Miracle-dz/UniFAR-FTUs huggingface dataset:
Osteoblast cell death triggers a pro-osteogenic inflammatory response regulated by reactive oxygen species and glucocorticoid signaling in zebrafish

In zebrafish, transgenic labeling approaches, robust regenerative responses and excellent in vivo imaging conditions enable precise characterization of immune cell behavior in response to injury. Here, we monitored osteoblast-immune cell interactions in bone, a tissue which is particularly difficult to in vivo image in tetrapod species. Ablation of individual osteoblasts leads to recruitment of neutrophils and macrophages in varying numbers, depending on the extent of the initial insult, and initiates generation of cathepsinK+ osteoclasts from macrophages. Induced osteoblast death triggers the production of pro-inflammatory cytokines and reactive oxygen species, which are needed for successful macrophage recruitment. Excess glucocorticoid signaling as it occurs during the stress response inhibits macrophage recruitment, maximum speed and changes the macrophages’ phenotype. While osteoblast loss is compensated for within a day by contribution of committed osteoblasts, macrophages continue to populate the region. Their presence is required for osteoblasts to fill the lesion site. Our model enables visualization of homeostatic bone repair after microlesions at single cell resolution and demonstrates a pro-osteogenic function of tissue-resident macrophages in non-mammalian vertebrates. Summary statement Laser-mediated osteoblast ablation induces recruitment of tissue-resident macrophages by a release of reactive oxygen species. The presence of macrophages is required for osteoblasts to repopulate the lesion site and can be modulated by glucocorticoids.
Comparing Host Module Activation Patterns and Temporal Dynamics in Infection by Influenza H1N1 Viruses

Influenza is a serious global health threat that shows varying pathogenicity among different virus strains. Understanding similarities and differences among activated functional pathways in the host responses can help elucidate therapeutic targets responsible for pathogenesis. To compare the types and timing of functional modules activated in host cells by four influenza viruses of varying pathogenicity, we developed a new DYNAmic MOdule (DYNAMO) method that addresses the need to compare functional module utilization over time. This integrative approach overlays whole genome time series expression data onto an immune-specific functional network, and extracts conserved modules exhibiting either different temporal patterns or overall transcriptional activity. We identified a common core response to influenza virus infection that is temporally shifted for different viruses. We also identified differentially regulated functional modules that reveal unique elements of responses to different virus strains. Our work highlights the usefulness of combining time series gene expression data with a functional interaction map to capture temporal dynamics of the same cellular pathways under different conditions. Our results help elucidate conservation of the immune response both globally and at a granular level, and provide mechanistic insight into the differences in the host response to infection by influenza strains of varying pathogenicity.
Perigenual and Subgenual Anterior Cingulate Afferents Converge on Common Pyramidal Cells in Amygdala Subregions of the Macaque

The subgenual (sgACC) and perigenual (pgACC) anterior cingulate are important afferents of the amygdala, with different cytoarchitecture, connectivity, and function. The sgACC is associated with arousal mechanisms linked to salient cues, whereas the pgACC is engaged in conflict decision-making, including in social contexts. After placing same-size, small volume tracer injections into sgACC and pgACC of the same hemisphere in male macaques, we examined anterogradely labeled fiber distribution to understand how these different functional systems communicate in the main amygdala nuclei at both mesocopic and cellular levels. The sgACC has broad-based termination patterns. In contrast, the pgACC has a more restricted pattern, which was always nested in sgACC terminals. Terminal overlap occurred in subregions of the accessory basal and basal nuclei, which we termed “hotspots. ” In triple-labeling confocal studies, the majority of randomly selected CaMKIIα-positive cells (putative amygdala glutamatergic neurons) in hotspots received dual contacts from the sgACC and pgACC. The ratio of dual contacts occurred over a surprisingly narrow range, suggesting a consistent, tight balance of afferent contacts on postsynaptic neurons. Large boutons, which are associated with greater synaptic strength, were ∼3 times more frequent on sgACC versus pgACC axon terminals in hotspots, consistent with a fast “driver” function. Together, the results reveal a nested interaction in which pgACC (“conflict/social monitoring”) terminals converge with the broader sgACC (“salience”) terminals at both the mesoscopic and cellular level. The presynaptic organization in hotspots suggests that shifts in arousal states can rapidly and flexibly influence decision-making functions in the amygdala. SIGNIFICANCE STATEMENT The subgenual (sgACC) and perigenual cingulate (pgACC) have distinct structural and functional characteristics and are important afferent modulators of the amygdala. The sgACC is critical for arousal, whereas the pgACC mediates conflict-monitoring, including in social contexts. Using dual tracer injections in the same monkey, we found that sgACC inputs broadly project in the main amygdala nuclei, whereas pgACC inputs were more restricted and nested in zones containing sgACC terminals (hotspots). The majority of CaMKIIα + (excitatory) amygdala neurons in hotspots received converging contacts, which were tightly balanced. pgACC and sgACC afferent streams are therefore highly interdependent in these specific amygdala subregions, permitting “internal arousal” states to rapidly shape responses of amygdala neurons involved in conflict and social monitoring networks.
Neural correlates of individual differences in aversion to risk and choice inconsistency

When making financial choices, most people prefer smaller but more certain gains to larger but more uncertain ones with the same expected value (risk aversion). However, attitudes toward risk may vary greatly also within individuals (choice inconsistency). To examine the brain dynamics implementing risky and inconsistent decisions, we recorded event-related brain potentials (ERPs) from 24 adults engaged in a task requiring choices between certain but smaller gains and uncertain but larger ones. Choice consistency and risk aversion were quantified for each individual. Participants were classified into three groups according to their attitude toward risk. Relative neutrality to risk was accompanied by a higher consistency across trials than risk aversion or proneness. Choice consistency was related to the amplitude of the positive ERP peaking near 200 ms after stimulus onset (P200), while risk aversion was related to modulation of the medial frontal negativity (MFN) and to the amplitude of a late positive potential (LPP). Late ERP activity was related to the modulation of value signals by risk levels and associated with individual differences in behavior. Overall, this study suggests that individual differences in attitude toward risk and choice consistency are associated with distinct brain dynamics.
An improved fluorescent noncanonical amino acid for measuring conformational distributions using time-resolved transition metal ion FRET

With the recent explosion in high-resolution protein structures, one of the next frontiers in biology is elucidating the mechanisms by which conformational rearrangements in proteins are regulated to meet the needs of cells under changing conditions. Rigorously measuring protein energetics and dynamics requires the development of new methods that can resolve structural heterogeneity and conformational distributions. We have previously developed steady-state transition metal ion fluorescence resonance energy transfer (tmFRET) approaches using a fluorescent noncanonical amino acid donor (Anap) and transition metal ion acceptor, to probe conformational rearrangements in soluble and membrane proteins. Here, we show that the fluorescent noncanonical amino acid Acd has superior photophysical properties that extend its utility as a donor for tmFRET. Using maltose binding protein (MBP) expressed in mammalian cells as a model system, we show that Acd is comparable to Anap in steady-state tmFRET experiments and that its long, single-exponential lifetime is better suited for probing conformational distributions using time-resolved FRET. These experiments reveal differences in heterogeneity in the apo and holo conformational states of MBP and produce accurate quantification of the distributions among apo and holo conformational states at subsaturating maltose concentrations. Our new approach using Acd for time-resolved tmFRET sets the stage for measuring the energetics of conformational rearrangements in soluble and membrane proteins in near-native conditions.
Insect attraction to the six major types of traditional-style, residential light bulbs and implications for insect survival and light pollution

Artificial light at night can affect the behavior and survival of the arthropods attracted to it. Most light pollution research focuses on high-wattage street lamps, but lower-wattage lamps used to illuminate porches, paths, façades, and backyards vastly outnumber street lamps. Thus, residential consumers could potentially have an enormous influence on artificial light ecologies by their choice of lamp. This study compared insect attraction to the six major types of traditional-style, residential light bulb: incandescent, CFL, halogen, warm color temperature LED, cool color temperature LED, and the yellow “bug” lights marketed as reducing insect attraction. The bulbs were alternately used in a baffle-funnel light trap from early spring through late fall, and capture rates were determined for the orders of insects. Incandescent bulbs produced the highest trap captures; the warm color temperature LED bulb produced the fewest, even fewer than the yellow “bug” light. The yellow “bug” light attracted more Dermaptera (Leach) than the other bulbs. The data support a recommendation of LED bulbs, especially those with a warm color temperature, to minimize the effects of night lighting on insect behavior and mortality. Further, the use of yellow “bug” lights, in contrast to their marketing, could attract earwigs and other minor pests.
Rapid Inactivation of SARS-CoV-2 Variants by Continuous and Intermittent Irradiation with a Deep-Ultraviolet Light-Emitting Diode (DUV-LED) Device

More than 1 year has passed since social activities have been restricted due to the spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). More recently, novel SARS-CoV-2 variants have been spreading around the world, and there is growing concern of higher transmissibility of the variants and weaker protective efficacy of vaccine against the variants. Immediate measures are needed to reduce human exposure to the virus. In this study, the antiviral efficacy of deep-ultraviolet light-emitting diode (DUV-LED) irradiation (280 ± 5 nm, 3.75 mW/cm2) against three SARS-CoV-2 variants was evaluated. For the B.1. 1.7, B.1. 351, and P.1 strains, the infectious titer reduction rates of 96.3%, 94.6%, and 91.9%, respectively, were already recognized with the irradiation of virus stocks for 1 s, and the rates increased to 99.9%, 99.9%, and 99.8%, respectively, with irradiation for 5 s. We also tested the effect of pulsed DUV-LED irradiation (7.5 mW/cm2, duty rate: 50%, frequency: 1 KHz) under the same output conditions as continuous irradiation, and found that the antiviral efficacy of pulsed and continuous irradiation was the same. These findings suggest that SARS-CoV-2 may be instantly inactivated by DUV-LED irradiation if the DUV-LED device is further developed and optimized to increase its output.
The terminal heme synthetic enzyme, Coproheme Decarboxylase, coordinates heme synthesis and uptake in response to iron in Mycobacteria

Heme is both an essential cofactor and an abundant source of nutritional iron for the human pathogen Mycobacterium tuberculosis (Mtb). While heme is required for Mtb survival and virulence, it is also potentially cytotoxic. Since Mtb has the ability to both make and uptake heme, the de novo synthesis of heme and its acquisition from the host must be balanced in order to mitigate heme toxicity. However, the mechanisms employed by Mtb to regulate heme uptake, synthesis, and bioavailability are poorly understood. By integrating ratiometric heme sensors with mycobacterial genetics, cell biology, and biochemistry, we determined that the terminal heme biosynthetic enzyme, coproheme decarboxylase (ChdC), plays a role in regulating both heme bioavailability and uptake in Mtb. Moreover, we found that Mtb has a preference for scavenging reduced ferrous heme and exhibits a cell surface heme reductase activity that is regulated by ChdC. In Mtb, ChdC expression is down-regulated when iron is limiting, which in-turn increases both heme import and bioavailability. Such a mechanism may serve to protect cells from heme toxicity while trying to meet the nutritional demand for iron. Our results demonstrate that heme synthesis and uptake are tightly integrated in mycobacteria and represent the first example of a heme synthetic enzyme playing a role in controlling heme uptake. Significance Statement Heme is an essential but potentially cytotoxic cofactor and iron source for the pathogen, Mycobacterium tuberculosis (Mtb). To understand how Mtb coordinates heme uptake and synthesis to mitigate heme toxicity, we integrated heme sensors with mycobacterial genetics and biochemical approaches to probe the interplay between heme synthesis and scavenging. We discovered that the terminal heme synthetic enzyme, coproheme decarboxylase (ChdC), negatively regulates heme uptake and utilization in response to iron availability through a mechanism involving control of a ferric heme reductase. During iron limitation, ChdC is downregulated, thereby enhancing exogenous heme reduction, uptake and utilization while simultaneously suppressing heme synthesis, which allows Mtb to avoid heme toxicity. Our results highlight the close coordination between heme synthesis and uptake in mycobacteria. Classification Biological sciences : Biochemistry
Morphometric relationships and their contribution to biomass and cannabinoid yield in hybrids of hemp (Cannabis sativa)

The breeding of hybrid cultivars of hemp (Cannabis sativa L.) is not well described, especially the segregation and inheritance of traits that are important for yield. A total of 23 families were produced from genetically diverse parents to investigate the inheritance of morphological traits and their association with biomass accumulation and cannabinoid yield. In addition, a novel classification method for canopy architecture was developed. The strong linear relationship between wet and dry biomass provided an accurate estimate of final dry stripped floral biomass. Of all field and aerial measurements, basal stem diameter was determined to be the single best selection criterion for final dry stripped floral biomass yield. Along with stem diameter, canopy architecture and stem growth predictors described the majority of the explainable variation of biomass yield. Within-family variance for morphological and cannabinoid measurements reflected the heterozygosity of the parents. While selfed populations suffered from inbreeding depression, hybrid development in hemp will require at least one inbred parent to achieve uniform growth and biomass yield. Nevertheless, floral phenology remains a confounding factor in selection because of its underlying influence on biomass production highlighting the need to understand the genetic basis for flowering time in the breeding of uniform cultivars. Highlight Stem and canopy architecture traits are superior predictors of floral biomass yield and offer a good indication of hybrid uniformity in field plantings of genetically diverse cannabinoid hemp populations.
Receptor Activity-Modifying Protein 2 (RAMP2) alters glucagon receptor trafficking in hepatocytes with functional effects on receptor signalling

Objectives Receptor Activity-Modifying Protein 2 (RAMP2) is a chaperone protein which allosterically binds to and interacts with the glucagon receptor (GCGR). The aims of this study were to investigate the effects of RAMP2 on GCGR trafficking and signalling in the liver, where glucagon is important for carbohydrate and lipid metabolism. Methods Subcellular localisation of GCGR in the presence and absence of RAMP2 was investigated using confocal microscopy, trafficking assays and radioligand binding assays in human embryonic kidney (HEK293T) and human hepatoma (Huh7) cells. Mouse embryonic fibroblasts (MEFs) lacking Wiskott Aldrich Syndrome protein and scar homologue (WASH) complex were used to investigate the effect of a halt in recycling of internalised proteins on GCGR signalling in the absence of RAMP2. NanoBiT complementation and cyclic AMP assays were used to study the functional effect of RAMP2 on recruitment and activation of GCGR signalling mediators. Response to hepatic RAMP2 up-regulation in lean and obese adult mice using a bespoke adeno-associated viral vector was also studied. Results GCGR is predominantly localised at the plasma membrane in the absence of RAMP2 and exhibits remarkably slow internalisation in response to agonist stimulation. Rapid intracellular retention of glucagon-stimulated GCGR in cells lacking WASH complex indicates that activated GCGRs undergo continuous cycles of internalisation and recycling despite apparent GCGR plasma membrane localisation up to 40 minutes post-stimulation. Co-expression of RAMP2 induces GCGR internalisation both basally and in response to agonist-stimulation. The intracellular retention of GCGR in the presence of RAMP2 confers a bias away from β-arrestin-2 recruitment coupled to increased activation of Gαs proteins at endosomes. This is associated with increased short-term efficacy for glucagon-stimulated cAMP production, although long-term signalling is dampened by increased receptor lysosomal targeting for degradation. Despite these signalling effects, only minor disturbance of carbohydrate metabolism was observed in mice with up-regulated hepatic RAMP2. Conclusions By retaining GCGR intracellularly, RAMP2 alters the spatiotemporal pattern of GCGR signalling. Further exploration of the effects of RAMP2 on GCGR in vivo is warranted. Graphical abstract Icons sourced from [1]
Rbfox1 is required for myofibril development and maintaining fiber-type specific isoform expression in Drosophila muscles

Protein isoform transitions confer distinct properties on muscle fibers and are regulated predominantly by differential transcription and alternative splicing. RNA-binding Fox protein 1 (Rbfox1) can affect both transcript levels and splicing, and is known to control skeletal muscle function. However, the detailed mechanisms by which Rbfox1 contributes to normal muscle development and physiology remain obscure. In this study, we report that Rbfox1 contributes to the generation of adult muscle diversity in Drosophila. Rbfox1 is differentially expressed in tubular and fibrillar muscle fiber types. RNAi knockdown of Rbfox1 leads to a loss of flight, climbing and jumping ability, as well as eclosion defects. Myofibers in knockdown muscle are frequently torn, and sarcomeres are hypercontracted. These defects arise from mis-regulation of fiber-type specific gene and splice isoform expression, notably loss of an IFM-specific isoform of Troponin-I that is critical for regulating myosin activity. We find that Rbfox1 influences mRNA transcript levels through 1) direct binding of 3’-UTRs of target transcripts as well as 2) through regulation of myogenic transcription factors, including Mef2, Exd and Salm. Moreover, Rbfox1 modulates splice isoform expression through 1) direct regulation of target splice events in structural genes and 2) regulation of the CELF-family RNA-binding protein Bruno1. Our data indicate that cross-regulatory interactions observed between FOX and CELF family RNA-binding proteins in vertebrates are conserved between their counterparts, Rbfox1 and Bruno1 in flies. Rbfox1 thus affects muscle development by regulation of both fiber-type specific gene and gene isoform expression dynamics of identity genes and structural proteins.
Emerged human-like facial expression representation in a deep convolutional neural network

Face identity and expression play critical roles in social communication. Recent research found that the deep convolutional neural networks (DCNNs) trained to recognize facial identities spontaneously learn features that support facial expression recognition, and vice versa, suggesting an integrated representation of facial identity and expression. In the present study, we found that the expression-selective units spontaneously emerged in a VGG-Face trained for facial identity recognition and tuned to distinct basic expressions. Importantly, they exhibited typical hallmarks of human expression perception, i.e., the facial expression confusion effect and categorical perception effect. We then investigated whether the emergence of expression-selective units is attributed to either face-specific experience or domain-general processing, by carrying out the same analysis on a VGG-16 trained for object classification and an untrained VGG-Face without any visual experience, both of them having the identical architecture with the pretrained VGG-Face. Although Similar expression-selective units were found in both DCNNs, they did not exhibit reliable human-like characteristics of facial expression perception. Taken together, our computational findings revealed the necessity of domain-specific visual experience of face identity for the development of facial expression perception, highlighting the contribution of nurture to form human-like facial expression perception. Beyond the weak equivalence between human and DCNNS at the input-output behavior, emerging simulated algorithms between models and humans could be established through domain-specific experience.