Miracle-dz/UniFAR-FTUs huggingface dataset:
Seasonal Variations in the Heat and Water Balances for Nonvegetated Surfaces

Abstract A model is presented for estimating the seasonal variations of evaporation, soil-water content, and soil temperature over nonvegetated land surfaces, especially in arid and semiarid regions. In the model, several types of soil are taken into consideration. Verification of the model has been achieved by comparing the observed and calculated results for the volcanic ash soil surface in Tsukuba and a sand dune field in Tottori. Using the routine data of 30 observatories including moist, semiarid, and arid regions at different elevations in China, the heat and water balances are estimated by the model. At a station in a semiarid region such as Lanzhou, the sensible heat flux is found to be considerably greater than the latent heat flux during the dry season. Both fluxes, however, have comparable magnitudes during the rainy season. The annual mean value of the soil-water content increases with depth, and the rate of increase grows larger as the amount of annual precipitation increases. But for an arid.
Small ADP-ribosylation factor-like GTPase TITAN5 (TTN5/ARL2) is linked with the dynamic regulation of IRON-REGULATED TRANSPORTER1

The endomembrane system is the central sorting machinery for membrane proteins where signals can be integrated to control plant nutritional responses. IRON-REGULATED TRANSPORTER1 (IRT1) is tightly controlled through trafficking between the endomembrane system and the plasma membrane to balance the demands for iron (Fe) and toxic effects that may arise from excess of this micronutrient in roots. Small GTPases of the Ras superfamily regulate signaling inputs in endomembrane trafficking, but their functions and activities are poorly known in plants. One plant endomembrane system-associated regulatory component is the small ARF-like GTPase TITAN 5/ARL2/ARLC1/HALLIMASCH (hereafter termed TTN5). TTN5 is required during early embryo development but many open questions remain with regard to its physiological function during the later life cycle or in response to environmental cues. Here, we demonstrate that TTN5 interacts with IRT1vr, the large cytoplasmic variable region and protein-regulatory platform of IRT1. TTN5 also interacts with peripheral membrane proteins that are components of the IRT1 regulation machinery and can be involved in protein trafficking, like SNX1, the C2 domain protein EHB1 and the SEC14-GOLD domain-containing PATL2. We show that heterozygous ttn5-1+/- plants have a Fe reduction phenotype. Fluorescent fusion proteins of TTN5 and IRT1 colocalize at the plasma membrane and in endosomes/multivesicular bodies, where IRT1 sorting and cycling between the plasma membrane and the vacuole are coordinated. Hence, this work links IRT1 and iron nutritional regulation with a small GTPase. This opens up the possibility that iron nutrient levels are controlled via the cellular regulation of the endomembrane system. Highlights The small GTPase TITAN 5 (TTN5/ARL2) is linked to iron homeostasis TTN5 interacts with the large intracellular loop and variable region of IRON-REGULATED TRANSPORTER 1 (IRT1) and has a positive effect on root iron (Fe) reduction TTN5 interacts with peripheral membrane proteins of the IRT1 interactome, EHB1, PATL2 and SNX1 suggesting a coordinating role in IRT1 regulation TTN5 and IRT1 colocalize at the plasma membrane and the endomembrane system related to vesicle transport One-sentence summary ADP-ribosylation factor-like small GTPase TITAN 5 (TTN5/ARL2) links vesicle transport and iron homeostasis by binding the intracellular regulatory protein interaction region of IRON-REGULATED TRANSPORTER 1 (IRT1).
Translation in a Box: Orthogonal Evolution in the Saccharomyces cerevisiae Mitochondrion

The ability to re-engineer and creatively evolve the translation system (TS) would allow invention of new coded polymers by altering the amino acid sidechain inventory and by shifting the polypeptide backbone into new chemical spaces. Unfortunately, the TS is difficult to manipulate and is more constrained over evolution than any other biological system. An orthogonal TS, running in parallel to the primary TS within a given host cell, would release constraints and allow TS manipulation. A fully orthogonal TS requires dedicated rRNAs, rProteins, aminoacyl-tRNA synthetases, and initiation and termination factors, none of which interact with the primary TS. The S. cerevisiae mitochondrial TS is fully orthogonal to the cytosolic TS. Mito-rRNAs, mito- rProteins, mito-tRNAs, mito-aminoacyl tRNA synthetases, and mito-translation factors are distinct from, physically separated from, and functionally independent of their cytosolic counterparts. Here, the S. cerevisiae mitochondrial translation system was subjected to various stresses including antibiotics, mutagenesis and truncation of mito-rProteins, or wholesale replacement of mito-rProteins. Directed evolution of these stressed systems was facilitated by controlled transitions between fermentation and respiration, by changing the carbon source in the growth medium; the dependence of S. cerevisiae survival on mitochondrial translation can be toggled on and off. Specific recreation of the resulting mutations recapitulate the evolved phenotypes. The method developed here appears to be a general approach for discovering functional dependencies. Suppressor mutations reveal functional dependencies within the S. cerevisiae mitochondrial TS. For example proteins Rrg9 or Mrx1 interact with the mito-TS and have critical role in its function. The combined results indicate that the S. cerevisiae mitochondrial TS can be engineered and evolved in isolation of the cytosolic TS. Significance The Central Dogma of Molecular Biology rules life on Earth. Information flows from DNA to mRNA to protein. In the last step of the Central Dogma, the translation system decodes mRNA and produces coded proteins by linking amino acids into polymers. Engineering and evolving the translation system could permits full technical control over this process and could lead to the generation of novel polymers. Here, we use the mitochondrial translation system in the budding yeast Saccharomyces cerevisiae for directed evolution of translation. We modify and evolve the translation system both directly and indirectly using antibiotics and gene editing tools and then measure resulting functionality. Our results show this secondary translation system inside S. cerevisiae mitochondria can be used as an approach for translation engineering.
Leakage beyond the primary infarction: A temporal analysis of cerebrovascular dysregulation at sites of hippocampal secondary neurodegeneration following cortical photothrombotic stroke

We have previously demonstrated that a cortical stroke causes persistent impairment of hippocampal-dependent cognitive tasks concomitant with secondary neurodegenerative processes such as amyloid-β accumulation in the hippocampus, a region remote from the primary infarct. Interestingly, there is emerging evidence suggesting that deposition of amyloid-β around cerebral vessels may lead to cerebrovascular structural changes, neurovascular dysfunction, and disruption of blood-brain barrier integrity. However, there is limited knowledge about the temporal changes of hippocampal cerebrovasculature after cortical stroke. In the current study, we aimed to characterise the spatiotemporal cerebrovascular changes after cortical stroke. This was done using the photothrombotic stroke model targeting the motor and somatosensory cortices of mice. Cerebrovascular morphology as well as the colocalization of amyloid-β with vasculature and blood-brain-barrier integrity were assessed in the cortex and hippocampal regions at 7, 28 and 84 days post-stroke. Our findings showed transient cerebrovascular remodelling in the peri-infarct area up to 28 days post-stroke. Importantly, the cerebrovascular changes were extended beyond the peri-infarct region to the ipsilateral hippocampus and were sustained out to 84 days post-stroke. When investigating vessel diameter, we showed a decrease at 84 days in the peri-infarct and CA1 regions that was exacerbated in vessels with amyloid-β deposition. Lastly, we showed sustained vascular leakage in the peri-infarct and ipsilateral hippocampus, indicative of a compromised blood-brain-barrier. Our findings indicate that hippocampal vasculature may represent an important therapeutic target to mitigate the progression of post-stroke cognitive impairment.
RaptorX-Single: single-sequence protein structure prediction by integrating protein language models

Protein structure prediction has been greatly improved by deep learning in the past few years. However, the most successful methods rely on multiple sequence alignment (MSA) of the sequence homologs of the protein under prediction. In nature a protein folds in the absence of its sequence homologs and thus, a MSA-free structure prediction method is desired. Here we develop a single sequence-based protein structure prediction method RaptorX-Single by integrating several protein language models and a structure generation module and then study its advantage over MSA-based prediction methods. Our experimental results indicate that in addition to running much faster than MSA-based methods such as AlphaFold2, RaptorX-Single outperforms AlphaFold2 and other MSA-free methods in predicting the structure of antibodies, proteins of very few sequence homologs and single mutation effects. RaptorX-Single also compares favorably to MSA-based AlphaFold2 when the protein under prediction has a large number of sequence homologs.
Spatial and temporal changes in microbial communities and greenhouse gas emissions in a denitrifying woodchip bioreactor at low water temperatures

Nitrogen (N) pollution is a major threat to ecosystems and a driver of climate change through emissions of the greenhouse gas nitrous oxide (N2O). Mining activities are increasingly recognized for contributing to N pollution due to undetonated, N-based explosives. A woodchip denitrifying bioreactor, installed to treat nitrate-rich leachate from waste rock dumps in northern Sweden, was monitored for two years to determine the spatial and temporal distribution of microbial communities in pore water and woodchips and their genetic potential for different N transformation processes, and how this affected the N removal capacity and possible production of undesired N species, like ammonium, nitrite and N2O. About 80 and 65 % of the nitrate was removed from the leachate the first and second operational year, respectively, which agreed with a decrease in dissolved organic carbon in the outlet water. There was a succession in the microbial community over time and in space along the reactor length in both pore water and woodchips, which was reflected in the genetic potential for N cycling and ultimately also reactor performance. We conclude that DNRA had minimal impact on the overall N removal efficiency due to the low relative abundance of the key gene nrfA involved in DNRA and the low production of ammonium. However, nitrite, ammonium, and N2O were formed in the bioreactor and released in the effluent water, although direct emissions of N2O from the surface was low. The N2O production in the reactor might be explained by the ratio between the genetic potential for overall denitrification and N2O reduction in the woodchip and pore water communities, as indicated by the low ratio between the abundance of nir and nosZ genes. Altogether, the results indicate that the denitrification pathway was temporally as well as spatially separated along the reactor length, and that unwanted reactive N species were produced at different time points and locations in the reactor. Thus, the succession of microbial communities in woodchip denitrifying bioreactors treating mining impacted water develops slowly at low temperature, which impacts the reactor performance.
Replication elongates short DNA, reduces sequence bias and develops trimer structure

The origin of molecular evolution required the replication of short oligonucleotides to form longer polymers. Prebiotically plausible oligonucleotide pools tend to contain more of some nucleotide bases than others. It has been unclear whether this initial bias persists and how it affects replication. To investigate this, we examined the evolution of 12 mer biased short DNA pools during enzymatic templated polymerization. Our analysis using next-generation sequencing from different time points revealed that the initial nucleotide bias of the pool disappeared in the elongated pool after isothermal replication. In contrast, the nucleotide composition at each position in the elongated sequences remained biased and varied with both position and initial bias. Furthermore, we observed the emergence of highly periodic dimer and trimer motifs in the rapidly elongated sequences. This shift in nucleotide composition and the emergence of structure through templated replication could help explain how biased prebiotic pools could undergo molecular evolution and lead to complex functional nucleic acids.
Magnetic resonance biomarkers for timely diagnostic of radiation dose-rate effects

Diagnostic of radiation effects can be obtained within hours from delivery relying on spectroscopic detection of cell metabolite concentrations. Clinical and pre-clinical studies show that radiation delivery with elevated dose-rates can achieve tumor suppression while minimizing toxicity to surrounding areas. Diagnostic biomarkers detected on short timescales are needed to orient high dose-rate radiation delivery. We have designed an 1H magnetic resonance approach to observe metabolite concentrations, in particular Choline, Creatine, and Lactate, in order to detect radiation dose and dose-rate effects within hours from radiation delivery. The results of our metabolic profiling method in glioblastoma cells are consistent with observations from clinical studies guided by magnetic resonance spectroscopy for radiotherapy of head tumors. At 5 Gy/min we have observed increases in lactate concentrations and decreases in [Cho]/[Cr] ratios at increasing radiation doses. An increase of the radiation dose-rate to 35 Gy/min is correlated with an increase of [Cho]/[Cr] consistent with a reduction in radiation-induced oxidative effects at high dose-rates. The observed biomarkers can be translated for radiation pulse sequences optimization. One Sentence Summary Magnetic resonance biomarkers to monitor biological effectiveness within hours after radiation delivery can be optimized for glioblastoma cells and are of potential use for the design of radiotherapy with high dose-rates.
Plasma-free samples for transcriptomic analysis: a potential alternative to whole blood samples

RNA sequencing (RNAseq) technology has become increasingly important in precision medicine and clinical diagnostics and emerged as a powerful tool for identifying protein-coding genes, performing differential gene analysis, and inferring immune cell composition. Human peripheral blood samples are widely used for RNAseq, providing valuable insights into individual biomolecular information. Blood samples can be classified as whole blood (WB), plasma, serum, and remaining sediment samples, including plasma-free blood (PFB) and serum-free blood (SFB) samples. However, the feasibility of using PFB and SFB samples for transcriptome analysis remains unclear. In this study, we aimed to assess the viability of employing PFB or SFB samples as substitute RNA sources in transcriptomic analysis and performed a comparative analysis of WB, PFB, and SFB samples for different applications. Our results revealed that PFB samples exhibit greater similarity to WB samples in terms of protein-coding gene expression patterns, differential expression gene profiling, and immunological characterizations, suggesting that PFB can be a viable alternative for transcriptomic analysis. This contributes to the optimization of blood sample utilization and the advancement of precision medicine research.
Overexpression of the violaxanthin de-epoxidase confers faster NPQ and photosynthesis induction in rice

Plants in the field experience fluctuations in light conditions. Plants with swift responses to dynamic light conditions usually gain competitive advantage in the field. The dynamic photosynthesis can be reflected in dynamic changes in almost all processes in photosynthesis, with dominant factors being dynamic changes in non-photochemical quenching, Rubisco activation and stomatal dynamics. Each of these dynamic responses is controlled by defined mechanisms. In this study, we showed that overexpression of VDE, an enzyme involved in the xanthophyll cycle and non-photochemical quenching, in rice resulted in faster NPQ induction, less photoinhibition, and faster photosynthesis induction, which together caused increased biomass production by about 11∼16%. This study, demonstrating a previously unnoticed role of VDE in altering the dynamics of photosynthesis induction besides decreasing photoinhibition, offers a potential strategy to improve canopy photosynthesis through capitalizing the ability of plants to use dynamic light. Highlight The overexpression of VDE in rice resulted in faster NPQ induction, less photoinhibition, and faster photosynthesis induction, which together caused increased biomass in field.
EnGens: a computational framework for generation and analysis of representative protein conformational ensembles

Abstract Proteins are dynamic macromolecules that perform vital functions in cells. A protein structure determines its function, but this structure is not static, as proteins change their conformation to achieve various functions. Understanding the conformational landscapes of proteins is essential to understand their mechanism of action. Sets of carefully chosen conformations can summarize such complex landscapes and provide better insights into protein function than single conformations. We refer to these sets as representative conformational ensembles. Recent advances in computational methods have led to an increase in the number of available structural datasets spanning conformational landscapes. However, extracting representative conformational ensembles from such datasets is not an easy task and many methods have been developed to tackle it. Our new approach, EnGens (short for ensemble generation), collects these methods into a unified framework for generating and analyzing representative protein conformational ensembles. In this work, we: (1) provide an overview of existing methods and tools for representative protein structural ensemble generation and analysis; (2) unify existing approaches in an open-source Python package, and a portable Docker image, providing interactive visualizations within a Jupyter Notebook pipeline; (3) test our pipeline on a few canonical examples from the literature. Representative ensembles produced by EnGens can be used for many downstream tasks such as protein–ligand ensemble docking, Markov state modeling of protein dynamics and analysis of the effect of single-point mutations.
Cerebellar state estimation enables resilient coupling across behavioural domains

Cerebellar computations are necessary for fine behavioural control and are thought to rely on internal probabilistic models performing state estimation. We propose that the cerebellum infers how states contextualise (i.e., interact with) each other, and coordinates extra-cerebellar neuronal dynamics underpinning a range of behaviours. To support this claim, we describe a cerebellar model for state estimation that includes states interactions, and link the underlying inference with the neuronal architecture and dynamics observed empirically. This is formalised using the free energy principle, which provides a dual perspective on a system in terms of both the dynamics of its physical – in this case neuronal – states, and the inference process they entail. As a proof of principle, we simulate cerebellar-dependent synchronisation of whisking and respiration, which are known to be tightly coupled in rodents. In summary, we suggest that cerebellar-dependent contextualisation of behaviour can explain its ubiquitous involvement in most aspects of behaviour.
On the involvement of cell volume regulation mechanisms in post-hypertonic lysis and slow-freezing injury of human erythrocytes and its broader cryobiological significance

An effort is made to explain the salt loading of hypertonicity-treated human red blood cells (RBC) and their post-hypertonic lysis, which occurs upon resuspension to isotonic media. It is recognized that the salt loading is consistent with the regulatory volume increase response - a physiological response applied by cells to adapt to hypertonic conditions. It is therefore hypothesized that salt loading occurs via physiological ion transport pathways, allowing passive dissipative fluxes across the plasma membrane with the preservation of membrane integrity. It is argued that post-hypertonic lysis is essentially a hypotonic lysis occurring already in an isotonic medium due to the excess salt in the cytoplasm. A simplified physiological model accounting for transmembrane ion fluxes was applied to simulate the RBC physiological state to address the problem quantitatively. Instead of assuming the plasma membrane to be impermeable to ions, the dynamic nature of cell physiological state and capacity of cells to perform acute cell volume regulation by increasing passive cation plasma membrane permeability is recognized. It is shown that the RBC plasma membrane contains ion pathways capable of supporting a several-order increase in catio permeability, facilitating overall salt loading. The obtained picture, consistent with general physiology, predicts the experimentally observed RBC behavior. Although treated in theory, evidence supporting the proposed theory is provided, and the high explanatory power of the proposed idea is demonstrated. While focused on human RBCs, this study offers a general mechanism for the osmotic injury of cells exposed to hypertonic solutions - conditions relevant to cell cryopreservation - since many cells possess cell volume regulation mechanisms. Implications of the proposed hypothesis explaining the cryoprotective mechanism of common cryoprotectants are discussed, and additives targeting ion transport pathways are suggested as novel cryoprotectants.
Express barcoding with NextGenPCR and MinION for species-level sorting of ecological samples

DNA barcodes are useful for species-level sorting of specimen samples, but rarely used in time-sensitive projects that require species richness estimates or identification of pest or invasive species within hours. The main reason is that existing express barcoding workflows are either too expensive or can only be carried out in very well equipped laboratories by highly trained staff. We here introduce a simple workflow that combines rapid DNA extraction with HotSHOT, amplicon production with the aid of NextGenPCR® thermocyclers, and sequencing with low-cost MinION sequencers. We demonstrate the power of the approach by generating and identifying 250 barcodes for 285 specimens within 6 hours. The workflow only required the following major equipment that easily fits onto a lab bench: Conventional thermocycler, NextGenPCR® thermocycler, microplate sealer, Qubit, and MinION. We argue that species-level sorting with simplified barcoding workflows is now faster, more accurate, and sufficiently cost-effective that it can and should replace morphospecies sorting in many projects.