Rapid simulation of glycoprotein structures by grafting and steric exclusion of glycan conformer libraries

Most membrane proteins are modified by covalent addition of complex sugars through N- and O-glycosylation. Unlike proteins, glycans do not typically adopt specific secondary structures and remain very mobile, shielding potentially large fractions of protein surface. High glycan conformational freedom hinders complete structural elucidation of glycoproteins. Computer simulations may be used to model glycosylated proteins but require hundreds of thousands of computing hours on supercomputers, thus limiting routine use. Here, we describe GlycoSHIELD, a reductionist method that can be implemented on personal computers to graft realistic ensembles of glycan conformers onto static protein structures in minutes. Using molecular dynamics simulation, small-angle X-ray scattering, cryoelectron microscopy, and mass spectrometry, we show that this open-access toolkit provides enhanced models of glycoprotein structures. Focusing on N-cadherin, human coronavirus spike proteins, and gamma-aminobutyric acid receptors, we show that GlycoSHIELD can shed light on the impact of glycans on the conformation and activity of complex glycoproteins.

Identification and characterization of stromal-like cells with CD207+/low CD1a+/low phenotype derived from histiocytic lesions - a perspective in vitro model for drug testing

BACKGROUND

Histiocytoses are rare disorders manifested by increased proliferation of pathogenic myeloid cells sharing histological features with macrophages or dendritic cells and accumulating in various organs, i.a., bone and skin. Pre-clinical in vitro models that could be used to determine molecular pathways of the disease are limited, hence research on histiocytoses is challenging. The current study compares cytophysiological features of progenitor, stromal-like cells derived from histiocytic lesions (sl-pHCs) of three pediatric patients with different histiocytoses types and outcomes. The characterized cells may find potential applications in drug testing.

METHODS

Molecular phenotype of the cells, i.e. expression of CD1a and CD207 (langerin), was determined using flow cytometry. Cytogenetic analysis included GTG-banded metaphases and microarray (aCGH) evaluation. Furthermore, the morphology and ultrastructure of cells were evaluated using a confocal and scanning electron microscope. The microphotographs from the confocal imaging were used to reconstruct the mitochondrial network and its morphology. Basic cytophysiological parameters, such as viability, mitochondrial activity, and proliferation, were analyzed using multiple cellular assays, including Annexin V/7-AAD staining, mitopotential analysis, BrdU test, clonogenicity analysis, and distribution of cells within the cell cycle. Biomarkers potentially associated with histiocytoses progression were determined using RT-qPCR at mRNA, miRNA and lncRNA levels. Intracellular accumulation of histiocytosis-specific proteins was detected with Western blot. Cytotoxicyty and IC50 of vemurafenib and trametinib were determined with MTS assay.

RESULTS

Obtained cellular models, i.e. RAB-1, HAN-1, and CHR-1, are heterogenic in terms of molecular phenotype and morphology. The cells express CD1a/CD207 markers characteristic for dendritic cells, but also show intracellular accumulation of markers characteristic for cells of mesenchymal origin, i.e. vimentin (VIM) and osteopontin (OPN). In subsequent cultures, cells remain viable and metabolically active, and the mitochondrial network is well developed, with some distinctive morphotypes noted in each cell line. Cell-specific transcriptome profile was noted, providing information on potential new biomarkers (non-coding RNAs) with diagnostic and prognostic features. The cells showed different sensitivity to vemurafenib and trametinib.

CONCLUSION

Obtained and characterized cellular models of stromal-like cells derived from histiocytic lesions can be used for studies on histiocytosis biology and drug testing.

Structure of the two-component S-layer of the archaeon Sulfolobus acidocaldarius

Surface layers (S-layers) are resilient two-dimensional protein lattices that encapsulate many bacteria and most archaea. In archaea, S-layers usually form the only structural component of the cell wall and thus act as the final frontier between the cell and its environment. Therefore, S-layers are crucial for supporting microbial life. Notwithstanding their importance, little is known about archaeal S-layers at the atomic level. Here, we combined single-particle cryo electron microscopy, cryo electron tomography, and Alphafold2 predictions to generate an atomic model of the two-component S-layer of Sulfolobus acidocaldarius. The outer component of this S-layer (SlaA) is a flexible, highly glycosylated, and stable protein. Together with the inner and membrane-bound component (SlaB), they assemble into a porous and interwoven lattice. We hypothesise that jackknife-like conformational changes in SlaA play important roles in S-layer assembly.

Sex Hormone-Binding Globulin (SHBG) Maintains Proper Equine Adipose-Derived Stromal Cells (ASCs)' Metabolic Functions and Negatively Regulates their Basal Adipogenic Potential

BACKGROUND

Sex hormone binding globulin (SHBG) deteriorated expression has been recently strongly correlated to increased level of circulating pro-inflammatory cytokines and insulin resistance, which are typical manifestations of equine metabolic syndrome (EMS). Despite previous reports demonstrated the potential therapeutic application of SHBG for liver-related dysfunctions, whether SHBG might modulate equine adipose-derived stem/stromal cells (EqASCs) metabolic machinery remains unknown. Therefore, we evaluated for the first time the impact of SHBG protein on metabolic changes in ASCs isolated from healthy horses.

METHODS

Beforehand, SHBG protein expression has been experimentally lowered using a predesigned siRNA in EqASCs to verify its metabolic implications and potential therapeutic value. Then, apoptosis profile, oxidative stress, mitochondrial network dynamics and basal adipogenic potential have been evaluated using various molecular and analytical techniques.

RESULTS

The SHBG knockdown altered the proliferative and metabolic activity of EqASCs, while dampening basal apoptosis via Bax transcript suppression. Furthermore, the cells treated with siRNA were characterized by senescent phenotype, accumulation of reactive oxygen species (ROS), nitric oxide, as well as decreased mitochondrial potential that was shown by mitochondrial membrane depolarization and lower expression of key mitophagy factors: PINK, PARKIN and MFN. The addition of SHBG protein reversed the impaired and senescent phenotype of EMS-like cells that was proven by enhanced proliferative activity, reduced apoptosis resistance, lower ROS accumulation and greater mitochondrial dynamics, which is proposed to be related to a normalization of Bax expression. Crucially, SHBG silencing enhanced the expression of key pro-adipogenic effectors, while decreased the abundance of anti-adipogenic factors namely HIF1-α and FABP4. The addition of exogenous SHBG further depleted the expression of PPARγ and C/EBPα and restored the levels of FABP4 and HIF1-α evoking a strong inhibitory potential toward ASCs adipogenesis.

CONCLUSION

Herein, we provide for the first time the evidence that SHBG protein in importantly involved in various key metabolic pathways governing EqASCs functions, and more importantly we showed that SHBG negatively affect the basal adipogenic potential of tested ASCs through a FABP4-dependant pathway, and provide thus new insights for the development of potential anti-obesity therapeutic approach in both animals and humans.

Interaction of SARS-CoV-2 with host cells and antibodies: experiment and simulation

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of the devastating global COVID-19 pandemic announced by WHO in March 2020. Through unprecedented scientific effort, several vaccines, drugs and antibodies have been developed, saving millions of lives, but the fight against COVID-19 continues as immune escape variants of concern such as Delta and Omicron emerge. To develop more effective treatments and to elucidate the side effects caused by vaccines and therapeutic agents, a deeper understanding of the molecular interactions of SARS-CoV-2 with them and human cells is required. With special interest in computational approaches, we will focus on the structure of SARS-CoV-2 and the interaction of its spike protein with human angiotensin-converting enzyme-2 (ACE2) as a prime entry point of the virus into host cells. In addition, other possible viral receptors will be considered. The fusion of viral and human membranes and the interaction of the spike protein with antibodies and nanobodies will be discussed, as well as the effect of SARS-CoV-2 on protein synthesis in host cells.

Sex hormone-binding globulin (SHBG) mitigates ER stress and improves viability and insulin sensitivity in adipose-derived mesenchymal stem cells (ASC) of equine metabolic syndrome (EMS)-affected horses

BACKGROUND

Equine metabolic syndrome (EMS), which encompasses insulin resistance, low-grade inflammation and predisposition to laminitis is a critical endocrine disorder among the most prevalent conditions affecting horses from different breeds. According to the most recent research, low human sex hormone-binding globulin (SHBG) serum levels correlate with an increased risk of obesity, insulin resistance and diabetes, and may contribute to overall metabolic dysregulations. This study aimed to test whether exogenous SHBG could protect EMS affected adipose-derived stromal stem cells (EqASCEMS) from apoptosis, oxidative stress, ER stress and thus improve insulin sensitivity.

METHODS

EqASCEMS wells were treated with two different concentrations (50 and 100 nM) of exogenous SHBG, whose biocompatibility was tested after 24, 48 and 72 h of incubation. Several parameters including cell viability, apoptosis, cell cycle, reactive oxygen species levels, ER stress, Pi3K/MAPK activation and insulin transducers expression were analysed.

RESULTS

Obtained data demonstrated that exogenous SHBG treatment significantly promoted ASCs cells proliferation, cell cycle and survival with reduced expression of p53 and p21 pro-apoptotic mediators. Furthermore, SHBG alleviated the oxidative stress caused by EMS and reduced the overaccumulation of intracellular ROS, by reducing ROS + cell percentage and regulating gene expression of endogenous antioxidant enzymes (Sod 1, Cat, GPx), SHBG treatment exhibited antioxidant activity by modulating total nitric oxide (NO) levels in EMS cells as well. SHBG treatment dampened the activation of ER stress sensors and effectors in EqASCEMS cells via the upregulation of MiR-7a-5p, the decrease in the expression levels of ATF-6, CHOP and eiF2A and the restoration of PDIA3 chaperone protein levels. As a consequence, SHBG application substantially improved insulin sensitivity through the modulation of Pi3K/Akt/Glut4 insulin signalling cascades.

CONCLUSION

Our results suggest that the SHBG is endowed with crucial beneficial effects on ASCs metabolic activities and could serve as a valuable therapeutic target for the development of efficient EMS treatment protocols. Video Abstract.

MiR-21-5p regulates the dynamic of mitochondria network and rejuvenates the senile phenotype of bone marrow stromal cells (BMSCs) isolated from osteoporotic SAM/P6 mice

BACKGROUND

Progression of senile osteoporosis is associated with deteriorated regenerative potential of bone marrow-derived mesenchymal stem/stromal cells (BMSCs). According to the recent results, the senescent phenotype of osteoporotic cells strongly correlates with impaired regulation of mitochondria dynamics. Moreover, due to the ageing of population and growing osteoporosis incidence, more efficient methods concerning BMSCs rejuvenation are intensely investigated. Recently, miR-21-5p was reported to play a vital role in bone turnover, but its therapeutic mechanisms in progenitor cells delivered from senile osteoporotic patients remain unclear. Therefore, the goal of this paper was to investigate for the first time the regenerative potential of miR-21-5p in the process of mitochondrial network regulation and stemness restoration using the unique model of BMSCs isolated from senile osteoporotic SAM/P6 mice model.

METHODS

BMSCs were isolated from healthy BALB/c and osteoporotic SAM/P6 mice. We analysed the impact of miR-21-5p on the expression of crucial markers related to cells' viability, mitochondria reconstruction and autophagy progression. Further, we established the expression of markers vital for bone homeostasis, as well as defined the composition of extracellular matrix in osteogenic cultures. The regenerative potential of miR-21 in vivo was also investigated using a critical-size cranial defect model by computed microtomography and SEM-EDX imaging.

RESULTS

MiR-21 upregulation improved cells' viability and drove mitochondria dynamics in osteoporotic BMSCs evidenced by the intensification of fission processes. Simultaneously, miR-21 enhanced the osteogenic differentiation of BMSCs evidenced by increased expression of Runx-2 but downregulated Trap, as well as improved calcification of extracellular matrix. Importantly, the analyses using the critical-size cranial defect model indicated on a greater ratio of newly formed tissue after miR-21 application, as well as upregulated content of calcium and phosphorus within the defect site.

CONCLUSIONS

Our results demonstrate that miR-21-5p regulates the fission and fusion processes of mitochondria and facilitates the stemness restoration of senile osteoporotic BMSCs. At the same time, it enhances the expression of RUNX-2, while reduces TRAP accumulation in the cells with deteriorated phenotype. Therefore, miR-21-5p may bring a novel molecular strategy for senile osteoporosis diagnostics and treatment.

Antibody accessibility determines location of spike surface mutations in SARS-CoV-2 variants

The steady emergence of SARS-CoV-2 variants gives us a real-time view of the interplay between viral evolution and the host immune defense. The spike protein of SARS-CoV-2 is the primary target of antibodies. Here, we show that steric accessibility to antibodies provides a strong predictor of mutation activity in the spike protein of SARS-CoV-2 variants, including Omicron. We introduce an antibody accessibility score (AAS) that accounts for the steric shielding effect of glycans at the surface of spike. We find that high values of the AAS correlate strongly with the sites of mutations in the spike proteins of newly emerging SARS-CoV-2 variants. We use the AAS to assess the escapability of variant spike proteins, i.e., their ability to escape antibody-based immune responses. The high calculated escapability of the Omicron variant BA.5 with respect to both wild-type (WT) vaccination and BA.1 infection is consistent with its rapid spread despite high rates of vaccination and prior infection with earlier variants. We calculated the AAS from structural and molecular dynamics simulation data that were available early in the pandemic, in the spring of 2020. The AAS thus allows us to prospectively assess the ability of variant spike proteins to escape antibody-based immune responses and to pinpoint regions of expected mutation activity in future variants.

The PTP1B inhibitor MSI-1436 ameliorates liver insulin sensitivity by modulating autophagy, ER stress and systemic inflammation in Equine metabolic syndrome affected horses

BACKGROUND

Equine metabolic syndrome (EMS) is a multifactorial pathology gathering insulin resistance, low-grade inflammation and past or chronic laminitis. Among the several molecular mechanisms underlying EMS pathogenesis, increased negative insulin signalling regulation mediated by protein tyrosine phosphatase 1 B (PTP1B) has emerged as a critical axis in the development of liver insulin resistance and general metabolic distress associated to increased ER stress, inflammation and disrupted autophagy. Thus, the use of PTP1B selective inhibitors such as MSI-1436 might be considered as a golden therapeutic tool for the proper management of EMS and associated conditions. Therefore, the present investigation aimed at verifying the clinical efficacy of MSI-1436 systemic administration on liver metabolic balance, insulin sensitivity and inflammatory status in EMS affected horses. Moreover, the impact of MSI-1436 treatment on liver autophagy machinery and associated ER stress in liver tissue has been analysed.

METHODS

Liver explants isolated from healthy and EMS horses have been treated with MSI-1436 prior to gene and protein expression analysis of main markers mediating ER stress, mitophagy and autophagy. Furthermore, EMS horses have been intravenously treated with a single dose of MSI-1436, and evaluated for their metabolic and inflammatory status.

RESULTS

Clinical application of MSI-1436 to EMS horses restored proper adiponectin levels and attenuated the typical hyperinsulinemia and hyperglycemia. Moreover, administration of MSI-1436 further reduced the circulating levels of key pro-inflammatory mediators including IL-1β, TNF-α and TGF-β and triggered the Tregs cells activation. At the molecular level, PTP1B inhibition resulted in a noticeable mitigation of liver ER stress, improvement of mitochondrial dynamics and consequently, a regulation of autophagic response. Similarly, short-term ex vivo treatment of EMS liver explants with trodusquemine (MSI-1436) substantially enhanced autophagy by upregulating the levels of HSC70 and Beclin-1 at both mRNA and protein level. Moreover, the PTP1B inhibitor potentiated mitophagy and associated expression of MFN2 and PINK1. Interestingly, inhibition of PTP1B resulted in potent attenuation of ER stress key mediators' expression namely, CHOP, ATF6, HSPA5 and XBP1.

CONCLUSION

Presented findings shed for the first time promising new insights in the development of an MSI-1436-based therapy for proper equine metabolic syndrome intervention and may additionally find potential translational application to human metabolic syndrome treatment.

Force-tuned avidity of spike variant-ACE2 interactions viewed on the single-molecule level

Recent waves of COVID-19 correlate with the emergence of the Delta and the Omicron variant. We report that the Spike trimer acts as a highly dynamic molecular caliper, thereby forming up to three tight bonds through its RBDs with ACE2 expressed on the cell surface. The Spike of both Delta and Omicron (B.1.1.529) Variant enhance and markedly prolong viral attachment to the host cell receptor ACE2, as opposed to the early Wuhan-1 isolate. Delta Spike shows rapid binding of all three Spike RBDs to three different ACE2 molecules with considerably increased bond lifetime when compared to the reference strain, thereby significantly amplifying avidity. Intriguingly, Omicron (B.1.1.529) Spike displays less multivalent bindings to ACE2 molecules, yet with a ten time longer bond lifetime than Delta. Delta and Omicron (B.1.1.529) Spike variants enhance and prolong viral attachment to the host, which likely not only increases the rate of viral uptake, but also enhances the resistance of the variants against host-cell detachment by shear forces such as airflow, mucus or blood flow. We uncover distinct binding mechanisms and strategies at single-molecule resolution, employed by circulating SARS-CoV-2 variants to enhance infectivity and viral transmission.

Global Structure of the Intrinsically Disordered Protein Tau Emerges from Its Local Structure

The paradigmatic disordered protein tau plays an important role in neuronal function and neurodegenerative diseases. To disentangle the factors controlling the balance between functional and disease-associated conformational states, we build a structural ensemble of the tau K18 fragment containing the four pseudorepeat domains involved in both microtubule binding and amyloid fibril formation. We assemble 129-residue-long tau K18 chains with atomic detail from an extensive fragment library constructed with molecular dynamics simulations. We introduce a reweighted hierarchical chain growth (RHCG) algorithm that integrates experimental data reporting on the local structure into the assembly process in a systematic manner. By combining Bayesian ensemble refinement with importance sampling, we obtain well-defined ensembles and overcome the problem of exponentially varying weights in the integrative modeling of long-chain polymeric molecules. The resulting tau K18 ensembles capture nuclear magnetic resonance (NMR) chemical shift and J-coupling measurements. Without further fitting, we achieve very good agreement with measurements of NMR residual dipolar couplings. The good agreement with experimental measures of global structure such as single-molecule Förster resonance energy transfer (FRET) efficiencies is improved further by ensemble refinement. By comparing wild-type and mutant ensembles, we show that pathogenic single-point P301L, P301S, and P301T mutations shift the population from the turn-like conformations of the functional microtubule-bound state to the extended conformations of disease-associated tau fibrils. RHCG thus provides us with an atomically detailed view of the population equilibrium between functional and aggregation-prone states of tau K18, and demonstrates that global structural characteristics of this intrinsically disordered protein emerge from its local structure.

Bone marrow stromal cells (BMSCs CD45- /CD44+ /CD73+ /CD90+ ) isolated from osteoporotic mice SAM/P6 as a novel model for osteoporosis investigation

Available therapies aimed at treating age‐related osteoporosis are still insufficient. Therefore, designing reliable in vitro model for the analysis of molecular mechanisms underlying senile osteoporosis is highly required. We have isolated and characterized progenitor cells isolated from bone marrow (BMSCs) of osteoporotic mice strain SAM/P6 (BMSC_SAM/P6). The cytophysiology of BMSC_SAM/P6 was for the first time compared with BMSCs isolated from healthy BALB/c mice (BMSC_BALB/c). Characterization of the cells included evaluation of their multipotency, morphology and determination of specific phenotype. Viability of BMSCs cultures was determined in reference to apoptosis profile, metabolic activity, oxidative stress, mitochondrial membrane potential and caspase activation. Additionally, expression of relevant biomarkers was determined with RT‐qPCR. Obtained results indicated that BMSC_SAM/P6 and BMSC_BALB/c show the typical phenotype of mesenchymal stromal cells (CD44+, CD73+, CD90+) and do not express CD45. Further, BMSC_SAM/P6 were characterized by deteriorated multipotency, decreased metabolic activity and increased apoptosis occurrence, accompanied by elevated oxidative stress and mitochondria depolarisation. The transcriptome analyses showed that BMSC_SAM/P6 are distinguished by lowered expression of molecules crucial for proper osteogenesis, including Coll‐1, Opg and Opn. However, the expression of Trap, DANCR1 and miR‐124‐3p was significantly up‐regulated. Obtained results show that BMSC_SAM/P6 present features of progenitor cells with disturbed metabolism and could serve as appropriate model for in vitro investigation of age‐dependent osteoporosis.

Nanohydroxyapatite (nHAp) Doped with Iron Oxide Nanoparticles (IO), miR-21 and miR-124 Under Magnetic Field Conditions Modulates Osteoblast Viability, Reduces Inflammation and Inhibits the Growth of Osteoclast - A Novel Concept for Osteoporosis Treatment: Part 1

Purpose

Osteoporosis results in a severe decrease in the life quality of many people worldwide. The latest data shows that the number of osteoporotic fractures is becoming an increasing international health service problem. Therefore, a new kind of controllable treatment methods for osteoporotic fractures is extensively desired. For that reason, we have manufactured and evaluated nanohydroxyapatite (nHAp)-based composite co-doped with iron oxide (IO) nanoparticles. The biomaterial was used as a matrix for the controlled delivery of miR-21-5p and miR-124-3p, which have a proven impact on bone cell metabolism.

Methods

The nanocomposite Ca₅(PO₄)₃OH/Fe₃O₄ (later called nHAp/IO) was obtained by the wet chemistry method and functionalised with microRNAs (nHAp/IO@miR-21/124). Its physicochemical characterization was performed using XRPD, FT-IR, SEM-EDS and HRTEM and SAED methods. The modulatory effect of the composite was tested in vitro using murine pre-osteoblasts MC3T3-E1 and pre-osteoclasts 4B12. Moreover, the anti-inflammatory effects of biomaterial were analysed using a model of LPS-treated murine macrophages RAW 264.7. We have analysed the cells’ viability, mitochondria membrane potential and oxidative stress under magnetic field (MF+) and without (MF-). Moreover, the results were supplemented with RT-qPCR and Western blot assays to evaluate the expression profile for master regulators of bone metabolism.

Results

The results indicated pro-osteogenic effects of nHAp/IO@miR-21/124 composite enhanced by exposure to MF. The enhanced osteogenesis guided by nHAp/IO@miR-21/124 presence was associated with increased metabolism of progenitor cells and activation of osteogenic markers (Runx-2, Opn, Coll-1). Simultaneously, nanocomposite decreased metabolism and differentiation of pre-osteoclastic 4B12 cells accompanied by reduced expression of CaII and Ctsk. Obtained composite regulated viability of bone progenitor cells and showed immunomodulatory properties inhibiting the expression of inflammatory markers, ie, TNF-α, iNOs or IL-1β, in LPS-stimulated RAW 264.7 cells.

Conclusion

We have described for the first time a new concept of osteoporosis treatment based on nHAp/IO@miR-21/124 application. Obtained results indicated that fabricated nanocomposite might impact proper regeneration of osteoporotic bone, restoring the balance between osteoblasts and osteoclast.

Computational epitope map of SARS-CoV-2 spike protein

The primary immunological target of COVID-19 vaccines is the SARS-CoV-2 spike (S) protein. S is exposed on the viral surface and mediates viral entry into the host cell. To identify possible antibody binding sites, we performed multi-microsecond molecular dynamics simulations of a 4.1 million atom system containing a patch of viral membrane with four full-length, fully glycosylated and palmitoylated S proteins. By mapping steric accessibility, structural rigidity, sequence conservation, and generic antibody binding signatures, we recover known epitopes on S and reveal promising epitope candidates for structure-based vaccine design. We find that the extensive and inherently flexible glycan coat shields a surface area larger than expected from static structures, highlighting the importance of structural dynamics. The protective glycan shield and the high flexibility of its hinges give the stalk overall low epitope scores. Our computational epitope-mapping procedure is general and should thus prove useful for other viral envelope proteins whose structures have been characterized.

Profiling circulating microRNAs in the serum of pregnant and non-pregnant pigs reveals a plethora of reproductive status-dependent microRNAs

Circulating, non-coding RNAs, such as microRNAs (miRNAs) have been proposed to be powerful pathophysiological indicators of pregnancy in animals and humans. Since their discovery, it is known that miRNAs can take part in numerous biological processes, including cell proliferation and differentiation during early embryonic development and establishment of pregnancy. Our recent studies have indicated that maternal blood can carry miRNAs reported previously at the embryo-maternal interface in pigs. To expand the scope of our research, we tested the hypothesis that miRNAs previously identified in conceptuses, trophoblasts, endometrium and uterine lumen-derived extracellular vesicles (EVs) collected before Day 20 of pregnancy can show reproductive status-dependent profiles in the serum of cyclic and pregnant crossbred pigs. Custom-designed TaqMan arrays, multiplex real-time reverse transcription (RT)-PCR and real-time RT-PCR allowed us to identify a number of reproductive status-dependent miRNAs in serum samples collected from pigs during the estrous cycle or pregnancy (Days 16 and 20). We found that serum samples were enriched with miRNAs involved in processes important during the estrous cycle and early pregnancy, e.g. cell sensitivity and viability, angiogenesis, embryonic cell proliferation and differentiation. Further validation revealed different abundance of ssc-miR-143-3p and ssc-miR-125b in pregnant and non-pregnant animals and correlation of ssc-miR-125b levels with litter size. In addition, analyzed serum samples contained both EVs and Argonaute2 proteins, which are known to be involved in miRNA transportation and intercellular communication. In summary, we identified several circulating miRNAs that differ in abundance between cyclic and pregnant animals and could serve as potential indicators of reproductive status in pigs during breeding management.

Optimization of barbel (Barbus Barbus L.) fertilization and effects of ovarian fluid when there are controlled conditions for gamete activations

Fertilization is one of the most important procedures in artificial reproduction and it directly affects the reproduction outcome. When there is optimization of fertilization, there can be a positive effect on subsequent reproductive processes and economic aspects of aquaculture. This study was conducted to determine time for which oocytes and sperm of barbel Barbus barbus retain fertilization capacity following placement in freshwater. Furthermore, the amount of ovarian fluid, excreted by fish during spawning with eggs (OFI; %) was determined, along with the chemical composition and effects on fertilization were determined. Gametes, ovarian fluid, and seminal plasma from barbel spawning specimens of the F₄ generation were used to conduct the study. Ovarian fluid accounted for 14%-68% of contents of the mass released at spawning and post-spawning composition differed depending on whether hormonal treatments were utilized for control of reproduction. There was an association (R² = 0.982; P = 0.000) between the pH of ovarian fluid and the barbel embryo survival rate. There was the greatest survival rate (>60 %) when the pH range of 7.9-8.4 and there was a lesser embryo viability when pH values were lesser or greater than values within this range (P <  0.05). The results from the study indicate that barbel eggs retain fertilization capacity longer (as long as 210 s) after activation by placement in fresh water than spermatozoa (about 30 s).

Titanium Dioxide Thin Films Obtained by Atomic Layer Deposition Promotes Osteoblasts' Viability and Differentiation Potential While Inhibiting Osteoclast Activity-Potential Application for Osteoporotic Bone Regeneration

Atomic layer deposition (ALD) technology has started to attract attention as an efficient method for obtaining bioactive, ultrathin oxide coatings. In this study, using ALD, we have created titanium dioxide (TiO2) layers. The coatings were characterised in terms of physicochemical and biological properties. The chemical composition of coatings, as well as thickness, roughness, wettability, was determined using XPS, XRD, XRR. Cytocompatibillity of ALD TiO2 coatings was accessed applying model of mouse pre-osteoblast cell line MC3T3-E1. The accumulation of transcripts essential for bone metabolism (both mRNA and miRNA) was determined using RT-qPCR. Obtained ALD TiO2 coatings were characterised as amorphous and homogeneous. Cytocompatibility of the layers was expressed by proper morphology and growth pattern of the osteoblasts, as well as their increased viability, proliferative and metabolic activity. Simultaneously, we observed decreased activity of osteoclasts. Obtained coatings promoted expression of Opn, Coll-1, miR-17 and miR-21 in MC3T3-E1 cells. The results are promising in terms of the potential application of TiO2 coatings obtained by ALD in the field of orthopaedics, especially in terms of metabolic- and age-related bone diseases, including osteoporosis.

In situ structural analysis of SARS-CoV-2 spike reveals flexibility mediated by three hinges

The spike protein (S) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is required for cell entry and is the primary focus for vaccine development. In this study, we combined cryo-electron tomography, subtomogram averaging, and molecular dynamics simulations to structurally analyze S in situ. Compared with the recombinant S, the viral S was more heavily glycosylated and occurred mostly in the closed prefusion conformation. We show that the stalk domain of S contains three hinges, giving the head unexpected orientational freedom. We propose that the hinges allow S to scan the host cell surface, shielded from antibodies by an extensive glycan coat. The structure of native S contributes to our understanding of SARS-CoV-2 infection and potentially to the development of safe vaccines.

Theranostic Applications of Nanostructured Silicate-Substituted Hydroxyapatite Codoped with Eu3+ and Bi3+ Ions-A Novel Strategy for Bone Regeneration

In this paper, nanocrystalline silicate-substituted hydroxyapatites (nSi-HAps) codoped with Eu³⁺ were functionalized with Bi³⁺ ions. Biomaterials were synthesized using a microwave-assisted hydrothermal method and heat-treated at 700 °C. The concentration of Eu³⁺ ions was established at 1 mol %, and the concentration of Bi³⁺ was in the range of 0.5-2 mol %. The physicochemical properties of the obtained biomaterials were determined using previously established methods, including X-ray powder diffraction, scanning electron microscopy techniques, and IR spectroscopy. Particle sizes obtained in this study were in the range of 22-65 nm, which was established by the Rietveld method. The luminescence properties of the Eu³⁺ ion-doped silicate-substituted apatite were recorded depending on the bismuth(III) concentration. The cytocompatibility of obtained biomaterials was tested using the model of mouse pre-osteoblasts cell line, that is, MC3T3-E1. We showed that the obtained biomaterials exerted anti-apoptotic effect, reducing the number of early and late apoptotic cells and decreasing caspase activity and reactive oxygen species accumulation. The transcripts levels of genes associated with apoptosis confirmed the anti-apoptotic effect of the biomaterials. Increased metabolic activity of MC3T3-E1 in cultures with biomaterials functionalized with Bi³⁺ ions has been observed. Moreover, the determined profile of osteogenic markers indicates that the obtained matrices, that is, Eu³⁺:nSi-HAp functionalized with Bi³⁺ ions, exert pro-osteogenic properties. The biological features of Eu³⁺:nSi-HAp modified with Bi³⁺ ions are highly desired in terms of functional tissue restoration and further efficient osteointegration.

An adhesion code ensures robust pattern formation during tissue morphogenesis

Animal development entails the organization of specific cell types in space and time, and spatial patterns must form in a robust manner. In the zebrafish spinal cord, neural progenitors form stereotypic patterns despite noisy morphogen signaling and large-scale cellular rearrangements during morphogenesis and growth. By directly measuring adhesion forces and preferences for three types of endogenous neural progenitors, we provide evidence for the differential adhesion model in which differences in intercellular adhesion mediate cell sorting. Cell type-specific combinatorial expression of different classes of cadherins (N-cadherin, cadherin 11, and protocadherin 19) results in homotypic preference ex vivo and patterning robustness in vivo. Furthermore, the differential adhesion code is regulated by the sonic hedgehog morphogen gradient. We propose that robust patterning during tissue morphogenesis results from interplay between adhesion-based self-organization and morphogen-directed patterning.

In situ structural analysis of SARS-CoV-2 spike reveals flexibility mediated by three hinges

The spike protein (S) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is required for cell entry and is the primary focus for vaccine development. In this study, we combined cryo-electron tomography, subtomogram averaging, and molecular dynamics simulations to structurally analyze S in situ. Compared with the recombinant S, the viral S was more heavily glycosylated and occurred mostly in the closed prefusion conformation. We show that the stalk domain of S contains three hinges, giving the head unexpected orientational freedom. We propose that the hinges allow S to scan the host cell surface, shielded from antibodies by an extensive glycan coat. The structure of native S contributes to our understanding of SARS-CoV-2 infection and potentially to the development of safe vaccines.

Mechanical Unfolding of Proteins-A Comparative Nonequilibrium Molecular Dynamics Study

Mechanical signals regulate functions of mechanosensitive proteins by inducing structural changes that are determinant for force-dependent interactions. Talin is a focal adhesion protein that is known to extend under mechanical load, and it has been shown to unfold via intermediate states. Here, we compared different nonequilibrium molecular dynamics (MD) simulations to study unfolding of the talin rod. We combined boxed MD (BXD), steered MD, and umbrella sampling (US) techniques and provide free energy profiles for unfolding of talin rod subdomains. We conducted BXD, steered MD, and US simulations at different detail levels and demonstrate how these different techniques can be used to study protein unfolding under tension. Unfolding free energy profiles determined by BXD suggest that the intermediate states in talin rod subdomains are stabilized by force during unfolding, and US confirmed these results.

Small and Long Non-coding RNAs as Functional Regulators of Bone Homeostasis, Acting Alone or Cooperatively

Emerging knowledge indicates that non-coding RNAs, including microRNAs (miRNAs) and long-noncoding RNAs (lncRNAs), have a pivotal role in bone development and the pathogenesis of bone-related disorders. Most recently, miRNAs have started to be regarded as potential biomarkers or targets for various sets of diseases, while lncRNAs have gained attention as a new layer of gene expression control acting through versatile interactions, also with miRNAs. The rapid development of RNA sequencing techniques based on next-generation sequencing (NGS) gives us better insight into molecular pathways regulated by the miRNA-lncRNA network. In this review, we summarize the current knowledge related to the function of miRNAs and lncRNAs as regulators of genes that are crucial for proper bone metabolism and homeostasis. We have characterized important non-coding RNAs and their expression signatures, in relationship to bone. Analysis of the biological function of miRNAs and lncRNAs, as well as their network, will pave the way for a better understanding of the pathogenesis of various bone disorders. We also think that this knowledge may lead to the development of innovative diagnostic tools and therapeutic approaches for bone-related disorders.

Zirconium Oxide Thin Films Obtained by Atomic Layer Deposition Technology Abolish the Anti-Osteogenic Effect Resulting from miR-21 Inhibition in the Pre-Osteoblastic MC3T3 Cell Line

Introduction

The development of the field of biomaterials engineering is rapid. Various bioactive coatings are created to improve the biocompatibility of substrates used for bone regeneration, which includes formulation of thin zirconia coatings with pro-osteogenic properties. The aim of this study was to assess the biological properties of ZrO₂ thin films grown by Atomic Layer Deposition (ALD) technology (ZrO₂^ALD).

Methodology

The cytocompatibility of the obtained layers was analysed using the mice pre-osteoblastic cell line (MC3T3) characterized by decreased expression of microRNA 21-5p (miR-21-5p) in order to evaluate the potential pro-osteogenic properties of the coatings. The in vitro experiments were designed to determine the effect of ZrO₂^ALD coatings on cell morphology (confocal microscope), proliferative activity (cell cycle analysis) and metabolism, reflected by mitochondrial membrane potential (cytometric-based measurement). Additionally, the influence of layers on the expression of genes associated with cell survival and osteogenesis was studied using RT-qPCR. The following genes were investigated: B-cell lymphoma 2 (Bcl-2), Bcl-2-associated X protein (Bax), p53 and p21, as well as osteogenic markers, i.e. collagen type 1 (Coll-1), osteopontin (Opn), osteocalcin (Ocl) and runt-related transcription factor 2 (Runx-2). The levels of microRNA (miRNA/miR) involved in the regulation of osteogenic genes were determined, including miR-7, miR-21, miR-124 and miR-223.

Results

The analysis revealed that the obtained coatings are cytocompatible and may increase the metabolism of pre-osteoblast, which was correlated with increased mitochondrial membrane potential and extensive development of the mitochondrial network. The obtained coatings affected the viability and proliferative status of cells, reducing the population of actively dividing cells. However, in cultures propagated on ZrO₂^ALD coatings, the up-regulation of genes essential for bone metabolism was noted.

Discussion

The data obtained indicate that ZrO₂ coatings created using the ALD method may have pro-osteogenic properties and may improve the metabolism of bone precursor cells. Given the above, further development of ZrO₂^ALD layers is essential in terms of their potential clinical application in bone regenerative medicine.

Noncollinear Ordering of the Orbital Magnetic Moments in Magnetite

The magnitude of the orbital magnetic moment and its role as a trigger of the Verwey transition in the prototypical Mott insulator, magnetite, remain contentious. Using 1s2p resonant inelastic x-ray scattering angle distribution (RIXS-AD), we prove the existence of noncollinear orbital magnetic ordering and infer the presence of dynamical distortion creating a polaronic precursor for the metal to insulator transition. These conclusions are based on a subtle angular shift of the RIXS-AD spectral intensity as a function of the magnetic field orientation. Theoretical simulations show that these results are only consistent with noncollinear magnetic orbital ordering. To further support these claims we perform Fe K-edge x-ray magnetic circular dichroism in order to quantify the Fe average orbital magnetic moment.

Dynamics of mercury content in adult sichel (Pelecus cultratus L.) tissues from the Baltic Sea before and during spawning

This study compares the content of mercury in the muscles, liver, kidneys, gonads and gills of male and female individuals of sichel (Pelecus cultratus). Moreover, the trend of changes of mercury concentration before (March) and during (May) the spawning season was examined. Sichel brooders were caught in the Vistula Lagoon during commercial fishing. The mercury content in tissues was determined by atomic absorption using a Milestone DMA-80. The tests revealed a statistically higher mercury concentration in muscles, liver and gonads in male vs. female fish. Moreover, significantly higher mercury concentration was found in male and female fish caught during the spawning season (May) than in those caught before this season (March). Moreover, testes (0.011 ± 0.007 mg kg^-1 w/w) were found to contain 12 times, and ovaries (0.004 ± 0.001 mg kg^-1 w/w) - approx. 19 times less mercury than the muscular tissue of those same fish. This may suggest the existence of a protective barrier, defending future offspring against the transfer of toxic mercury from the parent body to gonads and gametes.

The value of dermoscopy in diagnosing eyebrow loss in patients with alopecia areata and frontal fibrosing alopecia

INTRODUCTION

Alopecia areata and frontal fibrosing alopecia are common causes of eyebrow loss (madarosis).

OBJECTIVE

Assessment of trichoscopic markers of eyebrow loss in alopecia areata and frontal fibrosing alopecia.

MATERIALS AND METHODS

The analysis included 50 patients with scalp alopecia areata with madarosis, 50 patients with scalp frontal fibrosing alopecia with madarosis and 50 healthy controls. In every case, trichoscopy of the eyebrow area was performed.

RESULTS

Empty follicular and eccrine duct openings were observed in all patients and presented predominantly as yellow dots. Exclamation mark hairs were only detected in patients with alopecia areata (30%). Tapered hairs, broken hair, black dots and Pohl-Pinkus constrictions were observed in 14%, 36%, 26% and 4% of patients with alopecia areata, respectively, 4%, 16%, 2% and 0% of patients with frontal fibrosing alopecia, respectively, and they were not present in healthy controls. Dystrophic hairs and whitish areas were observed only in patients with frontal fibrosing alopecia (28% and 32%, respectively). Eyebrow regrowth in distinct directions was present in 32% of patients with frontal fibrosing alopecia, 8% of patients with alopecia areata and 4% of healthy controls. Diffuse erythema was detected in 60% of patients with alopecia areata and frontal fibrosing alopecia and 56% of healthy controls. Vellus hairs and upright regrowing hairs were observed in patients with alopecia areata (62% and 58%, respectively), frontal fibrosing alopecia (60% and 84%, respectively) and healthy controls (100% and 100%, respectively).

CONCLUSION

Trichoscopy of the eyebrow area is useful in diagnosing patients with isolated eyebrow loss. The most characteristic trichoscopic features of eyebrow loss in alopecia areata include exclamation mark hairs, tapered hairs, broken hairs and black dots. Frontal fibrosing alopecia of the eyebrows is characterized by the presence of dystrophic hairs, white areas and eyebrow regrowth in distinct directions.

Censoring Weighted Separate-and-Conquer Rule Induction from Survival Data

Objectives: Rule induction is one of the major methods of machine learning. Rule-based models can be easily read and interpreted by humans, that makes them particularly useful in survival studies as they can help clinicians to better understand analysed data and make informed decisions about patient treatment. Although of such usefulness, there is still a little research on rule learning in survival analysis. In this paper we take a step towards rule-based analysis of survival data.

Methods: We investigate so-called covering or separate-and-conquer method of rule induction in combination with a weighting scheme for handling censored observations. We also focus on rule quality measures being one of the key elements differentiating particular implementations of separate-and-conquer rule induction algorithms. We examine 15 rule quality measures guiding rule induction process and reflecting a wide range of different rule learning heuristics.

Results: The algorithm is extensively tested on a collection of 20 real survival datasets and compared with the state-of-the-art survival trees and random survival forests algorithms. Most of the rule quality measures outperform Kaplan-Meier estimate and perform at least equally well as tree-based algorithms.

Conclusions: Separate-and-conquer rule induction in combination with weighting scheme is an effective technique for building rule-based models of survival data which, according to predictive accuracy, are competitive with tree-based representations.

Predominance of Comorbidities in the Detriment of Daily Activity in Sarcoidosis Patients

Sarcoidosis may affect lung function, working ability, overall mobility, and daily activity. In the present study we performed an analysis of clinical settings in patients with sarcoidosis to disentangle its influence on daily physical activity (PA). PA assessment (number of steps per day, daily energy expenditure) was performed by accelerometry during consecutive 7 days after discharge from hospital. Thirty patients with sarcoidosis, aged 46.4 ± 10.5, were enrolled in the study. Clinical data (age, gender, steroid consumption, weight, and comorbidities), lung function tests (forced expiratory volume in one second - FEV1, forced vital capacity - FVC, and lung diffusion for carbon monoxide - DLCO), mobility (6-minute walk test - 6 MWT) and physical performance (oxygen consumption at anaerobic threshold - VO2/AT) were estimated. The mean daily PA (5214 ± 2699 steps/day) and VO2max (22.3 ± 7.0 ml/kg/min) were lower when referenced to the age-group predicted values. A significant greater daily PA was observed in sarcoidosis patients without comorbidities compared with those having more than two comorbidities (p = 0.046). No association was found between steroid use, lung function, and 6MWT. Daily PA was associated with patients aerobic efficacy and VO2max (r = 0.38, p < 0.04). The findings demonstrate a significant influence of comorbidities on sarcoidosis patients' exercise tolerance and daily PA. Special treatment considerations, including the potential impact of comorbidities, may help optimize exercise regimes, link physical activity with health, and prevent sarcoidosis complications.

Physical Functioning and Symptoms of Chronic Fatigue in Sarcoidosis Patients

Scientific reports underscore the importance of measuring the health-related quality of life in sarcoidosis patients. The present study seeks to define how sarcoidosis patients' quality of life, daily physical activity, and physical performance are related to each other. Seventeen patients (mean age 46.8 ± 8.8 years) suffering from sarcoidosis completed the following questionnaires: the fatigue assessment scale (FAS), the quality of life scale (SF-36 questionnaire), and the Borg dyspnea scale. Physical activity (PA) was assessed using accelerometry. Respiratory function, consisting of forced expiratory volume in one second (FEV1), forced vital capacity (FVC), forced expiratory volume in one second as a percentage of vital capacity (FEV1/%FVC), and diffusing capacity of the lungs for carbon monoxide (DLCO), were assessed. In addition, performance in 6-min walk test (MWT), aerobic capacity assessed from maximal oxygen uptake (VO2max), and the metabolic equivalent of task (MET) were evaluated. We found that daily PA (4566 ± 2378 steps/day) and VO2max (21.8 ± 5.9 ml/kg/min) were lower in sarcoidosis patients than the known predicted values in healthy age-matched individuals. There were significant inverse associations between the FAS score and 6MWT (r = -0.62; p < 0.01), and between SF-36 score and 6MWT (r = -0.55; p < 0.03). In contrast, SF-36 scores associated with fatigue and dyspnea scores (r = 0.72; p < 0.001 and r = 0.85; p < 0.001). These findings imply that sarcoidosis patients are less active compared with healthy subjects. The FAS and SF-36 scales seem to be effective tools for assessing the severity of fatigue in sarcoidosis patients.

An Effective Feedback Loop between Cell-Cell Contact Duration and Morphogen Signaling Determines Cell Fate

Cell-cell contact formation constitutes an essential step in evolution, leading to the differentiation of specialized cell types. However, remarkably little is known about whether and how the interplay between contact formation and fate specification affects development. Here, we identify a positive feedback loop between cell-cell contact duration, morphogen signaling, and mesendoderm cell-fate specification during zebrafish gastrulation. We show that long-lasting cell-cell contacts enhance the competence of prechordal plate (ppl) progenitor cells to respond to Nodal signaling, required for ppl cell-fate specification. We further show that Nodal signaling promotes ppl cell-cell contact duration, generating a positive feedback loop between ppl cell-cell contact duration and cell-fate specification. Finally, by combining mathematical modeling and experimentation, we show that this feedback determines whether anterior axial mesendoderm cells become ppl or, instead, turn into endoderm. Thus, the interdependent activities of cell-cell signaling and contact formation control fate diversification within the developing embryo.

55Mn NMR observation of colossal magnetoresistance effect in Sm0.55Sr0.45MnO3

Temperature dependent ⁵⁵Mn NMR study of Sm_0.55Sr_0.45MnO₃ is reported. Previous bulk magnetization measurements have shown that below T _C ~ 125 K the sample is ferromagnetic metallic (FMM) and above T_C it is charge ordered and insulating. In present report, we show that from zero-field NMR a single line double-exchange (DE) signal is observed at temperatures up to 139 K, which is due to a presence of FMM clusters also above T _C. The intensity of the DE line follows the temperature dependence of the magnetization measured at 0.01 T. When a magnetic field up to 2 T is applied at 139 K (i.e. 14 K above T _C), a strong increase in NMR intensity of the DE line is observed indicating that content of FMM regions increases. This reveals that metallicity is induced in the material by the applied magnetic field and explains the observed colossal magnetoresistance (CMR) effect at the microscopic level. The observation agrees with previous results, which confirm that the percolation of the FMM clusters is responsible for the CMR effect. The shift of the resonant frequency in the applied field is three times smaller compared to decrease expected from gyromagnetic ratio, which indicates an antiferromagnetic coupling between the FMM clusters.

The Lack of Association between FCN2 Gene Promoter Region Polymorphisms and Dental Caries in Polish Children

The aim of this study was to examine the association of single-nucleotide polymorphisms (SNPs) in the gene encoding ficolin-2 protein (FCN2 gene) at positions -986 (rs17514136), -602 (rs3124953), and -4 (rs3124952) with dental caries in Polish children. Two hundred and sixty Polish Caucasian children aged 15 years were enrolled in this study: 82 with "higher" caries experience (DMFT >5) and 178 with "lower" caries experience (DMFT ≤5). In addition, subjects with caries experience (DMFT ≥1) and caries-free subjects (DMFT = 0) were compared. FCN2 SNPs were genotyped with PCR-RFLP methods. There were no significant differences in the genotype, allele, or haplotype distributions in 3 analyzed SNPs of the FCN2 gene between children with "higher" and those with "lower" caries experience as well as between children with caries experience and caries-free children. In conclusion, we did not find any association of FCN2 promoter polymorphisms at positions -986, -602, and -4 with dental caries in Polish children.

Use of Modified Starches as Thickeners of Cocoa Syrups

Elaboration of cocoa syrups by the use of modified starches such as acetylated distarch adipate (ADA) and oxidised starch (OS) were described and analysed the influence of different amounts of ADA and OS on physical and sensory properties of cocoa syrups. The sensory, textural and rheological properties of syrups produced in the laboratory conditions were compared to the properties of commercially produced ones. The quantity of modified starch added affected textural and rheological properties of syrups. All analysed syrups showed non-Newtonian, pseudoplastic flow and thixotropy. Values of yield stresses, viscosities of Casson, and consistency coefficients of syrups prepared in laboratory conditions increased with an increase in the addition of modified starches.