title: Genomic and phenotypic characterization of experimentally selected resistant Leishmania donovani reveals a role for dynamin-1 like protein in the mechanism of resistance to a novel anti-leishmanial compound

abstract:
The implementation of prospective drug resistance (DR) studies in the R&D pipelines is a common practice for many infectious diseases, but not for Neglected Tropical Diseases. Here, we explored and demonstrated the importance of this approach, using as paradigms Leishmania donovani, the etiological agent of Visceral Leishmaniasis (VL), and TCMDC-143345, a promising compound of the GSK  Leishbox to treat VL. We experimentally selected resistance to TCMDC-143345 in vitro and characterized resistant parasites at genomic and phenotypic levels. We found that it took more time to develop resistance to TCMDC-143345 than to other drugs in clinical use and that there was no cross resistance to these drugs, suggesting a new and unique mechanism. By whole genome sequencing, we found two mutations in the gene encoding the L. donovani dynamin-1-like protein (LdoDLP1) that were fixed at highest drug pressure. Through phylogenetic analysis, we identified LdoDLP1 as a family member of the dynamin-related proteins, a group of proteins that impacts the shapes of biological membranes by mediating fusion and fission events, with a putative role in mitochondrial fission. We found that L. donovani lines genetically engineered to harbor the two identified LdoDLP1 mutations were resistant to TCMDC-143345 and displayed altered mitochondrial properties. By homology modeling, we showed how the two LdoDLP1 mutations may influence protein structure and function. Taken together, our data reveal a clear involvement of LdoDLP1 in the adaptation/resistance of L. donovani to TCMDC-143345.

ImportanceHumans and their pathogens are continuously locked in a molecular arms race during which the eventual emergence of pathogen drug resistance (DR) seems inevitable. For neglected tropical diseases (NTDs), DR is generally studied retrospectively, once it has already been established in clinical settings. We previously recommended to keep one step ahead in the host-pathogen arms race and implement prospective DR studies in the R&D pipeline, a common practice for many infectious diseases, but not for NTDs. Here, using Leishmania donovani, the etiological agent of Visceral Leishmaniasis (VL), and TCMDC-143345, a promising compound of the GSK  Leishbox to treat VL, as paradigms, we experimentally selected resistance to the compound and proceeded to genomic and phenotypic characterization of DR parasites. The results gathered in the present study suggest a new DR mechanism involving the L. donovani dynamin-1 like protein (LdoDLP1) and demonstrate the practical relevance of prospective DR studies.


title: Maribellus comscasis sp. nov., isolated from the deep-sea cold seep

abstract: A facultatively anaerobic, Gram-stain-negative, non-motile, curved rod-shaped bacterium, designated WC007T, was isolated from the deep-sea cold seep, P. R. China. Strain WC007T was found to grow at temperatures from 28 to 37 {degrees}C (optimum, 30 {degrees}C), at pH values between pH 6.0 and 8.0 (optimum, pH 7.0) and in 0-5.0% (w/v) NaCl (optimum, 1.0%). The major fatty acids (>10.0%) were iso-C15:0, C16:0, summed feature 3 and summed feature 8. The major isoprenoid quinone was MK-7. Predominant polar lipids were phosphatidylethanolamine, one unidentified phospholipid, one unidentified aminolipid and one unidentified lipid. The G+C content of the genomic DNA was 38.38%. The average nucleotide identity (ANIb and ANIm), amino acid identity (AAI), the tetranucleotide signatures (Tetra) and in silico DNA-DNA hybridization (isDDH) similarities between the genome sequences of isolate WC007T and Maribellus luteus XSD2T were 70.11%, 84.94%, 71.0%, 0.92022 and 20.40%, respectively, indicating that strain WC007T was distinguished from M. luteus. Phylogenetic analysis based on 16S rRNA gene sequences placed strain WC007T within the genus Maribellus and showed the highest similarity to strain XSD2T (95.70%). In combination of the results of phylogenetic analysis and phenotypic and chemotaxonomic data, strain WC007T was considered to represent a novel species of the genus Maribellus, for which the name Maribellus comscasis sp. nov. is proposed. The type strain is WC007T (=KCTC 25169T = MCCC 1K04777T). The available of the genome sequence of strain WC007T would be helpful in understanding the degradation mechanism of difficult-to-degrade polysaccharides.

category: microbiology


title: Predictors of virus prevalence and diversity across a wild bumblebee community

abstract: Viruses are key regulators of natural populations. Despite this, we have limited knowledge of the diversity and ecology of viruses that lack obvious fitness effects on their host. This is even the case in wild host populations that provide ecosystem services, where small fitness effects may have major ecological and financial impacts in aggregate. One such group of hosts are the bumblebees, which have a major role in the pollination of food crops and have suffered population declines and range contractions in recent decades. In this study, we used a multivariate generalised linear mixed model to investigate the ecological factors that determine the prevalence of four recently discovered bumblebee viruses (Mayfield virus 1, Mayfield virus 2, River Liunaeg virus and Loch Morlich virus), and two previously known viruses that infect both wild bumblebees and managed honeybees (Acute bee paralysis virus and Slow bee paralysis virus). We show that the recently discovered bumblebee viruses were more genetically diverse than the viruses shared with honeybees, potentially due to spillover dynamics of shared viruses. We found evidence for ecological drivers of prevalence in our samples, with relatively weak evidence for a positive effect of precipitation on the prevalence of River Luinaeg virus. Coinfection is potentially important in shaping prevalence: we found a strong positive association between River Liunaeg virus and Loch Morlich virus presence after controlling for host species, location and other relevant ecological variables. This study represents a first step in the description of predictors of bumblebee infection in the wild not driven by spillover from honeybees.


title: Harnessing Escherichia coli for bio-based production of formate under pressurized H2 and CO2 gases.

abstract: ABSRACTEscherichia coli is gram-negative bacterium that is a workhorse of the biotechnology industry. The organism has a flexible metabolism and can perform a mixed-acid fermentation under anaerobic conditions. Under these conditions E. coli synthesises a formate hydrogenlyase isoenzyme (FHL-1) that can generate molecular hydrogen and carbon dioxide from formic acid. The reverse reaction is hydrogen-dependent carbon dioxide reduction (HDCR), which has exciting possibilities in bio-based carbon capture and storage if it can be harnessed. In this study, an E. coli host strain was optimised for the production of formate from H2 and CO2 during bacterial growth in a pressurised batch bioreactor. A host strain was engineered that constitutively produced the FHL-1 enzyme and incorporation of tungsten in to the enzyme, in place of molybdenum, helped poise the reaction in the HDCR direction. The engineered E. coli strain showed an ability to grow under fermentative conditions while simultaneously producing formate from gaseous H2 and CO2 supplied in the bioreactor. However, while a sustained pressure of 10 bar N2 had no adverse effect on cell growth, when the culture was placed at or above 4 bar pressure of a H2:CO2 mixture then a clear growth deficiency was observed. Taken together, this work demonstrates that growing cells can be harnessed to hydrogenate carbon dioxide and provides fresh evidence that the FHL-1 enzyme may be intimately linked with bacterial energy metabolism.


title: The mechanism of full activation of tumor suppressor PTEN at the phosphatidylinositol-enriched membrane

abstract: Tumor suppressor PTEN, the second most highly mutated protein in cancer, dephosphorylates signaling lipid PIP3 produced by PI3Ks. Excess PIP3 promotes cell proliferation. The mechanism at the membrane of this pivotal phosphatase is unknown hindering drug discovery. Exploiting explicit solvent simulations, we tracked full-length PTEN trafficking from the cytosol to the membrane. We observed its interaction with membranes composed of zwitterionic phosphatidylcholine, anionic phosphatidylserine, and phosphoinositides, including signaling lipids PIP2 and PIP3. We tracked its moving away from the zwitterionic and getting absorbed onto anionic membrane that harbors PIP3. We followed it localizing on microdomains enriched in signaling lipids, as PI3K does, and observed PIP3 allosterically unfolding the N-terminal PIP2 binding domain, positioning it favorably for the polybasic motif interaction with PIP2. Finally, we determined PTEN catalytic action at the membrane, all in line with experimental observations, deciphering the mechanisms of how PTEN anchors to the membrane and restrains cancer.

category: molecular biology


title: The mechanism of full activation of tumor suppressor PTEN at the phosphoinositide-enriched membrane


title: The telomere regulatory gene POT1 responds to stress and predicts performance in nature: implications for telomeres and life history evolution

abstract: Long telomeres have become nearly synonymous with a variety of fitness-related traits and may be mediators of ecologically relevant variation in life history strategies. Growing evidence suggests that telomere dynamics are more predictive of performance than length itself, but very little work considers how telomere regulatory mechanisms respond to environmental challenges or influence performance in nature. Here, we combine observational and experimental datasets from free-living tree swallows (Tachycineta bicolor) to assess how performance is predicted by the telomere regulatory gene POT1, which encodes a shelterin protein that sterically blocks telomerase from repairing the telomere. First, we show that lower POT1 gene expression was associated with higher female quality, i.e. earlier breeding, and heavier body mass. We next challenged mothers with an immune stressor (lipopolysaccharide injection) that led to  sickness in mothers and 24h of food restriction in their offspring. While POT1 did not respond to maternal injection, females with lower constitutive gene expression were better able to maintain feeding rates following treatment. Maternal injection also generated a one-day stressor for chicks, who responded with decreased POT1 gene expression and elongated telomeres. Other putatively stress-responsive mechanisms (i.e. glucocorticoids, antioxidants) were not significantly different between control and stress-exposed chicks. Model comparisons indicated that POT1 mRNA abundance was a largely better predictor of performance than telomere dynamics, indicating that telomere regulators may be powerful modulators of variation in life history strategies.


title: Genome-wide screening of circadian and non-circadian impact of Neat1 genetic deletion

abstract: The functions of the long non-coding RNA, Nuclear enriched abundant transcript 1 (Neat1), are poorly understood. Neat1 is required for the formation of paraspeckles, but its respective paraspeckle-dependent or independent functions are unknown. Several studies including ours reported that Neat1 is involved in the regulation of circadian rhythms. We characterized the impact of Neat1 genetic deletion in a rat pituitary cell line. The mRNAs whose circadian expression pattern or expression level is regulated by Neat1 were identified after high-throughput RNA sequencing of the circadian transcriptome of wild-type cells compared to cells in which Neat1 was deleted by CRISPR/Cas9. The numerous RNAs affected by Neat1 deletion were found to be circadian or non-circadian, targets or non-targets of paraspeckles, and to be associated with many key biological processes showing that Neat1, interacting or independently of the circadian system, could play crucial roles in key physiological functions through diverse mechanisms.


title: Maintenance of Complex I and respiratory super-complexes by NDUF-11 is essential for respiratory function, mitochondrial structure and health in C. elegans

abstract: Mitochondrial super-complexes form around a conserved core of monomeric complex I and dimeric complex III; wherein subunit NDUFA11, of the former, is conspicuously situated at the interface. We identified B0491.5 (NDUF-11) as the C. elegans homologue, of which animals homozygous for a CRISPR-Cas9 generated knockout allele arrested at the L2 development stage. Reducing expression by RNAi allowed development to the adult stage, enabling characterisation of the consequences: destabilisation of complex I and its super-complexes, and perturbation of respiratory function. The loss of NADH-dehydrogenase activity is compensated by enhanced complex II activity, resulting in excessive detrimental ROS production. Meanwhile, electron cryo-tomography highlight aberrant cristae morphology and widening of the inter-membrane space and cristae junctions. The requirement of NDUF-11 for balanced respiration, mitochondrial morphology and development highlights the importance of complex I/ super-complex maintenance. Their perturbation by this, or other means, is likely to be the cause of metabolic stress and disease.


title: The Ran pathway uniquely regulates cytokinesis in cells with different fates in the early C. elegans embryo

abstract: Cytokinesis occurs at the end of mitosis and occurs due to the ingression of a contractile ring that cleaves the daughter cells. This process is tightly controlled to prevent cell fate changes or aneuploidy, and the core machinery is highly conserved among metazoans. Multiple mechanisms regulate cytokinesis, but their requirement in different cell types is not known. Here, we show that differently fated AB and P1 cells in the early C. elegans embryo have unique cytokinesis kinetics supported by distinct levels and cortical patterning of myosin. Through perturbation of polarity regulators and the generation of stable tetraploid strains, we demonstrate that these differences depend on both cell fate and size. Additionally, these parameters could influence the Ran pathway, which coordinates the contractile ring with chromatin position, and controls cytokinesis differently in AB and P1 cells. Our findings demonstrate the need to consider multiple parameters when modeling ring kinetics.

category: cell biology


title: Are we missing the forest for the trees? Conspecific negative density dependence in a temperate deciduous forest

abstract: One of the central goals of ecology is to determine the mechanisms that enable coexistence among species. Evidence is accruing that conspecific negative density dependence (CNDD), the process by which plant seedlings are unable to survive in the area surrounding adults of their same species, is a major contributor to tree species coexistence. However, for CNDD to maintain diversity, three conditions must be met. First, CNDD must maintain diversity for the majority of the woody plant community (rather than merely specific groups). Second, the pattern of repelled recruitment must increase in with plant size. Third, CNDD must occurs across life history strategies and not be restricted to a single life history strategy. These three conditions are rarely tested simultaneously. In this study, we simultaneously test all three conditions in a woody plant community in a North American temperate forest. We examined whether the different woody plant growth forms (shrubs, understory trees, mid-story trees, canopy trees, and lianas) at different ontogenetic stages (seedling, sapling, and adult) were overdispersed - a spatial pattern indicative of CNDD - using spatial point pattern analysis across life history stages and strategies. We found that there was a strong signal of overdispersal at the community level. However, this pattern was driven by adult canopy trees. By contrast, understory plants, which can constitute up to 80% of temperate forest plant diversity, were not overdispersed as adults. The lack of overdispersal suggests that CNDD is unlikely to be a major mechanism maintaining understory plant diversity. The focus on trees for the vast majority of CNDD studies may have biased the perception of the prevalence of CNDD as a dominant mechanism that maintains community-level diversity when, according to our data, CNDD may be restricted largely to trees.

category: ecology


title: Evolution to alternative levels of stable diversity leaves areas of niche space unexplored

abstract:
One of the oldest and most persistent questions in ecology and evolution is whether natural communities tend to evolve toward saturation and maximal diversity. Robert MacArthurs classical theory of niche packing and the theory of adaptive radiations both imply that populations will diversify and fully partition any available niche space. However, the saturation of natural populations is still very much an open area of debate and investigation. Additionally, recent evolutionary theory suggests the existence of alternative evolutionary stable states (ESSs), which implies that some stable communities may not be fully saturated. Using models with classical Lokta-Volterra ecological dynamics and three formulations of evolutionary dynamics (a model using adaptive dynamics, an individual-based model, and a partial differential equation model), we show that following an adaptive radiation, communities can often get stuck in low diversity states when limited by mutations of small phenotypic effect. These low diversity metastable states can also be maintained by limited resources and finite population sizes. When small mutations and finite populations are considered together, it is clear that despite the presence of higher-diversity stable states, natural populations are likely not fully saturating their environment and leaving potential niche space unfilled. Additionally, within-species variation can further reduce community diversity from levels predicted by models that assume species-level homogeneity.

Author summaryUnderstanding if and when communities evolve to saturate their local environments is imperative to our understanding of natural populations. Using computer simulations of classical evolutionary models, we study whether adaptive radiations tend to lead toward saturated communities, in which no new species can invade or remain trapped in alternative, lower diversity stable states. We show that with asymmetric competition and small effect mutations, evolutionary Red Queen dynamics can trap communities in low diversity metastable states. Moreover, limited resources not only reduces community population sizes, but also reduces community diversity, denying the formation of saturated communities and stabilizing low diversity, non-stationary evolutionary dynamics. Our results are directly relevant to the longstanding questions important to both ecological empiricists and theoreticians on the species packing and saturation of natural environments. Also, by showing the ease evolution can trap communities in low diversity metastable states, we demonstrate the potential harm in relying solely on ESSs to answer questions of biodiversity.

category: evolutionary biology


title: Pixelwise H-score: a novel digital image analysis based-metric to quantify membrane biomarker expression from immunohistochemistry images

abstract: Immunohistochemistry (IHC) assays play a central role in evaluating biomarker expression in tissue sections for diagnostic and research applications. Manual scoring of IHC images, which is the current standard of practice, is known to have several shortcomings in terms of reproducibility and scalability to large scale studies. Here, by using a digital image analysis-based approach, we introduce a new metric called the pixelwise H-score (pix H-score) that quantifies biomarker expression from whole-slide scanned IHC images. The pix H-score is an unsupervised algorithm that only requires the specification of intensity thresholds for the biomarker and the nuclear-counterstain channels. We present the detailed implementation of the pix H-score in two different whole-slide image analysis software packages Visiopharm and HALO. We consider three biomarkers P-cadherin, PD-L1, and 5T4, and show how the pix H-score exhibits tight concordance to multiple orthogonal measurements of biomarker abundance such as the biomarker mRNA transcript and the pathologist H-score. We also compare the pix H-score to existing automated image analysis algorithms and demonstrate that the pix H-score provides either comparable or significantly better performance over these methodologies. We also present results of an empirical resampling approach to assess the performance of the pix H-score in estimating biomarker abundance from select regions within the tumor tissue relative to the whole tumor resection. We anticipate that the new metric will be broadly applicable to quantify biomarker expression from a wide variety of IHC images. Moreover, these results underscore the benefit of digital image analysis-based approaches which offer an objective, reproducible, and highly scalable strategy to quantitatively analyze IHC images.

category: pathology


title: Incidence and Characteristics of Co-infection and Secondary Infection in Patients with COVID-19

abstract:
ObjectiveThe etiology and epidemiology of co-infection and secondary infection in COVID-19 patients remain unknown. The study aims to investigate the occurrence and characteristics of co-infection and secondary infection in COVID-19 patients, mainly focusing on Streptococcus pneumoniae co-infections.

MethodsThis study was a prospective, observational cohort study of the inpatients diagnosed with COVID-19 in two designated hospitals in south China enrolled between Jan 11 and Feb 22, 2020. The urine specimen was collected on admission and applied for pneumococcal urinary antigen tests (PUATs). Demographic, clinical and microbiological data of patients were recorded simultaneously.

ResultA total of 146 patients with a confirm diagnosis of COVID-19 at the median age of 50.0 years (IQR 36.0-61.0) were enrolled, in which, 16 (11.0%) were classified as severe cases and 130 (89.0%) as non-severe cases. Of the enrolled patients, only 3 (2.1%) were considered to present the co-infection, in which 1 was co-infected with S.pneumoniae, 1 with B. Ovatus infection and the other one with Influenza A virus infection. Secondary infection occurred in 16 patients, with S. maltophilia as the most commonly isolated pathogen (43.8%), followed by P. aeruginosa (25.0%), E. aerogenes (25.0%), C. parapsilosis (25.0%) and A. fumigates (18.8%).

ConclusionPatients with confirmed COVID-19 were rarely co-infected with Streptococcus pneumoniae or other pathogens, indicating that the application of antibiotics against CAP on admission may not be necessary in the treatment of COVID-19 cases.


title: Complex Systems Analysis Informs on the Spread of COVID-19

abstract: The non-linear progression of new infection numbers in a pandemic poses challenges to the evaluation of its management. The tools of complex systems research may aid in attaining information that would be difficult to extract with other means. To study the COVID-19 pandemic, we utilize the reported new cases per day for the globe, nine countries and six US states through October 2020. Fourier and univariate wavelet analyses inform on periodicity and extent of change. Evaluating time-lagged data sets of various lag lengths, we find that the autocorrelation function, average mutual information and box counting dimension represent good quantitative readouts for the progression of new infections. Bivariate wavelet analysis and return plots give indications of containment versus exacerbation. Homogeneity or heterogeneity in the population response, uptick versus suppression, and worsening or improving trends are discernible, in part by plotting various time lags in three dimensions. The analysis of epidemic or pandemic progression with the techniques available for observed (noisy) complex data can aid decision making in the public health response.

category: bioinformatics


title: Heterogeneity versus the COVID-19 Pandemic

abstract: In this paper, heterogeneity is formally defined, and its properties are explored. We define and distinguish observable versus non-observable heterogeneity. It is proposed that heterogeneity among the vulnerable is a significant factor in the contagion impact of COVID-19, as demonstrated with incidence rates on a Diamond Princess Cruise ship in February 2020. Given the nature of the disease, its heterogeneity and human social norms, pre-voyage and post-voyage quick testing procedures may become the new standard for cruise ship passengers and crew. The technological advances in testing available today would facilitate more humanistic treatment as compared to more archaic quarantine and isolation practices for all onboard ship. With quick testing, identification of those infected and thus not allowed to embark on a cruise or quarantining those disembarking and other mitigation strategies, the popular cruise adventure could be available safely again. Whatever the procedures implemented, the methodological purpose of this study should add valuable insight in the modeling of disease and specifically, the COVID-19 virus.

category: scientific communication and education


title: Metabolite discovery through global annotation of untargeted metabolomics data

abstract: Liquid chromatography-high resolution mass spectrometry (LC-MS)-based metabolomics aims to identify and quantitate all metabolites, but most LC-MS peaks remain unidentified. Here, we present a global network optimization approach, NetID, to annotate untargeted LC-MS metabolomics data. The approach aims to generate, for all experimentally observed ion peaks, annotations that match the measured masses, retention times, and (when available) MS/MS fragmentation patterns. Peaks are connected based on mass differences reflecting adducting, fragmentation, isotopes, or feasible biochemical transformations. Global optimization generates a single network linking most observed ion peaks, enhances peak assignment accuracy, and produces chemically-informative peak-peak relationships, including for peaks lacking MS/MS spectra. Applying this approach to yeast and mouse data, we identified five novel metabolites (thiamine derivatives and N-glucosyl-taurine). Isotope tracer studies indicate active flux through these metabolites. Thus, NetID applies existing metabolomic knowledge and global optimization to annotate untargeted metabolomics data, revealing novel metabolites.


title: Independent Genomic Sources of Brain Structure and Function

abstract:
IntroductionThe last decade has seen a surge in well powered genome-wide association studies (GWASs) of complex behavioural traits, disorders, and more recently, of brain structural and functional neuroimaging features. However, the extreme polygenicity of these complex traits makes it difficult to translate the GWAS signal into mechanistic biological insights. We postulate that the covariance of SNP-effects across many brain features, as be captured by latent genomic components of SNP effect sizes. These may partly reflect the concerted multi-locus genomic effects through known molecular pathways and protein-protein interactions. Here, we test the feasibility of a new data-driven method to derive such latent components of genome-wide effects on more than thousand neuroimaging derived traits, and investigate their utility in interpreting the complex biological processes that shape the GWAS signal.

MethodsWe downloaded the GWAS summary statistics of 3,143 brain imaging-derived phenotypes (IDPs) from the UK Biobank, provided by the Oxford Brain Imaging Genetics (BIG) Server (Elliott et al. 2018). Probabilistic independent component analysis (ICA) was used to extract two hundred independent genomic components from the matrix of SNP-effect sizes. We qualitatively describe the distribution of the latent components loadings in the neuroimaging and the genomic dimensions. Gene-wide statistics were calculated for each genomic component. We tested the genomic components enrichment for molecular pathways using MSigDB, and for single-cell RNA-sequencing of adult and foetal brain cells.

Results200 components explained 80% of the variance in SNP-effects sizes. Each MRI modality and data processing method projected the imaging data into a clearly distinct cluster in the genomic component embedded space. Among the 200 genomic components, 157 were clearly driven by a single locus, while 39 were highly polygenic. Together, these 39 components were significantly enriched for 2,274 MSigDB gene sets (fully corrected for multiple testing across gene-sets and components). Several components were sensitive to molecular pathways, single cell expression profiles, and brain traits in patterns consistent with knowledge across these biological levels. To illustrate this, we highlight a component that implicated axonal regeneration pathways, which was specifically enriched for gene expression in oligodendrocyte precursors, microglia and astrocytes, and loaded highly on white matter neuroimaging traits. We highlight a second component that implicated synaptic function and neuron projection organization pathways that was specifically enriched for neuronal cell transcriptomes.

ConclusionWe propose genomic ICA as a new method to identify latent genetic factors influencing brain structure and function by multimodal MRI. The derived latent genomic dimensions are highly sensitive to known molecular pathways and cell-specific gene expression profiles. Genomic ICA may help to disentangle the many different biological routes by which the genome defines the inter-individual variation of the brain. Future research is aimed at using this method to profile individual subjects genomic data along the new latent dimensions and evaluating the utility of these dimensions in stratifying heterogeneous patient populations.

category: neuroscience


title: Domain-general conflict monitoring predicts neural and behavioral indices of linguistic error processing during reading comprehension

abstract: The ability to detect and respond to linguistic errors is critical for successful reading comprehension, but these skills can vary considerably across readers. In the current study, healthy adults (age 18-35) read short discourse scenarios for comprehension while monitoring for the presence of semantic anomalies. Using a factor analytic approach, we examined if performance in non-linguistic conflict monitoring tasks (Stroop, AX-CPT) would predict individual differences in neural and behavioral measures of linguistic error processing. Consistent with this hypothesis, domain-general conflict monitoring predicted both readers end-of-trial acceptability judgments and the amplitude of a late neural response (the P600) evoked by linguistic anomalies. Interestingly, the influence on the P600 was non-linear, suggesting that online neural responses to linguistic errors are influenced by both the effectiveness and efficiency of domain-general conflict monitoring. These relationships were also highly specific and remained after controlling for variability in working memory capacity and verbal knowledge. Finally, we found that domain-general conflict monitoring also predicted individual variability in measures of reading comprehension, and that this relationship was partially mediated by behavioral measures of linguistic error detection. These findings inform our understanding of the role of domain-general executive functions in reading comprehension, with potential implications for the diagnosis and treatment of language impairments.


title: Neuron-type specificity of dorsal raphe projections to ventral tegmental area

abstract: The midbrain dorsal raphe (DR) and ventral tegmental area (VTA) contain two of the brains main ascending neuromodulatory transmitters: serotonin and dopamine. We studied the pathway from DR to VTA using single-cell RNA sequencing, anatomical tracing, and electrophysiology and behavior in mice. Single-cell sequencing confirmed a differential distribution of dopamine cell types between medial and lateral aspects of the VTA. This molecular diversity included differential expression of a subset of glutamatergic and serotonergic receptors. Anatomical data showed that distinct serotonergic and glutamatergic populations of DR neurons project to distinct medial-lateral locations in VTA. Physiological data showed that serotonergic neurons are positioned to excite putative dopaminergic neurons in lateral VTA on short timescales (within trial), and inhibit them on long timescales (on the next trial). Our results reveal precise anatomical specificity of DR projections to VTA, and suggest a functional role for serotonergic modulation of dopaminergic function across multiple timescales.


title: A failure of β-amyloid physiological function due to genetic deletion of α7 nicotinic acetylcholine receptors induces an Alzheimer's disease-like pathology

abstract:
The accumulation of amyloid-beta peptide (A{beta}) and the failure of cholinergic transmission are key players in Alzheimers disease (AD). However, in the healthy brain, A{beta} contributes to synaptic plasticity and memory acting through 7 subtype nicotinic acetylcholine receptors (7nAChRs). Here, we hypothesized that the 7nAChR deletion blocks A{beta} physiological function and promotes a compensatory increase in A{beta} levels that, in turn, triggers an AD-like pathology.

To validate this hypothesis, we studied the age-dependent phenotype of 7 knock out mice. We found that 7nAChR deletion caused an impairment of hippocampal synaptic plasticity and memory at 12 months of age, paralleled by an increase of Amyloid Precursor Protein expression and A{beta} levels. This was accompanied by other classical AD features such as a hyperphosphorylation of tau at residues Ser 199, Ser 396, Thr 205, a decrease of GSK-3{beta} at Ser 9, the presence of paired helical filaments and neurofibrillary tangles, neuronal loss and astrocytosis.

Our findings suggest that 7nAChR malfunction might precede A{beta} and tau pathology, offering a different perspective to interpret the failure of anti-A{beta} therapies against AD and to find novel therapeutical approaches aimed at restoring 7nAChRs-mediated A{beta} function at the synapse.


title: A meta-analysis of transcriptomic profiles from Huntington's disease patients substantiates the pathophysiological role of CDC42, NFY, DLX1 and PRMT3

abstract: Description of robust transcriptomic alterations in Huntingtons disease is essential to identify targets for biochemical studies and drug development. We analysed publicly available transcriptome data from the brain and blood of 220 HD patients and 241 healthy controls and identified 737 and 661 genes with robustly altered mRNA levels in the brain and blood of HD patients, respectively. In the brain, a subnetwork of 320 genes strongly correlated with HD and was enriched in transport-related genes. Bioinformatical analysis of this subnetwork highlighted CDC42, PAK1, YWHAH, NFY, DLX1, HMGN3, and PRMT3. Moreover, we found that CREB1 can regulate 78.0 % of genes whose mRNA levels correlated with HD in the blood of patients. Alterations in protein transport, metabolism, transcriptional regulation, and CDC42-mediated functions are likely central features of HD. Further our data substantiate the role of transcriptional regulators that have not been reported in the context of HD (e.g. DLX1, HMGN3 and PRMT3) and strongly suggest dysregulation of NFY and its target genes across tissues. A large proportion of the identified genes such as CDC42 were also altered in Parkinsons (PD) and Alzheimers disease (AD). The observed dysregulation of CDC42 and YWHAH in samples from HD, AD and PD patients indicates that those genes and their upstream regulators may be interesting therapeutic targets.


title: A meta-analysis of transcriptomic profiles from Huntington's disease patients points to a pathophysiological role of CDC42, NFY, DLX1 and PRMT3


title: PTEN regulates adipocyte progenitor growth, differentiation and cellular aging

abstract: The tumor suppressor phosphatase and tensin homolog (PTEN) negatively regulates the insulin signaling pathway. Germline PTEN pathogenic variants cause PTEN Hamartoma Tumor Syndrome (PHTS), associated with lipoma development in children. It remains unclear which mechanisms trigger this aberrant adipose tissue growth. Adipocyte progenitor cells (APCs) lose their capacity to differentiate into adipocytes during continuous culture, while APCs from PHTS patients lipomas retain their adipogenic potential over a prolonged period. To investigate the role of PTEN in adipose tissue development we performed functional assays and RNA sequencing of control and PTEN knockdown APCs. Reduction of PTEN levels using siRNA or CRISPR lead to an enhanced proliferation and differentiation of APCs. FOXO1 was downregulated on the mRNA level while inactivation through phosphorylation increased. FOXO1 phosphorylation initiates the expression of the lipogenesis activating transcription factor SREBP1. SREBP1 levels were higher after PTEN knockdown and may account for the enhanced adipogenesis. To validate this we overexpressed constitutively active FOXO1 in PTEN CRISPR cells and found reduced adipogenesis, accompanied by a SREBP1 downregulation. We observed that PTEN levels were upregulated during long term culture of wild type APCs. PTEN CRISPR cells showed less senescence compared to controls and the senescence marker CDKN1A (p21) was downregulated in PTEN knockdown cells. Cellular senescence was the most significantly enriched pathway found in RNA sequencing of PTEN knockdown vs. control cells. These results provide evidence that PTEN is involved in the regulation of APCs proliferation, differentiation and senescence, thereby contributing to aberrant adipose tissue growth in PHTS patients.


title: PTEN regulates adipocyte progenitor growth, differentiation and replicative aging


title: Increased male mating success in the presence of prey and rivals in a sexually cannibalistic mantis

abstract:
Pre-copulatory sexual cannibalism--or cannibalism without mating--is expected to promote the evolution of male strategies that enhance mating success and reduce the risk of cannibalism, such as preferential mating with feeding females. However, sexual selection on male competitiveness may alter male courtship decisions in the face of cannibalism risk. We investigated the effect of prey availability and rival presence on male mating decisions in the highly cannibalistic Springbok mantis, Miomantis caffra. We found that males approached females more rapidly and mated more often in the presence of prey, suggesting that females distracted with foraging may be less of a threat. The presence of a rival also hastened the onset of copulation and led to higher mating success, with very large effects occurring in the presence of both prey and rivals, indicating that intrasexual competition may intensify attraction to foraging females. Taken together, our results suggest that pre-copulatory cannibalism has selected for male preference for foraging females, and that males adjust their mating strategy to both the risk of competition and the threat of cannibalism.

LAY SUMMARYDeciding when to approach a mate is critical for male mantises at risk of being cannibalised. A male might do well to pounce when a female is distracted with prey, but what if a nearby male has the same intention? In the Springbok mantis, we show that males mate faster and with greater success when both prey and a rival are present, suggesting that mating decisions depend on the dual threats of cannibalism and competition.

category: animal behavior and cognition


title: From Decellurization to Imaging to 3-D Printing: low-cost plant-derived 3D-printed tissue scaffolds for tissue engineering

abstract: Natures most abundant carbohydrate, cellulose, has incredible structural properties that can be leveraged as scaffolds for tissue engineering. With plants being an inexpensive and easily accessible source, it is more feasible to experiment with these techniques and progress in the field of regenerative tissue engineering. In this study, we set out to optimize a low-cost method to obtain cellulose scaffolds that could potentially mimic a blood vessels after recellularization with endothelial cells. We chose a readily available plant specimen, i.e. cauliflower stalk, which offers anatomical similarity to blood vessels, vascular architecture and interconnected porosity. We went on to capture the cellulose scaffold digitally and created a 3-D model using a computer-aided design (CAD) software which was then used for 3-D printing the scaffold in two different sizes. We believe the decellularize-image-print cycle allows for skipping decellularization processes of new scaffolds every time a scaffold is required and therefore cutting cost and time needed, enables instant dissemination between individual researchers and communities and allows scalable printing at any size and level of detail. We hope this will catalyze even faster innovation in the space of tissue engineering and regenerative medicine.

category: bioengineering


title: DeepStrain: A Deep Learning Workflow for the Automated Characterization of Cardiac Mechanics

abstract: Myocardial strain analysis from cinematic magnetic resonance imaging (cine-MRI) data could provide a more thorough characterization of cardiac mechanics than volumetric parameters such as left-ventricular ejection fraction, but sources of variation including segmentation and motion estimation have limited its wide clinical use. We designed and validated a deep learning (DL) workflow to generate both volumetric parameters and strain measures from cine-MRI data, including strain rate (SR) and regional strain polar maps, consisting of segmentation and motion estimation convolutional neural networks developed and trained using healthy and cardiovascular disease (CVD) subjects (n=150). DL-based volumetric parameters were correlated (>0.98) and without significant bias relative to parameters derived from manual segmentations in 50 healthy and CVD subjects. Compared to landmarks manually-tracked on tagging-MRI images from 15 healthy subjects, landmark deformation using DL-based motion estimates from paired cine-MRI data resulted in an end-point-error of 2.9 {+/-} 1.5 mm. Measures of end-systolic global strain from these cine-MRI data showed no significant biases relative to a tagging-MRI reference method. On 4 healthy subjects, intraclass correlation coefficient for intra-scanner repeatability was excellent (>0.95) for strain, moderate to excellent for SR (0.690-0.963), and good to excellent (0.826-0.994) in most polar map segments. Absolute relative change was within ~5% for strain, within ~10% for SR, and <1% in half of polar map segments. In conclusion, we developed and evaluated a DL-based, end-to-end fully-automatic workflow for global and regional myocardial strain analysis to quantitatively characterize cardiac mechanics of healthy and CVD subjects based on ubiquitously acquired cine-MRI data.


title: Cortico-autonomic local arousals and heightened somatosensory arousability during NREM sleep of mice in neuropathic pain

abstract: Chronic pain patients frequently suffer from sleep disturbances. Improvement of sleep quality alleviates pain, but neurophysiological mechanisms underlying sleep disturbances require clarification to advance therapeutic strategies. Chronic pain causes high-frequency electrical activity in pain-processing cortical areas that could disrupt the normal process of low-frequency sleep rhythm generation. We found that the spared-nerve-injury (SNI) mouse model, mimicking human neuropathic pain, had preserved sleep-wake behavior. However, when we probed spontaneous arousability based on infraslow continuity-fragility dynamics of non-rapid-eye-movement sleep (NREMS), we found more numerous local cortical arousals accompanied by heart rate increases in hindlimb primary somatosensory, but not in prelimbic, cortices of SNI mice. Closed-loop mechanovibrational stimulation revealed higher sensory arousability in SNI. Sleep in chronic pain thus looked preserved in conventional measures but showed elevated spontaneous and evoked arousability. Our findings develop a novel moment-to-moment probing of NREMS fragility and propose that chronic pain-induced sleep complaints arise from perturbed arousability.

category: physiology


title: Complexome profiling on the lpa2 mutant reveals insights into PSII biogenesis and new PSII associated proteins

abstract:
We have identified the homolog of LOW PSII ACCUMULATION 2 (LPA2) in Chlamydomonas. A Chlamydomonas lpa2 mutant grew slower in low light and was hypersensitive to high light. PSII maximum quantum efficiency was reduced by 38%. Synthesis and stability of newly made PSII core subunits D1, D2, CP43, and CP47 were not impaired. Complexome profiling revealed that in the mutant CP43 was reduced to [~]23%, D1, D2, and CP47 to [~]30% of wild-type levels, while small PSII core subunits and components of the oxygen evolving complex were reduced at most by factor two. PSII supercomplexes, dimers, and monomers were reduced to 7%, 26%, and 60% of wild-type levels, while RC47 was increased [~]6-fold. Our data indicate that LPA2 acts at a step during PSII assembly without which PSII monomers and especially further assemblies become intrinsically unstable and prone to degradation. Levels of ATP synthase and LHCII were 29% and 27% higher in the mutant than in the wild type, whereas levels of the cytochrome b6f complex were unaltered. While the abundance of PSI core subunits and antennae hardly changed, LHCI antennae were more disconnected in the lpa2 mutant, presumably as an adaptive response to reduce excitation of PSI. The disconnection of LHCA2,9 together with PSAH and PSAG was the prime response, but independent and additional disconnection of LHCA1,3-8 along with PSAK occurred as well. Finally, based on co-migration profiles, we identified three novel putative PSII associated proteins with potential roles in regulating PSII complex dynamics, assembly, and chlorophyll breakdown.

One-sentence summaryWe provide evidence that the Chlamydomonas LPA2 homolog acts at a step in PSII biogenesis without which PSII monomers and further assemblies become unstable and prone to degradation.

category: plant biology


title: Influence of chemically and biosynthesized silver nanoparticles on in vitro viability and infectivity of Trichinella spiralis muscle larvae

abstract:
Back groundTrichinellosis is a serious worldwide parasitic zoonosis. The available therapy for the treatment of Trichinella spiralis is not satisfactory. This work aimed at evaluating of the in vitro effect of silver Therefore, the recovery of effective treatment is required.nanoparticles (AgNPs) on muscle larvae of Trichinella.

Methodology / principal findingThe present study investigated the larvicidal properties of chemical and myrrh AgNPs on muscle larvae (ML) of T. spiralis. The used AgNPs were chemically prepared using NaBH4 as reducing agent and biosynthesized using methanolic myrrh extract. Characterization of synthesized AgNPs was monitored via UV-Vis spectrophotometry, Fourier transform infrared spectroscopy and transmission electron microscopy (TEM) studies. The ML incubated with AgNPs at concentrations ranged from 1g/ml to 20g/ml.

Conclusions /SignificanceChemical and biosynthesized AgNPs revealed marked larvicidal effect against ML of Trichinella. Additionally, this in vitro study showed degenerative changes affecting the cuticle of AgNPs treated ML. The effectiveness of AgNPs on the infectivity of Trichinella ML was also assessed. The results showed complete inhibition of the infectivity of ML exposed to sublethal doses of chemical and myrrh prepared AgNPs when used to infect animal models. This is the first report where myrrh synthesized AgNPs have been tested for their anthelminthic activity against Trichinella in an in vitro model.

Author summaryTrichinellosis is a serious worldwide parasitic zoonosis. The available therapy for the treatment of Trichinella spiralis is not satisfactory. Therefore, the recovery of effective treatment is required. The present study investigated the larvicidal properties of chemical and myrrh AgNPs on muscle larvae (ML) of T. spiralis. The ML incubated with AgNPs at concentrations ranged from 1g/ml to 20g/ml. Chemical and biosynthesized AgNPs revealed marked larvicidal effect against ML of Trichinella. Additionally, this in vitro study showed degenerative changes affecting the cuticle of AgNPs treated ML. Also the results showed complete inhibition of the infectivity of ML exposed to sublethal doses of chemical and myrrh prepared AgNPs when used to infect animal models.


title: Bacillus sp. RZ2MS9, a tropical PGPR, colonizes maize endophytically and alters the plant's production of volatile organic compounds both independently and when co-inoculated with Azospirillum brasilense Ab-V5

abstract:
Bacillus spp. are among the most efficient known plant growth-promoting rhizobacteria (PGPR). The PGPR Bacillus sp. strain RZ2MS9 is a multi-trait maize growth promoter previously isolated from guarana plants cultivated in the Amazon rainforest. However, there are several aspects of its interaction with the host that need further investigation. To achieve effective performance of microbial inoculants in crop production, it is necessary to monitor the plants colonization by a PGPR and to assess the potential synergy among beneficial strains. Here, we obtained a stable mutant of RZ2MS9 labelled with green fluorescent protein (RZ2MS9-GFP). We verified that the insertion of the plasmid did not affect either bacterial growth nor its ability to promote maize growth in vitro. Using fluorescent microscopy and qPCR, we demonstrated that RZ2MS9-GFP successfully colonizes maizes roots and leaves endophytically. Subsequently, we evaluated whether RZ2MS9 has a synergistic effect on plant growth promotion when co-inoculated with Azospirillum brasilense Ab-V5, a commercial inoculant for maize. The two strains combined enhanced maizes roots and shoots dry weight by 50.8% and 79.6%, respectively, when compared to the non-inoculated control. In addition, we used co-inoculation experiments in glass chambers to analyze the plants Volatile Organic Compounds (VOCs) production during the maize-RZ2MS9 and maize-RZ2MS9-Ab-V5 interaction. We found that the single and co-inoculation altered maizes VOCs emission profile, with an increase in the production of indoles in the co-inoculation. Collectively, these results increase our knowledge about the interaction between the tropical PGPR Bacillus sp. RZ2MS9 and maize, and provide a new possibility of combined application with the commercial inoculant A. brasilense Ab-V5.

ImportanceBacillus sp. RZ2MS9 is a PGPR, previously isolated from guarana plants cultivated in the Brazilian Amazon, which successfully promotes the growth of maize and soybean plants. To improve our knowledge about the interaction between this very promising PGPR and maize, we labelled RZ2MS9 with gfp and monitored its maize colonization. The transformation did not affect either RZ2MS9 growth nor its ability to promote maize growth in vitro. We demonstrated that RZ2MS9 colonizes endophytically maizes roots and leaves. We also verified that the co-inoculation of RZ2MS9 and Azospirillum brasilense Ab-V5, a known commercial maize inoculant enhanced maizes roots and shoots growth. Moreover, the co-inoculation altered the maizes volatile organic compounds, increasing the production of indoles, that is related with decreased upon the reduction of fertilization. Certainly, our research contributed with better Bacillus sp. RZ2MS9 - maize interaction understanding and also provided new information concerning RZ2MS9 activity when applied with A. brasilense Ab-V5.


title: Improving variant calling using population data and deep learning

abstract: Large-scale population variant data is often used to filter and aid interpretation of variant calls in a single sample. These approaches do not incorporate population information directly into the process of variant calling, and are often limited to filtering which trades recall for precision. In this study, we develop population-aware DeepVariant models with a new channel encoding allele frequencies from the 1000 Genomes Project. This model reduces variant calling errors, improving both precision and recall in single samples, and reduces rare homozygous and pathogenic clinvar calls cohort-wide. We assess the use of population-specific or diverse reference panels, finding the greatest accuracy with diverse panels, suggesting that large, diverse panels are preferable to individual populations, even when the population matches sample ancestry. Finally, we show that this benefit generalizes to samples with different ancestry from the training data even when the ancestry is also excluded from the reference panel.


title: An epigenetic switch regulates the ontogeny of AXL positive/EGFR-TKI resistant cells by modulating miR-335 expression

abstract: Lung cancer remains the leading cause of cancer-related mortality worldwide, despite current advancements in research and therapeutics. Many patients diagnosed with lung cancer will develop resistance to chemotherapeutic agents. In the context of non-small cell lung cancers (NSCLC) harboring EGFR oncogenic mutations, augmented levels of AXL and GAS6 have been found to drive Erlotinib resistance in certain tumors with mesenchymal-like features. By studying the ontogeny of AXL-positive cells, we have identified a novel non-genetic mechanism of drug resistance based on cell-state transition. We demonstrate that AXL-positive cells are already present as a sub-population of cancer cells in Erlotinib-naive tumors and tumor-derived cell lines, and that the expression of AXL is regulated through a stochastic mechanism centered on the epigenetic regulation of miR-335. The existence of a cell-intrinsic program through which AXL-positive/Erlotinib-resistant cells emerge infers the need of treating tumors harboring EGFR-oncogenic mutations upfront with combinatorial treatments targeting both AXL-negative and AXL-positive cancer cells.

category: cancer biology


title: A simple Agrobacterium-mediated stable transformation technique for the hornwort model Anthoceros agrestis

abstract: We have developed a simple Agrobacterium-mediated method for the stable transformation of the hornwort Anthoceros agrestis, the fifth bryophyte species for which a genetic manipulation technique becomes available. High transformation efficiency was achieved by using thallus tissue grown under low-light conditions. We generated a total of 216 transgenic A. agrestis lines expressing the {beta}-Glucuronidase (GUS), cyan, green, and yellow fluorescent proteins under the control of the CaMV 35S promoter and several endogenous promoters. Nuclear and plasma membrane localization with multiple color fluorescent proteins was also confirmed. The transformation technique described here should pave the way for detailed molecular and genetic studies of hornwort biology, providing much needed insight into the molecular mechanisms underlying symbiosis, carbon-concentrating mechanism, RNA editing, and land plant evolution in general.


title: Guanosine tetraphosphate (ppGpp) accumulation inhibits chloroplast gene expression and promotes super grana formation in the moss Physcomitrium (Physcomitrella) patens

abstract: The nucleotides guanosine tetraphosphate and pentaphosphate (or ppGpp) are implicated in the regulation of chloroplast function in plants. ppGpp signalling is best understood in the model vascular plant Arabidopsis thaliana where it acts to regulate plastid gene expression to influence photosynthesis, plant development and immunity. However, little is known about the conservation or diversity of ppGpp signaling in other land plants. Here, we studied the function of ppGpp in the moss Physcomitrium (previously Physcomitrella) patens using an inducible system for triggering ppGpp accumulation. We used this approach to investigate the effects of ppGpp on chloroplast function, photosynthesis and growth. We demonstrate that ppGpp accumulation causes a dramatic drop in photosynthetic capacity by inhibiting chloroplast gene expression. This was accompanied by the unexpected reorganisation of the thylakoid system into super grana. Surprisingly, these changes did not affect gametophore growth, suggesting that bryophytes and vascular plants may have different tolerances to defects in photosynthesis. Our findings point to the existence of both highly conserved and more specific targets of ppGpp signalling in the land plants that may reflect different growth strategies.


title: Biosynthesis of Steroidal Alkaloids Are Coordinately Regulated and Differ Among Tomatoes in the Red-Fruited Clade

abstract:
1.1O_LIWe quantitatively profiled and genotyped two tomato populations representing diversity in the red-fruited clade to address the lack of knowledge regarding the chemical diversity, concentration, and genetic architecture controlling tomato steroidal alkaloids.
C_LIO_LIWe grew 107 genetically diverse fresh market, processing, land-race, and wild tomatoes in multiple environments. Nine steroidal alkaloids were quantified using ultra-high performance liquid chromatography tandem mass spectrometry. The diversity panel and a biparental population segregating for high alpha-tomatine, were genotyped to identify and validate quantitative trait loci (QTL) associated with steroidal alkaloids.
C_LIO_LILand-races and wild material exhibited higher alkaloid concentrations and more chemical diversity. Average total content of steroidal alkaloids, often dominated by lycoperoside F/G/esculeoside A, ranged from 1.9 to 23.3 mg/100 g fresh weight across accessions. Land-race and wild cherry accessions distinctly clustered based on elevated early or late steroidal alkaloid concentrations. Significant correlations were observed among early and late steroidal alkaloids in a species-dependent manner. A QTL controlling multiple, early steroidal alkaloid pathway intermediates on chromosome 3 was identified by genome wide association (GWAS) and validated in a backcross population.
C_LIO_LITomato steroidal alkaloids are diverse in the red-fruited tomato clade and their biosynthesis is regulated in a coordinated manner.
C_LI


title: Quantitative proteomics reveals extensive lysine ubiquitination in the Arabidopsis root proteome and uncovers novel transcription factor stability states

abstract: Protein activity, abundance, and stability can be regulated by posttranslational modification including ubiquitination. Ubiquitination is conserved among eukaryotes and plays a central role in modulating cellular function and yet we lack comprehensive catalogs of proteins that are modified by ubiquitin in plants. In this study, we describe an antibody-based approach to enrich peptides containing the di-glycine (diGly) remnant of ubiquitin and coupled that with isobaric labeling to enable quantification, from up to 16-multiplexed samples, for plant tissues. Collectively, we identified 7,130 diGly-modified lysine residues sites arising from 3,178 proteins in Arabidopsis primary roots. These data include ubiquitin proteasome dependent ubiquitination events as well as ubiquitination events associated with auxin treatment. Gene Ontology analysis indicated that ubiquitinated proteins are associated with numerous biological processes including hormone signaling, plant defense, protein homeostasis, and root morphogenesis. We determined the ubiquitinated lysine residues that directly regulate the stability of the transcription factors CRYPTOCHROME-INTERACTING BASIC-HELIX-LOOP-HELIX 1 (CIB1), CIB1 LIKE PROTEIN 2 (CIL2), and SENSITIVE TO PROTON RHIZOTOXICITY (STOP1) using site directed mutagenesis and in vivo degradation assays. These comprehensive site-level ubiquitinome profiles provide a wealth of data for future studies related to modulation of biological processes mediated by this posttranslational modification in plants.


title: The LEAFY floral regulator displays pioneer transcription factor properties

abstract: Pioneer transcription factors (TFs) are a special category of TFs with the capacity to bind to closed chromatin regions in which DNA is wrapped around histones and often highly methylated. Subsequently, they are able to modify the chromatin state to initiate gene expression. In plants, LEAFY (LFY) is a master floral regulator and has been suggested to act as a pioneer TF in Arabidopsis. Here, we demonstrate that LFY is able to bind both methylated and non-methylated DNA using a combination of in vitro genome-wide binding experiments and structural modeling. Comparisons between regions bound by LFY in vivo and chromatin accessibility data suggest that LFY binds a subset of regions occupied by nucleosomes. We confirm that LFY is able to bind nucleosomal DNA in vitro using reconstituted nucleosomes. Finally, we show that constitutive LFY expression in seedling tissues is sufficient to induce chromatin accessibility in the LFY direct target genes, APETALA1 and AGAMOUS. Taken together, our study suggests that LFY possesses key pioneer TF features that contribute to launch the floral gene expression program.


title: Protection against reinfection with D614- or G614-SARS-CoV-2 isolates in hamsters

abstract: Reinfections with SARS-CoV-2 have already been documented in humans, although its real incidence is currently unknown. Besides having great impact on public health, this phenomenon raises the question if immunity generated by a single infection is sufficient to provide sterilizing/protective immunity to a subsequent SARS-CoV-2 re-exposure. The Golden Syrian hamster is a manageable animal model to explore immunological mechanisms able to counteract COVID-19, as it recapitulates pathological aspects of mild to moderately affected patients. Here, we report that SARS-CoV-2-inoculated hamsters resolve infection in the upper and lower respiratory tracts within seven days upon inoculation with the Cat01 (G614) SARS-CoV-2 isolate. Three weeks after primary challenge, and despite high titers of neutralizing antibodies, half of the animals were susceptible to reinfection by both identical (Cat01, G614) and variant (WA/1, D614) SARS-CoV-2 isolates. However, upon re-inoculation, only nasal tissues were transiently infected with much lower viral replication than those observed after the first inoculation. These data indicate that a primary SARS-CoV-2 infection is not sufficient to elicit a sterilizing immunity in hamster models but protects against lung disease.


title: To make or take: bacterial lipid homeostasis during infection

abstract:
Bacterial fatty acids are critical components of the cellular membrane. A shift in environmental conditions or in the bacteriums lifestyle may result in the requirement for a distinct pool of fatty acids with unique biophysical properties. This can be achieved by the modification of existing fatty acids or via de novo synthesis. Furthermore, bacteria have evolved efficient means to acquire these energy-rich molecules from their environment. However, the balance between de novo fatty acid synthesis and exogenous acquisition during pathogenesis is poorly understood. Here we studied the mouse fatty acid landscape prior and post infection with Acinetobacter baumannii, a Gram-negative, opportunistic human pathogen. The lipid fluxes observed following infection revealed fatty acid- and niche-specific changes. Lipidomic profiling of A. baumannii isolated from the pleural cavity of mice identified novel A. baumannii membrane phospholipid species and an overall increased abundance of unsaturated fatty acid species. Importantly, we found that A. baumannii relies largely upon fatty acid acquisition in all but one of the studied niches, the blood, where the pathogen biosynthesises its own fatty acids. This work is the first to reveal the significance of balancing the making and taking of fatty acids in a Gram-negative bacterium during infection, which provides new insights into the validity of targeting fatty acid synthesis as a treatment strategy.

ImportanceAcinetobacter baumannii is one of the worlds most problematic superbugs, and is associated with significance morbidity and mortally in the hospital environment. The critical need for new antimicrobial strategies is recognised, but our understanding of its behaviour and adaptation to a changing environment during infection is limited. Here, we investigated the role of fatty acids at the host-pathogen interface using a mouse model of disease. We provide comprehensive insights into the bacterial membrane composition when they colonise the pleural cavity. Further, we show that A. baumannii heavily relies upon making its fatty acids when residing in the blood, whereas the bacterium favours fatty acid acquisition in most other host niches. Our new knowledge aids in understanding the importance of host fatty acids in infectious diseases. Further, fatty acid synthesis is an attractive target for the development of new antimicrobial strategies, but our work emphasizes the critical need to understand the microbial lipid homeostasis before this can be deemed suitable.


title: Overexpression of a G-protein coupled receptor-like gene affects encystment of Acanthamoeba castellanii

abstract:
Acanthamoeba castellanii is an amphizoic free-living amoeba as it can be found in humans and in the environment. This amoeba represents an important reservoir of pathogenic microorganisms. Persistence of A. castellanii in the environment or in humans is allowed by the ability of the vegetative form to differentiate under cysts when surrounding conditions are unfavorable. In this study, we investigate the role of the ACA1_383450 gene during encystment of A. castellanii. This gene encodes a putative G-protein coupled receptor, which shares homology with human GPR107 and murine GPR108. Expression of the ACA1_383450 gene is transiently repressed at the early phase of encystment and its overexpression affects encystment of A. castellanii. This study reveals a new Acanthamoeba gene which could affect the encystment process.

HighlightsO_LIThe ACA1_383450 gene encodes for a putative G-protein coupled receptor (GPCR).
C_LIO_LIThe ACA1_383450 mRNA levels are down-regulated during the early phase of encystment.
C_LIO_LIOverexpression of the ACA1_383450 gene affects formation of cysts.
C_LI


title: New targets for drug design: Importance of nsp14/nsp10 complex formation for the 3'-5' exoribonucleolytic activity on SARS-CoV-2

abstract:
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus has triggered a global pandemic with devastating consequences for health-care and social-economic systems. Thus, the understanding of fundamental aspects of SARS-CoV-2 is of extreme importance.

In this work, we have focused our attention on the viral ribonuclease (RNase) nsp14, since this protein was considered one of the most interferon antagonists from SARS-CoV-2, and affects viral replication. This RNase is a multifunctional protein that harbors two distinct activities, an N-terminal 3-to-5 exoribonuclease (ExoN) and a C-terminal N7-methyltransferase (N7-MTase), both with critical roles in coronaviruses life cycle. Namely, SARS-CoV-2 nsp14 ExoN knockout mutants are non-viable, indicating nsp14 as a prominent target for the development of antiviral drugs.

Nsp14 ExoN activity is stimulated through the interaction with the nsp10 protein, which has a pleiotropic function during viral replication. In this study, we have performed the first biochemical characterization of the complex nsp14-nsp10 from SARS-CoV-2. Here we confirm the 3-5 exoribonuclease and MTase activities of nsp14 in this new Coronavirus, and the critical role of nsp10 in upregulating the nsp14 ExoN activity in vitro. Furthermore, we demonstrate that SARS-CoV-2 nsp14 N7-MTase activity is functionally independent of the ExoN activity. The nsp14 MTase activity also seems to be independent of the presence of nsp10 cofactor, contrarily to nsp14 ExoN.

Until now, there is no available structure for the SARS-CoV-2 nsp14-nsp10 complex. As such, we have modelled the SARS-CoV-2 nsp14-nsp10 complex based on the 3D structure of the complex from SARS-CoV (PDB ID 5C8S). We also have managed to map key nsp10 residues involved in its interaction with nsp14, all of which are also shown to be essential for stimulation of the nsp14 ExoN activity. This reinforces the idea that a stable interaction between nsp10 and nsp14 is strictly required for the nsp14-mediated ExoN activity of SARS-CoV-2, as observed for SARS-CoV.

We have studied the role of conserved DEDD catalytic residues of SARS-CoV-2 nsp14 ExoN. Our results show that motif I of ExoN domain is essential for the nsp14 function contrasting to the functionality of these conserved catalytic residues in SARS-CoV, and in the Middle East respiratory syndrome coronavirus (MERS). The differences here revealed can have important implications regarding the specific pathogenesis of SARS-CoV-2.

The nsp10-nsp14 interface is a recognized attractive target for antivirals against SARS-CoV-2 and other coronaviruses. This work has unravelled a basis for discovering inhibitors targeting the specific amino acids here reported, in order to disrupt the assembly of this complex and interfere with coronaviruses replication.


title: CpG-adjuvanted stable prefusion SARS-CoV-2 spike protein protected hamsters from SARS-CoV-2 challenge

abstract: The COVID-19 pandemic presents an unprecedented challenge to global public health. Rapid development and deployment of safe and effective vaccines are imperative to control the pandemic. In the current study, we applied our adjuvanted stable prefusion SARS-CoV-2 spike (S-2P)-based vaccine, MVC-COV1901, to hamster models to demonstrate immunogenicity and protection from virus challenge. Golden Syrian hamsters immunized intramuscularly with two injections of 1 {micro}g or 5 {micro}g of S-2P adjuvanted with CpG 1018 and aluminum hydroxide (alum) were challenged intranasally with SARS-CoV-2. Prior to virus challenge, the vaccine induced high levels of neutralizing antibodies with 10,000-fold higher IgG level and an average of 50-fold higher pseudovirus neutralizing titers in either dose groups than vehicle or adjuvant control groups. Six days after infection, vaccinated hamsters did not display any weight loss associated with infection and had significantly reduced lung pathology and most importantly, lung viral load levels were reduced to lower than detection limit compared to unvaccinated animals. Vaccination with either 1 g or 5 g of adjuvanted S-2P produced comparable immunogenicity and protection from infection. This study builds upon our previous results to support the clinical development of MVC-COV1901 as a safe, highly immunogenic, and protective COVID-19 vaccine.


title: Hydraulic diversity stabilizes productivity in a large-scale subtropical tree biodiversity experiment

abstract: Extreme climatic events threaten forests and their climate mitigation potential globally. Understanding the drivers promoting ecosystem stability is therefore considered crucial to mitigate adverse climate change effects on forests. Here, we use structural equation models to explain how tree species richness, asynchronous species dynamics and diversity in hydraulic traits affect the stability of forest productivity along an experimentally manipulated biodiversity gradient ranging from 1 to 24 tree species. Tree species richness improved stability by increasing species asynchrony. That is, at higher species richness, inter-annual variation in productivity among tree species buffered the community against stress-related productivity declines. This effect was mediated by the diversity of species hydraulic traits regarding drought tolerance and stomatal control, but not by the community-weighted means of these traits. The identified mechanisms by which tree species richness stabilizes forest productivity emphasize the importance of hydraulically diverse, mixed-species forests to adapt to climate change.


title: Nonadaptive radiation of the gut microbiome in an adaptive radiation of Cyprinodon pupfishes with minor shifts for scale-eating

abstract: Adaptive radiations offer an excellent opportunity to understand the eco-evolutionary dynamics of gut microbiota and host niche specialization. In a laboratory common garden, we compared the gut microbiota of two novel trophic specialists, a scale-eater and a molluscivore, to a set of four outgroup generalist populations from which this adaptive radiation originated. We predicted an adaptive and highly divergent microbiome composition in the specialists matching their rapid rates of craniofacial diversification in the past 10 kya. We measured gut lengths and sequenced 16S rRNA amplicons of gut microbiomes from lab-reared fish fed the same high protein diet for one month. In contrast to our predictions, gut microbiota largely reflected 5 Mya phylogenetic divergence times among generalist populations in support of phylosymbiosis. However, we did find significant enrichment of Burkholderiaceae bacteria in both lab-reared scale-eater populations. These bacteria sometimes digest collagen, the major component of fish scales, supporting an adaptive shift. We also found some enrichment of Rhodobacteraceae and Planctomycetacia in lab-reared molluscivore populations, but these bacteria target cellulose. Minor shifts in gut microbiota appear adaptive for scale-eating in this radiation, whereas overall microbiome composition was phylogenetically conserved. This contrasts with predictions of adaptive radiation theory and observations of rapid diversification in all other trophic traits in these hosts, including craniofacial morphology, foraging behavior, aggression, and gene expression, suggesting that microbiome divergence proceeds as a nonadaptive radiation.


title: Genetic Characteristics and Phylogeny of 969-bp S Gene Sequence of SARS-CoV-2 from Hawaii Reveals the Worldwide Emerging P681H Mutation

abstract: COVID-19 pandemic has ravaged the world, caused over 1.8 million deaths in the first year, and severely affected the global economy. Hawaii is not spared from the transmission of SARS-CoV-2 in the local population, including high infection rates in racial and ethnic minorities. Early in the pandemic, we described in this journal various technologies used for the detection of SARS-CoV-2. Herein we characterize a 969-bp SARS-CoV-2 segment of the S gene downstream of the receptor-binding domain. At the John A. Burns School of Medicine Biocontainment Facility, RNA was extracted from an oropharyngeal swab and a nasal swab from two patients from Hawaii who were infected with the SARS-CoV-2 in August 2020. Following PCR, the two viral strains were sequenced using Sanger sequencing, and phylogenetic trees were generated using MEGAX. Phylogenetic tree results indicate that the virus has been introduced to Hawaii from multiple sources. Further, we decoded 13 single nucleotide polymorphisms across 13 unique SARS-CoV-2 genomes within this region of the S gene, with one non-synonymous mutation (P681H) found in the two Hawaii strains. The P681H mutation has unique and emerging characteristics with a significant exponential increase in worldwide frequency when compared to the plateauing of the now universal D614G mutation. The P681H mutation is also characteristic of the new SARS-CoV-2 variants from the United Kingdom and Nigeria. Additionally, several mutations resulting in cysteine residues were detected, potentially resulting in disruption of the disulfide bridges in and around the receptor-binding domain. Targeted sequence characterization is warranted to determine the origin of multiple introductions of SARS-CoV-2 circulating in Hawaii.


title: Structural Basis of KAI2 Divergence in Legume

abstract: KAI2 are plant /{beta} hydrolase receptors, which perceive smoke-derived butenolide signals (karrikins) and putative endogenous, yet unidentified phytohormones (KAI2-ligands, KLs). The number of functional KAI2 receptors varies among plant species. It has been suggested that KAI2 gene duplication and sub-functionalization plays an adaptative role for diverse environments or ligand diversification by altering the receptor responsiveness to specific KLs. Legumes represent one of the largest families of flowering plants and contain many essential agronomic crops. Prior to legume diversification, KAI2 underwent duplication, resulting in KAI2A and KAI2B. Integrating plant genetics, ligand perception and enzymatic assays, and protein crystallography, we demonstrate that Pisum sativum KAI2A and KAI2B act as receptors and enzymes with divergent ligand stereoselectivity. KAI2B has a stronger affinity than KAI2A towards the KAI2-ligand (-)-GR24 and remarkably hydrolyses a broader range of substrates including the strigolactone-like isomer (+)-GR24. We determine the crystal structures of PsKAI2B in apo and butenolide-bound states. The biochemical and structural analyses as well as recorded mass spectra of KAI2s reveal a transient intermediate on the catalytic serine and a stable adduct on the catalytic histidine, further illuminating the role of KAI2 not only as receptors but also as bona fide enzymes. Our work uncovers the stereoselectivity of ligand perception and catalysis by evolutionarily diverged KAI2 receptors in KAR/KL signaling pathways and proposes adaptive sensitivity to KAR/KL and strigolactone phytohormones by KAI2B.

category: biochemistry


title: Structural and Functional Analyses Explain Pea KAI2 Receptor Diversity and Reveal Stereoselective Catalysis During Signal Perception


title: Molecular dynamics simulations and functional studies reveal that hBD-2 binds SARS-CoV-2 spike RBD and blocks viral entry into ACE2 expressing cells

abstract: New approaches to complement vaccination are needed to combat the spread of SARS-CoV-2 and stop COVID-19 related deaths and long-term medical complications. Human beta defensin 2 (hBD-2) is a naturally occurring epithelial cell derived host defense peptide that has antiviral properties. Our comprehensive in-silico studies demonstrate that hBD-2 binds the site on the CoV-2-RBD that docks with the ACE2 receptor. Biophysical and biochemical assays confirm that hBD-2 indeed binds to the CoV-2-receptor binding domain (RBD) (KD [~] 300 nM), preventing it from binding to ACE2 expressing cells. Importantly, hBD-2 shows specificity by blocking CoV-2/spike pseudoviral infection, but not VSV-G mediated infection, of ACE2 expressing human cells with an IC50 of 2.4{+/-} 0.1 M. These promising findings offer opportunities to develop hBD-2 and/or its derivatives and mimetics to safely and effectively use as novel agents to prevent SARS-CoV-2 infection.


title: Comprehensive comparison of transcriptomes in SARS-CoV-2 infection: alternative entry routes and innate immune responses

abstract: The pathogenesis of COVID-19 emerges as complex, with multiple factors leading to injury of different organs. Several studies on underlying cellular processes have produced contradictory claims, e.g. on SARS-CoV-2 cell entry or innate immune responses. However, clarity in these matters is imperative for therapy development. We therefore performed a meta-study with a diverse set of transcriptomes under infections with SARS-CoV-2, SARS-CoV and MERS-CoV, including data from different cells and COVID-19 patients. Using these data, we investigated viral entry routes and innate immune responses. First, our analyses support the existence of cell entry mechanisms for SARS and SARS-CoV-2 other than the ACE2 route with evidence of inefficient infection of cells without expression of ACE2; expression of TMPRSS2/TPMRSS4 is unnecessary for efficient SARS-CoV-2 infection with evidence of efficient infection of A549 cells transduced with a vector expressing human ACE2. Second, we find that innate immune responses in terms of interferons and interferon simulated genes are strong in relevant cells, for example Calu3 cells, but vary markedly with cell type, virus dose, and virus type.


title: Careless: A Variational Bayesian Model for Merging X-ray Diffraction Data

abstract: AO_SCPLOWBSTRACTC_SCPLOWThe primary data in X-ray diffraction experiments are images which contain bright spots known as reflections. In order to compute the electron density of the crystal which yields these reflections, the intensity of each reflection must be estimated. Redundant observations must be parsimoniously reduced to a set of summary intensities and corresponding error estimates. This task is confounded by a range of systematic effects leading to equivalent reflections being expressed on different scales. Here, we present a modern Bayesian solution to this problem, careless, which uses deep learning and variational inference to simultaneously merge and scale reflection observations. We successfully apply this method to conventional monochromatic X-ray diffraction data, polychromatic diffraction data, and finally X-ray free-electron laser data. Thereby, we find that this single model is generally applicable to many types of X-ray diffraction experiments.

category: biophysics


title: Neuropilin-1 Assists SARS-CoV-2 Infection by Stimulating the Separation of Spike Protein Domains S1 and S2

abstract: The cell surface receptor Neuropilin-1 (Nrp1) was recently identified as a host factor for SARS-CoV-2 entry. As the Spike protein of SARS-CoV-2 is cleaved into the S1 and the S2 domain by furin protease, Nrp1 binds to the newly created C-terminal RRAR amino acid sequence of the S1 domain. In this study, we model the association of a Nrp1 (a2-b1-b2) protein with the Spike protein computationally and analyze the topological constraints in the SARS-CoV-2 Spike protein for binding with Nrp1 and ACE2. Importantly, we study the exit mechanism of S2 from the S1 domain with the assistance of ACE2 as well as Nrp1 by molecular dynamics pulling simulations. In the presence of Nrp1, by binding the S1 more strongly to the host membrane, there is a high probability of S2 being pulled out, rather than S1 being stretched. Thus, Nrp1 binding could stimulate the exit of S2 from the S1 domain, which will likely increase virus infectivity as the liberated S2 domain mediates the fusion of virus and host membranes. Understanding of such a Nrp1-assisted viral infection opens the gate for the generation of protein-protein inhibitors, such as antibodies, which could attenuate the infection mechanism and protect certain cells in a future combination therapy.


title: Stable Interaction Of The UK B.1.1.7 lineage SARS-CoV-2 S1 Spike N501Y Mutant With ACE2 Revealed By Molecular Dynamics Simulation

abstract:
Corona Virus Disease of 2019 (COVID-19) caused by Severe Acute Respiratory Syndrome Corona Virus 2 (SARS-CoV-2) has caused a massive health crisis across the globe, with some genetic variants gaining enhanced infectivity and competitive fitness, and thus significantly aggravating the global health concern. In this regard, the recent SARS-CoV-2 alpha variant, B.1.1.7 lineage, reported from the United Kingdom (UK), is of great significance in that it contains several mutations that increase its infection and transmission rates as evident from clinical reports. Specifically, the N501Y mutation in the SARS-CoV-2 spike S1 receptor binding domain (S1-RBD) has been shown to possess an increased affinity for ACE2, although the basis for this is not entirely clear yet. Here, we dissect the mechanism underlying the increased affinity using molecular dynamics (MD) simulations of the available ACE2-S1-RBD complex structure (6M0J) and show a prolonged and stable interfacial interaction of the N501Y mutant S1-RBD with ACE2 compared to the wild type S1-RBD. Additionally, we find that the N501Y mutant S1-RBD displays altered dynamics that likely aids in its enhanced interaction with ACE2. By elucidating a mechanistic basis for the increased affinity of the N501Y mutant S1-RBD for ACE2, we believe that the results presented here will aid in developing therapeutic strategies against SARS-CoV-2 including designing drugs targeting the ACE2-S1-RBD interaction.

SignificanceThe emergence of the new SARS-CoV-2 lineage in the UK in December 2020 has further aggravated the COVID-19 pandemic due to an increased ability of the variant to infect human hosts, likely due to mutations in the viral S1 spike protein including the N501Y S1-RBD mutation that is located at the interface of S1-RBD and ACE2, the host cell receptor for SARS-CoV-2. Given its location at the interface, N501Y S1-RBD mutation can therefore potentially alter the interfacial interaction. Multiple, all-atom, explicit solvent MD simulations of the ACE2-S1-RBD complex carried here indicated a more stable interaction between the N501Y mutant S1-RBD and ACE2 through stabilizing interfacial interactions of residues at one end of the interface that are either sequentially or physically near the mutation site. These mechanistic details will aid in better understanding the mechanism by which the alpha variant has increased infectivity as well as in designing better therapeutics including ACE2-S1 spike protein inhibitors that will, in turn, help thwarting the current and future pandemic.

HighlightsO_LIN501 in the wild type SARS-CoV-2 S1-RBD forms unsustained hydrogen bonds with residues in the ACE2, namely Y41 and K353
C_LIO_LIY501 in the N501Y mutant SARS-CoV-2 S1-RBD is not capable of forming substantial hydrogen bonds with ACE2 within the time span of the current simulation
C_LIO_LIEvidence from analyzing the simulation results suggests that Y501 of S1-RBD could form other types of non-covalent interactions with ACE2, such as van der Waals interactions
C_LIO_LIN501Y S1-RBD mutation stabilizes the position of interfacial residues neighboring to the mutation site, as well as other non-interfacial residues that are distant from the mutation site
C_LIO_LIThese altered dynamics results in more stable interaction of S1-RBD with ACE2 which could be the main reason underlying the reported enhanced affinity of S1-RBD in the SARS-CoV-2 alpha variant (UK B.1.1.7 lineage) to ACE2
C_LI


title: Decreased Interfacial Dynamics Caused by the N501Y Mutation in the SARS-CoV-2 S1 Spike:ACE2 Complex


title: Rhizoliths identified as prehistoric filing tools for fishhook production on San Nicolas Island, California

abstract: Chemical analysis of archeological objects can provide important clues about their purpose and function. In this study, we used scanning electron microscopy (SEM) and chemical spectroscopy (SEM-EDS and XRD) to identify a white residue present on cylindrical rhizoliths from a component at an archaeological site (CA-SNI-25) on San Nicolas Island, California, dated ca. AD 1300 to 1700. The residue was found to consist of biogenic calcite and aragonite particles, different in composition and morphology from the CaCO3 particles in the rhizoliths, but identical to marine shell material. These results, together with observations of surface micro-wear patterning on fishhooks and rhizoliths, replicative experiments, in situ spatial analysis, and other archaeological evidence, show that rhizoliths were used as files in a larger tool kit for crafting shell fishhooks. Our findings shed new light on the technological innovations devised by Native Americans to exploit the rich marine resources surrounding the Channel Islands, and provide the first analytical evidence for the use of rhizoliths as a production tool.

category: paleontology


title: Tracking the relation between gist and item memory over the course of long term memory consolidation

abstract: Our experiences in the world support memories not only of specific episodes but also of the generalities (the  gist) across related experiences. It remains unclear how these two types of memories evolve and influence one another over time. 173 human participants encoded spatial locations from a distribution and reported both item memory (specific locations) and gist memory (center for the locations) across one to two months. After one month, gist memory was preserved relative to item memory, despite a persistent positive correlation between them. Critically, item memories were biased towards the gist over time; however, with a spatial outlier item, the local center excluding the outlier became the source of bias, instead of the reported center overweighting the outlier. Our results suggest that the extraction of gist is sensitive to the regularities of items, and that the gist starts to guide item memories over longer durations as their relative strengths change.


title: Association between breastfeeding during infancy and white matter microstructure in early childhood

abstract:
IntroductionAssociations between breastfeeding and brain development, in the context of child, perinatal, and sociodemographic variables, remain unclear. This study investigates whether exclusive breastfeeding for the first 6 months and total duration of any breastfeeding are associated with brain white matter microstructure in young children.

MethodsThis study included a sample of 83 mothers and 85 typically developing children (42 males). Children underwent their first diffusion tensor imaging scan between ages 2.34-6.97 years; some children returned multiple times, providing a total of 331 datasets. Feeding information was collected from the mothers at 3, 6, and 12 months postpartum and at their childs scan to calculate breastfeeding status at 6 months (exclusive or not) as well as total duration of any breastfeeding. Linear regression was used to investigate associations between breastfeeding exclusivity/duration and fractional anisotropy (FA, a measure sensitive to myelination/axonal packing/fibre coherence) for the whole brain and 10 individual white matter tracts.

ResultsBreastfeeding exclusivity and duration were associated with global and regional white matter microstructure, even after controlling for perinatal and sociodemographic factors. Greater exclusivity was associated with higher FA in females and lower FA in males.

ConclusionsThese findings suggest white matter differences associated with breastfeeding that differ by sex. These may stem from different trajectories in white matter development between males and females in early childhood and suggest possible long-term white matter differences associated with breastfeeding.


title: White Matter Alterations in Young Children with Prenatal Alcohol Exposure

abstract: Prenatal alcohol exposure (PAE) can lead to cognitive, behavioural, and social-emotional challenges. Previous neuroimaging research has identified alterations to brain structure in newborns, older children, adolescents, and adults with PAE; however, little is known about brain structure in young children. Extensive brain development takes place during early childhood; therefore, understanding the neurological profiles of young children with PAE is critical for early identification and effective intervention. We studied 54 children (5.21{+/-}1.11 years; 27 males) with confirmed PAE compared to 54 age- and sex-matched children without PAE. Children underwent diffusion tensor imaging between 2 and 7 years of age. Mean fractional anisotropy (FA) and mean diffusivity (MD) were obtained for 10 major white matter tracts, along with tract volume, axial and radial diffusivity (AD, RD). A univariate analysis of covariance was conducted to test for group differences (PAE vs. control) controlling for age, sex and tract volume. Our results reveal white matter microstructural differences between young children with PAE and unexposed controls. The PAE group had higher FA and/or lower MD (as well as lower AD and RD) in the genu and the body of the corpus callosum, as well as the bilateral uncinate fasciculus and pyramidal tracts. Our findings align with studies of newborns with PAE finding lower AD, but contrast those in older populations with PAE, which consistently report lower FA and higher MD. These findings may reflect premature development of white matter that may then plateau too early, leading to the lower FA/higher MD observed at older ages.


title: Glycogen Synthase Kinase 3 regulates the genesis of the rare displaced ganglion cell retinal subtype

abstract: Glycogen Synthase Kinase 3 (GSK) proteins (GSK3 and GSK3{beta}) are key mediators of signaling pathways, with crucial roles in coordinating fundamental biological processes during neural development. Here we show that the complete loss of GSK3 signaling in mouse retinal progenitors leads to microphthalmia with broad morphological defects. Both proliferation of retinal progenitors and neuronal differentiation are impaired and result in enhanced cell death. A single wild-type allele of either Gsk3 or Gsk3{beta} is able to rescue these phenotypes. In this genetic context, all cell types are present with a functional retina. However, we unexpectedly detect a large number of cells in the inner nuclear layer expressing retinal ganglion cell (RGC)-specific markers (called displaced RGCs, dRGCs) when at least one allele of Gsk3 is expressed. Excess dRGCs lead to increased number of axons projecting into the ipsilateral medial terminal nucleus, an area of the brain belonging to the non-image-forming visual circuit and poorly targeted by RGCs in wild-type retina. Transcriptome analysis and optomotor response assay suggest that at least a subset of dRGCs in Gsk3 mutant mice are direction-selective RGCs. Our study thus uncovers a unique role of GSK3 in controlling the genesis of dRGCs, a rare and poorly characterized retinal cell type.


title: Human B cell lineages engaged by germinal centers following influenza vaccination are measurably evolving

abstract: Poor efficacy of seasonal influenza virus vaccines is often attributed to pre-existing immunity interfering with the persistence and maturation of vaccine-induced B cell responses.1 Consistent with this notion, no significant increase in somatic hypermutation (SHM) among circulating influenza-binding lineages was detected following seasonal vaccination in humans.2 A more recent study showed that at least a subset of vaccine-induced B cell lineages are recruited into germinal centers (GCs) following vaccination, suggesting that affinity maturation of these lineages can occur.3 Crucially, however, it has not been demonstrated whether these GC-engaged lineages actually accumulate additional SHM. Here, we address this point using a phylogenetic test of measurable evolution. We first validate this test through simulations and demonstrate measurable B cell evolution in known examples of affinity maturation such as the response to HIV infection. We then show that lineages in the blood are rarely measurably evolving following influenza vaccination, but that GC-engaged lineages - likely derived from memory B cells - are frequently measurably evolving. These findings confirm that seasonal influenza virus vaccination can stimulate additional SHM among responding B cell lineages.

category: immunology


title: Enhancing cancer targeting of γ9δ2TCR through modified NKG2D co-stimulation

abstract: Despite the ability of {gamma}{delta}T cells to mediate tumor killing independently of MHC recognition, all the clinical trials that have been carried out using these cells showed low response rate in patients, in part due to its poor proliferation ability. Recently, a new generation of CAR-T cells called {beta}T cells engineered to express a defined {gamma}{delta}TCR (TEG) has been developed. TEGs are {beta}T cells engineered to express a defined {gamma}{delta}TCR. These cells are able to mediate effective antitumor reactivity without showing any reactivity towards healthy tissue, and combine the best qualities of both {beta}T and {gamma}{delta}T cells. In fact, the high affinity {gamma}9{delta}2TCR clone 5 has recently been selected within the TEG format as a clinical candidate (TEG001). Here we present a strategy to improve the antitumor activity of TEG001 by co-expressing an activating chimeric co-receptor together with {gamma}{delta}TCR-Cl5.Therefore, we developed three different co-receptors by fusing the extracellular domain of the activating cell surface receptor NKG2D, that is able to bind stress induced ligands typically expressed on tumor cells, to the cytoplasmic signaling domains of the T cell costimulatory proteins ICOS, CD28 and 4-1BB. We determined that introduction of the chimeric co-receptors NKG2D-CD28wt and NKG2D-4-1BBCD28TM improved the activity of TEG001 against tumors that were recognized by {gamma}{delta}TCR-Cl5 and expressed NKG2D ligands, but did not affect tumors that either were not recognized by {gamma}{delta}TCR-Cl5 or did not express NKG2D ligands. This  chimeric co-receptors approach open a wide range of opportunities that lead to a next generation of TEGs.