title: Single-cell sequencing of the adult killifish (N. furzeri) brain identifies an atypical progenitor, glial and neuronal heterogeneity

abstract:
The African turquoise killifish uniquely combines a short lifespan with vertebrate-specific features, including age-dependent loss of neuroregenerative capacity, that are missing from the currently used model organisms. In this study, we investigate the cellular landscape that shapes adult neuro- and gliogenesis using single-cell sequencing. Our analysis identifies seventeen cell types including neuronal cells (NC), and progenitors (PC) of glial and non-glial nature in the adult killifish telencephalon. PC subclustering unveils four radial glia types, one atypical non-glial progenitor (NGP) and two clusters representing transitioning states. NC subclustering classified neurons into immature and mature excitatory or inhibitory sub-clusters. Using lineage inference analysis, we discovered neuroepithelial-like radial glia to be the source of neuro- and gliogenesis, and a central role for NGP. Our findings are evidence for specialized progenitors within telencephalon and the data is accessible via an online database, providing a resource to understand normal brain function, as well as the role of cellular relationships in response to injury and disease.

HighlightsO_LISingle-cell transcriptomics reveals four radial glial and one non-glial progenitor cell types relevant to the neurogenic potential of the adult killifish telencephalon
C_LIO_LIIterative clustering of neuronal cell types identified two immature and multiple mature neuron subclasses
C_LIO_LILineage inference analysis of progenitor cell types suggests a neuroepithelial-like radial glia population as the start point of neuro- and gliogenesis, that generates the proliferative non-glial progenitor
C_LIO_LIKillifish-specific marker genes are identified for all the telencephalic cell types, with a special emphasis on markers for the non-glial progenitor, neuron subclasses and radial glia sub-types
C_LI

category: neuroscience


title: Severe neural tube defects due to failure of closure initiation can arise without abnormality of neuroepithelial convergent extension

abstract: Planar cell polarity (PCP) signalling is vital for initiation of neural tube closure in mice, with diminished convergent extension (CE) cell movements leading to a severe form of neural tube defect (NTD), termed craniorachischisis (CRN). Some human NTDs are also associated with PCP gene mutations, but affected individuals are generally heterozygous, whereas PCP homozygosity or compound heterozygosity is needed to produce CRN in mice. This suggests human NTDs may involve other genetic or environmental factors, that interact with partial loss of PCP function. We found that reduced sulfation OF glycosaminoglycans (GAGs) interacts with heterozygosity for the Lp allele of Vangl2 (a core PCP gene), to cause CRN in mice. Here, we hypothesised that this GAG-PCP interaction may regulate convergent extension movements, and hence lead to severe NTDs in the context of only partial loss of PCP function. Both Lp and null alleles of Vangl2 gave similar findings. Culture of E8.5 embryos in the presence of chlorate (a GAG sulfation inhibitor), or enzymatic cleavage of GAG chains, led to failure of NT closure initiation in the majority of Lp/+ embryos, whereas few +/+ littermates exhibited CRN. The chlorate effect was rescued by exogenous sulphate. Surprisingly, DiO labeling of the embryonic node demonstrated no abnormality of midline axial extension in chlorate-treated Lp/+ embryos that developed CRN. In contrast, positive control Lp/Lp embryos displayed severe convergent extension defects in this assay. Morphometric analysis of the closure initiation site revealed abnormalities in the size and shape of somites that flank the closing neural tube in chlorate-treated Lp/+ embryos. We conclude that severe NTDs involving failure of closure initiation can arise by a mechanism other than faulty neuroepithelial convergent extension. Matrix-mediated expansion of somites, flanking the closing neural tube, may be required for closure initiation.

category: developmental biology


title: Gene drive that results in addiction to a temperature sensitive version of an essential gene triggers population collapse in Drosophila

abstract:
One strategy for population suppression seeks to use gene drive to spread genes that confer conditional lethality or sterility, providing a way of combining population modification with suppression. Stimuli of potential interest could be introduced by humans, such as an otherwise benign virus or chemical, or occur naturally on a seasonal basis, such as a change in temperature. Cleave and Rescue (ClvR) selfish genetic elements use Cas9 and gRNAs to disrupt endogenous versions of an essential gene, while also including a Rescue version of the essential gene resistant to disruption. ClvR spreads by creating loss-of-function alleles of the essential gene that select against those lacking it, resulting in populations in which the Rescue provides the only source of essential gene function. In consequence, if function of the Rescue, a kind of Trojan horse now omnipresent in a population, is condition-dependent, so too will be the survival of that population. To test this idea we created a ClvR in Drosophila in which Rescue activity of an essential gene, dribble, requires splicing of a temperature-sensitive intein (TS-ClvRdbe). This element spreads to transgene fixation at 23{degrees}C, but when populations now dependent on Ts-ClvRdbe are shifted to 29{degrees}C death and sterility result in a rapid population crash. These results show that conditional population elimination can be achieved. A similar logic, in which Rescue activity is conditional, could also be used in HEG-based drive, and to bring about suppression and/or killing of specific individuals in response to other stimuli..

SIGNIFICANCE STATEMENTGene drive can be used to spread traits of interest through wild populations. In some contexts the goal is to suppress or eliminate the population. In principle, one way to achieve this goal is if the trait being spread confers on carriers conditional lethality in response to an environmental stimulus that is either introduced by humans into the target area at a specific time (a virus, otherwise benign chemical; a kind of species-specific insecticide), or that occurs naturally on a seasonal basis, such as a change in temperature. Here we show that ClvR selfish elements can be used to spread a gene that confers lethality and sterility in response to increased temperature, demonstrating that conditional population elimination can be achieved.

category: genetics


title: De novo human brain enhancers created by single nucleotide mutations

abstract: Advanced human cognition is attributed to increased neocortex size and complexity, but the underlying gene regulatory mechanisms are unknown. Using deep learning model of embryonic neocortical enhancers, and human and macaque embryonic neocortex H3K27ac data, we identified ~4000 enhancers gained de novo in the human, largely attributable to single-nucleotide essential mutations. The genes near de novo gained enhancers exhibit increased expression in human embryonic neocortex relative to macaque, are involved in critical neural developmental processes, and are expressed specifically in the progenitor cells and interneurons. The gained enhancers, especially the essential mutations, are associated with central nervous system disorders/traits. Integrative computational analyses suggest that the essential mutations establish enhancer activities through affecting binding of key transcription factors of embryonic neocortex. Overall, our results suggest that non-coding mutations may have led to de novo enhancer gains in the embryonic human neocortex, that orchestrate the expression of genes involved in critical developmental processes associated with human cognition.

category: genomics


title: Dopaminergic axon tracts within a hyaluronic acid hydrogel encasement for implantation to restore the nigrostriatal pathway

abstract:
Parkinsons disease (PD) affects 10 million patients worldwide, making it the second most prevalent neurodegenerative disease. Motor symptoms emerge from the loss of dopamine in the striatum after the death of dopaminergic neurons and the long-projecting axons of the nigrostriatal pathway. Current treatments, such as dopamine replacement, deep brain stimulation or cell therapies, disregard the loss of this pathway at the core of symptoms. We sought to address this by improving our tissue-engineered nigrostriatal pathway (TE-NSP) technology, which consists of a tubular hydrogel with a collagen/laminin core that encases an aggregate of dopaminergic neurons and their axons in a way that resembles the nigrostriatal pathway. These constructs can be implanted to replace the lost neurons and axons with fidelity to the pathway, and thus provide dopamine according to feedback from the host circuitry. While TE-NSPs have been traditionally fabricated with agarose, here we utilized a hyaluronic acid (HA) hydrogel to expand the functionality of the encasement and our control over its properties. Using rat ventral midbrain neurons, we found that TE-NSPs exhibited longer and faster neurite growth with HA relative to agarose, with no differences observed in electrically-evoked dopamine release. When transplanted, HA hydrogels reduced host neuron loss and inflammation around the implant compared to agarose, and the cells and axons within TE-NSPs survived and maintained their cytoarchitecture for at least 2 weeks.

HighlightsO_LIWe fabricated engineered dopaminergic axons encased in a tubular hydrogel.
C_LIO_LIWe made hydrogels from methacrylated hyaluronic acid and compared them to agarose.
C_LIO_LIAxons in HA hydrogels had longer and faster axon growth and displayed evoked dopamine release.
C_LIO_LIHA hydrogels reduced the host inflammatory response and supported neuron and axon survival in vivo.
C_LIO_LIThis platform may be used to reconstruct the nigrostriatal pathway to treat Parkinsons disease.
C_LI

category: bioengineering


title: Mice and primates use distinct strategies for visual segmentation

abstract: The rodent visual system has attracted great interest in recent years due to its experimental tractability, but the fundamental mechanisms used by the mouse to represent the visual world remain unclear. In the primate, researchers have argued from both behavioral and neural evidence that a key step in visual representation is "figure-ground segmentation," the delineation of figures as distinct from backgrounds [1-4]. To determine if mice also show behavioral and neural signatures of figure-ground segmentation, we trained mice on a figure-ground segmentation task where figures were defined by gratings and naturalistic textures moving counterphase to the background. Unlike primates, mice were severely limited in their ability to segment figure from ground using the opponent motion cue, with segmentation behavior strongly dependent on the specific carrier pattern. Remarkably, when mice were forced to localize naturalistic patterns defined by opponent motion, they adopted a strategy of brute force memorization of texture patterns. In contrast, primates, including humans, macaques, and mouse lemurs, could readily segment figures independent of carrier pattern using the opponent motion cue. Consistent with mouse behavior, neural responses to the same stimuli recorded in mouse visual areas V1, RL, and LM also did not support texture-invariant segmentation of figures using opponent motion. Modeling revealed that the texture dependence of both the mouses behavior and neural responses could be explained by a feedforward neural network lacking explicit segmentation capabilities. These findings reveal a fundamental limitation in the ability of mice to segment visual objects compared to primates.


title: GLIS1 regulates trabecular meshwork function and intraocular pressure and is associated with glaucoma in humans

abstract: Chronically elevated intraocular pressure (IOP) is the major risk factor of primary open- angle glaucoma, a leading cause of blindness. Dysfunction of the trabecular meshwork (TM), which controls the outflow of aqueous humor (AqH) from the anterior chamber, is the major cause of elevated IOP. Here, we demonstrate that mice deficient in the Kruppel- like zinc finger transcriptional factor GLI-similar-1 (GLIS1) develop chronically elevated IOP. Magnetic resonance imaging and histopathological analysis reveal that deficiency in GLIS1 expression induces progressive degeneration of the TM, leading to inefficient AqH drainage from the anterior chamber and elevated IOP. Transcriptome and cistrome analyses identified several glaucoma- and extracellular matrix-associated genes as direct transcriptional targets of GLIS1. We also identified a significant association between GLIS1 variant rs941125 and glaucoma in humans (P=4.73x10-6), further supporting a role for GLIS1 into glaucoma etiology. Our study identifies GLIS1 as a critical regulator of TM function and maintenance, AqH dynamics, and IOP.

category: molecular biology


title: Mechanics defines the spatial pattern of compensatory proliferation

abstract: The number of cells in tissues is tightly controlled by cell division and cell death, and misregulation of cell numbers could lead to pathological conditions such as cancer. To maintain cell numbers in a tissue, a cell elimination process named programmed cell death or apoptosis, stimulates the proliferation of neighboring cells. This mechanism is called apoptosis-induced compensatory proliferation, which was originally reported more than 40 years ago. While only a limited number of the neigboring cells need to divide to compensate for apoptotic cell loss, the mechanisms that select cells for undergoing division remain an open question. Here we found that the spatial inhomogeneity in mechanotransduction through a growth-promoting transcription co-activator Yes-associated protein (YAP) in the neighboring tissue, accounts for the inhomogeneity of compensatory proliferation. Such inhomogeneous mechanotransduction arises from the combination of the non-uniform distribution of nuclear size, which is inherent in tissues, and the non-uniform pattern of mechanical force applied to the neighboring cells upon apoptosis. Our findings from a mechanical perspective complement the current biochemical understanding of compensatory growth and provide additional insights into cellular functions of how tissue precisely maintains its homeostasis.

category: cell biology


title: Convergent evolution of venom gland transcriptomes across Metazoa

abstract: Animals have repeatedly evolved specialized organs and anatomical structures to produce and deliver a cocktail of potent bioactive molecules to subdue prey or predators - venom. This makes it one of the most widespread convergent functions in the animal kingdom. Whether animals have adopted the same genetic toolkit to evolved venom systems is a fascinating question that still eludes us. Here, we performed the first comparative analysis of venom gland transcriptomes from 20 venomous species spanning the main Metazoan lineages, to test whether different animals have independently adopted similar molecular mechanisms to perform the same function. We found a strong convergence in gene expression profiles, with venom glands being more similar to each other than to any other tissue from the same species, and their differences closely mirroring the species phylogeny. Although venom glands secrete some of the fastest evolving molecules (toxins), their gene expression does not evolve faster than evolutionarily older tissues. We found 15 venom gland specific gene modules enriched in endoplasmic reticulum stress and unfolded protein response pathways, indicating that animals have independently adopted stress response mechanisms to cope with mass production of toxins. This, in turn, activates regulatory networks for epithelial development, cell turnover and maintenance which seem composed of both convergent and lineage-specific factors, possibly reflecting the different developmental origins of venom glands. This study represents the first step towards an understanding of the molecular mechanisms underlying the repeated evolution of one of the most successful adaptive traits in the animal kingdom.

category: evolutionary biology


title: Population bottlenecks constrain microbiome diversity and host genetic variation impeding fitness

abstract:
It is becoming increasingly clear that microbial symbionts influence key aspects of their hosts fitness, and vice versa. This may fundamentally change our thinking about how microbes and hosts interact in influencing fitness and adaptation to changing environments. Here we explore how reductions in population size commonly experienced by threatened species influence microbiome diversity. Consequences of such reductions are normally interpreted in terms of a loss of genetic variation, increased inbreeding and associated inbreeding depression. However, fitness effects of population bottlenecks might also be mediated through microbiome diversity, such as through loss of functionally important microbes. Here we utilise 50 Drosophila melanogaster lines with different histories of population bottlenecks to explore these questions. The lines were phenotyped for egg-to-adult viability and their genomes sequenced to estimate genetic variation. The bacterial 16S rRNA gene was amplified in these lines to investigate microbial diversity. We found that 1) host population bottlenecks constrained microbiome richness and diversity, 2) core microbiomes of hosts with low genetic variation were constituted from subsets of microbiomes found in flies with higher genetic variation, 3) both microbiome diversity and host genetic variation contributed to host population fitness, 4) connectivity and robustness of bacterial networks was low in the inbred lines regardless of host genetic variation, 5) reduced microbial diversity was associated with weaker evolutionary responses of hosts in stressful environments, and 6) these effects were unrelated to Wolbachia density. These findings suggest that population bottlenecks reduce hologenomic variation (combined host and microbial genetic variation). Thus, while the current biodiversity crisis focuses on population sizes and genetic variation of eukaryotes, an additional focal point should be the microbial diversity carried by the eukaryotes, which in turn may influence host fitness and adaptability with consequences for the persistence of populations.

Author summaryIt is becoming increasingly clear that organisms and the microbes that live on or in them - their microbiome - affect each other in profound ways that we are just beginning to understand. For instance, a diverse microbiome can help maintain metabolic functions or fight pathogens causing diseases. A disrupted microbiome may be especially critical for animals and plants that occur in low numbers because of threats from e.g. human exploitation or climate change, as they may already suffer from genetic challenges such as inbreeding and reduced evolutionary potential. The importance of such a reduction in population size, called a bottleneck, on the microbial diversity and the potential interactive effects on host health remains unexplored. Here we experimentally test these associations by investigating the microbiomes of 50 inbred or non-inbred populations of vinegar flies. We found that restricting the population size constrain the hosts genetic variation and simultaneously decreases the diversity of the microbiome that they harbor, and that both effects were detrimental to host fitness. The microbial communities in inbred host populations were less robust than in their non-inbred counterparts, suggesting that we should increasingly consider the microbiome diversity, which may ultimately influence the health and persistence of threatened species.


title: Population bottlenecks constrain host microbiome diversity and genetic variation impeding fitness


title: Novel measures of Morris water maze performance that use vector field maps to assess accuracy, uncertainty, and intention of navigational searches

abstract: Most commonly used behavioural measures for testing learning and memory in the Morris water maze (MWM) involve comparisons of an animals residence time in different quadrants of the pool. Such measures are limited in their ability to test different aspects of the animals performance. Here, we describe novel measures of performance in the MWM that use vector fields to capture the motion of mice as well as their search pattern in the maze. Using these vector fields, we develop quantitative measures of performance that are intuitive and more sensitive than classical measures. First, we describe search patterns in terms of vector field properties and use these properties to define three metrics of spatial memory namely Spatial Accuracy, Uncertainty and, Intensity of Search. We demonstrate the usefulness of these measures using four different data sets including comparisons between different strains of mice, an analysis of two mouse models of Noonan syndrome (Ptpn11 D61G and Ptpn11 N308D/+), and a study of goal reversal training. Importantly, besides highlighting novel aspects of performance in this widely used spatial task, our measures were able to uncover previously undetected differences, including in an animal model of Noonan syndrome, which we rescued with the mitogen activated protein kinase kinase (MEK) inhibitor SL327. Thus, our results show that our approach breaks down performance in the Morris water maze into sensitive measurable independent components that highlight differences in spatial learning and memory in the MWM that were undetected by conventional measures.

category: animal behavior and cognition


title: Which Index Should I Use? A Comparison of Indices for Enclosure Use Studies

abstract: Enclosure use assessments have gained popularity as one of the tools for animal welfare assessments and Post Occupancy Evaluations. There are now a plethora of studies and enclosure use indices available in published literature, and identification of the most appropriate index for each research question is often challenging. The benefits and limitations of four different enclosure use indices; Original and Modified Spread of Participation Index, Entropy, and Electivity Index were compared. Three artificial data sets were developed to represent the challenges commonly found in animal exhibits, and these indices were applied to these contrived enclosure settings. Three of the indices (Original SPI, Modified SPI, and Entropy) were used to assess a single measure of enclosure use variability. When zones within an exhibit were comparable in size, all three indices performed similarly. However, with less equal zone sizes, Modified SPI outperformed Original SPI and Entropy, suggesting that the Modified formula was more useful for assessing overall enclosure use variability under such conditions. Electivity Index assessed the use of individual zones, rather than the variability of use across the entire exhibit, and therefore could not be compared directly to the other three indices. This index is therefore most valuable for assessing individual resources, especially after exhibit modifications.


title: Self-organization of collective escape in pigeon flocks

abstract:
Bird flocks under predation demonstrate complex patterns of collective escape. These patterns may emerge by self-organization from simple interactions among group-members. Computational models have been shown to be valuable for identifying the behavioral rules that may govern these interactions among individuals during collective motion. However, our knowledge of such rules for collective escape is limited by the lack of quantitative data on bird flocks under predation in the field. In the present study, we analyze the first dataset of GPS trajectories of pigeons in airborne flocks attacked by a robotic falcon in order to build a species-specific model of collective escape. We use our model to examine a recently identified distance-dependent pattern of collective behavior that shows an increase in the escape frequency of pigeons when the predator is closer. We first extract from the empirical data the characteristics of pigeon flocks regarding their shape and internal structure (bearing angle and distance to nearest neighbours). Combining these with information on their coordination from the literature, we build an agent-based model tuned to pigeons collective escape. We show that the pattern of increased escape frequency closer to the predator arises without flock-members prioritizing escape when the predator is near. Instead, it emerges through self-organization from an individual rule of predator-avoidance that is independent of predator-prey distance. During this self-organization process, we uncover a role of hysteresis and show that flock members increase their consensus over the escape direction and turn collectively as the predator gets closer. Our results suggest that coordination among flock-members, combined with simple escape rules, reduces the cognitive costs of tracking the predator. Such rules that are independent of predator-prey distance can now be examined in other species. Finally, we emphasize on the important role of computational models in the interpretation of empirical findings of collective behavior.

Author summaryBird flocks show fascinating patterns of collective motion, particularly when escaping a predator. Little is however known about their underlying mechanisms. We fill this gap by firstly analyzing GPS data of pigeon flocks under attack by a robotic-predator and secondly, studying their collective escape in a computer simulation. Previous research on pigeons has revealed that flock-members turn away from the predator more the closer the predator gets. Using computer simulations that are based on pigeon-specific characteristics of motion and coordination among individuals, we study what escape rules at the individual level may underlie this distance-dependent pattern. We show that even if individuals do not intend to escape more when the predator is closer, their escape frequency still increases the closer they get to the predator. This happens by self-organization from the coordination among individuals and despite their tendency to turn away from the predator being constant. A key aspect of this process is the increasing consensus among flock members over the escape direction when the predator gets closer.


title: Open-source personal pipetting robots with live-cell incubation and microscopy compatibility

abstract: Liquid handling robots have the potential to automate many procedures in life sciences. However, they are not in widespread use in academic settings, where funding, space and maintenance specialists are usually limiting. In addition, current robots require lengthy programming by specialists and are incompatible with most academic laboratories with constantly changing small-scale projects. Here, we present the Pipetting Helper Imaging Lid (PHIL), an inexpensive, small, open-source personal liquid handling robot. It is designed for inexperienced users, with self-production from cheap commercial and 3D-printable components and custom control software. PHIL successfully automated pipetting for e.g. tissue immunostainings and stimulations of live stem and progenitor cells during time-lapse microscopy. PHIL is cheap enough for any laboratory member to have their own personal pipetting robot(s), and enables users without programming skills to easily automate a large range of experiments.


title: Based on the identification of tumor antigens and immune subtypes in renal clear cell carcinoma for mRNA vaccine development

abstract:
BackgroundCancer vaccine based on mRNA is considered as a promising strategy and has become a new hot spot in cancer immunotherapy. However, its application to KIRC is not clear. A growing body of research has shown that immunotyping can reflect the comprehensive immune status and immune microenvironment of tumor, which is closely related to treatment response and vaccination potential. The aim of this study was to identify the potential antigens of KIRC for the development of anti-KIRC mRNA vaccines, and to further differentiate the immune subtypes of KIRC to construct an immune landscape for the selection of appropriate patients for vaccination.

MethodsGene expression profiles and corresponding clinical information of 265 KIRC patients and RNA-seq data of 539 KIRC patients were retrieved from were collected from GEO and TCGA. cBioPortal was used to visualize and compare genetic alterations, while GEPIA2 was used to calculate the prognostic index of selected antigens. The relationship between the infiltration of antigen presenting cells and the expression of the identified antigen was visualized with TIMER, and consensus clustering analysis was used to determine the immune subtypes. Finally, the immune landscape of KIRC is visualized through the dimensionality reduction analysis based on graph learning.

ResultsTwo tumor antigens associated with prognostic and antigen-presenting infiltrating cells were identified in KIRC, including LRP2, and DOCK8. KIRC patients were classified into six immune subtypes based on different molecular, cellular, and clinical characteristics. Patients with IS5 and IS6 tumors had an immune "hot" and immunosuppressive phenotype, which was associated with better survival compared to other subtypes, whereas patients with IS1-4 tumors had an immune "cold" phenotype, which was associated with a higher tumor mutation burden. In addition, the expression of immune checkpoints and immunogenic cell death modulators differed significantly in different immunosubtypes of tumors. Finally, the immune landscape of KIRC shows a high degree of heterogeneity across patients.

ConclusionsLRP2 and FEM2 are potential KIRC antigens for mRNA vaccine development, and patients with immune subtypes IS1-4 are suitable for vaccination.

category: bioinformatics


title: Deleting in vivo β-catenin degradation domain in mouse hepatocytes drives hepatocellular carcinoma or hepatoblastoma-like tumors

abstract:
Background and aimsOne-third of hepatocellular carcinomas (HCCs) have mutations that activate the {beta}-catenin pathway with mostly CTNNB1 mutations. Mouse models using Adenomatous polyposis coli (Apc) loss-of-functions (LOF) are widely used to mimic {beta}-catenin-dependent tumorigenesis. Considering the low prevalence of APC mutations in human HCCs we aimed to generate hepatic tumors through CTNNB1 exon 3 deletion ({beta}cat{Delta}ex3) and to compare them to hepatic tumors with Apc LOF engineered through a frameshift in exon 15 (Apcfs-ex15).

MethodsWe used hepatic-specific and inducible Cre-lox mouse models as well as a hepatic-specific in vivo CRISPR/Cas9 approach using AAV vectors, to generate Apcfs-ex15 and {beta}cat{Delta}ex3 hepatic tumors harboring activation of the {beta}-catenin pathway. Tumors generated by the Cre-lox models were analyzed phenotypically using immunohistochemistry and were selected for transcriptomic analysis using RNA-sequencing. Mouse RNAseq data were compared to human RNAseq data (normal tissues (8), HCCs (48) and hepatoblastomas (9)) in an integrative analysis. Tumors generated via CRISPR were analyzed using DNA sequencing and immunohistochemistry.

ResultsMice with {beta}cat{Delta}ex3 alteration in hepatocytes developed liver tumors. Generated tumors were indistinguishable from those arising in Apcfs-ex15 mice. Both Apcfs-ex15 and {beta}cat{Delta}ex3 mouse models induced two phenotypically distinct tumors (differentiated or undifferentiated). Integrative analysis of human and mouse tumors showed that mouse differentiated tumors are close to human well differentiated CTNNB1-mutated tumors, while undifferentiated ones are closer to human mesenchymal hepatoblastomas, and are activated for YAP signaling.

ConclusionApcfs-ex15 and {beta}cat{Delta}ex3 mouse models similarly induce tumors transcriptionally close to either well differentiated {beta}-Catenin activated human HCCs or mesenchymal hepatoblastomas.

category: cancer biology


title: PHENOTYPIC CHARACTERIZATION OF TWO NOVEL CELL LINE MODELS OF CASTRATION RESISTANT PROSTATE CANCER.

abstract:
BACKGROUNDResistance to androgen deprivation therapies is a major driver of mortality in advanced prostate cancer. Therefore, there is a need to develop new pre-clinical models that allow the investigation of resistance mechanisms and the assessment of drugs for the treatment of castration resistant prostate cancer.

METHODSWe generated two novel cell line models (LAPC4-CR and VCaP-CR) which were derived by passaging LAPC4 and VCaP cells in vivo and in vitro under castrate conditions. We performed detailed transcriptomic (RNA-seq) and proteomic analyses (SWATH-MS) to delineate expression differences between castration-sensitive and castration-resistant cell lines. Furthermore, we characterized the in vivo and in vitro growth characteristics of the novel cell line models.

RESULTSThe two cell line derivatives LAPC4-CR and VCaP-CR showed castration resistant growth in vitro and in vivo which was only minimally inhibited by AR antagonists, enzalutamide and bicalutamide. High-dose androgen treatment resulted in significant growth arrest of VCaP-CR but not in LAPC4-CR cells. Both cell lines maintained AR expression, but exhibited distinct expression changes on the mRNA and protein level. Integrated analyses including data from LNCaP and the previously described castration resistant LNCaP-abl cells revealed an expression signature of castration resistance.

CONCLUSIONSThe two novel cell line models LAPC4-CR and VCaP-CR and their comprehensive characterization on the RNA and protein level represent important resources to study the molecular mechanisms of castration resistance.


title: Functional characterisation of the Nep1-like protein effectors of the necrotrophic pathogen - Alternaria brassicae

abstract: Alternaria brassicae is an important necrotrophic pathogen that infects the Brassicaceae family. Alternaria brassicae, like other necrotrophs, also secretes various proteinaceous effectors and metabolites that cause cell death to establish itself in the host. However, there has been no systematic study of A. brassicae effectors and their roles in pathogenesis. The availability of the genome sequence of A. brassicae in public domain has enabled the search for effectors and their functional characterisation. Nep1-like proteins are a superfamily of proteins that induce necrosis and ethylene biosynthesis. They have been reported from a variety of microbes including bacteria, fungi, and oomycetes. In this study, we identified two NLPs from A. brassicae viz. AbrNLP1 and AbrNLP2 and functionally characterised them. Although both AbrNLPs were found to be secretory in nature, they localised differentially inside the plant. AbrNLP2 was found to induce necrosis in both host and nonhost species, while AbrNLP1 could not induce necrosis in both species. Additionally, AbrNLP2 was shown to induce pathogen-associated molecular pattern (PAMP)-triggered immunity in both host and nonhost species. Overall, our study indicates that AbrNLPs are functionally and spatially (subcellular location) distinct and may play different but important roles during the pathogenesis of A. brassicae.

category: plant biology


title: Detection of Ramularia collo-cygni from barley (Hordeum vulgare) in Australia using triplex quantitative and digital PCR

abstract: Ramularia leaf spot (RLS), caused by Ramularia collo-cygni, is an emerging threat to barley (Hordeum vulgare) production. RLS has been reported in Australia; however only minimal information is available regarding its detection and distribution. Due to initial asymptomatic growth in planta, slow growth in vitro and symptomatic similarities to net blotch and physiological leaf spots, detection of this pathogen can be challenging. Quantitative PCR-based methods for R. collo-cygni-specific identification and detection have been described, however these assays (based upon the internal transcribed spacer [ITS] region) have been demonstrated to lack specificity. False-positive detections may have serious implications, thus we aimed to design a robust R. collo-cygni-specific PCR method. Using the phylogenetically informative RNA polymerase II second largest subunit (rpb2) and translation elongation factor 1- (tef1-) genes, along with the tef1- gene of H. vulgare, a triplex assay was developed for both quantitative and digital PCR. The triplex assay was used to assess DNA of barley leaves from New South Wales, South Australia, Tasmania, Victoria and Western Australia, along with DNA of seeds from Western Australia. Detection of R. collo-cygni DNA was confirmed for leaf samples from New South Wales, South Australia, Tasmania, Victoria and Western Australia, indicating a distribution ranging across the southern barley growing regions of Australia. No R. collo-cygni DNA was detected in seed from Western Australia. The R. collo-cygni-specific assay will be a valuable tool to assist with monitoring the distribution of R. collo-cygni in Australia and other regions.


title: Automated verification, assembly, and extension of GBM stem cell network model with knowledge from literature and data

abstract: Signaling network models are usually assembled from information in literature and expert knowledge or inferred from data. The goal of modeling is to gain mechanistic understanding of key signaling pathways and provide predictions on how perturbations affect large-scale processes such as disease progression. For glioblastoma multiforme (GBM), this task is critical, given the lack of effective treatments and pace of disease progression. Both manual and automated assembly of signaling networks from data or literature have drawbacks. Existing GBM networks, as well as networks assembled using state-of-the-art machine reading, fall short when judged by the quality and quantity of information, as well as certain attributes of the overall network structure. The contributions of this work are two-fold. First, we propose an automated methodology for verification of signaling networks. Next, we discuss automation of network assembly and extension that relies on methods and resources used for network verification, thus, implicitly including verification in these processes. In addition to these methods, we also present, and verify a comprehensive GBM network assembled with a hybrid of manual and automated methods. Finally, we demonstrate that, while an automated network assembly is fast, such networks still lack precision and realistic network topology.

category: systems biology


title: Towards a Neurometric-based Construct Validity of Trust

abstract: Trust is a nebulous construct central to successful cooperative exchanges and interpersonal relationships. In this study, we introduce a new approach to establishing construct validity of trust using "neurometrics". We develop a whole-brain multivariate pattern capable of classifying whether new participants will trust a relationship partner in the context of a cooperative interpersonal investment game (n=40) with 90% accuracy and find that it also generalizes to a variant of the same task collected in a different country with 82% accuracy (n=17). Moreover, we establish the convergent and discriminant validity by testing the pattern on eleven separate datasets (n=496) and find that trust is reliably related to beliefs of safety, inversely related to negative affect, but unrelated to reward, cognitive control, social perception, and self-referential processing. Together these results provide support for the notion that the psychological experience of trust contains elements of beliefs of reciprocation and fear of betrayal aversion. Contrary to our predictions, we found no evidence that trust is related to anticipated reward. This work demonstrates how "neurometrics" can be used to characterize the psychological processes associated with brain-based multivariate representations.


title: Pseudocritical and Precritical States in Brain Dynamics

abstract: Scale-free brain dynamics under external stimuli raises an apparent paradox since the critical point of the brain dynamics locates at the limit of zero external drive. Here, we demonstrate that relaxation of the membrane potential removes the critical point but facilitates scale-free dynamics in the presence of strong external stimuli. These findings feature biological neural networks as systems that have no real critical point but bear critical-like behaviors. Attainment of such pseudocritical states relies on processing neurons into a precritical state where they are made readily activatable. We discuss supportive signatures in existing experimental observations and advise new ones for these intriguing properties. These newly revealed repertoires of neural states call for reexamination of brains working states and open fresh avenues for the investigation of critical behaviors in complex dynamical systems.


title: Frequency-specific coactivation patterns in resting-state and their alterations in schizophrenia: an fMRI study

abstract: The resting-state human brain is a dynamic system that shows frequency-specific characteristics. Coactivation pattern (CAP) analysis has been recently used to identify recurring brain states sharing similar coactivation configurations. However, whether and how CAPs differ across different sub-frequency bands are unknown. In the current study, in addition to the typical low-frequency range (0.01 - 0.08 Hz), the spatial and temporal characteristics of CAPs in four sub-frequency bands, slow-5 (0.01 - 0.027 Hz), slow-4 (0.027 - 0.073 Hz), slow-3 (0.073 - 0.198 Hz), and slow-2 (0.198 - 0.25 Hz), were studied. Six CAP states were obtained for each band., The CAPs from the typical frequency range were spatially largely overlapped with those in slow-5, slow-4 and slow-3 but not with those in slow-2. With the increase of frequency, the CAP state became more unstable and resulted in an overall shorter persistence. The spatial and temporal characteristics of slow-4 and slow-5 were further compared, because they constitute most power of the resting-state fMRI signals. In general, slow-4 showed stronger coactivations or co-deactivations in subcortical regions, while slow-5 showed stronger coactivations or co-deactivations in large-scale cortical networks such as the dorsal attention network. Lastly, frequency-dependent dynamic alterations were also observed in schizophrenia patients. Combining the information obtained from both slow-5 and slow-4 increased the classification accuracy of schizophrenia patients than only using the typical range. In conclusion, our results revealed that the spatial and temporal characteristics of CAP state varied at different frequency bands, which could be helpful for identifying brain alterations in schizophrenia.


title: Pro-inflammatory Cytokine GM-CSF Improves Learning/Memory and Brain Pathology in Dp16 Down Syndrome Mice and Improves Learning/Memory in Wild-Type Mice

abstract: Down syndrome (DS) is characterized by chronic neuroinflammation, peripheral inflammation, astrogliosis, imbalanced excitatory/inhibitory neuronal function, and cognitive deficits in both humans and mouse models. Suppression of inflammation has been proposed as a therapeutic approach to treating DS co-morbidities, including intellectual disability (DS/ID). Conversely, we discovered previously that treatment with the pro-inflammatory cytokine granulocyte-macrophage colony-stimulating factor (GM-CSF) improved cognition and reduced biomarkers of brain pathology in humans with Alzheimers disease (AD), another inflammatory disorder, and in a mouse model of AD. To investigate the effects of GM-CSF treatment on DS/ID, we assessed behavior and brain pathology in 12-14 month-old DS mice (Dp[16]1Yey) and their wild-type (WT) littermates, neither of which develop amyloid, and found that GM-CSF treatment improved performance in the radial arm water maze in both Dp16 and WT mice compared to placebo. Dp16 mice also showed abnormal astrocyte morphology and aggregation and fewer calretinin-positive interneurons, both of which were improved by GM-CSF treatment. These findings suggest that stimulating and/or modulating inflammation and the innate immune system with GM-CSF treatment may enhance cognition in both people with DS/ID and in the typical aging population.


title: Tactile suppression stems from sensation-specific sensorimotor predictions

abstract: The ability to sample sensory information with our hands is crucial for smooth and efficient interactions with the world. Despite this important role of touch, tactile sensations on a moving hand are perceived weaker than when presented on the same but stationary hand.1-3 This phenomenon of tactile suppression has been explained by predictive mechanisms, such as forward models, that estimate future sensory states of the body on the basis of the motor command and suppress the associated predicted sensory feedback.4 The origins of tactile suppression have sparked a lot of debate, with contemporary accounts claiming that suppression is independent of predictive mechanisms and is instead akin to unspecific gating.5 Here, we target this debate and provide evidence for sensation-specific tactile suppression due to sensorimotor predictions. Participants stroked with their finger over textured surfaces that caused predictable vibrotactile feedback signals on that finger. Shortly before touching the texture, we applied external vibrotactile probes on the moving finger that either matched or mismatched the frequency generated by the stroking movement. We found stronger suppression of the probes that matched the predicted sensory feedback. These results show that tactile suppression is not limited to unspecific gating but is specifically tuned to the predicted sensory states of a movement.


title: Isolation and characterization of a Cyprinid herpesvirus strain YZ01 from apparently healthy goldfish after rising water temperature

abstract: A Cyprinid herpesvirus 2 (CyHV-2) strain YZ01 was isolated from an apparently healthy goldfish with history of exposure to CyHV-2 when the water temperature was heated from 3-6{square} to 25{square}. Brain, kidney, spleen (referred to as BKS) and intestine of sick and dead fish as well as crucian carp (CrCB) or goldfish brain cell (GFB) suspensions inoculated with above tissue homogenate were collected for PCR assay.Infected cell layers were prepared into ultrathin sections for transmission electron microscopy. Virus DNA were purified from cell suspensions for whole genome sequencing and analysis. Intestine and mixed brain, kidney and spleen fluid (BKS) of dead goldfish and BKS-infected CrCB suspensions as well as their subsequent passages were tested positive by PCR. Nucleus deformation, lattice-like arrangement of inclusion bodies and various forms of immature and mature virions in the nucleus, cytoplasm and outside of cell membranes were observed. Whole genome analysis of 7 CyHV-2 strains available in GeneBank showed that all strains genomes share very high homology while YZ01 was more close to CyHV-2 CNDF-TB2015 and SY-C1 which are classified as C genotype.

category: microbiology


title: Examining the effects of an anti-Salmonella bacteriophage preparation, BAFASAL, on ex vivo human gut microbiome composition and function using a multi-omics approach

abstract:
Salmonella infections (salmonellosis) pose serious health risks to humans, usually via contamination in our food chain. This foodborne pathogen causes major food losses and human illnesses that result in significant economic impacts. Pathogens such as Salmonella have traditionally been kept at bay through the use of antibiotics, but antibiotic overuse within the food industry has led to the development of numerous multidrug-resistant bacterial strains. Thus, governments are now restricting antibiotic use, forcing the industry to search for alternatives to secure safe food chains. Bacteriophages, viruses that infect and kill bacteria, are currently being investigated and used as replacement treatments and prophylactics due to their specificity and efficacy. They are generally regarded as safe alternatives to antibiotics as they are natural components of the ecosystem. One example is BAFASEL, a commercial bacteriophage mixture that specifically targets Salmonella and is currently approved for use in poultry farming. However, when specifically used in the industry they can also make their way into humans through our food chain or exposure as is the case for antibiotics. In particular, agricultural workers could be repeatedly exposed to bacteriophages supplemented in animal feeds. To the best of our knowledge, no studies have investigated the effects of such exposure to bacteriophages on the human gut microbiome. In this study, we used a novel in vitro assay called RapidAIM to investigate BAFASALs potential impact on five individual human gut microbiomes. Multi-omics analyses, including 16S rRNA gene sequencing and metaproteomic, revealed that ex vivo human gut microbiota composition and function were unaffected by BAFASAL treatment providing an additional measure for its safety. Due to the critical role of the gut microbiome in human health and the known role of bacteriophages in regulation of microbiome composition and function, we suggest assaying the impact of bacteriophage-cocktails on the human gut microbiome as a part of their safety assessment.

Graphical Abstract O_FIG_DISPLAY_L [Figure 1] M_FIG_DISPLAY C_FIG_DISPLAY


title: A SUBTILISIN-LIKE SERINE PROTEASE1 (OsSUBSrP1), plays an important role in the wax and cutin pathway, is essential for panicle development in rice

abstract:
Panicle degeneration is a severe physiological defect and causes reduction in grain yield. In this study, we characterized and presented the functional analysis of our previously reported mutant apa1331 (apical panicle abortion1331) that showed apical spikelet degeneration. The anthers from the apical spikelets of apa1331 were degenerated, pollen-less and showed lack of cuticle formation. Transverse sections showed normal meiosis till stage 5-6, however, defects in post-meiotic microspore development were found at stage 8-9 in apa1331. Measurement of wax and cutin analysis showed a significant reduction in anthers of apa1331 compared to Wildtype (WT). Quantification of H2O2 and MDA has indicated the excessive ROS (reactive oxygen species) in apa1331. Trypan blue staining, and TUNEL assay revealed cell death and excessive DNA fragmentation in apa1331. Map-based cloning and Mutmap analysis identified a candidate gene (LOC_Os04g40720) that is a SUBTILISIN-LIKE SERINE PROTEASE (OsSUBSrP1) which harbored an SNP (A>G) in apa1331. CRISPR-mediated knock-out lines of OsSUBSrP1 displayed spikelet degeneration comparable to apa1331. Global gene expression analysis revealed a significant downregulation of wax and cutin biosynthesis genes e.g., OsWDA1, OsMS2 and OsCER4 in apa1331. Our study reports the novel role of SUBSrP1 in ROS-mediated cell death in panicle development.

Highlights1. OsSUBSrP1 plays an important role in maintaining ROS-mediated programmed cell death.
2. OsSUBSrP1 is essential for apical spikelet development.
3. OsSUBSrP1 regulates the expression of wax and cutin biosynthesis pathway genes.


title: A new transgene mouse model using an extravesicular EGFP tag to elucidate the in vivo function of extracellular vesicles

abstract: The in vivo function of cell-derived extracellular vesicles (EVs) is challenging to establish since cell-specific EVs are difficult to isolate. We therefore created an EV reporter using CD9 to display enhanced green fluorescent protein (EGFP) on the EV surface. CD9-EGFP expression in cells did not affect EV size and concentration, but allowed for co-precipitation of EV markers TSG101 and ALIX from cell-conditioned medium by anti-GFP immunoprecipitation. We created a transgenic mouse where CD9-EGFP was inserted in the inverse orientation and double-floxed, ensuring Cre recombinase-dependent EV reporter expression. We crossed the EV reporter mice with mice expressing Cre ubiquitously (CMV- Cre), in cardiomyocytes (AMHC-Cre) and kidney epithelium (Pax8-Cre), respectively. The mice showed tissue-specific EGFP expression, and plasma and urine samples were used to immunoprecipitate EVs. CD9-EGFP EVs was detected in plasma samples from CMV-Cre/CD9-EGFP and AMHC-Cre/CD9-EGFP mice, but not in PAX8-Cre/CD9-EGFP mice. On the other hand, CD9-EGFP EVs were detected in urine samples from CMV-Cre/CD9-EGFP and PAX8-Cre/CD9-EGFP mice, but not AMHC-Cre/CD9-EGFP, indicating that plasma EVs are not filtered to the urine. In conclusion, our EV reporter mouse model enables Cre-dependent EV labeling, providing a new approach to study cell-specific EVs in vivo and gain new insight into their physiological and pathophysiological function.


title: The BLMP-1 transcription factor promotes oscillatory gene expression to achieve timely molting

abstract: Gene expression oscillators can coordinate developmental events in space and time. In C. elegans, a gene expression oscillator directs rhythmic accumulation of [~]25% of the transcriptome, and thus thousands of transcripts, presumably to control molting, a process of rhythmic skin regeneration. Recently, a reverse genetic screen identified several transcription factors important for molting. Here, we characterize one of these, BLMP-1, orthologous to the mammalian transcription repressor PRDM1. We find it to be important for timely molting, and oscillatory gene expression. We propose a dual function for BLMP-1 in shaping oscillatory gene expression and coupling it to a set of direct targets, which ensures cuticular integrity. With mammalian PRDM1/BLIMP1 promoting regular cycles of postnatal hair follicle regeneration, our findings point to the possible existence of a fundamentally conserved clock mechanism in control of rhythmic skin regeneration.


title: Gut microbial diversity in stingless bees is linked to host wing size and is influenced by geography

abstract:
Stingless bees are globally important social corbiculate bees, fulfilling critical pollination roles in many ecosystems; however, their gut microbiota, especially fungal communities, are not well characterized to date. We collected 121 bee samples from two species, Tetragonula carbonaria and Austroplebeia australis, across a distance of 1,200 km of eastern Australia, and analysed their gut microbiomes. We found that the gut bacterial richness of T. carbonaria was influenced by geography (latitude and longitude) and positively correlated to an established fitness indicator in insects; namely, host forewing length/size that relates to flight capacity of stingless bees. We characterized the core microbiomes of the two bees and found that they consisted of the bacterial taxa Snodgrassella, Lactobacillus, Acetobacteraceae and Bombella, and the fungal taxa Didymellaceae, Monocilium mucidum, Malassezia restricta and Aureobasidium pullulans. Both host species identity and management (wild or managed) significantly influenced the gut microbial diversity and composition, and similarity between colonies declined as the geographical distance between them increased. This result was also supported by our co-existing network analyses. Overall, we have thoroughly analysed stingless bee gut microbiomes, and provided novel evidence that T. carbonaria bees with larger wings or from more southern populations have higher microbial diversity in their guts.

Originality-Significance StatementBeneficial interactions between insects and their microbial symbionts are pivotal for their fitness. In this study, we analysed the gut microbiomes of two stingless bee species, Tetragonula carbonaria and Austroplebeia australis, that are widespread and important pollinators in Australia. We characterized their gut microbiomes and detected a significant positive correlation between gut bacterial richness and host forewing size for T. carbonaria; the first time that gut microbial diversity has been linked to a morphological trait in stingless bees. Furthermore, we found that host species identity, management type (wild or managed) and geography all significantly influenced bee gut microbial diversity and composition, and were able to describe both bacterial and fungal core microbial taxa. This study reveals novel understandings of stingless bee gut microbiomes and provides the basis for utilizing microbial strategies to maintain colony health.

category: ecology


title: Phylogenomic analysis of Uganda influenza type-A viruses to assess their relatedness to the vaccine strains and other Africa viruses: a molecular epidemiology study.

abstract:
BackgroundGenetic characterisation of circulating influenza viruses is essential for vaccine selection and mitigation of viral transmission. The current scantiness of viral genomic data and underutilisation of advanced molecular analysis methods on influenza viruses circulating in Africa has limited their extensive study and representation in the global influenza ecology. We aimed to sequence influenza type-A viruses (IAVs) that previously circulated in Uganda and characterised their genetic relatedness to the vaccine viruses and publicly available Africa IAVs.

MethodsThis was an observational study nested to the Uganda national influenza surveillance programme. We used Next-generation sequencing to locally generate genomes from 116 A(H1N1)pdm09 and 118 A(H3N2) viruses collected between 2010 and 2018 from 7 districts across Uganda. A total of 206 hemagglutinin (HA), 207 neuraminidase (NA), and 213 matrix protein (MP) sequences were genetically compared to the WHO-recommended vaccines and other viruses isolated from Africa since 1994. Viral temporal and spatial divergence and circulating genetic clades were characterised using phylogenetic methods.

FindingsWe successfully generated gene sequences for 91{middle dot}9% (215/234) viruses. Uganda A(H1N1)pdm09 and A(H3N2) virus HA, NA, and MP proteins had 96{middle dot}36-99{middle dot}09%, 96{middle dot}49-99{middle dot}39%, and 97{middle dot}48-99{middle dot}95% amino acid similarity, respectively, to vaccines recommended from 2010 through 2020. The local viruses incorporated amino acid substitutions (AAS) in their antigenic, receptor binding, and glycosylation sites each year causing them to antigenically drift away from vaccines. For seasons when vaccine formulations differed, Uganda IAV antigenic sites had 1-2 extra AAS relative to the Southern than Northern hemisphere vaccine viruses. All Uganda IAVs carried the adamantine-resistance marker S31N but not the neuraminidase inhibitor (NAI) resistance markers H274Y and H275Y. However, some A(H1N1)pdm09 viruses had permissive substitutions V234I, N369K, and V241I typical of NAI-resistant viruses. The 2017-2018 A(H1N1)pdm09 viruses belonged to global genetic clade 6B.1, while the A(H3N2) viruses isolated in 2017 belonged to clades 3C.2a and 3C.3a. Uganda IAVs obtained before 2016 clustered distinctly from other Africa viruses while later viruses mixed with other Africa, especially Kenya and Congo, and global viruses. Several unique viral lineages (bootstrap >90) persisted in Uganda and other countries for 1-3 years.

InterpretationThe study reveals Uganda as part of the global influenza ecology with continuous importation, antigenic drift, and extensive local transmission of IAVs, presenting a potential risk of future outbreaks. For a country with limited health resources and where social distancing is not sustainable, viral prevention by vaccination should be prioritized. The notable viral diversity in Africa is a warning to countries to broaden and incorporate genome analysis in routine surveillance to monitor circulating and detect new viruses. This knowledge can inform virus selection for vaccine production and assist in developing cost-effective virus control strategies.

FundingThis work was supported by the Makerere University-Uganda Virus Research Institute Centre of Excellence for Infection and Immunity Research and Training (MUII). MUII is supported through the Developing Excellence in Leadership, Training and Science (DELTAS) Africa Initiative (Grant no. 107743). The DELTAS Africa Initiative is an independent funding scheme of the African Academy of Sciences (AAS), Alliance for Accelerating Excellence in Science in Africa (AESA), and supported by the New Partnership for Africas Development Planning and Coordinating Agency (NEPAD Agency) with funding from the Wellcome Trust (Grant no. 107743) and the UK Government. The work was also funded in part by a Wellcome Trust grant (102975).


title: ribofootPrinter: A precision python toolbox for analysis of ribosome profiling data

abstract: Ribosome profiling is a valuable methodology for measuring changes in a cells translational program. The approach can report how efficiently mRNA coding sequences are translated and pinpoint positions along mRNAs where ribosomes slow down or arrest. It can also reveal when translation takes place outside coding regions, often with important regulatory consequences. While many useful software tools have emerged to facilitate analysis of these data, packages can become complex and challenging to adapt to specialized needs. In particular, the results of meta analysis of average footprint data around sequence motifs of interest can vary substantially depending on the normalization method that is utilized. We therefore introduce ribofootPrinter, a suite of Python tools designed to offer an accessible and modifiable set of code for analysis of ribosome profiling data. Footprint alignments are made to a simplified transcriptome, keeping the code intuitive, and multiple normalization options help facilitate interpretation of meta analysis, particularly outside coding regions. We believe this tool has promise to carry out sophisticated analysis yet offer simplicity to make it readily understandable and adaptable.


title: Fly Cell Atlas: a single-cell transcriptomic atlas of the adult fruit fly

abstract: The ability to obtain single cell transcriptomes for stable cell types and dynamic cell states is ushering in a new era for biology. We created the Tabula Drosophilae, a single cell atlas of the adult fruit fly which includes 580k cells from 15 individually dissected sexed tissues as well as the entire head and body. Over 100 researchers from the fly community contributed annotations to >250 distinct cell types across all tissues. We provide an in-depth analysis of cell type-related gene signatures and transcription factor markers, as well as sexual dimorphism, across the whole animal. Analysis of common cell types that are shared between tissues, such as blood and muscle cells, allowed the discovery of rare cell types and tissue-specific subtypes. This atlas provides a valuable resource for the entire Drosophila community and serves as a comprehensive reference to study genetic perturbations and disease models at single cell resolution.


title: High Sensitivity and Low-Cost Flavin luciferase (FLUX)-based Reporter Gene for Mammalian Cell Expression

abstract: Luciferase-based gene reporters generating bioluminescence signals are important tools for biomedical research. Amongst the luciferases, flavin-dependent enzymes use the most common, and thus most economical chemicals. However, their applications in mammalian cells are limited due to their low signals compared to other systems. Here, we constructed Flavin Luciferase for Mammalian Cell Expression (FLUX) by engineering luciferase from Vibrio campbellii (the most thermostable bacterial luciferase reported to date) and optimizing its expression and reporter assays in mammalian cells. We found that the FLUX reporter gene can be overexpressed in various cell lines and showed outstanding signal-to-background in HepG2 cells, significantly higher than that of firefly luciferase (Fluc). The combined use of FLUX/Fluc as target/control vectors gave the most stable signals, better than the standard set of Fluc(target)/Rluc(control). We demonstrated that FLUX can be used for testing inhibitors of the NF-{kappa}B signaling pathway, validating FLUX applications for various assays in the future.

category: biochemistry


title: C-STEM: ENGINEERING NICHE-LIKE MICRO-COMPARTMENTS FOR OPTIMAL AND SCALE-INDEPENDENT EXPANSION OF HUMAN PLURIPOTENT STEM CELLS IN BIOREACTORS

abstract:
Human pluripotent stem cells (hPSCs) have emerged as the most promising cellular source for cell therapies. To overcome scale up limitations of classical 2D culture systems, suspension cultures have been developed to meet the need of large-scale culture in regenerative medicine. Despite constant improvements, current protocols relying on the generation of micro-carriers or cell aggregates only achieve moderate amplification performance. Here, guided by reports showing that hPSCs can self-organize in vitro into cysts reminiscent of the epiblast stage in embryo development, we developed a physio-mimetic approach for hPSC culture. We engineered stem cell niche microenvironments inside microfluidics-assisted core-shell microcapsules. We demonstrate that lumenized three-dimensional colonies maximize viability and expansion rates while maintaining pluripotency. By optimizing capsule size and culture conditions, we scale-up this method to industrial scale stirred tank bioreactors and achieve an unprecedented hPSC amplification rate of 282-fold in 6.5 days.

TEASEROptimizing human pluripotent stem cells amplification by recapitulating and protecting biomimetic colonies in a bioreactor


title: Molecular Determinants of Complexin Clamping in Reconstituted Single-Vesicle Fusion

abstract: Previously we reported that Synaptotagmin-1 and Complexin synergistically clamp the SNARE assembly process to generate and maintain a pool of docked vesicles that fuse rapidly and synchronously upon Ca2+ influx (Ramakrishnan et al. 2020). Here using the same in vitro single-vesicle fusion assay, we establish the molecular details of the Complexin clamp and its physiological relevance. We find that a delay in fusion kinetics, likely imparted by Synaptotagmin-1, is needed for Complexin to block fusion. Systematic truncation/mutational analyses reveal that continuous alpha-helical accessory-central domains of Complexin are essential for its inhibitory function and specific interaction of the accessory helix with the SNAREpins, analogous to the trans clamping model, enhances this functionality. The c-terminal domain promotes clamping by locally elevating Complexin concentration through interactions with the membrane. Further, we find that Complexin likely contributes to rapid Ca2+-synchronized vesicular release by preventing un-initiated fusion rather than by directly facilitating vesicle fusion.

category: biophysics


title: ProXs drive the formation of membraneless organelles in plants

abstract: Membraneless organelles (MLOs) are non-membranous structures inside cells that organize cellular space and processes. The recent discovery that MLOs can be assembled via liquid-liquid phase separation (LLPS) advanced our understanding of these structures. However, the proteins that are capable of forming MLOs are largely unknown, especially in plants. In this study, we developed a method to identify proteins that we referred as ProXs (Proteins enriched by b-isoX) in Arabidopsis. Heterologous expression in yeast cells showed that most ProXs were capable of forming MLOs autonomously. We applied this method to several model and crop species including early and higher plants. This allowed us to generate an atlas of ProXs for studying plant MLOs. Analysis of ProXs from different species revealed high degree of conservation, supporting that they play important roles in cellular functions and are positively selected during evolution. Our method will be a valuable tool to characterize novel MLOs from desired cells and the data generated in present study will be instrumental for the plant research community to investigate MLO biology.


title: The Cl- channel TMEM16A controls the generation of cochlear Ca2+ waves and promotes the refinement of auditory brainstem networks

abstract: Before hearing onset (postnatal day 12 in mice), inner hair cells (IHC) spontaneously fire action potentials thereby driving pre-sensory activity in the ascending auditory pathway. The rate of IHC action potential bursts is modulated by inner supporting cells (ISC) of Kollikers organ through the activity of the Ca2+ activated Cl- channel TMEM16A. Here we show that conditional deletion of Tmem16a in mice disrupts the generation of Ca2+ waves within Kollikers organ, reduces the burst firing activity and the frequency-selectivity of auditory brainstem neurons in the medial nucleus of the trapezoid body (MNTB), and also impairs the refinement of MNTB projections to the lateral superior olive (LSO). These results reveal the importance of the activity of Kollikers organ for the refinement of central auditory connectivity. In addition, our study suggests a mechanism for the generation of Ca2+ waves, which may also apply to other tissues expressing TMEM16A.

category: neuroscience


title: Early life trauma leads to violent behavior and its inheritance by impairing local thyroid hormone availability in brain

abstract: Escalated and inappropriate levels of aggressive behavior referred to as pathological in psychiatry can lead to violent outcomes with detrimental impact on health and society. Early life trauma triggers adulthood violence and criminality, though molecular mechanisms remain elusive. Here, we provide prefrontal cortex and hypothalamus specific transcriptome profiles of peripubertal stress (PPS) exposed Balb/c adult male mice exhibiting escalated aggression and adult female mice resilient to such aberrant behavioral responses. We identify transthyretin (TTR) as a key regulator of PPS induced escalated aggression and its intergenerational inheritance. TTR mediated long-term perturbation in hypothalamic thyroid hormone (TH) availability contributed to male aggressive behavior without affecting circulating hormone. Ttr gene ablation in hypothalamus impaired local TH signaling including levels of TH transporters (Mct8, Oatp1c1), deiodinase 2(DIO2) and TH responsive genes (Nrgn, Trh and Hr). Escalated aggressive behavior and impaired TTR-TH signaling was also inherited in F1 male progenies. Further, we deciphered Ttr promoter hyper methylation in hypothalamus of such abnormally aggressive males across generations. Interestingly prefrontal cortex showed opposite pattern of Ttr expression as well as long term epigenetic changes. Also, T4 increase by levothyroxine in PFC did not produce any behavioral changes. Our findings reveal that trauma during puberty trigger lasting escalated aggression by epigenetic programming of TTR and consequent impaired thyroid availability in brain. TTR-TH signaling in brain can serve as potential target in reversal of escalated aggression and related psychopathologies.


title: Early life trauma leads to escalated aggressive behavior and its inheritance by impairing thyroid hormone availability in brain


title: Divergent effects of absolute evidence magnitude on decision accuracy and confidence in perceptual judgements

abstract: Whether people change their mind after making a perceptual judgement may depend on how confident they are in their decision. Recently, it was shown that, when making perceptual judgements about stimuli containing high levels of  absolute evidence (i.e., the overall magnitude of sensory evidence across choice options), people make less accurate decisions and are also slower to change their mind and correct their mistakes. Here we report two studies that investigated whether high levels of absolute evidence also lead to increased decision confidence. We used a luminance judgment task in which participants decided which of two dynamic, flickering stimuli was brighter. After making a decision, participants rated their confidence. We manipulated relative evidence (i.e., the mean luminance difference between the two stimuli) and absolute evidence (i.e., the summed luminance of the two stimuli). In the first experiment, we found that higher absolute evidence was associated with decreased decision accuracy but increased decision confidence. In the second experiment, we additionally manipulated the degree of luminance variability to assess whether the observed effects were due to differences in perceived evidence variability. We replicated the results of the first experiment but did not find substantial effects of luminance variability on confidence ratings. Our findings support the view that decisions and confidence judgments are based on partly dissociable sources of information, and suggest that decisions initially made with higher confidence may be more resistant to subsequent changes of mind.


title: Coding of interceptive saccades in parietal cortex of macaque monkeys

abstract: The oculomotor system can initiate remarkably accurate saccades towards moving targets (interceptive saccades) the processing of which is still under debate. The generation of these saccades requires the oculomotor centers to have information about the motion parameters of the target that then must be extrapolated to bridge the inherent processing delays. We investigated to what degree the information about motion of a saccade target is available in the lateral intra-parietal area (area LIP) of macaque monkeys for generation of accurate interceptive saccades. When a multi-layer neural network was trained based on neural discharges from area LIP around the time of saccades towards stationary targets it was also able to predict the end points of saccades directed towards moving targets. This prediction, however, lagged behind the actual post-saccadic position of the moving target by ~80 ms when the whole neuronal sample of 105 neurons was used. We further found that single neurons differentially code for the motion of the target. Selecting neurons with the strongest representation of target motion reduced this lag to ~30 ms which represents the position of the moving target approximately at the onset of the interceptive saccade. We conclude that - similarly to recent findings from the Superior Colliculus (Goffart et al., 2017) - there is a continuum of contributions of individual LIP neurons to the accuracy of interceptive saccades. A contribution of other gaze control centers (like the cerebellum or the frontal eye field) that further increase the saccadic accuracy is, however, likely.


title: Efficient breeding of industrial brewing yeast strains using CRISPR/Cas9-aided mating-type switching

abstract:
Yeast breeding is a powerful tool for developing and improving brewing yeast in a number of industry-relevant respects. However, breeding of industrial brewing yeast can be challenging, as strains are typically sterile and have large complex genomes. To facilitate breeding, we used the CRISPR/Cas9 system to generate double-stranded breaks in the MAT locus, generating transformants with a single specified mating type. The single mating type remained stable even after loss of the Cas9 plasmid, despite the strains being homothallic, and these strains could be readily mated with other brewing yeast transformants of opposite mating type. As a proof of concept, we applied this technology to generate yeast hybrids with an aim to increase {beta}-lyase activity for fermentation of beer with enhanced hop flavour. First, a genetic and phenotypic pre-screening of 38 strains was carried out in order to identify potential parent strains with high {beta}-lyase activity. Mating-competent transformants of eight parent strains were generated, and these were used to generate over 60 hybrids that were screened for {beta}-lyase activity. Selected phenolic off-flavour positive (POF+) hybrids were further sporulated to generate meiotic segregants with high {beta}-lyase activity, efficient wort fermentation and lack of POF; all traits that are desirable in strains for the fermentation of modern hop-forward beers. Our study demonstrates the power of combining the CRISPR/Cas9 system with classic yeast breeding to facilitate development and diversification of brewing yeast.

Key PointsO_LICRISPR/Cas9-based mating type switching was applied to industrial yeast strains
C_LIO_LITransformed strains could be readily mated to form intraspecific hybrids
C_LIO_LIHybrids exhibited heterosis for a number of brewing-relevant traits
C_LI


title: Global evolutionary dynamics and resistome analysis of Clostridioides difficile ribotype 017

abstract:
Clostridioides difficile PCR ribotype (RT) 017 ranks among the most successful strains of C. difficile in the world. In the past three decades, it has caused outbreaks on four continents, more than other "epidemic" strains, however, our understanding of the genomic epidemiology underpinning the spread of C. difficile RT 017 is limited. Here, we performed high-resolution phylogenomic and Bayesian evolutionary analyses on an updated and more representative dataset of 282 non-clonal C. difficile RT 017 isolates collected worldwide between 1981 and 2019. These analyses place an estimated time of global dissemination between 1953 and 1983 and identified the acquisition of the ermB-positive transposon Tn6194 as a key factor behind global emergence. This coincided with the introduction of clindamycin, a key inciter of C. difficile infection, into clinical practice in the 1960s. Based on the genomic data alone, the origin of C. difficile RT 017 could not be determined, however, geographical data and records of population movement suggest that C. difficile RT 017 had been moving between Asia and Europe since the Middle Ages and was later transported to North America around 1860 (95% CI: 1622 - 1954). A focused epidemiological study of 45 clinical C. difficile RT 017 genomes from a cluster in a tertiary hospital in Thailand revealed that the population consisted of two groups of multidrug-resistant (MDR) C. difficile RT 017 and a group of early, non-MDR C. difficile RT 017. The significant genomic diversity within each MDR group suggests that although they were all isolated from hospitalised patients, there was likely a reservoir of C. difficile RT 017 in the community that contributed to the spread of this pathogen.

Impact statementThis study utilises genomic sequence data from 282 non-clonal C. difficile ribotype (RT) 017 isolates collected from around the world to delineate the origin and spread of this epidemic lineage, as well as explore possible factors that have driven its success. It also reports a focused epidemiological investigation of a cluster of C. difficile RT 017 in a tertiary hospital in Thailand to identify possible sources of transmission in this specific setting.

Data summaryAll new WGS data generated in this study has been submitted to the European Nucleotide Archive under the BioProject PRJEB44406 (sample accession ERS6268756 - ERS6268798). The complete genome of C. difficile MAR286 was submitted to GenBank under BioProject PRJNA679085 (accession CP072118). Details of all genomes included in the final analyses are available in the Supplementary Document, available at 10.6084/m9.figshare.14544792.


title: A bacterial derived plant- mimicking cytokinin hormone regulates social behaviour in a rice pathogen

abstract: Many plant-associated bacteria produce plant- mimicking hormones which are involved in modulating host physiology. However, their function in modulating bacterial physiology has not been reported. Here we show that the XopQ protein, a type-III effector of the rice pathogen, Xanthomonas oryzae pv. oryzae (Xoo), is involved in cytokinin biosynthesis. Xoo produces and secretes an active form of cytokinin which enables the bacterium to maintain a planktonic lifestyle and promotes virulence. RNA-seq analysis indicates that the cytokinin produced by Xoo is required for the regulation of several genes which are involved in biofilm formation. We have also identified the Xoo isopentenyl transferase gene, which is involved in the cytokinin biosynthesis pathway and is required for maintaining planktonic behaviour and virulence. Furthermore, mutations in the predicted cytokinin receptor kinase (PcrK) and the downstream response regulator (PcrR) of Xoo phenocopy the cytokinin biosynthetic mutants, but are not complemented by supplementation with exogenous cytokinin. Cytokinin biosynthetic functions are encoded in a number of diverse bacterial genomes suggesting that cytokinin may be a widespread signalling molecule in the bacterial kingdom.


title: circFL-seq reveals full-length circular RNAs with rolling circular reverse transcription and nanopore sequencing

abstract: Circular RNAs (circRNAs) act through multiple mechanisms with their sequence features to fine-tune gene expression networks. Due to overlapping sequences with linear cognates, identifying internal sequences of circRNAs remains a great challenge, which hinders comprehensive understanding of circRNA functions and mechanisms. Here, based on rolling circular reverse transcription (RCRT) and nanopore sequencing, we developed circFL-seq, a full-length circRNA sequencing method, to profile circRNA at the isoform level. With a customized computational pipeline circfull to directly identify full-length sequences from rolling circular reads, we reconstructed 77,606 high-quality circRNAs from seven human cell lines and two human tissues. Benefiting from rolling circles and long-read sequencing, circFL-seq showed more than tenfold enrichment of circRNA reads and advantages for both detection and quantification at the isoform level compared to short-read RNA sequencing. The concordance of RT-qPCR and circFL-seq results for the identification of differential alternative splicing suggested wide application prospects for functional studies of internal variants in circRNAs. Moreover, the detection of cancer-related fusion circRNAs at the omics scale may further expand the application of circFL-seq. Together, the accurate identification and quantification of full-length circRNAs make circFL-seq a potential tool for large-scale screening of functional circRNAs.


title: Transcriptomic response of Cinachyrella cf. cavernosa sponges to spatial competition

abstract: Spatial competition in the intertidal zones drives the community structure in marine benthic habitats. Organisms inhabiting these areas not only need to withstand fluctuations of temperature, water level, pH, and salinity, but also need to compete for the best available space. Sponges are key members of the intertidal zones, and their life history processes (e.g. growth, reproduction, and regeneration) are affected by competition. Here we used transcriptomics to investigate the effects of interspecific competition between the tetillid sponge Cinachyrella cf. cavernosa, the zoantharid Zoanthus sansibaricus, and the macroalgae Dictyota ciliolata. The analysis of differentially expressed genes showed that Z. sansibaricus was the most stressful competitor to C. cf. cavernosa, which showed an increased rate of cellular respiration under stress of competition. Similarly, an up-regulation of energy metabolism, lipid metabolism, and the heat-shock protein (HSP) 70 was also observed along with an indication of a viral infection and decreased ability to synthesise protein. A down-regulation of purine and pyrimidine metabolism indicated reduction in physiological activities of the competing sponges. Moreover, a putative case of possible kleptocnidism, not previously reported in Cinachyrella cf. cavernosa was also observed. This study opens the door for more detailed investigations of marine organisms competing for spatial resources using transcriptome data.


title: Polygenic routes lead to parallel altitudinal adaptation in Heliosperma pusillum (Caryophyllaceae)

abstract: Understanding how organisms adapt to the environment is a major goal of modern biology. Parallel evolution - the independent evolution of similar phenotypes in different populations - provides a powerful framework to investigate the evolutionary potential of populations, the constraints of evolution, its repeatability and therefore its predictability. Here, we quantified the degree of gene expression and functional parallelism across replicated ecotype formation in Heliosperma pusillum (Caryophyllaceae), and gained insights into the architecture of adaptive traits. Population structure analyses and demographic modelling support a previously formulated hypothesis of parallel polytopic divergence of montane and alpine ecotypes. We detect a large proportion of differentially expressed genes (DEGs) underlying divergence within each replicate ecotype pair, with a strikingly low amount of shared DEGs across pairs. Functional enrichment of DEGs reveals that the traits affected by significant expression divergence are largely consistent across ecotype pairs, in strong contrast to the non-shared genetic basis. The remarkable redundancy of differential gene expression indicates a polygenic architecture for the diverged adaptive traits. We conclude that polygenic traits appear key to opening multiple routes for adaptation, widening the adaptive potential of organisms.


title: SELECTION DRIVES THE EVOLUTION OF CONVERGENT GENE EXPRESSION CHANGES DURING TRANSITIONS TO CO-SEXUALITY IN HAPLOID SEXUAL SYSTEMS

abstract: AO_SCPLOWBSTRACTC_SCPLOWCo-sexuality has evolved repeatedly from ancestors with separate sexes across a wide range of taxa. The switch to co-sexuality is expected to involve major molecular readjustments at the level of gene expression patterns, as modified males or females will express the opposite sexual function for which their phenotypes have been optimized. However, the molecular changes underpinning this important transition remain unknown, particularly in organisms with haploid sexual systems such as bryophytes, red and brown algae. Here, we explore four independent events of emergence of co-sexuality from uni-sexual (dioicous) ancestors in brown algal clades in order to examine the nature, evolution and degree of convergence of gene expression changes that accompany the breakdown of dioicy. The amount of male versus female phenotypic differences in dioicous species were not correlated with the extent of sex-biased gene expression, in strike contrast to what is observed in animals. Although sex-biased genes exhibited a high turnover rate during brown alga diversification, their predicted functions were remarkably conserved. Transition to co-sexuality consistently involved adaptive gene expression shifts and rapid sequence evolution, particularly of male-biased genes. The gene expression profiles of co-sexual species were more similar to those of females than to males of related dioicous species, suggesting that the former may have arisen from ancestral females. Finally, we identified extensive convergent gene expression changes associated with the transition to co-sexuality, and these changes appear to be driven by selection. Together, our observations provide novel insights on how co-sexual systems arise from ancestral, haploid UV sexual systems.


title: Identification of potential carboxylic acid-containing drug candidate to design novel competitive NDM inhibitors: An in-silico approach comprising combined virtual screening and molecular dynamics simulation

abstract: Metallo-{beta}-lactamases (MBLs) producing bacteria especially the ones with New Delhi metallo-beta-lactamase-1 (NDM-1) and its variants can potentially hydrolyse all the major {beta}-lactam antibiotics, ultimately escalating anti-microbial resistance world-wide. There is a dearth of approved inhibitors to combat NDM and other MBLs producing bacteria. Hence we focussed to find novel inhibitor(s) in-silico which can potentially suppress the activity of NDM/ MBLs. 2400 compounds were virtually screened to identify a promising carboxylic acid-containing compound (CID-53986787) analogous to NDM antagonist Captopril. Our lead compound can bind adjacent to the active site zinc ions (Zn1 and Zn2) in all highly resistant NDM variants. CID-53986787 possesses ~5-8% higher binding affinity than Captopril, exhibiting molecular interactions with crucial residues that can destabilize the hydrolytic activity of NDM. CID-53986787 was virtually evaluated to ascertain its safe pharmacological/ toxicity profile. Molecular dynamics simulation studies elucidated its stable interaction with the target protein (NDM-1).


title: Topography-induced large-scale anti-parallel collective migration in vascular endothelium

abstract: Collective migration of vascular endothelial cells is central for embryonic development, angiogenesis, and wound closure. Although physical confinement of cell assemblies has been shown to elicit specific patterns of collective movement in various cell types, endothelial migration in vivo often occurs without confinement. Here we show that unconfined endothelial cell monolayers on microgrooved substrates that mimic the anisotropic organization of the extracellular matrix exhibit a new type of collective movement that takes the form of a periodic pattern of anti-parallel cell streams. We further establish that the development of these streams requires intact cell-cell junctions and that stream sizes are particularly sensitive to groove depth. Finally, we show that modeling the endothelial cell sheet as an active fluid with the microgrooves acting as constraints on cell orientation predicts the occurrence of the periodic anti-parallel cell streams as well as their lengths and widths. We posit that in unconfined cell assemblies, physical factors that constrain or bias cellular orientation such as anisotropic extracellular matrix cues or directed flow-derived shear forces dictate the pattern of collective cell movement.


title: Insula to mPFC reciprocal connectivity differentially underlies novel taste neophobic response and learning

abstract: To survive in an ever-changing environment, animals must detect and learn salient information. The anterior insular cortex (aIC) and medial prefrontal cortex (mPFC) are heavily implicated in salience and novelty processing, and specifically, the processing of taste sensory information. Here, we examined the role of aIC-mPFC reciprocal connectivity in novel taste neophobia and memory formation, in mice. Using pERK and neuronal intrinsic properties as markers for neuronal activation, and retrograde AAV (rAAV) constructs for connectivity, we demonstrate a correlation between aIC-mPFC activity and novel taste experience. Furthermore, by expressing inhibitory chemogenetic receptors in these projections, we show that aIC-to-mPFC activity is necessary for both taste neophobia and its attenuation. However, activity within mPFC-to-aIC projections is essential only for the neophobic reaction but not for the learning process. These results provide an insight into the cortical circuitry needed to detect, react to- and learn salient stimuli, a process critically involved in psychiatric disorders.


title: Naturalistic Audiovisual Stimulation Reveals the Topographic Organization of Human Auditory Cortex

abstract: Despite the importance of audition in spatial, semantic, and social function, there is no consensus regarding the detailed organisation of human auditory cortex. Using a novel computational model to analyse a high-powered naturalistic audiovisual movie-watching dataset, we simultaneously estimate spectral tuning properties and category selectivity to reveal the modes of organisation and computational motifs that characterise human auditory cortex. We find that regions more remote from the auditory core exhibit more compressive, non-linear response properties and finely-tuned, speech-selective receptive fields in low frequency portions of the tonotopic map. These patterns of organisation mirror aspects of the visual cortical hierarchy, wherein tuning properties progress from a stimulus category-agnostic  front end towards more advanced regions increasingly optimised for behaviorally relevant stimulus categories.


title: Novel microbial syntrophies identified by longitudinal metagenomics

abstract:
Identifying species interactions in a microbial community and how this relates to community function is a key challenge. Towards addressing this challenge, we present here an extensive genome-resolved, longitudinal dataset and associated metadata. We collected weekly samples of microbial communities and recorded operating conditions from industrial methane producing anaerobic digestion reactors for a year. This allowed us to recover 2240 dereplicated metagenome assembled genomes (dMAGs), together with their coverage dynamics and functional annotations from which functional traits were inferred. Of these dMAGs, 1910 were novel species, with 22 representing novel orders and classes. Methanogenic communities are expected to be strongly structured by syntrophic and other associations between the methanogens and syntrophs that produce their substrates. We identified 450 potential syntrophic dMAGs by searching for pairs of methanogenic and non-methanogenic dMAGs that had highly correlated time-series. Genomes of potential syntrophs were enriched for oxidoreductases and sugar transport genes and there was a strong taxonomic signal in their associations with methanogens. Of particular note, we found that Bathyarchaeiea associated specifically with methanogens from the Thermoplasmata, and Thermococci classes. Same syntrophic associations were only rarely observed across multiple reactors, suggesting that syntrophies might be facultative, with particular strains within a species forming syntrophic associations only sometimes and not necessarily always with the same methanogenic partner. The presented results show that longitudinal metagenomics is a highly valuable approach for identifying species and their interactions in microbial communities.

One Sentence SummaryLongitudinal study of microbial communities identifies novel species and predicts their interactions and role in community function.


title: Reversal of the renal hyperglycemic memory by targeting sustained tubular p21 expression

abstract:
A major therapeutic obstacle in diabetes mellitus is the metabolic or hyperglycemic memory: the persistence of impaired organ function despite improvement of blood glucose. Therapies reversing the hyperglycemic memory and thus improving already established organ-dysfunction are lacking, but urgently needed considering the increasing prevalence of diabetes mellitus worldwide. Here we show that glucose-mediated changes in gene expression largely persist in diabetic kidney disease (DKD) despite reversing hyperglycemia. The senescence-associated cyclin-dependent kinase inhibitor p21 (Cdkn1a) was the top hit among genes persistently induced by hyperglycemia and was associated with sustained induction of the p53-p21 pathway. Persistent p21 induction was confirmed in various animal models, in several independent human samples and in in vitro models. Tubular p21 expression and urinary p21-levels were associated with DKD severity and remained elevated despite improved blood glucose levels in humans, suggesting that p21 may be a biomarker indicating persistent ("memorized") kidney damage. Glucose-mediated p21 induction and tubular senescence were enhanced in mice with reduced levels of the disease resolving protease activated protein C (aPC). Mechanistically, glucose-induced and sustained tubular p21 expression is linked with demethylation of its promoter and reduced DNMT1 expression. aPC reverses already established p21 expression independent of its anticoagulant function through receptor signaling. Accordingly, new pharmacological approaches specifically mimicking aPC signaling (3K3A-aPC, parmodulin-2) enabled the reversal of glucose-mediated sustained tubular p21 expression, tubular senescence, and DKD. Thus, p21-dependent tubular senescence contributes to the hyperglycemic memory but can be therapeutically targeted.

Single sentence summaryaPC signaling targets persistent p21 expression and tubular senescence and reverses the hyperglycemic memory in diabetic kidney disease.


title: A chromatin phase transition protects mitotic chromosomes against microtubule perforation

abstract: Dividing eukaryotic cells package extremely long chromosomal DNA molecules into discrete bodies to enable microtubule-mediated transport of one genome copy to each of the newly forming daughter cells1-3. Assembly of mitotic chromosomes involves DNA looping by condensin4-8 and chromatin compaction by global histone deacetylation9-13. While condensin confers mechanical resistance towards spindle pulling forces14-16, it is not known how histone deacetylation affects material properties and segregation mechanics of mitotic chromosomes. Here, we show how global histone deacetylation at the onset of mitosis induces a chromatin-intrinsic phase transition that endows chromosomes with specific characteristics necessary for their precise movement during cellular division. Deacetylation-mediated compaction of chromatin forms a structure dense in negative charge and allows mitotic chromosomes to resist perforation by microtubules as they are pushed to the metaphase plate. Hyperacetylated mitotic chromosomes lack a defined surface boundary, are frequently perforated by microtubules, and are prone to missegregation. Our study highlights the different contributions of DNA loop formation and chromatin-intrinsic phase separation to genome segregation in dividing cells.