Miracle-dz/UniFAR-FTUs huggingface dataset:
New Drosophila models to uncover the intrinsic and extrinsic factors mediating the toxicity of the human prion protein

Misfolded conformations of the prion protein (PrP) are responsible for devastating neurological disorders in humans and mammals. An unresolved problem is unraveling the mechanisms governing PrP conformational dynamics, misfolding, and the cellular mechanism leading to neurodegeneration. The variable susceptibility of mammals to prion diseases can be exploited to understand the conformational dynamics of PrP. Here we present a new fly model expressing human PrP with robust phenotypes in brain neurons and the eye. Using comparable attP2 insertions, we demonstrate the heightened toxicity of human PrP compared to that of mouse and hamster PrP along with a specific interaction with the amyloid-beta peptide. Using this new highly toxic new model, we started to uncover the intrinsic (sequence / structure) and extrinsic (interactions) factors regulating PrP toxicity. As extrinsic factors, we describe the importance of the PERK - ATF4 branch of the unfolded protein response as a key cellular mechanism mediating the toxicity of human PrP. For intrinsic factors, we introduced point mutations in human PrP (N159D, D167S, N174S) that were partially protective, revealing its high propensity to misfold into toxic conformations.
Metric Multidimensional Scaling for Large Single-Cell Data Sets using Neural Networks

Metric multidimensional scaling is one of the classical methods for embedding data into low-dimensional Euclidean space. It creates the low-dimensional embedding by approximately preserving the pairwise distances between the input points. However, current state-of-the-art approaches only scale to a few thousand data points. For larger data sets such as those occurring in single-cell RNA sequencing experiments, the running time becomes prohibitively large and thus alternative methods such as PCA are widely used instead. Here, we propose a neural network based approach for solving the metric multidimensional scaling problem that is orders of magnitude faster than previous state-of-the-art approaches, and hence scales to data sets with up to a few million cells. At the same time, it provides a non-linear mapping between high- and low-dimensional space that can place previously unseen cells in the same embedding.
A random forest classifier for protein–protein docking models

Herein, we present the results of a machine learning approach we developed to single out correct 3D docking models of protein-protein complexes obtained by popular docking software. To this aim, we generated a set of ≈7×106 docking models with three different docking programs (HADDOCK, FTDock and ZDOCK) for the 230 complexes in the protein-protein interaction benchmark, version 5 (BM5). Three different machine-learning approaches (Random Forest, Supported Vector Machine and Perceptron) were used to train classifiers with 158 different scoring functions (features). The Random Forest algorithm outperformed the other two algorithms and was selected for further optimization. Using a features selection algorithm, and optimizing the random forest hyperparameters, allowed us to train and validate a random forest classifier, named CoDES (COnservation Driven Expert System). Testing of CoDES on independent datasets, as well as results of its comparative performance with machine-learning methods recently developed in the field for the scoring of docking decoys, confirm its state-of-the-art ability to discriminate correct from incorrect decoys both in terms of global parameters and in terms of decoys ranked at the top positions.
Bioaffinity-based surface immobilization of antibodies to capture endothelial colony-forming cells

Maximizing the re-endothelialization of vascular implants such as prostheses or stents has the potential to significantly improve their long-term performance. Endothelial progenitor cell capture stents with surface-immobilized antibodies show significantly improved endothelialization in the clinic. However, most current antibody-based stent surface modification strategies rely on antibody adsorption or direct conjugation via amino or carboxyl groups which leads to poor control over antibody surface concentration and/or molecular orientation, and ultimately bioavailability for cell capture. Here, we assess the utility of a bioaffinity-based surface modification strategy to immobilize antibodies targeting endothelial cell surface antigens. A cysteine-tagged truncated protein G polypeptide containing three Fc-binding domains was conjugated onto aminated polystyrene substrates via a bi-functional linking arm, followed by antibody immobilization. Different IgG antibodies were successfully immobilized on the protein G-modified surfaces. Covalent grafting of the protein G polypeptide was more effective than surface adsorption in immobilizing antibodies at high density based on fluorophore-labeled secondary antibody detection, as well as endothelial colony-forming cell capture through anti-CD144 antibodies. This work presents a potential avenue for enhancing the performance of cell capture strategies by using covalent grafting of protein G polypeptides to immobilize IgG antibodies.
Searching sequence databases for functional homologs using profile HMMs: how to set bit score thresholds?

Motivation UniProt and BFD databases together have 2.5 billion protein sequences. A large majority of these proteins have been electronically annotated. Automated annotation pipelines, vis-à-vis manual curation, have the advantage of scale and speed but are fraught with relatively higher error rates. This is because sequence homology does not necessarily translate to functional homology, molecular function specification is hierarchic and not all functional families have the same amount of experimental data that one can exploit for annotation. Consequently, customization of annotation workflow is inevitable to minimize annotation errors. Results We discuss possible ways of customizing the search of sequence databases for functional homologs using profile HMMs. Choosing an optimal bit score threshold is a critical step in the application of HMMs, which is illustrated using four Case Studies; the single domain nucleotide sugar 6-dehydrogenase and lysozyme-C families, and SH3 and GT-A domains which are typically found as a part of multi-domain proteins. We also discuss the limitations of using profile HMMs for functional annotation and suggests some possible ways to partially overcome such limitations. Supplementary information Supplementary_material containing Figures S1-S7 and Tables S1 and S2 Supplementary_dataset. xlsx
PpRPK2 modulates auxin homeostasis and transport to specify stem cell identity and plant shape in the moss Physcomitrella

Plant shape is determined by the activity of stem cells in the growing tips, and evolutionary changes in shape are linked to changes in stem cell function. The CLAVATA pathway is a key regulator of stem cell function in the multicellular shoot tips of Arabidopsis, acting via the WUSCHEL transcription factor to modulate hormone homeostasis. Broad scale evolutionary comparisons have shown that CLAVATA is a conserved regulator of land plant stem cell function, but CLAVATA acts independently of WUSCHEL-like (WOX) proteins in bryophytes, raising questions about the evolution of stem cell function and the role of the CLAVATA pathway. Here we show that the moss (Physcomitrella) CLAVATA pathway affects stem cell activity and overall plant shape by modulating hormone homeostasis. CLAVATA pathway components are expressed in the tip cells of filamentous tissues, regulating cell identity, filament branching patterns and plant spread. The PpRPK2 receptor-like kinase plays the major role and is expressed more strongly than other receptor-encoding genes. Pprpk2 mutants have abnormal responses to cytokinin, and auxin transport inhibition and show reduced PIN auxin transporter expression. We propose a model whereby PpRPK2 modulates PIN activity to determine stem cell identity and overall plant form in Physcomitrella. Our data indicate that CLAVATA-mediated auxin homeostasis is a fundamental property of plant stem cell function likely exhibited by the last shared common ancestor of land plants.
Quantitative Modeling of Protein Synthesis Using Ribosome Profiling Data

Quantitative prediction on protein synthesis requires accurate translation initiation and codon translation rates. Ribosome profiling data, which provide steady-state distribution of relative ribosome occupancies along a transcript, can be used to extract these rate parameters. Various methods have been developed in the past few years to measure translation-initiation and codon translation rates from ribosome profiling data. In the review, we provide a detailed analysis of the key methods employed to extract the translation rate parameters from ribosome profiling data. We further discuss how these approaches were used to decipher the role of various structural and sequence-based features of mRNA molecules in the regulation of gene expression. The utilization of these accurate rate parameters in computational modeling of protein synthesis may provide new insights into the kinetic control of the process of gene expression.
Dynamics of Foliar Responses to O3 Stress as a Function of Phytotoxic O3 Dose in Hybrid Poplar

With background concentrations having reached phytotoxic levels during the last century, tropospheric ozone (O3) has become a key climate change agent, counteracting carbon sequestration by forest ecosystems. One of the main knowledge gaps for implementing the recent O3 flux-based critical levels (CLs) concerns the assessment of effective O3 dose leading to adverse effects in plants. In this study, we investigate the dynamics of physiological, structural, and morphological responses induced by two levels of O3 exposure (80 and 100 ppb) in the foliage of hybrid poplar, as a function of phytotoxic O3 dose (POD0) and foliar developmental stage. After a latency period driven by foliar ontological development, the gas exchanges and chlorophyll content decreased with higher POD0 monotonically. Hypersensitive response-like lesions appeared early during exposure and showed sigmoidal-like dynamics, varying according to leaf age. At current POD1_SPEC CL, notwithstanding the aforementioned reactions and initial visible injury to foliage, the treated poplars had still not shown any growth or biomass reduction. Hence, this study demonstrates the development of a complex syndrome of early reactions below the flux-based CL, with response dynamics closely determined by the foliar ontological stage and environmental conditions. General agreement with patterns observed in the field appears indicative of early O3 impacts on processes relevant, e.g., biodiversity ecosystem services before those of economic significance – i.e., wood production, as targeted by flux-based CL.
GDF11 Alleviates Pathological Myocardial Remodeling in Diabetic Cardiomyopathy Through SIRT1-Dependent Regulation of Oxidative Stress and Apoptosis

Growth differentiation factor 11 (GDF11) is a member of the transforming growth factor β superfamily that alleviates cardiac hypertrophy, myocardial infarction, and vascular injury by regulating oxidative stress, inflammation, and cell survival. However, the roles and underlying mechanisms of GDF11 in diabetic cardiomyopathy (DCM) remain largely unknown. In this study, we sought to determine whether GDF11 could prevent DCM. After establishing a mouse model of diabetes by administering a high-fat diet and streptozotocin, intramyocardial injection of an adeno-associated virus was used to achieve myocardium-specific GDF11 overexpression. GDF11 remarkably improved cardiac dysfunction and interstitial fibrosis by reducing the levels of reactive oxygen species and protecting against cardiomyocyte loss. Mechanistically, decreased sirtuin 1 (SIRT1) expression and activity were observed in diabetic mice, which was significantly increased after GDF11 overexpression. To further explore how SIRT1 mediates the role of GDF11, the selective inhibitor EX527 was used to block SIRT1 signaling pathway, which abolished the protective effects of GDF11 against DCM. In vitro studies confirmed that GDF11 protected against H9c2 cell injury in high glucose and palmitate by attenuating oxidative injury and apoptosis, and these effects were eliminated by SIRT1 depletion. Our results demonstrate for the first time that GDF11 protects against DCM by regulating SIRT1 signaling pathway.
Analysis of Age-Related White Matter Microstructures Based on Diffusion Tensor Imaging

Population aging has become a serious social problem. Accordingly, many researches are focusing on changes in brains of the elderly. In this study, we used multiple parameters to analyze age-related changes in white matter fibers. A sample cohort of 58 individuals was divided into young and middle-age groups and tract-based spatial statistics (TBSS) were used to analyze the differences in fractional anisotropy (FA), mean diffusion (MD), axial diffusion (AD), and radial diffusion (RD) between the two groups. Deterministic fiber tracking was used to investigate the correlation between fiber number and fiber length with age. The TBSS analysis revealed significant differences in FA, MD, AD, and RD in multiple white matter fibers between the two groups. In the middle-age group FA and AD were lower than in young people, whereas the MD and RD values were higher. Deterministic fiber tracking showed that the fiber length of some fibers correlated positively with age. These fibers were observed in the splenium of corpus callosum (SCC), the posterior limb of internal capsule (PLIC), the right posterior corona radiata (PCR_R), the anterior corona radiata (ACR), the left posterior thalamic radiation (include optic radiation; PTR_L), and the left superior longitudinal fasciculus (SLF_L), among others. The results showed that the SCC, PLIC, PCR_R, ACR, PTR_L, and SLF_L significantly differed between young and middle-age people. Therefore, we believe that these fibers could be used as image markers of age-related white matter changes.
Erhöhte Laserabsorption in ausgedehnten Clustermedien

Nach gegenwartigen Modellen fur Absorption von Ultrakurzpulslasern in Edelgasclustern verlauft die Absorption in zwei Phasen. Am Anfang ist die Elektronendichte uberkritisch bzgl. der Laserfrequenz. Die Stosabsorption dominiert und es werden uberwiegend die Elektronen geheizt. Infolgedessen expandieren die Elektronen, wodurch die Elektronendichte und damit die Plasmafrequenz abnimmt. Wenn die abnehmende Plasmafrequenz gleich der Laserfrequenz wird, es folgt starke resonante Kopplung, wodurch die zweite Phase der Absorption eintritt. In dieser Arbeit werden zwei zusatzliche Absorptionsmechanismen vorgestellt. Erstens wird die kollektive Wechselwirkung durch Berucksichtigung von nichtresonanten Anregungen erganzt.Zweitens wird gezeigt, dass der Clusterkern bzgl. der Elektronstreuung wie ein riesiger Atomkern fungiert und eine Erhohung der Stosabsorption hervorruft. Die nichtresonanten Anregungen werden im Rahmen eines Globaldipolmodells untersucht und es wird gezeigt, wie diese nichtresonanten Anregungen zur Heizung der Elektronen bis zu einigen keV fuhren konnen, was schon experimentell gemessen wurde. Auserdem wird gezeigt, dass die im Rahmen von Globaldipolmodellen berechnete Umwandlungseffizienz der Laserenergie in Harmonische der Laserfrequenz annahernd mit gemessenen Ergebnissen ubereinstimmt. Der berechnete Absorptionskoeffizient als Funktion von Spitzenlaserintensitat und Laserfrequenz ist sehr irregular. Wir zeigen durch die Berechnung von Lyapulnovexponenten, dass diese Irregularitat ein Ausdruck des chaotischen Verhaltens des Globaldipols ist. Ferner wird gezeigt, dass ein sich im thermischen Gleichgewicht befindender Cluster masgeblich geladen ist. Die Elektronenstreuung durch den Clusterkern wird ausfuhrlich untersucht und es wird gezeigt, dass die sehr grose Ladung (~10000e) des Clusterkerns zu wesentlich erhohter Stosabsorption fuhrt.
Bioprospecting of Palmyra Palm (Borassus flabellifer) Nectar: Unveiling the Probiotic and Therapeutic Potential of the Traditional Rural Drink

The present study investigates the therapeutic and probiotic attributes of traditional Toddy Palm Nectar (TPN). Glucose was found to be the highest with 4.37 mg/ml and arabinose was the least with 2.85 mg/ml. The average ethanol concentration of fresh TPN was found to be 0.3 mg/ml. The nutritional profile of TPN revealed 18 volatile fatty acids, the major one being hexadecenoic acid (M/Z 74). Amino acid profiling showed 26 amino acids, with OH-lysine-2 the highest (12.86%). About 120 morphologically distinct lactic acid bacteria (LAB) were isolated from 26 TPN samples, based on differential growth and in vitro probiotic characteristics. After 16S rRNA sequencing, four indigenous LAB strains were identified as Lactobacillus plantarum group OUBN1, Enterococcus faecium OUBN3, Pediococcus acidilactici OUBN4, and Pediococcus pentosaceous OUBN5 and their sequences were deposited to NCBI. Microbiological safety evaluation studies showed the absence of hemolytic, gelatinolytic and proteolytic activity. The bacterial isolate OUBN3 showed a maximum survival rate of 6.91 ± 0.04 log cfu/ml at acidic pH 2.5 and isolate OUBN5 showed 6.94 ± 0.02 log cfu/ml at pH 3.0. Similarly, the isolate OUBN5 showed 7.92 ± 0.03 log cfu/ml to 0.3% ox-bile after 4 h and 8.94 ± 0.03 log cfu/ml to simulated gastric juice after 3 h of treatments. OUBN1 expressed the highest autoaggregation (81.76 ± 1.25%), cell surface hydrophobicity (79.71 ± 3.42%), and displayed the maximum coaggregation with E. coli MTCC452 (76.96%), K. pneumoniae MTCC109 (75.62%), and S. aureus MTCC902 (70.69%). All strains showed significant antibiotic and antimicrobial activity. Isolate OUBN1 displayed hydroxyl radical scavenging activity (68.71 ± 1.0%) with an IC50 value of 75.62 μg/ml and the highest anti-cancer activity (percentage inhibition of 88.55) against HT-29 cells. Based on the characteristics observed, L. plantarum group OUBN1 and P. pentosaceous OUBN5 were found to be potential isolates to employ as probiotic microbiota in food and forage preparations. These findings reinforce the fact that LAB isolated from TPN could be exploited as an alternative means toward potential therapeutic applications. Graphical Abstract
Coordinated Cut and Bypass: Replication of Interstrand Crosslink-Containing DNA

DNA interstrand crosslinks (ICLs) are covalently bound DNA lesions, which are commonly induced by chemotherapeutic drugs, such as cisplatin and mitomycin C or endogenous byproducts of metabolic processes. This type of DNA lesion can block ongoing RNA transcription and DNA replication and thus cause genome instability and cancer. Several cellular defense mechanism, such as the Fanconi anemia pathway have developed to ensure accurate repair and DNA replication when ICLs are present. Various structure-specific nucleases and translesion synthesis (TLS) polymerases have come into focus in relation to ICL bypass. Current models propose that a structure-specific nuclease incision is needed to unhook the ICL from the replication fork, followed by the activity of a low-fidelity TLS polymerase enabling replication through the unhooked ICL adduct. This review focuses on how, in parallel with the Fanconi anemia pathway, PCNA interactions and ICL-induced PCNA ubiquitylation regulate the recruitment, substrate specificity, activity, and coordinated action of certain nucleases and TLS polymerases in the execution of stalled replication fork rescue via ICL bypass.
LYG1 Deficiency Attenuates the Severity of Acute Graft-Versus-Host Disease via Skewing Allogeneic T Cells Polarization Towards Treg Cells

Acute graft-versus-host disease (aGVHD) is a lethal complication after allogeneic hematopoietic stem cell transplantation. The mechanism involves the recognition of host antigens by donor-derived T cells which induces augmented response of alloreactive T cells. In this study, we characterized the role of a previously identified novel classical secretory protein with antitumor function-LYG1 (Lysozyme G-like 1), in aGVHD. LYG1 deficiency reduced the activation of CD4+ T cells and Th1 ratio, but increased Treg ratio in vitro by MLR assay. By using major MHC mismatched aGVHD model, LYG1 deficiency in donor T cells or CD4+ T cells attenuated aGVHD severity, inhibited CD4+ T cells activation and IFN-γ expression, promoted FoxP3 expression, suppressed CXCL9 and CXCL10 expression, restrained allogeneic CD4+ T cells infiltrating in target organs. The function of LYG1 in aGVHD was also confirmed using haploidentical transplant model. Furthermore, administration of recombinant human LYG1 protein intraperitoneally aggravated aGVHD by promoting IFN-γ production and inhibiting FoxP3 expression. The effect of rhLYG1 could partially be abrogated with the absence of IFN-γ. Furthermore, LYG1 deficiency in donor T cells preserved graft-versus-tumor response. In summary, our results indicate LYG1 regulates aGVHD by the alloreactivity of CD4+ T cells and the balance of Th1 and Treg differentiation of allogeneic CD4+ T cells, targeting LYG1 maybe a novel therapeutic strategy for preventing aGVHD.
Evaluation of Heterologous Biosynthetic Pathways for Methanol-Based 5-Aminovalerate Production by Thermophilic Bacillus methanolicus

The use of methanol as carbon source for biotechnological processes has recently attracted great interest due to its relatively low price, high abundance, high purity, and the fact that it is a non-food raw material. In this study, methanol-based production of 5-aminovalerate (5AVA) was established using recombinant Bacillus methanolicus strains. 5AVA is a building block of polyamides and a candidate to become the C5 platform chemical for the production of, among others, δ-valerolactam, 5-hydroxy-valerate, glutarate, and 1,5-pentanediol. In this study, we test five different 5AVA biosynthesis pathways, whereof two directly convert L-lysine to 5AVA and three use cadaverine as an intermediate. The conversion of L-lysine to 5AVA employs lysine 2-monooxygenase (DavB) and 5-aminovaleramidase (DavA), encoded by the well-known Pseudomonas putida cluster davBA, among others, or lysine α-oxidase (RaiP) in the presence of hydrogen peroxide. Cadaverine is converted either to γ-glutamine-cadaverine by glutamine synthetase (SpuI) or to 5-aminopentanal through activity of putrescine oxidase (Puo) or putrescine transaminase (PatA). Our efforts resulted in proof-of-concept 5AVA production from methanol at 50°C, enabled by two pathways out of the five tested with the highest titer of 0.02 g l–1. To our knowledge, this is the first report of 5AVA production from methanol in methylotrophic bacteria, and the recombinant strains and knowledge generated should represent a valuable basis for further improved 5AVA production from methanol.