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RNAi therapeutics possess the potential to cure many uncurable human diseases. For instance, RNAi therapeutics using liposomes showed remarkable survival benefits in patients with liver diseases. However, the extension of liposomes to deliver RNA to cure other ailments has largely been unsuccessful. Therefore, researchers are focusing on designing and testing different combinations of materials for versatile RNA delivery applications. Yet, an efficient and safe RNA delivery platform has not been identified. In this work, we have developed a new class of RNA-delivery vehicle called “Gelasomes,” using an incongruous combination of gelatin and lipidoid to exploit each material's unique properties while overcoming their inherent limitations. The low in vivo toxicity of Gelasomes is attributed to the exterior gelatin layers that shield the exposure of cationic lipidoid-siRNA clusters and yet present a biocompatible surface. Indeed, toxicity studies in mice indicate that repeated administration of Gelasomes (up to 48 mg/kg BW) is well-tolerated with no notable changes in body weight, hematology, or serum chemistry. Interestingly, the gelatin outer layer efficiently protects siRNA from serum degradation (48 h), preserving its functionality beyond two months of storage. Notably, Gelasomes possess dual siRNA conjugation modes, i.e., electrostatic binding with lipidoid core and covalent attachment to gelatin surface. The bivalency coupled with lipidoids' high transfection efficiency rendered Gelasomes with remarkably high gene silencing efficiency (>90 %) at very low treatment doses in vitro (40 μg/mL). In vivo studies further confirmed the high gene silencing ability of Gelasomes in non-small cell lung tumor mouse models. This new platform is tunable on all fronts: size, degree of surface coating, and biomolecule functionalization. Truncating the lipidoid C14-tail to a C8-tail yielded Gelasomes of reduced size. As lipidoids with different carbon lengths are synthesizable, we can develop a library of Gelasomes with different sizes. The surface coating with less gelatin resulted in high transfection efficiency at low doses of Gelasomes. The structure of Gelasomes offers chemical handles to couple target-specific molecules like antibodies to tune their properties for efficient biological application.

Abstract Objective miR-497/195, located at 17p13.1, is a highly conserved miRNA cluster whose abnormal expression is a key regulator of carcinogenesis. We performed a comprehensive analysis of the miR-497/195 cluster to determine its prognostic utility and role in cervical cancer (CC) using publicly available datasets. Results In silico analysis and validation revealed that this cluster is downregulated in CC. A total of 60 target genes of miR-497/195 cluster were identified as differentially expressed between normal and CC samples. ShinyGO, STRING, CytoHubba, Timer 2.0, HPA, and HCMBD were used for functional enrichment, PPIN network construction, hub gene identification, immune infiltration correlation, histopathological expression, and determination of the metastatic potential of miR-497/195 cluster and their target genes. PPIN analysis identified CCNE1, CCNE2, ANLN, RACGAP1, KIF23, CHEK1, CDC25A, E2F7, CDK1, and CEP55 as the top 10 hub genes (HGs). Furthermore, the upregulation of RECK, ATD5, and BCL2, downregulation of OSBPL3, RCAN3, and HIST1H3H effected overall survival of CC patients. We identified 6 targets (TFAP2A, CLSPN, RASEF, HIST1H3H, AKT3, and ITPR1) of miR-497/195 cluster to influence metastasis. In addition, 8 druggable genes and 38 potential drugs were also identified. Our study identified miR-497/195 cluster target genes and pathways that could be used for prognostic and therapeutic applications in CC.

Abstract Global biodiversity gradients are generally expected to reflect greater species replacement closer to the equator. However, empirical validation of global biodiversity gradients largely relies on vertebrates, plants, and other less diverse taxa. Here we assess the temporal and spatial dynamics of global arthropod biodiversity dynamics using a beta-diversity framework. Sampling includes 129 sampling sites whereby malaise traps are deployed to monitor temporal changes in arthropod communities. Overall, we encountered more than 150,000 unique barcode index numbers (BINs) (i.e. species proxies). We assess between site differences in community diversity using beta-diversity and the partitioned components of species replacement and richness difference. Global total beta-diversity (dissimilarity) increases with decreasing latitude, greater spatial distance and greater temporal distance. Species replacement and richness difference patterns vary across biogeographic regions. Our findings support long-standing, general expectations of global biodiversity patterns. However, we also show that the underlying processes driving patterns may be regionally linked.

Abstract Fluorescence microscopy data describe protein localization patterns at single-cell resolution and have the potential to reveal whole-proteome functional information with remarkable precision. Yet, extracting biologically meaningful representations from cell micrographs remains a major challenge. Existing approaches often fail to learn robust and noise-invariant features or rely on supervised labels for accurate annotations. We developed PIFiA (Protein Image-based Functional Annotation), a self-supervised approach for protein functional annotation from single-cell imaging data. We imaged the global yeast ORF-GFP collection and applied PIFiA to generate protein feature profiles from single-cell images of fluorescently tagged proteins. We show that PIFiA outperforms existing approaches for molecular representation learning and describe a range of downstream analysis tasks to explore the information content of the feature profiles. Specifically, we cluster extracted features into a hierarchy of functional organization, study cell population heterogeneity, and develop techniques to distinguish multi-localizing proteins and identify functional modules. Finally, we confirm new PIFiA predictions using a colocalization assay, suggesting previously unappreciated biological roles for several proteins. Paired with a fully interactive website ( https://thecellvision.org/pifia/ ), PIFiA is a resource for the quantitative analysis of protein organization within the cell.

ABSTRACTPrebiotic nutritional ingredients have received attention due to their health-promoting potential and related uses in the food and nutraceutical industries. Recent times have witnessed an increasing interest in the use of fructooligosaccharides (FOS) as prebiotics and their generation using microbial enzymes. FOS consumption is known to confer health benefits such as protection against colon cancer, improved mineral absorption, lowering effect on serum lipid and cholesterol concentration, antioxidant properties, favourable dietary modulation of the human colonic microbiota, and immuno-modulatory effects. Comparative analysis of molecular models of various fructosyltransferases (FTases) reveals the mechanism of action and interaction of substrate with the active site. Microbial FTases carry out transfructosylation of sucrose into fructooligosaccharides (kestose, nystose, and fructofuranosylnystose), the most predominantly used prebiotic oligosaccharides. Furthermore, FOS has also been used for other purposes, such as low-calorie sweeteners, dietary fibres, and as the substrates for fermentation. This review highlights the occurrence, characteristics, immobilisation, and potential applications of FOS-generating fungal FTases. Production, heterologous expression, molecular characteristics, and modelling of fungal FTases underpinning their biotechnological prospects are also discussed.

ADP ribosylation factor-like GTPase 2 (Arl2) is crucial for controlling mitochondrial fusion and microtubule assembly in various organisms. Arl2 regulates the asymmetric division of neural stem cells in Drosophila via microtubule growth. However, the function of mammalian Arl2 during cortical development was unknown. Here, we demonstrate that mouse Arl2 plays a new role in corticogenesis via regulating microtubule growth, but not mitochondria functions. Arl2 knockdown (KD) leads to impaired proliferation of neural progenitor cells (NPCs) and neuronal migration. Arl2 KD in mouse NPCs significantly diminishes centrosomal microtubule growth and delocalization of centrosomal proteins Cdk5rap2 and γ-tubulin. Moreover, Arl2 physically associates with Cdk5rap2 by in silico prediction using AlphaFold multimer, which was validated by co-immunoprecipitation and proximity ligation assay. Remarkably, Cdk5rap2 overexpression significantly rescues the neurogenesis defects caused by Arl2 KD. Therefore, Arl2 plays an important role in mouse cortical development through microtubule growth via the centrosomal protein Cdk5rap2.

Summary: Reactive changes of glial cells during neuroinflammation impact brain disorders and disease progression. Elucidating the mechanisms that control reactive gliosis may help us to understand brain pathophysiology and improve outcomes. Here, we report that adult ablation of autism spectrum disorder (ASD)-associated CHD8 in astrocytes attenuates reactive gliosis via remodeling chromatin accessibility, changing gene expression. Conditional Chd8 deletion in astrocytes, but not microglia, suppresses reactive gliosis by impeding astrocyte proliferation and morphological elaboration. Astrocyte Chd8 ablation alleviates lipopolysaccharide-induced neuroinflammation and septic-associated hypothermia in mice. Astrocytic CHD8 plays an important role in neuroinflammation by altering the chromatin landscape, regulating metabolic and lipid-associated pathways, and astrocyte-microglia crosstalk. Moreover, we show that reactive gliosis can be directly mitigated in vivo using an adeno-associated virus (AAV)-mediated Chd8 gene editing strategy. These findings uncover a role of ASD-associated CHD8 in the adult brain, which may warrant future exploration of targeting chromatin remodelers in reactive gliosis and neuroinflammation in injury and neurological diseases.

The prevalence of polymer usage in everyday activities has emerged as a detriment to both human life and the environment. A large number of studies describe severe impacts of micropolymers (MP) and nanopolymers (NP) on various organ systems, including the endocrine system. Additionally, plasticizers utilized as additives have been identified as endocrine-disrupting chemicals (EDCs). MP/NP, along with associated plasticizers, affect principal signalling pathways of endocrine glands such as the pituitary, thyroid, adrenal, and gonads, thereby disrupting hormone function and metabolic processes crucial for maintaining homeostasis, fertility, neural development, and fetal growth. This review delves into the sources, distribution, and effects of micropolymers, nanopolymers, and associated plasticizers acting as EDCs. Furthermore, it provides a detailed review of the mechanisms underlying endocrine disruption in relation to different types of MP/NP.

Background Onion thrips (Thrips tabaci) is a complex of cryptic species with subtle morphological differences and distinct genetic backgrounds; thus, species identification using traditional methods remains challenging. The existence of different haplotypes and genotypes within a species can significantly influence various aspects of its biology, including host preference, reproductive capacity, resistance to pesticides, and vector competence for plant viruses. Understanding the genetic diversity and population structure of cryptic species within T. tabaci will not only aid in the development of more effective control strategies tailored to specific genetic variants but also in monitoring population dynamics, tracking invasive species, and implementing quarantine measures to prevent the spread of economically damaging thrips biotypes. Methods This study aims to explore intraspecies genetic diversity and molecular evolutionary relationships of the mitochondrial cytochrome oxidase gene subunit I (mtCOI) in T. tabaci populations from India. To capture diversity within the Indian T. tabaci populations, amplicon sequencing was performed for the thrips mtCOI gene from eight diverse localities in India. A total of 48 sequences retrieved for the mtCOI gene from the NCBI Nucleotide database were analysed. Results Multiple insertions and deletions were detected at various genomic positions across the populations from different localities, with the highest variation observed in the 300–400 genome position range. Molecular diversity analyses identified 30 haplotypes within the population, with certain subpopulations exhibiting higher gene flow. Analysis of single nucleotide polymorphism patterns within the mtCOI gene across diverse Indian locales revealed significant intrapopulation genetic heterogeneity and its potential repercussions on gene functionality. Elevated F statistics (Fst) values in the northern–western subpopulations suggested high genetic variability, particularly evident in haplotype networks originating mainly from the northern region, notably Delhi. While most populations displayed stable and ancient evolutionary histories, thrips populations from northern, western, and north-eastern regions indicated rapid growth.

The Myddosome is a key innate immune signalling platform. It forms at the cell surface and contains MyD88 and IRAK proteins which ultimately coordinate the production of pro-inflammatory cytokines. Toll-like receptor 4 (TLR4) signals via the Myddosome when triggered by lipopolysaccharide (LPS) or amyloid-beta (Aβ) aggregates but the magnitude and time duration of the response are very different for reasons that are unclear. Here, we followed the formation of Myddosomes in live macrophages using local delivery of TLR4 agonist to the cell surface and visualisation with 3D rapid light sheet imaging. This was complemented by super-resolution imaging of Myddosomes in fixed macrophages to determine the size of the signalling complex at different times after triggering. Myddosomes formed more rapidly after LPS than in response to sonicated Aβ 1–42 fibrils (80 vs 372 s). The mean lifetimes of the Myddosomes were also shorter when triggered by LPS compared to sonicated Aβ fibrils (170 and 220 s), respectively. In both cases, a range of Myddosome of different sizes (50–500 nm) were formed. In particular, small round Myddosomes around 100 nm in size formed at early time points, then reduced in proportion over time. Collectively, our data suggest that compared to LPS the multivalency of Aβ fibrils leads to the formation of larger Myddosomes which form more slowly and, due to their size, take longer to disassemble. This explains why sonicated Aβ fibrils results in less efficient triggering of TLR4 signalling and may be a general property of protein aggregates.

Abstract Background Wistar rats are extensively used as the model for assessing toxicity and efficacy in preclinical research. Hematological and biochemical laboratory data are essential for evaluating specific variations in the physiological and functional profile of a laboratory animal. Establishing hematological and biochemical reference values for Wistar (han) rats at various age intervals was the goal of this work. Male and female Wistar rats (n = 660) of ages 6–8 weeks, 10–14 weeks and > 6 months were used in the experiment. Blood and serum were collected from these rats under fasting conditions. Results We observed that the majority of hematological and biochemical parameters were significantly influenced by sex and age. Hematological changes were significantly correlated to aging were increased red blood cells, hemoglobin, hematocrit, neutrophils, monocytes and eosinophils in both sexes, as well as decreased platelet, mean corpuscular volume, mean corpuscular hemoglobin and lymphocytes in both sexes. White blood cells of male rats were considerably higher than those of female rats in all age ranges. For biochemistry, increase in glucose, total protein and creatinine were seen in both sexes, along with increases in urea in females and alanine aminotransferase in males. Age was significantly associated with decreased alkaline phosphatase in both sexes. Conclusions When using Wistar rats as a model, these reference values may be useful in evaluating the results.

Abstract Terrestrial ecosystems evolved substantially through the Palaeozoic, especially the Permian, gaining much new complexity, especially among predators. Key among these predators were non-mammalian synapsids. Predator ecomorphology reflect interactions with prey and competitors, which are key controls on carnivore diversity and ecology. Therefore, carnivorous synapsids may offer insight on wider ecological evolution as the first complex, tetrapod-dominated, terrestrial ecosystems formed through the late Palaeozoic. Using morphometric and phylogenetic comparative methods, we chart carnivorous synapsid trophic morphology from the latest Carboniferous to the earliest Triassic (307-251.2 Ma). We find a major morphofunctional shift in synapsid carnivory between the early and middle Permian, via the addition of new feeding modes increasingly specialised for greater biting power or speed that captures the growing antagonism and dynamism of terrestrial tetrapod predator-prey interactions. The further evolution of new hypo- and hypercarnivorous synapsids highlight the nascent intrinsic pressures and complexification of terrestrial ecosystems across the mid-late Permian.

Abstract Background Archetypical cross-β spines sharpen the boundary between functional and pathological proteins including β-amyloid, tau, α-synuclein and transthyretin are linked to many debilitating human neurodegenerative and non-neurodegenerative amyloidoses. An increased focus on development of pathogenic β-sheet specific fluid and imaging structural biomarkers and conformation-specific monoclonal antibodies in targeted therapies has been recently observed. Identification and quantification of pathogenic oligomers remain challenging for existing neuroimaging modalities. Results We propose two artificial β-sheets which can mimic the nanoscopic structural characteristics of pathogenic oligomers and fibrils for evaluating the performance of a label free, X-ray based biomarker detection and quantification technique. Highly similar structure with elliptical cross-section and parallel cross-β motif is observed among recombinant α-synuclein fibril, Aβ-42 fibril and artificial β-sheet fibrils. We then use these β-sheet models to assess the performance of spectral small angle X-ray scattering (sSAXS) technique for detecting β-sheet structures. sSAXS showed quantitatively accurate detection of antiparallel, cross-β artificial oligomers from a tissue mimicking environment and significant distinction between different oligomer packing densities such as diffuse and dense packings. Conclusion The proposed synthetic β-sheet models mimicked the nanoscopic structural characteristics of β-sheets of fibrillar and oligomeric states of Aβ and α-synuclein based on the ATR-FTIR and SAXS data. The tunability of β-sheet proportions and shapes of structural motifs, and the low-cost of these β-sheet models can become useful test materials for evaluating β-sheet or amyloid specific biomarkers in a wide range of neurological diseases. By using the proposed synthetic β-sheet models, our study indicates that the sSAXS has potential to evaluate different stages of β-sheet-enriched structures including oligomers of pathogenic proteins.

Abstract The ongoing evolution of SARS-CoV-2 into more easily transmissible and infectious variants has provided unprecedented insight into mutations enabling immune escape. Understanding how these mutations affect the dynamics of antibody-antigen interactions is crucial to the development of broadly protective antibodies and vaccines. Here we report the characterization of a potent neutralizing antibody (N3-1) identified from a COVID-19 patient during the first disease wave. Cryogenic electron microscopy revealed a quaternary binding mode that enables direct interactions with all three receptor-binding domains of the spike protein trimer, resulting in extraordinary avidity and potent neutralization of all major variants of concern until the emergence of Omicron. Structure-based rational design of N3-1 mutants improved binding to all Omicron variants but only partially restored neutralization of the conformationally distinct Omicron BA.1. This study provides new insights into immune evasion through changes in spike protein dynamics and highlights considerations for future conformationally biased multivalent vaccine designs.

Summary: The locomotor role of dopaminergic neurons is traditionally attributed to their ascending projections to the basal ganglia, which project to the mesencephalic locomotor region (MLR). In addition, descending dopaminergic projections to the MLR are present from basal vertebrates to mammals. However, the neurons targeted in the MLR and their behavioral role are unknown in mammals. Here, we identify genetically defined MLR cells that express D1 or D2 receptors and control different motor behaviors in mice. In the cuneiform nucleus, D1-expressing neurons promote locomotion, while D2-expressing neurons stop locomotion. In the pedunculopontine nucleus, D1-expressing neurons promote locomotion, while D2-expressing neurons evoke ipsilateral turns. Using RNAscope, we show that MLR dopamine-sensitive neurons comprise a combination of glutamatergic, GABAergic, and cholinergic neurons, suggesting that different neurotransmitter-based cell types work together to control distinct behavioral modules. Altogether, our study uncovers behaviorally relevant cell types in the mammalian MLR based on the expression of dopaminergic receptors.

Gastrointestinal (GI) cancers account for one-fourth of the global cancer incidence and are incriminated to cause one-third of cancer-related deaths. GI cancer includes esophageal, gastric, liver, pancreatic, and colorectal cancers, mostly diagnosed at advanced stages due to a lack of accurate markers for early stages. The invasiveness of diagnostic methods like colonoscopy for solid biopsy reduces patient compliance as it cannot be frequently used to screen patients. Therefore, minimally invasive approaches like liquid biopsy may be explored for screening and early identification of gastrointestinal cancers. Liquid biopsy involves the qualitative and quantitative determination of certain cancer-specific biomarkers in body fluids such as blood, serum, saliva, and urine to predict disease progression, therapeutic tolerance, toxicities, and recurrence by evaluating minimal residual disease and its correlation with other clinical features. In this review, we deliberate upon various tumor-specific cellular and molecular entities such as circulating tumor cells (CTCs), tumor-educated platelets (TEPs), circulating tumor DNA (ctDNA), cell-free DNA (cfDNA), exosomes, and exosome-derived biomolecules and cite recent advances pertaining to their use in predicting disease progression, therapy response, or risk of relapse. We also discuss the technical challenges associated with translating liquid biopsy into clinical settings for various clinical applications in gastrointestinal cancers.

Summary: Histone deacetylases (HDACs) regulate gene expression and innate immunity. Previously, we showed that HDAC5 is degraded during Vaccinia virus (VACV) infection and is a restriction factor for VACV and herpes simplex virus type 1. Here, we report that HDAC5 promotes interferon regulatory factor 3 (IRF3) activation downstream of Toll-IL-1 receptor (TIR) domain-containing adaptor molecule-1 or Sendai virus-mediated stimulation without requiring HDAC activity. Loss of HDAC5-mediated IRF3 activation is restored by re-introduction of HDAC5 but not HDAC1 or HDAC4. The antiviral activity of HDAC5 is antagonized by VACV protein C6 and orthologs from the orthopoxviruses cowpox, rabbitpox, camelpox, monkeypox, and variola. Infection by many of these viruses induces proteasomal degradation of HDAC5, and expression of C6 alone can induce HDAC5 degradation. Mechanistically, C6 binds to the dimerization domain of HDAC5 and prevents homodimerization and heterodimerization with HDAC4. Overall, this study describes HDAC5 as a positive regulator of IRF3 activation and provides mechanistic insight into how the poxviral protein C6 binds to HDAC5 to antagonize its function.

Abstract Background Computational methods of predicting protein stability changes upon missense mutations are invaluable tools in high-throughput studies involving a large number of protein variants. However, they are limited by a wide variation in accuracy and difficulty of assessing prediction uncertainty. Using a popular computational tool, FoldX, we develop a statistical framework that quantifies the uncertainty of predicted changes in protein stability. Results We show that multiple linear regression models can be used to quantify the uncertainty associated with FoldX prediction for individual mutations. Comparing the performance among models with varying degrees of complexity, we find that the model precision improves significantly when we utilize molecular dynamics simulation as part of the FoldX workflow. Based on the model that incorporates information from molecular dynamics, biochemical properties, as well as FoldX energy terms, we can generally expect upper bounds on the uncertainty of folding stability predictions of ± 2.9 kcal/mol and ± 3.5 kcal/mol for binding stability predictions. The uncertainty for individual mutations varies; our model estimates it using FoldX energy terms, biochemical properties of the mutated residue, as well as the variability among snapshots from molecular dynamics simulation. Conclusions Using a linear regression framework, we construct models to predict the uncertainty associated with FoldX prediction of stability changes upon mutation. This technique is straightforward and can be extended to other computational methods as well.

An imperative requisite of tissue-engineered scaffolds is to promote host cell regeneration and concomitantly thwart microbial growth. Antibacterial agents are often added to prevent implant-related infections, which, however, aggravates the risk of bacterial resistance. For the first time, we report a fiber-based platform that selectively promotes the growth of mammalian cells and alleviates bacteria by varying fiber size, orientation, and material of polymeric yarns. The interactions of Gram-positive and -negative bacterial species with mammalian mesenchymal stem cells (MSC) were investigated on poly-€-caprolactone (PCL) yarns, polyethylene terephthalate (PET), poly-L-lactic acid (PLLA), and cotton. Various yarn configurations were studied by altering the fiber diameter (from nano- to microscale) and fiber orientations (aligned, twisted, and random) of PCL yarns. PCL nanofibrous yarn decreased the adhesion of S. aureus and E. coli, with a 2.7-fold and 1.5-fold reduction, respectively, compared to PCL microfibrous yarn. Among different fiber orientations, nanoaligned fibers resulted in an 8-fold and 30-fold reduction of S. aureus and E. coli adhesion compared to random fibers. Moreover, aligned orientation was superior in retarding the S. aureus adhesion by 14-fold compared to nanotwisted fibers. Our data demonstrate that polymeric yarns comprising fibers with nanoscale features and aligned orientation promote mammalian cell adhesion and spreading and concomitantly mitigate bacterial interaction. Moreover, we unveil the wicking of cells through polymeric yarns, facilitating early cell adhesion in fibrous scaffolds. Overall, this study provides insight to engineer scaffolds that couple superior interaction of mammalian cells with high-strength fibrous yarns for regenerative applications devoid of antibacterial agents or other surface modification strategies.

Cutting tool coolant channels play a pivotal role in machining processes, facilitating the efficient supply of cooling agents to high-stress areas and effective heat dissipation. Achieving optimal cooling at the tool’s cutting-edge is essential for enhancing production processes. Experimental investigations into tribological stress analysis can be limited in accessing complex tool–workpiece contact zones, prompting the use of numerical modelling to explore fluid dynamics and tribology. In this study, the coolant flow dynamics and heat dissipation in drilling operations were comprehensively investigated through computational fluid dynamics (CFD) modelling. Four twist drill models with varying coolant channel arrangements were studied: standard model drill, standard model drill with notch, profile model drill, and profile model drill with notch. Two distinct approaches are applied to the coolant inlet to assess the impact of operating conditions on fluid flow and heat dissipation at the cutting-edge. The findings emphasize that cutting-edge zones have insufficient coolant supply, particularly in modified drill models such as the standard model drill with notch and profile model drills with and without notch. Moreover, enhanced coolant supply at the cutting-edge is achieved under high-pressure inlet conditions. The standard model drill with a notch exhibited exceptional performance in reducing thermal load, facilitating efficient coolant escape to the flute for improved heat dissipation at the cutting-edge. Despite challenges like dead zones in profile models, the standard-with-notch model yielded the most promising results. Further analyses under constant pressure conditions at 40 and 60 bar exhibited enhanced fluid flow rates, particularly at the cutting-edge, leading to improved heat dissipation. The temperature distribution along the cutting-edge and outer corner demonstrated a decrease as the pressure increased. This study underscores the critical role of both coolant channel design and inlet pressure in optimizing coolant flow dynamics and heat transfer during drilling operations. The findings provide valuable insights for designing and enhancing coolant systems in machining processes, emphasizing the significance of not only coolant channel geometry but also inlet pressure for effective heat dissipation and enhanced tool performance.

D-amino acid oxidase (DAO) is a flavoenzyme that metabolizes D-amino acids by oxidative deamination, producing hydrogen peroxide (H 2 O 2 ) as a by-product. The generation of intracellular H 2 O 2 may alter the redox-homeostasis mechanism of cells and increase the oxidative stress levels in tissues, associated with the pathogenesis of age-related diseases and organ decline. This study investigates the effect of DAO knockdown using clustered regularly interspaced short palindromic repeats (CRISPR) through an in silico approach on its protein-protein interactions (PPIs) and their potential roles in the process of aging. The target sequence and guide RNA of DAO were designed using the CCTop database, PPI analysis using the Search Tool for the Retrieval of Interacting Genes/Proteins (STRING) database, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses, Reactome biological pathway, protein docking using GalaxyTongDock database, and structure analysis. The translated target sequence of DAO lies between amino acids 43 to 50. The 10 proteins that were predicted to interact with DAO are involved in peroxisome pathways such as acyl-coenzyme A oxidase 1 (ACOX1), alanine-glyoxylate and serine-pyruvate aminotransferase (AGXT), catalase (CAT), carnitine O-acetyltransferase (CRAT), glyceronephosphate O-acyltransferase (GNPAT), hydroxyacid oxidase 1 (HAO1), hydroxyacid oxidase 2 (HAO2), trans-L-3-hydroxyproline dehydratase (L3HYPDH), polyamine oxidase (PAOX), and pipecolic acid and sarcosine oxidase (PIPOX). In summary, DAO mutation would most likely reduce activity with its interacting proteins that generate H 2 O 2 . However, DAO mutation may result in peroxisomal disorders, and thus, alternative techniques should be considered for an in vivo approach.

Background and purpose: The increasing rate of opportunistic infections caused by Candida and other yeasts is becoming a major health concern worldwide. However,systematic data on the epidemiology and the yeast species infections in Malaysia is still limited. In this regard, the present research aimed to identify pathogenic yeasts utilizing an economically practical and easily available molecular technique and evaluate the prevalence of pathogenic yeasts in a Malaysian tertiary care hospital.Materials and Methods: Yeast isolates were collected from Sultan Abdul Halim Hospital, Kedah, Malaysia, from October 2020 to October 2021. Molecular identification of the isolates was performed by one enzyme-based polymerase chain reaction restriction fragment length polymorphism method.Results: Candida albicans was the most prevalent species, accounting for 120 isolates (59%) in total. The most prevalent non albicans Candida species were C. tropicalis (n=33,16%), C. krusei (Pichia kudriavzevii) (n=12, 5.8%), C. glabrata (n=12, 5.8%), and C.parapsilosis (n=6, 3%). Other unusual Candida species were C. guilliermondii (2), C.metapsilosis (2), C. orthopsilosis (1), C. lusitaniae (1), C. rugosa (1), C. haemulonii (1), C. bracarensis (1), and C. dubliniensis (1). Moreover, Talaromyces marneffei (1), Kodamaea ohmeri (1), Cryptococcus neoformans (3), and Cryptococcus laurentii (1) were among the other yeasts identified.Conclusion: The Molecular technique used in this study identified 96% of isolates,including mixed species. According to the findings, the most prevalent species are C. albicans, C. tropicalis, C. krusei, and C. glabrata.

Surface functionalization of iron oxide nanoparticles (Fe2O3 NPs) with antibiotics is a novel approach that opens the door to drug delivery applications. In the present work, we report iron oxide nanoparticles synthesized by chemical co-precipitation method. As-synthesized nanoparticles were characterized using field emission scanning electron microscopy (FESEM) , energy dispersive X-ray (EDX), X-ray diffraction (XRD), ultraviolet (UV)–visible (Vis) spectroscopy, Fourier transform infrared (FTIR), and vibrating sample magnetometer (VSM). The poly-shaped Fe2O3 NPs of size (34 ± 10) nm with hematite (α-Fe2O3) phase were synthesized. The antibacterial activity of chloramphenicol and gentamicin and their formulation with encapsulated iron oxide nanoparticles was investigated by the agar well diffusion technique. Drug-encapsulated Fe2O3 NPs showed antibacterial activity against Escherichia coli and Staphylococcus aureus strains, possibly in a dose-dependent manner. Significant effectiveness was confirmed by the increase in the single range of inhibition against the tested microorganisms. Furthermore, the effect of iron oxide nanoparticle concentrations ranging from 1 to 9 μg/μL on bacterial growth was examined.

Alloy based implants have made a great impact in the clinic and in preclinical research. Immune responses are one of the major causes of failure of these implants in the clinic. Although the immune responses toward non-degradable alloy implants are well documented, there is a poor understanding of the immune responses against degradable alloy implants. Recently, there have been several reports suggesting that degradable implants may develop substantial immune responses. This phenomenon needs to be further studied in detail to make the case for the degradable implants to be utilized in clinics. Herein, we review these new recent reports suggesting the role of innate and potentially adaptive immune cells in inducing immune responses against degradable implants. First, we discussed immune responses to allergen components of non-degradable implants to give a better overview on differences in the immune response between non-degradable and degradable implants. Furthermore, we also provide potential areas of research that can be undertaken that may shed light on the local and global immune responses that are generated in response to degradable implants.

The size of nanocarriers determines the biological property of the materials, especially as it relates to intratumoral distribution. Previous research has shown that sizes of 10–50 nm penetrate deep inside the tumor, resulting in better efficacy. On the other hand, studies have shown that gelatin exhibits excellent biological properties, including compatibility, degradability, and toxicity. Therefore, FDA approved gelatin as a safe material to use as an excipient in injectables. The bottleneck is the nonexistence of smaller-sized gelatin nanoparticles (GNPs) to realize the full potential of these biomaterials. Yet, GNPs with sizes of less than 50 nm have not been reported; the synthetic strategy reported in the literature uses “uncontrolled crosslinking coupled with nanoprecipitation”, resulting in larger particle size. We have developed a new method to self-assemble gelatin strands by using an anionic, phosphate-based crosslinker and controlled precipitation. The method we developed produced ultra-small gelatin nanoparticles (GX) of size 10 nm with a high degree of reproducibility, and it was characterized using dynamic light scattering (DLS), Energy-dispersive X-ray spectroscopy (EDS), High-resolution transmission, and scanning electron microscopy (HR-TEM/STEM). We also explored GX as a bioactive platform to encapsulate imaging and therapy agents within the cavity. Interestingly, we were able to encapsulate 2 nm size gold nanoparticles within the void of GX. The versatile nature of the GX particles was further demonstrated by surface functionalizing with larger size gelatin nanoparticles to form core-satellite nanocomposites. Additionally, we studied the tumor penetrability of dye-tagged 10, 50, and 200 nm gelatin nanoparticles. The study showed that smaller size gelatin nanoparticles penetrate deeper tumor regions than larger particles. In general, GX was efficient in penetrating the inner region of the spheroids. The results demonstrate the potential capabilities of ultra-small GX nanoparticles for multi-staged payload delivery, diagnostics, and cancer therapy.

Background: Phosphine resistance in Tribolium castaneum challenges grain storage. This study investigates the impact of cytochrome P450 (CYP) enzymes and CYP346 family genes on phosphine resistance in Indian Tribolium castaneum populations. Methods: Seven field populations of T. castaneum were compared with Lab- susceptible population for their resistance to phosphine. The levels of cytochrome P450 enzyme and expression of certain CYP346 family genes were tracked in these populations. Results: The highly resistant Patiala population showed significantly increased CYP450 activity (11.26 ± 0.14 nmol/min/mg protein, 7.41-fold higher) compared to the lab-susceptible population (1.52 ± 0.09 nmol/min/mg protein) when assayed using 8 mM p-nitroanisole as the substrate. The mRNA expression was measured relative to the standard gene RPS18 and revealed significant upregulation of CYP346B1 and CYP346B3 in highly resistant populations Moga and Patiala (CYP346B1: 12.09 ± 2.19 to 21.74 ± 3.82; CYP346B3: 59.097 ± 10.265 to 50.148 ± 8.272). Patiala’s CYP346B1 exhibited an impressive 685.76-fold change, and Moga’s CYP346B3 showed a 361.893-fold change compared to lab-susceptible. Linear regression confirmed robust fits for each gene (R2: 0.693 to 0.756). Principal component analysis (PCA) demonstrated a strong positive correlation between CYP346 genes expression; and cytochrome P450 activity. Patiala, Moga, and Hapur populations showed conformity, associating higher resistance with increased P450 activity and CYP346 gene expression. Cluster analysis highlighted a potential correlation between CYP346B1, CYP346B2, and CYP346B3 and P450 activity, with Patiala and Moga clustering together. Conclusions: Variability in CYP346B1 and CYP346B3 in strong resistance populations may contribute to adaptation and resistance mechanisms. The study provides insights into specific CYP346 family genes associated with phosphine resistance, emphasizing the intricate interaction between CYP450 detoxifying enzymes, CYP346 family genes, and resistance mechanisms. The upregulation of CYP346 genes suggests a survival advantage for T. castaneum against phosphine, diminishing phosphine’s efficacy as a pest control measure.

MTX-211 is a first-in-class dual inhibitor of epidermal growth factor receptor (EGFR) and phosphoinositide-3 kinase (PI3K) signaling pathways with a compelling pharmaceutical profile and could enhance the effectiveness of mitogen-activated protein kinase kinase (MEK) inhibitor therapy in colorectal tumors with KRAS mutations. However, the specific mechanisms contributing to the acquired resistance to MTX-211 in human cancers remain elusive. Here, we discovered that the overexpression of the ATP-binding cassette (ABC) drug transporter ABCG2, a prevalent mechanism associated with multidrug resistance (MDR), could diminish the effectiveness of MTX-211 in human cancer cells. We showed that the drug efflux activity of ABCG2 substantially decreased the intracellular accumulation of MTX-211 in cancer cells. As a result, the cytotoxicity and effectiveness of MTX-211 in suppressing the activation of the EGFR and PI3K pathways were significantly attenuated in cancer cells overexpressing ABCG2. Moreover, the enhancement of the MTX-211-stimulated ATPase activity of ABCG2 and the computational molecular docking analysis illustrating the binding of MTX-211 to the substrate-binding sites of ABCG2 offered a further indication for the interaction between MTX-211 and ABCG2. In summary, our findings indicate that MTX-211 acts as a substrate for ABCG2, underscoring the involvement of ABCG2 in the emergence of resistance to MTX-211. This finding carries clinical implications and merits further exploration.

The intention of the Special Issue “Advances in Spectroscopy for Materials: Bridging Science and Engineering” is to include various enthusiastic works that focus on the use of various analytical spectroscopic techniques while characterizing materials [...]

Excessive fibrosis and resultant poor control of intraocular pressure (IOP) reduce the efficacy of glaucoma surgeries. Historically, corticosteroids and anti-fibrotic agents, such as mitomycin C (MMC) and 5-fluorouracil (5-FU), have been used to mitigate post-surgical fibrosis, but these have unpredictable outcomes. Therefore, there is a need to develop novel treatments which provide increased effectiveness and specificity. This review aims to provide insight into the pathophysiology behind wound healing in glaucoma surgery, as well as the current and promising future wound healing agents that are less toxic and may provide better IOP control.

In cholinergic urticaria (CholU), small, itchy wheals are induced by exercise or passive warming and reduced sweating has been reported. Despite the described reduced muscarinic receptor expression, sweat duct obstruction, or sweat allergy, the underlying pathomechanisms are not well understood. To gain further insights, we collected skin biopsies before and after pulse-controlled ergometry and sweat after sauna provocation from CholU patients as well as healthy controls. CholU patients displayed partially severely reduced local sweating, yet total sweat volume was unaltered. However, sweat electrolyte composition was altered, with increased K+ concentration in CholU patients. Formalin-fixed, paraffin-embedded biopsies were stained to explore sweat leakage and tight junction protein expression. Dermcidin staining was not found outside the sweat glands. In the secretory coils of sweat glands, the distribution of claudin-3 and -10b as well as occludin was altered, but the zonula occludens-1 location was unchanged. In all, dermcidin and tight junction protein staining suggests an intact barrier with reduced sweat production capability in CholU patients. For future studies, an ex vivo skin model for quantification of sweat secretion was established, in which sweat secretion could be pharmacologically stimulated or blocked. This ex vivo model will be used to further investigate sweat gland function in CholU patients and decipher the underlying pathomechanism(s).

Genetic information in eukaryotic organisms is stored, replicated, transcribed, and inherited through the nucleus of a cell. Epigenetic modifications in the genetic material, including DNA methylation, histone modification, changes in non-coding RNA (ncRNA) biogenesis, and chromatin architecture play important roles in determining the genomic landscape and regulating gene expression. Genome architecture (structural features of chromatin, affected by epigenetic modifications) is a major driver of genomic functions/activities. Segregation of euchromatin (transcriptionally active) from heterochromatin (transcriptionally repressed chromosome) and positioning of genes in specific nuclear space in eukaryotic cells emphasise non-randomness in the organization of the genetic information. Not only does the base sequence of a gene carry the genetic information but the covalent modifications of bases, three-dimensional positioning of the genome, and chromatin loops are vital for switching on/off the gene and regulating its expression during growth/environmental stress. The epigenetic dynamics depend on the activities of writers and erasers under changing environmental conditions. The discovery of non-coding RNAs (one of the players in de novo methylation of DNA), increased DNA methylation protein (guide for the DNA demethylase), and methylation monitoring sequence (that helps keep a balance between DNA demethylation and methylation) have been some of the new developments in the era of epigenomics. To respond to environmental stimuli, plants depend on modulating gene expression through different mechanisms including biochemical, molecular, genetic, and epigenetic alterations. Studies on plants might provide better insights into epigenetic stress memory and molecular bases of adaptability to enable (epi)genome editing of crops for climate resilience and sustainable agriculture in the present era of multifaceted climate change.

The effects of Mesua ferrea Linn flower (MFE) extract on the pathogenic cascade of Alzheimer’s disease (AD) were determined by an in vitro and cell culture model in the search for a potential candidate for the treatment of AD. The 2,2′-azino-bis-3-ethylbenzthiazoline-6-sulphonic acid (ABTS) and 1,1-diphenyl-2-picrylhydrazyl (DPPH) assay exhibited that the MFE extract had antioxidant activities. According to the Ellman and the thioflavin T method’s result, the extracts could inhibit acetylcholinesterase and β-amyloid (Aβ) aggregation. Studies on neuroprotection in cell culture found that the MFE extract could reduce the death of human neuroblastoma cells (SH-SY5Y) caused by H2O2 and Aβ. Western blot analysis exhibited that the MFE extract alleviated H2O2-induced neuronal cell damage by downregulating the pro-apoptotic proteins, including cleaved caspase-3, Bax, and by enhancing the expression of anti-apoptotic markers including MCl1, BClxl, and survivin. Moreover, MFE extract inhibited the expression of APP, presenilin 1, and BACE, and increased the expression of neprilysin. In addition, the MFE extract could enhance scopolamine-induced memory deficit in mice. Overall, results showed that the MFE extract had several modes of action related to the AD pathogenesis cascade, including antioxidants, anti-acetylcholinesterase, anti-Aβ aggregation, and neuroprotection against oxidative stress and Aβ. Therefore, the M. ferrea L. flower might be a possibility for further development as a medication for AD.

Rice field bunds and edges can act as near crop habitats, available for planting flowering plants to attract and conserve the natural enemies. We evaluated the effect of ecological engineering on the incidence of Brown Planthopper (BPH), Nilaparvata lugens (Stål) (Hemiptera; Delphacidae) and the abundance of its predators in the rice variety Pusa Basmati-1121. Plots included the oilseed crops viz. sesamum, sunflower and soybean, with plantings of flowering crops marigold, balsam and gaillardia as bund flora around the edges of rice plots. Ecologically engineered plots contained both crops+flowers and resulted in a significantly reduced BPH population per hill in rice plots for 2019 (6.3) and 2020 (9.4) compared to the control plots (9.8 and 14.4). Ecologically engineered plots also witnessed the delayed appearance of BPH during each growing season. Peak BPH populations are lower in the ecologically engineered plots than in the control grounds. Furthermore, the activity of natural enemies, viz., spiders, mirid bugs and rove beetles was the highest in rice fields planted with oilseed crops like sesamum, sunflower and soybean. Olfactory response studies showed that the attraction response of spiders toward sesamum and balsam leaves was more significant than in other crop plants. Rice yield was enhanced in plots planted with crops+flowers during both seasons compared to control plots. Planting of oilseed crops plants such as sesamum, sunflower and soybean with flowering crops such as marigold, balsam and gaillardia as bund flora on the bunds around the main rice field enhanced the natural enemy activity, suppressed the planthopper population, and increased yields. Based on the results, we recommend including ecological engineering techniques as one of the management components in the Integrated Pest Management programme for rice crops.

Summary: Neurotransmitter release requires assembly of the SNARE complex fusion machinery, with multiple SNARE-binding proteins regulating when and where synaptic vesicle fusion occurs. The presynaptic protein Complexin (Cpx) controls spontaneous and evoked neurotransmitter release by modulating SNARE complex zippering. Although the central SNARE-binding helix is essential, post-translational modifications to Cpx’s C-terminal membrane-binding amphipathic helix regulate its ability to control synaptic vesicle fusion. Here, we demonstrate that RNA editing of the Cpx C-terminus modifies its ability to clamp SNARE-mediated fusion and alters presynaptic output. RNA editing of Cpx across single neurons is stochastic, generating up to eight edit variants that fine tune neurotransmitter release by altering the subcellular localization and clamping properties of the protein. Similar stochastic editing rules for other synaptic genes were observed, indicating editing variability at single adenosines and across multiple mRNAs generates unique synaptic proteomes within the same population of neurons to fine tune presynaptic output.

Abstract Background Protein S-nitrosylation (SNO) plays a key role in transferring nitric oxide-mediated signals in both animals and plants and has emerged as an important mechanism for regulating protein functions and cell signaling of all main classes of protein. It is involved in several biological processes including immune response, protein stability, transcription regulation, post translational regulation, DNA damage repair, redox regulation, and is an emerging paradigm of redox signaling for protection against oxidative stress. The development of robust computational tools to predict protein SNO sites would contribute to further interpretation of the pathological and physiological mechanisms of SNO. Results Using an intermediate fusion-based stacked generalization approach, we integrated embeddings from supervised embedding layer and contextualized protein language model (ProtT5) and developed a tool called pLMSNOSite (protein language model-based SNO site predictor). On an independent test set of experimentally identified SNO sites, pLMSNOSite achieved values of 0.340, 0.735 and 0.773 for MCC, sensitivity and specificity respectively. These results show that pLMSNOSite performs better than the compared approaches for the prediction of S-nitrosylation sites. Conclusion Together, the experimental results suggest that pLMSNOSite achieves significant improvement in the prediction performance of S-nitrosylation sites and represents a robust computational approach for predicting protein S-nitrosylation sites. pLMSNOSite could be a useful resource for further elucidation of SNO and is publicly available at https://github.com/KCLabMTU/pLMSNOSite .

The term “Liver disease” refers to a broad category of disorders affecting the liver. There are a variety of common liver ailments, such as hepatitis, cirrhosis, and liver cancer. Accurate and early diagnosis is an emergent demand for the prediction and diagnosis of liver disease. Conventional diagnostic techniques, such as radiological, CT scan, and liver function tests, are often time-consuming and prone to inaccuracies in several cases. An application of machine learning (ML) and deep learning (DL) techniques is an efficient approach to diagnosing diseases in a wide range of medical fields. This type of machine-related learning can handle various tasks, such as image recognition, analysis, and classification, because it helps train large datasets and learns to identify patterns that might not be perceived by humans. This paper is presented here with an evaluation of the performance of various DL models on the estimation and subtyping of liver ailment and prognosis. In this manuscript, we propose a novel approach, termed CNN+LSTM, which is an integration of convolutional neural network (CNN) and long short-term memory (LSTM) networks. The results of the study prove that ML and DL can be used to improve the diagnosis and prognosis of liver disease. The CNN+LSTM model achieves a better accuracy of 98.73% compared to other models such as CNN, Recurrent Neural Network (RNN), and LSTM. The incorporation of the proposed CNN+LSTM model has better results in terms of accuracy (98.73%), precision (99%), recall (98%), F1 score (98%), and AUC (Area Under the Curve)-ROC (Receiver Operating Characteristic) (99%), respectively. The use of the CNN+LSTM model shows robustness in predicting the liver ailment with an accurate diagnosis and prognosis.

Microorganisms colonizing modern water-based metalworking fluids (MWFs) have been implicated in various occupational respiratory health hazards to machinists. An understanding of the exposure risks from specific microbial groups/genera/species (pathogenic or allergenic) and their endotoxins and the need for strategies for effective, timely fluid management warrant real-time extended tracking of the establishment of microbial diversity and the prevailing fluid-related factors. In the current study, the microbial community composition, succession, and dynamics of a freshly recharged industrial semi-synthetic MWF operation was tracked in real-time over a period of 50 weeks, using a combination of microbiological and molecular approaches. Substantial initial bacterial count (both viable and non-viable) even in the freshly recharged MWF pointed to the inefficiency of the dumping, cleaning, and recharge (DCR) process. Subsequent temporal analysis using optimized targeted genus/group-specific qPCR confirmed the presence of Pseudomonads, Enterics, Legionellae, Mycobacteria (M. immunogenum), Actinomycetes, and Fungi. In contrast, selective culturing using commercial culture media yielded non-specific isolates and collectively revealed Gram-negative (13 genera representing 19 isolates) and Gram-positive (2 genera representing 6 isolates) bacteria and fungi but not mycobacteria. Citrobacter sp. and Bacillus cereus represented the most frequent Gram-negative and Gram-positive isolates, respectively, across different media and Nectria haematococca isolation as the first evidence of this fungal pathogen colonizing semi-synthetic MWF. Unbiased PCR-DGGE analysis revealed a more diverse whole community composition revealing 22 bacterial phylotypes and their succession. Surges in the endotoxin level coincided with the spikes in Gram-negative bacterial population and biocide additions. Taken together, the results showed that semi-synthetic MWF is conducive for the growth of a highly diverse microbial community including potential bacterial and fungal pathogens, the current DCR practices are inefficient in combating microbial reestablishment, and the practice of periodic biocide additions facilitates the build-up of endotoxins and non-viable bacterial population.

Nanogels are highly recognized as adaptable drug delivery systems that significantly contribute to improving various therapies and diagnostic examinations for different human diseases. These three-dimensional, hydrophilic cross-linked polymers have the ability to absorb large amounts of water or biological fluids. Due to the growing demand for enhancing current therapies, nanogels have emerged as the next-generation drug delivery system. They effectively address the limitations of conventional drug therapy, such as poor stability, large particle size, and low drug loading efficiency. Nanogels find extensive use in the controlled delivery of therapeutic agents, reducing adverse drug effects and enabling lower therapeutic doses while maintaining enhanced efficacy and patient compliance. They are considered an innovative drug delivery system that highlights the shortcomings of traditional methods. This article covers several topics, including the involvement of nanogels in the nanomedicine sector, their advantages and limitations, ideal properties like biocompatibility, biodegradability, drug loading capacity, particle size, permeability, non-immunological response, and colloidal stability. Additionally, it provides information on nanogel classification, synthesis, drug release mechanisms, and various biological applications. The article also discusses barriers associated with brain targeting and the progress of nanogels as nanocarriers for delivering therapeutic agents to the central nervous system.

Alzheimer's disease (AD) is a type of dementia that affects a vast number of people around the world, causing a great deal of misery and death. Evidence reveals a relationship between the presence of soluble Aβ peptide aggregates and the severity of dementia in Alzheimer's patients. The BBB (Blood Brain Barrier) is a key problem in Alzheimer's disease because it prevents therapeutics from reaching the desired places. To address the issue, lipid nanosystems have been employed to deliver therapeutic chemicals for anti-AD therapy in a precise and targeted manner. The applicability and clinical significance of lipid nanosystems to deliver therapeutic chemicals (Galantamine, Nicotinamide, Quercetin, Resveratrol, Curcumin, HUPA, Rapamycin, and Ibuprofen) for anti-AD therapy will be discussed in this review. Furthermore, the clinical implications of the aforementioned therapeutic compounds for anti-AD treatment have been examined. Thus, this review will pave the way for researchers to fashion therodiagnostics approaches based on nanomedicine to overcome the problems of delivering therapeutic molecules across the blood brain barrier (BBB).

The increasing availability of high-throughput sequencing (frequently termed next-generation sequencing (NGS)) data has created opportunities to gain deeper insights into the mechanisms of a number of diseases and is already impacting many areas of medicine and public health. The area of infectious diseases stands somewhat apart from other human diseases insofar as the relevant genomic data comes from the microbes rather than their human hosts. A particular concern about the threat of antimicrobial resistance (AMR) has driven the collection and reporting of large-scale datasets containing information from microbial genomes together with antimicrobial susceptibility test (AST) results. Unfortunately, the lack of clear standards or guiding principles for the reporting of such data is hampering the field’s advancement. We therefore present our recommendations for the publication and sharing of genotype and phenotype data on AMR, in the form of 10 simple rules. The adoption of these recommendations will enhance AMR data interoperability and help enable its large-scale analyses using computational biology tools, including mathematical modelling and machine learning. We hope that these rules can shed light on often overlooked but nonetheless very necessary aspects of AMR data sharing and enhance the field’s ability to address the problems of understanding AMR mechanisms, tracking their emergence and spread in populations, and predicting microbial susceptibility to antimicrobials for diagnostic purposes. Author summary The growing worldwide threat of antimicrobial resistance (AMR) makes the sharing of resistance data a priority for both researchers and public health practitioners. In particular, the growth of high-throughput sequencing data, in conjunction with AMR phenotypes, has the potential to revolutionise AMR diagnostics and surveillance. However, there is a significant heterogeneity in the ways that this type of data is currently shared, which makes it challenging to perform its analysis at scale. As both producers and users of publicly available genotype–phenotype data on AMR, we propose 10 simple rules that can mitigate this situation and nudge the field towards the adoption of better practices.

The increasing availability of high-throughput sequencing (frequently termed next-generation sequencing (NGS)) data has created opportunities to gain deeper insights into the mechanisms of a number of diseases and is already impacting many areas of medicine and public health. The area of infectious diseases stands somewhat apart from other human diseases insofar as the relevant genomic data comes from the microbes rather than their human hosts. A particular concern about the threat of antimicrobial resistance (AMR) has driven the collection and reporting of large-scale datasets containing information from microbial genomes together with antimicrobial susceptibility test (AST) results. Unfortunately, the lack of clear standards or guiding principles for the reporting of such data is hampering the field's advancement. We therefore present our recommendations for the publication and sharing of genotype and phenotype data on AMR, in the form of 10 simple rules. The adoption of these recommendations will enhance AMR data interoperability and help enable its large-scale analyses using computational biology tools, including mathematical modelling and machine learning. We hope that these rules can shed light on often overlooked but nonetheless very necessary aspects of AMR data sharing and enhance the field's ability to address the problems of understanding AMR mechanisms, tracking their emergence and spread in populations, and predicting microbial susceptibility to antimicrobials for diagnostic purposes.

Ehretia microphylla of the Boraginaceae family has been extensively used as a folklore remedy for the treatment of a wide range of ailments such as cough, cancer, allergies, and gastrointestinal and venereal disorders. Extensive literature review reports have revealed these findings due to the presence of numerous phytomolecules. To validate traditional claims for cytotoxic activity of E. microphylla, the present study was undertaken. Dried leaves of the plant were powdered and defatted with petroleum ether followed by hot continuous extraction with chloroform. The chloroform extract was subjected to in vitro cytotoxic screening against a panel of human cancer cell lines such as HCT-116 (colon), MCF-7 (breast), PC-3 (prostate), A-549 (lung), HL-60 (leukemia) and MiaPaCa-2 (pancreatic) at 50 µM using SRB assay. The extract exhibited noteworthy cytotoxicity activity against breast and lung cancer. It exhibited 85.55% and 77.93% inhibition against MCF-7 and A-549 cancer cell lines, respectively. The mechanism behind cell death was determined using the DAPI staining method, which induces alteration in nuclear morphology in MCF-7 cell lines evidenced through DAPI staining. Phytochemical screening of E. microphylla extract showed the presence of saponins, steroids, lipids, tannins and triterpenoids. The chemoprofile of the chloroform extract of E. microphylla leaves was established using an n-hexane:ethyl acetate solvent system in a ratio of 6:4. The developed chromatogram showed five spots both in visible and UV light at 254 nm. The information provided in the present study will enable further studies on the isolation and characterization of bioactive compounds/fractions by following bioactivity-guided fractionation, and thus, the plant has the potential to reduce proliferation and may induce cell death via apoptosis in breast cancer cells.

Background and Purpose: Invasive candidiasis is one of the most common systemicmycoses, and studies have shown mixed yeast infections. Malaysia lacks mixed yeastculture data.Materials and Methods: Yeast isolates were collected in Sultan Abdul Halim Hospital,North Malaysia, from October 2020 to October 2021. Chromogenic Candida differentialagar media and PCR-RFLP were used to identify yeast species.Results: A total of 206 yeast isolates were collected from different body sites of patients.The majority of the yeast isolates (n=104) were obtained from the urine. Other isolates were extracted from blood (n=52), vaginal swabs (n=45), ear discharge (n=2), tracheal aspirate (n=2), tissue (n=2), skin (n=1), nail (n=1), sputum (n=1), and cerebrospinal fluid (n=1). In total, 200 yeast samples were identified as single species, and six isolates were a mixture of Candida species.Conclusion: Malaysia lacks accurate epidemiological data on mixed yeast infections.We identified all samples to the species level, including mixed yeast cultures, using theMspI enzyme and PCR-RFLP.

Abstract Critical functions of the blood–brain barrier (BBB), including cerebral blood flow, energy metabolism, and immunomodulation, are regulated by insulin signaling pathways. Therefore, endothelial insulin resistance could lead to BBB dysfunction, which is associated with neurodegenerative diseases such as Alzheimer’s disease (AD). The current study aims to map the dynamics of insulin-responsive pathways in polarized human cerebral microvascular endothelial cell (hCMEC/D3) monolayers. RNA-Sequencing was performed on hCMEC/D3 monolayers with and without insulin treatment at various time points. The Short Time-series Expression Miner (STEM) method was used to identify gene clusters with distinct and representative expression patterns. Functional annotation and pathway analysis of genes from selected clusters were conducted using Webgestalt and Ingenuity Pathway Analysis (IPA) software. Quantitative expression differences of 16,570 genes between insulin-treated and control monolayers were determined at five-time points. The STEM software identified 12 significant clusters with 6880 genes that displayed distinct temporal patterns upon insulin exposure, and the clusters were further divided into three groups. Gene ontology (GO) enrichment analysis demonstrated that biological processes protecting BBB functions such as regulation of vascular development and actin cytoskeleton reorganization were upregulated after insulin treatment (Group 1 and 2). In contrast, GO pathways related to inflammation, such as response to interferon-gamma, were downregulated (Group 3). The IPA analyses further identified insulin-responsive cellular and molecular pathways that are associated with AD pathology. These findings unravel the dynamics of insulin action on the BBB endothelium and inform about downstream signaling cascades that are potentially disrupted due to brain insulin resistance prevalent in AD.

An in vivo transcriptomic analysis of Staphylococcus aureus infection in mice provides further insight into how this pathogen responds to changes in the host environment over time.

The 20th International Medical, Pharmaceutical, Cosmeceutical & Health Science Symposium (iMPaCHS) is an annual symposium co-organized by Faculty of Life and Health Sciences, International Medical School, School of Pharmacy, Management & Science of the Management & Science University, Malaysia. With the theme 'Advancing Health Science Innovations through Interdisciplinary Collaboration', the 20th iMPaCHS aims to promote holistic research skills for future betterment. Advancing health science innovations requires a multidisciplinary approach, which involves the collaboration of experts from various fields. Interdisciplinary collaboration enables the integration of knowledge, perspectives, and methodologies from different disciplines, leading to the development of novel and effective solutions to complex health challenges. By fostering interdisciplinary collaboration, health science can leverage the strengths of each field and accelerate the translation of research findings into clinical practice, ultimately improving and advancing the overall state of health science. This is in line with the sustainable development goal and collaborative research activity in the university. The 20th International Medical, Pharmaceutical, Cosmeceutical & Health Science Symposium (iMPaCHS) is an annual symposium co-organized by Faculty of Life and Health Sciences, International Medical School, School of Pharmacy, Management & Science of the Management & Science University, Malaysia. With the theme 'Advancing Health Science Innovations through Interdisciplinary Collaboration', the 20th iMPaCHS aims to promote holistic research skills for future betterment. Advancing health science innovations requires a multidisciplinary approach, which involves the collaboration of experts from various fields. Interdisciplinary collaboration enables the integration of knowledge, perspectives, and methodologies from different disciplines, leading to the development of novel and effective solutions to complex health challenges. By fostering interdisciplinary collaboration, health science can leverage the strengths of each field and accelerate the translation of research findings into clinical practice, ultimately improving and advancing the overall state of health science. This is in line with the sustainable development goal and collaborative research activity in the university.

EngA is an essential and unique bacterial GTPase involved in ribosome biogenesis. The essentiality and species-specific variations among EngA homologues make the protein a potential target for future drug development. In this aspect, it is important to understand the variations of EngA among probiotic organisms and non-probiotic bacteria to understand species specificity. The search for variations among EngA homologues revealed a unique variant, exclusively found in Bifidobacterium and a few Actinobacteria species. Bifidobacterium possesses a multifunctional fusion protein, wherein EngA is fused with an N-terminal CMK (Cytidylate Monophosphate Kinase) domain. The resulting protein is therefore a large (70kDa size) with 3 consecutive P-loops and a 50 amino acid long linker connecting the EngA and CMK domains. EngA is known to regulate ribosome biogenesis via nucleotide-dependent conformational changes. The additional domain may introduce further intricate regulation in ribosome biogenesis or participate in newer biological processes. This study is the first attempt to characterise this novel class of bacterial EngA found in the Genus of Bifidobacteria.

O-linked β-N-acetylglucosamine (O-GlcNAc) is a distinct monosaccharide modification of serine (S) or threonine (T) residues of nucleocytoplasmic and mitochondrial proteins. O-GlcNAc modification (i.e., O-GlcNAcylation) is involved in the regulation of diverse cellular processes, including transcription, epigenetic modifications, and cell signaling. Despite the great progress in experimentally mapping O-GlcNAc sites, there is an unmet need to develop robust prediction tools that can effectively locate the presence of O-GlcNAc sites in protein sequences of interest. In this work, we performed a comprehensive evaluation of a framework for prediction of protein O-GlcNAc sites using embeddings from pre-trained protein language models. In particular, we compared the performance of three protein sequence-based large protein language models (pLMs), Ankh, ESM-2, and ProtT5, for prediction of O-GlcNAc sites and also evaluated various ensemble strategies to integrate embeddings from these protein language models. Upon investigation, the decision-level fusion approach that integrates the decisions of the three embedding models, which we call LM-OGlcNAc-Site, outperformed the models trained on these individual language models as well as other fusion approaches and other existing predictors in almost all of the parameters evaluated. The precise prediction of O-GlcNAc sites will facilitate the probing of O-GlcNAc site-specific functions of proteins in physiology and diseases. Moreover, these findings also indicate the effectiveness of combined uses of multiple protein language models in post-translational modification prediction and open exciting avenues for further research and exploration in other protein downstream tasks. LM-OGlcNAc-Site’s web server and source code are publicly available to the community.

The global demand for bottled king coconut water has led to a significant accumulation of empty king coconut husks in nut water export industries, posing challenges in managing and disposing of this agricultural waste. To address this issue, the production of king coconut husk ash (KCHA) has emerged as an eco-friendly solution. This product can be applied as a fertilizer, soil amendment, or after mixing with compost to enhance its nutrient value. This study aimed to determine the optimal cut size and moisture level for obtaining a high yield of KCHA with the maximum potassium content. The experiment involved drying full-, half-, quarter-, and chip-sized husks in a dehydrator at 60 °C for 0, 2, 4, 8, 12, 24, and 48 h. The findings revealed that reducing the particle size of the husks accelerated the drying process. The ash produced with chips exhibited the most favorable characteristics, reaching the desired dryness in a relatively shorter time while yielding the highest KCHA content. Moreover, the results indicated that the optimal duration for dehydrating the husks to produce ash was 24 h at 60 °C, resulting in the highest moisture loss. This processing condition facilitated the efficient conversion of king coconut husks into potassium-rich ash. Implementing these findings into the production of KCHA as a nutrient-rich fertilizer or soil amendment offers a sustainable approach to improving agricultural practices while reducing the dependence on synthetic fertilizers and mitigating the environmental challenges associated with their accumulation.