title: Utilizing Multimodal Imaging to Visualize Potential Mechanism for Sudden Death in Epilepsy

abstract:
Sudden death in epilepsy, or SUDEP, is a fatal condition that accounts for more than 4000 deaths each year. Limited clinical and preclinical data on sudden death suggests critical contributions from autonomic, cardiac, and respiratory pathways. Recent animal (rat) studies on kainic acid induced seizure models explored a potential mechanism for such sudden and severe cardiorespiratory dysregulation being linked to acid reflux induced laryngospasm. Here, we expand on those previous investigations and utilize a multimodal approach to provide visual evidence of acid reflux-initiated laryngospasm and subsequent fatal cardiorespiratory distress in seizing rats.

We used systemic kainic acid to acutely induce seizure activity in Long Evans rats, under urethane anesthesia. We recorded electroencephalography (EEG), electrocardiography (ECG), chest plethysmography and esophageal pH signals during simultaneous fast MRI scans of the rat stomach and esophagus. MRI images, in conjunction with electrophysiology data were used to identify seizure progression, stomach acid movement up the esophagus, cardiorespiratory changes, and sudden death.

In all cases of sudden death, esophageal pH recordings alongside MRI images visualized stomach acid movement up the esophagus. Severe cardiac (ST segment elevation), respiratory (intermittent apnea) and brain activity (EEG narrowing due to hypoxia) changes were observed only after acid reached the larynx, which strongly suggests onset of laryngospasm following acid reflux. Additionally, absence of stomach acid in the esophagus of animals that survived acute seizure, provided evidence of a causal relationship between acid reflux and sudden death. The complimentary information coming from electrophysiology and fast MRI scans provided insight into the mechanism of esophageal reflux, laryngospasm, obstructive apnea, and subsequent sudden death in seizing animals. The results carry clinical significance as they outline a potential mechanism that may be relevant to SUDEP in humans.


title: Enhanced detection of nucleotide repeat mRNA with hybridization chain reaction

abstract: RNAs derived from expanded nucleotide repeats form detectable foci in patient cells and these foci are thought to contribute to disease pathogenesis. The most widely used method for detecting RNA foci is fluorescence in situ hybridization (FISH). However, FISH is prone to low sensitivity and photo-bleaching that can complicate data interpretation. Here we applied hybridization chain reaction (HCR) as an alternative approach to repeat RNA foci detection of GC-rich repeats in two neurodegenerative disorders: GGGGCC (G4C2) hexanucleotide repeat expansions in C9orf72 that cause amyotrophic lateral sclerosis and frontotemporal dementia (C9 ALS/FTD) and CGG repeat expansions in FMR1 that cause Fragile X-associated tremor/ataxia syndrome. We found that HCR of both G4C2 and CGG repeats has comparable specificity to traditional FISH, but is >40x more sensitive and shows repeat-length dependence in its intensity. HCR is better than FISH at detecting both nuclear and cytoplasmic foci in human C9 ALS/FTD fibroblasts, patient iPSC derived neurons, and patient brain samples. We used HCR to determine the impact of integrated stress response (ISR) activation on RNA foci number and distribution. G4C2 repeat RNA did not readily co-localize with the stress granule marker G3BP1, but ISR induction increased both the number of detectible nuclear RNA foci and the nuclear/cytoplasmic foci ratio in patient fibroblasts and patient derived neurons. Taken together, these data suggest that HCR can be a useful tool for detecting repeat expansion mRNA in C9 ALS/FTD and other repeat expansion disorders.

category: neuroscience


title: Multi-antigen recognition circuits overcome challenges of specificity, heterogeneity, and durability in T cell therapy for glioblastoma

abstract: Treatment of solid cancers with chimeric antigen receptor (CAR) T cells is plagued by the lack of target antigens that are both tumor-specific and homogeneously expressed. We show that multiantigen prime-and-kill recognition circuits have the flexibility and precision to overcome these challenges in attacking glioblastoma. A synNotch receptor that recognizes a specific priming antigen - the heterogeneous glioblastoma neoantigen EGFRvIII or a brain tissue-specific antigen - is used to locally induce expression of a CAR, enabling thorough but controlled tumor killing by targeting of homogeneous antigens that are not absolutely tumor specific. Moreover, regulated CAR expression maintains a higher fraction of the T cells in the naive-like state which is associated with higher durability in vivo. In summary, using circuits that integrate recognition of multiple imperfect but complementary antigens, we improve the specificity and persistence of T cells directed against glioblastoma, providing a general recognition strategy applicable to other solid tumors.

category: immunology


title: Site-directed crosslinking identifies the stator-rotor interaction surfaces in a hybrid bacterial flagellar motor

abstract: The bacterial flagellum is the motility organelle powered by a rotary motor. The rotor and stator elements of the motor are embedded in the cytoplasmic membrane. The stator units assemble around the rotor, and an ion flux (typically H+ or Na+) conducted through a channel of the stator induces conformational changes that generate rotor torque. Electrostatic interactions between the stator protein PomA in Vibrio (MotA in Escherichia coli) and the rotor protein FliG have been suggested by genetic analyses, but have not been demonstrated directly. Here, we used site-directed photo- and disulfide-crosslinking to provide direct evidence for the interaction. We introduced a UV-reactive amino acid, p-benzoyl-L-phenylalanine (pBPA), into the cytoplasmic region of PomA or the C-terminal region of FliG in intact cells. After UV irradiation, pBPA inserted at a number of positions formed a crosslink with FliG. PomA residue K89 gave the highest yield of crosslinks, suggesting that it is the PomA residue nearest to FliG. UV-induced crosslinking stopped motor rotation, and the isolated hook-basal body contained the crosslinked products. pBPA inserted to replace residues R281 or D288 in FliG formed crosslinks with the Escherichia coli stator protein, MotA. A cysteine residue introduced in place of PomA K89 formed disulfide crosslinks with cysteine inserted in place of FliG residues R281 and D288, and some other flanking positions. These results provide the first demonstration of direct physical interaction between specific residues in FliG and PomA/MotA.

category: microbiology


title: Transcriptomics provides a genetic signature of vineyard site with insight into vintage-independent regional wine characteristics

abstract:
In wine fermentations, the metabolic activity of both Saccharomyces cerevisiae and non-Saccharomyces organisms impact wine chemistry. Ribosomal DNA amplicon sequencing of grape musts has demonstrated that microorganisms occur non-randomly and are associated with the vineyard of origin, suggesting a role for the vineyard, grape, and wine microbiome in shaping wine fermentation outcomes. We used ribosomal DNA amplicon sequencing of grape must and RNA sequencing of primary fermentations to profile fermentations from 15 vineyards in California and Oregon across two vintages. We find that the relative abundance of fungal organisms detected by ribosomal DNA amplicon sequencing did not correlate with transcript abundance from those organisms within the RNA sequencing data, suggesting that the majority of the fungi detected in must by ribosomal DNA amplicon sequencing are not active during these inoculated fermentations. Additionally, we detect genetic signatures of vineyard site and region during fermentation that are predictive for each vineyard site, identifying nitrogen, sulfur, and thiamine metabolism as important factors for distinguishing vineyard site and region.

ImportanceThe wine industry generates billions of dollars of revenue annually, and economic productivity is in part associated with regional distinctiveness of wine sensory attributes. Microorganisms associated with grapes and wineries are influenced by region of origin, and given that some microorganisms play a role in fermentation, it is thought that microbes may contribute to the regional distinctiveness of wine. We show that while the presence of microbial DNA is associated with wine region and vineyard site, the presence of microbial DNA is not associated with gene expression of those microorganisms during fermentation. We further show that detected gene expression signatures associated with wine region and vineyard site provide a means to address differences in fermentations that may drive regional distinctiveness.


title: Topoisomerase 2b induces DNA breaks to regulate human papillomavirus replication

abstract: Topoisomerases regulate higher order chromatin structures through the transient breaking and re-ligating of one or both strands of the phosphodiester backbone of duplex DNA. TOP2{beta} is a type II topoisomerase that induces double strand DNA breaks at topological-associated domains (TADS) to relieve torsional stress arising during transcription or replication. TADS are anchored by CTCF and SMC1 cohesin proteins in complexes with TOP2{beta}. Upon DNA cleavage a covalent intermediate DNA-TOP2{beta} (TOP2{beta}cc) is transiently generated to allow for strand passage. The tyrosyl-DNA phosphodiesterase TDP2 can resolve TOP2{beta}cc but failure to do so quickly can lead to long-lasting DNA breaks. Given the role of CTCF/SMC1 proteins in the HPV life cycle we investigated if TOP2{beta} proteins contribute to HPV pathogenesis. Our studies demonstrated that levels of both TOP2{beta} and TDP2 were substantially increased in cells with high risk HPV genomes and this correlated with high amounts of DNA breaks. Knockdown of TOP2{beta} with shRNAs reduced DNA breaks by over 50% as determined through COMET assays. Furthermore this correlated with substantially reduced formation of repair foci such as {gamma}H2AX, pCHK1 and pSMC1 indicative of impaired activation of DNA damage repair pathways. Importantly, knockdown of TOP2{beta} also blocked HPV genome replication. Our previous studies demonstrated that CTCF /SMC1 factors associate with HPV genomes at sites in the late regions of HPV31 and these correspond to regions that also bind TOP2{beta}. This study identifies TOP2{beta} as responsible for enhanced levels of DNA breaks in HPV positive cells and as a regulator of viral replication.


title: Nectar bacteria stimulate pollen germination and bursting to enhance their fitness

abstract: For many flower visitors, pollen is the primary source of non-carbon nutrition, but pollen has physical defenses that make it difficult for consumers to access nutrients. Nectar-dwelling microbes are nearly ubiquitous among flowers and can reach high densities, despite the fact that floral nectar is nitrogen limited, containing only very low concentrations of non-carbon nutrients. Pollen contains trace micronutrients and high protein content but is protected by a recalcitrant outer shell. Here, we report that a common genus of nectar-dwelling bacteria, Acinetobacter, exploits pollen nutrition by inducing pollen germination and bursting. We use time course germination assays to quantify the effect of Acinetobacter species on pollen germination and pollen bursting. Inoculation with Acinetobacter species resulted in increased germination rates within 15 minutes, and bursting by 45 minutes, as compared to uninoculated pollen. The pollen germination and bursting phenotype is density-dependent, with lower concentrations of A. pollinis SCC477 resulting in a longer lag time before the spike in germination, which is then closely followed by a spike in bursting. Lastly, A. pollinis grows to nearly twice the density with germinable pollen vs ungerminable pollen, indicating that their ability to induce and exploit germination plays an important role in rapid growth. To our knowledge, this is the first direct test of non-plant biological induction of pollen germination, as well as the first evidence of induced germination as a method of nutrient procurement, as the microbes appear to hijack the pollens normally tightly controlled germination mechanisms for their benefit. Our results suggest that further study of microbe-pollen interactions may inform many aspects of pollination ecology, including microbial ecology in flowers, the mechanisms of pollinator nutrient acquisition from pollen, and cues of pollen germination for plant reproduction.

category: ecology


title: Substantial intraspecific variation in energy budgets: biology or artefact?

abstract:
O_LIDynamic energy budget (DEB) models provide a mechanistic description of life-histories in terms of fluxes of energy through biological processes. In these models, life-histories are a function of environmental conditions and of fundamental traits of the organism relating to the acquisition, allocation, and use of energy.
C_LIO_LIThese traits are described by the parameters of the DEB model, which have been estimated for over 2500 species. Recent work has aimed to compare species on the basis of differences in DEB parameters.
C_LIO_LIWe show that caution is required in such analyses, because (i) parameter estimates vary considerably as an artefact of the types of data used to fit the models, and (ii) there is substantial intraspecific variation in parameter values, reflecting biological differences among populations.
C_LIO_LIWe show that similar patterns of growth and reproduction can be reproduced with very different parameter sets. Our results imply that direct comparison of DEB parameters across populations or species may be invalid. However, valid comparisons are possible if differences in the types of data used to fit the models are taken into account.
C_LIO_LIWe estimated DEB parameters for 16 populations of Trinidadian guppy, identifying differences in resource allocation and metabolic rate consistent with evolved life-history differences among these populations.
C_LIO_LIVariation in parameter values was substantial: if intraspecific variation in DEB parameters is greater than currently measured levels of interspecific variation, the detection of broad-scale patterns in energy budgets across species will be challenging.
C_LI

category: evolutionary biology


title: Allopatric divergence limits cheating range and alters genetic requirements for a cooperative trait

abstract:
Social defectors may meet diverse cooperators. Genotype-by-genotype interactions may constrain the ranges of cooperators upon which particular defectors can cheat, limiting cheater spread. The bacterium Myxococcus xanthus undergoes cooperative multicellular development, but some developmental defectors cheat on cooperators during this process. In this study, interactions between a cheater disrupted at the signaling gene csgA and allopatrically diversified cooperators reveal a very small cheating range. Expectedly, the cheater failed to cheat on all natural-isolate cooperators owing to non-cheater-specific antagonisms. Surprisingly, lab-evolved cooperators that diverged from their cheating-susceptible ancestor by fewer than 20 mutations and without experiencing cheating had already exited the csgA mutants cheating range. Cooperators might also diversify in the potential for a mutation to reduce expression of cooperative trait or generate a cheating phenotype. A new csgA mutation constructed in several highly diverged cooperators generated diverse sporulation phenotypes, ranging from a complete defect to no defect, indicating that genetic backgrounds can limit the set of genomes in which a mutation creates a defector. Our results suggest that natural populations feature geographic mosaics of cooperators that have diversified in their susceptibility to particular cheaters and in the phenotypes generated by any given cooperation-gene mutation.

Significance statementSelection on cooperators exploited by obligate cheaters can induce evolution of resistance to cheating. Here we show that cooperators can also rapidly evolve immunity to cheating simply as a byproduct of evolutionary divergence in environments in which cooperation and cheating at the focal trait do not occur because the trait is not expressed. We also find that differences in the genomic context in which a cooperation-gene mutation arises can profoundly alter its phenotypic effect and determine whether the mutation generates a social defect at all - a pre-requisite for obligate cheating. These findings suggest that general divergence of social populations under a broad range of environmental conditions can restrict both the set of mutations that might generate social defectors in the first place and the host range of such defectors once they arise.


title: Allopatric divergence of cooperators limits cheating range and effects of a defector mutation


title: Allopatric divergence of cooperators confers cheating resistance and limits the effects of a defector mutation


title: Oxidative stress alters transcript localization of disease-causing genes in the retinal pigment epithelium

abstract: Nuclear retention is a mechanism whereby RNA transcripts are held in the nucleus to maintain a proper nuclear-to-cytoplasmic balance or as a stockpile for use in responding to stimuli. Many mechanisms are employed to determine whether transcripts are retained or exported to the cytoplasm, though the extent to which tissue- or cell-type, stressors, or disease pathogenesis affect this process remains unclear. As the most biochemically active tissue in the body, the retina must mitigate endogenous and exogenous stressors to maintain cell health and tissue function. Oxidative stress, believed to contribute to the pathogenesis, or progression, of age-related macular degeneration (AMD) and inherited retinal dystrophies (IRDs), is produced both internally from biochemical processes, as well as externally from environmental insult. To evaluate the effect of oxidative stress on transcript localization in the retinal pigment epithelium (RPE), we performed poly-A RNA sequencing on nuclear and cytoplasmic fractions from induced pluripotent stem cell-derived retinal pigment epithelium (iPSC-RPE) cells exposed to hydrogen peroxide, as well as untreated controls. Under normal conditions, the number of mRNA transcripts retained in the nucleus exceeded that found in studies of other tissues. Further, the nuclear-to-cytoplasmic ratio of transcripts is altered following oxidative stress, as is the retention of genes associated with AMD, IRDs, and those important for RPE physiology. These results provide a retention catalog of all expressed mRNA in iPSC-RPE under normal conditions and after exposure to hydrogen peroxide, offering insight into one of the potential roles oxidative stress plays in the progression of visual disorders.

category: genetics


title: To denoise or to cluster? That is not the question. Optimizing pipelines for COI metabarcoding and metaphylogeography

abstract: The recent blooming of metabarcoding applications to biodiversity studies comes with some relevant methodological debates. One such issue concerns the treatment of reads by denoising or by clustering methods, which have been wrongly presented as alternatives. It has also been suggested that denoised sequence variants should replace clusters as the basic unit of metabarcoding analyses, missing the fact that sequence clusters are a proxy for species-level entities, the basic unit in biodiversity studies. We argue here that methods developed and tested for ribosomal markers have been uncritically applied to highly variable markers such as cytochrome oxidase I (COI) without conceptual or operational (e.g., parameter setting) adjustment. COI has a naturally high intraspecies variability that should be assessed and reported, as it is a source of highly valuable information. We contend that denoising and clustering are not alternatives. Rather, they are complementary and both should be used together in COI metabarcoding pipelines. Using a typical dataset from benthic marine communities, we compared two denoising procedures (based on the UNOISE3 and the DADA2 algorithms), set suitable parameters for denoising and clustering COI datasets, and compared the outcome of applying these processes in different orders. Our results indicate that denoising based on the UNOISE3 algorithm preserves a higher intra-cluster variability. We suggest and test ways to improve this algorithm taking into account the natural variability of each codon position in coding genes. The order of the steps (denoising and clustering) has little influence on the final outcome. We recommend researchers to consider reporting their results in terms of both denoised sequences (a proxy for haplotypes) and clusters formed (a proxy for species), and to avoid collapsing the sequences of the latter into a single representative. This will allow studies at the cluster (ideally equating species-level diversity) and at the intra-cluster level, and will ease additivity and comparability between studies.


title: Therapeutic adenine base editing corrects nonsense mutation and improves visual function in a mouse model of Leber congenital amaurosis

abstract: Leber congenital amaurosis (LCA) is an inherited retinal degeneration that causes severe visual dysfunction in children and adolescents. In patients with LCA, pathogenic variants are evident in specific genes, such as RPE65, which are related to the functions of retinal pigment epithelium and photoreceptors. Base editing confers a way to correct pathogenic substitutions without double-stranded breaks in contrast to the original Cas9. In this study, we prepared dual adeno-associated virus vectors containing the split adenine base editors with trans-splicing intein (AAV-ABE) for in vivo adenine base editing in retinal degeneration 12 (rd12) mice, an animal model of LCA, which possess a nonsense mutation of C to T transition in the Rpe65 gene (p.R44X). AAV-ABE induced an A to G transition in retinal pigment epithelial cells of rd12 mice when injected into the subretinal space. The on-target editing was sufficient to recover wild-type mRNA, RPE65 protein, and light-induced electrical responses of retinal tissues. We suggest adenine base editing to correct pathogenic variants in the treatment of LCA.


title: Z4-11Al mediates olfactory attraction and courtship in Drosophila melanogaster

abstract:
Specific mate communication and recognition underlies reproduction and hence speciation. Mate communication evolves during adaptation to ecological niches and makes use of social signals and habitat cues.

Our study provides new insights in Drosophila melanogaster premating olfactory communication, showing that female pheromone (Z)-4-undecenal (Z4-11Al) and male pheromone cVA interact with food odour in a sex-specific manner. Furthermore, Z4-11Al, which mediates upwind flight attraction in both sexes, also elicits courtship in experienced males.

Twin variants of the olfactory receptor Or69a are co-expressed in the same olfactory sensory neurons, and feed into the same glomerulus in the antennal lobe. Z4-11Al is perceived via Or69aB, while the food odorant (R)-linalool is a main ligand for the other variant, Or69aA. That Z4-11Al mediates courtship in experienced males, not (R)- linalool, is probably due to courtship learning. Behavioural discrimination is reflected by calcium imaging of the antennal lobe, showing distinct glomerular activation patterns by these two compounds.

Male sex pheromone cVA is known to affect male and female courtship at close range, but does not elicit upwind flight attraction as a single compound, in to contrast to Z4-11Al. A blend of cVA and the food odour vinegar attracted females, while a blend of female pheromone Z4-11Al and vinegar attracted males instead.

Sex-specific upwind flight attraction to blends of food volatiles and male and female pheromone, respectively, adds a new element to Drosophila olfactory premating communication and is an unambiguous paradigm for identifying the behaviourally active components, towards a more complete concept of food-pheromone odour objects.

SummaryThe female-produced, species-specific volatile pheromone of D. melanogaster attracts both sexes from a distance, alone and in concert with food odorants, and elicits courtship in experienced males.

category: animal behavior and cognition


title: The female pheromone (Z)-4-undecenal mediates flight attraction and courtship in Drosophila melanogaster


title: Impact of gene annotation choice on the quantification of RNA-seq data

abstract: RNA sequencing is currently the method of choice for genome-wide profiling of gene expression. A popular approach to quantify expression levels of genes from RNA-seq data is to map reads to a reference genome and then count mapped reads to each gene. Gene annotation data, which include chromosomal coordinates of exons for tens of thousands of genes, are required for this quantification process. There are several major sources of gene annotations that can be used for quantification, such as Ensembl and RefSeq databases. However, there is very little understanding of the effect that the choice of annotation has on the accuracy of gene expression quantification in an RNA-seq analysis. In this paper, we present results from our comparison of Ensembl and RefSeq human annotations on their impact on gene expression quantification using a benchmark RNA-seq dataset generated by the SEquencing Quality Control (SEQC) consortium. We show that the use of RefSeq gene annotation models led to better quantification accuracy, based on the correlation with ground truths including expression data from >800 real-time PCR validated genes, known titration ratios of gene expression and microarray expression data. We also found that the recent expansion of the RefSeq annotation has led to a decrease in its annotation accuracy. Finally, we demonstrated that the RNA-seq quantification differences observed between different annotations were not affected by the use of different normalization methods.

category: bioinformatics


title: A Self-Supervised Machine Learning Approach for Objective Live Cell Segmentation and Analysis

abstract: Machine learning algorithms hold the promise of greatly improving live cell image analysis by way of (1) analyzing far more imagery than can be achieved by more traditional manual approaches and (2) by eliminating the subjective nature of researchers and diagnosticians selecting the cells or cell features to be included in the analyzed data set. Currently, however, even the most sophisticated model based or machine learning algorithms require user supervision, meaning the subjectivity problem is not removed but rather incorporated into the algorithms initial training steps and then repeatedly applied to the imagery. To address this roadblock, we have developed a self-supervised machine learning algorithm that recursively trains itself directly from the live cell imagery data, thus providing objective segmentation and quantification. The approach incorporates an optical flow algorithm component to self-label cell and background pixels for training, followed by the extraction of additional feature vectors for the automated generation of a cell/background classification model. Because it is self-trained, the software has no user-adjustable parameters and does not require curated training imagery. The algorithm was applied to automatically segment cells from their background for a variety of cell types and five commonly used imaging modalities - fluorescence, phase contrast, differential interference contrast (DIC), transmitted light and interference reflection microscopy (IRM). The approach is broadly applicable in that it enables completely automated cell segmentation for long-term live cell phenotyping applications, regardless of the input imagerys optical modality, magnification or cell type.


title: dynUGENE: an R package for uncertainty-aware gene regulatory network inference, simulation, and visualization

abstract: Methods for gene regulatory network inference focus on network architecture identification but neglect model selection and simulation. We implement an extension to the dynGENIE3 algorithm that accounts for model uncertainty as an R package, providing users with an easy to use interface for model selection and gene expression profile simulation. Source code is available at https://github.com/tianyu-lu/dynUGENE with a detailed user guide. A webserver with interactive controls is available at https://tianyulu.shinyapps.io/dynUGENE/.


title: Cancer phylogenetics using single-cell RNA-seq data

abstract: AO_SCPLOWBSTRACTC_SCPLOWPhylogenetic methods are emerging as a useful tool to understand cancer evolutionary dynamics, including tumor structure, heterogeneity, and progression. Most currently used approaches utilize either bulk whole genome sequencing (WGS) or single-cell DNA sequencing (scDNA-seq) and are based on calling copy number alterations and single nucleotide variants (SNVs). Here we explore the potential of single-cell RNA sequencing (scRNA-seq) to reconstruct cancer evolutionary dynamics. scRNA-seq is commonly applied to explore differential gene expression of cancer cells throughout tumor progression. The method exacerbates the single-cell sequencing problem of low yield per cell with uneven expression levels. This accounts for low and uneven sequencing coverage and makes SNV detection and phylogenetic analysis challenging. In this paper, we demonstrate for the first time that scRNA-seq data contains sufficient evolutionary signal and can be utilized in phylogenetic analyses. We explore and compare results of such analyses based on both expression levels and SNVs called from scRNA-seq data. Both techniques are shown to be useful for reconstructing phylogenetic relationships between cells, reflecting the clonal composition of a tumor. Both standardized expression values and SNVs appear to be equally capable of reconstructing a similar pattern of phylogenetic relationship. This pattern is stable even when phylogenetic uncertainty is taken in account. Our results open up a new direction of somatic phylogenetics based on scRNA-seq data. Further research is required to refine and improve these approaches to capture the full picture of somatic evolutionary dynamics in cancer.

category: cancer biology


title: Testing for phylogenetic signal in single-cell RNA-seq data


title: GLS-driven glutamine catabolism contributes to prostate cancer radiosensitivity by regulating the redox state, stemness and ATG5-mediated autophagy

abstract: Radiotherapy is one of the curative treatment options for localized prostate cancer (PCa). The curative potential of radiotherapy is mediated by irradiation-induced oxidative stress and DNA damage in tumor cells. However, PCa radiocurability can be impeded by tumor resistance mechanisms and normal tissue toxicity. Metabolic reprogramming is one of the major hallmarks of tumor progression and therapy resistance. Here, we found that radioresistant PCa cells and prostate cancer stem cells (CSCs) have a high glutamine demand. Glutaminase (GLS)-driven catabolism of glutamine serves not only for energy production but also for the maintenance of the redox state. Consequently, glutamine depletion or inhibition of critical regulators of glutamine utilization, such as glutaminase (GLS) and the transcription factor MYC results in PCa radiosensitization. On the contrary, we found that a combination of glutamine metabolism inhibitors with irradiation does not cause toxic effects on nonmalignant prostate cells. Glutamine catabolism contributes to the maintenance of CSCs through regulation of the alpha-ketoglutarate (-KG)-dependent chromatin-modifying dioxygenase. The lack of glutamine results in the inhibition of CSCs with a high aldehyde dehydrogenase (ALDH) activity, decreases the frequency of the CSC populations in vivo and reduces tumor formation in xenograft mouse models. Moreover, this study shows that activation of the ATG5-mediated autophagy in response to a lack of glutamine is a tumor survival strategy to withstand radiation-mediated cell damage. In combination with autophagy inhibition, the blockade of glutamine metabolism might be a promising strategy for PCa radiosensitization. High blood levels of glutamine in PCa patients significantly correlate with a shorter prostate-specific antigen (PSA) doubling time. Furthermore, high expression of critical regulators of glutamine metabolism, GLS1 and MYC, is significantly associated with a decreased progression-free survival in PCa patients treated with radiotherapy. Our findings demonstrate that GLS-driven glutaminolysis is a prognostic biomarker and therapeutic target for PCa radiosensitization.


title: IRGM/Irgm1 Aggravates Progression of Atherosclerosis by Inducing Macrophage Apoptosis

abstract:
AimsAtherosclerosis underlies most cardiovascular diseases, among which acute coronary syndrome (ACS) caused by plaque rupture (PR) often leads to death. Immune-related GTPases (IRGM/Irgm1) have been extensively studied in inflammatory diseases, but their role in atherosclerosis is unclear. Determining how IRGM/Irgm1 promotes atherosclerotic plaque vulnerability will provide information for new biomarkers and/or therapeutic targets.

Methods and resultsWe identified ruptured and unruptured plaques by optical coherence tomography, and found that serum IRGM was highly expressed in patients with ST-segment elevation myocardial infarction in PR. We used ApoE-/-Irgm1+/+, ApoE-/-Irgm1+/- mice and chimeric mice to establish a model of advanced atherosclerosis. The results of pathological experiments showed that Irgm1 caused plaque necrosis. The ratio of neutral lipids and cholesterol crystals increases, while the content of collagen fibers decreases, aggravating the destabilization of atherosclerotic plaques. In vitro, we used multiple approaches to confirm that Irgm1 promotes macrophage apoptosis by promoting the production of reactive oxygen species and activating the MAPK signaling pathway.

ConclusionsIRGM may be a potential risk factor for PR. Mechanistic studies have shown that IRGM/Irgm1 contributes to the formation and rupture of fragile plaques. This is partly mediated by the induction of macrophage apoptosis via the MAPK signaling pathway. IRGM may offer new strategies for early treatment of ACS.

Translation viewOur findings indicate that IRGM/Irgm1 contributes to formation and rupture of vulnerable plaques. It suggests that IRGM may provide a new target for the early treatment of ACS.

category: pathology


title: IRGM/Irgm1 Aggravates Progression of Atherosclerosis by Inducing Macrophage Apoptosis through the MAPK Signaling Pathway


title: Institutional Differences in the Stewardship and Research Output of United States Herbaria

abstract: Public policy decisions regarding institutional frameworks that govern the stewardship of biodiversity data at public and private institutions are an area of increasing importance. Museums, government agencies, and academic institutions across the United States maintain collections of biological specimens and information critical to scientific discovery. One subset of these natural history collections are herbaria, or collections of preserved plant matter and their associated data. In this study, I evaluate the current state of the digitization and databasing of herbariums contributing data to the SEInet Regional Network of North American Herbaria, and assess the impact of characteristics, particularly institution type (cultural sector institutions, public universities, private universities, or public land institutions), on the metrics of herbaria richness, digitization, and research usage. The results of this study suggest that institution type is significantly associated with the size, diversity, and digitization efforts of a herbarium collection. Specifically, cultural sector institutions tend to have larger and more diverse collections, followed by public and private universities, and finally public land institutions. Additionally, as herbarium size and richness increases, the research output of associated staff also increases. These results highlight that some institutions, particularly larger institutions located at universities or cultural sector institutions, may be better supported in the curation, stewardship, and digitization of large collections, allowing long-term access to the associated biodiversity data. Smaller institutions at public land institutions may need additional support in these endeavors, and may represent an area of unmet needs for digitization and curatorial funding and resources.

category: plant biology


title: A class I hydrophobin in Trichoderma virens influences plant-microbe interactions through enhancement of enzyme activity and MAMP recognition

abstract: The filamentous fungus, Trichoderma virens, is a well-known mycoparasitic plant symbiont, valued for its biocontrol capabilities. T. virens initiates a symbiotic relationship with a plant host through the colonization of its roots. To achieve colonization, the fungus must communicate with the host and evade its innate defenses. Hydrophobins from Trichoderma spp. have previously been demonstrated to be involved in colonization of host roots. In this study, the class I hydrophobin, HFB9A from T. virens was characterized for a potential role in root colonization. {Delta}hfb9a gene deletion mutants colonized less than the wild-type strain, were unable to induce systemic resistance against Colletotrichum graminicola, and showed a reduction in the activity of its cell wall degrading enzymes. The purified HFB9A protein was able to complement the enzyme activity of mutant culture filtrates as well as enhance the activity of commercially sourced cellulase. When exogenously applied to Arabidopsis plants, HFB9A protein induced phosphorylation of AtMAPK3/6, suggesting that it functions as a microbe-associated molecular pattern.


title: Synthetic Promoter Designs Enabled by a Comprehensive Analysis of Plant Core Promoters

abstract: Targeted engineering of plant gene expression holds great promise for ensuring food security and for producing biopharmaceuticals in plants. However, this engineering requires thorough knowledge of cis-regulatory elements in order to precisely control either endogenous or introduced genes. To generate this knowledge, we used a massively parallel reporter assay to measure the activity of nearly complete sets of promoters from Arabidopsis, maize and sorghum. We demonstrate that core promoter elements - notably the TATA-box - as well as promoter GC content and promoter-proximal transcription factor binding sites influence promoter strength. By performing the experiments in two assay systems, leaves of the dicot tobacco and protoplasts of the monocot maize, we detect species-specific differences in the contributions of GC content and transcription factors to promoter strength. Using these observations, we built computational models to predict promoter strength in both assay systems, allowing us to design highly active promoters comparable in activity to the viral 35S minimal promoter. Our results establish a promising experimental approach to optimize native promoter elements and generate synthetic ones with desirable features.


title: A role for prefoldins in H2A.Z deposition in Arabidopsis

abstract: The prefoldin complex (PFDc) participates in cellular proteostasis in eukaryotes by acting as cochaperone of the chaperonin CTT. This role is mainly exerted in the cytoplasm where it contributes to the correct folding of client proteins, thus preventing them to form aggregations and cellular damage. Several reports indicate, however, that they also play a role in transcriptional regulation in the nucleus in several model species. In this work, we have investigated how extended is the role of PFDs in nuclear processes by inspecting their interactome and their coexpression networks in yeast, fly, and humans. The analysis indicates that they may perform extensive, conserved functions in nuclear processes. The construction of the predicted interactome for Arabidopsis PFDs, based on the ortholog interactions, has allowed us to identify many putative PFD interactors linking them to unanticipated processes, such as chromatin remodeling. Based on this analysis, we have investigated the role of PFDs in H2A.Z deposition through their interaction with the chromatin remodeling complex SWR1c. Our results show that PFDs have a positive effect on SWR1c, which is reflected in defects in H2A.Z deposition in hundreds of genes in seedlings defective in PFD3 and PFD5 activities.


title: Identification of hub molecules of FUS-ALS by Bayesian gene regulatory network analysis of iPSC model: iBRN

abstract:
Fused in sarcoma/translated in liposarcoma (FUS) is a causative gene of amyotrophic lateral sclerosis (ALS). Mutated FUS causes accumulation of DNA damage and cytosolic stress granule (SG) formation, thereby motor neuron (MN) death. However, key molecular aetiology remains unclear. Here, we applied a novel platform technology, iBRN, "Non-biased" Bayesian gene regulatory network analysis based on induced pluripotent stem cell (iPSC)-derived cell model, to elucidate the molecular aetiology using transcriptome of iPSC-derived MNs harboring FUSH517D. iBRN revealed "hub molecules", which strongly influenced transcriptome network, such as miR-125b-5p-TIMELESS axis and PRKDC for the molecular aetiology. Next, we confirmed miR-125b-5p-TIMELESS axis in FUSH517D MNs such that miR-125b-5p regulated several DNA repair-related genes including TIMELESS. In addition, we validated both introduction of miR-125b-5p and knocking down of TIMELESS caused DNA damage in the cell culture model. Furthermore, PRKDC was strongly associated with FUS mis-localization into SGs by DNA damage under impaired DNA-PK activity. Collectively, our iBRN strategy provides the first compelling evidence to elucidate molecular aetiology in neurodegenerative diseases.

HighlightsO_LIA new platform technology, "iBRN", Bayesian gene regulatory network analysis based on iPSC cells
C_LIO_LIiBRN identifies hub molecules to strongly influence the gene network in FUS-ALS
C_LIO_LIPRKDC specifically acts as a guardian against FUS mis-localization during DNA damage stress
C_LIO_LImiR-125b-5p-TIMELESS axis regulates DNA repair-related genes in FUS-ALS.
C_LI


title: Differential encoding of safe and risky offers

abstract: Common currency theories in neuroeconomics hold that neurons in specific brain regions specifically encode subjective values of offers and not stimulus-specific information. The rationale behind these theories is that abstract value encoding lets the decision maker compare qualitatively different options. Alternatively, expectancy-based theories hold that the brain preferentially tracks the relationship between options and their outcomes, and thus does not abstract away details of offers. To adjudicate between these theories, we examined responses of neurons in six reward regions to risky and safe offers while macaques performed a gambling task. In all regions, responses to safe options are unrelated to responses evoked by equally preferred risky options. Nor does any region appear to contain a specialized subset of value-selective neurons. Finally, in all regions, responses to risky and safe options occupy distinct response subspaces, indicating that the organizational framework for encoding risky and safe offers is different. Together, these results argue against the idea that putative reward regions carry abstract value signals, and instead support the idea that these regions carry information that links specific options to their outcomes in support of a broader cognitive map.


title: Heart rate variability predicts decline in sensorimotor rhythm control

abstract: Voluntary control of sensorimotor rhythms (SMR, 8-12 Hz) can be used for brain-computer interface (BCI)-based operation of an assistive hand exoskeleton, e.g., in finger paralysis after stroke. To gain SMR control, stroke survivors are usually instructed to engage in motor imagery (MI) or to attempt moving the paralyzed fingers resulting in task- or event-related desynchronization (ERD) of SMR (SMR-ERD). However, as these tasks are cognitively demanding, especially for stroke survivors suffering from cognitive impairments, BCI control performance can deteriorate considerably over time. It would thus be important to identify biomarkers that predict decline in BCI control performance within an ongoing session in order to optimize the man-machine interaction scheme. Here we determine the link between BCI control performance over time and heart rate variability (HRV). Specifically, we investigated whether HRV can be used as a biomarker to predict decline during voluntary control of SMR-ERD across 17 healthy participants using Granger causality. SMR-ERD was visually displayed on a screen. Participants were instructed to engage in MI-based SMR-ERD control over two consecutive runs of 8.5 minutes each. During the second run, task difficulty was gradually increased. While control performance (p = .18) and HRV (p = .16) remained unchanged across participants during the first run, during the second run, both measures declined over time at high correlation (performance: -0.61%/10s, p = 0; HRV: -0.007ms/10s, p < .001). We found that HRV Granger-caused BCI control performance (p < .001) exhibited predictive characteristics of HRV on an individual participant level. These results suggest that HRV can predict decline in BCI performance paving the way for adaptive BCI control paradigms, e.g., to individualize and optimize assistive BCI systems in stroke.


title: Commercial vaccines do not confer protection against two genetic strains of Piscirickettsia salmonis, LF-89-like and EM-90-like, in Atlantic salmon.

abstract: In Atlantic salmon, vaccines have failed to control and prevent Piscirickettsiosis, for reasons that remain elusive. In this study, we report the efficacy of a commercial vaccine developed with the Piscirickettsia salmonis isolate AL100005 against other two isolates which are considered highly and ubiquitously prevalent in Chile: LF-89-like and EM-90-like. Two cohabitation trials were performed to mimic real-life conditions and vaccine performance: 1) post smolt fish were challenged with a single infection of LF-89-like, 2) adults were coinfected with EM-90-like and a low coinfection of sea lice. In the first trial, the vaccine delayed smolt mortalities by two days; however, unvaccinated and vaccinated fish did not show significant differences in survival (unvaccinated: 60.3%, vaccinated: 56.7%; p = 0.28). In the second trial, mortality started three days later for vaccinated fish than unvaccinated fish. However, unvaccinated and vaccinated fish did not show significant differences in survival (unvaccinated: 64.6%, vaccinated: 60.2%, p= 0.58). Thus, we found no evidence that the evaluated vaccines confer effective protection against of LF-89-like or EM-90-like with estimated relative survival proportions (RPSs) of -9% and -12%, respectively. More studies are necessary to evaluate whether pathogen heterogeneity is a key determinant of the vaccine efficacy against P. salmonis.


title: Leishmania donovani metacyclic promastigotes impair phagosome properties in inflammatory monocytes

abstract: Leishmaniasis, a debilitating disease with clinical manifestations ranging from self-healing ulcers to life-threatening visceral pathologies, is caused by protozoan parasites of the Leishmania genus. These professional vacuolar pathogens are transmitted by infected sand flies to mammalian hosts as metacyclic promastigotes and are rapidly internalized by various phagocyte populations. Classical monocytes are among the first myeloid cells to migrate to infection sites. Recent evidence shows that recruitment of these cells contributes to parasite burden and to the establishment of chronic disease. However, the nature of Leishmania-inflammatory monocyte interactions during the early stages of host infection has not been well investigated. Here, we aimed to assess the impact of Leishmania donovani metacyclic promastigotes on antimicrobial responses within these cells. Our data showed that inflammatory monocytes were readily colonized by L. donovani metacyclic promastigotes, while infection with Escherichia coli was efficiently cleared. Upon internalization, metacyclic promastigotes inhibited superoxide production at the parasitophorous vacuole (PV) through a mechanism involving exclusion of NADPH oxidase subunits gp91phox and p47phox from the PV membrane. Moreover, we observed that unlike phagosomes enclosing zymosan particles, vacuoles containing parasites acidified poorly. Interestingly, whereas the parasite surface coat virulence glycolipid lipophosphoglycan was responsible for the inhibition of PV acidification, impairement of the NADPH oxidase assembly was independent of lipophosphoglycan and of the metalloprotease GP63. Collectively, these observations indicate that permissiveness of inflammatory monocytes to L. donovani may thus be related to the ability of this parasite to impair the microbicidal properties of phagosomes.


title: Hunting Eagles with glass mice: revisiting the inoculum effect for Streptococcus pyogenes with a hollow fibre infection model

abstract:
BackgroundSevere, invasive Streptococcus pyogenes (Strep A) infections result in greater than 500,000 deaths annually. First line treatment for such infections is combination benzylpenicillin and clindamycin, but treatment failure can occur with this regimen. This failure has been partially attributed to the inoculum effect, which presents as reduced antibiotic susceptibility during high bacterial density and plateau-phase growth. Hollow fibre infection models (HFIM) have been proposed as an alternative to in vivo research to study these effects.

ObjectivesTo re-evaluate the inoculum effect for benzylpenicillin, clindamycin, linezolid and trimethoprim-sulfamethoxazole using a Strep A HFIM.

MethodsDifferential antibiotic susceptibility of Strep A was measured in a HFIM starting from low- and high-density inocula. Dynamic antibiotic concentrations were delivered over 48 hours to simulate human pharmacokinetics. Differences in antibiotic susceptibility were determined at 24 and 48 hours by plate count of remaining viable colony-forming units.

ResultsInoculum effects were seen in benzylpenicillin and linezolid at 24 hours, and benzylpenicillin, linezolid and clindamycin at 48 hours. The effect size was greatest for continuously infused benzylpenicillin. No inoculum effect was seen in trimethoprim-sulfamethoxazole.

ConclusionsInoculum effects were seen in the HFIM model using benzylpenicillin, linezolid and clindamycin, which may predict reduced clinical efficacy following treatment delay. The model has proven robust and largely in agreeance with published data, recommending it for further Strep A study.


title: Targeted capture and sequencing of Orientia tsutsugamushi genomes from chiggers and humans

abstract: Scrub typhus is a febrile disease caused by Orientia tsutsugamushi, transmitted by larval stage Trombiculid mites (chiggers), whose primary hosts are small mammals. The phylogenomics of O. tsutsugamushi in chiggers, small mammals and humans remains poorly understood. To combat the limitations imposed by the low relative quantities of pathogen DNA in typical O. tsutsugamushi clinical and ecological samples, along with the technical, safety and cost limitations of cell culture, a novel probe-based target enrichment sequencing protocol was developed. The method was designed to capture variation among conserved genes and facilitate phylogenomic analysis at the scale of population samples. A whole-genome amplification step was incorporated to enhance the efficiency of sequencing by reducing duplication rates. This resulted in on-target capture rates of up to 93% for a diverse set of human, chigger, and rodent samples, with the greatest success rate in samples with real-time PCR Ct values below 35. Analysis of the best-performing samples revealed phylogeographic clustering at local, provincial and international scales. Applying the methodology to a comprehensive set of samples could yield a more complete understanding of the ecology, genomic evolution and population structure of O. tsutsugamushi and other similarly challenging organisms, with potential benefits in the development of diagnostic tests and vaccines.


title: Design-of-Experiments In Vitro Transcription Yield Optimization of Self-Amplifying RNA

abstract: Self-amplifying RNA (saRNA) vaccines are able to induce a higher antigen-specific immune response with a more cost-effective and rapid production process compared to plasmid DNA vaccines. saRNAs are synthesized through in vitro transcription (IVT) however; this process has mainly been optimized for relatively short mRNAs. Here, we optimized the IVT process for long saRNAs, approximately 9.4 kb through a design of experiment (DoE) approach to produce a maximal RNA yield and validated the optimal IVT method on various sizes of RNA. We found that magnesium has the highest impact on RNA yield with acetate ions enabling a higher yield than chloride ions. In addition, the interaction between magnesium and nucleoside triphosphates (NTPs) is highly essential for IVT. Further addition of sodium acetate (NaOAc) during IVT provided no added benefit in RNA yield. Moreover, pyrophosphatase was not essential for productive IVT. The optimal IVT method can be used to synthesize different lengths of RNA. These findings emphasize the ability to synthesize high quality and quantity of saRNA through IVT and that the optimal amount of each component is essential for their interactions to produce a high RNA yield.

category: molecular biology


title: Telomerase Prevents Emphysema in Old Mice by Sustaining Subpopulations of Endothelial and AT2 Cells

abstract: Accumulation of senescent cells has been causally linked to the development of age-related pathologies. Here, we characterized a new mouse model (p21+/Tert) whose telomerase (TERT) is expressed from the p21 promoter that can be activated in response to telomere dysfunction. Lung parenchyma from p21+/Tert old mice accumulated fewer senescent cells with age and this correlated with a reduction in age-related alveolar space enlargement, a feature of pulmonary emphysema. This protection against emphysema depends on TERT catalytic activity and is associated with increased proliferation of pulmonary endothelial cells (EC) and capillary density. Single-cell RNA sequencing of lung cells revealed that TERT expression was associated with the enrichment of ECs expressing genes involved in vessel regeneration and in AT2 cells overexpressing S/G2M markers. These findings indicate that p21-promoter-dependent expression of catalytically active telomerase prevents emphysema by sustaining the proliferation of subclasses of EC and AT2 cells.


title: Sexually Transmitted Infections Select for Different Levels of Immunocompetence And Reproductive Efforts in The Two Sexes

abstract: 1.Sex differences in immunity have been described in humans and other mammal species. Females have a lower incidence of infections and non-reproductive malignancies and exhibit higher antibody levels after vaccination. Existing evolutionary explanations are based on differences in reproductive strategies and reaction to extrinsic differences in susceptibility and virulence between the sexes. Here, we test the hypothesis that known differences in the probability of transmission and outcome of sexually transmitted infections contribute to sex differences in immunocompetence. We modelled reproductive and immune investments against a fertility limiting Sexually Transmitted Infection (STI). We show that, in line with previous findings, increased susceptibility selects for tolerance to the parasite while increased virulence selects for resistance against it. Differences in reproductive strategies between the sexes lead to sex differences in immunocompetence, mostly with higher competence in females. Extrinsic differences in susceptibility and virulence between the sexes can augment or alleviate the evolutionary consequences of intrinsic differences depending on their direction and magnitude. This indicates that the selection of sex-specific immune strategies is less predictable than thought before and explains why sex differences in immunity have been found to be not universal and pervasive across animal species.


title: Is Palmer's elm leaf goldenrod real? The Angiosperms353 kit provides within-species signal in Solidago ulmifolia s.l.

abstract: The genus Solidago represents a taxonomically challenging group due to its sheer number of species, putative hybridization, polyploidy, and shallow genetic divergence among species. Here we use a dataset obtained exclusively from herbarium specimens to evaluate the status of Solidago ulmifolia var. palmeri, a morphologically subtle taxon potentially confined to Alabama, Arkansas, Mississippi, and Missouri. A multivariate analysis of both discrete and continuous morphological data revealed no clear distinction between S. ulmifolia var. palmeri and Solidago ulmifolia var. ulmifolia. Solidago ulmifolia var. palmeris status was also assessed with a phylogenomic and SNP clustering analysis of data generated with the "Angiosperms353" probe kit. Neither analysis supported Solidago ulmifolia var. palmeri as a distinct taxon, and we suggest that this name should be discarded. The status of Solidago delicatula (formerly known as Solidago ulmifolia var. microphylla) was also assessed. Both morphological and phylogenic analyses supported the species status of S. delicatula and we suggest maintaining this species at its current rank. These results highlight the utility of the Angiosperms353 probe kit, both with herbarium tissue and at lower taxonomic levels. Indeed, this is the first study to utilize this kit to identify genetic groups within a species.


title: Monitoring the promoter activity of long noncoding RNAs and stem cell differentiation through knock-in of sgRNA flanked by tRNA in an intron

abstract: Mammalian genomes encode thousands of long noncoding RNAs (lncRNAs) that are often expressed in a tissue and cell specific manner. Therefore, a reporter that can faithfully reflect the expression or activity of lncRNAs can provide tools useful not only for uncovering the regulators of lncRNAs, but also for tracking cell fate and disease status. Here, we design a sgRNA precursor in an intron (GRIT) strategy that can monitor the promoter activity of lncRNAs. We used this strategy to report the expression of Lncenc1 and Neat1 in mouse embryonic stem cells (ESCs). Furthermore, we show that GRIT may be used to track differentiation status of stem cells. We anticipate that GRIT will be applicable in dissecting regulatory mechanisms underlying the transcription of lncRNAs, tracking cell fate switch during differentiation or disease progression and integrating the promoter activity of various RNAs for synthetic biology applications.


title: No evidence for general intelligence in a fish

abstract: Differences in human general intelligence or reasoning ability can be quantified with the psychometric factor g, because individual performance across cognitive tasks is positively correlated. g also emerges in mammals and birds, is correlated with brain size and may similarly reflect general reasoning ability and behavioural flexibility in these species. To exclude the alternative that these positive cross-correlations may merely reflect the general biological quality of an organism or an inevitable by-product of having brains it is paramount to provide solid evidence for the absence of g in at least some species. Here, we show that wild-caught cleaner fish Labroides dimidiatus, a fish species otherwise known for its highly sophisticated social behaviour, completely lacks g when tested on ecologically non-relevant tasks. Moreover, performance in these experiments was not or negatively correlated with an ecologically relevant task, and in none of the tasks did fish caught from a high population density site outperform fish from a low-density site. g is thus unlikely a default result of how brains are designed, and not an automatic consequence of variation in social complexity. Rather, the results may reflect that g requires a minimal brain size, and thus explain the conundrum why the average mammal or bird has a roughly 10 times larger brain relative to body size than ectotherms. Ectotherm brains and cognition may therefore be organized in fundamentally different ways compared to endotherms.


title: DeepFrag: A Deep Convolutional Neural Network for Fragment-based Lead Optimization

abstract: 1Machine learning has been increasingly applied to the field of computer-aided drug discovery in recent years, leading to notable advances in binding-affinity prediction, virtual screening, and QSAR. Surprisingly, it is less often applied to lead optimization, the process of identifying chemical fragments that might be added to a known ligand to improve its binding affinity. We here describe a deep convolutional neural network that predicts appropriate fragments given the structure of a receptor/ligand complex. In an independent benchmark of known ligands with missing (deleted) fragments, our DeepFrag model selected the known (correct) fragment from a set over 6,500 about 58% of the time. Even when the known/correct fragment was not selected, the top fragment was often chemically similar and may well represent a valid substitution. We release our trained DeepFrag model and associated software under the terms of the Apache License, Version 2.0. A copy can be obtained free of charge from http://durrantlab.com/deepfragmodel.

category: pharmacology and toxicology


title: Competitive outcomes between native and invasive plants are linked to shifts in the bacterial rhizosphere microbiome

abstract: Rhizosphere microbiomes have received growing attention in recent years for their role in plant health, stress tolerance, soil nutrition, and invasion. Still, relatively little is known about how these microbial communities are altered under plant competition, and even less about whether these shifts are tied to competitive outcomes between native and invasive plants. We investigated the structure and diversity of rhizosphere bacterial and fungal microbiomes of native annual forbs and invasive annual grasses individually and in competition using high-throughput amplicon sequencing of the bacterial 16S rRNA gene and the fungal ITS region. We assessed how differentially abundant microbial families correlate to plant biomass under competition We find that bacterial diversity and structure differ between native forbs and invasive grasses, but fungal diversity and structure do not. Further, bacterial community structures under competition are distinct from individual bacterial community structures. We also identified five bacterial families that varied in normalized abundance between treatments and that were correlated with plant biomass under competition. We speculate that invasive grass dominance over these natives may be partially due to effects on the rhizosphere community, with changes in specific bacterial families potentially benefiting invaders at the expense of natives.


title: Invasive grass dominance over native forbs is linked to shifts in the bacterial rhizosphere microbiome


title: Dimerisation of the PICTS complex via LC8/Cut-up drives co-transcriptional transposon silencing in Drosophila

abstract: In animal gonads, the PIWI-interacting RNA (piRNA) pathway guards genome integrity in part through the co-transcriptional gene silencing of transposon insertions. In Drosophila ovaries, piRNA-loaded Piwi detects nascent transposon transcripts and instructs heterochromatin formation through the Panoramix-induced co-transcriptional silencing (PICTS) complex, containing Panoramix, Nxf2 and Nxt1. Here, we report that the highly conserved dynein light chain LC8/Cut-up (Ctp) is an essential component of the PICTS complex. Loss of Ctp results in transposon de-repression and a reduction in repressive chromatin marks specifically at transposon loci. In turn, Ctp can enforce transcriptional silencing when artificially recruited to RNA and DNA reporters. We show that Ctp drives dimerisation of the PICTS complex through its interaction with conserved motifs within Panoramix. Artificial dimerisation of Panoramix bypasses the necessity for its interaction with Ctp, demonstrating that conscription of a protein from a ubiquitous cellular machinery has fulfilled a fundamental requirement for a transposon silencing complex.


title: Spatiotemporal Determination of Metabolite Activities in Multiple Corneal Epithelium Barriers on a Chip

abstract: The corneal epithelial barrier maintains the metabolic activities of the ocular surface by regulating membrane transporters and metabolic enzymes responsible for the homeostasis of the eye as well as the pharmacokinetic behavior of drugs. Despite its importance, no established biomimetic in vitro methods are available to perform the spatiotemporal investigation of corneal metabolism and determine the transportation of endogenous and exogenous molecules. This study introduces multiple corneal epithelium barriers on a chip, namely, Cornea-Chip, which enables the spatiotemporal collection as well as analysis of micro-scaled extracellular metabolites from both the apical and basolateral sides of the barriers. Longitudinal samples collected during 48 h period were analyzed using untargeted liquid chromatography-mass spectrometry metabolomics method, and 104 metabolites were annotated. The shifts in extracellular metabolites and quantitative analysis of the mRNA associated with membrane transporters could allow the investigation of the correlation between the expression of and the secretion and transportation of metabolites across the polarized corneal epithelial barrier. The Cornea-Chip might provide a non-invasive, simple, and effectively informative method to determine pharmacokinetics and pharmacodynamics as well as to discover novel biomarkers for drug toxicological and safety tests as an alternative to animal experiments.

category: bioengineering


title: UCsim2: 2D Structured Illumination Microscopy using UC2

abstract: State-of-the-art microscopy techniques enable the imaging of sub-diffraction barrier biological structures at the price of high-costs or lacking transparency. We try to reduce some of these barriers by presenting a super-resolution upgrade to our recently presented open-source optical toolbox UC2. Our new injection moulded parts allow larger builds with higher precision. The 4x lower manufacturing tolerance compared to 3D printing makes assemblies more reproducible. By adding consumer-grade available open-source hardware such as digital mirror devices (DMD) and laser projectors we demonstrate a compact 3D multimodal setup that combines image scanning microscopy (ISM) and structured illumination microscopy (SIM). We demonstrate a gain in resolution and optical sectioning using the two different modes compared to the widefield limit by imaging Alexa Fluor 647- and SiR-stained HeLa cells. We compare different objective lenses and by sharing the designs and manuals of our setup, we make super-resolution imaging available to everyone.

category: cell biology


title: HBO1-MLL interaction promotes AF4/ENL/P-TEFb-mediated leukemogenesis

abstract: Leukemic oncoproteins cause uncontrolled self-renewal of hematopoietic progenitors by aberrant gene activation, eventually causing leukemia. However, the molecular mechanism of aberrant gene activation remains elusive. Here, we showed that leukemic MLL fusion proteins associate with the HBO1 histone acetyltransferase (HAT) complex through their TRX2 domain. Among many MLL fusions, MLL-ELL particularly depended on its association with the HBO1 complex for leukemic transformation. The C-terminal portion of ELL provided a binding platform for multiple factors including AF4, EAF1 and p53. MLL-ELL activated gene expression by loading an AF4 /ENL/P-TEFb complex (AEP) onto the target promoters. The HBO1 complex promoted the use of AEP over EAF1 and p53. Moreover, the NUP98-HBO1 fusion protein exerted its oncogenic properties via interaction with MLL but not its intrinsic HAT activity. Thus, the interaction between HBO1 and MLL is an important nexus in leukemic transformation, which may serve as a therapeutic target for drug development.


title: Strong and tunable anti-CRISPR/Cas9 activity of AcrIIA4 in plants

abstract: This study describes the strong anti-CRISPR activity of the bacterial AcrIIA4 protein in Nicotiana benthamiana, a model plant used as molecular farming platform. The results demonstrate that AcrIIA4 abolishes site-directed mutagenesis in leaves when transiently co-expressed with CRISPR/Cas9. We also show that AcrIIA4 represses CRISPR/dCas9-based transcriptional activation (CRISPRa) of both reporter and endogenous genes in a highly efficient, dose-dependent manner. Furthermore, the fusion of an auxin degron to AcrIIA4 results in auxin-regulated activation of a downstream reporter gene. The strong anti-Cas9 activity of AcrIIA4 reported here opens new possibilities for customized control of gene editing and gene expression in plants.

category: synthetic biology


title: Humanization of antibodies using a machine learning approach on large-scale repertoire data

abstract: Monoclonal antibody therapeutics are often produced from non-human sources (typically murine), and can therefore generate immunogenic responses in humans. Humanization procedures aim to produce antibody therapeutics that do not elicit an immune response and are safe for human use, without impacting efficacy. Humanization is normally carried out in a largely trial-and-error experimental process. We have built machine learning classifiers that can discriminate between human and non-human antibody variable domain sequences using the large amount of repertoire data now available. Our classifiers consistently outperform existing best-in-class models, and our output scores exhibit a negative relationship with the experimental immunogenicity of existing antibody therapeutics. We used our classifiers to develop a novel, computational humanization tool, Hu-mAb, that suggests mutations to an input sequence to reduce its immunogenicity. For a set of existing therapeutics with known precursor sequences, the mutations suggested by Hu-mAb show significant overlap with those deduced experimentally. Hu-mAb is therefore an effective replacement for trial- and-error humanization experiments, producing similar results in a fraction of the time. Hu-mAb is freely available to use at opig.stats.ox.ac.uk/webapps/humab.


title: An optimized retroviral toolbox for overexpression and genetic perturbation of primary lymphocytes

abstract: Genetic manipulation of primary lymphocytes is crucial for both clinical purposes and fundamental research. Despite their broad use, we encountered a paucity of data on systematic comparison and optimization of retroviral vectors, the workhorses of genetic modification of primary lymphocytes. Here, we report the construction and validation of a versatile range of retroviral expression vectors. These vectors can be used for the knockdown or overexpression of genes of interest in primary human and murine lymphocytes, in combination with a wide choice of selection and reporter strategies. By streamlining the vector backbone and insert design, these publicly available vectors allow easy interchangeability of the independent building blocks, such as different promoters, fluorescent proteins, surface markers and antibiotic resistance cassettes. We validated these vectors and tested the optimal promoters for in vitro and in vivo overexpression and knockdown of the murine T cell antigen receptor. By publicly sharing these vectors and the data on their optimization, we aim to facilitate genetic modification of primary lymphocytes for researchers entering this field.


title: Neutralizing antibodies targeting the SARS-CoV-2 receptor binding domain isolated from a naïve human antibody library

abstract: Infection with SARS-CoV-2 elicits robust antibody responses in some patients, with a majority of the response directed at the receptor binding domain (RBD) of the spike surface glycoprotein. Remarkably, many patient-derived antibodies that potently inhibit viral infection harbor few to no mutations from the germline, suggesting that naive antibody libraries are a viable means for discovery of novel SARS-CoV-2 neutralizing antibodies. Here, we used a yeast surface-display library of human naive antibodies to isolate and characterize three novel neutralizing antibodies that target the RBD: one that blocks interaction with angiotensin-converting enzyme 2 (ACE2), the human receptor for SARS-CoV-2, and two that target other epitopes on the RBD. These three antibodies neutralized SARS-CoV-2 spike-pseudotyped lentivirus with IC50 values as low as 60 ng/mL in vitro. Using a biolayer interferometry-based binding competition assay, we determined that these antibodies have distinct but overlapping epitopes with antibodies elicited during natural COVID-19 infection. Taken together, these analyses highlight how in vitro selection of naive antibodies can mimic the humoral response in vivo, yielding neutralizing antibodies and various epitopes that can be effectively targeted on the SARS-CoV-2 RBD.


title: Targeting evolutionary conserved sequences circumvents the evolution of resistance in a viral gene drive against human cytomegalovirus

abstract: Gene drives are genetic systems designed to efficiently spread a modification through a population. They have been designed almost exclusively in eukaryotic species, and especially in insects. We recently developed a CRISPR-based gene drive system in herpesviruses that relies on similar mechanisms and could efficiently spread into a population of wildtype viruses. A common consequence of gene drives in insects is the appearance and selection of drive-resistant sequences that are no longer recognized by CRISPR-Cas9. Here, we analyze in cell culture experiments the evolution of resistance in a viral gene drive against human cytomegalovirus. We report that after an initial invasion of the wildtype population, a drive-resistant population is positively selected over time and outcompetes gene drive viruses. However, we show that targeting evolutionary conserved sequences ensures that drive-resistant viruses acquire long-lasting mutations and are durably attenuated. As a consequence, and even though engineered viruses dont stably persist in the viral population, remaining viruses have a replication defect, leading to a long-term reduction of viral levels. This marks an important step toward developing effective gene drives in herpesviruses, especially for therapeutic applications.


title: Targeting conserved sequences circumvents the evolution of resistance in a viral gene drive against human cytomegalovirus


title: Artemisia annua L. extracts prevent in vitro replication of SARS-CoV-2

abstract:
Ethnopharmacological relevanceArtemisia annua L. has been used for millennia in Southeast Asia to treat "fever". Many infectious microbial and viral diseases have been shown to respond to A. annua and communities around the world use the plant as a medicinal tea, especially for treating malaria.

Aim of the StudySARS-CoV-2 (the cause of Covid-19) globally has infected and killed millions of people. Because of the broad-spectrum antiviral activity of artemisinin that includes blockade of SARS-CoV-1, we queried whether A. annua suppressed SARS-CoV-2.

Materials and MethodsUsing Vero E6 and Calu-3 cells, we measured anti viral activity SARS-CoV-2 activity against fully infectious virusof dried leaf extracts of seven cultivars of A. annua sourced from four continents. IC50s were calculated and defined as (the concentrations that inhibited viral replication by 50%.) and CC50s (the concentrations that kill 50% of cells) were calculated.

ResultsHot-water leaf extracts based on artemisinin, total flavonoids, or dry leaf mass showed antiviral activity with IC50 values of 0.1-8.7 M, 0.01-0.14 g, and 23.4-57.4 g, respectively. Antiviral efficacy did not correlate with artemisinin or total flavonoid contents of the extracts. One dried leaf sample was >12 years old, yet the hot-water extract was still found to be active. The UK and South African variants, B1.1.7 and B1.351, were similarly inhibited. While all hot water extracts were effective, concentrations of artemisinin and total flavonoids varied by nearly 100-fold in the extracts. Artemisinin alone showed an estimated IC50 of about 70 M, and the clinically used artemisinin derivatives artesunate, artemether, and dihydroartemisinin were ineffective or cytotoxic at elevated micromolar concentrations. In contrast, the antimalarial drug amodiaquine had an IC50 = 5.8 M. Extracts had minimal effects on infection of Vero E6 or Calu-3 cells by a reporter virus pseudotyped by the SARS-CoV-2 spike protein. There was no cytotoxicity within an order of magnitude above the antiviral IC90 values.

ConclusionsA. annua extracts inhibit SARS-CoV-2 infection, and the active component(s) in the extracts is likely something besides artemisinin or a combination of components that block virus infection at a step downstream of virus entry. Further studies will determine in vivo efficacy to assess whether A. annua might provide a cost-effective therapeutic to treat SARS-CoV-2 infections.

List of compounds studiedAmodiaquine
Artemisinin
Artesunate
Artemether
Deoxyartemisinin
Dihydroartemisinin

HighlightsO_LIArtemisia annua is effective in stopping replication of SARS-CoV-2 including 2 new variants.
C_LIO_LIThe anti-viral effect does not correlate to artemisinin, nor to the total flavonoid content.
C_LIO_LIThe anti-viral mechanism does not appear to involve blockade virus entry into cell.
C_LIO_LIThe plant offers two additional benefits: a decreased inflammatory response and blunting of fibrosis.
C_LIO_LIA. annua may provide a safe, low-cost alternative for treating patients infected with SARS-CoV-2.
C_LI


title: Artemisia annua L. extracts inhibit the in vitro replication of SARS-CoV-2 and two of its variants


title: Clr4SUV39H1 and Bdf2BRD4 ubiquitination mediate transcriptional silencing via heterochromatic phase transitions

abstract: Heterochromatin has crucial roles in genome stability by silencing repetitive DNA and by suppressing recombination1,2. In the fission yeast Schizosaccharomyces pombe, Clr4 methylates histone H3 lysine 9 (H3K9) to maintain centromeric heterochromatin during the cell cycle, guided by RNA interference (RNAi)3,4. Clr4 interacts with a specialized ubiquitination complex CLRC, which is recruited in part by small RNA and the RNAi transcriptional silencing complex (RITS) but otherwise, the role of CLRC is unknown5-8. Here we show that the E2 ubiquitin conjugating enzyme Ubc4 interacts with CLRC and targets Clr4 for mono-ubiquitination at an intrinsically disordered region. Mono-ubiquitination is essential for the transition from co-transcriptional (H3K9me2) to transcriptional (H3K9me3) gene silencing by transiently releasing Clr4 from centromeric heterochromatin, and is reversed by the deubiquitinating enzyme Ubp3. Addition of ubiquitin changes the liquid-liquid phase separation (LLPS) of Clr4 to enhance its dynamic activity. Ubc4-CLRC also poly-ubiquitinates Bdf2, the homologue of BET family double bromodomain protein BRD4 for degradation, which otherwise accumulates at centromeres to promote transcription and production of small RNAs.


title: Lamina-associated polypeptide 2α is required for intranuclear MRTF-A activity

abstract: Myocardin-related transcription factor A (MRTF-A), a coactivator of serum response factor (SRF), regulates the expression of many cytoskeletal genes in response to cytoplasmic and nuclear actin dynamics. Here we describe a novel mechanism to regulate MRTF-A activity within the nucleus by showing that lamina-associated polypeptide 2 (Lap2), the nucleoplasmic isoform of Lap2, is a direct binding partner of MRTF-A, and required for the efficient expression of MRTF-A/SRF target genes. Mechanistically, Lap2 is not required for MRTF-A nuclear localization, unlike most other MRTF-A regulators, but is required for binding of MRTF-A to its target genes. This regulatory step takes place prior to MRTF-A chromatin binding, because Lap2 neither interacts with, nor specifically influences active histone marks on MRTF-A/SRF target genes. Phenotypically, Lap2 is required for serum-induced cell migration, and deregulated MRTF-A activity may also contribute to muscle and proliferation phenotypes associated with loss of Lap2. Our studies therefore add another regulatory layer to the control of MRTF-A-SRF-mediated gene expression, and broaden the role of Lap2 in transcriptional regulation.


title: Synaptojanin1 deficiency upregulates basal level autophagosome formation in astrocytes

abstract: Macroautophagy (hereafter, autophagy) dysregulation is implicated in multiple neurological disorders. While the autophagy pathways are heavily investigated in heterologous cells and neurons, how autophagy is regulated in the astrocyte, the most abundant cell type in the mammalian brain, is less understood. Here we report that Synaptojanin1 (Synj1), a neuron enriched lipid phosphatase, is expressed in low levels in astrocytes and represses autophagy at the basal level. Synj1 is encoded by the Synj1 gene, whose missense mutations are linked to Parkinsonism with seizure. While the best-known role of Synj1 is to facilitate synaptic vesicle recycling, recent studies suggest that Synj1 also regulates autophagy. Our previous study using the Synj1 haploinsufficient (Synj1+/-) mouse demonstrated that Synj1 deficiency was associated with an age-dependent autophagy impairment in multiple brain regions. We now use cultured astrocytes from Synj1 deficient mice to investigate its role in astrocyte autophagy. We demonstrate that Synj1 deficient astrocytes exhibit increased LC3 puncta, which is more pronounced when lysosomal acidification is blocked. The increased autophagosome formation is accompanied by reduced autophagy substrate, p62, but an insensitivity to starvation induced autophagy clearance. Moreover, we show, for the first time, that the Parkinsonism associated R839C mutation impacts astrocyte autophagy. The profound impact of this mutation on Synj1s phosphatase functions results in elevated basal level autophagosome formation and clearance that mimics Synj1 deletion. We find that energy sensing molecules, including mTOR and AMPK, are altered in Synj1 deficient astrocytes, which may contribute to the enhanced basal level autophagy.


title: Microtubule-associated ROP interactors both delimit and transduce ROP signaling and regulate microtubule dynamics

abstract: Evidence suggests that ICR proteins function as adaptors that mediate ROP signaling. Here, we studied the functions of ICR2 and its homologs ICR5 and ICR3. We showed that ICR2 is a microtubule-associated protein that regulates microtubule dynamics. ICR2 can retrieve activated ROPs from the plasma membrane, and it is recruited to a subset of ROP domains. Secondary cell wall pits in the metaxylem of icr2 and icr5 Arabidopsis single mutants and icr2/icr5 double and icr2/icr5/icr3 triple mutants were denser and larger than those in wild-type Col-0 seedlings, implicating these three ICRs in restriction of ROP function. The icr2 but not the icr5 mutants developed split root hairs further implicating ICR2 in restriction of ROP signaling. Taken together, our results show that ICR2, and likely also ICR5 and ICR3, have multiple functions as ROP effectors and as regulators of microtubule dynamics.


title: Moving patronin foci and growing microtubule plus ends direct the spatiotemporal dynamics of Rho signaling and myosin during apical constriction

abstract: The contraction of the amnioserosa by apical constriction provides the major force for Drosophila dorsal closure. The nucleation, movement and dispersal of apicomedial actomyosin complexes generate pulsed constrictions during early dorsal closure whereas persistent apicomedial and circumapical actomyosin complexes drive the unpulsed constrictions that follow. What governs the spatiotemporal assembly of these distinct complexes, endows them with their pulsatile dynamics, and directs their motility remains unresolved. Here we identify an essential role for microtubule growth in regulating the timely contraction of the amnioserosa. We show that a symmetric cage of apical microtubules forms around the coalescing apicomedial myosin complex. An asymmetric tail of microtubules then trails the moving myosin complex and disperses as the myosin complex dissolves. Perturbing microtubule growth reduced the coalescence and movement of apicomedial myosin complexes and redistributed myosin and its activator, Rho kinase to the circumapical pool and altered the cell constriction and tissue contraction dynamics of the amnioserosa. We show that RhoGEF2, the activator of the Rho1 GTPase, is transiently associated with microtubule plus end binding protein EB1 and the apicomedial actomyosin complex. Our results suggest that microtubule growth from moving patronin platforms modulates actomyosin contractility through the spatiotemporal regulation of Rho1 activity. We propose that microtubule reorganisation enables a self-organising, mechanosensitive feedback loop that buffers the tissue against mechanical stresses by modulating actomyosin contractility.


title: Joint development recovery on resumption of embryonic movement following paralysis

abstract:
Fetal activity in utero is a normal part of pregnancy and reduced or absent movement can lead to long-term skeletal defects such as Fetal Akinesia Deformation Sequence (FADS), joint dysplasia and arthrogryposis. A variety of animal models with decreased or absent embryonic movements show a consistent set of developmental defects providing insight into the aetiology of congenital skeletal abnormalities. At developing joints defects include reduced joint interzones with frequent fusion of cartilaginous skeletal rudiments across the joint. At the spine defects include shortening and a spectrum of curvature deformations. An important question, with relevance to possible therapeutic interventions for human conditions, is the capacity for recovery with resumption of movement following short term immobilisation. Here we use the well-established chick model to compare the effects of sustained immobilisation from embryonic day (E) 4-10 to two different recovery scenarios: (i) natural recovery from E6 until E10 and (ii) the addition of hyperactive movement stimulation during the recovery period. We demonstrate partial recovery of movement and partial recovery of joint development under both recovery conditions, but no improvement in spine defects. The joints examined (elbow, hip and knee) showed better recovery in hindlimb than forelimb, with hyperactive mobility leading to greater recovery in the knee and hip. The hip joint showed the best recovery with improved rudiment separation, tissue organisation and commencement of cavitation. This work demonstrates that movement post paralysis can partially-recover specific aspects of joint development which could inform therapeutic approaches to ameliorate the effects of human fetal immobility.

Summary StatementThe study reveals that embryonic movement post paralysis can partially-recover specific aspects of joint development, which could inform therapeutic approaches to ameliorate the effects of restricted fetal movement in utero.

category: developmental biology


title: Low light intensity delays vegetative phase change in Arabidopsis thaliana

abstract: Plants that develop under low intensity light (LL) often display a phenotype known as the "shade tolerance syndrome (STS)". This syndrome is similar to the phenotype of plants in the juvenile phase of shoot development, but the basis for this similarity is unknown. We tested the hypothesis that the STS is regulated by the same mechanism that regulates the juvenile vegetative phase by examining the effect of LL on rosette development in Arabidopsis thaliana. We found that LL prolonged the juvenile vegetative phase and that this was associated with an increase the expression of the master regulators of vegetative phase change, miR156 and miR157, and a decrease in the expression of their SPL targets. Exogenous sucrose partially corrected the effect of LL on seedling development and miR156 expression. Our results suggest that the response of Arabidopsis to LL is mediated by an increase in miR156/miR157 expression and by factors that repress SPL gene expression independently of miR156/miR157, and is caused in part by a decrease in carbohydrate production. The effect of LL on vegetative phase change does not require the photoreceptors and transcription factors responsible for the shade avoidance syndrome, implying that light intensity and light quality regulate rosette development by different pathways.


title: Mitochondrial fusion regulates proliferation and differentiation in the type II neuroblast lineage in Drosophila

abstract: Optimal mitochondrial function determined by mitochondrial dynamics, morphology and activity is coupled to stem cell differentiation and organism development. However, the mechanisms of interaction of signaling pathways with mitochondrial morphology and activity are not completely understood. We assessed the role of mitochondrial fusion and fission in differentiation of neural stem cells called neuroblasts (NB) in the Drosophila brain. Depletion of mitochondrial inner membrane fusion protein Opa1 and mitochondrial outer membrane protein Marf in the Drosophila type II neuroblast lineage led to mitochondrial fragmentation and loss of activity. Opa1 and Marf depletion did not affect the numbers and polarity of type II neuroblasts but led to a decrease in proliferation and differentiation of cells in the lineage. On the contrary, loss of mitochondrial fission protein Drp1 led to mitochondrial fusion but did not show defects in proliferation and differentiation. Depletion of Drp1 along with Opa1 or Marf also led to mitochondrial fusion and suppressed fragmentation, loss of mitochondrial activity, proliferation and differentiation in the type II NB lineage. We found that Notch signaling depletion via the canonical pathway showed mitochondrial fragmentation and loss of differentiation similar to Opa1 mutants. An increase in Notch signaling required mitochondrial fusion for NB proliferation. Further, Drp1 mutants in combination with Notch depletion showed mitochondrial fusion and drove differentiation in the lineage suggesting that fused mitochondria can influence Notch signaling driven differentiation in the type II NB lineage. Our results implicate a crosstalk between Notch signalling, mitochondrial activity and mitochondrial fusion as an essential step in type II NB differentiation.


title: Gut microbiota of Drosophila subobscura contributes to its heat tolerance but is sensitive to transient thermal stress

abstract: Global warming impacts the animals fitness, leading to increasing extinction risk in ectotherm species. Gut microbiota can contribute to host physiology leading to an increase of resistance to abiotic stress conditions. Temperature has profound effects on ectotherms and gut microbiota can influence cold and heat tolerance of ectotherm species. Additionally, the gut microbiota is sensitive to environmental temperature, which induces changes in its composition and diversity. Here, we investigated the role of the gut microbiota on heat tolerance of Drosophila subobscura, comparing the knockdown time between conventional and axenic, and we also assessed the impact of heat stress on the diversity and community structure of the gut microbiota, comparing non-stressed and heat-stressed flies. Our findings provide evidence that gut microbiota influences heat tolerance, and that heat stress modifies the gut microbiota at taxonomical and structural levels. These results demonstrate that gut microbiota contributes to heat tolerance but it is also highly sensitive to transient heat stress, which could have important effects on host fitness, population risk extinction, and vulnerability of ectotherms to current and future climatic conditions.


title: Novel functional sequences uncovered through a bovine multi-assembly graph

abstract: Linear reference genomes are typically assembled from single individuals. They are unable to reflect the genetic diversity of populations and lack millions of bases. To overcome such limitations and make non-reference sequences amenable to genetic investigations, we build a multi-assembly graph from six reference-quality assemblies from taurine cattle and their close relatives. We uncover 70,329,827 bases that are missing in the bovine linear reference genome. The missing sequences encode novel transcripts that are differentially expressed between individual animals. Reads which were previously poorly or unmapped against the bovine reference genome now align accurately to the non-reference sequences. We show that the non-reference sequences contain polymorphic sites that segregate within and between breeds of cattle. Our efforts to uncover novel functional sequences from a multi-assembly graph pave the way towards the transition to a more representative bovine reference genome.

category: genomics


title: Measuring arterial pulsatility with Dynamic Inflow MAgnitude Contrast (DIMAC)

abstract:
The pulsatility of blood flow through cerebral arteries is clinically important, as it is intrinsically associated with cerebrovascular health. In this study we outline a new MRI approach to measuring the real-time pulsatile flow in cerebral arteries, which is based on the inflow phenomenon associated with fast gradient-recalled-echo acquisitions. Unlike traditional phase-contrast techniques, this new method, which we dub Dynamic Inflow Magnitude Contrast (DIMAC), does not require velocity-encoding gradients as sensitivity to flow velocity is derived purely from the inflow effect. We achieved this using a highly accelerated single slice EPI acquisition with a very short TR (15 ms) and a 90{degrees} flip angle, thus maximizing inflow contrast. We simulate the spoiled GRE signal in the presence of large arteries and perform a sensitivity analysis to demonstrate that in the regime of high inflow contrast it shows much greater sensitivity to flow velocity over blood volume changes. We support this theoretical prediction with in-vivo data collected in two separate experiments designed to demonstrate the utility of the DIMAC signal contrast. We perform a hypercapnia challenge experiment in order to experimentally modulate arterial tone within subjects, and thus modulate the arterial pulsatile flow waveform. We also perform a thigh-cuff release challenge, designed to induce a transient drop in blood pressure, and demonstrate that the continuous DIMAC signal captures the complex transient change in the pulsatile and non-pulsatile components of flow. In summary, this study proposes a new role for a well-established source of MR image contrast and demonstrates its potential for measuring both steady-state and dynamic changes in arterial tone.

HighlightsO_LIWe present a novel method for measuring pulsatility of cerebral arteries.
C_LIO_LIThe inflow effect on fast GRE imaging can be exploited to yield a flow velocity dependent signal.
C_LIO_LIWe measure pulsatile flow through cerebral arteries dynamically on a beat-to-beat basis.
C_LIO_LIWe use physiological challenges to demonstrate sensitivity to dynamic and steady-state changes in vascular tone.
C_LI


title: Auto-CORPus: Automated and Consistent Outputs from Research Publications

abstract:
To analyse large corpora using machine learning and other Natural Language Processing (NLP) algorithms, the corpora need to be standardised. The BioC format is a community-driven simple data structure for sharing text and annotations, however there is limited access to biomedical literature in BioC format and a lack of bioinformatics tools to convert online publication HTML formats to BioC. We present Auto-CORPus (Automated pipeline for Consistent Outputs from Research Publications), a novel NLP tool for the standardisation and conversion of publication HTML and table image files to three convenient machine-interpretable outputs to support biomedical text analytics. Firstly, Auto-CORPus can be configured to convert HTML from various publication sources to BioC. To standardise the description of heterogenous publication sections, the Information Artifact Ontology is used to annotate each section within the BioC output. Secondly, Auto-CORPus transforms publication tables to a JSON format to store, exchange and annotate table data between text analytics systems. The BioC specification does not include a data structure for representing publication table data, so we present a JSON format for sharing table content and metadata. Inline tables within full-text HTML files and linked tables within separate HTML files are processed and converted to machine-interpretable table JSON format. Finally, Auto-CORPus extracts abbreviations declared within publication text and provides an abbreviations JSON output that relates an abbreviation with the full definition. This abbreviation collection supports text mining tasks such as named entity recognition by including abbreviations unique to individual publications that are not contained within standard bio-ontologies and dictionaries.

AvailabilityThe Auto-CORPus package is freely available with detailed instructions from Github at https://github.com/omicsNLP/Auto-CORPus/.


title: Auto-CORPus: A Natural Language Processing Tool for Standardising and Reusing Biomedical Literature