title: Body mass, temperature, and depth shape the maximum intrinsic rate of population increase in sharks and rays

abstract: An important challenge in ecology is to understand variation in species maximum intrinsic rate of population increase, rmax, not least because rmax underpins our understanding of the limits of fishing, recovery potential, and ultimately extinction risk. Across many vertebrates, terrestrial and aquatic, body mass and environmental temperature across important correlates rmax across species. In sharks and rays, specifically, rmax is known be lower in larger species, but also in deep-sea ones. We use an information-theoretic approach that accounts for phylogenetic relatedness to evaluate the relative importance of body mass, temperature and depth on rmax. We show that both temperature and depth have separate effects on shark and ray rmax estimates, such that species living in deeper waters have lower rmax. Furthermore, temperature also correlates with changes in the mass scaling coefficient, suggesting that as body size increases, decreases in rmax are much steeper for species in warmer waters. These findings suggest that there (as-yet understood) depth-related processes that limit the maximum rate at which populations can grow in deep sea sharks and rays. While the deep ocean is associated with colder temperatures, other factors that are independent of temperature, such as food availability and physiological constraints, may influence the low rmax observed in deep sea sharks and rays. Our study lays the foundation for predicting the intrinsic limit of fishing, recovery potential, and extinction risk species based on easily accessible environmental information such as temperature and depth, particularly for data-poor species.


title: Clonal evolution in serially passaged Cryptococcus neoformans x deneoformans hybrids reveals a heterogenous landscape of mitotic recombination

abstract: Cryptococcus neoformans x deneoformans hybrids (also known as serotype AD hybrids) are basidiomycete yeasts that are common in a clinical setting. Like many hybrids, the AD hybrids are largely locked at the F1 stage and are mostly unable to undergo normal meiotic reproduction. However, these F1 hybrids, which display a high ([~]10%) sequence divergence are known to genetically diversify through mitotic recombination and aneuploidy, and this diversification may be adaptive. In this study, we evolved a single AD hybrid genotype in six diverse environments by serial passaging and then used genome resequencing of evolved clones to determine evolutionary mechanisms of adaptation. The evolved clones generally increased fitness after passaging, accompanied by an average of 3.3 point mutations, 2.9 loss of heterozygosity (LOH) events, and 0.7 trisomic chromosomes per clone. LOH occurred through nondisjunction of chromosomes, crossing over consistent with break-induced replication, and gene conversion, in that order of prevalence. The breakpoints of these recombination events were significantly associated with regions of the genome with lower sequence divergence between the parents and clustered in subtelomeric regions, notably in regions that had undergone introgression between the two parental species. Parallel evolution was observed, particularly through repeated homozygosity via nondisjunction, yet there was little evidence of environment-specific parallel change for either LOH, aneuploidy, or mutations. These data show that AD hybrids have both a remarkable genomic plasticity and yet are challenged in the ability to recombine through sequence divergence and chromosomal rearrangements, a scenario likely limiting the precision of adaptive evolution to novel environments.

category: genetics


title: Clonal evolution in serially passaged Cryptococcus neoformans x deneoformans hybrids reveals a heterogenous landscape of genomic change


title: Death comes for us all: an interplay of habitat selection, movement, and social behavior relate to cause specific mortality among grey wolves

abstract:
Avoiding death infects biological processes, including behavior. Habitat selection, movement, and sociality are highly flexible behaviors that influence the mortality risks and subsequent fitness of individuals. In the Anthropocene, animals are experiencing increased risks from direct human causes and increased spread of infectious diseases. Using integrated step selection analysis, we tested how the habitat selection, movement, and social behaviors of grey wolves vary as an individual dies due to humans or canine distemper virus (CDV) and how those behaviors may vary in the lead up to death. Behaviors that changed prior to death were strongly related to how an animal eventually died. Wolves killed by humans moved slower than wolves that survived and selected to be nearer roads closer in time to their death. Wolves that died due to CDV moved progressively slower as they neared death and reduced their avoidance of wet habitats. All animals, regardless of dying or not maintained strong selection to be near packmates across time, which seemingly contributed to disease dynamics in the packs that became infected with CDV. Habitat selection, movement, and sociality interact to put individuals and groups at greater risks, influencing their cause-specific mortality.

Lay SummaryNot much is known about behaviors prior to death in wild animals. Grey wolves killed by humans selected to be in riskier areas increasingly prior to their deaths. Wolves that died due to disease moved slower and changed their habitat selection to be in areas with more water as they became sicker. Sick wolves also continued to select for packmates, increasing the chances that the whole pack would succumb to the disease.

category: animal behavior and cognition


title: DeepMOCCA: A pan-cancer prognostic model identifies personalized prognostic markers through graph attention and multi-omics data integration

abstract:
Combining multiple types of genomic, transcriptional, proteomic, and epigenetic datasets has the potential to reveal biological mechanisms across multiple scales, and may lead to more accurate models for clinical decision support. Developing efficient models that can derive clinical outcomes from high-dimensional data remains problematical; challenges include the integration of multiple types of omics data, inclusion of biological background knowledge, and developing machine learning models that are able to deal with this high dimensionality while having only few samples from which to derive a model. We developed DeepMOCCA, a framework for multi-omics cancer analysis. We combine different types of omics data using biological relations between genes, transcripts, and proteins, combine the multi-omics data with background knowledge in the form of protein-protein interaction networks, and use graph convolution neural networks to exploit this combination of multi-omics data and background knowledge. DeepMOCCA predicts survival time for individual patient samples for 33 cancer types and outperforms most existing survival prediction methods. Moreover, DeepMOCCA includes a graph attention mechanism which prioritizes driver genes and prognostic markers in a patient-specific manner; the attention mechanism can be used to identify drivers and prognostic markers within cohorts and individual patients.

Author summaryLinking the features of tumors to a prognosis for the patient is a critical part of managing cancer. Many methods have been applied to this problem but we still lack accurate prognostic markers for many cancers. We now have more information than ever before on the state of the cancer genome, the epigenetic changes in tumors, and gene expression at both RNA and protein levels. Here, we address the question of how this data can be used to predict cancer survival and discover which tumor genes make the greatest contribution to the prognosis in individual tumor samples. We have developed a computational model, DeepMOCCA, that uses artificial neural networks underpinned by a large graph constructed from background knowledge concerning the functional interactions between genes and their products. We show that with our method, DeepMOCCA can predict cancer survival time based entirely on features of the tumor at a cellular and molecular level. The method confirms many existing genes that affect survival but for some cancers suggests new genes, either not implicated in survival before or not known to be important in that particular cancer. The ability to predict the important features in individual tumors provided by our method raises the possibility of personalized therapy based on the gene or network dominating the prognosis for that patient.

category: bioinformatics


title: Fragment-based computational design of antibodies targeting structured epitopes

abstract:
De novo design methods hold the promise of reducing the time and cost of antibody discovery, while enabling the facile and precise targeting of predetermined epitopes. Here we describe a fragment-based method for the combinatorial design of antibody binding loops and their grafting onto antibody scaffolds. We designed and tested six single-domain antibodies targeting different epitopes on three antigens, including the receptor-binding domain of the SARS-CoV-2 spike protein. Biophysical characterisation showed that all designs are highly stable, and bind their intended targets with affinities in the nanomolar range without any in vitro affinity maturation. We further discuss how a high-resolution input antigen structure is not required, as our method yields similar predictions when the input is a crystal structure or a computer-generated model. This computational procedure, which readily runs on a laptop, provides a starting point for the rapid generation of lead antibodies binding to pre-selected epitopes.

summaryA combinatorial method can rapidly design nanobodies for predetermined epitopes, which bind with KDs in the nanomolar range.


title: A study of the neuronal injury biomarkers pNF-H and UCHL1 in serum, CSF and urine in a cohort of thoracic endovascular aortic repair (TEVAR) patients.

abstract: A collection of longitudinal serum, cerebrospinal fluid (CSF) and urine samples were collected from a cohort of 50 patients undergoing thoracic endovascular aortic repairs (TEVAR). Samples were taken multiple time per day out to 5 days post operation and were probed with novel electrochemiluminescent assays specific for the phosphorylated axonal form of the major neurofilament subunit NF-H (pNF-H) and for ubiquitin C-terminal hydrolase 1 (UCHL1). Control blood samples showed small signals for pNF-H and in some cases rather larger signals for UCHL1. The presence of UCHL1 in these control blood samples was convincingly verified by western blotting with multiple well characterized UCHL1 antibodies and by mass spectroscopy. Elevated levels of both pNF-H and UCHL1 in blood and CSF in recovering TEVAR patients were associated with poorer outcomes. In particular release of UCHL1 into blood over several hours following TEVAR and peaking at any time over 1 ng/ml was a very strong predictor of patient death and was associated with renal failure and spinal cord ischemia (SCI). An unexpected finding was that high levels of UCHL1 were detected in certain urine samples, again in association with SCI, renal failure and poor patient outcome. We also present epitope mapping data on the UCHL1 monoclonal antibodies used including data on the widely used commercially available MCA-BH7. These studies suggest that measurement of the levels of both proteins in the blood, CSF and urine of TEVAR patients may be of clinical utility. However this study also raises questions about the origin and significance of UCHL1 both in control blood, in patient blood samples and in urine.

category: neuroscience


title: Slow rTMS to the left DLPFC enhances verbal memory formation

abstract: Encoding of episodic memories relies on stimulus-specific information processing and involves the left prefrontal cortex. We here present an incidental finding from a simultaneous EEG-TMS experiment as well as a replication of this unexpected effect. Our results reveal that stimulating the left dorsolateral prefrontal cortex (DLPFC) with slow repetitive transcranial magnetic stimulation (rTMS) leads to enhanced word memory performance. 40 healthy human participants engaged in a list learning paradigm. Half of the subjects (N=20) received 1 Hz rTMS to the left DLPFC while the other half (N=20) received 1 Hz rTMS to the vertex and served as a control group. Subjects receiving left DLPFC stimulation demonstrated enhanced memory performance compared to the control group. This effect was replicated in a double-blind within-subjects experiment where 24 participants received 1 Hz rTMS to the left DLPFC and vertex. In this second experiment, DLPFC stimulation also induced better memory performance compared to vertex stimulation. In addition to these behavioural effects, we found that 1 Hz rTMS to DLPFC induced stronger beta power modulation in posterior areas, a state which is known to be beneficial for memory encoding. Further analysis indicated, that beta modulations did not have an oscillatory origin. Instead, the observed beta modulations were a result of a spectral tilt, suggesting inhibition of these parietal regions. These results show that applying 1 Hz rTMS to DLPFC, an area involved in episodic memory formation, improves memory performance via modulating neural activity in parietal regions.


title: Rhythmic neuronal activities of the rat nucleus of the solitary tract are impaired by short-term high fat diet - implications for daily control of satiety by the brainstem

abstract:
Temporal partitioning of daily food intake is crucial for survival and involves the integration of internal circadian states and external influences such as the light-dark cycle and the composition of diet. These intrinsic and extrinsic factors are interdependent with misalignment of circadian rhythms promoting body weight gain, while consumption of a calorie dense diet elevates the risk of obesity and blunts circadian rhythms. Since cardiovascular disease, metabolic disorders, and cancer are comorbid with obesity, understanding the relationships between brain activity and diet is of pivotal importance. Recently, we defined for the first time the circadian properties of the dorsal vagal complex of the brainstem, a structure implicated in the control of food intake and autonomic tone, but if and how 24 h rhythms in this area are influenced by diet remains unresolved. Here we focused on a key structure of this complex, the nucleus of the solitary tract, and using a range of approaches, we interrogated how its neuronal and cellular rhythms are affected by high-fat diet. We report that short term consumption of this diet increases food intake during the day and blunts daily rhythms in gene expression and neuronal discharge in the nucleus of the solitary tract. These alterations in this structure occur without prominent body weight gain, suggesting that high-fat diet acts initially to reduce activity in the nucleus of the solitary tract, thereby disinhibiting mechanisms that suppress daytime feeding.

GRAPHICAL ABSTRACT

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title: BonZeb: Open-source, modular software tools for high-resolution zebrafish tracking and analysis

abstract: We present BonZeb - a suite of modular Bonsai packages which allow high-resolution zebrafish tracking with dynamic visual feedback. Bonsai is an increasingly popular software platform that is accelerating the standardization of experimental protocols within the neurosciences due to its speed, flexibility, and minimal programming overhead. BonZeb can be implemented into novel and existing Bonsai workflows for online behavioral tracking and offline tracking with batch processing. We demonstrate that BonZeb can run a variety of experimental configurations used for gaining insights into the neural mechanisms of zebrafish behavior. BonZeb supports head-fixed closed-loop and free-swimming virtual open-loop assays as well as multi-animal tracking, optogenetic stimulation, and calcium imaging during behavior. The combined performance, ease of use and versatility of BonZeb opens new experimental avenues for researchers seeking high-resolution behavioral tracking of larval zebrafish.


title: No balance between glutamate+glutamine and GABA+ in visual and motor cortices of the human brain

abstract: Theoretical work, supported by electrophysiological evidence, asserts that a balance between excitation and inhibition (E/I) is critical for healthy brain function. In magnetic resonance spectroscopy (MRS) studies, the ratio of excitatory (glutamate) and inhibitory ({gamma}-aminobutyric acid, GABA) neurotransmitters is often used as a proxy for this E/I balance. Recent MRS work found a positive correlation between GABA+ and Glx (glutamate+glutamine) in medial parietal cortex, providing validation for this proxy and supporting the link between the E/I balance observed in electrophysiology and that detected with MRS. Here we assess the same relationship, between GABA+ and Glx, in primary visual and motor cortices of resting male and female human participants. We find moderate to strong evidence that there is no positive correlation between these neurotransmitters in either location. We show this holds true when controlling for a range of other factors (i.e., demographics, signal quality, tissue composition, other neurochemicals) and regardless of the state of neural activity (i.e., resting/active). These results show that there is no brain-wide balance between excitatory and inhibitory neurotransmitters and indicates a dissociation between the E/I balance observed in electrophysiological work and the ratio of MRS-detected neurotransmitters.


title: Neutrophils require SKAP2 for reactive oxygen species production following C-type lectin and Candida stimulation

abstract: Signaling cascades that convert the recognition of pathogens to efficient inflammatory responses by immune cells, specifically neutrophils, are critical for host survival. SKAP2, an adaptor protein, is required for reactive oxygen species (ROS) generation following stimulation by integrins, formyl peptide receptors and gram-negative bacteria Klebsiella pneumoniae and Yersinia pseudotuberculosis in vitro (Nguyen et al., 2020, Shaban et al., 2020, Boras et al., 2017). SKAP2 is also required for the host defense against K. pneumoniae and{Delta} yopH Y. pseudotuberculosis infection in vivo in mouse models (Shaban et al., 2020, Nguyen et al., 2020). Another class of pattern recognition receptors (PRR) is the C-type lectin receptors (CLR), such as Dectin-1, Dectin-2 and Mincle, that are critical to trigger innate immune responses. Using neutrophils from murine HoxB8-immortalized progenitors, we show that SKAP2 is crucial for maximal ROS response to purified CLR agonists and to the fungal pathogens Candida glabrata and C. albicans, as well as for robust killing of C. glabrata. Skap2-/- murine neutrophils failed to generate ROS and exhibited reduced cellular adhesion in response to trehalose-6,6-dibehenate (TDB), furfurman, and curdlan, Mincle, Dectin-2, and Dectin-1 agonists, respectively. TDB, furfurman, and curdlan stimulation also led to SKAP2-independent integrin conformational changes, showing that inside-out signaling by these CLRs to integrin occurs in the absence of SKAP2. Pyk2 phosphorylation was significantly reduced after infection with C. glabrata in Skap2-/- neutrophils, while Syk phosphorylation was unaffected by the loss of SKAP2. These data strengthen the importance of SKAP2 in the activation of neutrophil ROS production by PRRs to include CLRs and extend the role of SKAP2 in host defense beyond antibacterial immunity to include Candida species.

category: immunology


title: Safety and Immunogenicity Evaluation of Inactivated whole-virus-SARS-COV-2 In Mice As Emerging Vaccine Development In Egypt

abstract: The current worldwide pandemic COVID-19 is causing severe human health problems, with high numbers of mortality rates and huge economic burdens that require an urgent demand for safe, and effective and vaccine development. Our study was the first trail to development and evaluation of safety and immune response to inactivated whole SARS-COV-2 virus vaccine adjuvanted with aluminium hydroxide. We used characterized SARS-COV-2 strain, severe acute respiratory syndrome coronavirus 2 isolates (SARS-CoV-2/human/EGY/Egy-SERVAC/2020) with accession numbers; MT981440; MT981439; MT981441; MT974071; MT974069 and MW250352 at GenBank that isolated from Egyptian patients SARS-CoV-2-positive. Development of the vaccine was carried out in a BSL - 3 facilities and the immunogenicity was determined in mice at two doses (55{micro}g and 100{micro}g per dose). All vaccinated mice were received a booster dose 14 days post first immunization. Our results demonstrated distinct cytopathic effect on the vero cell monolayers induced through SARS-COV-2 propagation and the viral particles were identified as Coronaviridae by transmission electron microscopy. SARS-CoV-2 was identified by RT-PCR performed on the cell culture. Immunogenicity of the developed vaccine indicated the high antigen-binding and neutralizing antibody titers, regardless the dose concentration, with excellent safety profiles.However, no deaths or clinical symptoms in mice groups. The efficacy of the inactivated vaccine formulation was tested by wild virus challenge the vaccinated mice and detection of viral replication in lung tissues. Vaccinated mice recorded complete protection from challenge infection three weeks post second dose. SARS-COV-2 replication was not observed in the lungs of mice following SARS-CoV-2 challenge, regardless of the level of serum neutralizing antibodies. This finding will support the future trials for evaluation an applicable SARS-CoV-2 vaccine candidate.


title: The phytonutrient cinnamaldehyde limits intestinal inflammation and enteric parasite infection

abstract: Phytonutrients such as cinnamaldehyde (CA) have been studied for their effects on metabolic diseases, but their influence on mucosal inflammation and immunity to enteric infection are not well documented. Here, we show that consumption of CA significantly down-regulates transcriptional pathways connected to inflammation in the small intestine of mice. During infection with the enteric helminth Heligomosomoides polygyrus, CA-treated mice displayed higher growth rates and less worms, concomitant with altered T-cell populations in mesenteric lymph nodes. Furthermore, infection-induced changes in gene pathways connected to cell cycle and mitotic activity were counteracted by CA. Mechanically, CA did not appear to exert activity through a prebiotic effect, as CA treatment did not significantly change the composition of the gut microbiota. Instead, in vitro experiments showed that CA directly induced xenobiotic metabolizing pathways in intestinal epithelial cells and suppressed endotoxin-induced inflammatory responses in macrophages. Thus, CA down-regulates inflammatory pathways in the intestinal mucosa and regulates host responses to enteric infection. These properties appear to be largely independent of the gut microbiota and instead connected to CAs ability to induce antioxidant pathways in intestinal cells. Our results encourage further investigation into the use of CA and related phytonutrients as functional food components to promote intestinal health in humans and animals.


title: In vitro evaluation of the activity of terpenes and cannabidiol against Human Coronavirus E229

abstract: The activity of a new, terpene-based formulation, code-named NT-VRL-1, against Human Coronavirus (HCoV) strain 229E was evaluated in human lung fibroblasts (MRC-5 cells), with and without the addition of cannabidiol (CBD). The tested formulation exhibited an antiviral effect when it was pre-incubated with the host cells prior to virus infection. The combination of NT-VRL-1 with CBD potentiated the antiviral effect better than the positive controls pyrazofurin and glycyrrhizin. There was a strong correlation between the quantitative results from a cell-viability assay and the cytopathic effect seen under the microscope after 72 h. To the best of our knowledge, this is the first report of activity of a combination of terpenes and CBD against a coronavirus.

category: microbiology


title: Microbial composition, diversity, and activity varies across different types of basal ice

abstract:
Glaciers and ice sheets possess layers of basal ice characterized by high amounts of entrained debris that can serve as sources of nutrients and organic matter, providing habitat for microorganisms adapted to the frozen conditions. Basal ice forms through various mechanisms and is classified based on its ice and debris content; however, little is known about variation in microbial composition, diversity, and activity across different basal ice types. We investigated these parameters in four different types of basal ice from a cold-based and temperate glacier and used a meta-analysis to compare our findings with microbiome studies from other frozen environments. We found basal ice environments harbor a diverse range of microbiomes whose composition and activity can vary significantly between basal ice types, even within adjacent facies from the same glacier. In some debris-rich basal ices, elevated ATP concentrations, isotopic gas signatures, and high ratios of amplified sequences for 16S rRNA relative to that for 16S rRNA genes implicated certain bacterial taxa (e.g., Paenisporosarcina, Desulfocapsa, Syntrophus, Desulfosporosinus) as being potentially active, with ice temperature appearing to be an important predictor for the diversity of taxa inferred to be active. Compared to those of other sympagic environments, these microbiomes often resembled those found in permafrost or perennial cave ice rather than other glacial ice environments. In contrast, debris-poor basal ices harbored microbiomes more like those found in oligotrophic englacial ice. Collectively, these results suggest that different basal ice types contain distinct microbiomes that are actively structured by the diagenesis of their habitat.

IMPORTANCEThe discharge of material from the basal ice zones of glaciers and ice sheets is an important source of dissolved organic matter, nutrients, and trace metals to downstream environments. Microorganisms with the ability to remain metabolically active while frozen have the potential to alter these substrates before they are released and may thus be a vital biogeochemical component of proglacial environments. However, basal ice environments are among the least explored areas of the cryosphere and information on their microbiology is limited. Here, we examine several basal ice types that were collected from different glaciers to investigate how their microbiomes varied. Our results indicate that sediment-rich basal ice from cold-based and temperate glaciers harbor microbiomes that conduct biogeochemical transformations at subzero temperatures and raises the intriguing possibility that subsurface regions of the cryosphere may be more biogeochemically active than previously thought.


title: Variation in bacterial composition, diversity, and activity across different subglacial basal ice types


title: Inter-tissue convergence of gene expression and loss of cellular identity during ageing

abstract: Developmental trajectories of gene expression may reverse in their direction during ageing, a phenomenon previously linked to cellular identity loss. Our analysis of cerebral cortex, lung, liver and muscle transcriptomes of 16 mice, covering development and ageing intervals, revealed widespread but tissue-specific ageing-associated expression reversals. Cumulatively, these reversals create a unique phenomenon: mammalian tissue transcriptomes diverge from each other during postnatal development, but during ageing, they tend to converge towards similar expression levels, a process we term Divergence followed by Convergence, or DiCo. We found that DiCo was most prevalent among tissue-specific genes and associated with loss of tissue identity, which is confirmed using data from independent mouse and human datasets. Further, using publicly available single-cell transcriptome data, we showed that DiCo could be driven both by alterations in tissue cell type composition and also by cell-autonomous expression changes within particular cell types.

category: genomics


title: Inter-tissue convergence of gene expression during ageing suggests age-related loss of tissue and cellular identity


title: ORT: A workflow linking genome-scale metabolic models with reactive transport codes

abstract:
MotivationNutrient and contaminant behavior in the subsurface are governed by multiple coupled hydrobiogeochemical processes which occur across different temporal and spatial scales. Accurate description of macroscopic system behavior requires accounting for the effects of microscopic and especially microbial processes. Microbial processes mediate precipitation and dissolution and change aqueous geochemistry, all of which impacts macroscopic system behavior. As  omics data describing microbial processes is increasingly affordable and available, novel methods for using this data quickly and effectively for improved ecosystem models are needed.

ResultsWe propose a workflow ( Omics to Reactive Transport - ORT) for utilizing metagenomic and environmental data to describe the effect of microbiological processes in macroscopic reactive transport models. This workflow utilizes and couples two open-source software packages: KBase (a software platform for systems biology) and PFLOTRAN (a reactive transport modeling code). We describe the architecture of ORT and demonstrate an implementation using metagenomic and geochemical data from a river system. Our demonstration uses microbiological drivers of nitrification and denitrification to predict nitrogen cycling patterns which agree with those provided with generalized stoichiometries. While our example uses data from a single measurement, our workflow can be applied to spatiotemporal metagenomic datasets to allow for iterative coupling between KBASE and PFLOTRAN.

Availability and ImplementationInteractive models available at https://pflotranmodeling.paf.subsurfaceinsights.com/pflotran-simple-model/. Microbiological data available at NCBI via BioProject ID PRJNA576070. ORT Python code available at https://github.com/subsurfaceinsights/ort-kbase-to-pflotran. KBase narrative available at https://narrative.kbase.us/narrative/71260 or static narrative (no login required) at https://kbase.us/n/71260/258

Contactrebecca.rubinstein@subsurfaceinsights.com or roelof.versteeg@subsurfaceinsights.com

Supplementary informationSupplementary data are available online.


title: Pneumococcal genetic variability influences age-dependent bacterial carriage

abstract: The pneumococcal conjugate vaccine (PCV) primarily reduces disease burden in adults through a reduction in carriage prevalence of invasive serotypes in children. Current vaccine formulations are the same for both adults and children, but tailoring these formulations to age category could optimize vaccine efficacy. Identification of specific pneumococcal genetic factors associated with carriage in younger or older age groups may suggest alternative formulations and contribute to a better mechanistic understanding of immunity. Here, we used whole genome sequencing to dissect pneumococcal variation associated with age. We performed genome sequencing in a large carriage cohort, and conducted a meta-analysis with an existing carriage study. We compiled a dictionary of pathogen genetic variation including serotype, sequence cluster, sequence elements, SNPs, burden combined rare variants, and clusters of orthologous genes (COGs) for each cohort - all of which used in a genome-wide association with host age. Age-dependent colonization had some heritability, though this varied between cohorts (h2 = 0.10, 0.00 - 0.69 95% CI in the first; h2 = 0.46, 0.33 - 0.60 95% CI in the second cohort). We found that serotypes and genetic background (strain) explained most of the heritability in each cohort (h2serotype = 0.06 and h2GPSC = 0.04 in the first; h2 serotype = 0.20 and h2 GPSC = 0.23 in the second cohort). We found one candidate association (p = 1.2x10-9) upstream of an accessory Sec-dependent serine-rich glycoprotein adhesin. Overall, association with age was highly cohort and strain dependent, supporting proposals for a future vaccination strategy which is primarily targeted using serotypes rather than proteins, and is tailored towards specific pathogen populations.


title: High molecular weight DNA extraction strategies for long-read sequencing of complex metagenomes

abstract: By offering extremely long contiguous characterization of individual DNA molecules, rapidly emerging long-read sequencing strategies offer comprehensive insights into the organization of genetic information in genomes and metagenomes. However, successful long-read sequencing experiments demand high concentrations of highly purified DNA of high molecular weight (HMW), which limits the utility of established DNA extraction kits designed for short-read sequencing. Challenges associated with input DNA quality intensify further when working with complex environmental samples of low microbial biomass, which requires new protocols that are tailored to study metagenomes with long-read sequencing. Here, we use human tongue scrapings to benchmark six HMW DNA extraction strategies that are based on commercially available kits, phenol-chloroform (PC) extraction, and agarose encasement followed by agarase digestion. A typical end goal of HMW DNA extractions is to obtain the longest possible reads during sequencing, which is often achieved by PC extractions as demonstrated in sequencing of cultured cells. Yet our analyses that consider overall read-size distribution, assembly performance, and the number of circularized elements found in sequencing results suggest that non-PC methods may be more appropriate for long-read sequencing of metagenomes.


title: Lamp1 mediates lipid transport, but is dispensable for autophagy in Drosophila

abstract: The endolysosomal system not only is an integral part of the cellular catabolic machinery that processes and recycles nutrients for synthesis of biomaterials, but also acts as signaling hub to sense and coordinate the energy state of cells with growth and differentiation. Lysosomal dysfunction adversely influences vesicular transport-dependent macromolecular degradation and thus causes serious problems for human health. In mammalian cells, loss of the lysosome associated membrane proteins LAMP1/2 strongly impacts autophagy and cholesterol trafficking. Here we show that the previously uncharacterized Drosophila Lamp1 is a bona fide homolog of vertebrate LAMP1/2. Surprisingly and in contrast to Lamp1/2 double mutant mice, Drosophila Lamp1 is not required for viability or autophagy, suggesting that autophagy defects in Lamp1/2 mutants may have indirect causes. However, Lamp1 deficiency results in an expansion of the acidic compartment in flies. Furthermore, we find that Lamp1 mutant larvae have defects in lipid metabolism as they show elevated levels of sterols and diacylglycerols (DAGs). Since DAGs are the main lipid species used for transport though the hemolymph (blood) in insects, our results indicate broader functions of Lamp1 in lipid transport. Our findings make Drosophila an ideal model to study the role of LAMP proteins in lipid assimilation without the confounding effects of their storage and without interfering with autophagic processes.

category: cell biology


title: Contribution of epigenetic changes to escape from X-chromosome inactivation

abstract:
BackgroundX-chromosome inactivation (XCI) is the epigenetic inactivation of one of two X chromosomes in XX eutherian mammals. The facultatively heterochromatic inactive X chromosome acquires many chromatin changes including DNA methylation and histone modifications. Despite these changes, some genes escape or variably escape from inactivation, and to the extent that they have been studied, epigenetic marks correlate with expression.

ResultsWe downloaded data from the International Human Epigenome Consortium and compared previous XCI status calls to DNA methylation, H3K4me1, H3K4me3, H3K9me3, H3K27ac, H3K27me3 and H3K36me3. At genes subject to XCI we found heterochromatic marks enriched, and euchromatic marks depleted on the inactive X when compared to the active X. Similar results were seen for genes escaping XCI although with diminished effect with H3K27me3 being most enriched. Using sample-specific XCI status calls made using allelic expression or DNA methylation we also compared differences between samples with opposite XCI statuses at variably escaping genes. We found some marks significantly differed with XCI status, but which marks were significant was not consistent between genes. We trained a model to predict XCI status from these epigenetic marks and obtained over 75% accuracy for genes escaping and over 90% for genes subject to XCI. This model allowed us to make novel XCI status calls for genes without allelic differences or CpG islands required for other XCI status calling methods. Using these calls to examine a domain of variably escaping genes, we saw XCI status vary at the level of individual genes and not at the domain level.

ConclusionHere we show that epigenetic marks differ between genes that are escaping and those subject to XCI, and that genes escaping XCI still differ between the active and inactive Xs. We show epigenetic differences at variably escaping genes, between samples escaping and those subject to XCI. Lastly we show gene-level regulation of variably escaping genes within a domain.


title: miQC: An adaptive probabilistic framework for quality control of single-cell RNA-sequencing data

abstract:
MotivationSingle-cell RNA-sequencing (scRNA-seq) has made it possible to profile gene expression in tissues at high resolution. An important preprocessing step prior to performing downstream analyses is to identify and remove cells with poor or degraded sample quality using quality control (QC) metrics. Two widely used QC metrics to identify a  low-quality cell are (i) if the cell includes a high proportion of reads that map to mitochondrial DNA (mtDNA) encoded genes and (ii) if a small number of genes are detected. Current best practices use these QC metrics independently with either arbitrary, uniform thresholds (e.g. 5%) or biological context-dependent (e.g. species) thresholds, and fail to jointly model these metrics in a data-driven manner. Current practices are often overly stringent and especially untenable on lower-quality tissues, such as archived tumor tissues.

ResultsWe propose a data-driven QC metric (miQC) that jointly models both the proportion of reads mapping to mtDNA genes and the number of detected genes with mixture models in a probabilistic framework to predict the low-quality cells in a given dataset. We demonstrate how our QC metric easily adapts to different types of single-cell datasets to remove low-quality cells while preserving high-quality cells that can be used for downstream analyses.

AvailabilitySoftware available at https://github.com/greenelab/miQC. The code used to download datasets, perform the analyses, and reproduce the figures is available at https://github.com/greenelab/mito-filtering.

ContactStephanie C. Hicks (shicks19@jhu.edu) and Anna Vaharautio (anna.vaharautio@helsinki.fi)


title: Towards high spatially resolved microproteomics using expansion microscopy

abstract:
Expansion microscopy is an emerging approach for morphological examination of biological specimens at nanoscale resolution using conventional optical microscopy. To achieve physical separation of cell structures, tissues are embedded in a swellable polymer and expanded several folds in an isotropic manner. This work shows the development and optimization of physical tissue expansion as a new method for spatially resolved large scale proteomics. Herein, we established a novel method to enlarge the tissue section to be compatible with manual microdissection on regions of interest and to carry out MS-based proteomic analysis. A major issue in the Expansion microscopy is the loss of proteins information during the mechanical homogenization phase due to the use of Proteinase K. For isotropic expansion, different homogenization agents are investigated, both to maximize protein identification and to minimize protein diffusion. Better results are obtained with SDS. From a tissue section enlarge more than 3-fold, we have been able to manually cut out regions of 1mm in size, equivalent to 300{micro}m in their real size. We identified up to 655 proteins from a region corresponding to an average of 940 cells. This approach can be performed easily without any expensive sampling instrument. We demonstrated the compatibility of sample preparation for expansion microscopy and proteomic study in a spatial context.

Abstract graphic

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category: biochemistry


title: Site-specific phosphorylation of PSD-95 dynamically regulates the post-synaptic density as observed by phase separation

abstract:
Postsynaptic density protein 95 is a key scaffolding protein in the postsynaptic density of excitatory glutamatergic neurons, organizing signaling complexes primarily via its three PSD-95/Discs-large/Zona occludens domains. PSD-95 is regulated by phosphorylation, but technical challenges have limited studies of the molecular details. Here, we genetically introduced site-specific phosphorylations in single, tandem and full-length PSD-95 and generated a total of 11 phosphorylated protein variants. We examined how these phosphorylations affected binding to known interaction partners and the impact on phase separation of PSD-95 complexes, and identified two new phosphorylation sites with opposing effects. Phosphorylation of Ser78 inhibited phase separation with the glutamate receptor subunit GluN2B and the auxiliary protein stargazin, whereas phosphorylation of Ser116 induced phase separation with stargazin only. Thus, by genetically introducing phosphoserine site-specifically and exploring the impact on phase separation, we have provided new insights into the regulation of PSD-95 by phosphorylation and the dynamics of the PSD.

Graphical Abstract: Phosphorylation of PSD-95.

O_LIIllustration of the interaction between the PDZ domains of PSD-95 and the NMDA receptor (NMDAR) (PDB: 4PE5) at the plasma membrane. PSD-95 interacts with the AMPA receptor (AMPAR) (PDB: 3KG2) through Stargazin (PDB: 5KBU). Using the software Ranch, a model of FL PSD-95 was generated using known structural domains of PSD-95 connected via a fully-flexible linker (PDZ1-2, PDB: 3GSL; PDZ3, PDB: 5JXB; SH3-GK, PDB: 1KJW).
C_LIO_LIIllustration of the effect of phosphorylation of PSD-95 on the formation of condensates at the PSD. PSD-95 can phase separate with receptors and intracellular proteins, and phosphorylation is can affect this interaction and lead to alterations, both negative and positive, in the formation of condensates.
C_LI


title: Bi-directional protein-protein interactions control liquid-liquid phase separation of PSD-95 and its interaction partners

abstract: The organization of the postsynaptic density (PSD), a protein-dense semi-membraneless organelle, is mediated by numerous specific protein-protein interactions (PPIs) which constitute a functional post-synapse. Postsynaptic density protein 95 (PSD-95) interacts with a manifold of proteins, including the C-terminal of transmembrane AMPA receptor (AMAPR) regulatory proteins (TARPs). Here, we uncover the minimal essential peptide responsible for the stargazin (TARP-{gamma}2) mediated liquid-liquid phase separation (LLPS) formation of PSD-95 and other key protein constituents of the PSD. Furthermore, we find that pharmacological inhibitors of PSD-95 can facilitate formation of LLPS. We found that in some cases LLPS formation is dependent on multivalent interactions while in other cases short peptides carrying a high charge are sufficient to promote LLPS in complex systems. This study offers a new perspective on PSD-95 interactions and their role in LLPS formation, while also considering the role of affinity over multivalency in LLPS systems.


title: Ablating Ku70 phosphorylation results in defective DNA damage repair and spontaneous induction of hepatocellular carcinoma

abstract: Multiple pathways mediate the repair of DNA double-strand break (DSB), with numerous mechanisms responsible for driving choice between the pathways. Previously, we reported that phosphorylation of the non-homologous end joining (NHEJ) factor, Ku70, is required for the dissociation of the Ku heterodimer from DNA ends to allow DSB repair via homologous recombination (HR). A knock-in mouse, in which phosphorylation is ablated in the three conserved sites of Ku70 (Ku703A/3A), was generated in order to test the hypothesis that Ku70 phosphorylation is required for initiation of HR and that blocking this process results in enhanced genomic instability and tumorigenesis. Here, we show that Ku703A/3A mice develop spontaneous and have accelerated chemical-induced hepatocellular carcinoma (HCC) compared to wild-type (Ku70+/+) littermates. The HCC tumors from the Ku703A/3A mice have increased {gamma}H2AX and 8-oxo-G staining, suggesting DNA repair is decreased in these mice. Spontaneous transformed cell lines from Ku703A/3A mice are more radiosensitive, have a significant decrease in DNA end resection, and are more sensitive to the DNA cross-linking agent mitomycin C compared to cells from Ku70+/+ littermates. Collectively, these findings demonstrate that phosphorylation-mediated dissociation of Ku heterodimer from DNA ends is required for efficient DNA damage repair and disruption of this process results in genomic instability and accelerated development of HCC.

category: cancer biology


title: Patterns of gene content and co-occurrence constrain the evolutionary path toward animal association in CPR bacteria

abstract:
Candidate Phyla Radiation (CPR) bacteria are small, likely episymbiotic organisms found across Earths ecosystems. Despite their prevalence, the distribution of CPR lineages across habitats and the genomic signatures of transitions amongst these habitats remain unclear. Here, we expand the genome inventory for Absconditabacteria (SR1), Gracilibacteria, and Saccharibacteria (TM7), CPR bacteria known to occur in both animal-associated and environmental microbiomes, and investigate variation in gene content with habitat of origin. By overlaying phylogeny with habitat information, we show that bacteria from these three lineages have undergone multiple transitions from environmental habitats into animal microbiomes. Based on co-occurrence analyses of hundreds of metagenomes, we extend the prior suggestion that certain Saccharibacteria have broad bacterial host ranges and constrain possible host relationships for Absconditabacteria and Gracilibacteria. Full-proteome analyses show that animal-associated Saccharibacteria have smaller gene repertoires than their environmental counterparts and are enriched in numerous protein families, including those likely functioning in amino acid metabolism, phage defense, and detoxification of peroxide. In contrast, some freshwater Saccharibacteria encode a putative rhodopsin. For protein families exhibiting the clearest patterns of differential habitat distribution, we compared protein and species phylogenies to estimate the incidence of lateral gene transfer and genomic loss occurring over the species tree. These analyses suggest that habitat transitions were likely not accompanied by large transfer or loss events, but rather were associated with continuous proteome remodeling. Thus, we speculate that CPR habitat transitions were driven largely by availability of suitable host taxa, and were reinforced by acquisition and loss of some capacities.

IMPORTANCEStudying the genetic differences between related microorganisms from different environment types can indicate factors associated with their movement among habitats. This is particularly interesting for bacteria from the Candidate Phyla Radiation because their minimal metabolic capabilities require symbiotic associations with microbial hosts. We found that shifts of Absconditabacteria, Gracilibacteria, and Saccharibacteria between environmental ecosystems and mammalian mouths/guts probably did not involve major episodes of gene gain and loss; rather, gradual genomic change likely followed habitat migration. The results inform our understanding of how little-known microorganisms establish in the human microbiota where they may ultimately impact health.


title: On-site genomic epidemiological analysis of antimicrobial-resistant bacteria in Cambodia with portable laboratory equipment

abstract: The rapid emergence of carbapenemase-producing Gram-negative bacteria (CPGNB) is a global threat due to the high mortality of infection and limited treatment options. Although there have been many reports of CPGNB isolated from Southeast Asian countries, to date there has been no genetic analysis of CPGNB isolated from Cambodia. Sequence-based molecular epidemiological analysis enables a better understanding of the genotypic characteristics and epidemiological significance of antimicrobial-resistant (AMR) bacteria in each country, and allows countries to enact measures related to AMR issues. In this study, we performed on-site genomic epidemiological analysis of CPGNB isolated in Cambodia using a portable laboratory equipment called Bento Lab, which combines a PCR thermal cycler, microcentrifuge, gel electrophoresis apparatus, and LED transilluminator, along with the MinION nanopore sequencer. PCR targeting of major carbapenemase genes using Bento Lab revealed that two Escherichia coli isolates and one Acinetobacter baumannii isolate harbored carbapenemase genes: blaNDM, blaOXA-48, and blaOXA-23, respectively. The results of phenotypic diagnostic tests for CPGNB, such as the carbapenem inactivation method and double-disk diffusion test using a specific inhibitor of metallo-{beta}-lactamases, were consistent with their AMR genotypes. Whole-genome sequencing analysis using MinION suggested that blaNDM-5 and blaOXA-181 genes were carried on plasmids (93.9-kb plasmid with IncFIA, IncFIB, IncFII, and IncQ1 replicons, and 51.5-kb plasmid with the IncX3 replicon, respectively) in E. coli, and that blaOXA-23 was encoded in two locations on the chromosome of A. baumannii. Plasmids carrying blaNDM-5 or blaOXA-181 in E. coli were highly structurally identical to plasmids prevalent in Enterobacterales in China and other countries, suggesting that they disseminated from a common evolutionary origin. Our findings demonstrate the potential impact of portable laboratory equipment on AMR bacteria research in hospitals and research centers with limited research facilities, and provide the first glimpse into the genomic epidemiology of CPGNB in Cambodia.


title: SWI/SNF senses carbon starvation with a pH-sensitive low complexity sequence

abstract: It is increasingly appreciated that intracellular pH changes are important biological signals. This motivates the elucidation of molecular mechanisms of pH-sensing. We determined that a nucleocytoplasmic pH oscillation was required for the transcriptional response to carbon starvation in S. cerevisiae. The SWI/SNF chromatin remodeling complex is a key mediator of this transcriptional response. We found that a glutamine-rich low complexity sequence (QLC) in the SNF5 subunit of this complex, and histidines within this sequence, were required for efficient transcriptional reprogramming during carbon starvation. Furthermore, the SNF5 QLC mediated pH-dependent recruitment of SWI/SNF to a model promoter in vitro. Simulations showed that protonation of histidines within the SNF5 QLC lead to conformational expansion, providing a potential biophysical mechanism for regulation of these interactions. Together, our results indicate that that pH changes are a second messenger for transcriptional reprogramming during carbon starvation, and that the SNF5 QLC acts as a pH-sensor.

category: molecular biology


title: Paralogous gene modules derived from ancient hybridization drive vesicle traffic evolution in yeast

abstract: Modules of interacting proteins regulate vesicle budding and fusion in eukaryotes. Distinct paralogous copies of these modules act at distinct sub-cellular locations. The processes by which such large gene modules are duplicated and retained remain unclear. Here we show that interspecies hybridization is a potent source of paralogous gene modules. We study the dynamics of paralog doublets derived from the 100-million-year-old hybridization event that gave rise to the whole genome duplication clade of budding yeast. We show that paralog doublets encoding vesicle traffic proteins are convergently retained across species. Vesicle coats and adaptors involved in secretory and early-endocytic pathways are retained as doublets, while tethers and other machinery involved in intra-Golgi traffic and later endocytic steps are reduced to singletons. These patterns reveal common selective pressures that have sculpted traffic pathways in diverse yeast species. They suggest that hybridization may have played a pivotal role in the expansion of the endomembrane system.

category: evolutionary biology


title: The genome sequence of the cereal pest Sitophilus oryzae: an unprecedented transposable element content

abstract:
BackgroundThe rice weevil Sitophilus oryzae is one of the most important agricultural pests, causing extensive damage to cereal in fields and to stored grains. S. oryzae has an intracellular symbiotic relationship (endosymbiosis) with the Gram-negative bacterium Sodalis pierantonius and is a valuable model to decipher host-symbiont molecular interactions.

ResultsWe sequenced the Sitophilus oryzae genome using a combination of short and long reads to produce the best assembly for a Curculionidae species to date. We show that S. oryzae has undergone successive bursts of transposable element (TE) amplification, representing 72% of the genome. In addition, we show that many TE families are transcriptionally active, and changes in their expression are associated with insect endosymbiotic state. S. oryzae has undergone a high gene expansion rate, when compared to other beetles. Reconstruction of host-symbiont metabolic networks revealed that, despite its recent association with cereal weevils (30 Kyear), S. pierantonius relies on the host for several amino acids and nucleotides to survive and to produce vitamins and essential amino-acids required for insect development and cuticle biosynthesis.

ConclusionsHere we present the genome of an agricultural pest beetle, which may act as a foundation for pest control. In addition, S. oryzae may be a useful model for endosymbiosis, and studying TE evolution and regulation, along with the impact of TEs on eukaryotic genomes.


title: The genome of the cereal pest Sitophilus oryzae: a transposable element haven


title: The transposable element-rich genome of the cereal pest Sitophilus oryzae


title: Comparative analysis of codon usage patterns in SARS-CoV-2, its mutants and other respiratory viruses

abstract: The Coronavirus disease 2019 (COVID-19) outbreak caused by Severe Acute Respiratory Syndrome Coronavirus 2 virus (SARS-CoV-2) poses a worldwide human health crisis, causing respiratory illness with a high mortality rate. To investigate the factors governing codon usage bias in all the respiratory viruses, including SARS-CoV-2 isolates from different geographical locations (~62K), including two recently emerging strains from the United Kingdom (UK), i.e., VUI202012/01 and South Africa (SA), i.e., 501.Y.V2 codon usage bias (CUBs) analysis was performed. The analysis includes RSCU analysis, GC content calculation, ENC analysis, dinucleotide frequency and neutrality plot analysis. We were motivated to conduct the study to fulfil two primary aims: first, to identify the difference in codon usage bias amongst all SARS-CoV-2 genomes and, secondly, to compare their CUBs properties with other respiratory viruses. A biased nucleotide composition was found as most of the highly preferred codons were A/U-ending in all the respiratory viruses studied here. Compared with the human host, the RSCU analysis led to the identification of 11 over-represented codons and 9 under-represented codons in SARS-CoV-2 genomes. Correlation analysis of ENC and GC3s revealed that mutational pressure is the leading force determining the CUBs. The present study results yield a better understanding of codon usage preferences for SARS-CoV-2 genomes and discover the possible evolutionary determinants responsible for the biases found among the respiratory viruses, thus unveils a unique feature of the SARS-CoV-2 evolution and adaptation. To the best of our knowledge, this is the first attempt at comparative CUBs analysis on the worldwide genomes of SARS-CoV-2, including novel emerged strains and other respiratory viruses.


title: Emergence of function from single RNA sequences by Darwinian evolution

abstract: The spontaneous emergence of function from pools of random sequence RNA is widely considered an important transition in the origin of life. However, the plausibility of this hypothetical process and the number of productive evolutionary trajectories in sequence space are unknown. Here we demonstrate that function can arise starting from a single RNA sequence by an iterative process of mutation and selection. Specifically, we describe the discovery of both specific ATP or GTP aptamers - with micromolar affinity for their nucleotide ligand - starting each from a single, homopolymeric poly-A sequence flanked by conserved primer binding sites. Our results indicate that the ab initio presence of large, diverse random sequence pools is not a prerequisite for the emergence of functional RNAs and that the process of Darwinian evolution has the capacity to generate function even from single, largely unstructured RNA sequences with minimal molecular and informational complexity.

category: synthetic biology


title: Lymphocyte-specific Protein Tyrosine Kinase Regulates Homologous Recombination (HR) DNA Repair and Targeting Enhances PARPi Utility in HR Proficient Ovarian Cancer

abstract:
Poly-ADP Ribose Polymerase (PARP) targeted therapy is clinically approved for the treatment of homologous recombination (HR) repair deficient tumors. The remarkable success in treatment of HR repair deficient cancers has not translated to HR-proficient cancer. Our studies identify the mechanism of non-receptor lymphocyte-specific protein tyrosine kinase (LCK) in HR repair in endometrioid epithelial ovarian cancer (eEOC). LCK expression is induced and activation in the nucleus in response to DNA damage insult. LCK inhibition attenuates expression of RAD51, BRCA1, and BRCA2 proteins necessary for HR-mediated DNA repair, sufficient to suppress RAD51 foci formation, and augments {gamma}H2AX foci formation. Mechanistically, DNA damage leads to direct interaction of LCK with RAD51 and BRCA1 in a kinase dependent manner. Attenuation of LCK sensitized HR-proficient eEOC cells to PARP inhibitor in cell culture and pre-clinical mouse studies. These findings identify a new mechanism for expanding utility of PARP inhibitors in HR proficient ovarian cancer.

Graphical Abstract

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title: LCK Regulates Homologous Recombination DNA Repair Identifying a New Therapeutic Target for Sensitizing PARP Inhibitors in HR Proficient Ovarian Cancer


title: Loneliness and the social brain: how perceived social isolation impairs human interactions

abstract: Loneliness is a painful condition associated with increased risk for premature mortality. The formation of new, positive social relationships can alleviate feelings of loneliness, but requires rapid trustworthiness decisions during initial encounters and it is still unclear how loneliness hinders interpersonal trust. Here, we use a multimodal approach including behavioral, psychophysiological, hormonal, and neuroimaging measurements to probe a trust-based mechanism underlying impaired social interactions in loneliness. Pre-stratified healthy individuals with high loneliness scores (n = 42 out of a screened sample of 3678 adults) show reduced oxytocinergic and affective responsiveness to a positive conversation, report less interpersonal trust, and prefer larger social distances compared to controls (n = 40). Moreover, lonely individuals are rated as less trustworthy compared to controls and identified by the blinded confederate better than chance. During initial trust decisions, lonely individuals exhibit attenuated limbic and striatal activation and blunted functional connectivity between the anterior insula and occipitoparietal regions, which correlates with the diminished affective responsiveness to the positive social interaction. This neural response pattern is not mediated by loneliness-associated psychological symptoms. Thus, our results indicate compromised integration of trust-related information as a shared neurobiological component in loneliness, yielding a reciprocally reinforced trust bias in social dyads.


title: The connectome spectrum as a canonical basis for a sparse representation of fast brain activity

abstract: The functional organization of neural processes is constrained by the brain s intrinsic structural connectivity. Here, we explore the potential of exploiting this structure in order to improve the signal representation properties of brain activity and its dynamics. Using a multi-modal imaging dataset (electroencephalography, structural MRI and diffusion MRI), we represent electrical brain activity at the cortical surface as a time-varying composition of harmonic modes of structural connectivity. The harmonic modes are termed connectome harmonics, and their representation is known as the connectome spectrum of the signal. We found that: first, the brain activity signal is more compactly represented by the connectome spectrum than by the traditional area-based representation; second, the connectome spectrum characterizes fast brain dynamics in terms of signal broadcasting profile, revealing different temporal regimes of integration and segregation that are consistent across participants. And last, the connectome spectrum characterises fast brain dynamics with fewer degrees of freedom than area-based signal representations. Specifically, we show that with the connectome spectrum representation, fewer dimensions are needed to capture the differences between low-level and high-level visual processing, and the topological properties of the signal. In summary, this work provides statistical, functional and topological evidence supporting that by accounting for the brain s structural connectivity fosters a more comprehensive understanding of large-scale dynamic neural functioning.


title: Laminar-specific functional connectivity mapping with multi-slice line-scanning fMRI

abstract: Laminar BOLD-fMRI has been applied to better depict the neuronal input and output circuitry and functional connectivity across cortical layers by measuring local hemodynamic changes. Despite extensive studies detecting laminar fMRI signals to illustrate the canonical microcircuit, the spatiotemporal characteristics of laminar-specific information flow across different cortical regions remain to be fully investigated in both evoked and resting states. Here, we developed a multi-slice line-scanning fMRI (MS-LS) method to detect laminar fMRI signals in adjacent cortical regions with high spatial (50 {micro}m) and temporal resolution (100 ms) in anesthetized rats. Across different scanning trials, we detected both laminar-specific positive and negative BOLD responses in the surrounding cortical region adjacent to the most activated cortex under evoked condition. Specifically, in contrast to the typical Layer (L) 4 correlation across different regions due to the thalamocortical projections for trials with positive BOLD, a strong correlation pattern specific in L2/3 was detected for the trials with negative BOLD in adjacent regions, which indicate a brain state-dependent laminar-fMRI responses based on cortiocotical interaction from different trials. Also, we acquired the laminar-specific rs-fMRI signals across different cortical regions, of which the high spatiotemporal resolution allows us to estimate lag times based on the maximal cross-correlation of laminar-specific rs-fMRI signals. In contrast to the larger variability of lag times in L1 and 6, robust lag time differences in L2/3, 4, and 5 across multiple cortices represented the low-frequency rs-fMRI signal propagation from the caudal to the rostral slice. In summary, our work provides a unique laminar fMRI mapping scheme to better characterize trial-specific intra- and inter-laminar functional connectivity with MS-LS, presenting layer-specific spatiotemporal variation of both evoked and rs-fMRI signals.


title: Study on Changes in Tourism Land and Influence Factors in Mountain Areas?A Case Study of Luanchuan County, China

abstract: The rapid development of the tourism industry in mountain areas has resulted in intense changes in land use structure and exerts a strong influence on terrestrial ecosystems. This paper takes Luanchuan County (typical mountainous terrain in western Henan Province, China) as an example and employs land use data from different times and spaces and the binary logistic method to study tourism land spatial variation and influence factors in mountain areas. The research shows that: (1) spatial variation in land use in scenic spots reveals a chain reaction of land use type transformation caused by construction land expansion, a key driving force of spatial variation in land use and land use type transformation, and (2) the changes in tourism land use types result from human utilization and development of land for economic benefits. The key influence factors of spatial variation in land use are altitude; gradient; and the distance to rivers, highways and villages. (3) A plan of tourism land management and control should be established with construction land as the key indicator.

category: ecology


title: Autism spectrum disorder: understanding the impact of SNPs on biological pathways in the fetal and adult cortex.

abstract: Autism spectrum disorder (ASD) is a neurodevelopmental disorder characterized by significant and complex genetic etiology. GWAS studies have identified genetic variants associated with ASD, but the functional impacts of these variants remain unknown. Here, we integrated four distinct levels of biological information (GWAS, eQTL, spatial genome organization and protein-protein interactions) to identify potential regulatory impacts of ASD-associated SNPs (p < 5x10-8) on biological pathways within fetal and adult cortical tissues. We found 80 and 58 SNPs that mark regulatory regions (i.e. expression quantitative trait loci or eQTLs) in the fetal and adult cortex, respectively. These eQTLs were also linked to other psychiatric disorders (e.g. schizophrenia, ADHD, bipolar disorder). Functional annotation of ASD-associated eQTLs revealed that they are involved in diverse regulatory processes. In particular, we found significant enrichment of eQTLs within regions repressed by Polycomb proteins in the fetal cortex compared to the adult cortex. Furthermore, we constructed fetal and adult cortex-specific protein-protein interaction networks and identified that ASD-associated regulatory SNPs impact on immune pathways, fatty acid metabolism, ribosome biogenesis, aminoacyl-tRNA biosynthesis and spliceosome in the fetal cortex. By contrast in the adult cortex, they largely affect immune pathways. Overall, our findings highlight potential regulatory mechanisms and pathways important for the etiology of ASD in early brain development and adulthood. This approach, in combination with clinical studies on ASD, will contribute to individualized mechanistic understanding of ASD development.


title: Development and validation of FootNet; a new kinematic algorithm to improve foot-strike and toe-off detection in treadmill running

abstract: The accurate detection of foot-strike and toe-off is often critical in the assessment of running biomechanics. The gold standard method for step event detection requires force data which are not always available. Although kinematics-based algorithms can also be used, their accuracy and generalisability are limited, often requiring corrections for speed or foot-strike pattern. The purpose of this study was to develop FootNet, a novel kinematics and deep learning-based algorithm for the detection of step events in treadmill running. Five treadmill running datasets were gathered and processed to obtain segment and joint kinematics, and to identify the contact phase within each gait cycle using force data. The proposed algorithm is based on a long short-term memory recurrent neural network and takes the distal tibia anteroposterior velocity, ankle dorsiflexion/plantar flexion angle and the anteroposterior and vertical velocities of the foot centre of mass as input features to predict the contact phase within a given gait cycle. The chosen model architecture underwent 5-fold cross-validation and the final model was tested in a subset of participants from each dataset (30%). Non-parametric Bland-Altman analyses (bias and [95% limits of agreement]) and root mean squared error (RMSE) were used to compare FootNet against the force data step event detection method. The association between detection errors and running speed, foot-strike angle and incline were also investigated. FootNet outperformed previously published algorithms (foot-strike bias = 0 [-10, 7] ms, RMSE = 5 ms; toe-off bias = 0 [-10, 10] ms, RMSE = 6 ms; and contact time bias = 0 [-15, 15] ms, RMSE = 8 ms) and proved robust to different running speeds, foot-strike angles and inclines. We have made FootNets source code publicly available for step event detection in treadmill running when force data are not available.


title: PPIDomainMiner : Inferring domain-domain interactions from multiple sources of protein-protein interactions

abstract:
Many biological processes are mediated by protein-protein interactions (PPIs). Because protein domains are the building blocks of proteins, PPIs likely rely on domain-domain interactions (DDIs). Several attempts exist to infer DDIs from PPI networks but the produced datasets are heterogeneous and sometimes not accessible, while the PPI interactome data keeps growing.

We describe a new computational approach called "PPIDM" (Protein-Protein Interactions Domain Miner) for inferring DDIs using multiple sources of PPIs. The approach is an extension of our previously described "CODAC" (Computational Discovery of Direct Associations using Common neighbors) method for inferring new edges in a tripartite graph. The PPIDM method has been applied to seven widely used PPI resources, using as "Gold-Standard" a set of DDIs extracted from 3D structural databases. Overall, PPIDM has produced a dataset of 84, 552 non-redundant DDIs. Statistical significance (p-value) is calculated for each source of PPI and used to classify the PPIDM DDIs in Gold (9,175 DDIs), Silver (24, 934 DDIs) and Bronze (50, 443 DDIs) categories. Dataset comparison reveals that PPIDM has inferred from the 2017 releases of PPI sources about 46% of the DDIs present in the 2020 release of the 3did database, not counting the DDIs present in the Gold-Standard. The PPIDM dataset contains 10, 229 DDIs that are consistent with more than 13, 300 PPIs extracted from the IMEx database, and nearly 23,300 DDIs (27.5%) that are consistent with more than 214,000 human PPIs extracted from the STRING database. Examples of newly inferred DDIs covering more than 10 PPIs in the IMEx database are provided.

Further exploitation of the PPIDM DDI reservoir includes the inventory of possible partners of a protein of interest and characterization of protein interactions at the domain level in combination with other methods. The result is publicly available at http://ppidm.loria.fr/.

Author summaryWe revisit at a large scale the question of inferring DDIs from PPIs. Compared to previous studies, we take a unified approach accross multiple sources of PPIs. This approach is a method for inferring new edges in a tripartite graph setting and can be compared to link prediction approaches in knowledge graphs. Aggregation of several sources is performed using an optimized weighted average of the individual scores calculated in each source. A huge dataset of over 84K DDIs is produced which far exceeds the previous datasets. We show that a significant portion of the PPIDM dataset covers a large number of PPIs from curated (IMEx) or non curated (STRING) databases. Such a reservoir of DDIs deserves further exploration and can be combined with high-throughput methods such as cross-linking mass spectrometry to identify plausible protein partners of proteins of interest.


title: Bayesian calibration of a stochastic, multiscale agent-based model for predicting in vitro tumor growth

abstract: Hybrid multiscale agent-based models (ABMs) are unique in their ability to simulate individual cell interactions and microenvironmental dynamics. Unfortunately, the high computational cost of modeling individual cells, the inherent stochasticity due to probabilistic phenotypic transitions, and numerous model parameters that are difficult to measure directly are fundamental limitations of applying such models to predict tumor dynamics. To overcome these challenges, we have developed a coarse-grained two-scale ABM (cgABM) calibrated with a set of time-resolved microscopy measurements of cancer cells grown with different initial conditions. The multiscale model consists of a reaction-diffusion type model capturing the spatio-temporal evolution of glucose and growth factors in the tumor microenvironment (at tissue scale), coupled with a lattice-free ABM to simulate individual cell dynamics (at cellular scale). The experimental data consists of BT474 human breast carcinoma cells initialized with different glucose concentrations and tumor cell confluences. The confluence of live and dead cells was measured every three hours over four days.   Given this model and data, we perform a global sensitivity analysis to identify the relative importance of the model parameters. The subsequent cgABM with a reduced parameter space is calibrated within a Bayesian framework to the experimental data to estimate model parameters, which are then used to predict the temporal evolution of the living and dead cell populations. To this end, a moment-based Bayesian inference is proposed to account for the stochasticity of the cgABM while quantifying uncertainties in model parameters and observational data. The results indicate that the cgABM can reliably predict the spatiotemporal evolution of breast cancer cells observed by the microscopy data with an average error and standard deviation for live and dead cells being 7.61 [[EQUATION]] 2.01 and 5.78 [[EQUATION]] 1.13, respectively.


title: Loss of Tsc1 in cerebellar Purkinje cells induces transcriptional and translation changes in FMRP target transcripts

abstract: Tuberous sclerosis complex (TSC) is a genetic disorder that is associated with multiple neurological manifestations. Previously, we demonstrated that Tsc1 loss in cerebellar Purkinje cells (PCs) can cause altered social behavior in mice. Here, we performed detailed transcriptional and translational analyses of Tsc1-deficient PCs to understand the molecular alterations in these cells. We found that target transcripts of the Fragile X Mental Retardation Protein (FMRP) are reduced in mutant PCs with evidence of increased degradation. Surprisingly, we observed unchanged ribosomal binding for many of these genes using Translating Ribosome Affinity Purification (TRAP). Finally, we found that the FMRP target, SHANK2, was reduced in PC synapses, suggesting that compensatory increases in ribosomal binding efficiency may be unable to overcome reduced transcript levels. These data further implicate dysfunction of FMRP and its targets in TSC and suggest that treatments aimed at restoring the function of these pathways may be beneficial.


title: Dopaminergic signaling supports auditory social learning

abstract: Explicit rewards are commonly used to reinforce a behavior, a form of learning that engages the dopaminergic neuromodulatory system. In contrast, skill acquisition can display dramatic improvements from a social learning experience, even though the observer receives no explicit reward. Here, we test whether a dopaminergic signal contributes to social learning in naive gerbils that are exposed to, and learn from, a skilled demonstrator performing an auditory discrimination task. Following five exposure sessions, naive observer gerbils were allowed to practice the auditory task, and their performance was assessed across days. We first tested the effect of an explicit food reward in the observers compartment that was yoked to the demonstrators performance during exposure sessions. Naive observer gerbils with the yoked reward learned the discrimination task significantly faster, as compared to unrewarded observers. The effect of this explicit reward was abolished by administration of a D1/D5 dopamine receptor antagonist during the exposure sessions. Similarly, the D1/D5 antagonist reduced the rate of learning in unrewarded observers. To test whether a dopaminergic signal was sufficient to enhance social learning, we administered a D1/D5 receptor agonist during the exposure sessions in which no reward was present, and found that the rate of learning occurred significantly faster. Finally, a quantitative analysis of observer vocalizations and movements during the exposure sessions suggest behavioral strategies that contribute to social learning. Together, these results are consistent with a dopamine-dependent reward signal during social learning.


title: Modulation of early level EEG signatures by distributed facial emotion cues

abstract:
Face perception plays an important role in our daily social interactions, as it is essential to recognize emotions. The N170 Event Related Potential (ERP) component has been widely identified as a major face-sensitive neuronal marker. However, despite extensive investigations conducted to examine this electroencephalographic pattern, there is yet no agreement regarding its sensitivity to the content of facial expressions.

Here, we aim to clarify the EEG signatures of the recognition of facial expressions by investigating ERP components that we hypothesize to be associated with this cognitive process. We asked the question whether the recognition of facial expressions is encoded by the N170 as weel as at the level of P100 and P250. In order to test this hypothesis, we analysed differences in amplitudes and latencies for the three ERPs, in a sample of 20 participants. A visual paradigm requiring explicit recognition of happy, sad and neutral faces was used. The facial cues were explicitly controlled to vary only regarding mouth and eye components. We found that non neutral emotion expressions elicit a response difference in the amplitude of N170 and P250. In contrast with the P100, there by excluding a role for low level factors.

Our study brings new light to the controversy whether emotional face expressions modulate early visual response components, which have been often analysed apart. The results support the tenet that neutral and emotional faces evoke distinct N170 patterns, but go further by revealing that this is also true for P250, unlike the P100.


title: Identification of gene products involved in plant colonization by Pantoea sp. YR343 using a diguanylate cyclase expressed in the presence of plants

abstract: Microbial colonization of plant roots is a highly complex process that requires the coordination and regulation of many gene networks, yet the functions of many of these gene products remain poorly understood. Pantoea sp. YR343, a gamma-proteobacterium isolated from the rhizosphere of Populus deltoides, forms robust biofilms along the root surfaces of Populus and possesses plant growth-promoting characteristics. The mechanisms governing biofilm formation along plant roots by bacteria, including Pantoea sp. YR343, are not fully understood and many genes involved in this process have yet to be discovered. In this work, we identified three diguanylate cyclases in the plant-associated microbe Pantoea sp. YR343 that are expressed in the presence of plant roots, One of these diguanylate cyclases, DGC2884 localizes to discrete sites in the cells and its overexpression results in reduced motility and increased EPS production and biofilm formation. We then performed a genetic screen by expressing this diguanylate cyclase from an inducible promoter in order to identify candidate downstream effectors of c-di-GMP signaling which may be involved in root colonization by Pantoea sp. YR343. Further, we demonstrate the importance of other domains in DGC2884 to its activity, which in combination with the genes identified by transposon mutagenesis, may yield insights into activity and regulation of homologous enzymes in medically and agriculturally relevant microbes.


title: Effect of wall type, delayed mortality and mosquito age on the residual efficacy of a clothianidin-based indoor residual spray formulation (SumiShieldTM 50WG) in southern Mozambique

abstract:
BackgroundIndoor residual spraying (IRS) is one of the main malaria vector control strategies in Mozambique alongside the distribution of insecticide treated nets. As part of the national insecticide resistance management strategy, Mozambique introduced SumiShield 50WG, a third generation IRS product, in 2018. Its residual efficacy was assessed in southern Mozambique during the 2018-2019 malaria season.

MethodsTwo different wall surfaces, cement and mud-plastered surfaces, daily mosquito mortality up to 120 hours post-exposure, and older mosquitoes (13-26d old) were included in standard WHO (World Health Organization) cone bioassay tests. Lethal times (LT) 90, LT50 and LT10 were estimated using Bayesian models.

ResultsMortality 24h post exposure was consistently below 80%, the current WHO threshold value for effective IRS, in both young and old mosquitoes, regardless of wall surface type. Considering delayed mortality, residual efficacies (mosquito mortality equal or greater than 80%) ranged from 1 to [≥]12 months, with the duration depending on mortality time post exposure, wall type and mosquito age. Looking at mortality 72h after exposure, residual efficacy was between 6 and 9 months, depending on wall type and mosquito age. Mortality of older mosquitoes was significantly higher on mud-surfaces compared to cemented-surfaces 24h post exposure, but this difference was not significant for the delayed mortalities. The LT50 and LT10 (i.e. 90% of the mosquitoes survive exposure to the insecticides) values were consistently higher for older mosquitoes using the 24h post-exposure observations and ranged from 0.2 to 5.7 months and 0.2 to 7.2 months for LT50 and LT10, respectively.

ConclusionsThe present study highlights the need for assessing mosquito mortality beyond the currently recommended 24h post exposure. Failure to do so may lead to underestimation of the residual efficacy of IRS products, as delayed mortality will lead to a further reduction in mosquito vector populations and potentially negatively impact disease transmission. Monitoring residual efficacy on relevant wall surfaces, including old mosquitoes that are ultimately responsible for malaria transmission, and assessing delayed mortalities are critical to provide accurate and actionable data to guide vector control programmes.


title: Left/right asymmetry disruptions and mirror-image reversals to behavior andbrain anatomy in Ciona

abstract:
BackgroundLeft-right asymmetries are a common feature of metazoan nervous systems. This is particularly pronounced in the comparatively simple larval central nervous system (CNS) of the tunicate Ciona, whose swimming tadpole larva shows a clear chordate ground plan. While common pathway elements for specifying the left-right axis are found in the chordates, particularly a requirement for Nodal signaling, Ciona differs from its vertebrate cousins by specifying its axis at the neurula stage, rather than at gastrula. Additionally, Ciona, and other ascidians, have a requirement for an intact chorionic membrane for proper left/right specification.

ResultsWe present here results showing that left-right asymmetry disruptions caused by removal of the chorion (dechorionation) are highly variable and present throughout the Ciona larval nervous system. While previous studies have documented disruptions to the conspicuously asymmetric sensory systems in the anterior brain vesicle, we document asymmetries in seemingly symmetric structures such as the posterior brain vesicle and motor ganglion. Moreover, defects caused by dechorionation include misplaced or absent neuron classes, loss of asymmetric gene expression, aberrant synaptic connectivity, and abnormal behaviors. In the motor ganglion, a brain structure that has been equated with the vertebrate hindbrain, we find that despite the apparent left/right symmetric distribution of interneurons and motor neurons, AMPA receptors are expressed exclusively on the left side, which equates with asymmetric swimming behaviors. We also find that within a population of dechorionated larvae, there is a small percentage with apparently normal left-right specification, and approximately equal population with inverted (mirror-image) asymmetry. We present a method based on a behavioral assay for isolating these larvae. When these two classes of larvae (normal and inverted) are assessed in a light dimming assay they display mirror-image behaviors, with normal larvae responding with counterclockwise swims, while inverted larvae respond with clockwise swims.

ConclusionsOur findings highlight the importance of left-right specification pathways not only for proper CNS anatomy, but also for correct synaptic connectivity and behavior.

category: developmental biology


title: Neuronal ROS-Induced Glial Lipid Droplet Formation is Altered by Loss of Alzheimers Disease-associated Genes

abstract: A growing list of Alzheimers disease (AD) genetic risk factors is being identified, but the contribution of these genetic mutations to disease remains largely unknown. Accumulating data support a role of lipid dysregulation and excessive ROS in the etiology of AD. Here, we identified cell-specific roles for eight AD risk-associated genes in ROS-induced glial lipid droplet (LD) formation. We demonstrate that ROS-induced glial LD formation requires two ABCA transporters (ABCA1 and ABCA7) in neurons, the APOE receptor (LRP1), endocytic genes (PICALM, CD2AP, and AP2A2) in glia, and retromer genes (VPS26 and VPS35) in both neurons and glia. Moreover, ROS strongly enhances A{beta}42-toxicity in flies and A{beta}42-plaque formation in mice. Finally, an ABCA1-activating peptide restores glial LD formation in the APOE4-associated loss of LD. This study places AD risk factors in a neuron-to-glia lipid transfer pathway with a critical role in protecting neurons from ROS-induced toxicity.


title: The landscape of accessible chromatin in quiescent and post-myocardial infarction cardiac fibroblasts

abstract: After myocardial infarction, quiescent cardiac fibroblasts are activated and undergo multiple proliferation and differentiation events, which contribute to the extracellular matrix remodeling of the infarcted myocardium. We recently found that cardiac fibroblasts of different differentiation states had distinct expression profiles closely related to their functions. Gene expression is directly regulated by chromatin state. However, the role of chromatin reorganization in the drastic gene expression changes during post-MI differentiation of cardiac fibroblast has not been revealed. In this study, the gene expression profiling and genome-wide mapping of accessible chromatin in mouse cardiac fibroblasts isolated from uninjured hearts and the infarcts at different time points were performed by RNA sequencing (RNA-seq) and the assay for transposase-accessible chromatin with high-throughput sequencing (ATAC-seq), respectively. ATAC-seq peaks were highly enriched in the promoter area and distal areas where enhancers might be located. A positive correlation was identified between the transcription level and promoter accessibility for many dynamically expressed genes. In addition, it was found that DNA methylation may contribute to the post-MI chromatin remodeling and gene expression in cardiac fibroblasts. Integrated analysis of ATAC-seq and RNA-seq datasets also identified transcription factors that possibly contributed to the differential gene expression between cardiac fibroblasts of different states.


title: Collective behavior emerges from genetically controlled simple behavioral motifs in zebrafish

abstract: Since Darwin, coordinated movement of animal groups has been believed to be essential to species survival, but it is not understood how changes in the genetic makeup of individuals might alter behavior of the collective. Here we find that even at the early larval stage, zebrafish regulate their proximity and alignment with each other. Two simple visual responses, one that measures relative visual field occupancy and the other global visual motion, suffice to account for the group behavior that emerges. We analyze how mutations in genes known to affect social behavior of humans perturb these simple reflexes in larval zebrafish and thereby affect their collective behaviors. We use model simulations to show that changes in reflexive responses of individual mutant animals predict well the distinctive collective patterns that emerge in a group. Hence group behaviors reflect in part genetically defined primitive sensorimotor "motifs", which are evident even in young larvae.


title: Autism-associated CHD8 keeps proliferation of human neural progenitors in check by lengthening the G1 phase of the cell cycle

abstract: CHD8 (Chromodomain Helicase DNA Binding Protein 8) is a chromatin remodeler that preferentially regulates expression of genes implicated in early development of the cerebral cortex. De novo mutations (DNMs) in CHD8 are strongly associated with a specific subtype of autism characterized by enlarged foreheads and distinct cranial features. The vast majority of these DNMs are heterozygous loss-of-function mutations with high penetrance for autism. How CHD8 haploinsufficiency alters the normal developmental trajectory of the human cortex is poorly understood and debated. Previous studies in the mammalian developing cortex have shown progressive lengthening of the G1 phase of the cell cycle as neural stem cells transition from proliferative to neurogenic divisions. G1 length has been proposed to operate as a molecular clock that controls timing of this crucial developmental switch. To determine the influence of CHD8 on cell cycle timing, we disrupted one allele of CHD8 in human embryonic stem cells (hESCs), differentiated these cells into neural precursor cells (NPCs), and imaged cell cycle progression of individual CHD8+/- NPCs -- in parallel with their isogenic CHD8+/+ counterparts -- during several rounds of cell division. We found a specific and marked decrease in G1 duration in CHD8+/- NPCs, resulting in an overall shortening of the cell cycle. Consistent with faster progression of CHD8+/- NPCs through G1 and the G1/S checkpoint, we observed increased expression of E cyclins and elevated phosphorylation of Erk in these mutant cells -- two central signalling pathways involved in S phase entry. Together, our findings show dysregulated proliferation of NPCs in a human stem cell model of CHD8 haploinsufficiency and predict enlargement of the neural progenitor pool in CHD8+/- developing brains, a phenotype that may explain macrocephaly in individuals with CHD8 DNMs. Furthermore, our work provides further evidence for a link between autism and cancer and identifies MAPK signaling as a potential therapeutic target for the treatment of this autism subtype.


title: CaSR modulates sodium channel-mediated Ca 2+ -dependent excitability

abstract: Increasing extracellular [Ca2+] ([Ca2+]o) strongly decreases intrinsic excitability in neurons but the mechanism is unclear. By one hypothesis, [Ca2+]o screens surface charge reducing voltage-dependent sodium channel (VGSC) activation and by another [Ca2+]o activates Calcium-sensing receptor (CaSR) closing the sodium-leak channel (NALCN). Here we report that action potential (AP) firing rates increased in wild-type (WT), but not CaSR null mutant (Casr-/-) neocortical neurons, following the switch from physiological to reduced Ca2+-containing Tyrode. However, after membrane potential correction, AP firing increased similarly in both genotypes inconsistent with CaSR regulation of NALCN. Activation of VGSCs was the dominant contributor to the increase in excitability after the [Ca2+]o change. VGSC conductance-voltage relationships were hyperpolarized by decreasing [Ca2+]o for Casr-/- neurons indicating CaSR contributes to [Ca2+]o-dependent excitability via VGSCs. Regulation of VGSC gating by [Ca2+]o is the key mechanism mediating [Ca2+]o-dependent changes in neocortical neuron excitability and CaSR influences neuronal excitability by its effects on VGSC gating.


title: Kinetic structure of recycling vesicle pool at the Calyx of Held synapse under in vivo-like activities

abstract:
Synaptic transmission at mammalian central synapses has ongoing background activity at physiological temperature. The recycling vesicle pool, with proper kinetics, ensures sustained synaptic transmission. However, the kinetic structure of recycling vesicle pool has never been quantitatively analyzed before, and most studies were performed at room temperature and under resting conditions. With the combination of presynaptic capacitance measurement and postsynaptic EPSC recording on calyx of Held synapses at physiological temperature, we studied vesicle recycling under sustained presynaptic stimulation. The kinetics of vesicle reuse was revealed by impeding transmitter refilling with folimycin. We kinetically dissected the recycling vesicle pool as sequentially connected sub-pools and depicted the complete kinetic structure. The sizes and transition rates among these sub-pools were dynamically regulated by neuronal activity, in order to ensure efficient synaptic transmission. Our work highlights the impact of the vesicle recycling machinery on stable and reliable synaptic transmission under variable levels of neuronal activity.

Impact statementThe recycling pool of vesicles are kinetically dissected as four populated pools ensuring stable and reliable synaptic transmission


title: Synaptic plasticity in distal dendrites can optimize probabilistic top-down predictions in pyramidal cells

abstract: Predictive coding has been identified as a key aspect of computation and learning in cortical microcircuits. But we do not know how synaptic plasticity processes install and maintain predictive coding capabilites in these neural circuits. Predictions are inherently uncertain, and learning rules that aim at discriminating linearly separable classes of inputs - such as the perceptron learning rule - do not perform well if the goal is learning to predict. We show that experimental data on synaptic plasticity in apical dendrites of pyramidal cells support another learning rule that is suitable for learning to predict. More precisely, it enables a spike-based approximation to logistic regression, a well-known gold standard for probabilistic prediction. We also show that data-based interactions between apical dendrites support learning of predictions for more complex probability distributions than those that can be handled by single dendrites. The resulting learning theory for top-down inputs to pyramidal cells provides a normative framework for evaluating experimental data, and suggests further experiments for tracking the emergence of predictive coding through synaptic plasticity in apical dendrites.


title: A normative framework for learning top-down predictions through synaptic plasticity in apical dendrites


title: Dopamine and serotonin interplay for valence-based spatial learning

abstract: Dopamine and serotonin are important modulators of synaptic plasticity and their action has been linked to our ability to learn the positive or negative outcomes or valence learning. In the hippocampus, both neuromodulators affect long-term synaptic plasticity but play different roles in the encoding of uncertainty or predicted reward. Here, we examine the differential role of these modulators on learning speed and cognitive flexibility in a navigational model. We compare two reward-modulated spike time-dependent plasticity (R-STDP) learning rules to describe the action of these neuromodulators. Our results show that the interplay of dopamine (DA) and serotonin (5-HT) improves overall learning performance and can explain experimentally reported differences in spatial task performance. Furthermore, this system allows us to make predictions regarding spatial reversal learning.