Browse Articles

Advanced hybrid intelligence evaluation of nanomedicine delivery to various organs using machine learning and adaptive tree structured Parzen estimator

AHP and Geospatial technology-based assessment of groundwater potential zones in Natham taluk, Tamil nadu, India

Liming promotes the leaching of carbon and nitrogen in a double-cropped rice system

Proteomic analysis of tumor cell nuclear expulsion reveals significant cell adhesion and RNA binding programs in extracellular chromatin

Abstract Understanding mechanisms of cancer cell death and the resulting effect on disease progression is crucial in cancer biology and the insight will likely offer better options for therapeutic treatment. Nuclear expulsion occurs in apoptotic cancer cells in a peptidylarginine deiminase 4 (Padi4) dependent manner. The resulting tumor cell nuclear expulsion product (TuNEP) promotes the outgrowth of neighboring cancer cells through chromatin-bound protein complexes. It is not clear what the protein compositions and functionalities are in these TuNEPs. In this study, we performed extensive proteomic profiling and identified key TuNEP protein components from mouse and human breast cancer cells as well as human lung cancer cells (4T1, MDA-MB-231, and PC9). We further compared TuNEP- specific proteins with those from apoptotic bodies or NETs from neutrophils. We found an enrichment of cellular adhesion molecules as well as increased citrullination of proteins associated with RNA binding. We showed that cellular adhesion molecules integrin and basigin (BSG) promote the growth of tumor spheroids. Our work revealed the unique TuNEP protein components distinct from neutrophil-derived NETs and shed light on potential mechanisms by which these cancer cell-derived TuNEPs promote tumor progression.

Adaptive clustering for medical image analysis using the improved separation index

Pilot study on the potential of low-salt brine with oregano essential oil for post-preservation of white brined cheese

Identification of palmitoylated biomarkers in non-alcoholic fatty liver disease via integrated bioinformatics analysis and machine learning

Elderly individuals exhibit dysregulated monocyte responses to viral immune complexes compared to adults and children

Abstract The severity of certain viral infectious diseases varies across the age; we hypothesize that these variations could be related to the variation of immune responses to viral immune complexes (ICs) among the age. This study aimed to investigate monocyte activation in response to ICs in children, adults, and elderly individuals. An experimental in vitro model was established using peripheral blood mononuclear cells from healthy individuals. Monocyte activation markers (CD169, CD38, HLA-DR), the negative co-stimulatory molecule (PD-L1), and cytokine production were measured under basal conditions and upon stimulation with human adenovirus 5-IgG immune complex (Ad5-ICs), interferon-alpha (IFN-α), and lipopolysaccharide (LPS). Monocytes from children and adults displayed similar activation profiles in response to ICs and IFN-α stimulation, characterized by increased expression of CD169 and PD-L1. In contrast, monocytes from elderly individuals exhibited weak or no overexpression of CD169 and PD-L1 coupled with a diminished PBMC cytokine response. Notably, cells from elderly participants produced high levels of TNF-α, IL-1α, and IL-6 in the absence of stimulation. Multiple comparisons confirmed reduced monocyte activation and PBMC cytokine responses in the elderly compared to adults and children. Although children exhibited a significant response to ICs, their secretion of IFN-α, IP-10, IFN-γ, IL-8, and IL-2 was lower than that observed in adults. Our findings suggest that elderly individuals have poor and dysregulated responses to ICs, likely due to immunosenescence and chronic inflammation. Adults exhibit a robust and balanced response to ICs, while children display a moderate response, possibly influenced by ‘trained immunity’ resulting from frequent early-life exposures to pathogens. These insights highlight the importance of further research to develop age-specific therapeutic strategies to modulate immune function during viral IC exposure.

Streptomyces rimosus-rich soil exposure alleviates depression-like behaviors by modulating neuroinflammation and synaptic plasticity in mice with stress

Influence of ATG SNPs on hip fracture patients’ functional status

Lung structural cells are altered by influenza virus leading to rapid immune protection following re-challenge

Abstract Lung structural cells form barriers against pathogens and trigger immune responses following infections. This leads to the recruitment of innate and adaptive immune cells some of which remain within the lung and contribute to enhanced pathogen control following subsequent infections. There is growing evidence that structural cells also display long-term changes following infection. Here we investigate long-term changes to mouse lung epithelial cells, fibroblasts, and endothelial cells following influenza virus infection finding that all three cell types maintain an imprint of the infection, particularly in genes linked to communication with T cells. MHCI and MHCII proteins continue to be expressed at higher levels in both differentiated epithelial cells and progenitor populations and several differentially expressed genes are downstream of the transcription factor, SpiB, a known orchestrator of antigen presentation. Lung epithelial cells from influenza-infected mice display functional changes, more rapidly controlling influenza virus than cells from naïve animals. This rapid anti-viral response and increased expression of molecules required to communicate with T cells demonstrates sustained and enhanced functions following infection. These data suggest lung structural cells display characteristics of immune memory which could affect outcomes that are protective in the context of infection or pathogenic in chronic inflammatory disorders.

Changes in host gene expression patterns underpin responses of the coral Stylophora pistillata to nutrient stress

Abstract The availability and stoichiometry of dissolved nutrients are known to have a significant effect on coral growth, biomineralisation, and stress tolerance. However, previous mechanistic studies have focused primarily on the photosynthetic symbionts. Here we studied the physiological and transcriptomic responses of the coral Stylophora pistillata exposed to four different concentration combinations of dissolved inorganic nitrogen (N) and phosphorus (P) over a period of eight weeks. Despite no significant effects on coral growth or calcification, corals from low P conditions bleached and had significantly fewer symbionts than those from high-phosphate treatments. Low P concentrations induced upregulation of ion transmembrane transporter activity, and downregulation of transcripts involved in phospholipid biosynthesis, protein processing, and protein maturation. Further, all enriched biological processes were related to phosphate metabolism. Our results suggest that S. pistillata controls a variety of molecular pathways to counteract the negative effects of insufficient nutrient supply.

Industrial applicability of enzymatic and whole-cell processes for the utilization of C1 building blocks

Experimental and numerical study of stick–slip phenomenon in granular materials

Abstract The stick–slip is a characteristic phenomenon of various mechanical systems, occurring when two bodies slide relative to each other. Friction plays a dominant role in this phenomenon, transitioning from static to dynamic when sudden movements take place. Studying this behaviour is particularly important for understanding stress transfer in granular materials. The study examines the development of the stick–slip phenomenon under plane strain conditions, which are commonly encountered in large-scale geotechnical structures. Experiments performed on glass bead samples investigate the effects of varying confining pressures, shear rates, initial void ratios, and degrees of bead wear on the development and characteristics of the stick–slip phenomenon. Additionally, a plane strain triaxial test is simulated using the discrete element method (DEM). Although the stick–slip events are not fully reproduced, some micro-slips are identified in the results. The physical mechanism underlying their development appears to correspond to the standard stick–slip behaviour reported in the experiments. Since micro-mechanical behaviour is a key to understanding the stick–slip phenomenon, incorporating DEM analyses opens a new route for determining micro-parameters and linking them to macro behaviour.

Structural basis of broad protection against influenza virus by human antibodies targeting the neuraminidase active site via a recurring motif in CDR H3

Abstract Influenza viruses evolve rapidly, driving seasonal epidemics and posing global pandemic threats. While neuraminidase (NA) has emerged as a vaccine target, shared molecular features of NA antibody responses are still not well understood. Here, we describe cryo-electron microscopy structures of the broadly protective human antibody DA03E17, which was previously identified from an H1N1-infected donor, in complex with NA from A/H1N1, A/H3N2, and B/Victoria-lineage viruses. DA03E17 targets the highly conserved NA active site using its long CDR H3, which features a DR (Asp–Arg) motif that engages catalytic residues and mimics sialic acid interactions. We further demonstrate that this motif is conserved among several NA active site-targeting antibodies, indicating a common receptor mimicry strategy. We also identified BCR sequences containing this DR motif across all donors in a healthy human repertoire database, suggesting that such precursors may be relatively common and have vaccine targeting potential. Our findings reveal shared molecular features in NA active site-targeting antibodies that can be harnessed to design broad, immune-focused influenza vaccines.

Fabrication and characterizations of 3D printed GelMA-Gel/bioactive glass scaffolds containing cerium for bone damage repair

The CCL2-CCR2 axis drives neuromuscular denervation in amyotrophic lateral sclerosis

Models for sustainable management of livestock waste based on neural network architectures

Ideal topological flat bands in chiral symmetric moiré systems from non-holomorphic functions

Dynamics and vibrational spectroscopy of quasi-one dimensional water wires inside carbon nanotubes of different diameter and chirality

Abstract Water strongly confined in nanostructures such as carbon nanotubes (CNTs) exhibits structural, dielectric, transport, dynamical and thermodynamical properties vastly different from bulk water, due to a strong modification of the (three-dimensional) hydrogen bond network. In this work, we mainly address the following aspects of extremely confined, quasi-one dimensional water chains in CNTs which have have not been emphasized much so far: The effect of chirality of the CNT, strong interactions with the hydrophobic walls and the (altered) vibrational response of confined water. Specifically, we have studied the (i) translation / diffusion, (ii) rotation / reorientation and (iii) vibrations of water chains confined within narrow carbon nanotubes (CNTs) with chirality indices (6,2), (6,4) and (6,6) using ab initio molecular dynamics. Special emphasis is on vibrational spectra, notably in the OH stretch region, obtained from fluctuations in the local OH stretching modes which were further employed to obtain two-dimensional infrared spectra and frequency-frequency correlation functions. We find that the vibrational distribution of water molecules under confinement is overall blue-shifted in comparison to bulk water, due to a breakdown of the three-dimensional hydrogen bond network. Further, the vibrational dynamics were found to dependent strongly upon the chirality and diameter of the CNTs, the latter causing stronger hydrophobic interactions with the walls of the nanotube. With respect to translational and rotational motion, the CNT-confined water molecules exhibit slower translational diffusion and faster reorientational motion compared to bulk liquid water for all cases simulated in this work.