Miracle-dz/UniFAR-FTUs huggingface dataset:
Optogenetic activation of striatal D1/D2 medium spiny neurons differentially engages downstream connected areas beyond the basal ganglia

The basal ganglia (BG) are a group of subcortical nuclei responsible for motor control, motor learning and executive function. Central to BG function are striatal medium spiny neurons (MSNs) expressing D1 and D2 dopamine receptors. D1 and D2 MSNs are typically considered functional antagonists that facilitate voluntary movements and inhibit competing motor patterns, respectively. While their opposite role is well documented for certain sensorimotor loops of the BG-thalamocortical network, it is unclear whether MSNs maintain a uniform functional role across the striatum and which influence they exert on brain areas outside the BG. Here, we addressed these questions by combining optogenetic activation of D1 and D2 MSNs in the mouse ventrolateral caudoputamen (vl CPu) with whole-brain functional MRI (fMRI) recordings. Neuronal excitation of either cell population in the vl CPu evoked distinct activity patterns in key regions of the BG-thalamocortical network including the pallidum, thalamus and motor cortex. Importantly, we report that striatal D1 and D2 MSN stimulation differentially engaged cerebellar and prefrontal regions. We characterised these long-range interactions by computational modelling of effective connectivity and confirmed that changes in D1 / D2 output drive functional relationships between regions within and beyond the BG. These results suggest a more complex functional organization of MSNs across the striatum than previously anticipated and provide evidence for the existence of an interconnected fronto - BG - cerebellar network modulated by striatal D1 and D2 MSNs. Graphical Abstract
Biophysical properties governing septin assembly

Septin filaments build structures such as rings, lattices and gauzes that serve as platforms for localizing signaling and organizing cell membranes. How cells control the geometry of septin assemblies in poorly understood. We show here that septins are isodesmic polymers, in contrast to cooperative polymerization exhibited by F-actin and microtubules. We constructed a physical model to analyze and interpret how septin assemblies change in the presence of regulators in yeast extracts. Notably filaments differ in length and curvature in yeast extract compared to pure protein indicating cellular regulators modulate intrinsic biophysical features. Combining analysis of extracts from regulatory mutants with simulations, we found increased filament flexibility and reduced filament fragmentation promote assembly of septin rings, whereas reduced flexibility in crowded environments promotes local filament alignment. This work demonstrates how tuning of intrinsic features of septin filament assembly by regulatory proteins yields a diverse array of structures observed in cells.
AN EXPERIMENTAL STUDY OF LIQUID-PARTICLE FLOW IN CIRCULATING FLUIDIZED BED

A liquid-solid circulating fluidized bed (LSCFB) is operated at high liquid velocity, where particle entrainment is highly significant and between the conventional liquid fluidized bed and the dilute phase liquid transport regimes. LSCFB has potential applications in the fields of food processing, biochemical processing, and petrochemical and metallurgical processing. It is well known that the flow characteristics in a liquid-solid circulating fluidized bed are different from those of a conventional liquid-solid fluidized bed. The limited studies available in literature do not provide complete understanding of the flow structure in this typical regime. In the present work, experiments were carried out in a 0.0762 m ID and 3 m height laboratory-scale liquid-solid circulating fluidized bed apparatus by using various solid particles and tap water as fluidizing medium. In the experimental setup, two distributors (specially designed) were used to monitor solid circulation rate in the riser. The effects of operating parameters, i.e., primary liquid flow rate in the riser (Up), solid circulation rate (Gs), and particle diameter (dp), were analyzed from the experimental data. Finally, a correlation was developed from the experimental data to estimate average solid holdup in the riser, and it was compared with present experimental and available data in the literature. They agree well with a maximum root-mean-square deviation of 7.83%.
Root carbon interaction with soil minerals is dynamic, leaving a legacy of microbially-derived residues

Minerals preserve the oldest most persistent soil carbon, and mineral characteristics appear to play a critical role in the formation of soil organic matter (SOM) associations. To test the hypothesis that carbon source and soil microorganisms also influence mineral-SOM associations, we incubated permeable minerals bags in soil microcosms with and without plants, in a 13CO2 labeling chamber. Mineral bags contained quartz, ferrihydrite, kaolinite, or native soil minerals isolated via density separation. Using 13C-NMR, FTICR-MS, and lipidomics, we traced plant-derived carbon onto minerals harvested from microcosms at three plant growth stages, characterizing total carbon, 13C enrichment, and SOM chemistry. While C accumulation was rapid and mineral-dependent, the accumulated amount was not significantly affected by the presence of plant roots. However, the rhizosphere did shape the chemistry of mineral-associated SOM. Minerals incubated in the rhizosphere were associated with a more diverse array of compounds with different C functional groups (carbonyl, aromatics, carbohydrates, lipids) than minerals incubated in a bulk soil control. These diverse rhizosphere-derived compounds may represent a “transient fraction” of mineral SOM, rapidly exchanging with mineral surfaces. Our results also suggest that many of the lipids which persist on minerals are microbially-derived with a large fraction of fungal lipids. Synopsis This study explores the interaction of rhizosphere carbon, minerals, and microbial influence on the fate of soil carbon. TOC
Synthesis, Properties, and Environmental Applications of Nanoscale Iron-Based Materials: A Review

Due to their special properties, people have been increasingly interested in studying applications of nanoscale metal materials in environmental engineering. Literature about the current research on the synthesis, properties, and environmental applications of nanoscale iron-based materials is reviewed and summarized in this article. Different physical and chemical methods used for synthesizing nano-iron-based particles with desired size, structure, and surface properties are described. We also emphasize important properties of nano-iron-based particles, including the density and intrinsic reactivity of surface sites. These properties directly influence the chemical behavior of such particles and, consequently, affect their applications in water and wastewater treatment and in air pollution control. Environmental applications of nano-iron particles are discussed in detail, including removal of chlorinated organics, heavy metals, and inorganics.
Insular cortex corticotropin-releasing factor integrates stress signaling with social decision making

Impairments in social cognition manifest in a variety of psychiatric disorders, making the neurobiological mechanisms underlying social decision making of particular translational importance. The insular cortex is consistently implicated in stress-related social and anxiety disorders, which are associated with diminished ability to make and use inferences about the emotions of others to guide behavior. We investigated how corticotropin releasing factor (CRF), a neuromodulator evoked by both self and social stressors, influenced the insula. In acute slices from male and female rats, CRF depolarized insular pyramidal neurons. In males, but not females, CRF suppressed presynaptic GABAergic inhibition leading to greater excitatory synaptic efficacy in a CRF receptor 1 (CRF1) and cannabinoid receptor 1 (CB1) dependent fashion. In males only, insular CRF increased social investigation, and CRF1 and CB1 antagonists interfered with social decision making. To investigate the molecular and cellular basis for the effect of CRF we examined insular CRF1 and CB1 mRNAs and found greater total insula CRF1 mRNA in females but greater CRF1 and CB1 mRNA colocalization in male insular cortex glutamatergic neurons which suggest complex, sex-specific organization of CRF and endocannabinoid systems. Together these results reveal a new sex-specific mechanism by which stress and affect contribute to social decision making.
Respiration, Heartbeat, and Conscious Tactile Perception

Previous studies have shown that timing of sensory stimulation during the cardiac cycle interacts with perception. Given the natural coupling of respiration and cardiac activity, we investigated here their joint effects on tactile perception. Forty-one healthy female and male human participants reported conscious perception of finger near-threshold electrical pulses (33% null trials) and decision confidence while electrocardiography, respiratory activity, and finger photoplethysmography were recorded. Participants adapted their respiratory cycle to expected stimulus onsets to preferentially occur during late inspiration/early expiration. This closely matched heart rate variation (sinus arrhythmia) across the respiratory cycle such that most frequent stimulation onsets occurred during the period of highest heart rate probably indicating highest alertness and cortical excitability. Tactile detection rate was highest during the first quadrant after expiration onset. Interindividually, stronger respiratory phase-locking to the task was associated with higher detection rates. Regarding the cardiac cycle, we confirmed previous findings that tactile detection rate was higher during diastole than systole and newly specified its minimum at 250–300 ms after the R-peak corresponding to the pulse wave arrival in the finger. Expectation of stimulation induced a transient heart deceleration which was more pronounced for unconfident decision ratings. Interindividually, stronger poststimulus modulations of heart rate were linked to higher detection rates. In summary, we demonstrate how tuning to the respiratory cycle and integration of respiratory-cardiac signals are used to optimize performance of a tactile detection task. SIGNIFICANCE STATEMENT Mechanistic studies on perception and cognition tend to focus on the brain neglecting contributions of the body. Here, we investigated how respiration and heartbeat influence tactile perception: respiration phase-locking to expected stimulus onsets corresponds to highest heart rate (and presumably alertness/cortical excitability) and correlates with detection performance. Tactile detection varies across the heart cycle with a minimum when the pulse reaches the finger and a maximum in diastole. Taken together with our previous finding of unchanged early event-related potentials across the cardiac cycle, we conclude that these effects are not a peripheral physiological artifact but a result of cognitive processes that model our body's internal state, make predictions to guide behavior, and might also tune respiration to serve the task.
Improved architectures for flexible DNA production using retrons across kingdoms of life

Exogenous DNA is a critical molecular tool for biology. This is particularly true for gene editing, where exogenous DNA can be used as a template to introduce precise changes to the sequence of a cell’s genome. This DNA is typically synthesized or assembled in vitro and then delivered to target cells. However, delivery can be inefficient, and low abundance of template DNA may be one reason that precise editing typically occurs at a low rate. It has recently been shown that producing DNA inside cells can using reverse transcriptases can increase the efficiency of genome editing. One tool to produce that DNA is a retron, a bacterial retroelement that has an endogenous role in phage defense. However, little effort has been directed at optimizing the retron for production of designed sequences when used as a component of biotechnology. Here, we identify modifications to the retron non-coding RNA that result in more abundant reverse transcribed DNA. We also test architectures of the retron operon that enable efficient reverse transcription across kingdoms of life from bacteria, to yeast, to cultured human cells. We find that gains in DNA production using modified retrons are portable from prokaryotic to eukaryotic cells. Finally, we demonstrate that increased production of RT-DNA results in more efficient genome editing in both prokaryotic and eukaryotic cells. These experiments provide a general framework for production of DNA using a retron for biotechnological applications.
Turning plants from passive to active material: FERONIA and microtubules independently contribute to mechanical feedback

To survive, cells must constantly resist mechanical stress. In plants, this involves the reinforcement of cell walls, notably through microtubule-dependent cellulose deposition, and thus wall sensing. Several receptor-like kinases have been proposed to act as mechanosensors. Here we tested whether the microtubule response to stress acts downstream of known wall sensors. Using a multi-step screen with eleven mutant lines, we identify FERONIA as the primary candidate for controlling the microtubule response to stress. However, when performing mechanical perturbations, we show that the microtubule response to stress can be independent from FER. We reveal that the feronia phenotype can be partially rescued by reducing tensile stress levels. Conversely, in the absence of both microtubules and FER, cells swell and burst like soap bubbles. Altogether, this shows that the microtubule response to stress acts as an independent pathway to resist stress, in parallel to FER. We propose that both pathways are key components to turn plant cells from passive to active material.
The Hox transcription factor Ultrabithorax binds RNA and regulates co-transcriptional splicing through an interplay with RNA polymerase II

Transcription Factors (TFs) play a pivotal role in cell fate decision by coordinating distinct gene expression programs. Although most TFs act at the DNA regulatory layer, few TFs can bind RNA and modulate mRNA splicing. Yet, the mechanistic cues underlying TFs function in splicing remain elusive. Focusing on the Drosophila Hox TF Ultrabithorax (Ubx), our work shed light on a novel layer of Ubx function at the RNA level. Transcriptome and genome-wide binding profiles in embryonic mesoderm and Drosophila cells indicate that Ubx regulates mRNA expression and splicing to promote distinct functions in defined cellular contexts. Ubx modulates splicing via its DNA-binding domain, the Homeodomain (HD). Our results demonstrate a new RNA-binding ability of Ubx in cells and in vitro. Notably, the N51 amino acid of the HD, which mediates Ubx-DNA interaction, is non-essential for Ubx-RNA interaction in vitro but is required in vivo. We find that the N51 amino acid is necessary to mediate interaction between Ubx and the active form of the RNA Polymerase II (Pol II S2Phos) in Drosophila cells. By combining molecular and imaging approaches, our results reveal that Ubx mediates elongation-coupled splicing via a dynamic interplay with active Pol II and chromatin binding. Overall, our work uncovered a novel role of the Hox TFs at the mRNA regulatory layer. This could be an essential function for other classes of TFs to control cell diversity.
Class I histone deacetylases (HDAC1–3) are histone lysine delactylases

Lysine l-lactylation [K(l-la)] is a newly discovered histone mark that can be stimulated under conditions of high glycolysis, such as the Warburg effect. K(l-la) is associated with functions that are different from the widely studied histone acetylation. While K(l-la) can be introduced by the acetyltransferase p300, histone delactylase enzymes remain unknown. Here, we report the systematic evaluation of zinc- and NAD+-dependent HDACs for their ability to cleave ε-N-l-lactyllysine marks. Our screens identified HDACs 1–3 and SIRT1–3 as delactylases in vitro. HDACs 1–3 show robust activity toward not only K(l-la) but also K(d-la) and diverse short-chain acyl modifications. We further confirmed the de-l-lactylase activity of HDACs 1 and 3 in cells. Identification of p300 and HDAC3 as regulatory enzymes suggests that histone lactylation is installed and removed by enzymes as opposed to spontaneous chemical reactivity. Our results therefore represent an important step toward full characterization of this pathway’s regulatory elements.
Neuronal ribosomes dynamically exchange ribosomal proteins in a context-dependent manner

Owing to their morphological complexity and dense network connections, neurons modify their proteomes locally, using mRNAs and ribosomes present in the neuropil (tissue enriched for dendrites and axons). Although ribosome biogenesis largely takes place in the nucleus and perinuclear region, neuronal ribosomal protein (RP) mRNAs have been frequently detected remotely, in dendrites and axons. Here, using imaging and ribosome profiling, we directly detected the RP mRNAs and their translation in the neuropil. Combining brief metabolic labeling with mass spectrometry, we found that a group of RPs quickly associated with translating ribosomes in the cytoplasm and that this incorporation is independent of canonical ribosome biogenesis. Moreover, the incorporation probability of some RPs was regulated by location (neurites vs. cell bodies) and changes in the cellular environment (in response to oxidative stress). Our results suggest new mechanisms for the local activation, repair and/or specialization of the translational machinery within neuronal processes, potentially allowing remote neuronal synapses a rapid solution to the relatively slow and energy-demanding requirement of nuclear ribosome biogenesis.
Pseudomonas aeruginosa isolates defective in function of the LasR quorum sensing regulator are frequent in diverse environmental niches

The saprophyte Pseudomonas aeruginosa is a versatile opportunistic pathogen causing infections in immunocompromised individuals. To facilitate its adaptation to a large variety of niches, this bacterium exploits population density-dependant gene regulation systems called quorum sensing. In P. aeruginosa, three distinct but interrelated quorum sensing systems (las, rhl and pqs) regulate the production of many survival and virulence functions. In prototypical strains, the las system, through its transcriptional regulator LasR, is important for the full activation of the rhl and pqs systems. Still, LasR-deficient isolates have been reported, mostly sampled from the lungs of people with cystic fibrosis, where they are considered selected by the chronic infection environment. In this study, we show that a defect in LasR activity appears to be an actually widespread mechanism of adaptation in this bacterium. Indeed, we found abundant LasR-defective isolates sampled from hydrocarbon-contaminated soils, hospital sink drains, and meat/fish market environments, using an approach based on phenotypic profiling, supported by gene sequencing. Interestingly, several LasR-defective isolates maintain an active rhl system or are deficient in pqs system signaling. The high prevalence of a LasR-defective phenotype among environmental P. aeruginosa isolates questions the role of quorum sensing in niche adaptation.
INPP4B promotes leukemia by restricting leukemic stem cell differentiation through regulation of lysosomal functions

Despite an increased understanding of leukemogenesis, specific mechanisms that underlie ‘stemness’ in leukemia remain largely undefined. Here, we report a novel pathway which regulates leukemic differentiation through control of lysosomal biology. We show that disruption of INPP4B results in dysregulated lysosomal gene networks, reduced lysosomal numbers and proteolytic capacity in leukemia. Inpp4b-deficient HSCs and LSCs are functionally compromised. Inpp4b-deficient leukemia models develop more differentiated leukemias with reduced disease initiating potential, and improved overall survival compared to Inpp4b-expressing leukemias. Together, our data is consistent with a model where INPP4B restricts differentiation of LSCs through regulation of lysosomal function. These data provide a mechanism to explain the association of INPP4B with aggressive AML and highlight avenues for LSC-specific leukemia therapies.This work is the first to show that the phosphoinositide phosphatase INPP4B regulates stemness and differentiation in AML, through a previously unknown role in lysosome function. Herein we describe a mechanism to explain why INPP4B overexpression is associated with poor clinical outcome in AML.
Integrating diverse data sources to predict disease risk in dairy cattle

Livestock farming is currently undergoing a digital revolution and becoming increasingly data-driven. Yet, such data often reside in disconnected silos making it impossible to leverage their full potential to improve animal well-being. Here, we introduce a precision medicine approach, bringing together information streams from a variety of life domains of dairy cattle to predict eight common and economically important diseases. Dairy cows are part of a highly industrialised environment. The animals and their surroundings are closely monitored and environmental, behavioural and physiological observations are readily accessible yet seldomly integrated. We use random forest classifiers trained on data from 5,828 animals in 166 herds in Austria to predict occurrences of lameness, acute and chronic mastitis, anoestrus, ovarian cysts, metritis, ketosis (hyperketonemia) and periparturient hypocalcemia (milk fever). To assess the importance of specific cattle life domains and individual features for these predictions, we use multivariate logistic regression and feature permutation approaches. We show that disease in dairy cattle is a product of the complex interplay between a multitude of life domains such as housing, nutrition or climate, and identify a range of features that were previously not associated with increased disease risk. For example, we can predict anoestrus with high sensitivity and specificity (F1=0.72) and find that housing, feed and husbandry variables such as barn design and time on pasture are most predictive of this disease. We also find previously unknown associations of features with disease risk, for example humid conditions, which significantly decrease the odds for ketosis. Our findings pave the way towards data-driven point-of-care interventions and demonstrate the added value of integrating all available data in the dairy industry to improve animal well-being and reduce disease risk.