Miracle-dz/UniFAR-FTUs huggingface dataset:
Re-assessing the phylogenetic status and evolutionary relationship of Forest Owlet [Athene blewitti (Hume 1873)] using genomic data

Phylogenetic relationships are often challenging to resolve in recent/younger lineage when only a few loci are used. Ultra Conserved Elements (UCE) are highly conserved regions across taxa that help resolve shallow and deep divergences. We utilized UCEs harvested from whole genomes to assess the phylogenetic position and taxonomic affiliation of an endangered endemic owlet in the family Strigidae – the Forest Owlet Athene blewitti. The taxonomic placement of this species has been revised multiple times. A multigene study attempted to address the question but showed a discrepancy across datasets in its placement of the species within genus Athene. We assembled a dataset of 5018 nuclear UCE loci with increased taxon sampling. Forest Owlet was found to be an early split from the Athene clade but sister to other Athene; and consistent across three approaches - maximum likelihood, bayesian, and the multispecies coalescence. Divergence dating using fossil calibrations suggest that the Athene lineage split from its ancestor about 7.6Mya, and the Forest Owlet diverged about 5.2Mya, consistent with previous multigene approaches. Despite osteological differences from other Athene, we suggest the placement of the Forest Owlet as a member of the Athene to emphasize its evolutionary relationship. Graphical Abstract HIGHLIGHTS Phylogenomics using genome-wide nuclear markers yielded a well-supported topology for Athene and Glaucidium lineages. Three different methods of phylogenetic tree construction showed that Forest Owlet is an early split from all other Athene species. Divergence dating in the bayesian framework puts the Forest Owlet age between 5.0my to 5.5my.
A Novel Activation Maximization-based Approach for Insight into Electrophysiology Classifiers

Spectral analysis remains a hallmark approach for gaining insight into electrophysiology modalities like electroencephalography (EEG). As the field of deep learning has progressed, more studies have begun to train deep learning classifiers on raw EEG data, which presents unique problems for explainability. A growing number of studies have presented explainability approaches that provide insight into the spectral features learned by deep learning classifiers. However, existing approaches only attribute importance to different frequency bands. Most of the methods cannot provide insight into the actual spectral values or the relationship between spectral features that models have learned. Here, we present a novel adaptation of activation maximization for electrophysiology time-series that generates samples that indicate the features learned by classifiers by optimizing their spectral content. We evaluate our approach within the context of EEG sleep stage classification with a convolutional neural network, and we find that our approach is able to identify spectral patterns known to be associated with each sleep stage. We also find surprising results suggesting that our classifier may have prioritized the use of eye and motion artifact when identifying Awake samples. Our approach is the first adaptation of activation maximization to the domain of raw electrophysiology classification. Additionally, our approach has implications for explaining any classifier trained on highly dynamic, long time-series.
Modular, robust, and extendible multicellular circuit design in yeast

Division of labor between cells is ubiquitous in biology but the use of multi-cellular consortia for engineering applications is only beginning to be explored. A significant advantage of multi-cellular circuits is their potential to be modular with respect to composition but this claim has not yet been extensively tested using experiments and quantitative modeling. Here, we construct a library of 24 yeast strains capable of sending, receiving or responding to three molecular signals, characterize them experimentally and build quantitative models of their input-output relationships. We then compose these strains into two- and three-strain cascades as well a four-strain bistable switch and show that experimentally measured consortia dynamics can be predicted from the models of the constituent parts. To further explore the achievable range of behaviors, we perform a fully automated computational search over all two-, three- and four-strain consortia to identify combinations that realize target behaviors including logic gates, band-pass filters and time pulses. Strain combinations that are predicted to map onto a target behavior are further computationally optimized and then experimentally tested. Experiments closely track computational predictions. The high reliability of these model descriptions further strengthens the feasibility and highlights the potential for distributed computing in synthetic biology.
LKB1 signalling in dendritic cells controls whole-body metabolic homeostasis by limiting T helper 17 priming

Obesity-associated metaflammation drives the development of insulin resistance and type 2 diabetes, notably through modulating innate and adaptive immune cells in metabolic organs. The nutrient sensor liver kinase B1 (LKB1) has recently been shown to control cellular metabolism and T cell priming functions of dendritic cells (DCs). Here, we report that hepatic DCs from high-fat diet (HFD)-fed obese mice display increased LKB1 phosphorylation and that LKB1 deficiency in DCs (CD11cΔLKB1) worsened HFD-driven hepatic steatosis, systemic insulin resistance and glucose intolerance. Loss of LKB1 in DCs was associated with increased cellular expression of Th17-polarizing cytokines and increased hepatic CD4+ IL-17A+ Th17 cells in HFD-fed mice. Importantly, IL-17A neutralization rescued metabolic perturbations in HFD-fed CD11cΔLKB1 mice. Mechanistically, disrupted metabolic homeostasis was independent of the canonical LKB1-AMPK axis. Instead, we provide evidence for involvement of the AMPK-related salt-inducible kinase(s) in controlling Th17-polarizing cytokine expression in LKB1-deficient DCs. Altogether, our data reveal a key role for LKB1 signalling in DCs in protection against obesity-induced metabolic dysfunctions by limiting hepatic Th17 differentiation.
Microscopic Quantification of Oxygen Consumption across Cortical Layers

The cerebral cortex is organized in cortical layers that differ in their cellular density, composition, and wiring. Cortical laminar architecture is also readily revealed by staining for cytochrome oxidase – the last enzyme in the respiratory electron transport chain located in the inner mitochondrial membrane. It has been hypothesized that a high-density band of cytochrome oxidase in cortical layer IV reflects higher oxygen consumption under baseline (unstimulated) conditions. Here, we tested the above hypothesis using direct measurements of the partial pressure of O2 (pO2) in cortical tissue by means of 2-photon phosphorescence lifetime microscopy (2PLM). We revisited our previously developed method for extraction of the cerebral metabolic rate of O2 (CMRO2) based on 2-photon pO2 measurements around diving arterioles and applied this method to estimate baseline CMRO2 in awake mice across cortical layers. To our surprise, our results revealed a decrease in baseline CMRO2 from layer I to layer IV. This decrease of CMRO2 with cortical depth was paralleled by an increase in tissue oxygenation. Higher baseline oxygenation and cytochrome density in layer IV may serve as an O2 reserve during surges of neuronal activity or certain metabolically active brain states rather than baseline energy needs. Our study provides the first quantification of microscopically resolved CMRO2 across cortical layers as a step towards informed interpretation and modeling of cortical-layer-specific Blood Oxygen Level Dependent (BOLD) functional Magnetic Resonance Imaging (fMRI) signals.
Loss of TBK1 activity leads to TDP-43 proteinopathy through lysosomal dysfunction in human motor neurons

Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disease characterized by motor neuron loss accompanied by cytoplasmic localization of TDP-43 proteins and their insoluble accumulations. Haploinsufficiency of TBK1 has been found to associate with or cause ALS. However, the cell-autonomous mechanisms by which reduced TBK1 activity contributes to human motor neuron pathology remain elusive. Here, we generated a human cellular model harboring loss-of-function mutations of TBK1 by gene editing and found that TBK1 deficiency was sufficient to cause TDP-43 pathology in human motor neurons. In addition to its functions in autophagy, we found that TBK1 interacted with endosomes and was required for normal endosomal maturation and subsequent lysosomal acidification. Surprisingly, TDP-43 pathology resulted more from the dysfunctional endo-lysosomal pathway than the previously recognized autophagy inhibition mechanism. Restoring TBK1 levels ameliorated lysosomal dysfunction and TDP-43 pathology and maintained normal motor neuron homeostasis. Notably, using patient-derived motor neurons, we found that haploinsufficiency of TBK1 sensitized neurons to lysosomal stress, and chemical regulators of endosomal maturation rescued the neurodegenerative process. Together, our results revealed the mechanism of TBK1 in maintaining TDP-43 and motor neuron homeostasis and suggested that modulating endosomal maturation was able to rescue neurodegenerative disease phenotypes caused by TBK1 deficiency.
Elevated transcriptional pausing of RNA polymerase II underlies acquired resistance to radiotherapy

As the mainstay modality for many malignancies, particularly inoperable solid tumors such as nasopharyngeal carcinoma (NPC), ionizing radiation (IR) induces a variety of lesions in genomic DNA, evoking a multipronged DNA damage response to interrupt many cellular processes including transcription. The turbulence in transcription, depending on the nature of DNA lesions, encompasses local blockage of RNA polymerase II (RNAPII) near the damage sites, as well as a less understood genome-wide alteration. How the transcriptional change influences the effectiveness of radiotherapy remains unclear. Using a panel of NPC and lung cancer cell lines, we observe increased phosphorylation at serine 5 (pS5) of the RNAPII after IR, indicating an accumulation of paused RNAPII. Remarkably, a similar increase of pS5 is seen in IR-resistant cells. ChIP-seq analysis of RNAPII distribution confirms this increased pausing both in IR-treated and IR-resistant NPC cells, notably on genes involved in radiation response and cell cycle. Accordingly, many of these genes show downregulated transcripts abundance in IR-resistant cells, and individual knockdown some of them such as TP53 and NEK7 endows NPC cells with varying degrees of IR-resistance. Decreasing pS5 of RNAPII and hence tuning down transcriptional pausing by inhibiting CDK7 reverses IR-resistance both in cell culture and xenograft models. Our results therefore uncover an unexpected link between elevated transcriptional pausing and IR-resistance. Given the recurrent NPC tissues display a steady increase in pS5 compared to the paired primary tissues, we suggest that CDK7 inhibitors can be used in combination with radiotherapy to increase sensitivity and thwart resistance.
Rhythmicity of Intestinal IgA Responses Confers Oscillatory Commensal Microbiota Mutualism

Mutualistic interactions with the commensal microbiota are enforced through a range of immune responses that confer metabolic benefits for the host and ensure tissue health and homeostasis. Immunoglobulin (Ig)A responses directly determine the composition of commensal species that colonize the intestinal tract but require significant metabolic resources to fuel antibody production by tissue-resident plasma cells. Here we demonstrate IgA responses are subject to diurnal regulation by dietary-derived metabolic cues and a cell-intrinsic circadian clock. Rhythmicity in IgA secretion conferred oscillatory patterns on the commensal microbial community and its associated metabolic activity, resulting in changes to metabolite availability over the course of the circadian day. Our findings suggest circadian networks comprising intestinal IgA, the diet and the microbiota align to ensure metabolic health. One-Sentence Summary We demonstrate diurnal rhythms in intestinal IgA act to cross-regulate oscillations in the abundance of commensal microbes to foster mutualism.
Ferroptosis regulation by the NGLY1/NFE2L1 pathway

Ferroptosis is an oxidative form of non-apoptotic cell death whose transcriptional regulation is poorly understood. Cap’n’collar (CNC) transcription factors including Nuclear Factor Erythroid-2 Related Factor 1 (NFE2L1/NRF1) and NFE2L2 (NRF2) are important regulators of oxidative stress responses. Here, we report that NFE2L1 expression inhibits ferroptosis, independent of NFE2L2. NFE2L1 inhibits ferroptosis by promoting expression of the key anti-ferroptotic lipid hydroperoxidase glutathione peroxidase 4 (GPX4). NFE2L1 abundance and function are regulated post-translationally by N-glycosylation. Functional maturation of NFE2L1 requires deglycosylation by cytosolic peptide:N-glycanase 1 (NGLY1). We find that loss of NGLY1 or NFE2L1 enhances ferroptosis sensitivity. Expression of wild-type NGLY1 but not a disease-associated NGLY1 mutant inhibits ferroptosis, and this effect is dependent on the presence of NFE2L1. Enhanced ferroptosis sensitivity in NFE2L1 and NFE2L2 knockout cells can be potently reverted by expression of an NFE2L1 mutant containing eight asparagine-to-aspartate protein sequence substitutions, which mimic NGLY1-catalyzed sequence editing. Enhanced ferroptosis sensitivity in NGLY1/NFE2L1 pathway mutants could also be reversed by overexpression of NFE2L2. These results suggest that ferroptosis sensitivity is regulated by NGLY1-catalyzed NFE2L1 deglycosylation, and highlight a broad role for CNC transcription factors in ferroptosis regulation. Significance Statement Ferroptosis is an oxidative form of cell death whose biochemical regulation remains incompletely understood. NFE2L1/NRF1 is a cap’n’collar (CNC) transcription factor whose role in ferroptosis regulation is unclear. Unlike the CNC family member NFE2L2/NRF2, NFE2L1 is an N-glycoprotein whose abundance is regulated by post-translational deglycosylation catalyzed by the enzyme peptide:N-glycanase 1 (NGLY1). Our results indicate that NGLY1-mediated NFE2L1 deglycosylation, resulting in ‘editing’ of the NFE2L1 amino acid sequence, is necessary for NFE2L1 to inhibit ferroptosis. Mechanistically, NFE2L1 inhibits ferroptosis by via the anti-ferroptotic protein GPX4. This work demonstrates that CNC transcription factors beyond NFE2L2 can regulate ferroptosis. This work may suggest a role of misregulation of ferroptosis in NGLY1 deficiency, an ultrarare genetic disorder.
Interventional Video Relation Detection

Video Visual Relation Detection (VidVRD) aims to semantically describe the dynamic interactions across visual concepts localized in a video in the form of subject, predicate, object. It can help to mitigate the semantic gap between vision and language in video understanding, thus receiving increasing attention in multimedia communities. Existing efforts primarily leverage the multimodal/spatio-temporal feature fusion to augment the representation of object trajectories as well as their interactions and formulate the prediction of predicates as a multi-class classification task. Despite their effectiveness, existing models ignore the severe long-tailed bias in VidVRD datasets. As a result, the models' prediction will be easily biased towards the popular head predicates (e.g., next-to and in-front-of), thus leading to poor generalizability. To fill the research gap, this paper proposes an Interventional Video Relation Detection (IVRD) approach that aims to improve not only the accuracy but also the robustness of the model prediction. Specifically, to better model the high-level visual predicate, our IVRD consists of two key components: 1) we first learn a set of predicate prototypes, where each prototype vector describes a set of relation references with the same predicate; and 2) we apply a causality-inspired intervention on the model input subject, object, which forces the model to fairly incorporate each possible predicate prototype into consideration. We expect the model to focus more on the visual content of the dynamic interaction between subject and object, rather than the spurious correlations between the model input and predicate labels. Extensive experiments on two popular benchmark datasets show the effectiveness of IVRD and also its advantages in reducing the bad long-tailed bias.
Is there magnocellular facilitation of early neural processes underlying visual word recognition? Evidence from masked repetition priming with ERPs

An influential theory in the field of visual object recognition proposes that fast magnocellular (M) information facilitates neural processing of spatially more fine-grained but slower parvocellular (P) information. While written words can be considered as a special type of visual objects, it is unknown whether magnocellular facilitation also plays a role in reading. We used a masked priming paradigm that has been shown to result in neural facilitation in visual word processing and tested whether these facilitating effects are mediated by the magnocellular system. In two experiments, we manipulated the influence of magnocellular and parvocellular systems on visual processing of a contextually predictable target character by contrasting high versus low spatial frequency and luminance versus color contrast, respectively. In addition, unchanged (normal) primes were included in both experiments as a manipulation check. As expected, unchanged primes elicited typical repetition effects in the N1, N250 and P3 components of the ERP in both experiments. In the experiment manipulating spatial contrast, we obtained repetition effects only for the N1 component for both M- and P-biased primes. In the luminance versus color contrast experiment, repetition effects were found in N1 and N250 for both M- and P- biased primes. Furthermore, no interactions were found between M- vs. P-biased prime types and repetition. Together these results indicate that M- and P- information contributes jointly to early neural processes underlying visual word recognition.
Conserved α-helix-3 is crucial for structure and functions of Rad6 E2 ubiquitin-conjugating enzymes

Rad6, an E2 ubiquitin-conjugating enzyme conserved from yeast to humans, functions in transcription, genome maintenance and proteostasis. The contributions of many conserved secondary structures of Rad6 and its human homologs UBE2A and UBE2B to their biological functions are not understood. A mutant RAD6 allele with a missense substitution at alanine-126 (A126) of α-helix-3 that causes defects in telomeric gene silencing, DNA repair and protein degradation was reported over two decades ago. Here, using a combination of genetics, biochemical, biophysical, and computational approaches, we discovered that α-helix-3 A126 mutations compromise the ability of Rad6 to ubiquitinate target proteins without disrupting interactions with partner E3 ubiquitin-ligases that are required for their various biological functions in vivo. Explaining the defective in vitro or in vivo ubiquitination activities, molecular dynamics simulations and NMR showed that α-helix-3 A126 mutations cause local disorder of the catalytic pocket of Rad6, and also disorganize the global structure of the protein to decrease its stability in vivo. We further demonstrate that α-helix-3 A126 mutations deform the structures of UBE2A and UBE2B, the human Rad6 homologs, and compromise the in vitro ubiquitination activity and folding of UBE2B. Molecular dynamics simulations and circular dichroism spectroscopy along with functional studies further revealed that cancer-associated mutations in α-helix-3 of UBE2A or UBE2B alter both structure and activity, providing an explanation for their pathogenicity. Overall, our studies reveal that the conserved α-helix-3 is a crucial structural constituent that controls the organization of catalytic pockets and biological functions of the Rad6-family E2 ubiquitin-conjugating enzymes.Contributions of the conserved α-helix-3 to the functions of E2 enzymes is not known.Mutations in alanine-126 of α-helix-3 impair in vitro enzymatic activity and in vivo biological functions of Rad6.Mutations in alanine-126 of α-helix-3 disorganize local or global protein structure, compromise folding or stability, and impair the catalytic activities of yeast Rad6 and its human homologs UBE2A and UBE2B.Cancer-associated mutations in α-helix-3 of human UBE2A or UBE2B alter protein flexibility, structure, and activity. α-helix-3 is a key structural component of yeast and human Rad6 E2 ubiquitin-conjugating enzymes.
Losses and gains of fallows impact farmland bird populations over three funding periods of the EU Common Agricultural Policy

Fallow land provides habitat for threatened and declining farmland biodiversity. Policy change under the EU’s Common Agricultural Policy (CAP) has been driving the area of fallows over the past decades and influenced trends in farmland biodiversity. We analyzed the relationships between fallow land area across Germany over three CAP funding periods and species richness and abundance of farmland birds. We examined whether the strength of the relationships with fallow land area were moderated by species habitat preferences and landscape configurational complexity (edge density). We combined spatial data on fallow land area from three agricultural censuses in Germany (2007, 2010 and 2016) with country-wide farmland bird monitoring data. Farmland bird species richness and the abundance of the majority of the studied farmland bird species were positively related to increases in fallows across three CAP funding periods. The relationship of fallows with bird richness was strongest at intermediate levels of edge density. There was generally little support for a moderating effect of edge density on the relations between fallows and bird abundance. We conclude that the loss of fallows in the period 2007 to 2016 resulted in strong declines of farmland birds. We predict that a future increase of the proportion of fallow land to 4% of the arable land, as envisaged in the German 2023-2027 CAP strategic plans, or to 10%, as foreseen in the EU Biodiversity Strategy, will lead to increases in farmland bird species richness and abundance depending on the landscape context and species-specific habitat preferences. Policy implications Increasing the proportion of fallow land will likely be a key lever to stabilize and revert negative farmland bird population trends. An increase of fallow area in all but the least complex landscapes will boost farmland bird richness and abundance. Increasing the proportion of fallow land to 4% should bring farmland bird richness and abundance back to the levels observed in 2007 acknowledging that farmland bird populations were already severely depleted in 2007. A more ambitious expansion of fallow land towards 10% should be targeted towards areas that experienced the strongest loss of fallows and towards landscapes with intermediate levels of edge density.