title: The Pathogenic R5L Mutation Disrupts Formation of Tau Complexes on the Microtubule by Altering Local N-Terminal Structure

abstract:
The microtubule-associated protein (MAP) Tau is an intrinsically disordered protein (IDP) primarily expressed in axons, where it functions to regulate microtubule dynamics, modulate motor protein motility, and participate in signaling cascades. Tau misregulation and point mutations are linked to neurodegenerative diseases, including Progressive Supranuclear Palsy (PSP), Picks Disease and Alzheimers disease. Many disease-associated mutations in Tau occur in the C-terminal microtubule-binding domain of the protein. Effects of C-terminal mutations in Tau have led to the widely accepted disease-state theory that missense mutations in Tau reduce microtubule-binding affinity or increase Tau propensity to aggregate. Here, we investigate the effect of an N-terminal disease-associated mutation in Tau, R5L, on Tau-microtubule interactions using an in vitro reconstituted system. Contrary to the canonical disease-state theory, we determine the R5L mutation does not reduce Tau affinity for the microtubule using Total Internal Reflection Fluorescence (TIRF) Microscopy. Rather, the R5L mutation decreases the ability of Tau to form larger order complexes, or Tau patches, at high concentrations of Tau. Using Nuclear Magnetic Resonance (NMR), we show that the R5L mutation results in a local structural change that reduces interactions of the projection domain in the presence of microtubules. Altogether, these results challenge both the current paradigm of how mutations in Tau lead to disease and the role of the projection domain in modulating Tau behavior on the microtubule surface.

Significance StatementThe microtubule-associated protein Tau is strongly linked to a number of neurological diseases. Disease onset is typically associated with weakened interaction with the microtubule, but this widely accepted model is based on hyperphosphorylation or mutations within the C-terminal microtubule-binding domain of Tau. Here, we find an N-terminal disease-associated mutation in Tau, R5L, does not reduce Tau affinity for microtubules, but instead modifies the N-terminal structure, altering Taus behavior and ability to condense on the microtubule surface. Our findings challenge the current paradigms of both how mutations in Tau lead to disease and the functional role of the N-terminal region of Tau.


title: PDXNet Portal: Patient-Derived Xenograft model, data, workflow, and tool discovery

abstract:
We created the PDX Network (PDXNet) Portal (https://portal.pdxnetwork.org/) to centralize access to the National Cancer Institute-funded PDXNet consortium resources (i.e., PDX models, sequencing data, treatment response data, and bioinformatics workflows), to facilitate collaboration among researchers, and to make resources easily available for research. The portal includes sections for resources, analysis results, metrics for PDXNet activities, data processing protocols, and training materials for processing PDX data.

The initial portal release highlights PDXNet model and data resources, including 334 new models across 33 cancer types. Tissue samples of these models were deposited in the NCIs Patient-Derived Model Repository (PDMR) for public access. These models have 2,822 associated sequencing files from 873 samples across 307 patients, which are hosted on the Cancer Genomics Cloud powered by Seven Bridges and the NCI Cancer Data Service for long-term storage and access with dbGaP permissions. The portal also includes results from standardized analysis workflows on PDXNet sequencing files and PDMR data (2,594 samples from 463 patients across 78 disease types). These 15 analysis workflows for whole-exome and RNA-Seq data are freely available, robust, validated, and standardized.

The model and data lists will grow substantially over the next two years and will be continuously updated as new data are available. PDXNet models support multi-agent treatment studies, determination of sensitivity and resistance mechanisms, and preclinical trials. The PDXNet portal is a centralized location for these data and resources, which we expect to be of significant utility for the cancer research community.

category: cancer biology


title: Generative modeling of histology tissue reduces human annotation effort for segmentation model development.

abstract: Segmentation of histology tissue whole side images is an important step for tissue analysis. Given enough annotated training data modern neural networks are capable accurate reproducible segmentation, however, the annotation of training datasets is time consuming. Techniques such as human in the loop annotation attempt to reduce this annotation burden, but still require a large amount of initial annotation. Semi-supervised learning, a technique which leverages both labeled and unlabeled data to learn features has shown promise for easing the burden of annotation. Towards this goal, we employ a recently published semi-supervised method: datasetGAN for the segmentation of glomeruli from renal biopsy images. We compare the performance of models trained using datasetGAN and traditional annotation and show that datasetGAN significantly reduces the amount of annotation required to develop a highly performing segmentation model. We also explore the usefulness of using datasetGAN for transfer learning and find that this greatly enhances the performance when a limited number of whole slide images are used for training.

category: pathology


title: Network-based analysis on the pharmacological mechanisms underlying the anti-diabetic property of Coix lachryma-jobi

abstract: Diabetes mellitus (DM) is the most common endocrine disorder and among the top 10 leading diseases causing death worldwide. Coicis semen [CS] (Coix lacryma-jobi), also known as adlay have been reported to display anti-diabetic properties. Unfortunately, studies on the pharmacological mechanisms involving adlay for the treatment of diabetes are nil. Thus, this study was conducted to evaluate the interactions and mechanisms of the bioactive compound targets of adlay in the treatment of diabetes using network analysis. Adlay bioactive compounds and potential target genes were obtained from SymMap. Diabetes related target genes were collected from CTD. Protein-Protein Interaction Network was analyzed using the STRING database. GO and KEGG pathway enrichment analyses were performed using DAVID to further explore the mechanisms of adlay in treating diabetes. PPI and compound-target-pathway were visualized using Cytoscape. A total of 25 bioactive compounds, 201 corresponding targets, and 35839 diabetes mellitus associated targets were obtained while 200 were considered potential therapeutic targets. The 9 bioactive compounds studied were berberine, oleic acid, beta-sitosterol, sitosterol, linoleic acid, berberrubine, jatrorrhizine, thalifendine, and stigmasterol. The identified 5 core targets were ESR1, JUN, MAPK14, and RXRA. Adlai targets enriched in GO terms were mostly involved with positive regulation of transcription, response to drugs, and negative regulation of apoptosis. This study provides novel research insights into the clinical properties of adlay in diabetes melitus treatment.

category: pharmacology and toxicology


title: SEX DIFFERENCES IN BLOOD PRESSURE RESPONSE TO CONTINUOUS ANG II INFUSION: ARE ONLY SEX HORMONES TO BLAME?

abstract:
To investigate the involvement of the sex chromosome complement (SCC), organizational and activational hormonal effects in changes in mean arterial pressure during acute Ang II infusion, we used gonadectomized (GDX) mice of the "four core genotypes" model, which dissociates the effect of gonadal sex and SCC, allowing comparisons of sexually dimorphic traits between XX and XY females as well as XX and XY males. Additionally, {beta}-estradiol and testosterone propionate (2ug/g) were daily injected for 4 days to evaluate activational hormonal effects.

Statistical analysis of the changes in mean arterial pressure revealed an interaction of SCC, organizational and activational hormonal effects during Ang II infusion {F(7,39=2,60 p<0.01)}. Our results indicate that, in absence of activational hormonal effects, interaction between the SCC and organizational hormonal action differentially modulates changes in arterial pressure. In GDX mice without hormone replacement, Ang II infusion resulted in an increase in mean arterial pressure in XX-male, XX-female and XY-female mice, while no changes were observed in XY-male mice. Furthermore, {beta}-estradiol replacement (GDX+E2 group) resulted in a decrease in blood pressure in XX-males, XX-females and XY-females (indicating an activational {beta}-estradiol effect), while no changes were observed in the XY-male group. Moreover, testosterone propionate replacement (GDX+TP group) showed a greater increase in blood pressure in XY-male mice than in XX-males and XX-females, demonstrating an activational hormonal effect of testosterone in XY-male mice.

Our data isolates and highlights the contribution and interaction of SCC, activational and organizational hormonal effects in sex differences in Ang II blood pressure regulation.

category: physiology


title: Alpha cell dysfunction in early type 1 diabetes

abstract: Multiple islet autoantibodies (AAb) predict type 1 diabetes (T1D) and hyperglycemia within 10 years. By contrast, T1D develops in just [~]15% of single AAb+ (generally against glutamic acid decarboxylase, GADA+) individuals; hence the single GADA+ state may represent an early stage of T1D amenable to interventions. Here, we functionally, histologically, and molecularly phenotype human islets from non-diabetic, GADA+ and T1D donors. Similar to the few remaining beta cells in T1D islets, GADA+ donor islets demonstrated a preserved insulin secretory response. By contrast, alpha cell glucagon secretion was dysregulated in both T1D and GADA+ islets with impaired glucose suppression of glucagon secretion. Single cell RNA sequencing (scRNASeq) of GADA+ alpha cells revealed distinct abnormalities in glycolysis and oxidative phosphorylation pathways and a marked downregulation of PKIB, providing a molecular basis for the loss of glucose suppression and the increased effect of IBMX observed in GADA+ donor islets. The striking observation of a distinct early defect in alpha cell function that precedes beta cell loss in T1D suggests that not only overt disease, but also the progression to T1D itself, is bihormonal in nature.


title: Connexin Hemichannels with Prostaglandin Release in Anabolic Function of Bone to Mechanical Loading

abstract: Mechanical stimulation, such as physical exercise, is essential for bone formation and health. Here, we demonstrate the critical role of osteocytic Cx43 hemichannels in anabolic function of bone in response to mechanical loading. Two transgenic mouse models, R76W and {Delta}130-136, expressing dominant-negative Cx43 mutants in osteocytes were adopted. Mechanical loading of tibial bone increased cortical bone mass and mechanical properties in wild-type and gap junction-impaired R76W mice through increased PGE2, endosteal osteoblast activity, and decreased sclerostin. These anabolic responses were impeded in gap junction/hemichannel-impaired {Delta}130-136 mice and accompanied by increased endosteal osteoclast activity. Specific inhibition of Cx43 hemichannels by Cx43(M1) antibody suppressed PGE2 secretion and impeded loading-induced endosteal osteoblast activity, bone formation and anabolic gene expression. PGE2 administration rescued the osteogenic response to mechanical loading impeded by impaired hemichannels. Together, osteocytic Cx43 hemichannels could be a potential new therapeutic target for treating bone loss and osteoporosis.


title: A video-based behavioural intervention associated with improved HPV knowledge and intention to vaccinate

abstract:
AimsThe aim of this study was to design, develop and evaluate a theory and evidence-based intervention to improve human papillomavirus (HPV) and HPV vaccine knowledge, and intention to vaccinate, among parent-daughter dyads.

MethodsA theory and evidence-based online behavioural intervention, "Is the HPV vaccine for me?" was developed to improve HPV and HPV vaccine knowledge, and intention to vaccinate. The impact and feasibility of the intervention was evaluated in a prospective randomised controlled feasibility trial.

ResultsA total of 49 parent-daughter dyads completed baseline knowledge assessment (n=24 control, n=25 intervention), and 35 dyads completed knowledge assessment at week 2 (n=17 control, n=18 intervention). The intervention was associated with a statistically significant increase in HPV, and HPV vaccine knowledge and intention to vaccinate. All intervention participants found the video interesting, while 96% found it useful.

ConclusionsThis intervention was found to be affordable, practicable, effective (cost-effective), acceptable, safe, and equitable, in this feasibility study.

category: scientific communication and education


title: Three-dimensional reconstruction of the face and feeding apparatus of the predatory nematode Pristionchus pacificus

abstract: Pristionchus pacificus is a nematode model for the developmental genetics of morphological polyphenism, especially at the level of individual cells. Morphological polyphenism in this species includes an evolutionary novelty, moveable teeth, which have enabled predatory feeding in this species and others in its family (Diplogastridae). From transmission electron micrographs of serial thin sections through an adult hermaphrodite of P. pacificus, we three-dimensionally reconstructed all epithelial and myoepithelial cells and syncytia, corresponding to 74 nuclei, of its face, mouth, and pharynx. We found that the epithelia that produce the predatory morphology of P. pacificus are identical to Caenorhabditis elegans in the number of cell classes and nuclei. However, differences in cell form, spatial relationships, and nucleus position correlate with gross morphological differences from C. elegans and outgroups. Moreover, we identified fine-structural features, especially in the anteriormost pharyngeal muscles, that underlie the conspicuous, left-right asymmetry that characterizes the P. pacificus feeding apparatus. Our reconstruction provides an anatomical map for studying the genetics of polyphenism, feeding behavior, and the development of novel form in a satellite model to C. elegans.

category: zoology


title: Comparative reconstruction of the predatory feeding structures of the polyphenic nematode Pristionchus pacificus

category: evolutionary biology


title: Brain functional connectome defines a transdiagnostic dimension associated with cognition and psychopathology in youth

abstract: The search for psychiatric biomarkers has remained elusive, in part, due to high comorbidity, low specificity, and poor concordance between neurobiological abnormalities and existing diagnostic categories. Developmental shifts in symptom expression and brain function across the lifespan further complicate biomarker identification. Recent studies suggest that focusing on cognition may be a pathway forward: Cognitive dysfunction is a common feature across psychiatric disorders. Individual differences in cognition may reflect variability in the connectivity of underlying neurocognitive brain networks, and predict psychopathology at different developmental periods. In the present study we identified brain-based dimensions of general cognitive capacity and psychopathology using sparse canonical correlation analysis (sCCA) in a sample of 7,383 preadolescents from the Adolescent Brian Cognitive Development (ABCD) study. This analysis revealed correlated patterns of functional connectivity with cognitive control capacity and psychopathology. Specifically, the results identified a single connectome-based latent brain variate that was positively correlated with performance on cognitive measures across domains and negatively correlated with parent-reported psychopathology across diagnoses and domains. Functional connectivity loadings for the brain variate were across distributed cortical and subcortical brain networks and a dose-dependent relationship with psychopathology based upon the cumulative number of psychiatric diagnoses was observed. These findings provide preliminary evidence for a connectome-based biomarker that indexes individual differences in cognitive control and predicts transdiagnostic psychopathology in a dose-dependent fashion.

category: neuroscience


title: Enhanced mismatch negativity responses in harmonic compared to inharmonic sound sequences

abstract: Many natural sounds have frequency spectra composed of integer multiples of a fundamental frequency. This property, known as harmonicity, plays an important role in auditory information processing. However, the extent to which harmonicity influences the processing of sound features beyond pitch is still unclear. This is interesting because harmonic sounds have lower information entropy than inharmonic sounds. According to predictive processing accounts of perception, this property could produce more salient neural responses due to the brains weighting of sensory signals according to their uncertainty. In the present study, we used electroencephalography to investigate brain responses to harmonic and inharmonic sounds commonly occurring in music: piano tones and hi-hat cymbal sounds. In a multi-feature oddball paradigm, we measured mismatch negativity (MMN) and P3a responses to timbre, intensity, and location deviants in listeners with and without congenital amusia--an impairment of pitch processing. As hypothesized, we observed larger amplitudes and earlier latencies for harmonic compared to inharmonic sounds for both MMN and P3a responses. These harmonicity effects were modulated by sound feature. Moreover, the difference in P3a latency between harmonic and inharmonic sounds was larger for controls than amusics. We propose an explanation of these results based on predictive coding and discuss the relationship between harmonicity, information entropy, and precision weighting of prediction errors.


title: Endogenous recruitment of frontal-sensory circuits during visual discrimination

abstract: A long-range circuit linking anterior cingulate cortex (ACC) to primary visual cortex (V1) has been previously proposed to mediate visual selective attention in mice during visually guided behaviour. Here we used in vivo two-photon functional imaging to measure endogenous activity of ACC neurons projecting to layer 1 of V1 (ACC-V1axons) in mice either passively viewing stimuli or performing a go/no-go visually guided task. We observed that while ACC-V1axons were recruited under these conditions, this was not linked to enhancement of neural or behavioural measures of sensory coding. Instead, ACC-V1axon activity was observed to be associated with licking behaviour, modulated by reward, and biased towards task relevant sensory cortex.


title: A network information theoretic framework to characterise muscle synergies in space and time

abstract:
ObjectiveCurrent approaches to muscle synergy extraction rely on linear dimensionality reduction algorithms that make specific assumptions on the underlying signals. However, to capture nonlinear time varying, large-scale but also muscle-specific interactions, a more generalised approach is required.

ApproachHere we developed a novel framework for muscle synergy extraction that relaxes model assumptions by using a combination of information- and network theory and dimensionality reduction. We first quantify informational dynamics between muscles, time-samples or muscle-time pairings using a novel mutual information formulation. We then model these pairwise interactions as multiplex networks and identify modules representing the network architecture. We employ this modularity criterion as the input parameter for dimensionality reduction, which verifiably extracts the identified modules, and also to characterise salient structures within each module.

Main resultsThis novel framework captures spatial, temporal and spatiotemporal interactions across two benchmark datasets of reaching movements, producing distinct spatial groupings and both tonic and phasic temporal patterns. Readily interpretable muscle synergies spanning multiple spatial and temporal scales were identified, demonstrating significant task dependence, ability to capture trial-to-trial fluctuations and concordance across participants. Furthermore, our framework identifies submodular structures that represent the distributed networks of co-occurring signal interactions across scales.

SignificanceThe capabilities of this framework are illustrated through the concomitant continuity with previous research and novelty of the insights gained. Several previous limitations are circumvented including the extraction of functionally meaningful and multiplexed pairwise muscle couplings under relaxed model assumptions. The extracted synergies provide a holistic view of the movement while important details of task performance are readily interpretable. The identified muscle groupings transcend biomechanical constraints and the temporal patterns reveal characteristics of fundamental motor control mechanisms. We conclude that this framework opens new opportunities for muscle synergy research and can constitute a bridge between existing models and recent network-theoretic endeavours.


title: Single-cell Networks Reorganise to Facilitate Whole-brain Supercritical Dynamics During Epileptic Seizures

abstract: Excitation-inhibition (EI) balance may be required for the organisation of brain dynamics to a phase transition, criticality, which confers computational benefits. Brain pathology associated with EI imbalance may therefore occur due to a deviation from criticality. However, evidence linking critical dynamics with EI imbalance-induced pathology is lacking. Here, we studied the effect of EI imbalance-induced epileptic seizures on brain dynamics, using in vivo whole-brain 2-photon imaging of GCaMP6s larval zebrafish at single-neuron resolution. We demonstrate the importance of EI balance for criticality, with EI imbalance causing a loss of whole-brain critical statistics. Using network models we show that a reorganisation of network topology drives this loss of criticality. Seizure dynamics match theoretical predictions for networks driven away from a phase transition into disorder, with the emergence of chaos and a loss of network-mediated separation, dynamic range and metastability. These results demonstrate that EI imbalance drives a pathological deviation from criticality.


title: Tiam1-mediated synaptic plasticity drives comorbid depressive symptoms in chronic pain

abstract: Hyperactivity in the anterior cingulate cortex (ACC) drives comorbid depressive symptoms in chronic pain, but the cause of ACC hyperactivity is currently unclear. Ketamine, an N-methyl-D-aspartate receptor (NMDAR) antagonist, induces rapid and sustained antidepressant-like effects in chronic pain-induced depression in both patients and animal models. However, the mechanisms underlying ketamines sustained antidepressant effects remain elusive. Here, we show that Tiam1, a Rac1-specific guanine nucleotide exchange factor (GEF) that was previously identified as a critical mediator of NMDAR-dependent dendritic spine development, is activated in the ACC in chronic pain mice displaying depressive-like behaviors. Conditional deletion of Tiam1 from postnatal forebrain excitatory neurons, specific deletion of Tiam1 from ACC neurons, or pharmacological inhibition of the Tiam1-Rac1 signaling pathway prevents chronic pain-induced depressive-like behaviors in mice. Biochemical, morphological, and electrophysiological assays reveal that Tiam1 orchestrates synaptic structural and functional remodeling in ACC neurons via actin cytoskeleton reorganization and synaptic NMDAR stabilization. This Tiam1-coordinated synaptic plasticity underpins ACC hyperactivity and drives chronic pain-induced depressive-like behaviors. Ketamine induces sustained antidepressant effects in chronic pain by blocking Tiam1-mediated synaptic structural and functional plasticity in ACC neurons. Our results reveal Tiam1 as a key factor in the pathophysiology of chronic pain-induced depression and in the sustained antidepressant effects of ketamine in ACC neurons. These findings highlight Tiam1 as a potential therapeutic target for the treatment of comorbid depressive symptoms in chronic pain.


title: Astrocytic urea cycle detoxifies Aβ-derived ammonia while impairing memory in Alzheimers Disease

abstract: Alzheimers disease (AD) is one of the foremost neurodegenerative diseases, characterized by beta-amyloid (A{beta}) plaques and significant progressive memory loss. In AD, astrocytes are known to take up and clear A{beta} plaques. However, how A{beta} induces pathogenesis and memory impairment in AD remains elusive. We report that normal astrocytes show non-cyclic urea metabolism, whereas A{beta}-treated astrocytes show switched-on urea cycle with upregulated enzymes and accumulated entering-metabolite aspartate, starting-substrate ammonia, end-product urea, and side-product putrescine. Gene-silencing of astrocytic ornithine decarboxylase-1 (ODC1), facilitating ornithine-to-putrescine conversion, boosts urea cycle and eliminates aberrant putrescine and its toxic by-products ammonia, H2O2, and GABA to recover from reactive astrogliosis and memory impairment in AD model. Our findings implicate that astrocytic urea cycle exerts opposing roles of beneficial A{beta} detoxification and detrimental memory impairment in AD. We propose ODC1-inhibition as a promising therapeutic strategy for AD to facilitate removal of toxic molecules and prevent memory loss.


title: Intrinsic maturation of sleep output neurons regulates sleep ontogeny in Drosophila

abstract: The maturation of sleep behavior across a lifespan (sleep ontogeny) is an evolutionarily conserved phenomenon. Mammalian studies have shown that in addition to increased sleep duration, early life sleep exhibits stark differences compared to mature sleep with regard to the amount of time spent in certain sleep states. How intrinsic maturation of sleep output circuits contributes to sleep ontogeny is poorly understood. The fruit fly Drosophila melanogaster exhibits multifaceted changes to sleep from juvenile to mature adulthood. Here, we use a non-invasive probabilistic approach to investigate changes in sleep architecture in juvenile and mature flies. Increased sleep in juvenile flies is driven primarily by a decreased probability of transitioning to wake, and characterized by more time in deeper sleep states. Functional manipulations of sleep-promoting neurons in the dFB suggest these neurons differentially regulate sleep in juvenile and mature flies. Transcriptomic analysis of dFB neurons at different ages and a subsequent RNAi screen implicate genes involved in distinct molecular processes in sleep control of juvenile and mature flies. These results reveal that dynamic transcriptional states of sleep output neurons contribute to changes in sleep across the lifespan.


title: Stratification in Microbial Communities with Depth and Redox Status in a Eutrophic Lake Across Two Years

abstract:
Bacteria have a profound impact on many key biogeochemical cycles in freshwater lake ecosystems; in turn, the composition of bacteria in the lake is contingent on the chemistry of the water. Many parameters that affect bacterial growth in freshwater ecosystems, such as water temperature, nutrient levels, and redox status, exhibit notable inter-annual differences in addition to seasonal changes. However, little is known about the impact of these inter- and intra-annual differences on the freshwater microbiome, especially in anoxic bottom waters. In this study, we paired biogeochemical field data with 16S rRNA gene amplicon sequencing of depth-discrete samples from a dimictic lake across two open-water seasons to observe variation in the microbiome relative to differences in water chemistry between two years. We found differences in the timing anoxia onset and the redox status in the water column across the two years. Changes in redox status led to major shifts in the microbial community composition. While there was little variation between years in the microbial taxonomic composition at the phyla level, there was substantial interannual variation at more resolved taxonomic levels. Some interannual differences can be explained by links between the predicted metabolic potential of those lineages and the different redox conditions between the two years. These results emphasize the need for repeated monitoring to deduce long-term trends in microbial communities in natural ecosystems and the importance of a comprehensive evaluation of environmental conditions contemporary with any microbiome analysis.

ImportanceThe results of this study add to the growing body of evidence that microbial communities in natural systems are temporally dynamic on multiple scales, and even more so at highly resolved taxonomic levels. By correlating our analysis of the microbial community with the redox status of the water column we find that many community differences between the years can be in part explained by these parameters. As collecting 16S rRNA data over many years is critical to understanding long term trends in microbial ecology, our study suggests that corresponding water chemistry data could be a powerful tool to help explain microbiome trends.

category: microbiology


title: Into the range: a latitudinal gradient or a center-margins differentiation of ecological strategies in Arabidopsis thaliana?

abstract:
Background and AimsDetermining within-species large-scale variation in phenotypic traits is central to elucidate the drivers of species ranges. Intraspecific comparisons offer the opportunity to understand how trade-offs and biogeographical history constrain adaptation to contrasted environmental conditions. Here we test whether functional traits, ecological strategies and phenotypic plasticity in response to abiotic stress vary along a latitudinal or a center-margins gradient within the native range of Arabidopsis thaliana.

MethodsThe phenotypic outcomes of plant adaptation at the center and margins of its geographic range were experimentally examined in 30 accessions from southern, central and northern Europe. The variation of traits related to stress tolerance, resource use, colonization ability as well as survival and fecundity was determined in response to high temperature (34{degrees}C) or frost (- 6{degrees}C), in combination with response to water deficit.

Key ResultsBoth evidence for a latitudinal and a center-margins differentiation was found. Traits related to the acquisitive/conservative strategy trade-off varied along a latitudinal gradient. Northern accessions presented a greater survival to stress than central and southern accessions. Traits related to a colonization-competition trade-off followed a center-margin differentiation. Central accessions presented a higher phenotypic plasticity and trait values associated with a higher colonization ability than northern and southern accessions which instead had a higher competition ability.

ConclusionsIntraspecific phenotypic variation helps us understand how the distribution range has evolved in Arabidopsis thaliana, which is shaped both by climate and the population migratory history. We advocate to consider intraspecific trait variation in species range studies instead of species means only as classically done in macroecology.

category: ecology


title: Admixture dynamics in colonial Mexico and the genetic legacy of the Manila Galleon

abstract: Mexico has considerable population substructure due to pre-Columbian diversity and subsequent variation in admixture levels from trans-oceanic migrations, primarily from Europe and Africa, but also, to a lesser extent, from Asia. Detailed analyses exploring sub-continental structure remain limited and post-Columbian demographic dynamics within Mexico have not been inferred with genomic data. We analyze the distribution of ancestry tracts to infer the timing and number of pulses of admixture in ten regions across Mexico, observing older admixture timings in the first colonial cities and more recent timings moving outward into southern and southeastern Mexico. We characterize the specific origin of the heterogeneous Native American ancestry in Mexico: a widespread western-central Native Mesoamerican component in northern Aridoamerican states and a central-eastern Nahua contribution in Guerrero (southern Mexico) and Veracruz to its north. Yucatan shows lowland Mayan ancestry, while Sonora exhibits a unique northwestern native Mexican ancestry matching no sampled reference, each consistent with localized indigenous cultures. Finally, in Acapulco, Guerrero a notable proportion of East Asian ancestry was observed, an understudied heritage in Mexico. We identified the source of this ancestry within Southeast Asia--specifically western Indonesian and non-Negrito Filipino--and dated its arrival to approximately thirteen generations ago (1620 CE). This points to a genetic legacy from the 17th century Manila Galleon trade between the colonial Spanish Philippines and the Pacific port of Acapulco in Spanish Mexico. Although this piece of the colonial Spanish trade route from China to Europe appears in historical records, it has been largely ignored as a source of genetic ancestry in Mexico, neglected due to slavery, assimilation as "Indios" and incomplete historical records.

category: genetics


title: Assessing species coverage and assembly quality of rapidly accumulating sequenced genomes

abstract: Ambitious initiatives to coordinate genome sequencing of Earths biodiversity mean that the accumulation of genomic data is growing rapidly. In addition to cataloguing biodiversity, these data provide the basis for understanding biological function and evolution. Accurate and complete genome assemblies offer a comprehensive and reliable foundation upon which to advance our understanding of organismal biology at genetic, species, and ecosystem levels. However, ever-changing sequencing technologies and analysis methods mean that available data are often heterogeneous in quality. In order to guide forthcoming genome generation efforts and promote efficient prioritisation of resources, it is thus essential to define and monitor taxonomic coverage and quality of the data. Here we present an automated analysis workflow that surveys genome assemblies from the United States National Center for Biotechnology Information (NCBI), assesses their completeness using the relevant Benchmarking Universal Single-Copy Orthologue (BUSCO) datasets, and collates the results into an interactively browsable resource. We apply our workflow to produce a community resource of available assemblies from the phylum Arthropoda, the Arthropoda Assembly Assessment Catalogue. Using this resource, we survey current taxonomic coverage and assembly quality at the NCBI, we examine how key assembly metrics relate to gene content completeness, and we compare results from using different BUSCO lineage datasets. These results demonstrate how the workflow can be used to build a community resource that enables large-scale assessments to survey species coverage and data quality of available genome assemblies, and to guide prioritisations for ongoing and future sampling, sequencing, and genome generation initiatives.

category: genomics


title: Thermal boldness: Volunteer exploration of extreme temperatures in Drosophila melanogaster

abstract: A dominant perception is that small and motile ectothermic animals must use behavior to avoid exposure to critical or sub-critical temperatures impairing physiological performance. Concomitantly, volunteer exploration of extreme environments by some individuals may promote physiological adjustments and enhance ecological opportunity. Here we introduce to the literature a Thermal Decision System (TDS) which is fully modular, thermally stable, versatile, and adaptable to study navigation through thermal landscapes in insects and other small motile animals. We used a specific setting of the TDS to investigate volunteer navigation through critical cold and hot temperatures in Drosophila melanogaster. We demonstrate that a thermally bold behavior (volunteer crossings through a Critical Temperature Zone, CTZ) characterized a fraction of flies in a sample, and that such a fraction was higher in an outbred population relative to isofemale lines. As set, the TDS generated a thermal gradient within the cold and hot CTZs, and the exploration of this gradient by flies did not relate simply with a tendency to be thermally bold. Mild fasting affected thermal exploration and boldness in complex manners, but thermal boldness was evident in both fasted and fed flies. Also, thermal boldness was not associated with individual critical temperatures. Finally, some flies showed consistent thermal boldness, as flies that performed an extreme thermal cross were more likely to perform a second cross compared with untested flies. We hypothesize that a simple "avoidance principle" is not the only behavioral drive for D. melanogaster facing extreme temperatures over space, and that this pattern may characterize other small motile ectothermic animals with analogous natural history. The physiological correlates, genetic architecture, and interspecific variation of thermal boldness deserve further consideration.

category: animal behavior and cognition


title: Using a Homeogram to Detect Sleep in Free-living Animals

abstract:
O_LISleep is appreciated as a behavior critical to homeostasis, performance, and fitness. Yet, most of what we know about sleep comes from humans or controlled laboratory experiments. Assessing sleep in wild animals is challenging, as it is often hidden from view, and electrophysiological recordings that define sleep states are difficult to obtain. Accelerometers have offered great insight regarding gross movement, although ambiguous quiescent states like sleep have been largely ignored, limiting our understanding of this ubiquitous behavior.
C_LIO_LIWe developed a broadly applicable sleep detection method called a homeogram that can be applied to accelerometer data collected from wild animals. We applied our methodology to detect sleep in free-ranging North American red squirrels (Tamiasciurus hudsonicus) in a region that experiences drastic seasonal shifts in light, temperature, and behavioral demands.
C_LIO_LIOur method characterized sleep in a manner consistent with limited existing studies and expanded those observations to provide evidence that red squirrels apply unique sleep strategies to cope with changing environments.
C_LIO_LIApplying our analytical strategy to accelerometer data from other species may open new possibilities to investigate sleep patterns for researchers studying wild animals.
C_LI


title: Polypolish: short-read polishing of long-read bacterial genome assemblies

abstract:
Long-read-only bacterial genome assemblies usually contain residual errors, most commonly homopolymer-length errors. Short-read polishing tools can use short reads to fix these errors, but most rely on short-read alignment which is unreliable in repeat regions. Errors in such regions are therefore challenging to fix and often remain after short-read polishing. Here we introduce Polypolish, a new short-read polisher which uses all-per-read alignments to repair errors in repeat sequences that other polishers cannot. Polypolish performed well in benchmarking tests using both simulated and real reads, and it almost never introduced errors during polishing. The best results were achieved by using Polypolish in combination with other short-read polishers.

Author summaryRecent improvements in Oxford Nanopore Technologies sequencing platforms and assembly algorithms have made it easier than ever to generate complete bacterial genome sequences. However, Oxford Nanopore genome sequences suffer from errors that limit their utility in downstream analyses. To fix these errors, one can  polish the genome with Illumina sequencing, exploiting the fact that Oxford Nanopore and Illumina sequencing have different error profiles. There are several polishing tools which can fix most errors in an Oxford Nanopore genome, but they struggle with errors in repetitive regions of the genome. With this in mind, we have developed a polisher, Polypolish, which uses a novel approach that allows it to fix more errors in genomic repeats. Our results show that Polypolish is both effective at repairing sequence errors and very unlikely to introduce new errors. Polypolish can often fix errors that other polishers cannot and vice versa, so the best results come from using a combination of tools. Polypolish therefore has an important role in bacterial genome assembly methods that aim for the highest possible sequence accuracy.

category: bioinformatics


title: Reproducible, high-dimensional imaging in archival human tissue by Multiplexed Ion Beam Imaging by Time-of-Flight (MIBI-TOF)

abstract: Multiplexed ion beam imaging by time-of-flight (MIBI-TOF) is a form of mass spectrometry imaging that uses metal labeled antibodies and secondary ion mass spectrometry to image dozens of proteins simultaneously in the same tissue section. Working with the National Cancer Institutes (NCI) Cancer Immune Monitoring and Analysis Centers (CIMAC), we undertook a validation study, assessing concordance across a dozen serial sections of a tissue microarray of 21 samples that were independently processed and imaged by MIBI-TOF or single-plex immunohistochemistry (IHC) over 12 days. Pixel-level features were highly concordant across all 16 targets assessed in both staining intensity (R2 = 0.94 {+/-} 0.04) and frequency (R2 = 0.95 {+/-} 0.04). Comparison to digitized, single-plex IHC on adjacent serial sections revealed similar concordance (R2 = 0.85 {+/-} 0.08) as well. Lastly, automated segmentation and clustering of eight cell populations found that cell frequencies between replicates yielded an average correlation of R2 = 0.92 {+/-} 0.06. Taken together, we demonstrate that MIBI-TOF, with well-vetted reagents and automated analysis, can generate consistent and quantitative annotations of clinically relevant cell states in archival human tissue, and more broadly, present a scalable framework for benchmarking multiplexed IHC approaches.


title: Propionate ameliorates diabetes-induced neurological dysfunction through regulating the PI3K-AKT-eNOS signaling pathway

abstract:
A large body of research has established diabetes-related cognitive deterioration, sometimes known as "diabetic encephalopathy." Current evidence supports that oxidative stress, neuronal apoptosis, and cerebral microcirculation weakness are associated with cognition deficits induced by diabetes. The present study explores the effect of propionate on neurological deficits, cerebral blood flow, and oxidative stress in diabetic mice. Propionate can markedly improve neurological function, which is correlated with its capabilities of stimulating nitric oxide (NO) production, increasing cerebral microcirculation, suppressing oxidative stress and reducing neuron loss in the hippocampus. In addition, the results of Western Blotting indicated that the brain-protective function of propionate in streptozocin (STZ)-induced insulin-dependent diabetes mellitus (IDDM) mice is related to phosphoinositide 3-kinase (PI3K)/serine-threonine protein kinase (Akt)/endothelial nitric oxide synthase(eNOS) signaling pathway. In a diabetic mouse model, propionate reduces cerebral microcirculation, hippocampus apoptosis, and neurological impairment. Thus, propionate, now employed as a food preservative, may also help slow diabetes-induced cognitive loss.

Graphical Abstract

O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=110 SRC="FIGDIR/small/464493v2_ufig1.gif" ALT="Figure 1">
View larger version (27K):
org.highwire.dtl.DTLVardef@81fa09org.highwire.dtl.DTLVardef@1469451org.highwire.dtl.DTLVardef@b37fa1org.highwire.dtl.DTLVardef@8037e7_HPS_FORMAT_FIGEXP  M_FIG C_FIG HighlightsO_LIPropionate ameliorates diabetic-induced depression-like behavior, spatial learning and memory deficits.
C_LIO_LIPropionate increases cerebral microcirculation by enhancing NO production in diabetic mice.
C_LIO_LIPropionate suppresses oxidative stress and reduces neuron loss in the hippocampus.
C_LIO_LIThe brain-protective function of propionate is related to PI3K/Akt/eNOS signaling pathway.
C_LI


title: Propionate ameliorates diabetes-induced neurological dysfunction through regulating the PI3K/Akt/eNOS signaling pathway


title: Molecular and functional characterization of the mouse intracardiac nervous system

abstract:
BackgroundThe intracardiac nervous system (ICNS) refers to clusters of neurons, located within the heart, which participate to the neuronal regulation of cardiac functions and which are involved in the initiation of cardiac arrhythmias. Therefore, deciphering its role in cardiac physiology and physiopathology is mandatory.

ObjectiveThe aim of this study is to provide a phenotypic, electrophysiological and pharmacological characterization of the mouse ICNS, which is still poorly characterized.

MethodsGlobal cardiac innervation and phenotypic diversity were investigated using immunohistochemistry on cleared murine heart and on tissue sections. Patch clamp technique was used for electrophysiological and pharmacological characterization of isolated mouse intracardiac neurons.

ResultsWe have identified the expression of seven distinct neuronal markers within mouse ICNS, thus proving the neurochemical diversity of this network. Of note, it was the first time that the existence of neurons expressing the calcium binding protein calbindin, the neuropeptide Y (NPY) and the cocain and amphetamine regulated transcript (CART) peptide, was described in the mouse. Electrophysiological studies also revealed the existence of four different neuronal populations based on their electrical behavior. Finally, we showed that these neurons can be modulated by several neuromodulators.

ConclusionThis study showed that mouse ICNS presents a molecular and functional complexity similar to other species, and is therefore a suitable model to decipher the role of individual neuronal subtypes regarding the modulation of cardiac function and the initiation of cardiac arrhythmias.


title: Diet-induced obese mice are resistant to improvements in cardiac function resulting from short-term adropin treatment

abstract: Previous studies have shown that treatment with recombinant adropin, a circulating peptide secreted by the liver and brain, restores glucose utilization in the hearts of diet-induced obese mice. This restoration of fuel substrate flexibility, which is lost in obese and diabetic animals, has the potential to improve contractile function in the diabetic heart. Using an ex vivo approach, we examined whether short-term adropin treatment could enhance cardiac function in a mouse model of diet-induced obesity. Our study showed that acute adropin treatment reduces inhibitory phosphorylation of pyruvate dehydrogenase in primary neonatal cardiomyocytes, and leads to moderate improvements in ex vivo cardiac function in mice fed a low fat diet. Conversely, short-term exposure to adropin led to a small decrease in cardiac function in mice fed a long-term high fat diet. Insulin treatment did not significantly alter cardiac function in adropin treated hearts from either low or high fat diet mice, however acute adropin treatment did moderately restore downstream insulin signaling in high fat diet fed mice. Overall, these data suggest that in an ex vivo setting, acute adropin treatment alone is not sufficient to promote improved cardiac function in obese animals.


title: Association of ocean macroplastic debris with stranded sea turtles in the Central Gulf of Thailand

abstract: The impact of macroplastic debris (> 5 mm in size) on marine life is a global concern but is rarely investigated in Thailand. Our objective was to investigate the relationship between stranded sea turtles and macroplastics found in the Central Gulf of Thailand. The turtle (n = 388) stranding record between 2017-2020 was analysed retrospectively to determine their size, species, and interaction with macroplastics. Thereafter, between 2019-2020, macroplastics were collected, from the gastrointestinal (GI) tract of dead turtles and from the beaches where stranded turtles were found. A stereomicroscope was used to visually categorise the macroplastics, and the plastic composition was analysed using a Fourier-transform infrared (FTIR) spectrometer. Green sea turtles (Chelonia mydas) were found to account for the majority of stranded turtles (74%, n = 251), and macroplastics were discovered in 74% of cases of entanglement and ingestion. At the juvenile stage, the stranded turtle was strongly related to macroplastics. Immature turtles were more likely to become entangled than adult turtles. Entangled turtles had a greater survival rate than turtles that had consumed plastic. The plastic fibres were the majority of macroplastics found in the GI tracts (62%, n = 152/244) and on the beach (64%, n = 74/115). Most fibres from GI tracts (83%, n = 126/152) and the beaches (93%, n = 68/74) were identified as the fishing net comprised of polyethylene or polypropylene. We concluded that fishing nets made of polyethylene or polypropylene might be one of the significant causes of sea turtle stranding in the Central Gulf of Thailand, and this issue requires immediate resolution.


title: Cortical Spheroid Model for Studying the Effects of Ischemic Brain Injury

abstract:
Stroke is a devastating neurological disorder and a leading cause of death and long-term disability. Despite many decades of research, there are still very few therapeutic options for patients suffering from stroke or its consequences. This is partially due to the limitations of current research models, including traditional in vitro models which lack the three-dimensional (3D) architecture and cellular make-up of the in vivo brain. 3D spheroids derived from primary postnatal rat cortex provide an in vivo-relevant model containing a similar cellular composition to the native cortex and a cell-synthesized extracellular matrix. These spheroids are costeffective, highly reproducible, and can be produced in a high-throughput manner, making this model an ideal candidate for screening potential therapeutics. To study the cellular and molecular mechanisms of stroke in this model, spheroids were deprived of glucose, oxygen, or both oxygen and glucose for 24 hours. Both oxygen and oxygen-glucose deprived spheroids demonstrated many of the hallmarks of stroke, including a decrease in metabolism, an increase in neural dysfunction, and an increase in reactive astrocytes. Pretreatment of spheroids with the antioxidant agent N-acetylcysteine (NAC) mitigated the decrease in ATP seen after 24 hours of oxygen-glucose deprivation. Together, these results show the utility of our 3D cortical spheroid model for studying ischemic injury and its potential for screening stroke therapeutics.

Significance StatementThose who survive after suffering a stroke often have long-term cognitive or physical disabilities. There is currently only one available therapeutic, tissue plasminogen activator (tPA), and it must be administered within a few hours after the onset of stroke. As stroke prevalence increases with our aging population, there is a growing need for therapies to mitigate or reverse the resulting brain damage. Three-dimensional (3D) culture systems have the potential to screen novel therapeutics more reliably than traditional in vitro models. Here we present a novel 3D cortical spheroid ischemia model which replicates many of the characteristics of stroke and has the potential to be an effective tool in therapeutic development.


title: Cholinergic modulation of distinct inhibitory domains in granule cells of the olfactory bulb

abstract: Early olfactory processing relies on a large population of inhibitory neurons in the olfactory bulb (OB), the granule cells (GCs). GCs inhibit the OB output neurons, the mitral and tufted cells (M/TCs), shaping their responses to odors both in the spatial and temporal domains, therefore, the activity of GCs is finely tuned by local and centrifugal excitatory and inhibitory inputs. While the circuit substrates underlying regulatory inputs onto GCs are well-established, how they are locally modulated remains unclear. Here, we examine the regulation of GABAergic inhibition onto GCs by acetylcholine, a main neuromodulatory transmitter released in the OB, by basal forebrain (BF) neurons. In acute brain slices from male and female mice, we show that activation of muscarinic acetylcholine receptors (mAChRs) produces opposing effects on local and centrifugal inhibition onto GCs. By using electrophysiology, laser uncaging and optogenetics we show that the kinetics of GABAergic currents in GCs could be correlated with distal and proximal spatial domains from where they originate, along the GC somatodendritic axis. Proximal inhibition from BF afferents, is suppressed by activation of M2/M4-mAChRs. In contrast, distal local inhibition from deep short axon cells (dSACs) is enhanced by activation of M3-mAChRs. Furthermore, we show that the cholinergic enhancement of distal inhibition in GCs reduces the extent of dendrodendritic inhibition in MCs. Interestingly, the excitatory cortical feedback, which also targets the proximal region of GCs, was not modulated by acetylcholine, suggesting that muscarinic activation shifts the synaptic balance towards excitation in GCs. Together, these results suggest that BF cholinergic inputs to the OB fine tune GC-mediated inhibition of M/TCs by differentially modulating the proximal and distal domains of inhibition in GCs.


title: Individual differences in visual search performance extend from artificial arrays to naturalistic environments.

abstract: Visual search is a universal human activity in naturalistic environments. Traditionally, visual search is investigated under tightly controlled conditions, where head-restricted participants locate a minimalistic target in a cluttered array presented on a computer screen. Do classic findings of visual search extend to naturalistic settings, where participants actively explore complex, real-world scenes? Here, we leverage advances in virtual reality (VR) technology to relate individual differences in classic visual search paradigms to naturalistic search behavior. In a naturalistic visual search task, participants looked for an object within their environment via a combination of head-turns and eye-movements using a head-mounted display. Then, in a classic visual search task, participants searched for a target within a simple array of colored letters using only eye-movements. We tested how set size, a property known to limit visual search within computer displays, predicts the efficiency of search behavior inside immersive, real-world scenes that vary in levels of visual clutter. We found that participants search performance was impacted by the level of visual clutter within real-world scenes. Critically, we also observed that individual differences in vi1-3sual search efficiency in classic search predicted efficiency in real-world search, but only when the comparison was limited to the forward-facing field of view for real-world search. These results demonstrate that set size is a reliable predictor of individual performance across computer-based and active, real-world visual search behavior.


title: Behavioral and molecular underpinnings of performance variability in eyeblink conditioning in male and female mice

abstract: The functional and molecular sources of behavioral variability in mice are not fully understood. As a consequence, the predominant use of male mice has become a standard in animal research, under the assumption that males are less variable than females. Similarly, to homogenize genetic background, neuroscience studies have almost exclusively used the C57BL/6 (B6) strain. Here, we examined individual differences in performance in the context of associative learning. We performed delayed eyeblink conditioning while recording locomotor activity in mice from both sexes in two strains (B6 and B6CBAF1). Further, we used a C-FOS immunostaining approach to explore brain areas involved in eyeblink conditioning across subjects and correlate them with behavioral performance. We found that B6 male and female mice show comparable variability in this task and that females reach higher learning scores. We found a strong positive correlation across sexes between learning scores and voluntary locomotion. C-FOS immunostainings revealed positive correlations between C-FOS positive cell density and learning in the cerebellar cortex, as well as multiple previously unreported extra-cerebellar areas. We found consistent and comparable correlations in eyeblink performance and C-fos expression in B6 and B6CBAF1 females and males. Taken together, we show that differences in motor behavior and activity across brain areas correlate with learning scores during eyeblink conditioning across strains and sexes.


title: Eyeblink conditioning performance and brain-wide C-fos expression in male and female mice


title: Intratumoral and extratumoral synapses are required for glioblastoma progression in Drosophila

abstract: Glioblastoma (GB) is the most aggressive, lethal and frequent primary brain tumor. It originates from glial cells and is characterized by rapid expansion through infiltration. GB cells interact with the microenvironment and healthy surrounding tissues, mostly neurons and vessels. GB cells project tumor microtubes (TMs) that contact with neurons and exchange signaling molecules related to Wingless/WNT, JNK, Insulin or Neuroligin-3 pathways. This cell to cell communication promotes GB expansion and neurodegeneration. Moreover, healthy neurons form glutamatergic functional synapses with GB cells which facilitate GB expansion and premature death in mouse GB xerograph models. Targeting signaling and synaptic components of GB progression may become a suitable strategy against glioblastoma. In a Drosophila GB model, we have determined the post-synaptic nature of GB cells with respect to neurons, and the contribution of post-synaptic genes expressed in GB cells to tumor progression. In addition, we document the presence of intratumoral synapses between GB cells, and the functional contribution of pre-synaptic genes to GB calcium dependent activity and expansion. Finally, we explore the relevance of synaptic genes in GB cells to the lifespan reduction caused by GB advance. Our results indicate that both presynaptic and postsynaptic proteins play a role in GB progression and lethality.


title: Bilaterally Reduced Rolandic Beta Band Activity in Minor Stroke Patients

abstract:
Stroke patients with hemiparesis display decreased beta band (13-25 Hz) rolandic activity, correlating to impaired motor function. However, patients without significant weakness, with small lesions far from sensorimotor cortex, nevertheless exhibit bilateral decreased motor dexterity and slowed reaction times. We investigate whether these minor stroke patients also display abnormal beta band activity.

Magnetoencephalographic (MEG) data were collected from nine minor stroke patients (NIHSS < 4) without significant hemiparesis, at ~1 and ~6 months postinfarct, and eight age-similar controls. Rolandic relative beta power during matching tasks and resting state, and Beta Event Related (De)Synchronization (ERD/ERS) during button press responses were analyzed.

Regardless of lesion location, patients had significantly reduced relative beta power and ERS compared to controls. Abnormalities persisted over visits, and were present in both ipsi- and contra-lesional hemispheres, consistent with bilateral impairments in motor dexterity and speed.

Minor stroke patients without severe weakness display reduced rolandic beta band activity in both hemispheres, which may be linked to bilaterally impaired dexterity and processing speed, implicating global connectivity dysfunction affecting sensorimotor cortex. Rolandic beta band activity may be a potential biomarker and treatment target, even for minor stroke patients with small lesions far from sensorimotor areas.


title: A Kernel-based Nonlinear Manifold Learning for EEG Channel Selection with Application to Alzheimer's Disease

abstract: This paper introduces a novel EEG channel selection method to determine which channel inter-relationships provide the best classification accuracy between a group of patients with Alzheimers disease (AD) and a cohort of age matched healthy controls (HC). Thereby, determine which inter-relationships are more important for the in-depth dynamical analysis to further understand how neurodegenerative diseases such as AD affects global and local brain dynamics. The channel selection methodology uses kernel-based nonlinear manifold learning via Isomap and Gaussian Process Latent Variable Model (Isomap-GPLVM). The Isomap-GPLVM method is employed to learn both the spatial and temporal local similarities and global dissimilarities present within the EEG data structures. The resulting kernel (dis)similarity matrix is used as a measure of synchrony between EEG channels. Based on this information, channel-specific linear Support Vector Machine (SVM) classification is then used to determine which spatio-temporal channel inter-relationships are more important for in-depth dynamical analysis. In this work, the analysis of EEG data from HCs and AD patients is presented as a case study. Our analysis shows that inter-relationships between channels in the fronto-parietal region and the rest are better at differentiating between AD and HC groups.


title: The Respiratory Resistance Sensitivity Task: An Automated Method for Quantifying Respiratory Interoception and Metacognition

abstract: The ability to sense, monitor, and control respiration - e.g., respiratory interoception (henceforth, respiroception) is a core homeostatic ability. Beyond the regulation of gas exchange, enhanced awareness of respiratory sensations is directly related to psychiatric symptoms such as panic and anxiety. Indeed, chronic breathlessness (dyspnea) is associated with a fourfold increase in the risk of developing depression and anxiety, and the regulation of the breath is a key aspect of many mindfulness-based approaches to the treatment of mental illness. Physiologically speaking, the ability to accurately monitor respiratory sensations is important for optimizing cardiorespiratory function during athletic exertion, and can be a key indicator of illness. Given the important role of respiroception in mental and physical health, it is unsurprising that there is increased interest in the quantification of respiratory psychophysiology across different perceptual and metacognitive levels of the psychological hierarchy. Compared to other more popular modalities of interoception, such as in the cardiac domain, there are relatively few methods available for measuring aspects of respiroception. Existing inspiratory loading tasks are difficult to administer and frequently require expensive medical equipment, or offer poor granularity in their quantification of respiratory-related perceptual ability. To facilitate the study of respiroception, we here present a new, fully automated and computer-controlled apparatus and psychophysiological method, which can flexibly and easily measure respiratory-related interoceptive sensitivity, bias and metacognition, in as little as 30 minutes of testing, using easy to make 3D printable parts.


title: Anti-TRAP/SSP2 monoclonal antibodies can inhibit sporozoite infection and enhance protection of anti-CSP monoclonal antibodies

abstract: Vaccine-induced sterilizing protection from infection by Plasmodium parasites, the pathogens that cause malaria, will be essential in the fight against malaria as it would prevent both malaria-related disease and transmission. Stopping the relatively small number of parasites injected by the mosquito before they can migrate from the skin to the liver is an attractive means to this goal. Antibody-eliciting vaccines have been used to pursue this objective by targeting the major parasite surface protein present during this stage, the circumsporozoite protein (CSP). While CSP-based vaccines have recently had encouraging success in disease reduction, this was only achieved with extremely high antibody titers and appeared less effective for a complete block of infection (i.e. sterile protection). While such disease reduction is important, these and other results indicate that strategies focusing on CSP alone may not achieve the high levels of sterile protection needed for malaria eradication. Here, we show that monoclonal antibodies (mAbs) recognizing another sporozoite protein, TRAP/SSP2, exhibit a range of inhibitory activity and that these mAbs can augment CSP-based protection despite conferring no sterile protection on their own. Therefore, pursuing a multivalent subunit vaccine immunization is a promising strategy for improving infection-blocking malaria vaccines.


title: Estimating the maximal growth rates of eukaryotic microbes from cultures and metagenomes via codon usage patterns

abstract: Microbial eukaryotes are ubiquitous in the environment and play important roles in key ecosystem processes, including accounting for a significant portion of global primary production. Yet, our tools for assessing the functional capabilities of eukaryotic microbes in the environment are quite limited because many microbes have yet to be grown in culture. Maximum growth rate is a fundamental parameter of microbial lifestyle that reveals important information about an organisms functional role in a community. We developed and validated a genomic estimator of maximum growth rate for eukaryotic microbes, enabling the assessment of growth potential for both cultivated and yet-to-be-cultivated organisms. We produced a database of over 700 growth predictions from genomes, transcriptomes, and metagenome-assembled genomes, and found that closely related and/or functionally similar organisms tended to have similar maximal growth rates. By comparing the maximal growth rates of existing culture collections with environmentally-derived genomes we found that, unlike for prokaryotes, culture collections of microbial eukaryotes are only minimally biased in terms of growth potential. We then extended our tool to make community-wide estimates of growth potential from over 500 marine metagenomes, mapping growth potential across the global oceans. We found that prokaryotic and eukaryotic communities have highly correlated growth potentials near the ocean surface, but that this relationship disappears deeper in the water column. This suggests that fast growing eukaryotes and prokaryotes thrive under similar conditions at the ocean surface, but that there is a decoupling of these communities as resources become scarce deeper in the water column.


title: Evolutionary epidemiology of a zoonosis

abstract:
Cryptosporidium parvum is a global zoonoses and a major cause of diarrhoea in humans and ruminants. The parasites life cycle comprises an obligatory sexual phase, during which genetic exchanges can occur between previously isolated lineages. Here, we compare 32 whole genome sequences from human- and ruminant-derived parasite isolates collected across Europe, Egypt and China. We identify three strongly supported clusters that comprise a mix of isolates from different host species, geographic origins, and subtypes. We show that: (1) recombination occurs between ruminant isolates into human isolates; (2) these recombinant regions can be passed on to other human subtypes through gene flow and population admixture; (3) there have been multiple genetic exchanges, and all are likely recent; (4) putative virulence genes are significantly enriched within these genetic exchanges, and (5) this results in an increase in their nucleotide diversity. We carefully dissect the phylogenetic sequence of two genetic exchanges, illustrating the long-term evolutionary consequences of these events. Our results suggest that increased globalisation and close human-animal contacts increase the opportunity for genetic exchanges between previously isolated parasite lineages, resulting in spillover and spillback events. We discuss how this can provide a novel substrate for natural selection at genes involved in host-parasite interactions, thereby potentially altering the dynamic coevolutionary equilibrium in the Red Queens arms race.

Data SummaryAll raw and processed sequencing data generated and analysed during the current study have been submitted to the NCBI Sequence Read Archive (https://www.ncbi.nlm.nih.gov/bioproject/), under BioProjects PRJNA634014 and PRJNA633764.


title: Population-specific patterns of toxin sequestration in monarch butterflies from around the world

abstract: Monarch butterflies are one of the preeminent examples of a toxin-sequestering animal, gaining protection against predators via cardenolides obtained from their milkweed host plants. Although cardenolide sequestration by monarchs has been studied in ecological, physiological, and phylogenetic contexts, relatively little research has surveyed genetic variation in the ability to sequester, nor has monarch sequestration been studied in relation to divergent host plant assemblages or variation in exposure to predation. Here, we use the monarchs recent global range expansion to test hypotheses about how cardenolide sequestration evolves over relatively contemporary time scales. First, we test for whether sympatric monarch/milkweed combinations have a sequestration advantage by rearing six geographically disparate monarch populations on six associated milkweed host species and measuring levels of sequestered cardenolides in a set of 440 adult butterflies. Second, we use monarchs from Guam--an oceanic island where birds have been functionally extirpated for approximately 40 years--to test hypotheses about how exposure to avian predation affects cardenolide sequestration. We find little overall evidence for increased sequestration on sympatric hosts. However, one monarch population (Puerto Rico) shows strong support for cross-host tradeoffs in sequestration ability, primarily driven by limited sequestration of polar cardenolides from two temperate North American milkweeds (Asclepias syriaca and A. speciosa). Monarchs from Guam show some evidence for reduced cardenolide sequestration in both a cross-island comparison of wild-caught butterflies as well as population-level comparisons of greenhouse-reared butterflies. Our results suggest that there is substantial genetic variation in sequestration ability (both within and between monarch populations) and that evolutionary history and contemporary species interactions may influence patterns of cardenolide sequestration.


title: In vivo adenine base editing corrects newborn murine model of Hurler syndrome

abstract: Mucopolysaccharidosis type I (MPS I) is a severe disease caused by loss-of-function mutations variants in the -L-iduronidase (IDUA) gene. In vivo genome editing represents a promising strategy to correct IDUA mutations, and has the potential to permanently restore IDUA function over the lifespan of the patients. Here, we used adenine base editing to directly convert A>G (TAG>TGG) in newborn murine model harboring Idua-W392X mutation, which recapitulates the human condition and is analogous to the highly prevalent human W402X mutation. We engineered a split-intein dual-adeno-associated virus (AAV) 9 in vivo adenine base editor to circumvent the package size limit of AAV vectors. Intravenous injection of AAV9-base editor system into MPS I newborn mice led to sustained enzyme expression sufficient for correction of metabolic disease (GAGs substrate accumulation) and prevention of neurobehavioral deficits. We observed a reversion of the W392X mutation in 22.46{+/-}6.74% of hepatocytes, 11.18{+/-}5.25% of heart and 0.34{+/-}0.12% of brain, along with decreased GAGs storage in peripheral organs (liver, spleen, lung and kidney). Collectively, these data showed the promise of a base editing approach to precisely correct a common genetic cause of MPS I in vivo and could be broadly applicable to the treatment of a wide array of monogenic diseases.


title: Multiplexed ultrasound imaging using clustered gas vesicles and spectral imaging

abstract: Current advances in ultrasound imaging techniques including super-resolution ultrasound imaging allows us to visualize microvasculature in biological specimens using microbubbles. However, microbubbles diffuse in blood stream limiting imaging acquisition and frame subtraction scheme of super-resolution ultrasound imaging cannot improve spatial resolution without moving microbubbles. Fluorescent proteins revolutionized to understand molecular and cellular functions in biological systems. Here, we devised a panel of gas vesicles to realize multiplexed ultrasound imaging to uniquely visualize locations of different species of gas vesicles. Mid-band fit spectral imaging technique demonstrated that stationary gas vesicles were efficiently localized in gel phantom and murine liver specimens by visualizing three-dimensional vessel structures. Clustered and unclustered gas vesicles were phagocytosed by murine macrophages to serve as carriers and beacons for the proposed multiplexed and single cell level imaging technique. The spatial distribution of macrophages containing clustered and unclustered gas vesicles were reconstructed by mid-band fit spectral imaging with pseudo-coloring scheme.

category: bioengineering


title: Mapping enzyme catalysis with metabolomic biosensing

abstract: Enzymes are represented across a vast space of protein sequences and structural forms and have activities that far exceed the best chemical catalysts; however, engineering them to have novel or enhanced activity is limited by technologies for sensing product formation. Here, we describe a general and scalable approach for characterizing enzyme activity that uses the metabolism of the host cell as a biosensor by which to infer product formation. Since different products consume different molecules in their synthesis, they perturb host metabolism in unique ways that can be measured by mass spectrometry. This provides a general way by which to sense product formation, to discover unexpected products and map the effects of mutagenesis.


title: scTriangulate: Decision-level integration of multimodal single-cell data

abstract: Hundreds of bioinformatics approaches now exist to define cellular heterogeneity from singlecell genomics data. Reconciling conflicts between diverse methods, algorithm settings, annotations or modalities have the potential to clarify which populations are real and establish reusable reference atlases. Here, we present a customizable computational strategy called scTrianguate, which leverages cooperative game theory to intelligently mix-and-match clustering solutions from different resolutions, algorithms, reference atlases, or multi-modal measurements. This algorithm relies on a series of robust statistical metrics for cluster stability that work across molecular modalities to identify high-confidence integrated annotations. When applied to annotations from diverse competing cell atlas projects, this approach is able to resolve conflicts and determine the validity of controversial cell population predictions. Tested with scRNA-Seq, CITE-Seq (RNA + surface ADT), multiome (RNA + ATAC), and TEA-Seq (RNA + surface ADT + ATAC), this approach identifies highly stable and reproducible, known and novel cell populations, while excluding clusters defined by technical artifacts (i.e., doublets). Importantly, we find that distinct cell populations are frequently attributed with features from different modalities (RNA, ATAC, ADT) in the same assay, highlighting the importance of multimodal analysis in cluster determination. As it is flexible, this approach can be updated with new user-defined statistical metrics to alter the decision engine and customized to new measures of stability for different measures of cellular activity.


title: Immunogenic potential of neopeptides depends on parent protein subcellular location

abstract:
Antigen presentation via the major histocompatibility complex (MHC) is essential for anti-tumor immunity, however the rules that determine what tumor-derived peptides will be immunogenic are still incompletely understood. Here we investigate whether protein subcellular location driven constraints on accessibility of peptides to the MHC associate with potential for peptide immunogenicity. Analyzing over 380,000 peptides from studies of MHC presentation and peptide immunogenicity, we find clear spatial biases in both eluted and immunogenic peptides. We find that including parent protein location improves prediction of peptide immunogenicity in multiple datasets. In human immunotherapy cohorts, location was associated with response to a neoantigen vaccine, and immune checkpoint blockade responders generally had a higher burden of neopeptides from accessible locations. We conclude that protein subcellular location adds important information for optimizing immunotherapies.

HighlightsO_LIPeptides eluted from class I and II MHC reflect biases in the subcellular location of the parent proteins
C_LIO_LIAn embedding-based indicator of parent protein location improves prediction of neoepitope immunogenicity and immunotherapy response
C_LIO_LINeoepitope location improves estimation of effective neoantigen burden and stratification of potential for immunotherapy response
C_LI


title: Airpart: Interpretable statistical models for analyzing allelic imbalance in single-cell datasets

abstract:
MotivationAllelic expression analysis aids in detection of cis-regulatory mechanisms of genetic variation which produce allelic imbalance (AI) in heterozygotes. Measuring AI in bulk data lacking time or spatial resolution has the limitation that cell-type-specific (CTS), spatial-, or time-dependent AI signals may be dampened or not detected.

ResultsWe introduce a statistical method airpart for identifying differential CTS AI from single-cell RNA-sequencing (scRNA-seq) data, or other spatially- or time-resolved datasets. airpart outputs discrete partitions of data, pointing to groups of genes and cells under common mechanisms of cis-genetic regulation. In order to account for low counts in single-cell data, our method uses a Generalized Fused Lasso with Binomial likelihood for partitioning groups of cells by AI signal, and a hierarchical Bayesian model for AI statistical inference. In simulation, airpart accurately detected partitions of cell types by their AI and had lower RMSE of allelic ratio estimates than existing methods. In real data, airpart identified differential AI patterns across cell states and could be used to define trends of AI signal over spatial or time axes.

AvailabilityThe airpart package is available as an R/Bioconductor package at https://bioconductor.org/packages/airpart.


title: Nanopore microscope identifies RNA isoforms with structural colors

abstract:
Identifying RNA transcript isoforms requires intricate protocols that suffer from various enzymatic biases. Here we design three-dimensional molecular constructs that enable identification of transcript isoforms at the single-molecule level using solid-state nanopore microscopy. We refold target RNA into RNA identifiers (IDs) with designed sets of complementary DNA strands. Each reshaped molecule carries a unique sequence of structural (pseudo)colors. Structural colors consist of DNA structures, protein labels, native RNA structures, or a combination of all three. The sequence of structural colors of RNA IDs enables simultaneous identification and relative quantification of multiple RNA targets without prior amplification. Our Amplification-free RNA TargEt Multiplex Isoform Sensing (ARTEMIS) reveals structural arrangements in native transcripts in agreement with published variants. ARTEMIS discriminates circular and linear transcript isoforms in a one step, enzyme-free reaction in a complex human transcriptome using single-molecule readout.

One sentence summaryHere we show enzyme-free identification and relative quantification of RNA isoforms using a nanopore microscope and structural colors.

category: biophysics


title: Identification of electroporation sites in the complex lipid organization of the plasma membrane

abstract: The plasma membrane of a biological cell is a complex assembly of lipids and membrane proteins, which tightly regulate transmembrane transport. When a cell is exposed to a strong electric field, the membrane integrity becomes transiently disrupted by formation of transmembrane pores. This phenomenon, termed electroporation, is already utilized in many rapidly developing applications in medicine including gene therapy, cancer treatment, and treatment of cardiac arrythmias. However, the molecular mechanisms of electroporation are not yet sufficiently well understood; in particular, it is unclear where exactly pores form in the complex organization of the plasma membrane. In this study we combine coarse-grained molecular dynamics simulations, machine learning methods, and Bayesian survival analysis to identify how formation of pores depends on the local lipid organization. We show that pores do not form homogeneously across the membrane, but colocalize with domains that have specific features, the most important being high density of polyunsaturated lipids. We further show that knowing the lipid organization is sufficient to reliably predict poration sites with machine learning. However, by analysing poration kinetics with Bayesian survival analysis we then show that poration does not depend solely on local lipid arrangement, but also on membrane mechanical properties and the polarity of the electric field. Finally, we discuss how the combination of atomistic and coarse-grained molecular dynamics simulations, machine learning methods, and Bayesian survival analysis can guide the design of future experiments and help us to develop an accurate description of plasma membrane electroporation on the whole-cell level. Achieving this will allow us to shift the optimization of electroporation applications from blind trial-and-error approaches to mechanistic-driven design.


title: Interactive 3D visualization and post-processing analysis of vertex-based unstructured polyhedral meshes with ParaView

abstract: The development of physics-based 3D models that investigate the behavior of biological tissues requires effective and efficient visualization tools. The open-source software ParaView has such capabilities, but often impose a steep learning curve due to the use of the Visualization Toolkit (VTK) data structures. To overcome this, I show how to setup the components of 3D vertex-like models, i.e., vertices, faces, and polyhedra, into the VTK data format and then output as ParaView unstructured grid files. I present a few relevant tools to visualize and analyze the files in ParaView. All sample codes are available in the Github repository vis3Dvertex.


title: Cyperus rotundus root extract inhibits progress of lymphedema in mouse tail model

abstract:
Lymphedema is clinically manifested as swelling due to abnormal accumulation of interstitial fluid attributed to inefficient fluid uptake and reduced lymphatic flow. Here we have evaluated the effect of Cyperus rotundus root (CRR) ethanolic extract in a mouse tail model of lymphedema and hypothesized that Cyperus rotundus plant known for its anti-inflammatory effect through inhibition of TNF alpha will be effective in managing this condition. The skin was removed after leaving 1cm of distance from the base of the trunk. Cut was introduced in sterile condition. The animals were divided into Experimental control(EC) and Cyperus rotundus (CRR) treated groups. A change in tail volume around the wound was monitored upto the 20 days. Kinetics of the swelling was calculated for statistical significance. Further TS of upper part of the wound was stained with H&E stain and documented for histological changes

RESULTSIn EC group, gradual rise in swelling was recorded, which peaked on 10th day and continued up to 15th day, followed by gradual decrease. In CR extract treated group, the swelling was significantly low and peak was obtained on 8th day, while in EC group the swelling was significantly higher and peak was obtained 11th day. The histological section show, fibrous band intersection the lobules of adipocyte and lymphatic vascular channel and muscles in the sub epithelium region in the EC group, which was very less in CRR group.

CONCLUSIONSPolar fraction of CRR significantly prevents the progress of lymphedema and which lays an important role of this plant as for the drug development in future.


title: A plasma membrane-localized polycystin-1/polycystin-2 complex in endothelial cells elicits vasodilation

abstract: Polycystin-1 (PC-1, PKD1), a receptor-like protein expressed by the Pkd1 gene, is present in a wide variety of cell types, but its cellular location, signaling mechanisms and physiological functions are poorly understood. Here, by studying tamoxifen-inducible, endothelial cell (EC)-specific Pkd1 knockout (Pkd1 ecKO) mice, we show that flow activates PC-1-mediated, Ca2+-dependent cation currents in ECs. EC-specific PC-1 knockout attenuates flow-mediated arterial hyperpolarization and vasodilation. PC-1-dependent vasodilation occurs over the entire functional shear stress range and primarily via the activation of nitric oxide synthase (NOS), with a smaller contribution from small-conductance Ca2+-activated K+ (SK) channels. EC-specific PC-1 knockout increases systemic blood pressure without altering kidney anatomy. PC-1 coimmunoprecipitates with polycystin-2 (PC-2, PKD2), a TRP polycystin channel, and clusters of both proteins locate in nanoscale proximity in the EC plasma membrane. Knockout of either PC-1 or PC-2 (Pkd2 ecKO mice) abolishes surface clusters of both PC-1 and PC-2 in ECs. Single knockout of PC-1 or PC-2 or double knockout of PC-1 and PC-2 (Pkd1/Pkd2 ecKO mice) similarly attenuates flow-mediated vasodilation. Flow stimulates non-selective cation currents in ECs that are similarly inhibited by either PC-1 or PC-2 knockout or by interference peptides corresponding to the C-terminus coiled-coil domains present in PC-1 or PC-2. In summary, we show that PC-1 regulates arterial contractility and demonstrate that this occurs through the formation of an interdependent signaling complex with PC-2 in endothelial cells. Flow stimulates PC-1/PC-2 clusters in the EC plasma membrane, leading to Ca2+ influx, NOS and SK channel activation, vasodilation and a reduction in blood pressure.


title: Sex Differences in Pubertal Circadian and Ultradian Rhythmic Development Under Naturalistic Conditions

abstract: Biological rhythms in core body temperature (CBT) provide informative markers of adolescent development under controlled laboratory conditions. However, it is unknown if these markers are preserved under more variable naturalistic conditions, and if CBT may therefore prove useful in a real-world setting. To evaluate this possibility, we examined fecal steroid concentrations and CBT rhythms from pre-adolescence (p26) through early adulthood (p76) in intact male and female rats under natural light and climate at the University of California, Berkeley Field Station. Despite greater environmental variability, CBT markers of pubertal onset and its rhythmic progression were comparable to those previously reported in laboratory conditions in female rats and extend actigraphy-based findings in males. Specifically, sex differences emerged in circadian rhythm (CR) power and temperature amplitude prior to pubertal onset and persisted into early adulthood, with females exhibiting elevated CBT and decreased CR power compared to males. Within-day (ultradian rhythm; UR) patterns also exhibited a pronounced sex difference associated with estrous cyclicity. Pubertal onset, defined by vaginal opening, preputial separation, and sex steroid concentrations, occurred later than previously reported under lab conditions for both sexes. Vaginal opening and increased fecal estradiol concentrations were closely tied to the commencement of 4-day oscillations in CBT and UR power in female rats. By contrast, preputial separation and the first rise in testosterone concentration were not associated with adolescent changes to CBT rhythms in male rats. Together, males and females exhibited unique temporal patterning of CBT and sex steroids across pubertal development, with tractable associations between hormonal concentrations, external development, and temporal structure in females. The preservation of these features outside the laboratory supports CBT as a strong candidate for translational pubertal monitoring under naturalistic conditions in females.


title: Genome scale modeling of the protein secretory pathway reveals novel targets for improved recombinant protein production in yeast

abstract: Eukaryal cells are used for the production of many recombinant pharmaceutical proteins, including several of the current top-selling products. The protein secretory pathway in eukaryal cells is complex and involves many different processes such as post-translational modifications, translocation, and folding. Furthermore, recombinant protein production competes with native secretory proteins for the limited energy and proteome resources allocated to the protein secretory pathway. Due to the complexity of this pathway, improvement through metabolic engineering has traditionally been relatively ad-hoc; and considering the industrial importance of this pathway, there is a need for more systematic approaches for novel design principles. Here, we present the first proteome-constrained genome-scale protein secretory model of a eukaryal cell, namely for the yeast Saccharomyces cerevisiae (pcSecYeast). The model contains all key processes of this pathway, i.e., protein translation, modification, and degradation coupled with metabolism. The model can capture delicate phenotypic changes such as the switch in the use of specific glucose transporters in response to changing extracellular glucose concentration. Furthermore, the model can also simulate the effects of protein misfolding on cellular growth, suggesting that retro-translocation of misfolded proteins contributes to protein retention in the Endoplasmic reticulum (ER). We used pcSecYeast to simulate various recombinant proteins production and identified overexpression targets for different recombinant proteins overproduction. We experimentally validated many of the predicted targets for -amylase production in this study, and the results show that the secretory pathways have more limited capacity than metabolism in terms of protein secretion.

category: systems biology


title: Dorsolateral prefrontal cortex supports speech perception in listeners with cochlear implants

abstract: Cochlear implants are neuroprosthetic devices that can restore hearing in individuals with severe to profound hearing loss by electrically stimulating the auditory nerve. Because of physical limitations on the precision of this stimulation, the acoustic information delivered by a cochlear implant does not convey the same level of spectral detail as that conveyed by normal hearing. As a result, speech understanding in listeners with cochlear implants is typically poorer and more effortful than in listeners with normal hearing. The brain networks supporting speech understanding in listeners with cochlear implants are not well understood, partly due to difficulties obtaining functional neuroimaging data in this population. In the current study, we assessed the brain regions supporting spoken word understanding in adult listeners with right unilateral cochlear implants (n=20) and matched controls (n=18) using high-density diffuse optical tomography (HD-DOT), a quiet and non-invasive imaging modality with spatial resolution comparable to that of functional MRI. We found that while listening to spoken words in quiet, listeners with cochlear implants showed greater activity in the left dorsolateral prefrontal cortex, overlapping with functionally-defined domain-general processing seen in a spatial working memory task. These results suggest that listeners with cochlear implants require greater cognitive processing during speech understanding than listeners with normal hearing, supported by compensatory recruitment in the left dorsolateral prefrontal cortex.


title: Amyloid-beta and tau pathologies are both necessary to induce novel stage-specific microglia subtypes during Alzheimer's disease progression.

abstract: It is unknown whether specific microglia are selectively induced by amyloid-{beta} (A{beta}), tau pathologies, or both in combination. To address this, we use single-cell RNA-sequencing to profile mice bearing both A{beta} and tau pathologies during Alzheimers disease (AD) progression. We identify novel microglia subtypes induced in a disease stage-specific manner. We show that during early-stage disease, interferon signaling induces a subtype of microglia termed EADAM. During late-stage disease, a second microglia subtype termed LADAM is detected. While EADAM and LADAM-like microglia are observed in other neurodegenerative models, the magnitude and composition of subtype markers are distinct from microglia observed with AD-like pathology. The pattern of EADAM- and LADAM-associated gene expression is observed in microglia from human AD, during the early and late stages of disease, respectively. Furthermore, we observe that several siglec genes are selectively expressed in either EADAM or LADAM. Siglecg is expressed in white-matter-associated LADAM, and expression of the human orthologue of Siglecg is progressively elevated in AD-stage-dependent manner but not shown in non-AD tauopathy. Our findings imply that both A{beta} and tau pathologies are required for disease stage-specific induction of EADAM and LADAM.


title: Propofol modulates functional connectivity signatures of sustained attention

abstract: Sustained attention is a critical cognitive function reflected in an individuals whole-brain pattern of fMRI functional connectivity. However sustained attention is not a purely static trait. Rather, attention waxes and wanes over time. Do functional brain networks that underlie individual differences in sustained attention also underlie changes in attentional state? To investigate, we replicate the finding that a validated connectome-based model of individual differences in sustained attention tracks pharmacologically induced changes in attentional state. Specifically, preregistered analyses revealed that participants exhibited functional connectivity signatures of stronger attention when awake than when under deep sedation with the anesthetic agent propofol. Furthermore, this effect was relatively specific to the predefined sustained attention networks: propofol administration modulated strength of the sustained attention networks more than it modulated strength of canonical resting-state networks and a network defined to predict fluid intelligence, and the functional connections most affected by propofol sedation overlapped with the sustained attention networks. Thus, propofol modulates functional connectivity signatures of sustained attention within individuals. More broadly these findings underscore the utility of pharmacological intervention in testing both the generalizability and specificity of network-based models of cognitive function.


title: A novel automated approach for improving standardization of the marble burying test enables quantification of burying bouts and activity characteristics

abstract:
The marble burying test is a commonly used paradigm to screen phenotypes in mouse models of neurodevelopmental and psychiatric disorders. The current methodological approach relies solely on reporting the number of buried marbles at the end of the test. By measuring the proxy of the behavior (buried marbles), rather than the behavior itself (burying bouts), many important characteristics regarding the temporal aspect of this assay are lost. Here we introduce a novel, automated method to quantify mouse behavior throughout the duration of the marble burying test with the focus on the burying bouts. Using open-source software packages, we trained a supervised machine learning algorithm (the "classifier") to distinguish burying behavior in freely moving mice. In order to confirm the classifiers accuracy and uncover the behavioral meaning of the marble burying test, we performed marble burying test in three mouse models: Ube3am-/p+ (Angelman Syndrome model), Shank2-/- (autism model), and Sapap3-/- (obsessive-compulsive disorder model) mice. The classifier scored burying behavior accurately and consistent with the literature in the Ube3am-/p+ mice, which showed decreased levels of burying compared to controls. Shank2-/- mice showed a similar pattern of decreased burying behavior, which was not found in Sapap3-/- mice. Tracking mouse behavior throughout the test enabled us to quantify activity characteristics, revealing hypoactivity in Ube3am-/p+ and hyperactivity in the Shank2-/- mice, indicating that mouse activity is unrelated to burying behavior. Together, we demonstrate that our classifier is an accurate method for the analysis of the marble burying test, providing more information than the currently used methods.

Significance StatementThe marble burying test is widely used in phenotyping neurodevelopmental and neuropsychiatric disorder mouse models. Currently, its analysis consists of manually scoring the number of buried marbles upon the completion of the assay. This approach is not standardized across laboratories, and leaves out important variables such as movement characteristics and information about the burying bouts. This leads to divergent interpretations of the marble burying test, ranging from anxiety to cognitive impairment. We introduce a method that reliably tracks mouse behavior throughout the experiment, classifies the duration and number of the burying bouts, and is generalizable across laboratories. Using machine learning for measuring the actual burying behavior standardizes this method, and provides rich information about the burying characteristics.