Sub-nucleosomal Genome Structure Reveals Distinct Nucleosome Folding Motifs.

Elucidating the global and local rules that govern genome-wide, hierarchical chromatin architecture remains a critical challenge. Current high-throughput chromosome conformation capture (Hi-C) technologies have identified large-scale chromatin structural motifs, such as topologically associating domains and looping. However, structural rules at the smallest or nucleosome scale remain poorly understood. Here, we coupled nucleosome-resolved Hi-C technology with simulated annealing-molecular dynamics (SA-MD) simulation to reveal 3D spatial distributions of nucleosomes and their genome-wide orientation in chromatin. Our method, called Hi-CO, revealed distinct nucleosome folding motifs across the yeast genome. Our results uncovered two types of basic secondary structural motifs in nucleosome folding: α-tetrahedron and ß-rhombus analogous to α helix and ß sheet motifs in protein folding. Using mutants and cell-cycle-synchronized cells, we further uncovered motifs with specific nucleosome positioning and orientation coupled to epigenetic features at individual loci. By illuminating molecular-level structure-function relationships in eukaryotic chromatin, our findings establish organizational principles of nucleosome folding.

Slide-tags enables single-nucleus barcoding for multimodal spatial genomics.

Recent technological innovations have enabled the high-throughput quantification of gene expression and epigenetic regulation within individual cells, transforming our understanding of how complex tissues are constructed1-6. However, missing from these measurements is the ability to routinely and easily spatially localize these profiled cells. We developed a strategy, Slide-tags, in which single nuclei within an intact tissue section are tagged with spatial barcode oligonucleotides derived from DNA-barcoded beads with known positions. These tagged nuclei can then be used as an input into a wide variety of single-nucleus profiling assays. Application of Slide-tags to the mouse hippocampus positioned nuclei at less than 10 µm spatial resolution and delivered whole-transcriptome data that are indistinguishable in quality from ordinary single-nucleus RNA-sequencing data. To demonstrate that Slide-tags can be applied to a wide variety of human tissues, we performed the assay on brain, tonsil and melanoma. We revealed cell-type-specific spatially varying gene expression across cortical layers and spatially contextualized receptor-ligand interactions driving B cell maturation in lymphoid tissue. A major benefit of Slide-tags is that it is easily adaptable to almost any single-cell measurement technology. As a proof of principle, we performed multiomic measurements of open chromatin, RNA and T cell receptor (TCR) sequences in the same cells from metastatic melanoma, identifying transcription factor motifs driving cancer cell state transitions in spatially distinct microenvironments. Slide-tags offers a universal platform for importing the compendium of established single-cell measurements into the spatial genomics repertoire.

JASPAR 2024: 20th anniversary of the open-access database of transcription factor binding profiles.

JASPAR (https://jaspar.elixir.no/) is a widely-used open-access database presenting manually curated high-quality and non-redundant DNA-binding profiles for transcription factors (TFs) across taxa. In this 10th release and 20th-anniversary update, the CORE collection has expanded with 329 new profiles. We updated three existing profiles and provided orthogonal support for 72 profiles from the previous release's UNVALIDATED collection. Altogether, the JASPAR 2024 update provides a 20% increase in CORE profiles from the previous release. A trimming algorithm enhanced profiles by removing low information content flanking base pairs, which were likely uninformative (within the capacity of the PFM models) for TFBS predictions and modelling TF-DNA interactions. This release includes enhanced metadata, featuring a refined classification for plant TFs' structural DNA-binding domains. The new JASPAR collections prompt updates to the genomic tracks of predicted TF binding sites (TFBSs) in 8 organisms, with human and mouse tracks available as native tracks in the UCSC Genome browser. All data are available through the JASPAR web interface and programmatically through its API and the updated Bioconductor and pyJASPAR packages. Finally, a new TFBS extraction tool enables users to retrieve predicted JASPAR TFBSs intersecting their genomic regions of interest.

Improving bioinformatics software quality through teamwork.

Since high-throughput techniques became a staple in biological science laboratories, computational algorithms, and scientific software have boomed. However, the development of bioinformatics software usually lacks software development quality standards. The resulting software code is hard to test, reuse, and maintain. We believe that the root of inefficiency in implementing the best software development practices in academic settings is the individualistic approach, which has traditionally been the norm for recognizing scientific achievements and, by extension, for developing specialized software. Software development is a collective effort in most software-heavy endeavors. Indeed, the literature suggests teamwork directly impacts code quality through knowledge sharing, collective software development, and established coding standards. In our computational biology research groups, we sustainably involve all group members in learning, sharing, and discussing software development while maintaining the personal ownership of research projects and related software products. We found that group members involved in this endeavor improved their coding skills, became more efficient bioinformaticians, and obtained detailed knowledge about their peers' work, triggering new collaborative projects. We strongly advocate for improving software development culture within bioinformatics through collective effort in computational biology groups or institutes with three or more bioinformaticians.

Overview of multifunctional Tregs in cardiovascular disease: From insights into cellular functions to clinical implications.

Regulatory T cells (Tregs) are crucial in regulating T-cell-mediated immune responses. Numerous studies have shown that dysfunction or decreased numbers of Tregs may be involved in inflammatory cardiovascular diseases (CVDs) such as atherosclerosis, hypertension, myocardial infarction, myocarditis, cardiomyopathy, valvular heart diseases, heart failure, and abdominal aortic aneurysm. Tregs can help to ameliorate CVDs by suppressing excessive inflammation through various mechanisms, including inhibition of T cells and B cells, inhibition of macrophage-induced inflammation, inhibition of dendritic cells and foam cell formation, and induction of anti-inflammatory macrophages. Enhancing or restoring the immunosuppressive activity of Tregs may thus serve as a fundamental immunotherapy to treat hypertension and CVDs. However, the precise molecular mechanisms underlying the Tregs-induced protection against hypertension and CVDs remain to be investigated. This review focuses on recent advances in our understanding of Tregs subsets and function in CVDs. In addition, we discuss promising strategies for using Tregs through various pharmacological approaches to treat hypertension and CVDs.

Reversible Protection and Targeted Delivery of DNA Origami with a Disulfide-Containing Cationic Polymer.

DNA nanostructures have considerable biomedical potential as intracellular delivery vehicles as they are highly homogeneous and can be functionalized with high spatial resolution. However, challenges like instability under physiological conditions, limited cellular uptake, and lysosomal degradation limit their use. This paper presents a bio-reducible, cationic polymer poly(cystaminebisacrylamide-1,6-diaminohexane) (PCD) as a reversible DNA origami protector. PCD displays a stronger DNA affinity than other cationic polymers. DNA nanostructures with PCD protection are shielded from low salt conditions and DNase I degradation and show a 40-fold increase in cell-association when linked to targeting antibodies. Confocal microscopy reveals a potential secondary cell uptake mechanism, directly delivering the nanostructures to the cytoplasm. Additionally, PCD can be removed by cleaving its backbone disulfides using the intracellular reductant, glutathione. Finally, the application of these constructs is demonstrated for targeted delivery of a cytotoxic agent to cancer cells, which efficiently decreases their viability. The PCD protective agent that is reported here is a simple and efficient method for the stabilization of DNA origami structures. With the ability to deprotect the DNA nanostructures upon entry of the intracellular space, the possibility for the use of DNA origami in pharmaceutical applications is enhanced.

Type II natural killer T cells use features of both innate-like and conventional T cells to recognize sulfatide self antigens.

Glycolipids presented by the major histocompatibility complex (MHC) class I homolog CD1d are recognized by natural killer T cells (NKT cells) characterized by either a semi-invariant T cell antigen receptor (TCR) repertoire (type I NKT cells or iNKT cells) or a relatively variable TCR repertoire (type II NKT cells). Here we describe the structure of a type II NKT cell TCR in complex with CD1d-lysosulfatide. Both TCR α-chains and TCR ß-chains made contact with the CD1d molecule with a diagonal footprint, typical of MHC-TCR interactions, whereas the antigen was recognized exclusively with a single TCR chain, similar to the iNKT cell TCR. Type II NKT cell TCRs, therefore, recognize CD1d-sulfatide complexes by a distinct recognition mechanism characterized by the TCR-binding features of both iNKT cells and conventional peptide-reactive T cells.

Vapor and Light Responsive Biocompatible Soft Actuator.

Bioinspired smart polymeric materials that undergo three-dimensional shape deformation in response to specific stimuli have gained significant attention in the field of soft robotics and intelligent devices. Despite the substantial advancements in soft robotics, there is a growing demand for the design of multistimuli-responsive soft actuators using a single layer of material due to its reduced complexity and ease of manufacturing and durability. Here, we report the actuation characteristics of a single-layer, dual-responsive soft actuator that overcomes the commonly encountered delamination issues often associated with bilayer systems by incorporating PEDOT:PSS with cassava starch. This soft actuator exhibits deformations in response to various solvent vapors, such as water, alcohol, and acetone. Remarkably, it demonstrates opposite deformations upon exposure to water and alcohol vapors. Additionally, the actuator responds to light triggers and folds upon exposure to sunlight and infrared light. The degree of folding can be precisely controlled by adjusting the intensity of the light source. Furthermore, the periodic geometric patterns imposed on the surface of the actuator provide an additional handle to control the bending axis. For proof of concept, we leverage the actuation capabilities of our actuator to showcase a range of potential applications, including its usage in wearable textiles, crawler robots, smart curtains, push-and-pull machines, and smart lifts.

Responsive soft actuator: harnessing multi-vapor, light, and magnetic field stimuli.

Bioinspired soft actuators, capable of undergoing shape deformation in response to external triggers, hold great potential in fields such as soft robotics, artificial muscles, drug delivery, and smart switches. However, their widespread application is hindered by limitations in responsiveness, durability, and complex fabrication processes. In this study, we propose a new approach to tackle these challenges by developing a single-layer soft actuator that responds to multiple stimuli using a straightforward solution-casting method. This actuator comprises bio-polymer gelatin, bio-compatible PEDOT:PSS, and iron oxide (Fe3O4) nanoparticles. Our actuator exhibits responsiveness to a range of organic solvent vapors, including water vapor, light, and magnetic fields. Notably, it exhibits rapid and reversible bending in distinct directions in response to different vapors, bending upwards in the presence of water vapor and downwards in the presence of alcohol vapor. Moreover, exposure to infrared (IR) light induces a bending toward the light source. The incorporation of magnet-responsive Fe3O4 nanoparticles induces multi-functionality in the actuator. The actuation characteristics of the actuator are controlled by leveraging its responsiveness to dual stimuli, such as water vapor and magnetic fields, as well as light and magnetic fields. For the proof of concept, we showcase several potential applications of our multi-stimuli responsive soft actuator, including magnet-triggered electrical switches, cargo transportation, soft grippers, targeted drug delivery, energy harvesting, and bio-mimicry.

PIDA-promoted metal-free [3 + 2] heteroannulation of ß-ketothioamides with 4-hydroxy coumarins: chemo-/regioselective access to furo[3,2-c]chromen-4-ones at room temperature.

Herein, we report a viable protocol to access furo[3,2-c]chromen-4-ones by engaging easily accessible 4-hydroxy coumarins as a three-atom CCO unit and thioamides as a C2 coupling partner, mediated by phenyliodine(III) diacetate (PIDA) at room temperature in a highly efficient and pot-/step-economical manner. This strategy not only avoids potential toxicity and tiresome workup conditions, but also features operational simplicity, a broad substrate scope, good functional group tolerance, high yields, easy scalability and exclusive selectivity. A mechanistic study has shown that this metal-free reaction is triggered by PIDA via activation of the ß-carbon of 4-hydroxy coumarin, followed by a nucleophilic addition/intramolecular cyclization/dethiohydration cascade. High-resolution mass spectra (HRMS) study confirms the key intermediates involved during the course of the reaction, elucidating the reaction pathways, and demonstrates the excellent regio- and chemoselectivity of this approach.

Influence of Ancillary Ligand on the Photosensitization and Photophysical Properties of Red Luminescent Tri-fluorinated Β-diketonate Eu(III) Complexes.

Highly emissive ternary Eu(III) complexes were synthesized with a tri-fluorinated ß-diketone as principal ligand and heterocyclic aromatic compounds as ancillary ligands to assess their utility as an illuminating material for display devices and other optoelectronics. The general characterizations, regarding the coordinating facets of complexes were accomplished via various spectroscopic techniques. Thermal stability was investigated via TGA/DTA. Photophysical analysis was accomplished by PL studies, Band gap value, color parameters and J-O analysis. DFT calculations were performed adopting geometrically optimized structure of complexes. Superb thermal stability has been achieved in complexes, which decides their concrete candidature for display devices. The bright red luminescence of complexes is ascribed to 5D0 → 7F2 transition of Eu(III) ion. Colorimetric parameters unlocked the applicability of complexes as warm light source and J-O parameters adequately summarized the coordinating surrounding around the metal ion. Various radiative properties were also evaluated which suggested the prospective use of complexes in lasers and other optoelectronic devices. The band gap and Urbach band tail, procured from absorption spectra, revealed the semiconducting behavior of synthesized complexes. DFT studies rendered the energies of FMO and various other molecular parameters. It can be summarized from the photophysical and optical analysis of synthesized complexes that these complexes are virtuous luminescent materials and possess potentiality to be used in diverse domain of display devices.

Heat-killed probiotic Levilactobacillus brevis MKAK9 and its exopolysaccharide promote longevity by modulating aging hallmarks and enhancing immune responses in Caenorhabditis elegans.

BACKGROUND: Proteostasis is a critical aging hallmark responsible for removing damaged or misfolded proteins and their aggregates by improving proteasomal degradation through the autophagy-lysosome pathway (ALP) and the ubiquitin-proteasome system (UPS). Research on the impact of heat-killed probiotic bacteria and their structural components on aging hallmarks and innate immune responses is scarce, yet enhancing these effects could potentially delay age-related diseases. RESULTS: This study introduces a novel heat-killed Levilactobacillus brevis strain MKAK9 (HK MKAK9), along with its exopolysaccharide (EPS), demonstrating their ability to extend longevity by improving proteostasis and immune responses in wild-type Caenorhabditis elegans. We elucidate the underlying mechanisms through a comprehensive approach involving mRNA- and small RNA sequencing, proteomic analysis, lifespan assays on loss-of-function mutants, and quantitative RT-PCR. Mechanistically, HK MKAK9 and its EPS resulted in downregulation of the insulin-like signaling pathway in a DAF-16-dependent manner, enhancing protein ubiquitination and subsequent proteasomal degradation through activation of the ALP pathway, which is partially mediated by microRNA mir-243. Importantly, autophagosomes engulf ubiquitinylated proteins, as evidenced by increased expression of the autophagy receptor sqst-3, and subsequently fuse with lysosomes, facilitated by increased levels of the lysosome-associated membrane protein (LAMP) lmp-1, suggesting the formation of autolysosomes for degradation of the selected cargo. Moreover, HK MKAK9 and its EPS activated the p38 MAPK pathway and its downstream SKN-1 transcription factor, which are known to regulate genes involved in innate immune response (thn-1, ilys-1, cnc-2, spp-9, spp-21, clec-47, and clec-266) and antioxidation (sod-3 and gst-44), thereby reducing the accumulation of reactive oxygen species (ROS) at both cellular and mitochondrial levels. Notably, SOD-3 emerged as a transcriptional target of both DAF-16 and SKN-1 transcription factors. CONCLUSION: Our research sets a benchmark for future investigations by demonstrating that heat-killed probiotic and its specific cellular component, EPS, can downregulate the insulin-signaling pathway, potentially improving the autophagy-lysosome pathway (ALP) for degrading ubiquitinylated proteins and promoting organismal longevity. Additionally, we discovered that increased expression of microRNA mir-243 regulates insulin-like signaling and its downstream ALP pathway. Our findings also indicate that postbiotic treatment may bolster antioxidative and innate immune responses, offering a promising avenue for interventions in aging-related diseases.

Prevalence of non-communicable disease risk factors among nursing staff in a low and middle-income country: A cross-sectional digital survey-based study.

AIM: To assess the prevalence of non-communicable disease risk factors among the nursing staff and educate them on prevention. BACKGROUND: Nursing staff is integral to the Indian community healthcare systems. Recent studies report a high prevalence of non-communicable diseases in Indian nursing staff. Therefore, data on the prevalence of non-communicable disease risk factors among nursing staff are crucial for education on prevention. DESIGN: A cross-sectional digital survey-based study. METHOD: We invited 4435 nursing staff to attend our online survey. We used a customized questionnaire for data collection, including a digitized version of the Community-Based Assessment Checklist form. A score of >4 was considered high risk and warranted screening. RESULT: Among 682 nursing staff who attended, 70% had never undergone screening for non-communicable diseases. The prevalence of non-communicable disease risk factors was significantly higher in male nursing staff. In addition, logistic regression analysis showed that age, tobacco and alcohol use, increased waist circumference, physical inactivity and family history of non-communicable diseases were significant risk factors among nursing staff. CONCLUSION: The study findings suggest that the nursing staff have suboptimal self-health concerns on non-communicable diseases. This situation warrants continued medical education, awareness campaigns on adopting a healthy lifestyle and health promotion.

Film Coating of Phosphorylated Mandua Starch on Matrix Tablets for pH-Sensitive Release of Mesalamine.

Chemically modified mandua starch was successfully synthesized and applied to coat mesalamine-loaded matrix tablets. The coating material was an aqueous dispersion of mandua starch modified by sodium trimetaphosphate and sodium tripolyphosphate. To investigate the colon-targeting release competence, chemically modified mandua starch film-coated mesalamine tablets were produced using the wet granulation method followed by dip coating. The effect of the coating on the colon-targeted release of the resultant delivery system was inspected in healthy human volunteers and rabbits using roentgenography. The results show that drug release was controlled when the coating level was 10% w/w. The release percentage in the upper gastric phase (pH 1.2, simulated gastric fluid) was less than 6% and reached up to 59.51% w/w after 14 h in simulated colonic fluid. In addition to in vivo roentgenographic studies in healthy rabbits, human volunteer studies proved the colon targeting efficiency of the formulation. These results clearly demonstrated that chemically modified mandua starch has high effectiveness as a novel aqueous coating material for controlled release or colon targeting.

Triplex-Forming Peptide Nucleic Acid Controls Dynamic Conformations of RNA Bulges.

RNA folding is driven by the formation of double-helical segments interspaced by loops of unpaired nucleotides. Among the latter, bulges formed by one or several unpaired nucleotides are one of the most common structural motifs that play an important role in stabilizing RNA-RNA, RNA-protein, and RNA-small molecule interactions. Single-nucleotide bulges can fold in alternative structures where the unpaired nucleobase is either looped-out (flexible) in a solvent or stacked-in (intercalated) between the base pairs. In the present study, we discovered that triplex-forming peptide nucleic acids (PNAs) had unusually high affinity for single-purine-nucleotide bulges in double-helical RNA. Depending on the PNA's sequence, the triplex formation shifted the equilibrium between looped-out and stacked-in conformations. The ability to control the dynamic equilibria of RNA's structure will be an important tool for studying structure-function relationships in RNA biology and may have potential in novel therapeutic approaches targeting disease-related RNAs.

Synthesis of fused polycyclic ß-carboline derivatives using Ugi-4CR followed by cascade cyclization.

Ugi-four component reaction (Ugi-4CR) is extremely attractive for diversity-oriented and step economical synthesis as evident from past applications. Here we report the synthesis of fused polycyclic ß-carboline derivatives by sequential Pictet-Spengler's and Ugi-4CR multi-component reaction followed by cascade cyclization. The post cyclisation of Ugi product provides conformationally stable heterocyclic molecule that is expected to be suitable for interaction with different biological targets. The methodology provides a simple and facile access to heterocycles embedded in polycyclic framework which otherwise seems difficult to synthesize by conventional methods. Synthesis of fused Polycyclic ß-Carboline Derivatives Using Ugi-4CR Followed by Cascade Cyclization.

Ligand-based designing of DPP-4 inhibitors via hybridization; synthesis, docking, and biological evaluation of pyridazine-acetohydrazides.

A series of novel pyridazine-acetohydrazide hybrids were designed, synthesized, and evaluated for their in vitro and in vivo antihyperglycemic activity. In this context, pyridazine-acetohydrazides (6a-6p) were synthesized by coupling substituted aldehyde with 2-(5-cyano-6-oxo-3,4-diphenylpyridazine-1-6H-yl) acetohydrazide, which was prepared via the reaction of pyridazine ester with hydrazine hydrate. The molecular docking study was carried out to examine the binding affinities and interaction of designed compounds against the DPP-4 enzyme. Compounds 6e, 6f, 6l, and 6n exhibited interaction with active residue. In silico ADMET properties, and toxicity studies corroborated that compounds were found to have good bioavailability and less toxic. The synthesized compounds were further estimated for in vitro DPP-4 activity. Compounds 6e and 6l were found as the most effective DPP-4 inhibitor in this series with IC50 values (6.48, 8.22 nM) when compared with sitagliptin (13.02 nM). According to the toxicity assay compound, 6l showed very less toxicity at a higher concentration so further selected for the in vivo antihyperglycemic activity.

Electronic and optical properties of Nb/V-doped WS2 monolayer: A first-principles study.

The electronic, dielectric, and optical properties of pure and Nb/V-doped WS2 monolayer are being investigated using the first-principles density functional theory (DFT). The electronic band structure calculations reveal that the pure and doped WS2 monolayer is a direct band gap semiconductor. It is seen that the doping not only slightly reduces the band gap but also changes the n-type character of pure WS2 monolayer to the p-type character. Hence, it may be useful for channel material in field effect transistors (FETs). Moreover, the optical studies reveal that the WS2 monolayer shows a significantly good optical response. However, a small ultraviolet shift is observed in the optical response of the doped case compared to the pristine WS2 monolayer. This study suggests that the WS2 monolayer can be a possible optical material for optoelectronic applications, and it can also be a replacement of MoS2 -based future electronics and optoelectronics.

A comprehensive study on the electronic structure, dielectric and optical properties of alkali-earth metals and transition metal hydroxides M(OH)2.

In the present work, the physical properties of alkali-earth metal and transition metal hydroxides are comprehensively investigated using the density functional theory. Here, the alkali-earth metals Ca, Mg, and transition metals Cd, Zn are considered from the II-A and II-B groups in the periodic table of elements. The first principle electronic structure calculations show that these bulk hydroxide materials are direct band gap material. Ca(OH)2 and Mg(OH)2 exhibit an insulating behavior with a very large band gap. However, Cd(OH)2 and Zn(OH)2 are found to be wide band gap semiconductors. The dielectric and optical studies reveal that these materials have a high degree of anisotropy. Hence, the light propagation in these materials behaves differently in the direction perpendicular and parallel to the optical axis, and exhibits birefringence. Therefore, these materials may be useful for optical communication. The calculated electron energy loss suggests that these materials can also be used for unwanted signal noise suppression. The wide band gap makes them useful for high-power applications. Moreover, Ca(OH)2 and Mg(OH)2 are found to be suitable for dielectric medium.