title: Using Deep Clustering to Improve fMRI Dynamic Functional Connectivity Analysis

abstract:
Dynamic functional connectivity (dFC) analysis of resting-state fMRI data is commonly performed by calculating sliding-window correlations (SWC), followed by k-means clustering in order to assign each window to a given state. Studies using synthetic data have shown that k-means performance is highly dependent on sliding window parameters and signal-to-noise ratio. Additionally, sources of heterogeneity between subjects may affect the accuracy of group-level clustering, thus affecting measurements of dFC state temporal properties such as dwell time and fractional occupancy. This may result in spurious conclusions regarding differences between groups (e.g. when comparing a clinical population to healthy controls). Therefore, is it important to quantify the ability of k-means to estimate dFC state temporal properties when applied to cohorts of multiple subjects, and to explore ways in which clustering performance can be maximised.

Here, we explore the use of dimensionality reduction methods prior to clustering in order to map high-dimensional data to a lower dimensional space, providing salient features to the subsequent clustering step. We assess the use of deep autoencoders for feature selection prior to applying k-means clustering to the encoded data. We compare this deep clustering method to feature selection using principle component analysis (PCA), uniform manifold approximation and projection (UMAP), as well as applying k-means to the original feature space using either L1 or L2 distance. We provide extensive quantitative evaluation of clustering performance using synthetic datasets, representing data from multiple heterogeneous subjects. In synthetic data we find that deep clustering gives the best performance, while other approaches are often insufficient to capture temporal properties of dFC states. We then demonstrate the application of each method to real-world data from human subjects and show that the choice of feature selection method has a significant effect on group-level measurements of state temporal properties. We therefore advocate for the use of deep clustering as a precursor to clustering in dFC.

category: neuroscience


title: Animal soil food web complexity triggers shifts in microbial communities, including PAH degraders, but without clear effects on phenanthrene phytoremediation

abstract:
The aim of this study was to determine whether the complexity of the animal soil food web (SFWC) is a significant factor influencing the soil microbial communities, the productivity of the willow, and the degradation rates of 100 mg kg-1 phenanthrene contamination. The SFWC treatment had eight levels: just the microbial community (BF), or the BF with nematodes (N), springtails (C), earthworms (E), CE, CN, EN, CEN. After eight weeks of growth, the height and biomass of willows were significantly affected by the SFWC, whereas the amount of phenanthrene degraded was not affected, reaching over 95% in all pots. SFWC affected the structure and the composition of the bacterial, archaeal and fungal communities, with significant effects of SFWC on the relative abundance of fungal genera such as Sphaerosporella, a known willow symbiont during phytoremediation, and bacterial phyla such as Actinobacteriota, containing many PAH degraders. These SFWC effects on microbial communities were not clearly reflected in the community structure and abundance of PAH degraders, even though some degraders related to the Actinobacteriota and the diversity of Gram-negative degraders were affected by the SFWC treatments. Overall, our results suggest that, under our experimental conditions, SFWC does not affect significantly willow phytoremediation outcomes.

ImportancePolycyclic aromatic hydrocarbons (PAH) pose a threat to soil ecosystems. Phytoremediation is a green technology that can help restore ecosystems health affected by PAH contamination. Past research on phytoremediation of PAH has focused on the roles of plant and microbes in contaminant fates. However, soil environments usually harbor large faunal communities that interact with both the plant and the microbial communities, potentially altering the phytoremediation process. We hypothesized that soil food web complexity (SFWC), represented by increasing levels of soil fauna, influences PAH degradation through interactions with the plant and the microbes. In this study, we demonstrated that SFWC increases the plant biomass and changes the composition of the microbial community, especially the fungal structure. In our pot experiment, more complex levels of SFWC did not contribute to higher degradation rates, but the increased plant biomass and the higher relative abundance of fungal genera associated with lower plant stress could indirectly contribute to better phytoremediation outcomes. Our results highlight the importance of considering the contributions of soil fauna to the success of phytoremediation.

category: microbiology


title: A putative cap binding protein and the methyl phosphate capping enzyme Bin3/MePCE function in telomerase biogenesis.

abstract: Telomerase reverse transcriptase (TERT) and the noncoding telomerase RNA (TR) subunit constitute the core of telomerase. Additional subunits are required for ribonucleoprotein complex assembly and in some cases remain stably associated with the active holoenzyme. Pof8, a member of the LARP7 protein family is such a constitutive component of telomerase in fission yeast. Using affinity purification of Pof8, we have identified two previously uncharacterized proteins that form a complex with Pof8 and participate in telomerase biogenesis. Both proteins participate in ribonucleoprotein complex assembly and are required for wildtype telomerase activity and telomere length maintenance. One factor we named Thc1 (Telomerase Holoenzyme Component 1) shares structural similarity with the nuclear cap binding complex and the poly-adenosine ribonuclease (PARN), the other is the ortholog of the methyl phosphate capping enzyme (Bin3/MePCE) in metazoans and was named Bmc1 (Bin3/MePCE 1) to reflect its evolutionary roots. Thc1 and Bmc1 function together with Pof8 in recognizing correctly folded telomerase RNA and promoting the recruitment of the Lsm2-8 complex and the catalytic subunit to assemble functional telomerase.

category: molecular biology


title: Revisiting The Role of Notch in Nephron Segmentation: Notch is required for proximal, not distal fate selection during mouse and human nephrogenesis

abstract:
Notch signaling promotes maturation of nephron epithelia, but its proposed contribution to nephron segmentation into proximal and distal domains has been called into doubt. We leveraged single cell and bulk RNA-seq, quantitative immunofluorescent lineage/fate tracing, and genetically modified human iPSC to revisit this question in developing mouse kidneys and human kidney organoids. We confirmed that Notch signaling is needed for maturation of all nephron lineages, and thus mature lineage markers fail to detect a fate bias. By contrast, early markers identified a distal fate bias in cells lacking Notch2, and a concomitant increase in early proximal and podocyte fates in cells expressing hyperactive Notch1 was observed. Orthogonal support for a conserved role for Notch signaling in the distal/proximal axis segmentation is provided by the ability of Nicastrin-deficient hiPSCs-derived organoids to differentiate into TFA2B+ distal tubule and CDH1 connecting segment progenitors, but not into HNF4A+ or LTL+ proximal progenitors.

SummaryNotch signaling acts in nephron segmentation to select early proximal, but not distal tubule fate downstream of a global role promoting epithelial growth and maturation in mouse and human.

category: developmental biology


title: Selective pressure on membrane proteins drives the evolution of Helicobacter pylori Colombian subpopulations

abstract: Helicobacter pylori have coevolved with mankind since its origins, adapting to different human groups. In America H. pylori has evolved in several subpopulations specific for regions or even countries. In this study we analyzed the genome of 163 Colombian strains along with 1,113 strains that represent worldwide H. pylori populations to better discern the ancestry and adaption to Colombian people. Population structure was inferred with FineStructure and chromosome painting identifying the proportion of ancestries in Colombian isolates. Phylogenetic relationship was analyzed using the SNPs present in the core genome. Also, a Fst analysis was done to identify the gene variants with the strongest fixation in the identified Colombian subpopulations in relation to their parent population hspSWEurope. Worldwide, population structure analysis allowed the identification of two Colombian subpopulations, the previously described hspSWEuropeColombia and a novel subpopulation named hspColombia. In addition, three subgroups of H. pylori were identified within hspColombia that follow their geographic origin. The Colombian H. pylori subpopulations represent an admixture of European, African and Native indigenous ancestry; although some genomes showed a high proportion of self-identity, suggesting a strong adaption to these mestizo Colombian groups. The Fst analysis identified 82 SNPs significantly fixed in 26 genes of the hspColombia subpopulation that encode mainly for outer membrane proteins and proteins involved in central metabolism. The strongest fixation indices were identified in genes encoding the membrane proteins HofC, HopE, FrpB-4 and Sialidase A. These findings demonstrate that H. pylori has evolved in Colombia to give rise to subpopulations following a geographical structure, evolving to an autochthonous genetic pool, drive by a positive selective pressure especially on genes encoding for outer membrane proteins.

category: genomics


title: PHASE: A MATLAB Based Program for the Analysis of Drosophila Phase, Activity, and Sleep under Entrainment

abstract: The problem of entrainment is central to circadian biology. In this regard, Drosophila has been an important model system. Owing to the simplicity of its nervous system and the availability of powerful genetic tools, the system has shed significant light on the molecular and neural underpinnings of entrainment. However, much remains to be learned regarding the molecular and physiological mechanisms underlying this important phenomenon. Under cyclic light/dark conditions, Drosophila melanogaster displays crepuscular patterns of locomotor activity with one peak anticipating dawn and the other anticipating dusk. These peaks are characterized through an estimation of their phase relative to the environmental light cycle and the extent of their anticipation of light transitions. In Drosophila chronobiology, estimations of phases are often subjective, and anticipation indices vary significantly between studies. Though there is increasing interest in building flexible analysis software tools in the field, none incorporates objective measures of Drosophila activity peaks in combination with the analysis of fly activity/sleep in the same program. To this end, we have developed PHASE, a MATLAB-based program that is simple and easy to use and (i) supports the visualization and analysis of activity and sleep under entrainment, (ii) allows analysis of both activity and sleep parameters within user-defined windows within a diurnal cycle, (iii) uses a smoothing filter for the objective identification of peaks of activity (and therefore can be used to quantitatively characterize them), and (iv) offers a series of analyses for the assessment of behavioral anticipation of environmental transitions.

category: animal behavior and cognition


title: Wavelength-dependent DNA photodamage in a 3-D human skin model over the far-UVC and germicidal-UVC wavelength ranges from 215 to 255 nm

abstract: The effectiveness of UVC to reduce airborne-mediated disease transmission is well-established. However conventional germicidal UVC (~254 nm) cannot be used directly in occupied spaces because of the potential for damage to the skin and eye. A recently studied alternative with the potential to be used directly in occupied spaces is far-UVC (200 to 235 nm, typically 222 nm), as it cannot penetrate to the key living cells in the epidermis. Optimal far-UVC use is hampered by limited knowledge of the precise wavelength dependence of UVC-induced DNA damage, and thus we have used a monochromatic UVC exposure system to assess wavelength-dependent DNA damage in a realistic 3-D human skin model. We exposed a 3-D human skin model to mono-wavelength UVC exposures of 100 mJ/cm2, at UVC wavelengths from 215 to 255 nm (5-nm steps). At each wavelength we measured yields of DNA-damaged keratinocytes, and their distribution within the layers of the epidermis. No increase in DNA damage was observed in the epidermis at wavelengths from 215 to 235 nm, but at higher wavelengths (240-255 nm) significant levels of DNA damage were observed. These results support use of far-UVC light to safely reduce the risk of airborne disease transmission in occupied locations.

category: biophysics


title: Sampling motion trajectories during hippocampal theta sequences

abstract: Efficient planning in complex environments requires that uncertainty associated with current inferences and possible consequences of forthcoming actions is represented. Representation of uncertainty has been established in sensory systems during simple perceptual decision making tasks but it remains unclear if complex cognitive computations such as planning and navigation are also supported by probabilistic neural representations. Here we capitalized on gradually changing uncertainty along planned motion trajectories during hippocampal theta sequences to capture signatures of uncertainty representation in population responses. In contrast with prominent theories, we found no evidence of encoding parameters of probability distributions in the momentary population activity recorded in an open-field navigation task in rats. Instead, uncertainty was encoded sequentially by sampling motion trajectories randomly in subsequent theta cycles from the distribution of potential trajectories. Our analysis is the first to demonstrate that the hippocampus is well equipped to contribute to optimal planning by representing uncertainty.


title: A glyphosate-based herbicide cross-selects for antibiotic resistance genes in bacterioplankton communities

abstract:
Agrochemicals often contaminate freshwater bodies, affecting microbial communities that underlie aquatic food webs. For example, Roundup, a widely-used glyphosate-based herbicide (GBH), has the potential to indirectly select for antibiotic resistant bacteria. Such cross-selection could occur, for example, if the same genes (e.g. encoding efflux pumps) confer resistance to both glyphosate and antibiotics. To test for cross-resistance in natural aquatic bacterial communities, we added Roundup to 1,000-L mesocosms filled with water from a pristine lake. Over 57 days, we tracked changes in bacterial communities with shotgun metagenomic sequencing, and annotated metagenome-assembled genomes (MAGs) for the presence of known antibiotic resistance genes (ARGs), plasmids, and resistance mutations in the enzyme targeted by glyphosate (enolpyruvyl-shikimate-3-phosphate synthase; EPSPS). We found that high doses of GBH significantly increased ARG frequency and selected for multidrug efflux pumps in particular. The relative abundance of MAGs after a high dose of GBH was predictable based on the number of ARGs encoded in their genomes (17% of variation explained) and, to a lesser extent, by resistance mutations in EPSPS. Together, these results indicate that GBHs have the potential to cross-select for antibiotic resistance in natural freshwater bacteria.

IMPORTANCEGlyphosate-based herbicides (GBHs) such as Roundup may have the unintended consequence of selecting for antibiotic resistance genes (ARGs), as demonstrated in previous experiments. However, the effects of GBHs on ARGs remains unknown in natural aquatic communities, which are often contaminated with pesticides from agricultural runoff. Moreover, the resistance provided by ARGs compared to canonical mutations in the glyphosate target enzyme, EPSPS, remains unclear. Here we used freshwater mesocosm experiments to show that GBHs strongly select for ARGs, particularly multidrug efflux pumps. These selective effects are evident after just a few days, and at glyphosate concentrations that are high but still within short-term (1-4 day) regulatory limits. The ability of bacteria to survive and thrive after GBH stress was predictable by the number of ARGs in their genomes, and to a lesser extent by mutations in EPSPS. GBHs are therefore likely to select for higher ARG frequencies in natural streams, lakes, and ponds.


title: Swift Formation of Optimal Single Spheroids towards In-Vitro 3-Dimensional Tumour Models

abstract: Monolayer cell culture, while useful for basic in vitro studies, are not physiologically relevant. Spheroids, on the other hand provide a more complex 3-dimensional (3D) structure which more resemble the in vivo tumour growth thereby allowing results obtained with those on proliferation, cell death, differentiation, metabolism, and various anti-tumour therapies to be more predictive of in vivo outcomes. However, the cost associated with their generation often involve expensive, plate, media, and growth supplements, which have limited their use for high throughput experiments. The protocol herein presents a novel and rapid generation for single spheroids of various cancer cell lines, U87 MG; SEBTA-027; SF188, brain cancer cells, DU-145, TRAMP-C1, prostate cancer cells, in 96-round bottom well plates. Cells are washed with anti-adherent solution, and the homogeneous compact spheroid morphology was evidenced as early as 24 hours after 10 minutes centrifugation for the seeded cells. By using confocal microscopy, the proliferating cells were traced in the rim and the dead cells were found inside the core region of the spheroid. The H&E stain of spheroid slices and the western blotting were utilised to investigate the tightness of the cell packaging by adhesion proteins. Carnosine was used as an example of treatment for U87 single spheroids. The protocol allows the rapid generation of spheroids, which will help towards reducing the number of tests performed on animals.

category: cell biology


title: Clustering and visualization of single-cell RNA-seq data using path metrics

abstract:
Recent advances in single-cell technologies have enabled high-resolution characterization of tissue and cancer compositions. Although numerous tools for dimension reduction and clustering are available for single-cell data analyses, these methods often fail to simultaneously preserve local cluster structure and global data geometry. This article explores the application of power-weighted path metrics for the analysis of single cell RNA data.

Extensive experiments on single cell RNA sequencing data sets confirm the usefulness of path metrics for dimension reduction and clustering. Distances between cells are measured in a data-driven way which is both density sensitive (decreasing distances across high density regions) and respects the underlying data geometry. By combining path metrics with multidimensional scaling, a low dimensional embedding of the data is obtained which respects both the global geometry of the data and preserves cluster structure. We evaluate the method both for clustering quality and geometric fidelity, and it outperforms other algorithms on a wide range of bench marking data sets.


title: An RNA-binding switch drives ribosome biogenesis and tumorigenesis downstream of RAS oncogene

abstract: Oncogenic RAS signaling reprograms gene expression through both transcriptional and post-transcriptional mechanisms. While transcriptional regulation downstream of RAS is relatively well characterized, how RAS post-transcriptionally modulates gene expression to promote malignancy is largely unclear. Using quantitative RNA Interactome Capture analysis, we reveal that oncogenic RAS signaling reshapes the RNA-bound proteomic landscape of cancer cells, with a network of nuclear proteins centered around Nucleolin displaying enhanced RNA-binding activity. We show that Nucleolin is phosphorylated downstream of RAS, which increases its binding to pre-ribosomal-RNA (rRNA), boosts rRNA production, and promotes ribosome biogenesis. This Nucleolin-dependent enhancement of ribosome biogenesis is crucial for RAS-induced cancer cell proliferation, and can be targeted therapeutically to inhibit tumor growth. Our results reveal that oncogenic RAS signaling drives ribosome biogenesis by regulating the RNA-binding activity of Nucleolin, and highlight the crucial role of this process in RAS-mediated tumorigenesis.

category: cancer biology


title: The phospho-docking protein 14-3-3 regulates microtubule-associated proteins in oocytes including the chromosomal passenger Borealin

abstract:
Global regulation of spindle-associated proteins is crucial in oocytes due to the absence of centrosomes and their very large cytoplasmic volume, but little is known about how this is achieved beyond involvement of the Ran-importin pathway. We previously uncovered a novel regulatory mechanism in Drosophila oocytes, in which the phospho-docking protein 14-3-3 suppresses microtubule binding of Kinesin-14/Ncd away from chromosomes. Here we report systematic identification of microtubule-associated proteins regulated by 14-3-3 from Drosophila oocytes. Proteins from ovary extract were co-sedimented with microtubules in the presence or absence of a 14-3-3 inhibitor. Through quantitative mass-spectrometry, we identified proteins or complexes whose ability to binding microtubules is suppressed by 14-3-3, including the chromosomal passenger complex (CPC), the centralspindlin complex and Kinesin-14/Ncd. We showed that 14-3-3 binds to the disordered region of Borealin, and this binding is regulated differentially by two phosphorylations on Borealin. Mutations at these two phospho-sites compromised normal Borealin localisation and centromere bi-orientation in oocytes, showing that phospho-regulation of 14-3-3 binding is important for Borealin localisation and function. The mass spectrometry data are available from ProteomeXchange, identifier <ID to be provided when available, PXD000xxx>.

Author SummaryAccurate segregation of chromosomes during cell division is fundamental for genome stability. Chromosome segregation is mediated by the spindle, which is made of dynamic microtubules and associated proteins that regulate microtubule behaviour. How these microtubule-associated proteins are regulated is not well understood. Furthermore, as oocytes have an exceptionally large volume of cytoplasm and lack centrosomes, regulation of microtubule-associated proteins is especially crucial for organisation and function of the meiotic spindle. In this study, we showed that 14-3-3, a protein that binds to phosphorylated proteins, plays an important role to regulate multiple microtubule-associated proteins in fly oocytes. The regulated proteins include subunits of the conserved kinase complex called the chromosomal passenger complex. We further found that interaction of one of the subunits with 14-3-3 is regulated by two phosphorylations, and that these phosphorylations are important for localisation and function of this subunit. As these proteins are widely conserved including humans, this study may provide an insight into chromosome mis-segregation in human oocytes, which is very frequent and a major cause of human infertility, miscarriages and congenital birth conditions.


title: Mitotic spindle formation in the absence of Polo kinase

abstract: Mitosis is a fundamental process in every eukaryote, in which chromosomes are segregated into two daughter cells by the action of the microtubule (MT)-based spindle. Despite this common principle, genes essential for mitosis are variable among organisms. This indicates that the loss of essential genes or bypass-of-essentiality (BOE) occurred multiple times during evolution. While many BOE relationships have been recently revealed experimentally, the BOE of mitosis regulators (BOE-M) has been scarcely reported and how this occurs remains largely unknown. Here, by mutagenesis and subsequent evolutionary repair experiments, we isolated viable fission yeast strains that lacked the entire coding region of Polo-like kinase (Plk), a versatile essential mitotic kinase. The BOE of Plk was enabled by specific mutations in the downstream machinery, including the MT-nucleating {gamma}-tubulin complex, and more surprisingly, through downregulation of glucose uptake, which is not readily connected to mitosis. The latter bypass was dependent on casein kinase I (CK1), which has not been considered as a major mitotic regulator. Our genetic and phenotypic data suggest that CK1 constitutes an alternative mechanism of MT nucleation, which is normally dominated by Plk. A similar relationship was observed in a human colon cancer cell line. Thus, our study shows that BOE-M can be achieved by simple genetic or environmental changes, consistent with the occurrence of BOE-M during evolution. Furthermore, the identification of BOE-M constitutes a powerful means to uncover a hitherto under-studied mechanism driving mitosis and also hints at the limitations and solutions for selecting chemotherapeutic compounds targeting mitosis.


title: RB1 loss triggers dependence on ESRRG in retinoblastoma

abstract: Retinoblastoma (Rb) is a deadly childhood eye cancer that is classically initiated by inactivation of the RB1 tumor suppressor. Clinical management continues to rely on nonspecific chemotherapeutic agents that are associated with treatment resistance and toxicity. Here, we analyzed 103 whole exomes, 16 whole transcriptomes, 5 single-cell transcriptomes, and 4 whole genomes from primary Rb tumors to identify novel Rb dependencies. Several recurrent genomic aberrations implicate estrogen-related receptor gamma (ESRRG) in Rb pathogenesis. RB1 directly interacts with and inhibits ESRRG, and RB1 loss uncouples ESRRG from negative regulation. ESRRG regulates genes involved in retinogenesis and oxygen metabolism in Rb cells. ESRRG is preferentially expressed in hypoxic Rb cells in vivo. Depletion or inhibition of ESRRG causes marked Rb cell death which is exacerbated in hypoxia. These findings reveal a novel dependency of Rb cells on ESRRG, and they implicate ESRRG as a potential therapeutic vulnerability in Rb.


title: Loss of Cohesin regulator PDS5A reveals repressive role of Polycomb loops

abstract: Polycomb Repressive Complexes 1 and 2 (PRC1, PRC2) are conserved epigenetic regulators that promote transcriptional silencing. PRC1 and PRC2 converge on shared targets, catalyzing repressive histone modifications. In addition, a subset of PRC1/PRC2 targets engage in long-range interactions whose functions in gene silencing are poorly understood. Using a CRISPR screen in mouse embryonic stem cells, we identified that the cohesin regulator PDS5A links transcriptional silencing by Polycomb and 3D genome organization. PDS5A deletion impairs cohesin unloading and results in derepression of subset of endogenous PRC1/PRC2 target genes. Importantly, derepression is not associated with loss of repressive Polycomb chromatin modifications. Instead, loss of PDS5A leads to aberrant cohesin activity, ectopic insulation sites and specific reduction of ultra-long Polycomb loops. We infer that these loops are important for robust silencing at a subset of Polycomb target genes and that maintenance of cohesin-dependent genome architecture is critical for Polycomb regulation.


title: Non-rapid eye movement sleep and wake neurophysiology in schizophrenia

abstract: Motivated by the potential of objective neurophysiological markers to index thalamocortical function in patients with severe psychiatric illnesses, we comprehensively characterized key NREM sleep parameters across multiple domains, their interdependencies, and their relationship to waking event-related potentials and symptom severity. In 130 schizophrenia (SCZ) patients and controls, we confirmed a marked reduction in sleep spindle density in SCZ and extended these findings to show that only slow spindles predicted symptom severity, and that fast and slow spindle properties were largely uncorrelated. We also describe a novel measure of slow oscillation and spindle interaction that was attenuated in SCZ. The main sleep findings were replicated in a demographically distinct sample, and a joint model, based on multiple NREM components, predicted disease status in the replication cohort. Although also altered in patients, auditory event-related potentials elicited during wake were unrelated to NREM metrics. Consistent with a growing literature implicating thalamocortical dysfunction in SCZ, our characterization identifies independent NREM and wake EEG biomarkers that may index distinct aspects of SCZ pathophysiology and point to multiple neural mechanisms underlying disease heterogeneity. This study lays the groundwork for evaluating these neurophysiological markers, individually or in combination, to guide efforts at treatment and prevention as well as identifying individuals most likely to benefit from specific interventions.


title: Cortical Temporal Integration Window for Binaural Cues accounts for Sluggish Auditory Spatial Perception

abstract: The auditory system has exquisite temporal coding in the periphery which is transformed into a rate-based code in central auditory structures like auditory cortex. However, the cortex is still able to synchronize, albeit at lower modulation rates, to acoustic fluctuations. The perceptual significance of this cortical synchronization is unknown. We estimated physiological synchronization limits of cortex (in humans with electroencephalography) and brainstem neurons (in chinchillas) to dynamic binaural cues using a novel system-identification technique, along with parallel perceptual measurements. We find that cortex can synchronize to dynamic binaural cues up to approximately 10 Hz, which aligns well with our measured limits of perceiving dynamic spatial information and utilizing dynamic binaural cues for spatial unmasking, i.e. measures of binaural sluggishness. We also find the tracking limit for frequency modulation (FM) is similar to the limit for spatial tracking, demonstrating that this sluggish tracking is a more general perceptual limit that can be accounted for by cortical temporal integration limits.


title: Sensory suppression and increased neuromodulation during actions disrupt memory encoding of unpredictable self-initiated stimuli

abstract: Actions modulate sensory processing by attenuating responses to self- compared to externally-generated inputs, which is traditionally attributed to stimulus-specific motor predictions. Yet, suppression has been also found for stimuli merely coinciding with actions, pointing to unspecific processes that may be driven by neuromodulatory systems. Meanwhile, the differential processing for self-generated stimuli raises the possibility of producing effects also on memory for these stimuli, however, evidence remains mixed as to the direction of the effects. Here, we assessed the effects of actions on sensory processing and memory encoding of concomitant, but unpredictable sounds, using a combination of self-generation and memory recognition task concurrently with EEG and pupil recordings. At encoding, subjects performed button presses that half of the time generated a sound (motor-auditory; MA) and listened to passively presented sounds (auditory-only; A). At retrieval, two sounds were presented and participants had to respond which one was present before. We measured memory bias and memory performance by having sequences where either both or only one of the test sounds were presented at encoding, respectively. Results showed worse memory performance - but no differences in memory bias - and attenuated responses and larger pupil diameter for MA compared to A sounds. Critically, the larger the sensory attenuation and pupil diameter, the worse the memory performance for MA sounds. Nevertheless, sensory attenuation did not correlate with pupil dilation. Collectively, our findings suggest that sensory attenuation and neuromodulatory processes coexist during actions, and both relate to disrupted memory for concurrent, albeit unpredictable sounds.


title: An explainable self-attention deep neural network for detecting mild cognitive impairment using multi-inputbdigital drawing tasks

abstract: Mild cognitive impairment (MCI) is an early stage of age-inappropriate cognitive decline, which could develop into dementia - an untreatable neurodegenerative disorder. An early detection of MCI is a crucial step for timely prevention and intervention. To tackle this problem, recent studies have developed deep learning models to detect MCI and various types of dementia using data obtained from the classic clock-drawing test (CDT), a popular neuropsychological screening tool that can be easily and rapidly implemented for assessing cognitive impairments in an aging population. While these models succeed at distinguishing severe forms of dementia, it is still difficult to predict the early stage of the disease using the CDT data alone. Also, the state-of-the-art deep learning techniques still face the black-box challenges, making it questionable to implement them in the clinical setting. Here, we propose a novel deep learning modeling framework that incorporates data from multiple drawing tasks including the CDT, cube-copying, and trail-making tasks obtained from a digital platform. Using self-attention and soft-label methods, our model achieves much higher classification performance at detecting MCI compared to those of a well-established convolutional neural network model. Moreover, our model can highlight features of the MCI data that considerably deviate from those of the healthy aging population, offering accurate predictions for detecting MCI along with visual explanation that aids the interpretation of the deep learning model.


title: Clemastine induces an impairment in developmental myelination

abstract: Abnormalities in myelination are associated to behavioral and cognitive dysfunction in neurodevelopmental psychiatric disorders. Thus, therapies to promote or accelerate myelination could potentially ameliorate symptoms in autism. Clemastine, a histamine H1 antagonist with anticholinergic properties against muscarinic M1 receptor, is the most promising drug with promyelinating properties (Mei et al., 2014). Clemastine penetrates the blood brain barrier efficiently and promotes remyelination in different animal models of neurodegeneration including multiple sclerosis, ischemia and Alzheimers disease. However, its role in myelination during development is unknown. We showed that clemastine treatment during development increase oligodendrocyte differentiation in both white and gray matter. However, despite the increase in the number of oligodendrocytes, conduction velocity of myelinated fibers of corpus callosum decreased in clemastine treated mice. Confocal and electron microscopy showed a reduction in the number of myelinated axons and nodes of Ranvier and a reduction of myelin thickness in corpus callosum. To understand the mechanisms leading to myelin formation impairment in the presence of an excess of myelinating oligodendrocytes, we focused on microglial cells which also express muscarinic M1 receptors. Importantly, the population of CD11c+microglia cells, necessary for myelination, as well as the levels of insulin growth factor-1 decrease in clemastine-treated mice. Altogether, these data suggest that clemastine impact on myelin development is more complex than previously thought and could be dependent on microglia-oligodendrocyte crosstalk. Further studies are needed to clarify the role of microglia cells on developmental myelination.


title: Opposing regulation of short-term memory by basal ganglia direct and indirect pathways that are coactive during behavior

abstract: The basal ganglia direct and indirect pathways are viewed to mediate opposing functions in movement. However, this classic model is challenged by recent findings that both pathways are coactive during behavior. We examined the roles of direct (dSPNs) and indirect (iSPNs) pathway spiny projection neurons in a decision-making task with a short-term memory (STM) component. Optogenetic stimulation of cortical-input-defined dSPNs and iSPNs during STM oppositely biased upcoming licking choice, without affecting licking execution. Optogenetically identified dSPNs and iSPNs showed similar response patterns, although with quantitative difference in spatiotemporal organization. To understand how coactive dSPNs and iSPNs play opposing roles, we recorded population activity in frontal cortex and the basal ganglia output nucleus SNr. Stimulation of dSPNs and iSPNs bidirectionally regulated cortical decision variable through the differential modulation of SNr ramping activity. These results reconcile different views by demonstrating that coactive dSPNs and iSPNs precisely shape cortical activity in a push-pull balance.


title: Astrocytes in the dorsal vagal complex are not activated by systemic glucoprivation and their chemogenetic activation does not elicit homeostatic glucoregulatory responses in mice

abstract: The dorsal vagal complex (DVC) is a brainstem site regulating diverse aspects of physiology including food intake and blood glucose homeostasis. Astrocytes are purported to play an active role in regulating DVC function and, by extension, physiological parameters. Previous work has demonstrated that DVC astrocytes directly sense hormones that regulate food intake and blood glucose and are critical for their effect. In addition, DVC astrocytes in ex vivo slices respond to low tissue glucose. The response of neurons, including catecholaminergic neurons, to low glucose is conditional on intact astrocyte signalling in slice preparations suggesting astrocytes are possibly the primary sensors of glucose deprivation (glucoprivation). Based on these findings we hypothesised that if DVC astrocytes act as glucoprivation sensors in vivo they would both show a response to systemic glucoprivation and drive physiological responses to restore blood glucose. We found that 2 hours of systemic glucoprivation induced neither FOS nor glial fibrillary acidic protein (GFAP)-immunoreactivity in DVC astrocytes, specifically those in the nucleus of the solitary tract (NTS). Furthermore, we found that while chemogenetic activation of DVC astrocytes suppressed food intake by reducing both meal size and meal number, this manipulation also suppressed food intake under conditions of glucoprivation. Chemogenetic activation of DVC astrocytes did not increase basal blood glucose nor protect against insulin-induced hypoglycaemia. In male mice chemogenetic DVC astrocyte activation did not alter glucose tolerance, in female mice the initial glucose excursion was reduced, suggesting enhanced glucose absorption. Taken together this suggests that as a whole-population DVC astrocytes do not function as glucoprivation sensors in vivo in mice. Instead, we propose that DVC astrocytes play an indispensable, homeostatic role to maintain the function of glucoregulatory neuronal circuitry.


title: Neural Readout of a Latency Code in the Active Electrosensory System

abstract: The latency of spikes relative to a stimulus conveys sensory information across modalities. However, in most cases it remains unclear whether and how such latency codes are utilized by postsynaptic neurons. In the active electrosensory system of mormyrid fish, a latency code for stimulus amplitude in electroreceptor afferent nerve fibers (EAs) is hypothesized to be read out by a central reference provided by motor corollary discharge (CD). Here we demonstrate that CD enhances sensory responses in postsynaptic granular cells of the electrosensory lobe, but is not required for reading out EA input. Instead, diverse latency and spike count tuning across the EA population gives rise to graded information about stimulus amplitude that can be read out by standard integration of converging excitatory synaptic inputs. Inhibitory control over the temporal window of integration renders two granular cell subclasses differentially sensitive to information derived from relative spike latency versus spike count.


title: A reusable benchmark of brain-age prediction from M/EEG resting-state signals

abstract:
Population-level modeling can define quantitative measures of individual aging by applying machine learning to large volumes of brain images. These measures of brain age, obtained from the general population, helped characterize disease severity in neurological populations, improving estimates of diagnosis or prognosis. Magnetoencephalography (MEG) and Electroencephalography (EEG) have the potential to further generalize this approach towards prevention and public health by enabling assessments of brain health at large scales in socioeconomically diverse environments. However, more research is needed to define methods that can handle the complexity and diversity of M/EEG signals across diverse real-world contexts. To catalyse this effort, here we propose reusable benchmarks of competing machine learning approaches for brain age modeling. We benchmarked popular classical machine learning pipelines and deep learning architectures previously used for pathology decoding or brain age estimation in 4 international M/EEG cohorts from diverse countries and cultural contexts, including recordings from more than 2500 participants. Our benchmarks were built on top of the M/EEG adaptations of the BIDS standard, providing tools that can be applied with minimal modification on any M/EEG dataset provided in the BIDS format. Our results suggest that, regardless of whether classical machine learning or deep learning was used, the highest performance was reached by pipelines and architectures involving spatially aware representations of the M/EEG signals, leading to R^2 scores between 0.60-0.71. Hand-crafted features paired with random forest regression provided robust benchmarks even in situations in which other approaches failed. Taken together, this set of benchmarks, accompanied by open-source software and high-level Python scripts, can serve as a starting point and quantitative reference for future efforts at developing M/EEG-based measures of brain aging. The generality of the approach renders this benchmark reusable for other related objectives such as modeling specific cognitive variables or clinical endpoints.

Highlights- We provide systematic reusable benchmarks for brain age from M/EEG signals
- The benchmarks were carried out on M/EEG from four countries > 2500 recordings
- We compared machine learning pipelines capable of handling the non-linear regression task of relating biomedical outcomes to M/EEG dynamics, based on classical machine learning and deep learning
- Next to data-driven methods we benchmarked template-based source localization as a practical tool for generating features less affected by electromagnetic field spread
- The benchmarks are built on top of the MNE ecosystem and the braindecode package and can be applied on any M/EEG dataset presented in the BIDS format


title: Identifying Uncertainty States during Wayfinding in Indoor Environments: An EEG Classification Study

abstract: The researchers used a machine-learning classification approach to better understand neurological features associated with periods of wayfinding uncertainty. The participants (n=30) were asked to complete wayfinding tasks of varying difficulty in a virtual reality (VR) hospital environment. Time segments when participants experienced navigational uncertainty were first identified using a combination of objective measurements (frequency of inputs into the VR controller) and behavioral annotations from two independent observers. Uncertainty time-segments during navigation were ranked on a scale from 1 (low) to 5 (high). The machine-learning model, a random forest classifier implemented using scikit-learn in Python, was used to evaluate common spatial patterns of EEG spectral power across the theta, alpha, and beta bands associated with the researcher-identified uncertainty states. The overall predictive power of the resulting model was 0.70 in terms of the area under the Receiver Operating Characteristics curve (ROC-AUC). These findings indicate that EEG data can potentially be used as a metric for identifying navigational uncertainty states, which may provide greater rigor and efficiency in studies of human responses to architectural design variables and wayfinding cues.


title: Leukocyte cytokine responses in adult patients with mitochondrial DNA defects

abstract: Patients with oxidative phosphorylation (OxPhos) defects causing mitochondrial diseases appear particularly vulnerable to infections. Although OxPhos defects modulate cytokine production in vitro and in animal models, little is known about how circulating leukocytes of patients with inherited mitochondrial DNA (mtDNA) defects respond to acute immune challenges. In a small cohort of healthy controls (n=21) and patients (n=12) with either the m.3243A>G mutation or single, large-scale mtDNA deletions, we examined: i) cytokine responses (IL-6, TNF-, IL-1{beta}) in response to acute lipopolysaccharide (LPS) exposure, and ii) sensitivity to the immunosuppressive effects of glucocorticoid signaling (dexamethasone) on cytokine production. In dose-response experiments to determine the half-maximal effective LPS concentration (EC50), relative to controls, leukocytes from patients with mtDNA deletions showed 74 - 79% lower responses for IL-6 and IL-1{beta} (pIL-6=0.031, pIL-1{beta}=0.009). Moreover, IL-6 response to LPS in presence of GC was also blunted in cells from patients with mtDNA deletions (pIL-6=0.006), but not in leukocytes from patients with the m.3243A>G mutation. Overall, these ex vivo data provide preliminary evidence that some systemic OxPhos defects may compromise immune cytokine responses and glucocorticoid sensitivity. Further work in larger cohorts is needed to define the nature of immune dysregulation in patients with mitochondrial disease, and their potential implications for disease phenotypes.

category: immunology


title: Age determination through DNA methylation patterns of fingernails and toenails

abstract: Over the past decade, age prediction based on DNA methylation has become a vastly investigated topic; many age prediction models have been developed based on different DNAm markers and using various tissues. However, the potential of using nails to this end has not yet been explored. Their inherent resistance to decay and ease of sampling would offer an advantage in cases where post-mortem degradation poses challenges concerning sample collection and DNA-extraction. In the current study, clippings from both fingernails and toenails were collected from 108 living test subjects (age range: 0 - 96 years). The methylation status of 15 CpGs located in 4 previously established age-related markers (ASPA, EDARADD, PDE4C, ELOVL2) was investigated through pyrosequencing of bisulphite converted DNA. Significant dissimilarities in methylation levels were observed between all four limbs, hence limb-specific age prediction models were developed using ordinary least squares, weighted least squares and quantile regression analysis. When applied to their respective test sets, these models yielded a mean absolute deviation between predicted and chronological age ranging from 6.71 to 8.48 years. In addition, the assay was tested on methylation data derived from 5 nail samples collected from deceased individuals, demonstrating its feasibility for application in post-mortem cases. In conclusion, this study provides the first proof that chronological age can be assessed through DNA methylation patterns in nails.

category: genetics


title: Simple contextual cueing prevents retroactive interference in short-term perceptual training of orientation detection tasks

abstract: Perceptual training of multiple tasks suffers from interference between the trained tasks. Here, we conducted four psychophysical experiments with separate groups of participants to investigate the possibility of preventing the interference in short-term perceptual training. We trained the participants to detect two orientations of Gabor stimuli in two adjacent days at the same retinal location and examined the interference of training effects between the two orientations. The results showed significant retroactive interference from the second orientation to the first orientation (Experiments 1 and 2). Introducing a 6-hour interval between the pre-test and training of the second orientation did not eliminate the interference effect, excluding the interpretation of disrupted reconsolidation as the pre-test of the second orientation may reactivate and destabilize the representation of the first orientation (Experiment 3). Finally, the training of the two orientations was accompanied by fixations in two colors, each served as a contextual cue for one orientation. The results showed that the retroactive interference was not evident after introducing these passively perceived contextual cues (Experiment 4). Our findings suggest that the retroactive interference effect in short-term perceptual training of orientation detection tasks was likely the result of higher-level factors such as shared contextual cues embedded in the tasks. The effect of multiple perceptual training could be facilitated by associating the trained tasks with different contextual cues.


title: Attention enhances category representations across the brain with strengthened residual correlations to ventral temporal cortex

abstract: How does attention enhance neural representations of goal-relevant stimuli while suppressing representations of ignored stimuli across regions of the brain? While prior studies have shown that attention enhances visual responses, we lack a cohesive understanding of how selective attention modulates visual representations across the brain. Here, we used functional magnetic resonance imaging (fMRI) while participants performed a selective attention task on superimposed stimuli from multiple categories and used a data-driven approach to test how attention affects both decodability of category information and residual correlations (after regressing out stimulus-driven variance) with category-selective regions of ventral temporal cortex (VTC). Our data reveal three main findings. First, when two objects are simultaneously viewed, the category of the attended object can be decoded more readily than the category of the ignored object, with the greatest attentional enhancements observed in occipital and temporal lobes. Second, after accounting for the response to the stimulus, the correlation in the residual brain activity between a cortical region and a category-selective region of VTC was elevated when that regions preferred category was attended vs. ignored, and more so in the right occipital, parietal, and frontal cortices. Third, we found that the stronger the residual correlations between a given region of cortex and VTC, the better visual category information could be decoded from that region. These findings suggest that heightened residual correlations by selective attention may reflect the sharing of information between sensory regions and higher-order cortical regions to provide attentional enhancement of goal-relevant information.


title: Shape variability of the central sulcus in the developing brain: a longitudinal descriptive and predictive study in preterm infants.

abstract:
Despite growing evidence of links between sulcation and function in the adult brain, the folding dynamics, occurring mostly before normal-term-birth, is vastly unknown. Looking into the development of cortical sulci in babies can give us keys to address fundamental questions: what is the sulcal shape variability in the developing brain? When are the shape features encoded? How are these morphological parameters related to further functional development?

In this study, we aimed to investigate the shape variability of the developing central sulcus, which is the frontier between the primary somatosensory and motor cortices. We studied a cohort of 71 extremely preterm infants scanned twice using MRI - once around 30 weeks post-menstrual age (w PMA) and once at term-equivalent age, around 40w PMA -, in order to quantify the sulcuss shape variability using manifold learning, regardless of age-group or hemisphere. We then used these shape descriptors to evaluate the sulcuss variability at both ages and to assess hemispheric and age- group specificities. This led us to propose a description of ten shape features capturing the variability in the central sulcus of preterm infants. Our results suggested that most of these features (8/10) are encoded as early as 30w PMA. We unprecedentedly observed hemispheric asymmetries at both ages, and the one captured at term-equivalent age seems to correspond with the asymmetry pattern previously reported in adults. We further trained classifiers in order to explore the predictive value of these shape features on manual performance at 5 years of age (handedness and fine motor outcome). The central sulcuss shape alone showed a limited but relevant predictive capacity in both cases. The study of sulcal shape features during early neurodevelopment may participate to a better comprehension of the complex links between morphological and functional organization of the developing brain.

Highlights- Shape features can be isolated to describe quantitatively the development of the central sulcus.
- Most shape characteristics of the central sulcus are already encoded at 30 weeks of post-menstrual age (w PMA) in preterm newborns.
- The central sulcus shows subtle hemispheric asymmetries as soon as 30w PMA.
- The early shape of the central sulcus can help predicting handedness and fine motor outcome at 5 years of age.


title: Disrupting inferior frontal cortex activity alters affect decoding efficiency from clear but not from ambiguous affective speech

abstract:
The evaluation of socio-affective sound information is accomplished by the primate neural auditory cortex in collaboration with limbic and inferior frontal brain nodes. For the latter, activity in inferior frontal cortex (IFC) is often observed during classification of voice sounds, especially if they carry affective information. Partly opposing views have been proposed, with IFC either coding cognitive processing challenges in case of sensory ambiguity or representing categorical object and affect information for clear vocalizations. Here, we presented clear and ambiguous affective speech to two groups of human participants during neuroimaging, while in one group we inhibited right IFC activity with transcranial magnetic stimulation (TMS) prior to brain scanning. Inhibition of IFC activity led to partly faster affective decisions, more accurate choice probabilities and reduced auditory cortical activity for clear affective speech, while fronto-limbic connectivity increased for clear vocalizations. This indicates that IFC inhibition might lead to a more intuitive and efficient processing of affect information in voices. Contrarily, normal IFC activity might represent a more deliberate form of affective sound processing (i.e., enforcing cognitive analysis) that flags categorial sound decisions with precaution (i.e., representation of categorial uncertainty). This would point to an intermediate functional property of the IFC between previously assumed mechanisms.

TeaserInferior frontal cortex enforces cognitive analyses during affect decisions with different levels of sensory ambiguity.


title: Macrogenetics reveals multifaceted influences of environmental variation on vertebrate population genetic diversity across the Americas

abstract: Relative to species diversity gradients, the broad scale distribution of population-specific genetic diversity (PGD) across taxa remains understudied. We used nuclear DNA data collected from 6285 vertebrate populations across the Americas to assess the role environmental variables play in structuring the spatial/latitudinal distribution of PGD, a key component of adaptive potential in the face of environmental change. Our results provide key evidence for taxa-specific responses and that temperature variability in addition to mean temperature may be a primary driver of PGD. Additionally, we found some positive influence of precipitation, productivity, and elevation on PGD; identified trends were dependent on the metric of PGD. In contrast to the classic negative relationship between species diversity and latitude, we report either a positive or taxa-dependent relationship between PGD and latitude, depending on the metric of PGD. The inconsistent latitudinal gradient in different metrics of PGD may be due to opposing processes diminishing patterns across latitudes that operate on different timescales, as well as the flattening of large-scale genetic gradients when assessing across species versus within species. Our study highlights the nuance required to assess broad patterns in genetic diversity, and the need for developing balanced conservation strategies that ensure population, species, and community persistence.

category: ecology


title: Crystal structures and functional analysis of the ZnF5-WWE1-WWE2 region of PARP13/ZAP define a new mode of engaging poly(ADP-ribose)

abstract: PARP13/ZAP acts against multiple viruses through recognizing and promoting degradation of cytoplasmic viral mRNA. PARP13 has four N-terminal Zn-finger motifs that bind CG-rich nucleotide sequences, and a C-terminal ADP ribosyltransferase fold similar to other PARPs. A central region predicted to contain a fifth Zn-finger and two tandem WWE domains is implicated in binding poly(ADP-ribose); however, there are limited insights into the structure and function of this PARP13 region (ZnF5-WWE1-WWE2). Here, we present crystal structures of ZnF5-WWE1-WWE2 from mouse PARP13 in complex with ADP-ribose and with ATP. ZnF5-WWE1-WWE2 crystallized as a dimer with major contacts formed between WWE1 and WWE2 originating from different monomers, indicative of a more compact monomeric arrangement of the tandem WWE domains. Solution scattering experiments and biophysical analysis indicated a monomer in solution, suggesting that the crystal dimer represents domain swapping that could potentially represent a PARP13 conformation assumed when signaling viral RNA detection. The crystal structure and binding studies demonstrate that WWE2 interacts with ADP-ribose and ATP, whereas WWE1 does not have a functional binding site. The shape of the WWE2 binding pocket disfavors interaction with the ribose-ribose linkage of poly(ADP-ribose). Binding studies with poly(ADP-ribose) ligands indicate that WWE2 serves as an anchor for preferential binding to the terminal end of poly(ADP-ribose), and the composite structure of ZnF5-WWE1-WWE2 forms an extended surface to engage polymer chains of ADP-ribose. This model represents a novel mode of poly(ADP-ribose) recognition and provides a structural framework for investigating poly(ADP-ribose) impact on PARP13 function.

category: biochemistry


title: Relationship between monomer packing and receptor binding domain pocket status in the spike trimer of SARS-CoV-2 variants

abstract: Existence of a SARS-CoV-2 spike protein trimer form with closer packing between monomers when receptor binding domains (RBDs) are all down, locked as opposed to closed, has been associated with linoleic acid (LA) binding at neutral pH, or can occur at acidic pH in the absence of LA binding. The relationship between degree of closure of the LA binding pocket of the RBD, and monomer burial in the trimer, is examined for a range of spike protein structures, including those with D614G mutation, and that of the Delta variant (which also carries D614G). Some spike protein structures with this aspartic acid mutation show monomer packing approaching that of the locked form (at neutral pH, without LA binding) for two segments, a third (around the RBD) remains less closely packed. Mutations in the RBD are a focus for the Omicron variant spike protein. Structure reports suggest that these mutations are involved in increased RBD-RBD interactions, and also that they could lead to a closing of the LA pocket, both of which could impact on pH-dependence. One potential outcome is that the extent of pH-dependent conformational transitions of the pre-fusion SARS-CoV-2 spike trimer are reduced in the Omicron variant.

category: bioinformatics


title: Relationship between monomer packing, receptor binding domain pocket status, and pH, in the spike trimer of SARS-CoV-2 variants


title: Spatially bivariate EEG-neurofeedback can manipulate interhemispheric rebalancing of M1 excitability

abstract: Human behavior requires interregional crosstalk to employ the sensorimotor processes in the brain. Although some external neuromodulation tools have been used to manipulate interhemispheric sensorimotor activity, a central controversy concerns whether this activity can be volitionally controlled. Experimental tools lack the power to up- or down-regulate the state of the targeted hemisphere over a large dynamic range and, therefore, cannot evaluate the possible volitional control of the activity. We overcame this difficulty by using the recently developed method of spatially bivariate electroencephalography (EEG)-neurofeedback to systematically enable participants to manipulate their bilateral sensorimotor activities. Herein, we report that bi-directional changes in ipsilateral excitability to the imagined hand (conditioning hemisphere) affect interhemispheric inhibition (IHI) assessed by paired-pulse transcranial magnetic stimulation paradigm. In addition, participants were able to robustly manipulate the IHI magnitudes. Further physiological analyses revealed that the self-manipulation of IHI magnitude reflected interhemispheric connectivity in EEG and TMS, which was accompanied by intrinsic bilateral cortical oscillatory activities. Our results provide clear neuroscientific evidence regarding the inhibitory interhemispheric sensorimotor activity and IHI manipulator, thereby challenging the current theoretical concept of recovery of motor function for neurorehabilitation.


title: Attenuated transcriptional response to pro-inflammatory cytokines in schizophrenia hiPSC-derived neural progenitor cells

abstract:
Maternal immune activation (MIA) during prenatal development is an environmental risk factor for psychiatric disorders including schizophrenia (SZ). This link is particularly well established in the case of schizophrenia. Converging lines of evidence from human and animal model studies have suggested that elevated cytokine levels in the maternal and fetal compartments are an important indication of the mechanisms driving this association. However, there is variability in susceptibility to the psychiatric risk conferred by MIA, likely influenced by genetic factors. How MIA interacts with a genetic profile susceptible to SZ is challenging to test in animal models. To address this gap, we examined whether differential gene expression responses occur in forebrain-lineage neural progenitor cells (NPCs) derived from human induced pluripotent stem cells (hiPSC) generated from three individuals with a diagnosis of schizophrenia and three healthy controls. Following acute (24 hour) treatment with either interferon-gamma (IFN{gamma}; 25 ng/l) or interleukin (IL)-1{beta} (10 ng/l), we identified, by RNA sequencing, 3380 differentially expressed genes (DEGs) in the IFN{gamma}-treated control lines (compared to untreated controls), and 1980 DEGs in IFN{gamma}-treated SZ lines (compared to untreated SZ lines). Of these, 359 genes responded differently to IFN{gamma} treatment in SZ relative to control lines, which were enriched for genes differentially expressed in adult SZ cases and in pathways related to the regulation of antigen processing, neuronal post-synaptic density, and the presynapse. There were no differentially expressed genes in the IL-1{beta}-treatment conditions after Benjamini-Hochberg correction. Gene set enrichment analysis however showed that IL-1{beta} impacts immune function and neuronal differentiation. Collectively, our data suggest that a) SZ NPCs show an attenuated transcriptional response to IFN{gamma} treatment compared to control NPCs; b) IL-1{beta} may be less relevant to NPC cultures than IFN{gamma} and c) the genes differentially regulated in schizophrenia lines are primarily mitochondrial, loss-of-function, pre- and post-synaptic genes. Our findings particularly highlight early synaptic development as a key target for future research into the mechanisms of association between maternal immune activation and schizophrenia risk.

Highlights* There is a significant transcriptional response to IFN{gamma} treatment in human induced cortical neural progenitor cells (NPCs)
* Differential expression implicates mitochondrial complex genes in this IFN{gamma}-dependent response, which are underexpressed in response to treatment in schizophrenia (SZ) NPCs.
* SZ NPCs do not upregulate pre- and post-synaptic genes in response to IFN{gamma} as much as control NPCs
* IL-1{beta} may be less relevant to NPC cultures than IFN{gamma} due to low IL1 receptor expression in NPCs.


title: IFN-γ-independent control of M. tuberculosis requires CD4 T cell-derived GM-CSF and activation of HIF-1α

abstract: The prevailing model of protective immunity to tuberculosis is that CD4 T cells produce the cytokine IFN-{gamma} to activate bactericidal mechanisms in infected macrophages. Recent evidence has expanded this model, and it is now clear that CD4 T cells can control M. tuberculosis infection in the absence of IFN-{gamma} production. To identify factors and pathways involved in IFN-{gamma}-independent control, we developed a co-culture model using CD4 T cells isolated from the lungs of infected mice and M. tuberculosis-infected murine bone marrow-derived macrophages (BMDMs). We show that IFN-{gamma}-independent control is primarily mediated by CD4 T cell production of the cytokine GM-CSF and requires activation of the macrophage transcription factor HIF-1. HIF-1 activation drives a metabolic shift toward aerobic glycolysis and leads to the production of lipid droplets, both of which support host defense against infection. Surprisingly, recombinant GM-CSF is insufficient to rescue the absence of control by GM-CSF-deficient CD4 T cells during co-culture with BMDMs. In peritoneal macrophages, GM-CSF is sufficient to control growth, induces lipid droplet biogenesis, and requires HIF-1 expression for control. While HIF-1-mediated control following IFN-{gamma} stimulation requires nitric oxide, we find that HIF-1 activation by CD4 T cells and recombinant GM-CSF is nitric oxide-independent, implying a distinct pathway of activation. In addition to GM-CSF, CD4 T cells produce a factor that helps maintain phagosome membrane integrity during infection and blocks bacterial access to host lipids, a primary nutrient source. These results advance our understanding of CD4 T cell-mediated immunity to M. tuberculosis, clarify the role of nitric oxide as primarily immunomodulatory during M. tuberculosis infection, and reveal a novel mechanism for the activation of HIF-1. Furthermore, we establish a previously unknown functional link between GM-CSF and HIF-1 and provide evidence that CD4 T cell-derived GM-CSF is a potent bactericidal effector.


title: SMAD4 and TGFβ are architects of inverse genetic programs during fate-determination of antiviral memory CD8 T cells

abstract: Transforming growth factor {beta} (TGF{beta}) is a morphogenic protein that augments antiviral immunity by altering the functional properties of pathogen-specific memory CD8 T cells. During infection, TGF{beta} inhibits formation of effector (TEFF) and circulating memory CD8 T cells, while encouraging tissue-resident memory CD8 T cells (TRM) to settle in peripheral tissues. SMAD proteins are signaling intermediates that are used by members of the TGF cytokine family to modify gene expression. Using RNA-sequencing we determined that SMAD4 altered the transcriptional profile of antiviral CTLs during respiratory infection. Our data show that SMAD4 and TGF{beta} use alternate signaling pathways to cooperatively regulate a collection of genes that determine whether pathogen-specific memory CD8 T cells localize in peripheral or lymphoid tissues. During infection, SMAD4 acts independently of TGF{beta} to inhibit TRM development, while inducing genes that support formation of circulating memory CD8 T cells. The genes that are modulated by SMAD4 include several homing receptors (CD103, KLRG1 and CD62L) and transcription factors (Hobit and EOMES) that support memory formation.


title: Emergence of compensatory mutations reveal the importance of electrostatic interactions between HIV-1 integrase and genomic RNA

abstract:
ABSTRACTHIV-1 integrase (IN) has a non-catalytic function in virion maturation through its binding to the viral RNA genome (gRNA). Allosteric integrase inhibitors (ALLINIs) and class II IN substitutions inhibit IN-gRNA binding and result in non-infectious viruses marked by mislocalization of the gRNA within virions. HIV-1 IN utilizes basic residues within its C-terminal domain (CTD) to bind to the gRNA. However, the molecular nature of how these residues mediate gRNA binding and whether other regions of IN are involved remain unknown. To address this, we have isolated compensatory substitutions in the background of a class II IN mutant virus bearing R269A/K273A substitutions within the IN-CTD. We found that the nearby D256N and D270N compensatory substitutions restored the ability of IN to bind gRNA and led to the formation of mature infectious virions. Reinstating the local positive charge of the IN-CTD through individual D256R, D256K, D278R and D279R substitutions was sufficient to restore IN-RNA binding and infectivity for the IN R269A/K273A as well as the IN R262A/R263A class II mutants. Structural modeling suggested that compensatory substitutions in the D256 residue created an additional interaction interface for gRNA binding. Finally, HIV-1 IN R269A/K273A, but not IN R262A/R263A, bearing compensatory mutations was more sensitive to ALLINIs providing key genetic evidence that specific IN residues required for RNA binding also influence ALLINI activity. Taken together, our findings highlight the essential role of CTD in gRNA binding and ALLINI sensitivity, and reveal the importance of pliable electrostatic interactions between the IN- CTD and the gRNA.

IMPORTANCEIn addition to its catalytic function, HIV-1 integrase (IN) binds to the viral RNA genome (gRNA) through positively charged residues within its C-terminal domain (CTD) and regulates proper virion maturation. Here we show that compensatory mutations in nearby acidic residues (i.e. D256N and D270N) restore the ability to bind gRNA for IN variants bearing substitutions in these positively charged CTD residues. Similarly, charge reversals through individual D-to-R and D-to-K substitutions at these positions enabled the respective IN mutants to bind gRNA and restore virion infectivity. Further, we show that specific residues within the IN-CTD required for RNA binding also influence sensitivity to allosteric integrase inhibitors, a class of novel IN- targeting compounds that target the non-catalytic function of IN. Taken together, our findings reveal the importance of electrostatic interactions in IN-gRNA binding and provide key evidence for a crucial role of the IN-CTD in allosteric integrase inhibitor mechanism of action.


title: Novel mechanism of plasmid-DNA transfer mediated by heterologous cell fusion in syntrophic coculture of Clostridium organisms

abstract:
The evolution of bacteria is driven by random genetic mutations and horizontal gene transfer (HGT) of genetic material from other bacteria. HGT can occur via transformation, transduction, and conjugation. Here, we present a potential new mechanism of HGT which occurs in a syntrophic Clostridium coculture. We have previously shown that in syntrophic cocultures of Clostridium acetobutylicum and Clostridium ljungdahlii, the two organisms undergo heterologous cell fusion, which includes fusion of the peptidoglycan cell walls and membranes. Heterologous cell fusion facilitated a large-scale exchange of cytoplasmic protein and RNA between the two organisms, leading to the formation of hybrid bacterial cells containing cytoplasmic material of the two parent organisms. Here we present new evidence that cell fusion events also facilitate the exchange of plasmid DNA between the two organisms of the syntrophic coculture. Through the use of a selective subculturing process, we successfully isolated wild-type C. acetobutylicum clones which have acquired a portion of the plasmid DNA - containing the antibiotic resistance marker - from a recombinant strain of C. ljungdahlii. Fusion events led to formation of persistent aberrant hybrid cells with distinct morphogenetic characteristics. Furthermore, our data support the concept of a novel, interspecies, mechanism of acquiring antibiotic resistance. Since neither organism contains any known conjugation machinery or mechanism, these findings expand our understanding of multi-species microbiomes, their survival strategies, and evolution.

IMPORTANCEInvestigations of natural multispecies microbiomes and the field of synthetic and syntrophic microbial cocultures are attracting renewed interest based on their potential application in biotechnology, ecology, and medical fields. A variety of synthetic and natural cocultures have been examined in terms of their metabolic output, but relatively few systems have been interrogated at the cellular and molecular level. Previously, we have shown the syntrophic coculture of C. acetobutylicum and C. ljungdahlii undergoes heterologous cell-to-cell fusion, which facilitates the exchange of cytoplasmic protein and RNA between the two organisms, and leads to the formation of hybrid bacterial cells. Continuing this line of investigation, we now show that heterologous cell fusion between the two Clostridium organisms can also facilitate the exchange of DNA between the two organisms. By applying selective pressures to this coculture system, we isolated clones of wild-type C. acetobutylicum which acquired the erythromycin resistance (erm) gene from the C. ljungdahlii strain carrying a plasmid with the erm gene. Fusion led to persistent hybrid cells containing DNA from both parents but with distinct properties and morphologies. Moreover, we provide evidence for a novel mechanism of acquiring antibiotic resistance mediated by the syntrophic interactions of this system. This is a major finding that may shed light on a new mechanism of bacterias ability to acquire antibiotic resistance.


title: Long term exposure of human gut microbiota with high and low emulsifier sensitivity to soy lecithin in M-SHIME model.

abstract:
In the context of the potential health hazards related to food processing, dietary emulsifiers have been shown to alter the structure and function of the gut microbial community, both in vivo and in vitro. In mouse models, these emulsifier exposed gut microbiota were shown to contribute to gut inflammation. Several knowledge gaps remain to be addressed though. As such, the impact from a longer timeframe of exposure on the gut microbiota is not known and interindividual variability in microbiome response needs to be measured.

To answer these research questions, in this study the faecal microbiota from two individuals, previously selected for high and low emulsifier sensitivity, were exposed to two concentrations of soy lecithin during a 7 day treatment phase in the dynamic mucosal simulator of the human intestinal microbial ecosystem (M-SHIME). The results showed mild effects from soy lecithin on the composition and functionality of these microbial communities, which depended on the original microbial composition. The effects also mostly levelled off after 3 days of exposure. The emulsifier sensitivity for which the microbiota were selected, was preserved. Some potentially concerning effects were also registered: butyrate levels, positively correlating with Faecalibacterium abundance, were lowered by soy lecithin. Also the abundance of the beneficial Bifidobacterium genus was lowered, while the abundance of the notorious unclassified Enterobacteriaceae was increased. Within the family of the unclassified Lachnospiraceae, several genera were either suppressed or stimulated.

The effects that these microbial alterations would have on a living host is not yet certain, especially given the fact that large fractions of soy lecithins constituents can be absorbed. Nevertheless, choline and phosphatidylcholine, both primary and absorbable constituents of soy lecithin, have recently been linked to cardiovascular disease via the generation of TMA by the gut microbiota. Further studies that validate our findings and link them to potential health outcomes are thus justified.


title: Transcription factor lineages in plant-pathogenic fungi, connecting diversity with fungal virulence

abstract: Plant-pathogenic fungi span diverse taxonomic lineages. Their host-infection strategies are often specialised and require the coordinated regulation of molecular virulence factors. Transcription factors (TFs) are fundamental regulators of gene expression, controlling development and virulence in plant pathogenic fungi. Recent research has established regulatory roles for several taxonomically conserved fungal TFs, but the evolution of specific virulence regulators is not well understood. This study sought to explore the representation of TFs across a taxonomically-diverse range of fungi, with a focus on plant pathogens. A significant trend was observed among the obligate, host-associated pathogens, which possess a reduced overall TF repertoire, alluding to a lack of pressure for maintaining diversity. A novel orthology-based analysis is then presented that refined TF classifications, traditionally based on the nature of the DNA-binding domains. Using this analysis, cases of TF over/underrepresentation across fungal pathogen lineages are systematically highlighted. Specific examples are then explored and discussed that included the TF orthologues of Ste12, Pf2 and EBR1, plus phytotoxic secondary-metabolite cluster regulators, which all presented novel and distinct evolutionary insights. Ultimately, as the examples presented demonstrate, this resource can be interrogated to guide functional studies that seek to characterise virulence-specific regulators and shed light on the factors underpinning plant pathogenicity.


title: Centromere identity is dependent on nuclear spatial organization

abstract: The establishment of centromere-specific CENP-A chromatin is influenced by epigenetic and genetic processes. Central domain sequences from fission yeast centromeres are preferred substrates for CENP-ACnp1 incorporation, but their use is context dependent, requiring adjacent heterochromatin. CENP-ACnp1 overexpression bypasses heterochromatin dependency, suggesting heterochromatin ensures exposure to conditions or locations permissive for CENP-ACnp1 assembly. Centromeres cluster around spindle-pole bodies (SPBs). We show that heterochromatin-bearing minichromosomes localize close to SPBs, consistent with this location promoting CENP-ACnp1 incorporation. We demonstrate that heterochromatin-independent de novo CENP-ACnp1 chromatin assembly occurs when central domain DNA is placed near, but not far from, endogenous centromeres or neocentromeres. Moreover, direct tethering of central domain DNA at SPBs permits CENP-ACnp1 assembly, suggesting that the nuclear compartment surrounding SPBs is permissive for CENP-ACnp1 incorporation because target sequences are exposed to high levels of CENP-ACnp1 and associated assembly factors. Thus, nuclear spatial organization is a key epigenetic factor that influences centromere identity.


title: The zinc-finger transcription factor LSL-1 is a major regulator of the germline transcriptional program in C. elegans

abstract: Specific gene transcriptional programs are required to ensure proper proliferation and differentiation processes underlying the production of specialized cells during development. Gene activity is mainly regulated by the concerted action of transcription factors and chromatin proteins. In the nematode C. elegans, mechanisms that silence improper transcriptional programs in germline and somatic cells have been well studied, however, how are tissue specific sets of genes turned on is less known. LSL-1 is herein defined as a novel crucial transcriptional regulator of germline genes in C. elegans. LSL-1 is first detected in the P4 blastomere and remains present at all stages of germline development, from primordial germ cell proliferation to the end of meiotic prophase. lsl-1 loss-of-function mutants exhibit many defects including meiotic prophase progression delay, a high level of germline apoptosis, and production of almost no functional gametes. Transcriptomic analysis and ChIP-seq data show that LSL-1 binds to promoters and acts as a transcriptional activator of germline genes involved in various processes, including homologous chromosome pairing, recombination, and genome stability. Furthermore, we show that LSL-1 functions by antagonizing the action of the heterochromatin proteins HPL-2/HP1 and LET-418/Mi2 known to be involved in the repression of germline genes in somatic cells. Based on our results, we propose LSL-1 to be a major regulator of the germline transcriptional program during development.


title: The 677C>T variant in methylenetetrahydrofolate reductase causes morphological and functional cerebrovascular deficits in mice

abstract: Vascular contributions to cognitive impairment and dementia (VCID) particularly Alzheimers disease and related dementias (ADRDs) are increasing; however, mechanisms driving cerebrovascular decline are poorly understood. Methylenetetrahydrofolate reductase (MTHFR) is a critical enzyme in the folate and methionine cycles. Variants in MTHFR, notably 677C>T, are associated with dementias, but no mouse model existed to identify mechanisms by which MTHFR677C>T increases risk. Therefore, MODEL-AD created a novel knock-in (KI) strain carrying the Mthfr677C>T allele on the C57BL/6J background (Mthfr677C>T) to characterize morphology and function perturbed by the variant. Consistent with human clinical data, Mthfr677C>T mice have reduced enzyme activity in the liver and elevated plasma homocysteine levels. MTHFR enzyme activity as well as critical metabolites in the folate and methionine cycles are reduced in the Mthfr677C>T brain. Mice showed reduced tissue perfusion in numerous brain regions by PET/CT as well as significantly reduced vascular density and increased GFAP-expressing astrocytes in frontal cortex. Electron microscopy revealed cerebrovascular damage including endothelial and pericyte apoptosis, reduced luminal size, and increased astrocyte and microglial presence in the microenvironment. Collectively, these data suggest critical perturbations to cerebrovascular function in Mthfr677C>T mice supporting its use as a model for preclinical studies of VCID.


title: Structure of human CST-pol-α/primase bound to a telomeric overhang poised for initiation of telomere C-strand synthesis

abstract: Telomere replication and regulation protect mammalian chromosome ends and promote genome stability. An essential step in telomere maintenance is the C-strand fill-in process, which is the de novo synthesis of the complementary strand of the telomere overhang. This step is catalyzed by polymerase-alpha/primase complex (pol-/primase) and coordinated by an accessory factor, CTC1-STN1-TEN1 (CST). Using cryogenic-electron microscopy single-particle analysis, we report the structure of the human telomere C-strand fill-in preinitiation complex (PIC) at 3.9 [A] resolution. The structure reveals a CST and a pol-/primase co-bound to a single telomere overhang, poised for de novo RNA primer synthesis. Upon PIC assembly, the pol-/primase undergoes large conformation change from its apo-state; CST partitions the DNA and RNA catalytic centers of pol-/primase into two separate domains and positions the 3' end of an extended telomere single-stranded DNA template towards the RNA catalytic center (PRIM1 or p49). The telomeric single-stranded DNA template is further positioned by the POLA1 (or p180) catalytically dead exonuclease domain. Together with CST, the exonuclease domain forms a tight-fit molecular tunnel for template direction. Given the structural homology of CST to Replication Protein A (RPA), our structure provides the structural basis for a new model of how pol-/primase lagging-strand DNA synthesis is coordinated by single-stranded DNA-binding accessory factors.


title: Human Mitochondrial AAA+ ATPase SKD3/CLPB forms Nucleotide-Stabilized Dodecamers

abstract: SKD3, also known as human CLPB, belongs to the AAA+ family of ATPases associated with various activities. Mutations in the SKD3/CLPB gene cause 3-methylglutaconic aciduria type VII and congenital neutropenia. SKD3 is upregulated in acute myeloid leukemia, where it contributes to anti-cancer drug resistance. SKD3 resides in the mitochondrial intermembrane space, where it forms ATP-dependent high-molecular weight complexes, but its biological function and mechanistic links to the clinical phenotypes are currently unknown. Using sedimentation equilibrium and dynamic light scattering, we show that SKD3 is monomeric at low protein concentration in the absence of nucleotides, but it forms oligomers at higher protein concentration or in the presence of adenine nucleotides. The apparent molecular weight of the nucleotide-bound SKD3 is consistent with self-association of 12 monomers. Image-class analysis and averaging from negative-stain electron microscopy (EM) of SKD3 in the ATP-bound state visualized cylinder-shaped particles with an open central channel along the cylinder axis. The dimensions of the EM-visualized particle suggest that the SKD3 dodecamer is formed by association of two hexameric rings. While hexameric structure has been often observed among AAA+ ATPases, a double-hexamer sandwich found for SKD3 appears uncommon within this protein family. A functional significance of the non-canonical structure of SKD3 remains to be determined.


title: Chemoproteomics of microbiota metabolites reveals small-molecule agonists for orphan receptor GPRC5A

abstract: The microbiota generates diverse metabolites that can engage multiple pathways to modulate host physiology and disease, but their protein targets and mechanism(s) of action have not been fully elucidated. To address this challenge, we focused on indole-3-acetic acid (IAA), a prominent microbiota metabolite, and developed IAA-based chemical reporters for proteomic studies. We discovered that IAA interacts with many proteins in host cells, including small-molecule transporters, receptors and metabolic enzymes. Notably, our functional studies revealed that IAA binds to orphan G protein-coupled receptors such as GPRC5A, but only aromatic monoamines were capable of inducing GPRC5A signaling. Functional profiling of microbiota uncovered specific bacterial species and enzymes that generate GPRC5A agonists. Finally, biochemical characterization of GPRC5A activation identified more potent synthetic agonists as well as key amino acid residues involved in ligand binding. These studies highlight the utility of chemoproteomics to dissect protein targets and mechanisms of action for microbiota metabolites.


title: Enrichment analysis on regulatory subspaces: a novel direction for the superior description of cellular responses to SARS-CoV-2

abstract:
StatementThe enrichment analysis of discriminative cell transcriptional responses to SARS-CoV-2 infection using biclustering produces a broader set of superiorly enriched GO terms and KEGG pathways against alternative state-of-the-art machine learning approaches, unraveling novel knowledge.

Motivation and methodsThe comprehensive understanding of the impacts of the SARS-CoV-2 virus on infected cells is still incomplete. This work identifies and analyses the main cell regulatory processes affected and induced by SARS-CoV-2, using transcriptomic data from several infectable cell lines available in public databases and in vivo samples. We propose a new class of statistical models to handle three major challenges, namely the scarcity of observations, the high dimensionality of the data, and the complexity of the interactions between genes. Additionally, we analyse the function of these genes and their interactions within cells to compare them to ones affected by IAV (H1N1), RSV and HPIV3 in the target cell lines.

ResultsGathered results show that, although clustering and predictive algorithms aid classic functional enrichment analysis, recent pattern-based biclustering algorithms significantly improve the number and quality of the detected biological processes. Additionally, a comparative analysis of these processes is performed to identify potential pathophysiological characteristics of COVID-19. These are further compared to those identified by other authors for the same virus as well as related ones such as SARS-CoV-1. This approach is particularly relevant due to a lack of other works utilizing more complex machine learning tools within this context.


title: Syndecan-1 is overexpressed in human thoracic aneurysm but is dispensable for the disease progression in vivo

abstract: Glycosaminoglycans (GAGs) pooling has been considered since long as one of the histopathological characteristics defining thoracic aortic aneurysm (TAA) together with smooth muscle cells (SMCs) apoptosis and elastin fibers degradation. However, few information is provided about GAGs composition or potential implication in TAA pathology. Syndecan-1 (Sdc-1) is a heparan sulfate proteoglycan that is implicated in extracellular matrix (ECM) interaction and assembly, regulation of SMCs phenotype and various aspects of inflammation in the vascular wall. In the current work, the regulation of Sdc-1 protein was examined in human TAA by ELISA and immunohistochemistry. In addition, the role of Sdc-1 was evaluated in descending TAA in vivo using a mouse model combining both aortic wall weakening and hypertension. Our results showed that Sdc-1 protein is over expressed in human TAA aortas compared to healthy counterparts and that SMCs are the major cell type expressing Sdc-1. Similarly, in the mouse model used, Sdc-1 expression was increased in TAA aortas compared to healthy samples. Although its protective role against abdominal aneurysm has been reported, we observed that Sdc-1 was dispensable for TAA prevalence or rupture. In addition, Sdc-1 deficiency did not alter the extent of aortic wall dilatation, elastin degradation, collagen deposition, or leukocyte recruitment in our TAA model. These findings suggest that Sdc-1 could be a biomarker revealing TAA pathology. Future investigations could uncover the underlying mechanisms leading to Sdc-1 expression alteration in TAA.

category: pathology


title: Flv3A facilitates O2 photoreduction and affects H2 photoproduction independently of Flv1A in diazotrophic Anabaena filaments

abstract: The model heterocyst-forming filamentous cyanobacterium, Anabaena sp. PCC 7120 (Anabaena) represents multicellular organisms capable of simultaneously performing oxygenic photosynthesis in vegetative cells and the O2-sensitive N2-fixation inside the heterocysts. The flavodiiron proteins (FDPs) have been shown to participate in photoprotection of photosynthesis by driving excess electrons to O2 (Mehler-like reaction). Here, we addressed the physiological relevance of the vegetative cell-specific Flv1A and Flv3A on the bioenergetic processes occurring in diazotrophic Anabaena under variable CO2. We demonstrate that both Flv1A and Flv3A are required for proper induction of the Mehler-like reaction upon a sudden increase in light intensity, which is likely important for the activation of carbon-concentrating mechanisms (CCM) and CO2 fixation. Under ambient CO2 diazotrophic conditions, Flv3A is capable of mediating moderate O2 photoreduction, independently of Flv1A, but in coordination with Flv2 and Flv4. Strikingly, the lack of Flv3A resulted in strong downregulation of the heterocyst-specific uptake hydrogenase, which led to enhanced H2 photoproduction under both oxic and micro-oxic conditions. These results reveal a novel regulatory network between the Mehler-like reaction and the diazotrophic metabolism, which is of great interest for future biotechnological applications.

category: plant biology


title: Establishing Normative Reference Values for the Utah Seated Medicine Ball Throw Protocol in Adolescents

abstract:
The seated medicine ball throw (SMBT) is a field test intended to assess upper-body muscular power by measuring the maximal distance an individual can throw a medicine ball from an isolated, seated position (25). The SMBT has been used to assess upper-body power in various populations and to establish concurrent validity for other measures of upper-body power such as the bench press power test and the plyometric push-up. The SMBT is less costly and simpler to incorporate into a field test battery than other upper body power assessments. While the SMBT is a valid, reliable field test for upper-body power, normative reference standards for most populations, including adolescent (12-15 years old) physical education students, do not exist.

PurposeThis study reports distances thrown in the SMBT to establish normative reference values in male and female physical education students, ages 12-15 years old.

MethodsOne hundred thirteen untrained male and female physical education students aged 12-15 years performed the SMBT field test three times on a single testing day. Participants threw a 2kg medicine ball with a 19.5 cm diameter while seated at a 90{degrees} after recording height, body mass, and BMI.

ResultsParticipant data was separated by age gender for analysis. Mean and standard deviation for the SMBT for males was 4.3{+/-}0.7m and 5.2{+/-}0.8 m for ages 12-13 and 14-15, respectively, and for females was 3.4{+/-}0.5m and 3.7{+/-}0.5m for ages 12-13 and 14-15, respectively. Pearson correlation coefficients for between-trials comparisons for males and females ranged from r=0.85-0.97. Pearson correlation coefficients for average SMBT and age of participants was r=0.93. Normative reference values as percentile ranks for the SMBT scores for age groups 12-13 and 14-15 among males and females, respectively, were also established.

ConclusionThe data presented provides an initial set of normative reference standards for coaches and students to determine upper-body muscular power using the SMBT.

category: scientific communication and education


title: The neural cell adhesion molecule NrCAM regulates development of hypothalamic tanycytes

abstract: Hypothalamic tanycytes are neural stem and progenitor cells, but little is known of how they are regulated. Here we provide evidence that the cell adhesion molecule, NrCAM, regulates tanycytes in the adult niche. NrCAM is strongly expressed in adult mouse tanycytes. Immunohistochemical and in situ hybridization analysis revealed that NrCAM loss of function leads to both a reduced number of tanycytes and reduced expression of tanycyte-specific cell markers, along with a small reduction in tyrosine hydroxylase-positive arcuate neurons. Similar analyses of NrCAM mutants at E16 identify few changes in gene expression or cell composition, indicating that NrCAM regulates tanycytes, rather than early embryonic hypothalamic development. Neurosphere and organotypic assays support the idea that NrCAM governs cellular homeostasis. Single-cell RNA sequencing (scRNA-Seq) shows that tanycyte-specific genes, including a number that are implicated in thyroid hormone metabolism, show reduced expression in the mutant mouse. However, the mild tanycyte depletion and loss of markers observed in NrCAM-deficient mice were associated with only a subtle metabolic phenotype.

category: neuroscience