Miracle-dz/UniFAR-FTUs huggingface dataset:
Licensing microgels prolong the immunomodulatory phenotype of mesenchymal stromal cells

Mesenchymal stromal cells (MSC) are sensors of inflammation, and they exert immunomodulatory properties through the secretion of cytokines and exosomes and direct cell-cell interactions. MSC are routinely used in clinical trials and effectively resolve inflammatory conditions. Nevertheless, inconsistent clinical outcomes necessitate the need for more robust therapeutic phenotypes. The immunomodulatory properties of MSC can be enhanced and protracted by priming (aka licensing) them with IFNγ and TNFα. Yet these enhanced properties rapidly diminish, and prolonged stimulation could tolerize their response. Hence a balanced approach is needed to enhance the therapeutic potential of the MSC for consistent clinical performance. Here, we investigated the concentration-dependent effects of IFNγ and TNFα and developed gelatin-based microgels to sustain a licensed MSC phenotype. We show that IFNγ treatment is more beneficial than TNFα in promoting an immunomodulatory MSC phenotype. We also show that the microgels possess integrin-binding sites to support MSC attachment and a net positive charge to sequester the licensing cytokines electrostatically. Microgels are enzymatically degradable, and the rate is dependent on the enzyme concentration and matrix density. Our studies show that one milligram of microgels by dry mass can sequester up to 641 ± 81 ng of IFNγ. Upon enzymatic degradation, microgels exhibited a sustained release of IFNγ that linearly correlated with their degradation rate. The MSC cultured on the IFNγ sequestered microgels displayed efficient licensing potential comparable to or exceeding the effects of bolus IFNγ treatment. When cultured with proinflammatory M1-like macrophages, the MSC-seeded on licensing microgel showed an enhanced immunomodulatory potential compared to untreated MSC and MSC treated with bolus IFNγ treatment. Specifically, the MSC seeded on licensing microgels significantly upregulated Arg1, Mrc1, and Igf1, and downregulated Tnfa in M1-like macrophages compared to other treatment conditions. These licensing microgels are a potent immunomodulatory approach that shows substantial promise in elevating the efficacy of current MSC therapies and may find utility in treating chronic inflammatory conditions.
Meta-analysis of metagenomes via machine learning and assembly graphs reveals strain switches in Crohn’s disease

Microbial strains have closely related genomes but may have different phenotypes in the same environment. Shotgun metagenomic sequencing can capture the genomes of all strains present in a community but strain-resolved analysis from shotgun sequencing alone remains difficult. We developed an approach to identify and interrogate strain-level differences in groups of metagenomes. We use this approach to perform a meta-analysis of stool microbiomes from individuals with and without inflammatory bowel disease (IBD; Crohn’s disease, ulcerative colitis; n = 605), a disease for which there are not specific microbial biomarkers but some evidence that microbial strain variation may stratify by disease state. We first developed a machine learning classifier based on compressed representations of complete metagenomes (FracMinHash sketches) and identified genomes that correlate with IBD subtype. To rescue variation that may not have been present in the genomes, we then used assembly graph genome queries to recover strain variation for correlated genomes. Lastly, we developed a novel differential abundance framework that works directly on the assembly graph to uncover all sequence variants correlated with IBD. We refer to this approach as dominating set differential abundance analysis and have implemented it in the spacegraphcats software package. Using this approach, we identified five bacterial strains that are associated with Crohn’s disease. Our method captures variation within the entire sequencing data set, allowing for discovery of previously hidden disease associations.
Integrating analog and digital modes of gene expression at Arabidopsis FLC

Quantitative gene regulation at the cell population-level can be achieved by two fundamentally different modes of regulation at individual gene copies. A “digital” mode involves binary ON/OFF expression states, with population-level variation arising from the proportion of gene copies in each state, while an “analog” mode involves graded expression levels at each gene copy. At the Arabidopsis floral repressor FLOWERING LOCUS C (FLC), “digital” Polycomb silencing is known to facilitate quantitative epigenetic memory in response to cold. However, whether FLC regulation before cold involves analog or digital modes is unknown. Using quantitative fluorescent imaging of FLC mRNA and protein, together with mathematical modelling, we find that FLC expression before cold is regulated by both analog and digital modes. We observe a temporal separation between the two modes, with analog preceding digital. The analog mode can maintain intermediate expression levels at individual FLC gene copies, before subsequent digital silencing, consistent with the copies switching OFF stochastically and heritably without cold. This switch leads to a slow reduction in FLC expression at the cell population-level. These data present a new paradigm for gradual repression, elucidating how analog transcriptional and digital epigenetic memory pathways can be integrated.
β-catenin programs a tissue-specific epigenetic vulnerability in aggressive adrenocortical carcinoma

Adrenocortical carcinoma (ACC) is a rare cancer in which tissue-specific differentiation is paradoxically associated with dismal outcomes. The differentiated ACC subtype CIMP-high is prevalent, incurable, and routinely fatal. CIMP-high ACC possess abnormal DNA methylation and frequent β-catenin activating mutations. Here, we demonstrate that ACC differentiation is maintained by a balance between nuclear, tissue-specific β-catenin-containing complexes and the epigenome. On chromatin, β-catenin binds master adrenal transcription factor SF1 and hijacks the adrenocortical super-enhancer landscape to maintain differentiation. Off chromatin, β-catenin binds histone methyltransferase EZH2, which is redistributed by the CIMP-high DNA methylation signature. SF1/β-catenin and EZH2/β-catenin complexes exist in normal adrenals and are selected for through all phases of ACC evolution. Pharmacologic EZH2 inhibition in CIMP-high ACC favors EZH2/β-catenin assembly and purges SF1/β-catenin from chromatin, erasing differentiation and restraining cancer growth in vitro and in vivo. Our studies illustrate how tissue-specific programs shape oncogene selection, surreptitiously encoding targetable therapeutic vulnerabilities.
Responses of the in vitro turtle brain to visual and auditory stimuli during severe hypoxia

North American pond turtles (Emydidae) are renowned for their ability to survive extreme hypoxia and anoxia, which enables several species to overwinter in ice-locked, anoxic freshwater ponds and bogs for months. Centrally important for surviving these conditions is a profound metabolic suppression, which enables ATP demands to be met entirely with glycolysis. Despite this, turtles have occasionally been observed exploring their natural and laboratory environments while anoxic and can still respond to sensory stimuli. To better understand whether anoxia limits a special sensory function, we recorded evoked potentials in a reduced brain preparation, in vitro, that was perfused with severely hypoxic artificial cerebral spinal fluid (aCSF). For recordings of visual responses, an LED light was flashed onto retinal eyecups while evoked potentials were recorded from the retina or the optic tectum. For recordings of auditory responses, a piezo motor-controlled glass actuator vibrated the tympanic membrane while evoked potentials were recorded from the cochlear nuclei. We found that visual responses decreased even with moderately hypoxic perfusate (aCSF PO2 = 30-60 torr) and completely abolished under severe hypoxia. In contrast, the evoked response within the cochlear nuclei was unattenuated with severe hypoxia (aCSF PO2 < 20 torr). These data provide further support that pond turtles have a limited ability to sense visual information in their environment even while moderately hypoxic, but that auditory input may become a principal avenue of sensory perception during extreme diving in this species. Summary Statement Severe hypoxia attenuates the visual, but not auditory responses in a reduced brain preparation from a pond turtle.
Single cell multi-omic mapping of subclonal architecture and pathway phenotype in primary gastric and metastatic colon cancers

Single cell genomics provides a high-resolution profile of intratumoral heterogeneity and subclonal structure in primary and metastatic tumors. Notably, metastases and therapeutic resistant tumors often originate from distinct subclones. These distinct cellular populations are an important contributor to adaptation and resistance to ongoing therapy. Single cell DNA-sequencing (scDNA-seq) defines subclones but does not provide biological information about cell types. Single cell RNA-sequencing (scRNA-seq) provides biological information but is less useful for identifying different subclones. The integrated scDNA-seq and scRNA-seq data from the same tumor cell population provides both subclone structure and biology. To understand the cellular genomic variation of different subclones in primary and metastatic cancers, we developed an approach to integrate multi-omics data from both types of single cells. This joint data set represented thousands of normal and tumor cells derived from a set of primary gastric and metastatic colorectal cancers. The extensive cellular sampling provided robust characterization of the subclonal architecture of gastric and colorectal cancers. We reconstructed the subclonal architecture using the cells in G0/G1 phase. The scDNA-seq provided a ground truth for copy number-based subclones. From the scRNA-seq data, the epithelial cells in G0/G1 were identified and assigned to specific subclones by a correlation algorithm based on gene dosage. The inferred CNV profiles from the scRNA-seq epithelial cells were assigned subclones identified from the scDNA-seq. Afterward, we determined the biological pathway activities of specific clones. Overall, integrative multi-omics analysis of single-cell datasets is more informative than any individual genomic modality, provides deep insights into the intratumoral heterogeneity, and reveals subclonal biology.
Wheat NAM genes regulate the majority of early monocarpic senescence transcriptional changes including nitrogen remobilization genes

Senescence enables the remobilisation of nitrogen and micronutrients from vegetative tissues of wheat (Triticum aestivum L.) into the grain. Understanding the molecular players in this process will enable the breeding of wheat lines with tailored grain nutrient content. The NAC transcription factor NAM-B1 is associated with earlier senescence and higher levels of grain protein, iron, and zinc content due to increased nutrient remobilisation. To investigate how related NAM genes control nitrogen remobilization at the molecular level, we carried out a comparative transcriptomic study at seven time points (3, 7, 10, 13, 19 and 26 days after anthesis) in wild type and NAM RNA interference (RNAi) lines with reduced NAM gene expression. Approximately 2.5 times more genes were differentially expressed in WT than NAM RNAi during this early senescence time course (6,508 vs 2,605 genes). In both genotypes, differentially expressed genes were enriched for GO terms related to photosynthesis, hormones, amino acid transport and nitrogen metabolism. However, nitrogen metabolism genes including glutamine synthetase (GS1 and GS2), glutamate decarboxylase (GAD), glutamate dehydrogenase (GDH) and asparagine synthetase (ASN1) showed stronger or earlier differential expression in WT than in NAM RNAi plants, consistent with higher nitrogen remobilisation. The use of time course data identified the dynamics of NAM-regulated and NAM-independent gene expression changes during senescence, and provides an entry point to functionally characterise the pathways regulating senescence and nutrient remobilisation in wheat.
Clonal breeding strategies to harness heterosis: insights from stochastic simulation

To produce genetic gain, hybrid crop breeding can change the additive as well as dominance genetic value of populations, which can lead to utilization of heterosis. A common hybrid breeding strategy is reciprocal recurrent selection (RRS), in which parents of hybrids are typically recycled within pools based on general combining ability (GCA). However, the relative performance of RRS and other possible breeding strategies have not been thoroughly compared. RRS can have relatively increased costs and longer cycle lengths which reduce genetic gain, but these are sometimes outweighed by its ability to harness heterosis due to dominance and increase genetic gain. Here, we used stochastic simulation to compare gain per unit cost of various clonal breeding strategies with different amounts of population inbreeding depression and heterosis due to dominance, relative cycle lengths, time horizons, estimation methods, selection intensities, and ploidy levels. In diploids with phenotypic selection at high intensity, whether RRS was the optimal breeding strategy depended on the initial population heterosis. However, in diploids with rapid cycling genomic selection at high intensity, RRS was the optimal breeding strategy after 50 years over almost all amounts of initial population heterosis under the study assumptions. RRS required more population heterosis to outperform other strategies as its relative cycle length increased and as selection intensity decreased. Use of diploid fully inbred parents vs. outbred parents with RRS typically did not affect genetic gain. In autopolyploids, RRS typically was not beneficial regardless of the amount of population inbreeding depression. Key Message Reciprocal recurrent selection sometimes increases genetic gain per unit cost in clonal diploids with heterosis due to dominance, but it typically does not benefit autopolyploids.
Identifying low risk insecticides that can enhance food production without increasing mortality of biocontrol agents for human schistosomiasis

Use of agrochemicals, including insecticides, is vital to food production and predicted to increase 2-5 fold by 2050. Previous studies have shown a positive association between agriculture and the human infectious disease schistosomiasis, which is problematic as this parasitic disease infects approximately 250 million people worldwide. Certain insecticides might runoff fields and be highly toxic to invertebrates, such as prawns in the genus Macrobrachium, that are biocontrol agents for snails that transmit the parasites causing schistosomiasis. We used a laboratory dose-response experiment and an observational field study to determine the relative toxicities of three pyrethroid (esfenvalerate, λ-cyhalothrin, and permethrin) and three organophosphate (chlorpyrifos, malathion, and terbufos) insecticides to Macrobrachium prawns. In the lab, pyrethroids were consistently several orders of magnitude more toxic than organophosphate insecticides, and more likely to runoff fields at lethal levels according to modeling data. In the field, we found that Macrobrachium prawn survival at 31 water contact sites in the lower basin of the Senegal River where schistosomiasis is endemic was predicted by pyrethroid application rates to nearby crop fields after controlling for abiotic and prawn-level factors. Our findings suggest that widely used pyrethroid insecticides can have strong non-target effects on Macrobrachium prawns that are biocontrol agents where 400 million people are at risk of human schistosomiasis. Understanding the ecotoxicology of high-risk insecticides may help improve human health in schistosomiasis-endemic regions undergoing agricultural expansion.
The curse of optimism: a persistent distraction by novelty

Human curiosity has been interpreted as a drive for exploration and modeled by intrinsically motivated reinforcement learning algorithms. An unresolved challenge in machine learning is that several of these algorithms get distracted by reward-independent stochastic stimuli. Here, we ask whether humans get distracted by the same stimuli as the algorithms. We design an experimental paradigm where human participants search for rewarding states in an environment with a highly ‘stochastic’ but reward-free sub-region. We show that (i) participants get repeatedly and persistently distracted by novelty in the stochastic part of the environment; (ii) optimism about the availability of other rewards increases this distraction; and (iii) the observed distraction pattern is consistent with the predictions of algorithms driven by novelty but not with ‘optimal’ algorithms driven by information-gain. Our results suggest that humans use suboptimal but computationally cheap curiosity-driven policies for exploration in complex environments.
Modulating hierarchical learning by high-definition transcranial alternating current stimulation at theta frequency

Considerable evidence highlights the dorsolateral prefrontal cortex (DLPFC) as a key region for hierarchical learning. In a previous electroencephalography (EEG) study we found that the low-level precision-weighted prediction errors (pwPEs) were encoded by frontal theta oscillations (4–7Hz), centered on F4 in the 10-20 EEG system corresponding to right DLPFC (rDLPFC). However, the causal relationship between frontal theta oscillations and hierarchical learning remains poorly understood. To investigate this question, in the current study, participants received theta (6Hz) and sham high-definition transcranial alternating current stimulation (HD-tACS) over the rDLPFC, while performing the probabilistic reversal learning task. Behaviorally, theta tACS induced a significant reduction in accuracy for the stable environment, but not for the volatile environment, relative to the sham condition. Computationally, we implemented a combination of a hierarchical Bayesian learning and a decision model. Theta tACS induced a significant increase in low-level (i.e., probability) learning rate and uncertainty of low-level estimation relative to sham condition. Instead, the temperature parameter of the decision model was not significantly altered due to theta stimulation. These results indicate that theta frequency may modulate the (low-level) learning rate. Furthermore, environmental features (e.g., its stability) may determine whether learning is optimized as a result.
Manipulation of neuronal activity in the entorhinal-hippocampal circuit affects intraneuronal amyloid-β levels

One of the neuropathological hallmarks of Alzheimer’s disease (AD) is the accumulation of amyloid-β (Aβ) plaques, which is preceded by intraneuronal build-up of toxic, aggregated Aβ during disease progression. Aβ plaques are first deposited in the neocortex before appearing in the medial temporal lobe, and tau pathology with subsequent neurodegeneration in the latter anatomical region causes early memory impairments in patients. Current research suggests that early intraneuronal Aβ build-up may begin in superficial layers of lateral entorhinal cortex (LEC). To examine whether manipulation of neuronal activity of LEC layer II neurons affected intraneuronal Aβ levels in LEC and in downstream perforant path terminals in the hippocampus (HPC), we used a chemogenetic approach to selectively and chronically silence superficial LEC neurons in young and aged 3xTg AD mice and monitored its effect on intraneuronal Aβ levels in LEC and HPC. Chronic chemogenetic silencing of LEC neurons led to reduced early intraneuronal Aβ in LEC and in projection terminals in the HPC, compared with controls. Early intraneuronal Aβ levels in the downstream HPC correlated with activity levels in superficial layers of LEC, with the subiculum being the earliest subregion involved, and our findings give evidence to early AD neuropathology originating in select neuronal populations.
A hair cell-specific peroxidase coordinates stomatal and prickle hair cell size to optimize epidermal cell functionality in grasses

and we selected candidate genes for a genetic screening. Candidates their gene function, their epidermis is cell it the a wide cell types stomata and hair individual cell it is poorly understood their number and size is coordinated. we identified a role for BdPRX76/BdPOX , a class III peroxidase, stomata and hair cell size in the Brachypodium distachyon . In bdpox stomata prickle hair cells were smaller. density remained unchanged, the negative correlation between stomatal size and density disrupted and resulted in higher stomatal conductance intrinsic water-use efficiency. Reporter lines that BdPOX was exclusively expressed in hair cells suggesting that BdPOX cell-autonomously hair cell size and non-cell-autonomously restricts stomatal length. Cell wall autofluorescence and lignin stainings indicated a role for BdPOX in lignification or crosslinking of related phenolic compounds at the hair cell base. Ectopic expression of BdPOX in the stomatal lineage increased phenolic content in cell walls and restricted stomatal elongation. Together, we reveal a developmental coordination between hair cells and stomata that optimizes epidermal functionality. We propose that a cell-type-specific disruption of this coordination leads to compensatory developmentaldefects in other epidermal cell types.
A Physcomitrella PIN protein acts in spermatogenesis and sporophyte retention

The auxin efflux PIN-FORMED (PIN) proteins are conserved in all land plants and important players in plant development. In the moss Physcomitrella (Physcomitrium patens) three canonical PINs (PpPINA-C) are expressed in the leafy shoot (gametophore). PpPINA and PpPINB show functional activity in vegetative growth and sporophyte development. Here, we examined the role of PpPINC in the life cycle of Physcomitrella. We established reporter and knockout lines for PpPINC and analysed vegetative and reproductive tissues using microscopy and transcriptomic sequencing of moss gametangia. PpPINC is expressed in immature leaves, mature gametangia and during sporophyte development. The sperm cells (spermatozoids) of pinC knockout mutants exhibit increased motility and an altered flagella phenotype. Further, the pinC mutants have a higher portion of differentially expressed genes (DEGs) related to spermatogenesis, increased fertility, and an increased abortion rate of premeiotic sporophytes. Here, we show that PpPINC is important for spermatogenesis and sporophyte retention. We propose an evolutionary conserved way of polar growth during early moss embryo development and sporophyte attachment to the gametophore, while suggesting the mechanical function in sporophyte retention of a ring structure, the Lorch ring.