by gene expression signatures linked to tissue phenotype or pathognomonic fusion proteins.

ResultsWe systematically assessed dissociation methods across different sarcoma subtypes. We compared gene expression from single-cell and single-nucleus RNA-sequencing of 125,831 whole-cells and nuclei from ES, DSRCT, and osteosarcoma PDXs. We detected warm dissociation artifacts in single-cell samples and gene length bias in single-nucleus samples. Classic sarcoma gene signatures were observed regardless of dissociation method. In addition, we showed that dissociation method biases can be computationally corrected.

ConclusionsWe highlighted transcriptional biases, including warm dissociation and gene-length biases, introduced by the dissociation method for various sarcoma subtypes. This work is the first to characterize how the dissociation methods used for sc/snRNA-seq may affect the interpretation of the molecular features in sarcoma PDXs.

category: cancer biology


title: Impact of neonatal activation of nuclear receptor CAR (Nr1i3) on Cyp2 gene expression in adult mouse liver

abstract: Perinatal exposure to environmental chemicals is proposed to reprogram development and alter disease susceptibility later in life. Supporting this, neonatal activation of the nuclear receptor CAR (Nr1i3) by TCPOBOP induces persistent expression of mouse hepatic Cyp2 genes into adulthood, attributed to long-term epigenetic memory of the early life exposure [Hepatology (2012) 56:1499-1509]. Here, we confirm that the same high-dose (15x ED50) neonatal TCPOBOP exposure used in that work induces prolonged (12 weeks) increases in hepatic Cyp2 expression; however, we show that the persistence of expression can be fully explained by the persistence of residual TCPOBOP in liver tissue. When the long-term presence of TCPOBOP in tissue was eliminated by decreasing the neonatal TCPOBOP dose 22-fold (0.67x ED50), strong neonatal increases in hepatic Cyp2 expression were still obtained but did not persist into adulthood. Furthermore, the neonatal ED50-range TCPOBOP exposure did not sensitize mice to a subsequent, low-dose TCPOBOP treatment. In contrast, neonatal treatment with phenobarbital, a short half-life (t1/2=8 h) agonist of CAR and of PXR (Nr1i2), induced high-level neonatal activation of Cyp2 genes and also altered their responsiveness to low-dose phenobarbital exposure at adulthood by either increasing (Cyp2b10) or decreasing (Cyp2c55) expression. Thus, neonatal xenobiotic exposure can reprogram hepatic Cyp2 genes and alter their responsiveness to exposures later in life. These findings highlight the need to carefully consider xenobiotic dose, half-life and persistence in tissue when evaluating the long-term effects of early life environmental chemical exposures.

category: pharmacology and toxicology


title: Chromatin reprogramming and transcriptional regulation orchestrate embryogenesis in hexaploid wheat

abstract: Embryogenesis represents the beginning of life cycle, but our understanding of the regulatory circuitry in plants is far lagged to animals. Here, we draw a transcriptome trajectory and chromatin landscape profile during embryogenesis of most cultivated crop hexaploid wheat, highlighting large-scale chromatin reconfiguration and distinct proximal and distal transcriptional regulation in defining cell fate transition. Upon fertilization, H3K27ac and H3K4me3 resetting were correlated with maternal genome silence, while de novo building of chromatin accessibility activated zygotic genome. Global depletion of H3K27me3 in pre-embryo results in a permissive chromatin environment with gain-of-chromatin accessibility, allowing subsequent hierarchical cis- and trans-regulation network mediated by key factors, such as LEC1, MYB, ZHD, LEC2, governing embryo pattern formation. By contrast, H3K27me3 restoration coordinating with chromatin compaction in developmental genes attenuated totipotency and prohibited extensive organogenesis during embryo maturation. In addition, dynamic biased expression of homeolog triads and diverse expression profiles after polyploidization were observed. This is correlated with asymmetric transposon elements insertion in accessible proximal and distal regions. Thus, our study revealed a plant-specific chromatin reprogramming process in facilitating the hierarchical transcription regulation circuits mediated "inverse hourglass model" and unveiled epigenetic regulation of evolutionary divergence among different sub-genome in shaping embryogenesis in polyploidy wheat.

category: plant biology


title: FOXO dictates initiation of B cell development and myeloid restriction in common lymphoid progenitors

abstract:
The development of B cells relies on an intricate network of transcription factors critical for developmental progression and lineage commitment. In the B cell developmental trajectory, a temporal switch from predominant Foxo3 to Foxo1 expression occurs at the CLP stage. Utilizing VAV-iCre mediated conditional deletion, we found that the loss of FOXO3 impaired B cell development from LMPP down to B cell precursors, while the loss of FOXO1 impaired B cell commitment and resulted in a complete developmental block at the CD25 negative proB cell stage. Strikingly, the combined loss of FOXO1 and FOXO3 resulted in the failure to restrict the myeloid potential of CLPs and the complete loss of the B cell lineage. This is underpinned by the failure to enforce the early B-lineage gene regulatory circuitry upon a predominantly pre-established open chromatin landscape. Altogether, this demonstrates that FOXO3 and FOXO1 cooperatively govern early lineage restriction and initiation of B-lineage commitment in CLPs.

SUMMARYCommon lymphoid progenitors co-express the transcription factors FOXO1 and FOXO3. Removing FOXO1 and FOXO3 at this developmental stage results in regained myeloid potential, failed establishment of the early B cell gene regulatory program, and the complete loss of the B cell lineage.


title: Novel orthonairovirus in rodents and shrews, Gabon

abstract: Small mammals harbor various zoonotic viruses and are natural reservoirs for emerging viruses. Here, we identified a novel orthonairovirus, which is genetically close to the virus suggested the association with human neural diseases. The virus was found in 24.6% of the small mammals captured in Gabon, Central Africa.

category: microbiology


title: Inflammasome-mediated glucose limitation induces antibiotic tolerance in Staphylococcus aureus

abstract: Staphylococcus aureus is a leading human pathogen that frequently causes relapsing infections. Host-pathogen interactions have been shown to have substantial impacts on antibiotic susceptibility and the formation of antibiotic tolerant cells. In this study, we interrogate how a major S. aureus virulence factor, -toxin, interacts with macrophages to alter the microenvironment of the pathogen, thereby influencing its susceptibility to antibiotics. We find -toxin-mediated activation of the NLRP3 inflammasome induces antibiotic tolerance in the host cell cytoplasm. Induction of antibiotic tolerance is driven by increased glycolysis in the host cells, resulting in glucose limitation and ATP depletion in S. aureus. Additionally, inhibition of NLRP3 activation improves antibiotic efficacy in vitro and in vivo. Our findings identify interactions between S. aureus and the host that result in metabolic crosstalk that can determine the outcome of antimicrobial therapy.


title: EFA6R suppresses ovarian cancer cell migration and invasion

abstract:
Exchange factor for ADP-ribosylation factor (Arf)6 (EFA6)R expression loss in ovarian cancer has shown to decrease patient survival. EFA6R contains the catalytic Sec7, pleckstrin homology (PH), and coiled-coil (CC) domains. To gain further insight into the role of EFA6R, this study further investigated EFA6R expression in OC and its putative role as a metastatic suppressor. EFA6R mRNA expression, assessed by RT-qPCR, was significantly downregulated in OC tissues and cell lines. OC tissue microarray staining with EFA6R antibody showed that loss of protein expression correlated with increased cancer grade. Furthermore, EFA6R protein levels, assessed by immunoblotting, were significantly reduced in OC tissues and cell lines. Treatment of SKOV-3 cells with 5-aza-2deoxycytidine, an epigenetic regulator, restored EFA6R expression and attenuated functional cell migration and invasion, which was reversed by siRNA-mediated knockdown of EFA6R expression. This study also revelated that exogenously expressed EFA6R localises to the plasma membrane, through its PH domain, and thereby inhibits cell migration and invasion in the CC domain-dependent and an Arf6-independent manner. EFA6R loss-of-function involves epigenetic mechanisms in which downregulation increases OC tumour cell migration and invasion.

Summary statementEFA6R expression is epigenetically regulated in ovarian cancer cells and loss of expression correlates with increased tumour grade and enhanced tumour cell migration. EFA6R appears to mediate these effects independently of Arf6.

category: cell biology


title: CRISPR-based targeted haplotype-resolved assemblies of a megabase region

abstract: Constructing high-quality haplotype-resolved genome assemblies has substantially improved the ability to detect and characterize genetic variants. A targeted approach providing readily access to the rich information from haplotype-resolved genome assemblies will be appealing to groups of basic researchers and medical scientists focused on specific genomic regions. Here, using the 4.5 megabase, notoriously difficult-to-assemble major histocompatibility complex (MHC) region as an example, we demonstrated an approach to construct haplotype-resolved de novo assemblies of targeted genomic regions with the CRISPR-based enrichment. Compared to the results from haplotype-resolved genome assemblies, our targeted approach achieved comparable completeness and accuracy with greatly reduced computing complexity, sequencing cost, as well as the amount of starting materials. Moreover, using the targeted assembled personal haplotypes as the reference both improves the quantification accuracy for sequencing data and enables allele-specific functional genomics analyses. Given its highly efficient use of resources, our approach can greatly facilitate population genetic studies of targeted regions, and may pave a new way to elucidate the molecular mechanisms in disease etiology.

category: genomics


title: Human genetic variations reveal Chromosomal Instability aiding Variants (CIVa) in kinetochore-microtubule associated proteins

abstract: The vast majority of Chromosomal Instability (CIN) promoting mutations remain unknown. We assess the prevalence of Chromosomal Instability aiding Variants (CIVa) by collating Loss-of-Function (LoF) variants predicted in 135 chromosome segregation genes from over 150,000 humans, including consanguineous individuals. Surprisingly, we observe heterozygous and homozygous CIVa in Astrin and SKA3 genes that encode evolutionarily conserved microtubule-associated proteins essential for chromosome segregation. By combining high-resolution microscopy and controlled protein expression, we show the naturally occurring Astrin variant, p.Q1012*, as potentially harmful because it fails to localise normally, delays anaphase onset, induces chromosome misalignment and promotes chromosome missegregation. We show that N-terminal frameshift variants in Astrin and SKA3 are likely to generate shorter isoforms that do not compromise chromosome segregation revealing resilient mechanisms to cope with harmful variants. This study provides a framework to predict and stratify naturally occurring CIVa, an important step towards precision medicine for CIN syndromes.


title: Multivalent binding proteins can drive collapse and reswelling of chromatin in confinement

abstract: Collapsed conformations of chromatin have been long suspected of being mediated by interactions with multivalent binding proteins, such as CTCF, which can bring together distant sections of the chromatin fiber. In this study, we use Langevin dynamics simulation of coarse grained chromatin polymer to show that the role of binding proteins can be more nuanced than previously suspected. In particular, for chromatin polymer in confinement, entropic forces can drive reswelling of collapsed chromatin with increasing binder concentrations. The reswelling transition happens at physiologically relevant binder concentrations and the extent of reswelling is mediated both by the concentration of binding proteins as well as the strength of confinement. We also study the kinetics of collapse and reswelling and show that both processes occur in similar timescales. We characterise this reswelling of chromatin in biologically relevant regimes and discuss implications for the spatial organisation of the genome.

category: biophysics


title: Population dynamics of epithelial-mesenchymal heterogeneity in cancer cells

abstract: Phenotypic heterogeneity is a hallmark of aggressive cancer behaviour and a clinical challenge. Despite much characterisation of this heterogeneity at a multi-omics level in many cancers, we have a limited understanding of how this heterogeneity emerges spontaneously in an isogenic cell population. Some longitudinal observations of dynamics in epithelial-mesenchymal heterogeneity, a canonical example of phenotypic heterogeneity, have offered us opportunities to quantify the rates of phenotypic switching that may drive such heterogeneity. Here, we offer a mathematical modeling framework that explains the salient features of population dynamics noted in PMC42-LA cells: a) predominance of EpCAMhigh subpopulation, b) re-establishment of parental distributions from the EpCAMhigh and EpCAMlow subpopulations, and c) enhanced heterogeneity in clonal populations established from individual cells. Our framework proposes that fluctuations or noise in content duplication and partitioning of SNAIL - an EMT-inducing transcription factor - during cell division can explain spontaneous phenotypic switching and consequent dynamic heterogeneity in PMC42-LA cells observed experimentally at both single-cell and bulk level analysis. Together, we propose that asymmetric cell division can be a potential mechanism for phenotypic heterogeneity.


title: Genetic control of neuronal activity enhances axonal growth only on permissive substrates

abstract: Neural tissue has limited regenerative ability, to cope with that, in the recent years a diverse set of novel tools have been used to tailor neurostimulation therapies and promote functional regeneration after axonal injuries. In this report, we explore cell-specific methods to modulate neuronal activity, including opto- and chemogenetics to assess the effect of specific neuronal stimulation in the promotion of axonal regeneration after injury. We found that opto- or chemogenetic modulations of neuronal activity on both dorsal root ganglia and corticospinal motor neurons increase their axonal growth capacity only on permissive substrates.


title: A survey of neurophysiological differentiation across mouse visual brain areas and timescales

abstract:
Neurophysiological differentiation (ND), a metric that quantifies the number of distinct activity states that the brain or its part visits over a period of time, has been used as a correlate of meaningfulness or subjective perception of visual stimuli. ND has largely been studied in non-invasive human whole-brain recordings where spatial resolution is limited. However, it is likely that perception is supported by discrete populations of spiking neurons rather than the whole brain. Therefore, in this study, we use Neuropixels recordings from the mouse brain to characterize the ND metric within neural populations recorded at single-cell resolution in localized regions. Using the spiking activity of thousands of simultaneously recorded neurons spanning 6 visual cortical areas as well as the visual thalamus, we show that the ND of stimulus-evoked activity of the entire visual cortex is higher for naturalistic stimuli relative to artificial ones. This finding holds in most individual areas throughout the visual hierarchy as well. For animals performing an image change detection task, ND of the entire visual cortex (though not individual areas) is higher for successful detection compared to failed trials, consistent with the assumed perception of the stimulus. Analysis of spiking activity allows us to characterize the ND metric across a wide range of timescales from 10s of milliseconds to a few seconds. This analysis reveals that although ND of activity of single neurons is often maximized at an optimal timescale around 100 ms, the optimum shifts to under 5 ms for ND of neuronal ensembles. Finally, we find that the ND of activations in convolutional neural networks (CNNs) trained on an image classification task shows distinct trends relative to the mouse visual system: ND is often higher for less naturalistic stimuli and varies by orders of magnitude across the hierarchy, compared to modest variation in the mouse brain. Together, these results suggest that ND computed on cellular-level neural recordings can be a useful tool highlighting cell populations that may be involved in subjective perception.

SummaryAdvances in our understanding on neural coding has revealed that information about visual stimuli is represented across several brain regions. However, availability of information does not imply that it is necessarily utilized by the brain, much less that it is subjectively perceived. Since percepts originate in neural activity, distinct percepts must be associated with distinct  states of neural activity, at least within the brain region that supports the percepts. Thus, one approach developed in this direction is to quantify the number of distinct  states that the activity of the brain goes through, called neurophysiological differentiation (ND). ND of the entire brain has been shown to reflect subjective reports of visual stimulus meaningfulness. But what specific subpopulations within the brain could be supporting conscious perception, and what is the correct timescale on which states should be quantified? In this study, we analyze ND of spiking neural activity in the mouse visual cortex recorded using Neuropixels probes, allowing us to characterize the ND metric across a wide range of timescales all the way down from 5 ms to a few seconds. It also allows us to understand the ND of neural activity of different ensembles of neurons, from individual thalamic or cortical ensembles to those spanning across multiple visual areas in the mouse brain.


title: The architecture of the actin network can balance the pushing forces produced by growing microtubules.

abstract: The position of centrosome, the main microtubule-organizing center (MTOC), is instrumental in the definition of cell polarity. It is defined by the balance of tension and pressure forces in the network of microtubules (MTs). As MTs polymerize against the cell periphery, pressure increases and produces pushing forces on the MTOC. How the mechanical interplay between MTs and the actin network is involved in the regulation of these forces remains poorly understood, in particular because its investigation is technically limited by the structural and biochemical complexity of the cell cytoplasm. Here, in a cell-free assay, we used purified proteins to reconstitute the interaction of an aster of dynamic MTs with actin networks of various compositions and architectures in cell-sized microwells. In the absence of actin filaments, the positioning of the MTOC was highly sensitive to variations in MT length. The presence of a bulk actin filament network limited MTs deformation and displacement, and MTOCs were hold in place. In contrast, the assembly of a dense and branched actin network along the edges of the wells centered the MTOCs by preventing MT slippage and thus maintaining an isotropic balance of pushing forces. In agreement with this, an asymmetric peripheral actin network caused the MTOC to decenter by creating an asymmetry in the pushing forces. Numerical simulations demonstrated that steric hindrance by actin networks, at the tip or along the entire length of MTs, can modulate MTOC positioning, as observed in the experiments. Overall, our results show that actin networks can limit the sensitivity of MTOC positioning to MT length and enforce robust MTOC centering or decentering depending on its architecture.


title: On the hormonal control of posterior regeneration in the annelid Platynereis dumerilii

abstract: Regeneration is the process by which many animals are able to restore lost or injured body parts. After amputation of the posterior part of its body, the annelid Platynereis dumerilii is able to regenerate the pygidium, the posteriormost part of its body that bears the anus, and a subterminal growth zone containing stem cells that allows the subsequent addition of new segments. The ability to regenerate their posterior part (posterior regeneration) is promoted in juvenile worms by a hormone produced by the brain and is lost when this hormonal activity becomes low at the time the worms undergo their sexual maturation. By characterizing posterior regeneration at the morphological and molecular levels in worms that have been decapitated, we show that the presence of the head is essential for multiple aspects of posterior regeneration, as well as for the subsequent production of new segments. We also show that methylfarnesoate, the molecule proposed to be the brain hormone, can partially rescue the posterior regeneration defects observed in decapitated worms. Our results are therefore consistent with a key role of brain hormonal activity in the control of regeneration and growth in P. dumerilii, and support the hypothesis of the involvement of methylfarnesoate in this control.

category: developmental biology


title: Trichomes on female reproductive tract: rapid diversification and underlying gene regulatory network in Drosophila suzukii and its related species

abstract:
BackgroundThe ovipositors of some insects are external female genitalia, which have their primary function to deliver eggs. Drosophila suzukii and its sibling species D. subpulchrella are known to have acquired highly sclerotized and enlarged ovipositors upon their shifts in oviposition sites from rotting to ripening fruits. Inside the ovipositor plates, there are scale-like polarized protrusions termed "oviprovector scales" that are likely to aid the mechanical movement of the eggs. The size and spatial distribution of the scales need to be rearranged following the divergence of the ovipositors. In this study, we examined the features of the oviprovector scales in D. suzukii and its closely related species. We also investigated whether the scales are single-cell protrusions comprised of F-actin under the same conserved gene regulatory network as the well-characterized trichomes on the larval cuticular surface.

ResultsThe oviprovector scales of D. suzukii and D. subpulchrella were distinct in size and spatial arrangement compared to those of a closely related species D. biarmipes and D. melanogaster. The comparisons of the size of the scales suggested that the apical cell area of the oviprovector has expanded upon the elongation of the ovipositor plates in these species. Our transcriptome analysis revealed that 43 out of the 46 genes known to be involved in the trichome gene regulatory network are expressed in the developing female genitalia of D. suzukii and D. subpulchrella. An antibody staining depicted the presence of Shavenbaby (Svb) in the inner cavity of the developing ovipositors of D. melanogaster at 44-48 h after puparium formation (APF). Also, shavenoid (sha) was expressed in the corresponding patterns in the developing ovipositors and showed differential expression levels between D. suzukii and D. subpulchrella at 48 h APF.

ConclusionsThe oviprovector scales have divergent size and spatial arrangements among species. Therefore, these scales may represent a rapidly diversifying morphological trait of the female reproductive tract reflecting ecological contexts. Furthermore, our results showed that the gene regulatory network underlying trichome formation is adopted to develop the rapidly evolving trichomes on the oviprovectors of these flies.


title: Delimiting the cryptic diversity and host preferences of Sycophila parasitoid wasps associated with oak galls using phylogenomic data

abstract: Cryptic species diversity is a major challenge for the species-rich community of parasitoids attacking oak gall wasps due to a high degree of sexual dimorphism, morphological plasticity, small size, and poorly known biology. As such, we know very little about the number of species present, nor the evolutionary forces responsible for generating this diversity. One hypothesis is that trait diversity in the gall wasps, including the morphology of the galls they induce, have evolved in response to selection imposed by the parasitoid community, with reciprocal selection driving diversification of the parasitoids. Using a rare continental scale data set of Sycophila parasitoid wasps reared from 44 species of cynipid galls from 18 species of oak across the US, we combined mitochondrial DNA barcodes, Ultraconserved Elements (UCEs), morphological, and natural history data to delimit putative species. We also generate the first large-scale assessment of ecological specialization and host association in this species-rich group with implications for evolutionary ecology and biocontrol. We find most Sycophila target multiple gall wasp species with similar gall morphologies and are generally associated with smaller galls. This result suggests that parasitoid wasps such as Sycophila have adaptations allowing them to exploit particular host trait combinations, while hosts with contrasting traits are resistant to attack. With our congruence-based method of species delimitation, our study has nearly doubled the number of Sycophila wasps among the lineages studied, which highlights the need for taxonomic revision of Sycophila, as many species cannot be identified morphologically or by using molecular delimitation methods.


title: Bee core venom genes predominantly originated before aculeate stingers evolved

abstract: Venoms have convergently evolved in all major animal lineages and are ideal candidates to unravel the genomic processes underlying convergent trait evolution. However, few animal groups have been studied in detail, and large-scale comparative genomic analyses to address toxin gene evolution are rare. The hyper-diverse hymenopterans are the most speciose group of venomous animals, but the origin of their toxin genes has been largely overlooked. We combined proteo-transcriptomics with comparative genomics compiling an up-to-date list of core bee venom proteins to investigate the origin of 11 venom genes in 30 hymenopteran genomes including two newly sequenced genomes of stingless bees. We found a more distinct pattern in which toxin genes originated predominantly by single gene co-option, a prevalent mechanism in parasitoid wasps. These are always accompanied by parallel expansion events in other bee and hymenopteran sister gene groups. The short toxic peptides melittin and apamin appear to be unique to bees, a result supported by a novel machine learning approach. Based on the syntenic pattern we propose here Anthophilin1 as a bee-unique gene family that includes apamin and MCDP. It appears that bees co-adapted their venom genes which predominantly already existed before the aculeate ovipositor evolved to a stinger which exclusively injects venom. Our results provide insight into the large-scale evolution of bee venom compounds, and we present here the first study revealing general processes of venom evolution at a comparative genomic level for this mega-diverse Hymenoptera.


title: Tropical origin, global diversification and dispersal in the pond damselflies (Coenagrionoidea) revealed by a new molecular phylogeny

abstract:
AimThe processes responsible for the formation of Earths most conspicuous diversity pattern, the latitudinal diversity gradient (LDG), remain unexplored for many clades in the Tree of Life. Here, we present a densely-sampled and dated molecular phylogeny for the most speciose clade of damselflies worldwide (Odonata: Coenagrionoidea), and investigate the role of time, macroevolutionary processes and dispersal dynamics in shaping the LDG in this ancient insect superfamily.

Locationglobal

Time period240-0 mya

Major taxa studiedpond damselflies (Coenagrionidae) and featherlegs (Platycnemididae)

MethodsWe used a process-based biogeographic model to jointly infer ancestral ranges and speciation times and to characterise dispersal dynamics between latitudinal regions. We then used this phylogenetic inference to investigate temporal and latitudinal variation in diversification rates.

ResultsOur results uncover a tropical origin of pond damselflies and featherlegs [~] 105 mya, with their common ancestor arising in either Northern South America or Western Africa. While diversification rates have declined since the origin of this clade, the tropics have acted as a net source of lineages dispersing into temperate areas, where both speciation and extinction rates have been relatively higher.

Main conclusionsThis study underscores the importance of biogeographic origin and time to diversify as important drivers of the LDG in pond damselflies. Diversification dynamics may have instead resulted in the formation of ephemeral species in temperate regions. Dispersal has played a role reducing the steepness of the LDG, rather than amplifying it, which would have been expected under strong tropical niche conservatism. With ongoing climate change and increasing northward range expansions of many damselfly taxa, the LDG may continue to shallow. Our results support recent calls to unify biogeographic and macroevolutionary approaches to increase our understanding of how latitudinal diversity gradients are formed and why they vary across time and among taxa.


title: Widespread transposon co-option in the Caenorhabditis germline regulatory network

abstract: The movement of selfish DNA elements can lead to widespread genomic alterations with potential to create novel functions. Here we show that transposon expansions in Caenorhabditis nematodes led to extensive rewiring of germline transcriptional regulation. We find that about one third of C. elegans germline-specific promoters have been co-opted from two related Miniature Inverted Repeat Transposable Elements (MITEs), CERP2 and CELE2. The promoters are regulated by HIM-17, a THAP domain-containing transcription factor related to a transposase. Expansion of CERP2 occurred prior to radiation of the Caenorhabditis genus, as did fixation of mutations in HIM-17 through positive selection, whereas CELE2 expanded only in C. elegans. Through comparative analyses in C. briggsae, we find evolutionary conservation of most CERP2 co-opted promoters, but a substantial fraction of events are species specific. Our work reveals the emergence of a novel transcriptional network driven by TE co-option with a major impact on regulatory evolution.


title: Effects of Neonicotinoid Seed Treatments on Soil Microbial Gene Expression Vary with Time in an Agricultural Ecosystem

abstract:
Neonicotinoids, a class of systemic insecticides, have been widely used for decades against various insect pests. Past studies have reported non-target effects of neonicotinoids on some beneficial macro- and micro-organisms. Given the crucial role that the soil microbiota plays in sustaining soil fertility, it is critical to understand how microbial taxonomic composition and gene expression respond to neonicotinoid exposure. To date, few studies have focused on this question, and these studies have evaluated the shifts in soil microbial taxonomic composition or used soil biochemical analyses to assess the changes in microbial functions. In this study, we have applied a metatranscriptomic approach to quantify the variability in soil microbial gene expression in a two-year soybean/corn crop rotation in Quebec, Canada. We identified weak and temporally inconsistent effects of neonicotinoid application on soil microbial gene expression, as well as a strong temporal variation in soil microbial gene expression among months and years. Neonicotinoid seed treatment altered the expression of a small number of microbial genes, including genes associated with heat shock proteins, regulatory functions, metabolic processes and DNA repair. These changes in gene expression varied during the growing season and between years. Overall, the composition of soil microbial expressed genes seems to be more resilient and less affected by neonicotinoid application than soil microbial taxonomic composition. Our study is among the first to document the effects of neonicotinoid seed treatment on microbial gene expression and highlights the strong temporal variability of soil microbial gene expression and its responses to neonicotinoid seed treatments.

IMPORTANCEThis work provides the first example of the impacts of neonicotinoid seed treatment on community-wide soil microbial gene expression in an experimental design representing real farming conditions. Neonicotinoid pesticides have attracted a great deal of attention in recent years due to their potential non-target impacts on ecological communities and their functions. Our paper represents the first use of metatranscriptomic sequencing to offer real-time and in-depth insights into the non-target effects of this pesticide on soil microbial gene expression and on potentially beneficial soil microorganisms.


title: Benchmark of Differential Gene Expression Analysis Methods for Inter-species RNA-Seq Data using a Phylogenetic Simulation Framework

abstract: Inter-species RNA-Seq datasets are increasingly common, and have the potential to answer new questions on gene expression patterns across the evolution. Single species differential expression analysis is a now well studied problem, that benefits from sound statistical methods. Extensive reviews on biological or synthetic datasets have provided the community with a clear picture on the relative performances of the available tools in various settings. Such benchmarks are still missing in the inter-species gene expression context. In this work, we take a first step in this direction by developing and implementing a new simulation framework. This tool builds on both the RNA-Seq and the Phylogenetic Comparative Methods literatures to generate realistic count datasets, while taking into account the phylogenetic relationships between the samples. We illustrate the features of this new framework through a targeted simulation study, that reveals some of the strengths and weaknesses of both the classical and phylogenetic approaches for inter-species differential expression analysis. The tool has been integrated in the R package compcodeR freely available on Bioconductor.

category: bioinformatics


title: SHARPIN serine 146 phosphorylation mediates ARP2/3 interaction, cancer cell invasion, and metastasis

abstract: The adaptor protein SHARPIN is involved in a number of cellular processes and promotes cancer progression and metastasis. However, how the choice between different functions of SHARPIN is post-translationally regulated is unclear. Here we have characterized SHARPIN phosphorylation by mass spectrometry and in vitro kinase assay. Focusing on two uncharacterized phosphorylation sites, serine 131 and 146, in the unstructured linker region of SHARPIN, we demonstrate their role in SHARPIN-ARP2/3 complex interaction, whereas they play no role in integrin inhibition or LUBAC activation. Consistent with its novel role in ARP2/3 regulation, serine 146 (S146) phosphorylation of SHARPIN promoted lamellopodia formation. Notably, CRISPR-Cas9 mediated knockout of SHARPIN abrogated three-dimensional (3D) invasion of several cancer cell lines. The 3D invasion of cancer cells was rescued by overexpression of the wild-type SHARPIN, but not by SHARPIN S146A mutant, identifying S146 as an invasion promoting phosphorylation switch. Finally, we demonstrate that inhibition of phosphorylation at S146 significantly reduces the in vivo metastasis in the zebrafish model. Collectively, these results demonstrate that SHARPIN S146 phosphorylation constitutes a single functional determinant of cancer cell invasion both in vitro and in vivo.


title: NELL-1 regulates the matrisome to alter osteosarcoma disease progression

abstract:
Sarcomas produce abnormal extracellular matrix (ECM) which in turn provides instructive cues for cell growth and invasion. Neural EGF Like-Like molecule 1 (NELL1) is a secreted glycoprotein characterized by its non-neoplastic osteoinductive effects, yet highly expressed in skeletal sarcomas. Here, NELL1 gene deletion markedly reduced invasive behavior across human osteosarcoma (OS) cell lines. This resulted in reduced OS disease progression, inhibited metastatic potential and improved survival in a xenograft model. These observations were recapitulated with Nell1 conditional knockout in mouse models of p53/Rb driven sarcomagenesis, including reduced tumor frequency, and extended tumor free survival.

Transcriptomic and phospho-proteomic analysis demonstrated that NELL1 loss skews the expression of matricellular proteins associated with reduced FAK signaling. Culture on OS enriched matricellular proteins reversed phenotypic and signaling changes among NELL1 knockout sarcoma cells. These findings in mouse and human models suggest that NELL1 expression alters the sarcoma matrix, thereby modulating cellular invasive potential and prognosis. Disruption of NELL1 signaling may represent a novel therapeutic approach to short circuit sarcoma disease progression.


title: Large-scale systematic feasibility study on the pan-cancer predictability of multi-omic biomarkers from whole slide images with deep learning

abstract: We assessed the pan-cancer predictability of multi-omic biomarkers from haematoxylin and eosin (H&E)-stained whole slide images (WSI) using deep learning (DL) throughout a systematic study. A total of 13,443 DL models predicting 4,481 multi-omic biomarkers across 32 cancer types were trained and validated. The investigated biomarkers included a broad range of genetic, transcriptomic, proteomic, and metabolic alterations. Furthermore, established markers relevant for prognosis, molecular subtypes and clinical outcomes were included. Overall, we established the general feasibility of predicting multi-omic markers directly from routine histology images with DL across solid cancer types, where 50% of the models could perform at an area under the curve (AUC) of more than 0.633 (with 25% of the models having an AUC larger than 0.711). A wide range of biomarkers were detectable from routine histology images across all investigated cancer types, with a mean AUC of at least 0.62 in almost all malignancies. Strikingly, we observed that biomarker predictability was mostly consistent and not dependent on sample size and class ratio, suggesting a degree of true predictability inherent in histomorphology. Together, the results of our study show the potential of DL to predict a multitude of biomarkers across the omics spectrum using only routine slides. This paves the way for accelerating diagnosis and developing more precise treatments for cancer patients.


title: Deep learning can predict multi-omic biomarkers from routine pathology images: A systematic large-scale study


title: The flavonoid nobiletin exhibits differential effects on cell viability in keratinocytes exposed to UVA versus UVB radiation

abstract: The polymethoxylated flavonoid nobiletin has been shown to suppress inflammatory responses to UVB radiation and to enhance circadian rhythms. Because expression of the core nucleotide excision repair (NER) factor XPA and the rate of removal of UV photoproducts from DNA are regulated by the circadian clock, we investigated whether the beneficial effects of nobiletin in UVB-exposed cells could be due in part to enhanced NER. Though nobiletin limited UVB-irradiated human keratinocytes from undergoing cell death, we found that this enhanced survival was not associated with increased NER or XPA expression. Instead, nobiletin reduced initial UV photoproduct formation and promoted a G1 cell cycle arrest. We then examined the implications of this findings for exposures to solar radiation through use of a solar simulated light (SSL) source that contains primarily UVA radiation. In striking contrast to the results obtained with UVB radiation, nobiletin instead sensitized keratinocytes to both the SSL and a more defined UVA light source. This enhanced cell death was correlated with a photochemical change in nobiletin absorption spectrum in the UVA range. We conclude that nobiletin is unlikely to be a useful compound for protecting keratinocytes against the harmful effects of solar UV radiation.


title: The role of rice SOG1 and SOG1-like in DNA damage response

abstract:
Higher plants are constantly exposed to environmental stresses, and therefore complicated defense systems, including DNA damage response (DDR) and DNA repair systems, have developed to protect plant cells. In Arabidopsis, the transcription factor SUPPRESSOR OF GAMMA RESPONSE 1 (SOG1) has been reported to play a key role in DDR. Here, we focus on DDR in rice--thought to be a simpler system compared with Arabidopsis due to lack of induction of endocycle even under DNA damage stress. Rice SOG1 (OsSOG1) and SOG1-like (OsSGL) were identified as putative AtSOG1 orthologs with complete or partial conservation of the serine-glutamine (SQ) motifs involved in activation via phosphorylation. In addition to OsSOG1- or OsSGL-knockout mutants, OsSOG1 non-phosphorylatable mutants (OsSOG1-7A) were generated by homologous recombination-mediated gene targeting. Based on DNA damage susceptibility and transcriptome analysis using these mutants, we demonstrated that OsSOG1, but not OsSGL, plays a central role in the DDR and DNA repair. OsSOG1 regulated target genes via CTT (N)7 AAG motifs reported previously as AtSOG1 recognition sites. The loss of transcription activities and DNA damage tolerance of OsSOG1-7A was not complete compared with OsSOG1-knockout mutants, raising the possibility that another phosphorylation site might be involved in the activation of OsSOG1. Furthermore, our findings have highlighted differences in SOG1-mediated DDR between rice and Arabidopsis, especially regarding induction of cell-cycle arrest and endocycle arrest, revealing rice-specific DDR mechanisms.

One sentence summaryRice transcription factor SUPPRESSOR OF GAMMA RESPONSE 1 controls DNA damage response and DNA repair through activation via phosphorylation and the direct regulation of expression of numerous genes.


title: REM sleep promotes bidirectional plasticity in developing visual cortex in vivo

abstract: Sleep is required for the full expression of plasticity during the visual critical period (CP). However, the precise role of rapid-eye-movement (REM) sleep in this process is undetermined. Previous studies in rodents indicate that REM sleep weakens cortical circuits following MD, but this has been explored in only one class of cortical neuron (layer 5 apical dendrites). We investigated the role of REM sleep in ocular dominance plasticity (ODP) in layer 2/3 neurons using 2-photon calcium imaging in awake CP mice. In contrast to findings in layer 5 neurons, we find that REM sleep promotes changes consistent with synaptic strengthening and weakening. This supports recent suggestions that the effects of sleep on plasticity are highly dependent upon the type of circuit and preceding waking experience.


title: Neuro-toxicogenomic mapping of TMT induced neurotoxicity using human minibrain reveals associated adverse outcome events

abstract: Genome-wide transcriptomic interrogation of organoids and 3D tissue models are increasingly used for characterizing drug, toxicity responses and neurodevelopmental disorders. We established here a neuro-toxicogenomic assay by utilizing "minibrain", a human in vitro 3D brain model system and a low-cost, highly multiplexable RNA-seq methodology (BRB-seq) for screening the effect of trimethyltin chloride (TMT) induced neurotoxicity. We demonstrate that transcriptomic profiling is insightful to the cellular composition and regional identity of the minibrain. Further, we characterize the transcriptomic changes associated with the dose-time neurotoxic response of minibrain upon exposure to TMT. The distinct gene expression changes and molecular candidates identified with our pipeline provides insight to map the key events involved in the adverse outcome pathway of TMT associated neurotoxicity. We identify processes such as endoplasmic reticulum stress, dysregulation of synaptic genes and downregulation of neuron-morphology associated genes upon exposure to TMT. In response to TMT, we identify activation of an early response homeostatic mechanism in minibrain and an interplay of STAT pathways correlating with the dose severity. In this study, we present a neuro-toxicogenomic assay that demonstrates the power of a low-cost transcriptomic screening to study chemical induced neurotoxicity.


title: Prostaglandin E1 as therapeutic molecule for Nephronophthisis and related ciliopathies

abstract:
Nephronophthisis (NPH) is an autosomal recessive tubulointerstitial nephropathy belonging to the ciliopathy disorders and known as the most common cause of hereditary end-stage renal disease in children. Yet, no curative treatment is available. The major gene, NPHP1, encodes a protein playing key functions at the primary cilium and cellular junctions. Using an in cellulo medium-throughput drug-screen, we identified 51 FDA-approved compounds and selected 11 for their physicochemical properties, including prostaglandin E1 (PGE1). PGE1 was further validated to rescue ciliogenesis in immortalized patient NPHP1-/- urine-derived renal tubular cells and corroborated by the effects of its analog PGE2. The two molecules reduced pronephric cyst occurrence in vivo in nphp4 zebrafish model, and PGE1 treatment in Nphp1-/- mice led to a significant reduction of renal tubular dilatations, partially restoring cilia length within tubules. Finally, comparative transcriptomics allowed identification of key molecules downstream PGE1. Altogether, our drug-screen strategy led to the identification of PGE1 as the first potential therapeutic molecule for NPH-associated ciliopathies.

Significant statementJuvenile nephronophthisis (NPH) is a renal ciliopathy due to a dysfunction of primary cilia and a common genetic cause of end-stage renal disease in children and young adults. No curative treatment is available. This paper describes the identification of Prostaglandin E1 (PGE1) as the first potential therapeutic molecule for NPH-associated ciliopathies. We demonstrated that PGE1 rescues defective ciliogenesis and ciliary composition in NPHP1-/- patient urine-derived renal tubular cells. Furthermore, PGE1 improves ciliary and kidney phenotypes in our NPH zebrafish and Nphp1-/- mouse models. Finally, in vitro experiments as well as transcriptomic analyses pointed out several pathways downstream PGE1 as cAMP, cell-cell/cell-matrix adhesion or actin cytoskeleton. Altogether, our findings provide a new alternative for treatment of NPH.


title: The UBR box E3 ligases Poe and Hyd are required for efficient Pericentrin degradation

abstract: Centrosomes are the major microtubule organizing centers (MTOC) of many cells and are composed of centrioles and the pericentriolar material (PCM). Centrosomes are an essential part of diverse cellular processes and require precise regulation of their protein levels. One protein whose levels must be regulated is Pericentrin - PCNT in humans and PLP in Drosophila. Increased PCNT expression and its protein accumulation is linked to clinical conditions including cancer, mental disorders, and ciliopathies. However, the mechanisms by which PCNT levels are regulated remains underexplored. Our previous study (Galletta, 2020) demonstrated that PLP levels are sharply downregulated during early spermatogenesis and this regulation is essential to spatially position PLP on the proximal end of centrioles. We hypothesized that the sharp drop in PLP protein was a result of a rapid protein degradation during the male pre-meiotic G2 phase. In this study we show that the N-terminal region of PLP is required for regulating its levels, which when elevated, extends PLPs position distally on centrioles. Consequently, PCM was also mispositioned leading to defects in spermatids. We then performed a targeted screen where we identified the E2 ligases, Rad6 and UbcD1, and the UBR box family E3 ligases, Poe (UBR4) and Hyd (UBR5) as factors that promote PLP degradation in spermatocytes. Collectively, our study suggests that Poe and Hyd directly bind the N-terminus of PLP and target it for degradation, ensuring proper centriole/basal body assembly and male fertility.


title: Within and among population differences in cuticular hydrocarbons in the seabird tick Ixodes uriae.

abstract: The hydrophobic layer of the arthropod cuticle acts to maintain water balance, but can also serve to transmit chemical signals via cuticular hydrocarbons (CHC), essential mediators of insect behavior. CHC signatures typically vary qualitatively among species, but also quantitatively among populations within a species, and have been used as taxonomic tools to differentiate species or populations in a variety of taxa. Most work in this area to date has focused on insects, with little known for other arthropod classes such as ticks. The worldwide distribution and extensive host-range of the seabird tick Ixodes uriae make it a good model to study the factors influencing CHC composition. Genetically differentiated host-races of I. uriae have evolved across the distribution of this species but the factors promoting sympatric population divergence are still unknown. To test for a potential role of host-associated CHC in population isolation, we collected I. uriae specimens from two of its seabird hosts, the Atlantic puffin (Fratercula arctica) and the common guillemot (Uria aalge) in different colonies in Iceland. Using gas-chromatography and mass-spectrometry, we detected a complex cuticular mixture of 22 hydrocarbons, including n-alkanes, methyl-alkanes and alkenes ranging from 17 to 33 carbons in length. We found that each population had a distinct CHC profile, with long-chain hydrocarbons tending to be more abundant in puffin tick populations. As profiles also varied between host-associated groups, future work will now be required to tests whether the different CHC signals may reinforce assortative mating patterns, and thus I. uriae population divergence.

category: ecology


category: zoology


title: Deciphering polymorphism in 61,157 Escherichia coli genomes via epistatic sequence landscapes

abstract: Characterizing the effect of mutations is key to understand the evolution of protein sequences and to separate neutral amino-acid changes from deleterious ones. Epistatic interactions between residues can lead to a context dependence of mutation effect. Context dependence constrains the amino-acid changes that can contribute to polymorphism in the short term, and the ones that can accumulate between species in the long term. We use computational approaches to accurately predict the polymorphisms segregating in a panel of 61,157 Escherichia coli genomes from the analysis of distant homologues. By comparing a context-aware Direct-Coupling Analysis modelling to a non-epistatic approach, we show that the genetic context strongly constrains the tolerable amino acids in 30% to 50% of amino-acid sites. The study of more distant species suggests the gradual build-up of genetic context over long evolutionary timescales by the accumulation of small epistatic contributions.


title: chromMAGMA: regulatory element-centric interrogation of risk variants

abstract: Genome-wide association studies (GWASs) have identified thousands of genetic variants associated with common polygenic traits. The candidate causal risk variants reside almost exclusively in noncoding regions of the genome and the underlying mechanisms remain elusive for most. Innovative approaches are necessary to understand their biological function. Multimarker analysis of genomic annotation (MAGMA) is a widely used program that nominates candidate risk genes by mapping single-nucleotide polymorphism (SNP) summary statistics from genome-wide association studies to gene bodies. We augmented MAGMA into chromatin-MAGMA (chromMAGMA), a novel method to nominate candidate risk genes based on the presence of risk variants within noncoding regulatory elements (REs). We applied chromMAGMA to a genetic susceptibility dataset for epithelial ovarian cancer (EOC), a rare gynecologic malignancy characterized by high mortality. Disease-specific RE landscapes were defined using H3K27ac chromatin immunoprecipitation-sequence data. This identified 155 unique candidate EOC risk genes across five EOC histotypes; 83% (105/127) of high-grade serous ovarian cancer risk genes had not previously been implicated in this EOC histotype. Risk genes nominated by chromMAGMA converged on mRNA splicing and transcriptional dysregulation pathways. chromMAGMA is a pipeline that nominates candidate risk genes through a gene regulation-focused approach and helps interpret the biological mechanism of noncoding risk variants in complex diseases.

category: genetics


title: Can double PPO mutations exist in a same allele and are such mutants functional?

abstract:
BackgroundResistance to PPO-inhibiting herbicides is primarily endowed by target site mutations at the PPO2 gene that compromise binding of the herbicide to the catalytic domain. In Amaranthus ssp. PPO2, the most prevalent target mutations are deletion of the G210 codon and the R128G and G339A substitutions. These mutations strongly affect the dynamic of the PPO2 binding pocket resulting in reduced affinity with the ligand. Here we investigated the likelihood of co-occurrence of the most widespread target site mutations in the same ppo2 allele.

ResultsPlants carrying R128G+/+ {Delta}G210+/-, where + indicates presence of the mutation, were crossed with each other. The ppo2 of the offspring was subjected to pyrosequencing and E. coli- based Sanger sequencing to determine mutation frequencies and allele co-occurrence. The data show that R128G {Delta}G210 can occur only in one allele; the second allele carries only one mutation. Double mutation in both alleles is less likely because of significant loss of enzyme activity. The segregation of offspring populations derived from a cross between heterozygous plants carrying {Delta}G210 G399A also showed no co-occurrence in the same allele. The offspring exhibited the expected mutation distribution patterns with few exceptions.

ConclusionsHomozygous double-mutants are not physiologically viable. Double-mutant plants can only exist in a heterozygous state. Alternatively, if two mutations are detected in one plant, each mutation would occur in a separate allele.

NomenclaturePalmer amaranth, Amaranthus palmeri S. Wats.; protoporphyrinogen oxidase, PPO; tall waterhemp, Amaranthus tuberculatus (Moq.) J.D.Sauer


title: Can double PPO mutations exist in the same allele and are such mutants functional?


title: GM1 asymmetry in the membrane stabilizes pores

abstract: Cell membranes are highly asymmetric and their stability against poration is crucial for survival. We investigated the influence of membrane asymmetry on electroporation of giant vesicles with membranes doped with GM1, a ganglioside asymmetri-cally enriched in neuronal cell membranes. Compared to symmetric membranes, the lifetimes of micronsized pores are about an order of magnitude longer suggesting that pores are stabilized by GM1. Internal membrane nanotubes caused by the GM1 asymmetry, obstruct and additionally slow down pore closure, effectively reducing pore edge tension and leading to leaky membranes. Our results point to the drastic effects this ganglioside can have on pore resealing in biotechnology applications based on poration as well as on membrane repair processes.


title: Energetic decoupling of phycobilisomes from photosystem II involved in nonphotochemical quenching in red algae

abstract:
To mitigate photodamage under fluctuating light conditions, photosynthetic organisms respond by regulating light energy absorbed by light-harvesting complexes and used for photochemistry. Nonphotochemical quenching acts as a frontline response to prevent excitation energy from reaching the photochemical reaction center of photosystem II. The mechanisms underlying nonphotochemical quenching in red algae, which display unique combination of light-harvesting transmembrane antenna proteins and membrane-attached phycobilisomes, appear to be different from those in cyanobacteria, green algae, and plants. Several single-process models have been proposed for red algal nonphotochemical quenching, yet the possibility of more than one process being involved in nonphotochemical quenching awaits further investigation. To assess multiple nonphotochemical quenching processes in the extremophilic red alga Cyanidioschyzon merolae, fluorescence analyses with light preferentially absorbed by phycobilisomes or photosystems were utilized. Energetic decoupling of phycobilisomes from photosystem II and intrinsic photosystem II quenching were identified as two dominant processes involved in nonphotochemical quenching and distinguished by their kinetics. Whereas the degrees of energetic decoupling remained similar after its induction, the degrees of intrinsic photosystem II quenching varied depending on the illumination period and intensity. The respective effects of protein crosslinkers, osmolytes, ionophores, and photosynthetic inhibitors on the kinetics of nonphotochemical quenching suggested that the energetic decoupling involved conformational changes associated with the connection between the PBS and PSII. Furthermore, the surface charge on the thylakoid membrane played a significant role in the modulation of red algal nonphotochemical quenching.

One-sentence summaryEnergetic decoupling of phycobilisomes from photosystem II and intrinsic photosystem II quenching were involved in nonphotochemical quenching of the extremophilic red alga Cyanidioschyzon merolae.


title: Out of sight: Surveillance strategies for emerging vectored plant pathogens.

abstract: Emerging pests and pathogens of plants are a major threat to natural and managed ecosystems worldwide. Whilst it is well accepted that surveillance activities are key to both the early detection of new incursions and the ability to identify pest-free areas, the performance of these activities must be evaluated to ensure they are fit for purpose. This requires consideration of the number of potential hosts inspected or tested as well as the epidemiology of the pathogen and the detection method used. In the case of plant pathogens, one particular concern is whether the visual inspection of plant hosts for signs of disease is able to detect the presence of these pathogens at low prevalences, given that it takes time for these symptoms to develop. One such pathogen is the ST53 strain of the vector-borne bacterial pathogen Xylella fastidiosa in olive hosts, which was first identified in southern Italy in 2013. Additionally, X. fastidiosa ST53 in olive has a rapid rate of spread, which could also have important implications for surveillance. In the current study, we evaluate how well visual surveillance would be expected to perform for this pathogen and investigate whether molecular testing of either tree hosts or insect vectors offer feasible alternatives. Our results identify the main constraints to each of these strategies and can be used to inform and improve both current and future surveillance activities.


title: Ethylene augments root hypoxia tolerance through amelioration of reactive oxygen species and growth cessation

abstract: Flooded plants experience impaired gas diffusion underwater, leading to oxygen deprivation (hypoxia). The volatile plant hormone ethylene is rapidly trapped in submerged plant cells and is instrumental for enhanced hypoxia acclimation. However, the precise mechanisms underpinning ethylene-enhanced hypoxia survival remain unclear. We studied the effect of ethylene pre-treatment on hypoxia survival of primary Arabidopsis thaliana root tips. Both hypoxia itself and re-oxygenation following hypoxia are highly damaging to root tip cells and ethylene pre-treatments reduced this damage. Ethylene pre-treatment alone altered the abundance of transcripts and proteins involved in hypoxia responses, root growth, translation and reactive oxygen species (ROS) homeostasis. Through imaging and manipulating ROS abundance in planta, we demonstrate that ethylene limits excessive ROS formation during hypoxia and subsequent re-oxygenation and improves oxidative stress survival. In addition, we show that ethylene leads to rapid root growth cessation and this quiescence behaviour contributes to enhanced hypoxia tolerance. Collectively, our results show that the early flooding signal ethylene modulates a variety of processes that all contribute to hypoxia survival.


title: Conserved Structural Motifs in the Hammerhead Ribozyme of a Chloroplast Viroid Mimic tRNA Anticodon Structure to Hijack tRNA Ligase for Viroid Circularization

abstract:
Viroids belonging to the family Avsunviroidae contain hammerhead ribozymes that process to unit length the oligomeric RNAs of both polarities generated during the rolling-circle replication that occurs in chloroplasts of host plants. Linear products, with 5-hydroxyl and 2,3-phosphodiester termini, are then recognized and circularized by the host chloroplastic isoform of the tRNA ligase. Here we analyze the circularization process of eggplant latent viroid (ELVd), an asymptomatic viroid that infects eggplants (Solanum melongena L.), using an Escherichia coli co-expression system in which longer-than-unit linear ELVd (+) precursors are expressed along with the eggplant chloroplastic tRNA ligase. The RNA precursor contains two copies of the hammerhead ribozyme and yields the appropriate termini for the tRNA ligase-mediated ligation in bacteria. We have determined that the ligation efficiency is highly dependent on the presence of ribozyme sequences in the ligatable termini, since the circularization of a series of viroid variants in which the ligation position was rearranged increased substantially in the presence of these sequences. Further in silico analysis showed sequence and structure similarity between the hammerhead ribozyme catalytic pocket and the anticodon loop of tRNAs, both of which harbor a characteristic U-turn of the phosphodiester backbone. Directed mutagenesis in the ribozyme domain supports the role of this U-turn loop in the ligation process. We propose that, in addition to its self-cleavage function, the viroid ribozymes have evolved to mimic the structure of the tRNA anticodon loop to recruit host tRNA ligase for the circularization of the monomeric linear replication intermediates.

IMPORTANCEViroids are a very particular class of infectious agents because they only consist of a small RNA that, to our current knowledge, does not encode for proteins. Consequently, viroids parasite host factors and structures to mediate all processes in the infectious cycle. How these small infectious RNAs are able to hijack host resources is currently a mystery. In this work, we shed some light on the functionality of hammerhead ribozymes during replication of viroids that belong to the family Avsunviroidae, which replicate in the chloroplasts. Our findings suggest that, in addition to mediate self-cleavage of replication intermediates, hammerhead ribozymes also recruit tRNA ligase for monomer circularization, likely mimicking a common host tRNA structural motif.


title: A draft genome assembly for the heterozygous wild tomato 	Solanum habrochaites highlights haplotypic structural variations of intracellular immune receptors

abstract: Solanum habrochaites LA1353 is a self-incompatible, highly heterozygous wild tomato that is a useful germplasm resource for the study of metabolism, reproduction and disease resistance. We generated a draft genome assembly with PacBio HiFi reads and genome annotations, which underscored the expansion of gene families associated with metabolite-production, self-incompatibility, DNA regulation and immunity. After manually curating intracellular nucleotide-binding leucine-rich repeat immune receptors (NLRs), we found that S. habrochaites LA1353 has a larger NLR inventory than other wild tomato species. A great number of heterozygous local copy number variations (CNVs) driven by haplotypic structural variations further expands the inventory, both enhancing NLR diversity and providing more opportunities for sequence evolution. The NLRs associated with local CNVs predominantly appear in the helper NLR (NRC)-related phylogenetic clades and are concentrated in a few physical NLR gene clusters. Synteny analysis points out that these genomic regions correspond to the known NLR clusters from which experimentally validated, functional NLRs, such as Hero, Mi-1.2 and Rpi-amr1, have been identified. Producing and incorporating Resistance Gene Enrichment Sequencing (RenSeq) data across wild tomato species, we reveal that the regions with local CNVs might have been shaped nearly equally by recent NLR gains and losses, along with enhanced sequence diversification that diminishes one-to-one orthology between heterozygous alleles. Our analysis suggests that these genomic regions may have accelerated evolutionary dynamics for NLR diversity generation in S. habrochaites LA1353.


title: Probabilistic Edge Weights Fine-tune Boolean Network Dynamics

abstract: Biological systems are noisy by nature. This aspect is reflected in our experimental measurements and should be reflected in the models we build to better understand these systems. Noise can be especially consequential when trying to interpret specific regulatory interactions, i.e. regulatory network edges. In this paper, we propose a method to explicitly encode edge-noise in Boolean dynamical systems by probabilistic edge-weight (PEW) operators. PEW operators have two important features: first, they introduce a form of edge-weight into Boolean models through the noise, second, the noise is dependent on the dynamical state of the system, which enables more biologically meaningful modeling choices. Moreover, we offer a simple-to-use implementation in the already well-established BooleanNet framework. In two application cases, we show how the introduction of just a few PEW operators in Boolean models can fine-tune the emergent dynamics and increase the accuracy of qualitative predictions. This includes fine-tuning interactions which cause non-biological behaviors when switching between asynchronous and synchronous update schemes in dynamical simulations. Moreover, PEW operators also open the way to encode more exotic cellular dynamics, such as cellular learning, and to implementing edge-weights for regulatory networks inferred from omics data.

category: systems biology


title: Scale-Dependent Coherence of Terrestrial Vertebrate Biodiversity with Environment

abstract: Disentangling contributions from environmental variables is crucial for explaining global biodiversity patterns. We use wavelet power spectra to separate wavelength-dependent trends across Earths surface. Spectra reveal scale- and location-dependent coherence between species richness and topography (E), annual precipitation (Pn), temperature (Tm) and temperature range ({Delta}T). > 97% of richness of carnivorans, bats, songbirds, hummingbirds and amphibians resides at wavelengths {gtrsim} 103 km. 30-69% is generated at scales {gtrsim} 104 km. At these scales, richness across the Americas is anti-correlated with E and {Delta}T, and positively correlated with Pn and Tm. Carnivoran richness is incoherent with {Delta}T, suggesting insensitivity to temperature seasonality. Conversely, amphibian richness is anti-correlated with {Delta}T at large scales. At scales [lsim] 103 km, richness is highest within the tropics. Terrestrial plateaux exhibit coherence between carnivoran richness and E at scales ~ 103 km, reflecting contributions of orogeny/epeirogeny to biodiversity. Similar findings result from transects across other continents. Scale-dependent sensitivities of vertebrate populations to climate are revealed.


title: Computational Model of Heterogeneity in Melanoma: Designing Therapies and Predicting Outcomes

abstract: Cutaneous melanoma is a highly invasive tumor and, despite the development of recent therapies, most patients with advanced metastatic melanoma have a poor clinical outcome. The most frequent mutations in melanoma affect the BRAF oncogene, a protein kinase of the MAPK signaling pathway. Therapies targeting both BRAF and MEK are effective for only 50% of patients and, almost systematically, generate drug resistance. Genetic and non-genetic mechanisms associated with the strong heterogeneity and plasticity of melanoma cells have been suggested to favor drug resistance but are still poorly understood. Recently, we have introduced a novel mathematical formalism allowing the representation of the relation between tumor heterogeneity and drug resistance and proposed several models for the development of resistance of melanoma treated with BRAF/MEK inhibitors. In this paper, we further investigate this relationship by using a new computational model that copes with multiple cell states identified by single cell mRNA sequencing data in melanoma treated with BRAF/MEK inhibitors. We use this model to predict the outcome of different therapeutic strategies. The reference therapy, referred to as "continuous" consists in applying one drug (or several drugs) without disruption. In "combination therapy", several drugs are used sequentially. In "adaptive therapy" drug application is interrupted when the tumor size is below a lower threshold and resumed when the size goes over an upper threshold. We show that, counter-intuitively, the optimal protocol in combination therapy of BRAF/MEK inhibitors with a hypothetical drug targeting cell states that develop later during the tumor response to kinase inhibitors, is to treat first with this hypothetical drug. Also, even though there is little difference in the timing of emergence of the resistance between continuous and adaptive therapies, the spatial distribution of the different melanoma subpopulations is more zonated in the case of adaptive therapy.


title: A unified Method for assessing the Observability of Dynamic Complex Systems in Biology

abstract:
AO_SCPLOWBSTRACTC_SCPLOWO_ST_ABSProblemC_ST_ABSSystems biology is essentially based on the assumption that the complexity of a system can be described by almost generic models to predict the behavior of many other similar systems. To this end, inductive (data-intensive) or deductive (mechanistic) models are currently being developed either to discover patterns and identify plausible correlations from past events, or to connect different causal relationships of interacting elements to construct predictive models. The use of any mathematical approach, or combination of mathematical approaches, presupposes the existence of constant and observable universal causal principles for all biological systems. However, there are currently no tools to assess the robustness of adoption over these universal causal principles, even considering that organisms not only respond to inherent processes and environmental stimuli across multiple scales, but also integrate information across and within these scales, introducing a degree of uncontrollable uncertainty.

MethodologyTo this end, we have developed a method to better evaluate these causal processes by evaluating the information contained in the dynamic trajectories, using concepts of geometric information theory and persistent homology to analyze patterns in time series, so that recognizing the persistence of these patterns over different time periods leads to the evaluation of stable causal relationships. Since we are assessing causal relationships from the patterns in the time series, we are here going beyond mere feature engineering. With this measure, and together with the evaluation of persistent entropy in the trajectories in relation to different individual systems, we have developed a method called the{Phi} -S Diagram as a measure of complexity to better recognize when organisms follow mechanistic pathways or respond autonomously and individually, which is a limitation for both the inductive and deductive modeling methods.

ResultsWe calculated the {Phi}-S Diagram using a deterministic data set available in the UCI repository for reference to test the interpretability of the method, as well as health data available in the same repository that includes the physiological response to movement measured in individuals outside of laboratory conditions. We were able to confirm the mechanistic character in both data sets. Although the current data show that the cardiac response to exercise could be explained in a mechanistic way, we have also discovered that some individuals have a more autonomous than aleatoric response, implying that there are persistent individual variations that limit the universal observability of the system, suggesting that such individuals need an empirical rather than a systemic approach. This proof of concept presents a step towards a clearer framework for the theoretical representation of complex biological systems.


title: Factors affecting post-breeding endometritis, pregnancy rate and embryonic/fetal death in sport mares in two French commercial stud farms: special focus on age, parity and lactating status effects

abstract: Fertility in mares depends on management and reproduction mode, but overall analyses have shown that there is an important and progressive decline in fertility in older mares. Age is often related to maternal parity, but the role of parity in the fertility decline in old mares is not known. Moreover, the positive or negative impacts of breeding mares yearly are a subject of controversy. The aim of this study was to identify whether these factors, as well as reproductive management, played a role on post-insemination endometritis and fertility in sports mares in commercial studs. Altogether, the breeding records of 277 mares (506 cycles) over one breeding season in two French commercial stud farms were analyzed. Age, parity, whether the mare was barren or suckling, follicular size before ovulation, the use of estrus and/or ovulation induction, artificial insemination (AI) protocol, post-breeding inflammation and treatment, Day 14 pregnancies and number of embryos, as well as subsequent foaling the next year were recorded. Data were analyzed using multivariate logistic regression models. The pregnancy rate by cycle was 41.9% and 76.5% of mares were pregnant at the end of the season. Mares older than 10 years, barren mares or mares inseminated in July or August were more likely to have inflammatory reaction after insemination (p<0.0001, OR=3.29, 5.389 and 3.329, respectively). Mares >10 years and mares inseminated with frozen semen were less likely to be pregnant on Day 14 vs younger mares and mares inseminated with fresh and refrigerated semen (p<0.05, OR=0.622 and 0.582, respectively). As expected, mares with multiple ovulations were more likely to be pregnant on Day 14 compared to mares that had only one ovulation (p<0.05, OR=1.791). Altogether, parity only tended to improve the likelihood of being pregnant on Day 14 (p=0.07, OR=1.434 in parous vs nulliparous) but in older mares (age >10), parity increased pregnancy rates (44.09% vs 30.89% in parous vs nulliparous, p<0.05). Post-breeding inflammation was not related to pregnancy rate on Day 14 (37.8% vs 44.2%, p=0.16) but all mares with post-breeding inflammation received a treatment. No effect of suckling at insemination was observed. None of the studied factor could be related to embryo/fetal mortality. In conclusion, maternal age seems to be more important than parity and lactating status for reproductive success in mare. Cumulative effects on parity and aging were observed on pregnancy rates.


title: DelaySSAToolkit.jl: stochastic simulation of reaction systems with time delays in Julia

abstract:
SummaryDelaySSAToolkit.jl is a Julia package for modelling reaction systems with non-Markovian dynamics, specifically those with time delays. These delays implicitly capture multiple intermediate reaction steps and hence serve as an effective model reduction technique for complex systems in biology, chemistry, ecology and genetics. The package implements a variety of exact formulations of the delay stochastic simulation algorithm.

Contactxmfu@ecust.edu.cn, zcao@ecust.edu.cn, or ramon.grima@ed.ac.uk

Availability and ImplementationThe source code and documentation of DelaySSAToolkit.jl are available at https://github.com/palmtree2013/DelaySSAToolkit.jl.


title: Functional gradients in the human lateral prefrontal cortex revealed by a comprehensive coordinate-based meta-analysis

abstract: The human lateral prefrontal cortex (LPFC) enables flexible goal-directed behavior. Yet, its organizing principles remain actively debated despite decades of research. Meta-analysis efforts to map the LPFC have either been restricted in scope or suffered from limited expressivity in meta-analysis tools. The latter short-coming hinders the complexity of questions that can be expressed in a meta-analysis and hence limits the specificity of structure-function associations. Here, we adopt NeuroLang, a novel approach to meta-analysis based on first-order probabilistic logic programming, to infer the organizing principles of the LPFC with greater specificity from 14,371 neuroimaging publications. Our results reveal a rostrocaudal and a dorsoventral gradient, respectively explaining the most and second-most variance in whole-brain meta-analytic connectivity in the LPFC. Moreover, we find a cross-study agreement on a spectrum of increasing abstraction from caudal to rostral LPFC both in specific network connectivity and structure-function associations that supports a domain-general role for the mid-LPFC. Furthermore, meta-analyzing inter-hemispheric asymmetries along the rostrocaudal gradient reveals specific associations with topics of language, memory, response inhibition, and error processing. Overall, we provide a comprehensive mapping of the organizing principles of task-dependent activity in the LPFC, grounding future hypothesis generation on a quantitative overview of past findings.

category: neuroscience


title: Delayed Oligodendrocyte Progenitor Cell Recruitment and Maturation in Large Volume Demyelination

abstract: Remyelination-inducing therapies have the potential to restore neurologic function and prevent progression in multiple sclerosis (MS). However, preclinical therapies capable of driving oligodendrocyte differentiation and enhancing remyelination in murine models have not yet yielded meaningful clinical improvement. These setbacks suggest that small animal models may be inadequate for the development and identification of promising regenerative therapies. Unlike MS, rodent models of demyelination undergo highly efficient remyelination, have typically very small volumes and exhibit abundant oligodendrocyte recruitment rapidly following demyelination. We hypothesized that oligodendrocyte progenitor cell (OPC) recruitment becomes rate-limiting as lesion volume increases leading to a failure of oligodendrocyte differentiation and endogenous remyelination. In this study, we utilized lysolecithin injection into the large white matter tracts of the rabbit to create demyelinated lesions that have cross-sectional areas 20-fold larger than those previously reported in mice, and volumes 8-fold larger. Unlike rodent lesions which show robust supernumerary OPC recruitment (representing a 3-10 fold increase in Olig2+ cell density), recruitment in the rabbit never exceeds normal levels. Importantly, the density of mature CC1+ oligodendrocytes failed to return to NAWM levels by 56 dpl and the percentage of differentiated oligodendrocytes drastically lagged behind that of rodent lesions. These results suggest that as lesion volume increases the requirement for increased OPC proliferation and migration becomes limiting. As oligodendrocyte differentiation from human OPCs is dependent on the local density of progenitors, the reduced density of progenitors in large lesions may contribute to failed differentiation and remyelination. Together, we show that large volume demyelination in the white matter of the rabbit recapitulates several key features of human MS lesions, and represents an important preclinical model for the assessment of remyelination therapies in human demyelinating disease.


title: Histochemical Examination of Changes In Testis After Vasectomy In Rats And Qualitative Analysis Of Tissue Zinc Content

abstract:
It is claimed that around 100 million men worldwide have undergone vasectomy for birth control. Vasectomy is an operation to prevent the transfer of sperm by preventing the luminal continuity of the vas deferens. Degenerative changes after vasectomy usually start with loss of spermatogenic cells in the germinal epithelium, while Sertoli cells are affected later. There is no change in Leydig cells. Zinc, which is found at high rates in the male reproductive system, is an element in the structure of many enzymes necessary for cell membrane integrity, growth and sexual maturity.

In this study, bilateral vasectomy was performed on 18 young adult male rats and control operation was performed on 18 rats. Afterwards, 6 animals from each group were sacrificed after 6 weeks, 12 weeks and 12 months. Germinal epithelium, tubule structure, basement membrane, interstitium and collagen fiber changes were examined at microscope and transmission electron microscope level. On the other hand, zinc content in testicular tissue was measured by Energy-dispersive X-ray spectroscopy (EDS). Six weeks after vasectomy, localized losses in the germinal epithelium and disorganization of spermatogenic cells were observed. In addition to the loss of spermatogenic cells at the 12th week, separations, thickening and an increase in the collagen fiber in the peritubular area were observed in the interstitium and perinuclear area. Tissue zinc content was also found to be the lowest in the 12 months group.

In conclusion, our study showed that the degenerative changes in the rat testis that increased with time after vasectomy were parallel to the decrease in tissue zinc content.


title: A Cyclisation and Docking Protocol for Cyclic Peptide-Protein Modelling using HADDOCK2.4

abstract: An emerging class of therapeutic molecules are cyclic peptides with over 40 cyclic peptide drugs currently in clinical use. Their mode of action is, however, not fully understood, impeding rational drug design. Computational techniques could positively impact their design but modeling them and their interactions remains challenging due to their cyclic nature and their flexibility. This study presents a step-by-step protocol for generating cyclic peptide conformations and docking them to their protein target using HADDOCK2.4. A dataset of 30 cyclic peptide-protein complexes was used to optimize both cyclisation and docking protocols. It supports peptides cyclized via an N- and C-terminus peptide bond and/or a disulfide bond. An ensemble of cyclic peptide conformations is then used in HADDOCK to dock them onto their target protein using knowledge of the binding site on the protein side to drive the modeling. The presented protocol predicts at least one acceptable model according to CAPRI criteria (Critical Assessment of Prediction of Interaction) for each complex of the dataset when the top 10 HADDOCK-ranked single structures are considered (100% success rate top10) both in the bound and unbound docking scenario. Moreover, its performance in both bound and fully unbound docking, is similar to the state-of-the-art software in the field, Autodock CrankPep. The presented cyclisation and docking protocol should make HADDOCK a valuable tool for rational cyclic peptide-based drug design and high-throughput screening.


title: Conserved mechanism for perception of root-active CLE peptides

abstract:
Precision in sensing the environmental cues and adjusting the growth and the physiology of the root system are necessary for plant robustness. Plants achieve their phenotypic plasticity by tightly controlling and buffering developmental decisions. In addition to the classical plant hormones that mediate plant development and stress responses, the CLE peptides constitute an additional crucial level of regulation. While the CLV3-CLV1 module appears to be highly conserved to control the proliferation of the shoot apical meristem stem cells, we do not yet fully understand the function of the additional CLE genes and whether they act in a similar way across the plant species, including tomato. Due to the small gene size and high sequence variability, it is extremely difficult to precisely annotate CLE genes in plant genomes. Here we present our analysis of the CLE family in tomato, based on a combination of iterative tBLASTn and Hidden-Markov-Model (HMM), which allowed us to identify thirty-seven new SlCLEs in addition to the fifteen reported previously. We could confirm the biological activities of selected SlCLEs in suppressing root meristematic cell divisions. We show that root response is mediated by SlCLAVATA2, indicating the conservation of CLE perception mechanism.

One-sentence summaryUsing a combination of iterative tBLASTn and Hidden-Markov-Model approaches, we uncovered 37 new tomato CLE genes predominantly expressed in roots, and we showed a conserved effect on root meristem arrest, that was SlCLAVATA2-dependent.

HighlightsO_LIWe applied a combined approach of iterative tBLASTn and Hidden-Markov-Model to identify fifty-two tomato SlCLE genes, including thirty-seven new genes
C_LIO_LIAll identified genes encode for pre-propeptides with a single CLE-domain containing conserved residues similar to Arabidopsis
C_LIO_LIAnalyzing the publicly available RNAseq datasets, we could confirm the expression of SlCLE genes that was often associated specifically with root or shoot, a certain developmental stage of the fruit, or with drought stress conditions
C_LIO_LIRemarkably, the majority of SlCLE genes are predominantly expressed in the root tissues
C_LIO_LIWe showed the conserved inhibitory effect on the root meristem and columella cells division for the selected SlCLE peptides that were SlCLAVATA2-dependent.
C_LI


title: New insights into tomato CLE peptide repertoire and perception mechanisms