title: A computational solution for bolstering reliability of epigenetic clocks: Implications for clinical trials and longitudinal tracking

abstract: Epigenetic clocks are widely used aging biomarkers calculated from DNA methylation data. Unfortunately, measurements for individual CpGs can be surprisingly unreliable due to technical noise, and this may limit the utility of epigenetic clocks. We report that noise produces deviations up to 3 to 9 years between technical replicates for six major epigenetic clocks. The elimination of low-reliability CpGs does not ameliorate this issue. Here, we present a novel computational multi-step solution to address this noise, involving performing principal component analysis on the CpG-level data followed by biological age prediction using principal components as input. This method extracts shared systematic variation in DNAm while minimizing random noise from individual CpGs. Our novel principal-component versions of six clocks show agreement between most technical replicates within 0 to 1.5 years, equivalent or improved prediction of outcomes, and more stable trajectories in longitudinal studies and cell culture. This method entails only one additional step compared to traditional clocks, does not require prior knowledge of CpG reliabilities, and can improve the reliability of any existing or future epigenetic biomarker. The high reliability of principal component-based epigenetic clocks will make them particularly useful for applications in personalized medicine and clinical trials evaluating novel aging interventions.


title: Learning latent embedding of multi-modal single cell data and cross-modality relationship simultaneously

abstract: It is a challenging task to integrate scRNA-seq and scATAC-seq data obtained from different batches. Existing methods tend to use a pre-defined gene activity matrix (GAM) to convert the scATAC-seq data into scRNA-seq data. The pre-defined GAM is often of low quality and does not reflect the dataset-specific relationship between the two data modalities. We propose scDART (single cell Deep learning model for ATAC-seq and RNA-seq Trajectory), a deep learning framework that integrates scRNA-seq and scATAC-seq data and learns cross-modalities relationships simultaneously. Specifically, the design of scDART allows it to preserve cell trajectories in continuous cell populations and can be applied to trajectory inference on integrated data.

category: bioinformatics


title: An Artificial Intelligence and Telemedicine Based Screening Tool to Identify Glaucoma Suspects from Color Fundus Imaging

abstract:
Backgrounds & ObjectiveGlaucomatous vision loss may be preceded by an enlargement of the cup-to-disc ratio (CDR). We propose to develop and validate an artificial intelligence based CDR grading system that may aid in effective glaucoma-suspect screening.

Design, Setting & Participants1546 disc-centered fundus images were selected including all 457 images from the Retinal Image Database for Optic Nerve Evaluation dataset, and images randomly selected from the Age-Related EyeDisease Study, and Singapore Malay Eye Study to develop the system. First, a proprietary semi-automated software was used by an expert grader to quantify vertical CDR. Then, using CDR below 0.5 (not suspect) and CDR above 0.5 (glaucoma-suspect), deep learning architectures were used to train and test a binary classifier system.

MeasurementsThe binary classifier, with glaucoma-suspect as positive, is measured using sensitivity, specificity, accuracy, and AUC.

ResultsThe system achieved an accuracy of 89.67% (sensitivity, 83.33%; specificity, 93.89%; AUC, 0.93). For external validation, the Retinal Fundus Image database for Glaucoma Analysis dataset, which has 638 gradable quality images, was used. Here the model achieved an accuracy of 83.54% (sensitivity, 80.11%; specificity, 84.96%; AUC, 0.85).

ConclusionsHaving demonstrated an accurate and fully automated glaucoma-suspect screening system that can be deployed on telemedicine platforms, we plan prospective trials to determine the feasibility of the system in primary care settings.


title: The United States Swine Pathogen Database: integrating veterinary diagnostic laboratory sequence data to monitor emerging pathogens of swine

abstract:
Veterinary diagnostic laboratories annually derive thousands of nucleotide sequences from clinical samples of swine pathogens such as porcine reproductive and respiratory syndrome virus (PRRSV), Senecavirus A, and swine enteric coronaviruses. In addition, next generation sequencing has resulted in the rapid production of full-length genomes. Presently, sequence data are released to diagnostic clients for the purposes of informing control measures, but are not publicly available as data may be associated with sensitive information. However, public sequence data can be used to objectively design field-relevant vaccines; determine when and how pathogens are spreading across the landscape; identify virus transmission hotspots; and are a critical component in genomic surveillance for pandemic preparedness. We have developed a centralized sequence database that integrates a selected set of previously private clinical data, using PRRSV data as an exemplar, alongside publicly available genomic information. We implemented the Tripal toolkit, using the open source Drupal content management system and the Chado database schema. Tripal consists of a collection of Drupal modules that are used to manage, visualize, and disseminate biological data stored within Chado. Hosting is provided by Amazon Web Services (AWS) EC2 cloud instance with resource scaling. New sequences sourced from diagnostic labs contain at a minimum four data items: genomic information; date of collection; collection location (state or province level); and a unique identifier. Users can download annotated genomic sequences from the database using a customized search interface that incorporates data mined from published literature; search for similar sequences using BLAST-based tools; and explore annotated reference genomes. Additionally, because the bulk of data presently are PRRSV sequences, custom curation and annotation pipelines have determined PRRSV genotype (Type 1 or 2), the location of open reading frames and nonstructural proteins, generated amino acid sequences, the occurrence of putative frame shifts, and restriction fragment length polymorphism (RFLP) classification of GP5 genes. Genomic data from seven major swine pathogens have been curated and annotated. The resource provides researchers timely access to sequences discovered by veterinary diagnosticians, allowing for epidemiological and comparative virology studies. The result will be a better understanding on the emergence of novel swine viruses in the United States (US), and how these novel strains are disseminated in the US and abroad.

Database URLhttps://swinepathogendb.org


title: Identification of a signature of evolutionarily conserved stress-induced mutagenesis in cancer

abstract: The clustering of mutations observed in cancer cells is reminiscent of the stress-induced mutagenesis (SIM) response in bacteria. SIM employs error-prone polymerases resulting in mutations concentrated around DNA double-strand breaks with an abundance that decays with genomic distance. We performed a quantitative study on single nucleotide variant calls for whole-genome sequencing data from 1,950 tumors and non-inherited mutations from 129 normal samples. We introduce statistical methods to identify mutational clusters and quantify their distribution patterns. Our results show that mutations in both normal and cancer samples are indeed clustered and have shapes indicative of SIM. We also found that clusters of mutations colocalize more prevalently in normal samples than in cancer, suggesting loss of regulation leading to increased randomness in the mutational process during carcinogenesis.

category: cancer biology


title: Evidence for a general neural signature of face familiarity

abstract:
We explored the neural signatures of face familiarity using cross-participant and cross-experiment decoding of event-related potentials, evoked by unknown and experimentally familiarized faces from a set of experiments with different participants, stimuli, and familiarization-types. Participants were either familiarized perceptually, via media exposure, or by personal interaction. We observed significant cross-experiment familiarity decoding involving all three experiments, predominantly over posterior and central regions of the right hemisphere in the 270 - 630 ms time window. This shared face familiarity effect was most prominent between the Media and Personal, as well as between the Perceptual and Personal experiments. Cross-experiment decodability makes this signal a strong candidate for a general neural indicator of face familiarity, independent of familiarization methods and stimuli. Furthermore, the sustained pattern of temporal generalization suggests that it reflects a single automatic processing cascade that is maintained over time.

HighlightsO_LIWe investigated if a general neural signature of face familiarity exist
C_LIO_LIA cross-experiment decoding analysis of EEG data was used
C_LIO_LIThe analysis involved perceptual, media and personal familiarization methods
C_LIO_LIWe found a preserved pattern of familiarity decoding across experiments between 270 and 630 ms post-stimulus
C_LIO_LIThis signature is consistent with previous reports on face familiarity effects
C_LI

category: neuroscience


title: Visualization of subcortical structures in non-human primates in vivo by Quantitative Susceptibility Mapping at 3T MRI

abstract:
Magnetic resonance imaging (MRI) is now an essential tool in the field of neuroscience involving non-human primates (NHP). Structural MRI scanning using T1-weighted (T1w) or T2-weighted (T2w) images provides anatomical information, particularly for experiments involving deep structures such as the basal ganglia and cerebellum. However, for certain subcortical structures, T1w and T2w images fail to reveal important anatomical details. To better visualize such structures in the macaque brain, we applied a relatively new method called quantitative susceptibility mapping (QSM), which enhances tissue contrast based on the local tissue magnetic susceptibility. To evaluate the visualization of important structures, we quantified the the contrast-to-noise ratios (CNRs) of the ventral pallidum (VP), globus pallidus external and internal segments (GPe and GPi), substantia nigra (SN), subthalamic nucleus (STN) in the basal ganglia and the dentate nucleus (DN) in the cerebellum. For these structures, the QSM method significantly increased the CNR, and thus the visibility, beyond that in either the T1w or T2w images. In addition, QSM values of some structures were correlated to the age of the macaque subjects. These results indicate that the QSM method can enable the clear identification of certain subcortical structures that are invisible in more traditional scanning sequences.

HighlightsO_LINHP subcortical structures are challenging to see in conventional T1w and T2w images
C_LIO_LIWe applied quantitative susceptibility mapping (QSM) to identify them easily
C_LIO_LIQSM clearly visualized basal ganglia and cerebellar nucleus of high brain iron content
C_LIO_LICNRs of some subcortical nucleus were significantly higher in QSM
C_LIO_LIQSM values of several subcortical nucleus increased with age
C_LI


title: The physiological basis for the computation of direction selectivity in the Drosophila OFF pathway

abstract: In Drosophila, direction-selective neurons implement a mechanism of motion computation similar to cortical neurons, using contrast-opponent receptive fields with ON and OFF subunits. It is not clear how the presynaptic circuitry of direction-selective neurons in the OFF pathway supports this computation, because all major inputs are OFF-rectified neurons. Here, we reveal the biological substrate for motion computation in the OFF pathway. Three interneurons, Tm2, Tm9 and CT1, also provide information about ON stimuli to the OFF direction-selective neuron T5 across its receptive field, supporting a contrast-opponent receptive field organization. Consistent with its prominent role in motion detection, variability in Tm9 receptive field properties is passed on to T5, and calcium decrements in Tm9 in response to ON stimuli are maintained across behavioral states, while spatial tuning is sharpened by active behavior. Together, our work shows how a key neuronal computation is implemented by its constituent neuronal circuit elements to ensure direction selectivity.


title: Speed tuning in head coordinates as an alternative explanation of depth selectivity from motion parallax in area MT

abstract: There are two distinct sources of retinal image motion: motion of objects in the world and movement of the observer. In cases where an object moves in a scene and the eyes also move, a coordinate transformation that involves smooth eye movements and retinal motion will be needed in order to estimate object motion in world coordinates. More recently, interactions between retinal and eye velocity signals have also been suggested to generate depth selectivity from motion parallax (MP) in the macaque middle temporal (MT) area. We explored whether the nature of the interaction between eye and retinal velocities in MT neurons favors one of these two possibilities or a mixture of both. We analyzed responses of MT neurons to retinal and eye velocities in a viewing context in which the observer translates laterally while maintaining visual fixation on a world-fixed target. In this scenario, the depth of an object can be inferred from the ratio between retinal velocity and eye velocity, according to the motion-pursuit law. Previous studies have shown that MT responses to retinal motion are gain-modulated by the direction of eye movement, suggesting a potential mechanism for depth tuning from MP. However, our analysis of the joint tuning profile for retinal and eye velocities reveals that some MT neurons show a partial coordinate transformation toward head coordinates. We formalized a series of computational models to predict neural spike trains as well as selectivity for depth, and we used factorial model comparisons to quantify the relative importance of each model component. Our findings for many MT neurons reveal that the data are equally well explained by gain modulation or a partial coordinate transformation toward head coordinates, although some responses can only be well fit by the coordinate transform model. Our results highlight the potential role of MT neurons in representing multiple higher-level sensory variables, including depth from MP and object motion in the world.


title: Time-oriented attention improves accuracy in a paced finger tapping task

abstract: Finger tapping is a task widely used in a variety of experimental paradigms, in particular to understand sensorimotor synchronization and time processing in the range of hundreds of milliseconds (millisecond timing). Normally, subjects dont receive any instruction about what to attend to and the results are seldom interpreted taking into account the possible effects of attention. In this work we show that attention can be oriented to the purely temporal aspects of a paced finger tapping task and that it affects performance. Specifically, time-oriented attention improves the accuracy in paced finger tapping and it also increases the resynchronization efficiency after a period perturbation. We use two markers of the attention level: auditory ERPs and subjective report of the mental workload. In addition, we propose a novel algorithm to separate the auditory, stimulus-related components from the somatosensory, response-related ones, which are naturally overlapped in the recorded EEG.


title: Evidence that faecal carriage of resistant Escherichia coli by 16-week-old dogs in the United Kingdom is associated with raw feeding and that E. coli from these dogs are shared with humans and cause opportunistic infections.

abstract: We report a survey (August 2017 to March 2018) and risk factor analysis of faecal carriage of antibacterial-resistant (ABR) Escherichia coli in 223 sixteen-week-old dogs in the United Kingdom. Raw feeding was associated with the presence of E. coli resistant to fluoroquinolones, tetracycline, amoxicillin, and streptomycin, but not to cefalexin or cefotaxime. Whole genome sequencing of 30 fluoroquinolone-resistant (FQ-R), 22 cefotaxime-resistant (CTX-R) and seven dual FQ-R/CTX-R E. coli isolates showed a wide range of sequence types (STs), an approximately 50:50 split of CTX-M:AmpC-mediated CTX-R, and almost exclusively mutational FQ-R dominated by ST744 and ST162. Comparisons between E. coli isolates from puppies known to be located within a 50 x 50 km region with those isolated from human urinary tract and bloodstream infections (isolated in parallel in the same region) identified a clone of ST963 E. coli carrying chromosomal blaCMY.2 in two puppies and causing two urinary tract infections and one bloodstream infection. Furthermore, an ST744 FQ-R clone was carried by one puppy and caused one urinary tract infection. Accordingly, we conclude that raw feeding is associated with carriage of ABR E. coli in dogs even at sixteen weeks of age and that bacteria carried by dogs are shared with humans.

category: microbiology


title: Evidence that faecal carriage of resistant Escherichia coli by 16-week-old dogs in the United Kingdom is associated with raw feeding


title: Multiview tiling light sheet microscopy for 3D high resolution live imaging

abstract: Light sheet or selective plane illumination microscopy (SPIM) is ideally suited for in toto imaging of living specimens at high temporal-spatial resolution. In SPIM, the light scattering that occurs during imaging of opaque specimens brings about limitations in terms of resolution and the imaging field of view. To ameliorate this shortcoming, the illumination beam can be engineered into a highly confined light sheet over a large field of view and multi-view imaging can be performed by applying multiple lenses combined with mechanical rotation of the sample. Here, we present a Multiview tiling SPIM (MT-SPIM) that combines the Multi-view SPIM (M-SPIM) with a confined, multi-tiled light sheet. The MT-SPIM provides high-resolution, robust and rotation-free imaging of living specimens. We applied the MT-SPIM to image nuclei and Myosin II from the cellular to subcellular spatial scale in early Drosophila embryogenesis. We show that the MT-SPIM improves the axial-resolution relative to the conventional M-SPIM by a factor of two. We further demonstrate that this axial resolution enhancement improves the automated segmentation of Myosin II distribution and of nuclear volumes and shapes.

category: developmental biology


title: The critical role of natural history museums in advancing eDNA for biodiversity studies: a case study with Amazonian fishes

abstract: Ichthyological surveys have traditionally been conducted using whole-specimen, capture-based sampling with varied, but conventional fishing gear. Recently, environmental DNA (eDNA) metabarcoding has emerged as a complementary, and possible alternative, approach to whole-specimen methodologies. In the tropics, where much of the diversity remains undescribed, vast reaches continue unexplored, and anthropogenic activities are constant threats; there have been few eDNA attempts for ichthyological inventories. We tested the discriminatory power of eDNA using MiFish primers with existing public reference libraries and compared this with capture-based methods in two distinct ecosystems in the megadiverse Amazon basin. In our study, eDNA provided an accurate snapshot of the fishes at higher taxonomic levels and corroborated its effectiveness to detect specialized fish assemblages. Some flaws in fish metabarcoding studies are routine issues addressed in natural history museums. Thus, by expanding their archives to include eDNA and adopting a series of initiatives linking collection-based research, training and outreach, natural history museums can enable the effective use of eDNA to survey Earths hotspots of biodiversity before taxa go extinct. Our project surveying poorly explored rivers and using DNA vouchered archives to build metabarcoding libraries for Neotropical fishes can serve as a model of this protocol.

category: ecology


title: Ultra-rare constrained missense variants in the epilepsies: Shared and specific enrichment patterns in neuronal gene-sets

abstract:
BackgroundBurden analysis in epilepsy has shown an excess of deleterious ultra-rare variants (URVs) in few gene-sets, such as known epilepsy genes, constrained genes, ion channel or GABAA receptor genes. We set out to investigate the burden of URVs in a comprehensive range of gene-sets presumed to be implicated in epileptogenesis.

MethodsWe investigated several constraint and conservation-based strategies to study whole exome sequencing data from European individuals with developmental and epileptic encephalopathies (DEE, n = 1,003), genetic generalized epilepsy (GGE, n = 3,064), and non-acquired focal epilepsy (NAFE, n = 3,522), collected by the Epi25 Collaborative, compared to 3,962 ancestry-matched controls. The burden of 12 non-synonymous URVs types in 92 gene-sets was compared between epilepsy cases (DDE, GGE, NAFE) and controls using logistic regression analysis.

ResultsBurden analysis of brain-expressed genes revealed an excess of different URVs types in all three epilepsy categories which was largest for missense variants in highly constrained sites (constrained missense variants). The URVs burden was prominent in neuron-specific, synaptic and developmental genes as well as genes encoding ion channels and receptors, and it was generally higher for DEE and GGE compared to NAFE. The patterns of URVs burden in gene-sets expressed in inhibitory vs. excitatory neurons or receptors suggested a high burden in both groups in DEE but a differential involvement of inhibitory genes in GGE, while excitatory genes were predominantly affected in NAFE. Top ranking susceptibility genes from a recent genome-wide association study (GWAS) of generalized and focal epilepsies displayed a higher URVs burden in constrained coding regions in GGE and NAFE, respectively.

ConclusionsUsing exome-based gene-set burden analysis, we demonstrate that missense URVs affecting mainly constrained sites are enriched in neuronal genes in both common and rare severe epilepsy syndromes. Our results indicate a differential impact of these URVs in genes expressed in inhibitory vs. excitatory neurons and receptors in generalized vs. focal epilepsies. The excess of URVs in top-ranking GWAS risk-genes suggests a convergence of rare deleterious and common risk-variants in the pathogenesis of generalized and focal epilepsies.

category: genomics


title: Adipose gene expression profiles reveal novel insights into the adaptation of northern Eurasian semi-domestic reindeer (Rangifer tarandus)

abstract: Reindeer (Rangifer tarandus) are semi-domesticated animals adapted to the challenging arctic conditions of northern Eurasia. Adipose tissues play a crucial role in animals living in northern environments by altering gene expression in their tissues to regulate energy homeostasis and thermogenic activity. Here, we performed transcriptome profiling by RNA sequencing of adipose tissues from three different anatomical depots: metacarpal (bone marrow), perirenal, and prescapular fat in Finnish and Even reindeer (in Sakha) during two seasonal time points (spring and winter). On average 36.5 million pair-ended clean reads were obtained for each sample, and a total of 16,362 genes were expressed in our data. Gene expression profiles in metacarpal tissue were distinct and clustered separately from perirenal and prescapular adipose tissues. Notably, metacarpal adipose tissue appeared to have a significant role in the regulation of the energy metabolism of reindeer in spring when their nutritional condition is poor after winter. During spring, when the animals are in less optimal condition, genes associated with the immune system (e.g., CCL2, CCL11, CXCL14, IGSF3, IGHM, IGLC7, IGKC, JCHAIN, and IGSF10) were upregulated in the perirenal and prescapular adipose tissue, while genes involved in energy metabolism (e.g., ACOT2, APOA1, ANGPTL1, ANGPTL8, ELOVL7, MSMO1, PFKFB1, and ST3GAL6) were upregulated in metacarpal tissue. Even reindeer harboured relatively fewer significantly differentially expressed genes than Finnish reindeer, irrespective of the season, possibly owing to climatic and management differences. Moreover, blood and tissue parameters reflecting general physiological and metabolic status showed less seasonal variation in Even reindeer than in Finnish reindeer. This study identified adipose candidate genes potentially involved in immune response, fat deposition, energy metabolism, development, cell growth, and organogenesis. Taken together, this study provides new information on the mechanisms by which reindeer adapt to less optimal arctic conditions.


title: Megapixel camera arrays for high-resolution animal tracking in multiwell plates

abstract: Tracking small laboratory animals such as flies, fish, and worms is used for phenotyping in neuroscience, genetics, disease modelling, and drug discovery. Current imaging systems are limited either in spatial resolution or throughput. A system capable of imaging a large number of animals with sufficient resolution to estimate their pose would enable a new class of experiments where detailed behavioural differences are quantified but at a scale where hundreds of treatments can be tested simultaneously. Here we report a new imaging system consisting of an array of six 12-megapixel cameras that can simultaneously record from all the wells of a 96-well plate with a resolution of 80 pixels/mm at 25 frames per second. We show that this resolution is sufficient to estimate the pose of nematode worms including head identification and to extract high-dimensional phenotypic fingerprints. We use the system to study behavioural variability across wild isolates, the sensitisation of worms to repeated blue light stimulation, the phenotypes of worm disease models, and worms behavioural responses to drug treatment. Because the system is compatible with standard multiwell plates, it makes computational ethological approaches accessible in existing high-throughput pipelines and greatly increases the scale of possible phenotypic screening experiments in C. elegans.

category: animal behavior and cognition


title: Modeling drug combination effects via latent tensor reconstruction

abstract:
AO_SCPLOWBSTRACTC_SCPLOWO_ST_ABSMotivationC_ST_ABSCombination therapies have emerged as a powerful treatment modality to overcome drug resistance and improve treatment efficacy. However, the number of possible drug combinations increases very rapidly with the number of individual drugs in consideration which makes the comprehensive experimental screening infeasible in practice. Machine learning models offer time- and cost-efficient means to aid this process by prioritising the most effective drug combinations for further pre-clinical and clinical validation. However, the complexity of the underlying interaction patterns across multiple drug doses and in different cellular contexts poses challenges to the predictive modelling of drug combination effects.

ResultsWe introduce comboLTR, highly time-efficient method for learning complex, nonlinear target functions for describing the responses of therapeutic agent combinations in various doses and cancer cell-contexts. The method is based on a polynomial regression via powerful latent tensor reconstruction. It uses a combination of recommender system-style features indexing the data tensor of response values in different contexts, and chemical and multi-omics features as inputs. We demonstrate that comboLTR outperforms state-of-the-art methods in terms of predictive performance and running time, and produces highly accurate results even in the challenging and practical inference scenario where full dose-response matrices are predicted for completely new drug combinations with no available combination and monotherapy response measurements in any training cell line.

Availability and implementationcomboLTR code is available at https://github.com/aalto-ics-kepaco/ComboLTR

Contacttianduanyi.wang@aalto.fi; juho.rousu@aalto.fi


title: Full-length Genome of the Ogataea polymorpha strain HU-11 reveals large duplicated segments in subtelomeic regions

abstract:
BackgroundCurrently, methylotrophic yeasts (e.g., Pichia pastoris, Ogataea polymorpha, and Candida boindii) are subjects of intense genomics studies in basic research and industrial applications. In the genus Ogataea, most research is focused on three basic O. polymorpha strains--CBS4732, NCYC495, and DL-1. However, the relationship between CBS4732, NCYC495, and DL-1 remains unclear, as the genomic differences between them have not be exactly determined without their high-quality complete genomes. As a nutritionally deficient mutant derived from CBS4732, the O. polymorpha strain CBS4732 ura3{Delta} (named HU-11) is being used for high-yield production of several important proteins or peptides. HU-11 has the same reference genome as CBS4732 (noted as HU-11/CBS4732), because the only genomic difference between them is a 5-bp insertion.

ResultsIn the present study, we have assembled the full-length genome of O. polymorpha HU-11/CBS4732 using high-depth PacBio and Illumina data. Long terminal repeat (LTR) retrotransposons, rDNA, 5 and 3 telomeric, subtelomeric, low complexity and other repeat regions were curated to improve the genome quality. Particularly, we detected large duplicated segments (LDSs) in the subtelomeric regions and exactly determined all the structural variations (SVs) between CBS4732 and NCYC495.

New findings mainly include(1) the genomic differences between HU-11/CBS4732 and NCYC495 include single nucleotide polymorphisms, small insertions and deletions, and only three SVs; (2) six genes were incorporated into CBS4732 from Cyberlindnera jadinii by horizontal gene transfer and may bring HU-11/CBS4732 new biological functions or physiological properties; (3) many recombination events may have occurred on chromosome 4 and 5 of CBS4732 and NCYC495 ancestors and two large segments were acquired by CBS4732 and NCYC495 from chromosome 6 and C. jadinii during recombination, respectively; and (4) the genome expansion in methylotrophic yeasts is mainly driven by large segment duplication in subtelomeric regions.

ConclusionsThe present study preliminarily revealed the complex relationship between CBS4732, NCYC495, and DL-1. The new findings provide new opportunities for in-depth understanding of genome evolution in methylotrophic yeasts and lay the foundations for the industrial applications of O. polymorpha CBS4732, NCYC495, DL-1, and their derivative strains. The full-length genome of the O. polymorpha strain HU-11/CBS4732 should be included into the NCBI RefSeq database for future studies of Ogataea spp..


title: Full-length Genome of a Ogataea polymorpha strain CBS4732 ura3Δ reveals large duplicated segments in subtelomeric regions


title: Shear Relaxation Governs Dynamic Processes of Biomolecular Condensates

abstract: Phase-separated biomolecular condensates must respond agilely to biochemical and environmental cues in performing their wide-ranging cellular functions, but our understanding of condensate dynamics is lagging. Ample evidence now indicates biomolecular condensates as viscoelastic fluids, where shear stress relaxes at a finite rate, not instantaneously as in viscous liquids. Yet the fusion dynamics of condensate droplets has only been modeled based on viscous liquids, with fusion time given by the viscocapillary ratio (viscosity over interfacial tension). Here we used optically trapped polystyrene beads to measure the viscous and elastic moduli and the interfacial tensions of four types of droplets. Our results challenge the viscocapillary model, and reveal that the relaxation of shear stress governs fusion and other dynamic processes of condensates.

category: biophysics


title: Gene clustering coordinates transcriptional output of disparate biological processes in eukaryotes

abstract: The establishment of distinct transcriptional programs in response to developmental or environmental cues is central to all life. This entails the concordant and discordant transcriptional regulation of several distinct biological processes (BP) often involving thousands of genes. Genomic clustering of genes in a BP is one strategy by which transcriptional coregulation of a BPs genes is achieved. However, whether gene clustering also plays a role in transcriptional coherence of several distinct BPs, often involving thousands of genes, remains unexplored. Here, by analyzing the genomes of eukaryotes ranging from yeast to human, we report the identification of thousands of conserved and species-specific discrete clustered BP pairs, many of which in normal human tissues are transcriptionally correlated. Strikingly, our results reveal that system-level transcriptional coordination is achieved in part by the genic proximity of regulatory nodes of disparate BPs whose coregulation drives the transcriptional coherence of their respective pathways. This, we hypothesize, is one strategy for creating coregulated, tunable modulons in eukaryotes.

category: systems biology


title: A new species of the genus Euphlyctis (Anura: Dicroglossidae) from West Bengal, India

abstract:
A new species of green frog of the genus Euphlyctis Fitzinger, 1843 is described from West Bengal, a state of eastern India. A robust frog, SVL of male 86mm and that of female 132mm. The species is diagnosed by the presence of following characters: green dorsum and female with a greenish white mid-dorsal line, tibiotarsal articulation reaches eye, male with two vocal sac openings at the junction of jaw, female is larger than male though body parameters is proportionately longer in male, nostril snout length 3.45% of SVL, nostril much closer to snout tip than eye, units of hind limb i. e. thigh, shank and foot are almost equal in length, relative length of finger: II < IV < I < III.

The new species is compared with existing eight species of the genus Euphlyctis.

category: zoology


title: A functional topography within the cholinergic basal forebrain for processing sensory cues associated with reward and punishment

abstract: Basal forebrain cholinergic neurons (BFCNs) project throughout the cortex to regulate arousal, stimulus salience, plasticity, and learning. Although often treated as a monolithic structure, the basal forebrain features distinct connectivity along its anteroposterior axis that could impart regional differences in BFCN processing. Here, we performed simultaneous bulk calcium imaging from anterior and posterior BFCNs over a one-month period of variable reinforcement learning in mice. BFCNs in both regions showed equivalently weak responses to unconditioned visual stimuli and anticipated rewards. Anterior BFCNs in the horizontal limb of the diagonal band were more responsive to reward omission, more accurately classified behavioral outcomes, and more closely tracked fluctuations in pupil-indexed global brain state. Posterior BFCNs in globus pallidus and substantia innominata were more responsive to unconditioned auditory stimuli, orofacial movements, aversive reinforcement, and showed robust associative plasticity for punishment-predicting cues. These results identify a functional topography that diversifies cholinergic modulatory signals broadcast to downstream brain regions.


title: A functional topography within the cholinergic basal forebrain for encoding sensory cues and behavioral reinforcement outcomes.


title: Post mortem mapping of connectional anatomy for the validation of diffusion MRI

abstract: Despite the impressive advances in diffusion MRI (dMRI) acquisition and analysis that have taken place during the Human Connectome era, dMRI tractography is still an imperfect source of information on the circuitry of the brain. In this review, we discuss methods for post mortem validation of dMRI tractography, fiber orientations, and other microstructural properties of axon bundles that are typically extracted from dMRI data. These methods include anatomic tracer studies, Klinglers dissection, myelin stains, label-free optical imaging techniques, and others. We provide an overview of the basic principles of each technique, its limitations, and what it has taught us so far about the accuracy of different dMRI acquisition and analysis approaches.


title: Drug metabolism activity is a Critical Intrinsic Selector for Hepatocytes to elongate cell lifespan by using a cell-killing antibiotic

abstract: Hepatocytes can be used to study the pathogenesis of liver diseases and drug discovery research. Human hepatocytes are, however, hardly expandable in vitro making it difficult to secure large numbers of cells from one donor. In this study, we aimed to establish an in vitro long-term culture system that enables stable proliferation and maintenance of human hepatocytes to ensure a constant supply. We purified human hepatocytes by selection with cytocidal puromycin, and cultured them for more than 60 population doublings over a span of more than 350 days. These results show that this simple culture system with usage of the cytocidal antibiotics enables efficient hepatocyte proliferation and is an effective method for generating a stable supply of hepatocytes for drug discovery research at a significant cost reduction.

category: cell biology


title: Food web aggregation: effects on key positions

abstract:
Providing standard definitions of what should be considered as a node in food webs is still an unsolved problem. Especially for comparative and predictive food web modelling, a more systematic understanding is needed for the effects of trophic aggregation procedures. Aggregation is unavoidable during data management. Therefore, it is crucial to know whether food web properties are conserved during this process.

Here, we study how different aggregation methods change the positional importance of species in food webs. In particular, we investigated the effects of various aggregation algorithms on 24 indices of importance. Our work was carried out on 76 aquatic food webs coming from the Ecopath with Ecosim database (EcoBase). We considered six main types of aggregation, according to the way that the nodes were clustered. These were (i) hierarchical clustering based on the Jaccard index, (ii) hierarchical clustering based on the regular equivalence index (REGE), (iii) maximisation of directed modularity, (iv) maximisation of modularity according to modules in which species fed on the same preys, (v) maximisation of modularity according to modules in which species are fed upon by the same predators, and (vi) clustering through the group model.

Hierarchical clustering based on the Jaccard index and REGE index outperformed the other four methods on maintaining the relative importance of species for all the indices of importance (except for the contrastatus index (s') and betweenness centrality (BC)). The choice between these two methods should follow our research question and the importance index we are interested in studying. The other four aggregation methods change more the centrality of species, especially the one based on maximising directed modularity. When using these aggregation algorithms, one has to keep in mind that the network will not only be smaller but also provides different information.


title: A variable-rate quantitative trait evolution model using penalized-likelihood

abstract: In recent years it has become increasingly popular to use phylogenetic comparative methods to investigate heterogeneity in the rate or process of quantitative trait evolution across the branches or clades of a phylogenetic tree. Here, I present a new method for modeling variability in the rate of evolution of a continuously-valued character trait on a reconstructed phylogeny. The underlying model of evolution is stochastic diffusion (Brownian motion), but in which the instantaneous diffusion rate ({sigma}2) also evolves by Brownian motion on a logarithmic scale. Unfortunately, its not possible to simultaneously estimate the rates of evolution along each edge of the tree and the rate of evolution of{sigma} 2 itself using Maximum Likelihood. As such, I propose a penalized-likelihood method in which the penalty term is equal to the log-transformed probability density of the rates under a Brownian model, multiplied by a  smoothing coefficient,{lambda} , selected by the user.{lambda} determines the magnitude of penalty thats applied to rate variation between edges. Lower values of{lambda} penalize rate variation relatively little; whereas larger{lambda} values result in minimal rate variation among edges of the tree in the fitted model, eventually converging on a single value of{sigma} 2 for all of the branches of the tree. In addition to presenting this model here, I have also implemented it as part of my phytools R package in the function multirateBM. Using different values of the penalty coefficient,{lambda} , I fit the model to simulated data with: Brownian rate variation among edges (the model assumption); uncorrelated rate variation; rate changes that occur in discrete places on the tree; and no rate variation at all among the branches of the phylogeny. I then compare the estimated values of{sigma} 2 to their known true values. In addition, I use the method to analyze a simple empirical dataset of body mass evolution in mammals. Finally, I discuss the relationship between the method of this article and other models from the phylogenetic comparative methods and finance literature, as well as some applications and limitations of the approach.

category: evolutionary biology


title: Expression signatures based on pyroptosis-related genes can robustly diagnose skin cutaneous melanoma and predict the prognosis.

abstract: Skin cutaneous melanoma (SKCM) is a chronically malignant tumor with a high mortality rate. Pyroptosis, a kind of pro-inflammatory programmed cell death, has been linked to cancer in recent studies. However, the value of pyroptosis in the diagnosis and prognosis of SKCM is not clear. In this study, it was discovered that 20 pyroptosis-related genes (PRGs) differed in expression between SKCM and normal tissues, which were related to diagnosis and prognosis. Firstly, based on these genes, nine machine-learning algorithms were shown to perform well in constructing diagnostic classifiers, including K-Nearest Neighbor (KNN), logistic regression, Support Vector Machine (SVM), Artificial Neural Network (ANN), decision tree, random forest, XGBoost, LightGBM, and CatBoost. Secondly, the least absolute shrinkage and selection operator (LASSO) Cox regression analysis was applied and the prognostic model was constructed based on 9 PRGs. Subgroups in low and high risks determined by the prognostic model were shown to have different survival. Thirdly, functional enrichment analyses were performed by applying the gene set enrichment analysis (GSEA), and results suggested that the risk was related to immune response. Finally, immune infiltration analysis was carried out, which showed that fractions of activated CD4+ memory T cells, {gamma}{delta} T cells, Ml macrophages, and M2 macrophages were significantly different between subgroups. In conclusion, the expression signatures of pyroptosis-related genes are effective and robust in the diagnosis and prognosis of SKCM, which is related to immunity.


title: Pyroptosis-related gene signatures can robustly diagnose skin cutaneous melanoma and predict the prognosis


title: RegVar: Tissue-specific Prioritization of Noncoding Regulatory Variants

abstract: Noncoding genomic variants constitute the majority of trait-associated genome variations; however, identification of functional noncoding variants is still a challenge in human genetics, and a method systematically assessing the impact of regulatory variants on gene expression and linking them to potential target genes is still lacking. Here we introduce a deep neural network (DNN)-based computational framework, RegVar, that can accurately predict the tissue-specific impact of noncoding regulatory variants on target genes. We show that, by robustly learning the genomic characteristics of massive variant-gene expression associations in a variety of human tissues, RegVar vastly surpasses all current noncoding variants prioritization methods in predicting regulatory variants under different circumstances. The unique features of RegVar make it an excellent framework for assessing the regulatory impact of any variant on its putative target genes in a variety of tissues. RegVar is available as a webserver at http://regvar.cbportal.org/.


title: The SARS CoV-1 3a protein disrupts Golgi complex morphology and cargo trafficking

abstract: Coronaviruses assemble by budding into the endoplasmic reticulum-Golgi intermediate compartment, but the pathway of egress from infected cells is not well understood. Efficient egress of infectious bronchitis virus (a gamma coronavirus, CoV) requires neutralization of Golgi pH by the envelope (E) protein. This results in reduced rates of cargo traffic and disrupts Golgi morphology, but it protects the spike protein from aberrant proteolysis. The severe acute respiratory syndrome (SARS) CoV-1 E protein does not disrupt the Golgi, however. We show here that in transfected cells, the ORF3a protein of SARS CoV-1 disrupts Golgi morphology, cargo trafficking and luminal pH. Unlike the infectious bronchitis virus E protein, these functions of the SARS CoV-1 3a protein appear to require its viroporin activity. Thus, neutralization of acidic compartments may be a universal feature of CoV infection, although different viral proteins and mechanisms may be used to achieve this outcome.


title: A biosensor to gauge protein homeostasis resilience differences in the nucleus compared to cytosol of mammalian cells

abstract: An extensive network of chaperones and other proteins maintain protein homeostasis and guard against inappropriate protein aggregation that is a hallmark of neurodegenerative diseases. Using a fluorescence resonance energy-based biosensor that simultaneously reports on intact cellular chaperone holdase activity and detrimental aggregation propensity, we investigated the buffering capacity of the systems managing protein homeostasis in the nucleus of the human cell line HEK293 compared to the cytosol. We found that the nucleus showed lower net holdase activity and reduced capacity to suppress protein aggregation, suggesting that the nuclear quality control resources are less effective compared to those in the cytosol. Aggregation of mutant huntingtin exon 1 protein (Httex1) in the cytosol appeared to deplete cytosolic chaperone supply by depleting holdase activity. Unexpectedly, the same stress increased holdase activity in the nucleus suggesting that proteostasis stress can trigger a rebalance of chaperone supply in different subcellular compartments. Collectively the findings suggest the cytosol has more capacity to manage imbalances in proteome foldedness than the nucleus, but chaperone supply can be redirected into the nucleus under conditions of proteostasis stress caused by cytosolic protein aggregation.

category: biochemistry


title: Inferring the stabilization effects of SARS-CoV-2 variants on the binding with ACE2 receptor

abstract: With the progression of the SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) pandemic, several variants of the virus are emerging with mutations distributed all over the viral sequence. While most of them are expected to have little to no effects at the phenotype level, some of these variants presenting specific mutations on the Spike protein are rapidly spreading, making urgent the need of characterizing their effects on phenotype features like contagiousness and antigenicity. With this aim, we performed extensive molecular dynamics simulations on a selected set of possible Spike variants in order to assess the stabilizing effect of particular amino acid substitutions, with a special focus on the mutations that are both characteristic of the top three most worrying variants at the moment, i.e the English, South African and Amazonian ones, and that occur at the molecular interface between SARS-CoV-2 Spike protein and its human ACE2 receptor. We characterize these variants effect in terms of (i) residues mobility, (ii) compactness, studying the network of interactions at the interface, and (iii) variation of shape complementarity via expanding the molecular surfaces in the Zernike basis. Overall, our analyses highlighted greater stability of the three variant complexes with respect to both the wild type and two negative control systems, especially for the English and Amazonian variants. In addition, in the three variants, we investigate the effects a not-yet observed mutation in position 501 could provoke on complex stability. We found that a phenylalanine mutation behaves similarly to the English variant and may cooperate in further increasing the stability of the South African one, hinting at the need for careful surveillance for the emergence of such kind of mutations in the population. Ultimately, we show that the observables we propose describe key features for the stability of the ACE2-spike complex and can help to monitor further possible spike variants.


title: Triggered reversible disassembly of an engineered protein nanocage

abstract: Protein nanocages play crucial roles in sub-cellular compartmentalization and spatial control in all domains of life and have been used as biomolecular tools for applications in biocatalysis, drug delivery, and bionanotechnology. The ability to control their assembly state under physiological conditions would further expand their practical utility. To gain such control, we introduced a peptide capable of triggering conformational change at a key structural position in the largest known encapsulin nanocompartment. We report the structure of the resulting engineered nanocage and demonstrate its ability to on-demand disassemble and reassemble under physiological conditions. We demonstrate its capacity for in vivo encapsulation of proteins of choice while also demonstrating in vitro cargo loading capabilities. Our results represent a functionally robust addition to the nanocage toolbox and a novel approach for controlling protein nanocage disassembly and reassembly under mild conditions.

category: synthetic biology


title: Stabilisation of Antithetic Control via Molecular Buffering

abstract: A key goal in synthetic biology is the construction of molecular circuits that robustly adapt to perturbations. Although many natural systems display perfect adaptation, whereby stationary molecular concentrations are insensitive to perturbations, its de novo engineering has proven elusive. The discovery of the antithetic control motif was a significant step toward a universal mechanism for engineering perfect adaptation. Antithetic control provides perfect adaptation in a wide range of systems, but it can lead to oscillatory dynamics due to loss of stability, and moreover, it can lose perfect adaptation in fast growing cultures. Here, we introduce an extended antithetic control motif that resolves these limitations. We show that molecular buffering, a widely conserved mechanism for homeostatic control in nature, stabilises oscillations and allows for near-perfect adaptation during rapid growth. We study multiple buffering topologies and compare their performance in terms of their stability and adaptation properties. We illustrate the benefits of our proposed strategy in exemplar models for biofuel production and growth rate control in bacterial cultures. Our results provide an improved circuit for robust control of biomolecular systems.


title: Intestinal helminth infection transforms the CD4+ T cell composition of the skin

abstract: Intestinal helminth parasites can alter immune responses to vaccines, other infections, allergens and autoantigens, indicating effects on host immune responses in distal barrier tissues. We herein show that C57BL/6 mice infected with the strictly intestinal nematode Heligmosomoides polygyrus have impaired capacity to initiate skin immune responses and develop skin-resident memory cells to mycobacterial antigens, both during infection and months after deworming therapy. Surprisingly, and in contrast to a previously noted loss of T cells in peripheral lymph nodes, the skin of worm-infected mice harboured higher numbers of CD4+ T cells compared to skin of uninfected controls. H. polygyrus-specific TH2 cells accumulated during infection and remained after worm expulsion. Accumulation of TH2 cells in the skin was associated with increased expression of the skin-homing chemokine receptors CCR4 and CCR10 on CD4+ T cells in blood and mesenteric lymph nodes draining intestinal tissues, indicating gut-to-skin trafficking of cells. In conclusion, we show that infection by a strictly intestinal helminth has long-term effects on immune cell composition and local immune responses to unrelated antigens in the skin, revealing a novel mechanism for T cell colonization and worm-mediated immunosuppression in this organ.

category: immunology


title: Computer-Vision Stabilized Intravital Imaging Reveals Lung Capillary Neutrophil Dynamics Crucial for Lung Host-Defense Function

abstract: Polymorphonuclear neutrophils (PMN) are highly dynamic innate immune cells which are essential for lung host defense. However, in vivo intravital imaging in moving organs such as the lung remains challenging due to motion artifacts. Here we describe a novel intravital imaging method with high-throughput analytical capability based on a computer vision stabilization algorithm, Computer-vision-Assisted STabilized intravital imaging (CASTii). The sub-micron precision of this approach enables analysis of compartmentalized intravital PMN dynamics. We quantified in real-time a novel patrolling function of lung intracapillary circulating PMN. We also describe the dynamics of intracapillary PMN pooling (marginated PMN pool) using direct imaging of PMNs. The pool was formed by repeated catch-and-release kinetics involving PMN deformation inside microvessels during the passage of PMNs in vessels. We observed rapid PMN recruitment into the lung tissue compartments from pooled PMNs in response to alveolar chemoattract exposure. In contrast, endotoxemia-induced intracapillary sequestration of PMN impaired PMN transmigration into the alveolar space and defective phagocytosis of live bacteria. Intravital imaging of PMN dynamics with CASTii provides fundamental insights into host-defense functions of lung capillary PMN.


title: Genome organisation and evolution of a eukaryotic nicotinate co-inducible pathway

abstract: In Aspergillus nidulans a regulon including 11 hxn genes (hxnS, T, R, P, Y, Z, X, W, V, M and N) is inducible by a nicotinate metabolic derivative, repressible by ammonium and under stringent control of the nitrogen-state sensitive GATA factor AreA and the specific transcription factor HxnR. This is the first report in a eukaryote of the genomic organisation of a possibly complete pathway of nicotinate utilisation. In A. nidulans the regulon is organised in three distinct clusters, this organisation is variable in the Ascomycota. In some Pezizomycotina species all the 11 genes map in a single cluster, in other in two clusters. This variable organisation sheds light on cluster evolution. Instances of gene duplication, followed by, or simultaneous with, integration in the cluster; partial or total cluster loss; horizontal gene transfer of several genes, including an example of whole cluster re-acquisition in Aspergillus of section Flavi were detected, together with the incorporation in some clusters of genes not found in the A. nidulans co-regulated regulon, which underlie both the plasticity and the reticulate character of metabolic cluster evolution. This study provides a comprehensive phylogeny of six members of the cluster across representatives of all Ascomycota classes.


title: Multiple acyl-CoA dehydrogenase deficiency kills Mycobacterium tuberculosis in vitro and during infection

abstract: The human pathogen Mycobacterium tuberculosis (Mtb) devotes a significant fraction of its genome to fatty acid metabolism. Although Mtb depends on host fatty acids as a carbon source, fatty acid {beta}-oxidation is mediated by genetically redundant enzymes, which has hampered the development of antitubercular drugs targeting this metabolic pathway. Here, we identify rv0338c, referred to as etfDMtb, to encode a membrane dehydrogenase essential for fatty acid {beta}-oxidation in Mtb. An etfD deletion mutant ({Delta}etfD) was incapable of growing on fatty acids in vitro, with long-chain fatty acids being bactericidal, and failed to grow and survive in mice. The {Delta}etfD metabolome revealed a block in {beta}-oxidation at the step catalyzed by acyl-CoA dehydrogenases (ACADs). In many organisms, including humans, ACADs are functionally dependent on an electron transfer flavoprotein (ETF) and cognate dehydrogenase. Immunoprecipitation identified EtfD in complex with FixA (EtfBMtb). FixA (EtfBMtb) and FixB (EtfAMtb) are homologous to the human ETF subunits. Our results demonstrate that EtfBAMtb constitutes Mtbs ETF, while EtfDMtb, although not homologous to human EtfD, functions as the dehydrogenase. These findings identify Mtbs fatty acid {beta}-oxidation as a novel potential target for TB drug development.


title: Eukaryotic ribosome recognizes 3 context and stimulates stop codon readthrough

abstract: It is known that the nucleotide context surrounding stop codons significantly affects the efficiency of translation termination. In eukaryotes, various 3' contexts have been described that are unfavourable for translation termination; however, the exact molecular mechanism that mediates their effect remains unknown. In this study, we used a reconstituted mammalian translation system to examine the efficiency of stop codons in different contexts, including several previously described weak 3' stop codon contexts. Our results revealed that ribosomes can independently recognize certain contexts and ignore stop codons that are followed by these sequences. Moreover, the efficiency of translation termination at the weak 3' contexts was almost equal to the one at the standard context. We propose that weak 3' contexts interact with the 18S rRNA provoking a conformational change in the U-turn-like structure of the stop codon in the A site of ribosome. This change makes incorporation of the near-cognate tRNA more preferable than recognition of the stop codon by the release factors and increases readthrough.

category: molecular biology


title: The DNA-to-cytoplasm ratio broadly activates zygotic gene expression in Xenopus

abstract: SummaryIn multicellular animals, the first major event after fertilization is the switch from maternal to zygotic control of development. During this transition, zygotic gene transcription is broadly activated in an otherwise quiescent genome in a process known as zygotic genome activation (ZGA). In fast developing embryos, ZGA often overlaps with the slowing of initially synchronous cell divisions at the mid-blastula transition (MBT). Initial studies of the MBT led to the nuclear-to-cytoplasmic ratio model where MBT timing is regulated by the exponentially increasing amounts of some nuclear component  N titrated against a fixed cytoplasmic component  C. However, more recent experiments have been interpreted to suggest that ZGA is independent of the N/C ratio. To determine the role of the N/C ratio in ZGA, we generated Xenopus frog embryos with [~]3-fold differences in genomic DNA (i.e., "N") by using X. tropicalis sperm to fertilize X. laevis eggs with or without their maternal genome. Resulting embryos have otherwise identical X. tropicalis genome template amounts, embryo sizes, and X. laevis maternal environments. We used the X. tropicalis paternally derived mRNA to identify a high confidence set of exclusively zygotic transcripts. Both ZGA and the increase in cell cycle duration are delayed in embryos with [~]3-fold less DNA per cell. Thus, DNA is an important component of the N/C ratio, which is indeed a critical regulator of zygotic genome activation in Xenopus embryos.


title: DNMT3A-dependent DNA methylation is required for spermatogonial stem cells to commit to spermatogenesis

abstract: DNA methylation plays a critical role in spermatogenesis, as evidenced by the male sterility of DNA methyltransferase (DNMT) mutant mice. Here, we report a striking division of labor in the establishment of the methylation landscape of male germ cells and its functions in spermatogenesis: while DNMT3C is essential for preventing retrotransposons from interfering with meiosis, DNMT3A broadly methylates the genome--at the exception of DNMT3C-dependent retrotransposons--and controls spermatogonial stem cell (SSC) plasticity. By reconstructing developmental trajectories through single-cell RNA-seq and by profiling chromatin states, we found that Dnmt3A mutant SSCs can only self-renew and no longer differentiate due to spurious enhancer activation that enforces an irreversible stem cell gene program. We therefore provide a novel function for DNA methylation in male fertility: the epigenetic programming of SSC commitment to differentiation and to life-long spermatogenesis supply.


title: Genetic lineage of the Amami islanders inferred from classical genetic markers

abstract: The genetic structure of the people of mainland Japan and Okinawa has been gradually unveiled in recent years. However, previous anthropological studies dealing with people in the Amami islands, located between mainland Japan and Okinawa, were less informative because of the lack of genetic data. In this study, we collected DNAs from 104 subjects in two of the Amami islands, Amami-Oshima island and Kikai island. We analyzed the D-loop region of mtDNA, four Y-STRs, and four autosomal nonsynonymous SNPs to clarify the Amami islanders genetic structure compared with peoples in Okinawa, mainland Japan, and other regions of East Asia. We found that the Amami islanders showed a genetically intermediate position between mainland Japan and Okinawa in mtDNA and Y-STR. However, the frequencies of several autosomal SNPs in the Amami islanders indicated a significant difference from mainland Japanese, which may be because of the gene flow from Okinawa but not natural selection. Moreover, extremely high or low frequencies of several alleles implied a founder effect in Kikai islanders. Note that there is room for the interpretation of the results because of the small sample size and number of alleles in the present study. Geographically broad and detailed samplings and genome-wide analyses are awaited.

category: genetics


title: Deep Mutagenesis of a Transporter for Uptake of a Non-Native Substrate Identifies Conformationally Dynamic Regions

abstract: The serotonin transporter, SERT, catalyzes serotonin reuptake at the synapse to terminate neurotransmission via an alternating access mechanism, and SERT inhibitors are the most widely prescribed antidepressants. Here, deep mutagenesis is used to determine the effects of nearly all amino acid substitutions on human SERT surface expression and transport of the fluorescent substrate analogue APP+, identifying many mutations that enhance APP+ import. Comprehensive simulations of the entire ion-coupled import process reveal that while binding of the native substrate, serotonin, reduces free energy barriers between conformational states to promote SERT dynamics, the conformational free energy landscape in the presence of APP+ instead resembles Na+ bound-SERT, with a higher free energy barrier for transitioning to an inward-facing state. The deep mutational scan for SERT-catalyzed import of APP+ finds mutations that promote the necessary conformational changes that would otherwise be facilitated by the native substrate. Indeed, hundreds of gain-of-function mutations for APP+ import are found along the permeation pathway, most notably mutations that favor opening of a solvent-exposed intracellular vestibule. The mutagenesis data support the simulated mechanism in which the neurotransmitter and a symported sodium share a common cytosolic exit pathway to achieve coupling. Furthermore, the mutational landscape for SERT surface trafficking, which likely filters out misfolded sequences, reveals that residues along the permeation pathway are mutationally tolerant, providing plausible evolutionary pathways for changes in transporter properties while maintaining folded structure.


title: Single-molecule imaging of IQGAP1 regulating actin filament dynamics in real time

abstract: IQGAP is a conserved family of actin-binding proteins with essential roles in cell motility, cytokinesis, and cell adhesion, yet it has remained poorly understood how IQGAP proteins directly regulate actin filament dynamics. To close this gap, we used single-molecule and single-filament TIRF microscopy to directly visualize IQGAP regulating actin dynamics in real time. To our knowledge, this is the first study to do so. Our results show that full-length human IQGAP1 forms dimers that stably bind to filament sides and transiently cap barbed ends. These interactions organize actin filaments into thin bundles, suppress barbed end growth, and inhibit filament disassembly. Surprisingly, each activity depends on distinct combinations of IQGAP1 domains and/or dimerization, suggesting that different mechanisms underlie each functional effect on actin. These observations have important implications for how IQGAP functions as a direct actin regulator in vivo, and how it is deployed and regulated in different biological settings.


title: Sequence determinants of in cell condensate assembly morphology, dynamics, and oligomerization as measured by number and brightness analysis

abstract:
BackgroundBiomolecular condensates are non-stoichiometric assemblies that are characterized by their capacity to spatially concentrate biomolecules and play a key role in cellular organization. Proteins that drive the formation of biomolecular condensates frequently contain oligomerization domains and intrinsically disordered regions (IDRs), both of which can contribute multivalent interactions that drive higher-order assembly. Our understanding of the relative and temporal contribution of oligomerization domains and IDRs to the material properties of in vivo biomolecular condensates is limited. Similarly, the spatial and temporal dependence of protein oligomeric state inside condensates has been largely unexplored in vivo.

MethodsIn this study, we combined quantitative microscopy with number and brightness analysis to investigate the aging, material properties, and protein oligomeric state of biomolecular condensates in vivo. Our work is focused on condensates formed by AUXIN RESPONSE FACTOR 19 (ARF19), which is a transcription factor integral to the signaling pathway for the plant hormone auxin. ARF19 contains a large central glutamine-rich IDR and a C-terminal Phox Bem1 (PB1) oligomerization domain and forms cytoplasmic condensates.

ResultsOur results reveal that the IDR amino acid composition can influence the morphology and material properties of ARF19 condensates. In contrast the distribution of oligomeric species within condensates appears insensitive to the IDR composition. In addition, we identified a relationship between the abundance of higher- and lower-order oligomers within individual condensates and their apparent fluidity.

ConclusionsIDR amino acid composition affects condensate morphology and material properties. In ARF condensates, altering the amino acid composition of the IDR did not greatly affect the oligomeric state of proteins within the condensate.


title: Exosome component 1 cleaves single-stranded DNA and sensitizes kidney renal clear cell carcinoma cells to poly(ADP-ribose) polymerase inhibitor

abstract: Targeting DNA repair pathway offers an important therapeutic strategy for cancers. However, the failure of DNA repair inhibitors to markedly benefit patients necessitates the development of new strategies. Here, we show that exosome component 1 (EXOSC1) promotes DNA damages and sensitizes kidney renal clear cell carcinoma (KIRC) cells to DNA repair inhibitor. Considering that endogenous source of mutation (ESM) constantly assaults genomic DNA and likely sensitize cancer cells to the inhibitor, we first analyzed the statistical relationship between the expression of individual genes and the mutations for KIRC. Among the candidates, EXOSC1 most notably promoted DNA damages and subsequent mutations via preferentially cleaving C site(s) in single-stranded DNA. Consistently, EXOSC1 was more significantly correlated with C>A transversions in coding strands than these in template strands in KIRC. Notably, KIRC patients with high EXOSC1 showed a poor prognosis, and EXOSC1 sensitized cancer cells to poly(ADP-ribose) polymerase inhibitor. These results show that EXOSC1 acts as an ESM in KIRC, and targeting EXOSC1 might be a potential therapeutic strategy.

category: cancer biology


title: Aberrant integration of Hepatitis B virus DNA promotes major restructuring of human hepatocellular carcinoma genome architecture

abstract: Most cancers are characterized by the somatic acquisition of genomic rearrangements during tumour evolution that eventually drive the oncogenesis. There are different mutational mechanisms causing structural variation, some of which are specific to particular cancer types. Here, using multiplatform sequencing technologies, we identify and characterize a remarkable mutational mechanism in human hepatocellular carcinoma caused by Hepatitis B virus, by which DNA molecules from the virus are inserted into the tumour genome causing dramatic changes in its configuration, including non-homologous chromosomal fusions and megabase-size telomeric deletions. This aberrant mutational process, present in at least 8% of all HCC tumours, is active early during liver cancer evolution and can provide the driver rearrangements that a cancer clone requires to survive and grow.


title: Development of Small Molecule Inhibitors Targeting PBX1 Transcription Signaling as a Novel Cancer Therapeutic Strategy

abstract: PBX1 (pre-B cell leukemia transcription factor 1) is a transcription factor involved in diverse cellular functions including organ development, stem cell renewal, and tumorigenesis. PBX1 is localized at chr1q23.3, a frequently amplified chromosomal region, and it is overexpressed in many human malignancies including breast, lung, melanoma, and ovarian carcinomas. Cancer cells with elevated PBX1 signaling are particularly vulnerable to PBX1-withdrawal. We designed a series of small molecule compounds capable of docking to the interface between PBX1 and its cognate DNA target sequence and identified a lead compound, T417, which efficiently hindered the formation of the PBX1 transcriptional complex and affected the transcription of PBX1 target genes. In cell-based assays, T417 significantly suppressed long-term self-renewal and proliferation of cancer cells expressing high levels of PBX1 but not of those expressing low levels of PBX1. T417 also re-sensitized platinum-resistant ovarian tumor cells to carboplatin and produced synergistic anti-tumorigenic effects in vivo in combination with carboplatin. Normal tissues were spared, likely due to the lower PBX1 expression levels. Since PBX1 functions as a molecular hub in developing cancer recurrence and treatment resistance, our data highlight the potential of targeting the PBX-DNA interface as a therapeutic strategy for patients whose tumors rely on PBX1 activation for survival.

category: pathology


title: CRISPR-Cas12a genome editing at the whole-plant level using two compatible RNA virus vectors

abstract: The use of viral vectors that can replicate and move systemically through the host plant to deliver bacterial clustered, regularly interspaced, short palindromic repeats (CRISPR) components enables genome editing at the whole-plant level and avoids the requirement for labor-intensive stable transformation. However, this approach usually relies on previously transformed plants that stably express a CRISPR-associated (Cas) nuclease. Here we describe successful DNA-free genome editing of Nicotiana benthamiana using two compatible RNA virus vectors, derived from tobacco etch virus (TEV; genus Potyvirus) and potato virus X (PVX; genus Potexvirus), which replicate in the same cells. The TEV and PVX vectors respectively express a Cas12a nuclease and the corresponding guide RNA. This novel two-virus vector system improves the toolbox for transformation-free virus-induced genome editing in plants and will advance efforts to breed more nutritious, resistant, and productive crops.

category: plant biology


title: Synchronization of iPS-derived cardiomyocytes to visitor heartbeat in an interactive museum exhibit

abstract: Science museums play an important role in science education, both engaging the public with science concepts and building support for scientific research. Designing museum exhibits to meet increasing public interests in the life sciences is particularly important, yet remains challenging. In this report we describe Give Heart Cells a Beat, a permanent interactive science exhibit that allows museum visitors to synchronize the beating of live stem cell-derived cardiomyocytes to their own heart rate in real-time. Evaluation with museum visitors reveals that the exhibit engaged the public with the specimen and prompted curiosity in heart biology and, to a lesser degree, stem cells and electrophysiology. Give Heart Cells a Beat is the product of a close collaboration between a museum and a research laboratory, and, to our knowledge, the first example of the use of live human heart cells in an interactive exhibit. We hope this exhibit will serve as an example for the implementation of stem cell technology in the field of informal science education and encourage others to pursue close working relationships between academia and public science venues such as museums.

category: scientific communication and education


title: A SARS-CoV-2 targeted siRNA-nanoparticle therapy for COVID-19

abstract: Coronavirus disease 2019 (COVID-19) is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection in humans. Despite several emerging vaccines, there remains no verifiable therapeutic targeted specifically to the virus. Here we present a highly effective siRNA therapeutic against SARS-CoV-2 infection using a novel lipid nanoparticle delivery system. Multiple small-interfering RNAs (siRNAs) targeting highly conserved regions of the SARS-CoV-2 virus were screened and three candidate siRNAs emerged that effectively inhibit virus by greater than 90% either alone or in combination with one another. We simultaneously developed and screened two novel lipid nanoparticle formulations for the delivery of these candidate siRNA therapeutics to the lungs, an organ that incurs immense damage during SARS-CoV-2 infection. Encapsulation of siRNAs in these LNPs followed by in vivo injection demonstrated robust repression of virus in the lungs and a pronounced survival advantage to the treated mice. Our LNP-siRNA approaches are scalable and can be administered upon the first sign of SARS-CoV-2 infection in humans. We suggest that an siRNA-LNP therapeutic approach could prove highly useful in treating COVID-19 disease as an adjunctive therapy to current vaccine strategies.


title: Alterations in protein translation and carboxylic acid catabolic processes in diabetic kidney disease

abstract: Diabetic kidney disease (DKD) remains the leading cause of end stage kidney disease despite decades of study. Alterations in the glomerulus and kidney tubules both contribute to the pathogenesis of DKD although the majority of investigative efforts have focused on the glomerulus. We sought to examine the differential expression signature of human DKD in the glomerulus and proximal tubule and corroborate our findings in the db/db mouse model of diabetes. A transcriptogram network analysis of RNAseq data from laser microdissected (LMD) human glomerulus and proximal tubule of DKD and reference nephrectomy samples revealed enriched pathways including rhodopsin-like receptors, olfactory signaling, and ribosome (protein translation) in the proximal tubule of human DKD biopsy samples. The translation pathway was also enriched in the glomerulus. Increased translation in diabetic kidneys was validated using polyribosomal profiling in the db/db mouse model of diabetes. Using single nuclear RNA sequencing (snRNAseq) of kidneys from db/db mice, we prioritized additional pathways identified in human DKD. The top overlapping pathway identified in the murine snRNAseq proximal tubule clusters and the human LMD proximal tubule compartment was carboxylic acid catabolism. Using ultra-performance liquid chromatography-mass spectrometry, the fatty acid catabolism pathway was also found to be dysregulated in the db/db mouse model. The Acetyl-CoA metabolite was down-regulated in db/db mice, aligning with the human differential expression of the genes ACOX1 and ACACB. In summary, our findings demonstrate that proximal tubular alterations in protein translation and carboxylic acid catabolism are key features in both human and murine DKD.


title: Network controllability enrichment analysis reveals that SARS-CoV-2 infection tends to target indispensable nodes of a directed human protein-protein interaction network

abstract: The COVID-19 disease has been a global threat caused by the new coronavirus species, SARS-CoV-2, since early 2020 with an urgent need for therapeutic interventions. In order to provide insight into human proteins targeted by SARS-CoV-2, here we study a directed human protein-protein interaction network (dhPPIN) based on our previous work on network controllability of virus targets. We previously showed that human proteins targeted by viruses tend to be those whose removal in a dhPPIN requires more control of the network dynamics, which were classified as indispensable nodes. In this study we introduce a more comprehensive rank-based enrichment analysis of our previous dhPPIN for SARS-CoV-2 infection and show that SARS-CoV-2 also tends to target indispensable nodes in the dhPPIN using multiple proteomics datasets, supporting validity and generality of controllability analysis of viral infection in humans. Also, we find differential controllability among SARS-CoV-2, SARS-CoV-1, and MERS-CoV from a comparative proteomics study. Moreover, we show functional significance of indispensable nodes by analyzing heterogeneous datasets from a genome-wide CRISPR screening study, a time-course phosphoproteomics study, and a genome-wide association study. Specifically, we identify SARS-CoV-2 ORF3A as most frequently interacting with indispensable proteins in the dhPPIN, which are enriched in TGF-beta signaling and tend to be sources nodes and interact with each other. Finally, we built an integrated network model of ORF3A-interacting indispensable proteins with multiple functional supports to provide hypotheses for experimental validation as well as therapeutic opportunities. Therefore, a sub-network of indispensable proteins targeted by SARS-CoV-2 could serve as a prioritized network of drug targets and a basis for further functional and mechanistic studies from a network controllability perspective.


title: Production of antibodies in egg whites of chickens.

abstract:
BackgroundIgM, which participates in the primary immune response, is the primary antibody in egg whites. There is scant information about the production of antibodies in egg whites. This study describes the preparation of antibodies against bacterial antigens.

MethodsEnzyme-linked immunosorbent assay (ELISA) was used to detect the presence of anti-egg white antibodies. The antibodies were purified using affinity chromatography. Statistical analyses were performed using SPSS version 22. Statistical significance was set at P<0.05.

ResultsLarge amounts of anti-protein A antibodies were produced in chicken egg whites. The generation of anti-SpA antibodies was demonstrated by affinity chromatography from 9 d post-immunization egg white samples. Inhibition of agglutination was observed in samples containing anti-SpA antibodies, and agglutination at the bottom of the wells was observed in the negative samples.

ConclusionAnti-protein A antibodies (IgM) were produced in the egg whites of the immunized hens. Bacterial growth in blood agar plates was observed only in specimens plated with egg whites from pre-immunized birds. Protein A-affinity chromatography was helpful for the characterization of anti-protein A antibodies. Inhibition of these antibodies was observed in vitro.


title: Antifungal siderophore conjugates for theranostic applications in invasive pulmonary aspergillosis using low molecular TAFC scaffolds

abstract:
Invasive pulmonary aspergillosis (IPA) is a life-threatening form of fungal infection, primarily in immunocompromised patients and associated with a significant mortality. Diagnostic procedures are often invasive and/or time consuming and existing antifungals can be constrained by dose limiting toxicity and drug interaction. In this study, we modified triacetylfusarinine C (TAFC), the main siderophore produced by the opportunistic pathogen Aspergillus fumigatus, with antifungal molecules to perform antifungal susceptibility tests and molecular imaging.

MethodsA variation of small organic molecules (eflornithine, fludioxonil, thiomersal, fluoroorotic acid (FOA), cyanine 5 (Cy5)) with antifungal activity were coupled to TAFC, resulting in a "Trojan horse" to deliver antifungal compounds specifically into Aspergillus fumigatus hyphae by the major facilitator transporter MirB. Radioactive labelling with gallium-68 allowed to perform in vitro characterization (LogD, stability, uptake assay) as well as biodistribution experiments and PET/CT imaging in an IPA rat infection model. Compounds labelled with stable gallium were used for antifungal susceptibility tests.

Results[Ga]DAFC-fludioxonil, -FOA and Cy5 revealed a MirB dependent active uptake with fungal growth inhibition at 16 g/mL after 24 h. Visualization of an Aspergillus fumigatus infection in lungs of a rat was possible with gallium-68 labelled compounds using PET/CT. Heterogeneous biodistribution patterns revealed the immense influence of the antifungal moiety conjugated to DAFC.

ConclusionOverall, novel antifungal siderophore conjugates with promising fungal growth inhibition and the possibility to perform PET-imaging, combine both therapeutic and diagnostic potential in a theranostic compound for IPA caused by Aspergillus fumigatus.

category: microbiology


title: Chemical phylogenetics of the staphylococcal quorum sensing landscape

abstract: Staphylococci utilize secreted autoinducing peptides (AIPs) to regulate group behaviour through a process called quorum sensing (QS). Here, we survey the QS interaction landscape within the Staphylococcus genus by assembling a unique compound collection, comprising all the currently known AIPs. These ribosomally synthesized and posttranslationally modified peptides (RiPPs) were obtained by chemical synthesis and mapping of their ability to modulate QS was evaluated using reporter strains of common human and animal colonizing pathogens (S. aureus, S. epidermidis, S. lugdunensis). The resulting map of >200 native QS interactions provides a holistic view of nodes that contribute to the complex signalling network within the Staphylococcus genus. This overview reveals surprising cross-species QS induction and identify the first pan-inhibitory AIP, which is then shown to attenuate MRSA induced skin infection in a mouse model. Our results expose a complex universe of possible staphylococcal interactions and provide further impetus for development of therapeutics based on QS modulators targeting antibiotic resistant pathogens.


title: Replication timing analysis in polyploid cells reveals Rif1 uses multiple mechanisms to promote underreplication in Drosophila.

abstract: Regulation of DNA replication and copy number are necessary to promote genome stability and maintain cell and tissue function. DNA replication is regulated temporally in a process known as replication timing (RT). Rif1 is key regulator of RT and has a critical function in copy number control in polyploid cells. In a previous study (Munden et al., 2018), we demonstrated that Rif1 functions with SUUR to inhibit replication fork progression and promote underreplication (UR) of specific genomic regions. How Rif1-dependent control of RT factors into its ability to promote UR is unknown. By applying a computational approach to measure RT in Drosophila polyploid cells, we show that SUUR and Rif1 have differential roles in controlling UR and RT. Our findings reveal that Rif1 functions both upstream and downstream of SUUR to promote UR. Our work provides new mechanistic insight into the process of UR and its links to RT.


title: Shared and specific functions of Arfs 1-5 at the Golgi revealed by systematic knockouts

abstract: The ADP-ribosylation factors (Arfs) are small GTPases regulating membrane traffic in the secretory pathway. They are closely related and appear to have overlapping functions, regulators, and effectors. The functional specificity of individual Arfs and the extent of redundancy in vivo are still largely unknown. We addressed these questions by CRISPR/Cas9-mediated genomic deletion of the human class I (Arfs 1 and 3) and class II (Arfs 4 and 5) Arfs, either individually or in combination. Cells lacking individual Arfs or certain combinations were viable with only a slight growth defect when lacking Arf1 or Arf4. However, Arf1 and 4, and Arf4 and 5 could not be deleted simultaneously. Hence, class I Arfs are not essential and Arf4 alone was found to be sufficient for cell viability. Remarkably, two single knockouts produced specific and distinct phenotypes. Upon deletion of Arf1, the Golgi complex was enlarged and recruitment of vesicle coats decreased, confirming a major role of Arf1 in coat formation at the Golgi. Cell lines deleted for Arf4 exhibited secretion of ER resident proteins, indicating a specific defect in coatomer-dependent ER protein retrieval by the KDEL receptors. The knockout cell lines will be a useful tool to study other Arf-dependent processes.


title: Ubiquity of the Symbiont Serratia symbiotica in the Aphid Natural Environment: Distribution, Diversity and Evolution at a Multitrophic Level

abstract: Bacterial symbioses are significant drivers of insect evolutionary ecology. However, despite recent findings that these associations can emerge from environmentally derived bacterial precursors, there is still little information on how these potential progenitors of insect symbionts circulates in the trophic systems. The aphid symbiont Serratia symbiotica represents a valuable model for deciphering evolutionary scenarios of bacterial acquisition by insects, as its diversity includes intracellular host-dependent strains as well as gut-associated strains that have retained some ability to live independently of their hosts and circulate in plant phloem sap. These strains represent a potential reservoir for the emergence of new and more intimate symbioses. Here, we conducted a field study to examine the distribution and diversity of S. symbiotica found in aphid populations, as well as in different compartments of their surrounding environment. A total of 250 aphid colonies, 203 associated insects, and 161 plant samples associated with aphid colonies were screened for S. symbiotica. Twenty percent of aphids were infected with S. symbiotica, and the symbiont includes a wide diversity of strains with varied tissue tropism corresponding to different lifestyle. We also showed that the prevalence of S. symbiotica is influenced by seasonal temperatures. For the first time, we found that S. symbiotica was present in non aphid species and in host plants, and that the prevalence of the bacterium in these samples was higher when associated aphid colonies were infected. Furthermore, phylogenetic analyses suggest the existence of horizontal transfers between the different trophic levels examined. These results provide a completely new picture of the ubiquity of an insect symbiont in nature. They suggest that ecological interactions promote the dissemination of strains that are still free-living and poorly specialized, and for which plants are a proabable reservoir for the acquisition of new bacterial partners in insects.


title: Bacteriophage Lambda RexA and RexB Functions Assist the Transition from Lysogeny to Lytic Growth

abstract: The CI and Cro repressors of bacteriophage {lambda} create a bistable switch between lysogenic and lytic growth. In {lambda} lysogens, CI repressor expressed from the PRM promoter blocks expression of the lytic promoters PL and PR to allow stable maintenance of the lysogenic state. When lysogens are induced, CI repressor is inactivated and Cro repressor is expressed from the lytic PR promoter. Cro repressor blocks PRM transcription and CI repressor synthesis to ensure that the lytic state proceeds. RexA and RexB proteins, like CI, are expressed from the PRM promoter in {lambda} lysogens; RexB is also expressed from a second promoter, PLIT, embedded in rexA. Here we show that RexA binds CI repressor and assists the transition from lysogenic to lytic growth, using both intact lysogens and defective prophages with reporter genes under control of the lytic PL and PR promoters. Once lytic growth begins, if the bistable switch does return to the immune state, RexA expression lessens the probability that it will remain there, thus stabilizing the lytic state and activation of the lytic PL and PR promoters. RexB modulates the effect of RexA and may also help establish phage DNA replication as lytic growth ensues.


title: Awareness-dependent normalization framework of visual bottom-up attention

abstract: Although bottom-up attention can improve visual performance with and without awareness, whether they are governed by a common neural computation remains unclear. Using a modified Posner paradigm with backward masking, we found that both the attention-triggered cueing effect with and without awareness displayed a monotonic gradient profile (Gaussian-like). The scope of this profile, however, was significantly wider with than without awareness. Subsequently, for each subject, the stimulus size was manipulated as their respective mean scopes with and without awareness while stimulus contrast was varied in a spatial cueing task. By measuring the gain pattern of contrast-response functions, we observed changes in the cueing effect consonant with changes in contrast gain for bottom-up attention with awareness and response gain for bottom-up attention without awareness. Our findings indicate an awareness-dependent normalization framework of visual bottom-up attention, placing a necessary constraint, namely, awareness, on our understanding of the neural computations underlying visual attention.

category: neuroscience


title: What canonical online and offline measures of statistical learning can and cannot tell us

abstract: Statistical learning (SL) allows individuals to rapidly detect regularities in the sensory environment. We replicated previous findings showing that adult participants become sensitive to the implicit structure in a continuous speech stream of repeating tri-syllabic pseudowords within minutes, as measured by standard tests in the SL literature: a target detection task and a 2AFC word recognition task. Consistent with previous findings, we found only a weak correlation between these two measures of learning, leading us to question whether there is overlap between the information captured by these two tasks. Representational similarity analysis on reaction times measured during the target detection task revealed that reaction time data reflect sensitivity to transitional probability, triplet position, word grouping, and duplet pairings of syllables. However, individual performance on the word recognition task was not predicted by similarity measures derived for any of these four features. We conclude that online detection tasks provide richer and multi-faceted information about the SL process, as compared with 2AFC recognition tasks, and may be preferable for gaining insight into the dynamic aspects of SL.


title: Independent information from PET, CSF and plasma biomarkers of tau pathology in Alzheimer's disease

abstract: PET, CSF and plasma biomarkers of tau pathology may be differentially associated with Alzheimers disease (AD) related demographic, cognitive, genetic and neuroimaging markers. We examined 771 participants with normal cognition, mild cognitive impairment or dementia from BioFINDER-2 (n=400) and ADNI (n=371). All had tau-PET ([18F]RO948 in BioFINDER-2, [18F]flortaucipir in ADNI) and CSF p-tau181 biomarkers available. Plasma p-tau181 and plasma/CSF p-tau217 were available in BioFINDER-2 only. Concordance between PET, CSF and plasma tau biomarkers ranged between 66% and 95%. Across the whole group, ridge regression models showed that increased CSF and plasma p-tau181 and p-tau217 levels were independently of tau PET associated with higher age, and APOE{varepsilon}4-carriership and A{beta}-positivity, while increased tau-PET signal in the temporal cortex was associated with worse cognitive performance and reduced cortical thickness. We conclude that biofluid and neuroimaging markers of tau pathology convey partly independent information, with CSF and plasma p-tau181 and p-tau217 levels being more tightly linked with early markers of AD (especially A{beta} pathology), while tau-PET shows the strongest associations with cognitive and neurodegenerative markers of disease progression.


title: Central nervous system infusion of TrkB agonist, 7,8-dihydroxyflavone, is ineffective in promoting myelin repair in cuprizone and experimental autoimmune encephalomyelitis mouse models of multiple sclerosis

abstract: Small molecular weight functional mimetics of brain-derived neurotrophic factor (BDNF) which act via the TrkB receptor have been developed to overcome the pharmacokinetic limitations of BDNF as a therapeutic agent for neurological disease. Activation of TrkB signalling on oligodendrocytes has been identified as a potential strategy for promoting myelin repair in demyelinating conditions such as Multiple Sclerosis (MS). Here, we tested the efficacy of intracerebroventricular infusion of TrkB agonist 7,8-dihydroxyflavone (DHF) to promote myelin repair in the cuprizone model of de- and remyelination and alter the course of experimental autoimmune encephalomyelitis (EAE), after the onset of clinical signs. In these two distinct, but common mouse models used for the preclinical testing of MS therapeutics, we found that DHF infusion increased the percentage of myelin basic protein and density of oligodendrocyte progenitor cells (OPCs) in the corpus callosum of female C57BL/6 mice after cuprizone demyelination. However, DHF did not alter the percentage of axons myelinated or increase the density of post-mitotic oligodendrocytes in this model. Direct central nervous system infusion of DHF infusion also had no effect on the clinical course of EAE in male and female C57BL/6 mice, and examination of the lumbar spinal cord after 21 days of treatment revealed extensive demyelination, with active phagocytosis of myelin debris by Iba1+ macrophages/microglia. These results indicate that direct central nervous system infusion of DHF is ineffective at promoting myelin repair in toxin-induced and inflammatory models of demyelination.


title: Structure-function interplay as signature for brain decoding and fingerprinting

abstract:
Brain signatures of functional activity have shown promising results in both decoding brain states, meaning distinguishing between different tasks, and fingerprinting, that is identifying individuals within a large group. Importantly, these brain signatures do not account for the underlying brain anatomy on which brain function takes place. Structure-function coupling based on graph signal processing (GSP) has recently revealed a meaningful spatial gradient from unimodal to transmodal regions, on average in healthy subjects during resting-state. Here, we explore the potential of GSP to introduce new imaging-based biomarkers to characterize tasks and individuals. We used multimodal magnetic resonance imaging of 100 unrelated healthy subjects from the Human Connectome Project both during rest and seven different tasks and adopted a support vector machine classification approach for both decoding and fingerprinting, with various cross-validation settings. We found that structurefunction coupling measures allow accurate classifications for both task decoding and fingerprinting. In particular, key information for fingerprinting is found in the more liberal portion of functional signals, that is the one decoupled from structure. A network mainly involving cortico-subcortical connections showed the strongest correlation with cognitive traits, assessed with partial least square analysis, corroborating its relevance for fingerprinting. By introducing a new perspective on GSP-based signal filtering and FC decomposition, these results show that brain structure-function coupling provides a new class of signatures of cognition and individual brain organization at rest and during tasks. Further, they provide insights on clarifying the role of low and high spatial frequencies of the structural connectome, leading to new understanding of where key structure-function information for characterizing individuals can be found across the structural connectome graph spectrum.

Highlights- The relation of brain function with the underlying structural wiring is complex
- We propose new structure-informed graph signal processing (GSP) of functional data
- GSP-derived features allow accurate task decoding and individual fingerprinting
- Functional connectivity from filtered data is more unique to subject and cognition
- The role of structurally aligned and liberal graph frequencies is elucidated


title: Brain structure-function coupling provides signatures for task decoding and individual fingerprinting