Miracle-dz/UniFAR-FTUs huggingface dataset:
Comparative transcriptomics of Hirschfeldia incana and relatives highlights differences in photosynthetic pathways

Photosynthesis is the only yield-related trait that has not yet been substantially improved by plant breeding. The limited results of previous attempts to increase yield via improvement of photosynthetic pathways suggest that more knowledge is still needed to achieve this goal. To learn more about the genetic and physiological basis of high photosynthetic light-use efficiency (LUE) at high irradiance, we study Hirschfeldia incana. Here, we compare the transcriptomic response to high light of H. incana with that of three other members of the Brassicaceae, Arabidopsis thaliana, Brassica rapa, and Brassica nigra, which have a lower photosynthetic LUE. First, we built a high-light, high-uniformity growing environment in a climate-controlled room. Plants grown in this system developed normally and showed no signs of stress during the whole growth period. Then we compared gene expression in low and high-light conditions across the four species, utilizing a panproteome to group homologous proteins efficiently. As expected, all species actively regulate genes related to the photosynthetic process. An in-depth analysis on the expression of genes involved in three key photosynthetic pathways revealed a general trend of lower gene expression in high-light conditions. However, H. incana distinguishes itself from the other species through higher expression of certain genes in these pathways, either through constitutive higher expression, as for LHCB8, ordinary differential expression, as for PSBE, or cumulative higher expression obtained by simultaneous expression of multiple gene copies, as seen for LHCA6. These differentially expressed genes in photosynthetic path-ways are interesting leads to further investigate the exact relationship between gene expression, protein abundance and turnover, and ultimately the LUE phenotype. In addition, we can also exclude thousands of genes from “explaining” the phenotype, because they do not show differential expression between both light conditions. Finally, we deliver a transcriptomic resource of plant species fully grown under, rather than briefly exposed to, a very high irradiance, supporting efforts to develop highly efficient photosynthesis in crop plants.
A molecularly distinct cell type in the dmPAG regulates intermale aggression behaviors in mice

The periaqueductal gray (PAG) has been suggested as a central hub for defensive responses to threatening stimuli and regulation of aggression. However, little is known on the circuitry and molecular mechanisms that govern this regulation. Here, we investigate the role of a molecularly distinct cell type, Taschykinin 2-expressing neurons (Tac2+), located in dorsomedial PAG (dmPAG), in modulating aggression in a mouse resident-intruder model. Using a rabies-assisted input mapping strategy, we found that dmPAGTac2 neurons received monosynaptic input from the ventromedial hypothalamus, a region implicated in mediating fighting behaviors. Whole-brain Fos mapping and in vivo Ca2+ recording in mice revealed that dmPAGTac2 neurons were exclusively activated by fighting behaviors. Further, we manipulated activity of dmPAGTac2 neurons using chemogenetic tools and found that activation of dmPAGTac2 neurons evoked, while inhibition or genetic ablation of dmPAGTac2 neurons suppressed fighting behaviors. To further reveal molecular pathways that govern this fighting behaviors, we profiled dmPAGTac2 neurons using a viral-based translating ribosome affinity purification (TRAP) approach and revealed that fighting behaviors specifically induced enrichment of serotonin-associated transcripts in dmPAGTac2 neurons. Last, we validated these findings by selectively delivering pharmacological agents into the dmPAG through guide cannula and reversed the behavioral outcomes induced by chemogenetic manipulation of dmPAGTac2 neurons. Collectively, we identify that dmPAGTac2 neuron as a molecularly distinct cell type that regulates mouse aggressive behavior in dmPAG region and thus suggest a novel molecular target for the treatment of exacerbated aggressive behaviors in populations that exhibit high-level of violence. Graphic Abstract
Detection of high potential gold mineralization areas using Landsat 8 data in Northeastern Sudan

This investigation used Landsat 8 data for mapping lithological units and alteration zones to detect high potential areas for gold mineralization in Red Sea Hills in Sudan part of the Arabian-Nubian Shield (ANS). The study area contains three gold mines part of Ariab mining district in Red Sea Hills, Northeastern Sudan. There are three types of gold deposits in the study area (Supergene deposits, polymetallic massive sulphide deposits and The Ganaet deposits) are being mined in Hadal Auatib mine, Hassai mine and Kamoeb mine. The objective of this study was to find new high potential areas for gold mineralization in the area. Color composite, band ratio, principle component analysis, directional filtering, minimum noise fraction (MNF), spectral angle mapper (SAM), matched filtering (MF) and Mixture-Tuned Matched-Filtering (MTMF) were used for geological mapping in this study. The results of this study showed the distribution of the lithological units and the hydrothermal alteration zones along with new high potential areas for gold mineralization which can be used in the future and proved the ability of Landsat data in mapping these feature. The results indicate that Landsat 8 data are capable to identify lithological units and alteration zones at a regional scale. However the identification of specific hydrothermal alteration zone is not feasible. High potential areas have been identified in the study area. Fieldwork verified the image processing results.
Chromosome size-dependent polar ejection force impairs mammalian mitotic error correction

Accurate chromosome segregation requires sister kinetochores to biorient, attaching to opposite spindle poles. To this end, the mammalian kinetochore destabilizes incorrect attachments and stabilizes correct ones, but how it discriminates between these is not yet clear. Here, we test the model that kinetochore tension is the stabilizing cue and ask how chromosome size impacts that model. We live image PtK2 cells, with just 14 chromosomes, widely ranging in size, and find that long chromosomes align at the metaphase plate later than short chromosomes. Enriching for errors and imaging error correction live, we show that long chromosomes exhibit a specific delay in correcting attachments. Using chromokinesin overexpression and laser ablation to perturb polar ejection forces, we find that chromosome size and force on arms determine alignment order. Thus, we propose a model where increased force on long chromosomes can falsely stabilize incorrect attachments, delaying their biorientation. As such, long chromosomes may require compensatory mechanisms for correcting errors to avoid chromosomal instability.
Efficient Drug Delivering of a Photodynamic Therapy Agent into Cellular Membranes Rationalized by Molecular Dynamics

Photodynamic Therapy (PDT) represents a most attractive therapeutic strategy to reduce side effects of chemotherapy and improve the global quality of life of patients. Yet, many PDT drugs suffer from a poor bioavailability and cellular intake, and thus, drug delivery strategy should be implemented. In this letter we report the behavior of a temoporfin-based PDT drug, commercialized under the name of Foscan, complexed by two ? -cyclodextrin units in presence of a lipid bilayer. Our all atom simulations have shown the internalization of the complex and its spontaneous dissociation inside the lipid bilayer. The factors favoring penetration and dissociation have also been analyzed, together with the membrane perturbation due to the interaction with the cyclodextrin complex. Our results confirm the suitability of the encapsulation strategy for PDT, and rationalize the experimental results concerning its efficacy. TOC GRAPHICS
Social Context and Reward Sensitivity Enhance Corticostriatal Function during Experiences of Shared Rewards

Although prior research has demonstrated enhanced striatal response when sharing rewards with close social connections, less is known about how individual differences affect ventral striatal (VS) activation and connectivity when experiencing rewards within social contexts. Given that self-reported reward sensitivity and level of substance use have been associated with differences in VS activation, we set out to investigate whether these factors would be independently associated with enhancements to neural reward responses within social contexts. In this pre-registered study, participants (N=45) underwent fMRI while playing a card guessing game in which correct or incorrect guesses resulted in monetary gains and losses that were shared evenly with either a close friend, stranger (confederate), or non-human partner. Consistent with our prior work, we found increased VS activation when sharing rewards with a socially close peer as opposed to an out-of-network stranger. As self-reported reward sensitivity increased, the difference in VS response to rewards shared with friends and strangers decreased. We also found enhanced connectivity between the VS and temporoparietal junction when sharing rewards with close friends as opposed to strangers. Finally, exploratory analyses revealed that as reward sensitivity and sub-clinical substance use increase, the difference in VS connectivity with the right fusiform face area increases as a function of social context. These findings demonstrate that responsivity to the context of close friends may be tied to individual reward sensitivity or sub-clinical substance use habits; together these factors may inform predictions of risk for future mental health disorders.
Genome sequencing and molecular networking analysis of the wild fungus Anthostomella pinea reveal its ability to produce a diverse range of secondary metabolites

Background Filamentous fungi are prolific producers of bioactive molecules and enzymes with important applications in industry. Yet, the vast majority of fungal species remain undiscovered or uncharacterized. Here we focus our attention to a wild fungal isolate that we identified as Anthostomella pinea . The fungus belongs to a complex polyphyletic genus in the family of Xylariaceae , which is known to comprise endophytic and pathogenic fungi that produce a plethora of interesting secondary metabolites. Despite that, Anthostomella is largely understudied and only two species have been fully sequenced and characterized at a genomic level. Results In this work, we used long-read sequencing to obtain the complete 53.7 Mb genome sequence including the full mitochondrial DNA. We performed extensive structural and functional annotation of coding sequences, including genes encoding enzymes with potential applications in biotechnology. Among others, we found that the genome of A. pinea encodes 91 biosynthetic gene clusters, more than 600 CAZymes, and 164 P450s. Furthermore, untargeted metabolomics and molecular networking analysis of the cultivation extracts revealed a rich secondary metabolism, and in particular an abundance of sesquiterpenoids and sesquiterpene lactones. We also identified the polyketide antibiotic xanthoepocin, to which we attribute the anti–Gram-positive effect of the extracts that we observed in antibacterial plate assays. Conclusions Taken together, our results provide a first glimpse into the potential of Anthstomella pinea to provide new bioactive molecules and biocatalysts and will facilitate future research into these valuable metabolites.
Ribosomal S6 kinase 1 regulates ‘inflammaging’ via the senescence secretome

Inhibition of the nutrient-responsive mTOR (mammalian target of rapamycin) signalling pathway including the key downstream effector S6 kinase 1 (S6K1) extends lifespan and improves healthspan in mice. However, the underlying mechanisms contributing to the broad range of age-related benefits observed with loss of S6K1 signalling are unclear. Cellular senescence is a stable growth arrest accompanied by an inflammatory phenotype (termed the senescence-associated secretory phenotype, or SASP). While both cellular senescence and SASP-mediated chronic inflammation contribute to age-related pathology, the specific role of S6K1 signalling in these processes has not been determined. Here, focussing on mouse liver, a key target tissue for the beneficial metabolic effects of loss of S6K1 signalling, we show that S6K1 deletion does not reduce senescence but ameliorates inflammation and immune cell infiltration in aged livers. Using human and mouse models of senescence, we demonstrated that reduced inflammation is a liver-intrinsic effect associated with S6K deletion. Furthermore, gene expression analysis suggested that downregulated cGAS/STING and IRF3 activation might mediate the impaired SASP observed upon S6K deletion. Using a hepatic oncogene induced senescence model, we showed in vivo that S6K1 deletion results in reduced IRF3 activation, impaired production of cytokines such as IL1ý and reduced immune infiltration. Overall, deletion of S6K reduces inflammation in the liver suggesting that suppression of the inflammatory SASP by loss of S6K could contribute to explain the beneficial effects of inhibiting this pathway on healthspan and lifespan.
Trait Reward Sensitivity Modulates Connectivity with the Temporoparietal Junction and Anterior Insula during Strategic Decision Making

Many decisions happen in social contexts such as negotiations, yet little is understood about how people balance fairness versus selfishness. Past investigations found that activation in brain areas involved in executive function and reward processing was associated with people offering less with no threat of rejection from their partner, compared to offering more when there was a threat of rejection. However, it remains unclear how trait reward sensitivity may modulate activation and connectivity patterns in these situations. To address this gap, we used task-based fMRI to examine the relation between reward sensitivity and the neural correlates of bargaining choices. Participants (N = 54) completed the Sensitivity to Punishment (SP)/Sensitivity to Reward (SR) Questionnaire and the Behavioral Inhibition System/Behavioral Activation System scales. Participants performed the Ultimatum and Dictator Games as proposers and exhibited strategic decisions by being fair when there was a threat of rejection, but being selfish when there was not a threat of rejection. We found that strategic decisions evoked activation in the Inferior Frontal Gyrus (IFG) and the Anterior Insula (AI). Next, we found elevated IFG connectivity with the Temporoparietal junction (TPJ) during strategic decisions. Finally, we explored whether trait reward sensitivity modulated brain responses while making strategic decisions. We found that people who scored lower in reward sensitivity made less strategic choices when they exhibited higher AI-Angular Gyrus connectivity. Taken together, our results demonstrate how trait reward sensitivity modulates neural responses to strategic decisions, potentially underscoring the importance of this factor within social and decision neuroscience.
Skimming genomes for systematics and DNA barcodes of corals

1: Numerous genomic methods developed over the past two decades have enabled the discovery and extraction of orthologous loci to help resolve phylogenetic relationships across various taxa and scales. Genome skimming (or low-coverage whole genome sequencing) remains a low-cost, promising method to not only extract high-copy loci, but also 100s to 1000s of phylogenetically informative single-copy nuclear loci (e.g., ultraconserved elements [UCEs] and exons) from contemporary and historical museum samples. The subphylum Anthozoa, which includes important ecosystem engineers (e.g., stony corals, black corals, anemones and octocorals) in the marine environment, is in critical need of phylogenetic resolution and thus might benefit from a genome-skimming approach. 2: Genome skimming was conducted on 242 hexacorals and octocorals collected from 1890 to 2022. Using previously developed target-capture baitsets, we bioinformatically obtained UCEs and exons from the genome-skimming data and incorporated them with data from previously published target-capture studies. We also extracted partial to whole mitogenomes and nuclear rRNA genes from the skim data. 3: The mean number of UCE and exon loci extracted from the genome skimming data was 1,837 ± 662 SD for octocorals and 1,422 ± 720 loci for hexacorals; phylogenetic relationships were well resolved within each class. A mean of 1,422 ± 720 loci were obtained from the historical museum specimens, with 1,253 loci recovered from the oldest specimen collected in 1886 and 1,336 loci recovered from a holotype. The nuclear rRNA genes and the majority of mitochondrial genes were successfully obtained from >95% of samples. Out of 99 circularized mitogenomes, 88% were recovered in samples from which we obtained >15M paired-end (PE) reads (>30M total reads); there was more variability in whether mitogenomes were circularized or not in samples with <15M PE reads. 4: Bioinformatically pulling UCEs, exons, mitochondrial genomes, and nuclear rRNA genes from genome skimming is a viable and low-cost option for phylogenetic studies. This approach can be used to review and support taxonomic revisions and reconstruct evolutionary histories, including historical museum and type specimens.
LKB1 suppresses growth and promotes the internalization of EGFR through the PIKFYVE lipid kinase

The tumor suppressor LKB1 is a serine/threonine protein kinase that is frequently mutated in human lung adenocarcinoma (LUAD). LKB1 regulates a complex signaling network that is known to control cell polarity and metabolism; however, the pathways that mediate the tumor suppressive activity of LKB1 are incompletely defined. To identify mechanisms of LKB1- mediated growth suppression we developed a spheroid-based cell culture assay to study LKB1- dependent growth. Using this assay, along with genome-wide CRISPR screens and validation with orthogonal methods, we discovered that LKB1 suppresses growth, in part, by activating the PIKFYVE lipid kinase, which promotes the internalization of wild-type EGFR. Our findings reveal a new mechanism of regulation of EGFR, which may have implications for the treatment of LKB1-mutant LUAD.
Early-life gut microbiota assembly patterns are conserved between laboratory and wild mice

Assembly of the mammalian gut microbiota during early life is known to shape key aspects of organismal development, including immunity, metabolism and behaviour. While house mice (Mus musculus) are the major laboratory model organism for gut microbiota research, their artificial lab-based lifestyle could fundamentally alter ecological processes of microbiota assembly and dynamics, in ways that affect their usefulness as a model system. To examine this, here we directly compared patterns of gut microbiota assembly in house mice from the lab and from the wild, making use of a tractable, individually-marked wild population where we could examine patterns of gut microbiota assembly during early life. Despite lab and wild mice harbouring taxonomically distinct communities, we identify striking similarities in multiple patterns of their gut microbiota assembly. Specifically, age-related changes in both alpha and beta diversity, as well as the abundance of predominant phyla and aerotolerance of the microbiota followed parallel trajectories in both settings. These results suggest some degree of intrinsic programme in gut microbiota assembly that transcends variation in taxonomic profiles, and the genetic and environmental background of the host. They further support the notion that despite their artificial environment, lab mice can provide meaningful insights into natural microbiota ecological dynamics in early life and their interplay with host development.
OPUS-Rota5: A Highly Accurate Protein Side-chain Modeling Method with 3D-Unet and RotaFormer

Accurate protein side-chain modeling is crucial for protein folding and design. This is particularly true for molecular docking as ligands primarily interact with side chains. A protein structure with large errors in side chains has limited usage such as in drug design. Previous research on AlphaFold2 (AF2) predictions of GPCR targets indicates that the docking of natural ligands back on AF2-predicted structures has limited successful rate presumably due to large errors in side chains. Here, we introduce a two-stage side-chain modeling approach called OPUS-Rota5. It leverages a modified 3D-Unet to capture the local environmental features including ligand information of each residue, and then employs RotaFormer module to aggregate various types of feature. Evaluation on three test sets, including recently released targets from CAMEO and CASP15, reveals that side chains modeled by OPUS-Rota5 are significantly more accurate than those predicted by other methods. We also employ OPUS-Rota5 to refine the side chains of 25 GPCR targets predicted by AF2 and then performed docking of their natural ligands back with a significantly improved successful rate. Such results suggest that OPUS-Rota5 could be a valuable tool for molecular docking, particularly for targets with relatively accurate predicted backbones, but not side chains.
Effects of non-retinal inputs in visual thalamus depend on visual responsiveness and stimulus context

In the dorsolateral geniculate nucleus (dLGN) of the thalamus, retinal signals are combined with non-retinal inputs such as corticothalamic (CT) feedback and behavioural state. How these shape dLGN activity remains an open question. We recorded extracellular responses in dLGN of awake mice to a movie stimulus, while photosuppressing CT feedback, tracking locomotion and pupil size. To assess the relative impact of retinal and non-retinal inputs, we fit single neuron responses using generalized linear models. While including CT feedback and behavioural state as predictors significantly improved the model’s overall performance, the improvement was especially pronounced for a sub-population of poorly visually responsive neurons. In addition, the impact of CT feedback was faster and more prevalent in the absence of a patterned visual stimulus. Finally, for CT feedback-sensitive dLGN neurons, visual stimuli could be discriminated better when CT feedback was suppressed. Together, these results show that effects of non-retinal inputs in dLGN depend on visual responsiveness and stimulus context.
Strontium isotopes of Tertiary phillipsites from the southern Pacific; timing of the geochemical evolution

ABSTRACT The Rb-Sr system of phillipsites from an indurated volcano-sedimentary mass sampled in the Southern Pacific Ocean became closed long after the deposition of the host rock: Middle Miocene (14.7 ± 3.3 Ma) and Middle Eocene, respectively. This isotopic age of about 15 Ma probably represents the end of an induration phenomenon which stopped the chemical exchanges between the zeolites and their environment. These minerals inherited Sr primarily from volcanic material, as demonstrated by their initial 87Sr/86Sr ratio at 0.70441 ± 0.00036 (2) which plots within the values of the known 87Sr/86Sr ratios of the nearby basalts. The leaching technique with diluted acid was checked by recalculation of the Rb and Sr contents of the leachates and residues according to their percentage in the untreated sample and comparison with their amounts in the corresponding untreated sample. Any discrepancy is, in most cases, smaller than 3.5 percent for both Rb and Sr amounts. This technique may, therefore, be used to obtain a correct amount of the distribution of these elements among the soluble and insoluble fractions. The examination of the leachates also showed that the volcano-sedimentary material forming the cores of nodules from the water-sediment interface experienced a more complex history than the underlying analogous volcano sedimentary level.