Assay Research Articles

Biological activity and chemical characteristics studies of new oligomannose produced by Erwinia gerundensis

Natural polymers have attracted considerable attention in recent decades among scientists due to their potential therapeutic uses, particularly as antimicrobial and antitumor agents. In this research, novel EPSs were extracted from garlic rhizosphere bacteria. The antibacterial and antitumor activities of the polymer were evaluated through biological assays. The antibacterial activity was tested against gram-positive microorganisms (such as Listeria monocytogenes, Bacillus cereus, and Staphylococcus aureus) and gram-negative organisms (such as Shigella sonnei and Escherichia coli). The most significant inhibition zone was observed with Listeria monocytogenes and S. typhi, measuring 35 mm, while the most miniature antibacterial effect was seen with Staphylococcus aureus at 23.67 mm.Furthermore, the inhibitory effect of the crude polymer was assessed using a broth medium with two strains of E. coli and Bacillus cereus. Electron microscope images displayed varying degrees of damage to bacterial cells in the treated broth. The antitumor activity was determined using the MTT test on colon carcinoma cells (HCT-116), hepatocellular carcinoma cells (HepG-2), and CaCO2 (intestinal carcinoma cells), with IC50 values of 188.86±6.17 µg/mL, 221.66±8.02 µg/mL, and 203.65±7.43 µg/mL, respectively, after 48 h. The bacteria responsible for polymer production were isolated from garlic plant rhizospheres and identified as Erwinia gerundensis CCASU-2024–69 through 16S rRNA sequencing. FTIR and NMR techniques determined the crude EPS's main components and functional groups, including carbonyl, carboxylic, methylene, and silanol. GC–MS analysis revealed 34 bioactive compounds, while HPLC analysis indicated that the EPS was a hetero-monosaccharide consisting of d-xylose, d-glucose, l-arabinose, ribose, and d-mannose. This research study represents the initial exploration into the exopolysaccharide derived from Erwinia gerundensis. To assess the interaction between the exopolysaccharide and the active sites of Bacillus cereus and E. coli, molecular docking experiments were conducted using five monosaccharides: d-xylose, d-glucose, l-arabinose, ribose, and d-mannose. The data obtained from the molecular docking analysis strongly correlates with the findings from biological studies.Furthermore, these highly active compounds exhibit a favorable proposed ADMET profile. This particular exopolysaccharide shows potential as a natural antibiotic and holds promise in treating gastrointestinal cancer. A comprehensive assessment of laboratory animals is essential before its potential use as a prebiotic in nutrition.

Salinity Tolerance Mechanism of Crithmum maritimum L.: Implications for Sustainable Agriculture in Saline Soils

Edible halophytes are attracting attention due to their potential for agriculture in saline and marginal areas. The salt tolerance mechanism was analyzed in Crithmum maritimum L., based on ionic, osmotic, and redox homeostasis strategies under salt stress. The methodology involved growing C. maritimum seeds in pots under controlled greenhouse conditions and exposing them to different NaCl concentrations (0, 100, 200, and 300 mM) for five months. High salinity levels decreased plant length and biomass, but the shoot-to-root length and biomass ratio increased significantly. Photosynthetic pigments (chlorophyll and carotenoids) were quantified using spectrophotometric analysis, while macro- and micro-nutrient contents were determined via the Kjeldahl method, flame photometry, and atomic absorption spectrophotometry. Osmolyte accumulation, including proline and glycine betaine, was analyzed using specific biochemical assays, and antioxidant enzyme activities (SOD, CAT, and POX) were measured to assess redox homeostasis. Photosynthetic pigments in C. maritimum leaves slightly increased at 100 mM NaCl, but significantly declined at 200 and 300 mM NaCl. A high Na content in the shoots indicated no restriction in mineral uptake in the roots. Nitrogen and phosphorus slightly decreased under high salinity. The cation content in the shoots varied: potassium decreased, while calcium and magnesium increased with salinity, although the Mg+2/Na+ and K+/Na+ ratios showed similar declining patterns. The micro-nutrients iron and manganese increased in the shoots, while copper remained unchanged. The content of osmolytes proline and glycine betaine significantly increased under the 200 and 300 mM NaCl treatments. Antioxidant enzyme activities (SOD, CAT, and POX) decreased at 100 and 200 mM NaCl, but were strongly induced at 300 mM NaCl. The total antiradical activity of the leaves increased with higher salinity levels. Our results indicated that the facultative halophyte characteristics of C. maritimum emerged after exposure to 200 mM NaCl. Increased calcium content may be a key factor in salinity tolerance. We concluded that C. maritimum employs strong osmotic adjustment and redox homeostasis mechanisms, making it a promising candidate for cultivation in saline environments.

Chronic sleep deprivation induces erectile dysfunction through increased oxidative stress, apoptosis, endothelial dysfunction, and corporal fibrosis in a rat model.

Sleep is foundational for nocturnal erections, facilitating nutrient exchange and waste removal, which has brought widespread attention to the relationship between sleep and erectile dysfunction (ED). However, there is currently a lack of basic research confirming whether chronic sleep deprivation (CSD) leads to erectile impairment and its underlying pathological mechanisms. The study sought to investigate whether CSD impairs erectile function in rats and the potential tissue damage it may cause in rats. The modified multiple platform method was employed to induce CSD in 14 rats, randomly divided into a platform control group and a CSD group. After 3 weeks, erectile function was evaluated by measuring intracavernosal pressure following cavernous nerve stimulation. Arterial blood samples were then analyzed for testosterone levels, and cavernous tissues were processed for advanced molecular biology assays, including Western blotting and immunofluorescence. After inducing CSD, rats exhibited a marked reduction in erectile function, yet their serum testosterone levels remained statistically unchanged when compared with the control group. More importantly, rats in the CSD group exhibited a significant increase in oxidative stress levels, accompanied by low expression of HO-1 and high expression of NOX1 and NOX4. Subsequently, elevated oxidative stress induced increased apoptosis in smooth muscle and endothelial cells, as evidenced by significant decreases in CD31 and α-smooth muscle actin expression in the CSD group, demonstrated through Western blotting and immunofluorescence assays. Endothelial cell apoptosis led to a significant decrease in endothelial nitric oxide synthase, resulting in lowered levels of nitric oxide and cyclic guanosine monophosphate, which severely impaired the erectile mechanism. Additionally, activation of the transforming growth factor β1 fibrotic pathway led to increased levels of tissue fibrosis, resulting in irreversible damage to the penile tissue in the CSD group. Our study lacks further exploration of the molecular mechanisms linking CSD and ED, representing a future research focus for potential targeted therapies. Our findings demonstrated that CSD significantly impairs erectile function in rats. CSD severely impairs erectile function in rats. When exposed to CSD, rats exhibit significantly elevated oxidative stress levels, which lead to increased tissue apoptosis, endothelial dysfunction, and ultimately irreversible fibrotic changes in the tissues. Further researches into the potential molecular mechanisms are needed to identify possible therapeutic targets for ED related to CSD.

Assessment of Antioxidant and Hepatoprotective Effects of Kappaphycus alvarezii (Doty) Doty ex Silva Against Carbon Tetrachloride-Induced Liver Injury in Rats

Kappaphycus alvarezii (Doty) Doty ex Silva, commonly known as red algae, holds economic significance as a primary source of κ-carrageenan, which exhibits promising medicinal and therapeutic properties. This study aims to assess the antioxidant potential as well as hepatoprotective activity of the ethanolic extract of K. alvarezii (EEKA). The assays utilised to determine the antioxidant properties of EEKA were total phenolic content (TPC) and 2,2-diphenyl-1-picrylhydrazyl (DPPH) radical scavenging. In addition, the ability of EEKA to ameliorate experimentally induced liver injury in Sprague-Dawley rats caused by carbon tetrachloride (CCl4) was evaluated. The biochemical assays involved measuring liver marker enzymes (AST and ALT) in serum as well as determining the levels of reduced glutathione (GSH), lipid peroxidation (LPO) via malondialdehyde, catalase (CAT), and glutathione S-transferase (GST) in liver homogenates. The TPC and DPPH radical scavenging activity of EEKA demonstrated relatively low antioxidant properties compared to standard references. However, CCl4-induced groups exhibited significantly increased levels of AST and ALT, along with depletion of antioxidant status (GSH, CAT, and GST) indicated by LPO. Pretreatment with EEKA resulted in slightly decreased liver marker enzyme activity and LPO, coupled with an increase in antioxidant status. These findings suggest that EEKA contains active principles capable of counteracting the hepatotoxic effects induced by CCl4.

Characterizations of Protein Arginine Deiminase 1 as a Substrate of NTMT1: Implications of Nα-Methylation in Protein Stability and Interaction.

α-N-Methylation (Nα-methylation), catalyzed by protein N-terminal methyltransferases (NTMTs), constitutes a crucial post-translational modification involving the transfer of a methyl group from S-adenosyl-l-methionine (SAM) to the Nα-terminal amino group of substrate proteins. NTMT1/2 are known to methylate canonical Nα sequences, such as X-P-K/R. With over 300 potential human protein substrates, only a small fraction has been validated, and even less is known about the functions of Nα-methylation. This study delves into the characterizations of protein arginine deiminase 1 (PAD1) as a substrate of NTMT1. By employing biochemical and cellular assays, we demonstrated NTMT1-mediated Nα-methylation of PAD1, leading to an increase in protein half-life and the modulation of protein-protein interactions in HEK293T cells. The methylation of PAD1 appears nonessential to its enzymatic activity or cellular localization. Proteomic studies revealed differential protein interactions between unmethylated and Nα-methylated PAD1, suggesting a regulatory role for Nα-methylation in modulating PAD1's protein-protein interactions. These findings shed light on the intricate molecular mechanisms governing PAD1 function and expand our knowledge of Nα-methylation in regulating protein function.

Identification of critical amino acids in the DNA binding domain of LuxO: Lessons from a constitutive active LuxO.

Quorum sensing plays a vital role in the environmental and host life cycles of Vibrio cholerae. The quorum-sensing circuit involves the consorted action of autoinducers, small RNAs, and regulatory proteins to control a plethora of physiological events in this bacterium. Among the regulatory proteins, LuxO is considered a low-cell-density master regulator. It is a homolog of NtrC, a two-component response regulator. NtrC belongs to an evolving protein family that works with the alternative sigma factor σ54 to trigger gene transcription. Structurally, these proteins comprise 3 domains: a receiver domain, a central AAA+ATPase domain, and a C-terminal DNA-binding domain (DBD). LuxO communicates with its cognate promoters by employing its DNA binding domain. In the present study, we desired to identify the critical residues in the DBD of LuxO. Our combined mutagenesis and biochemical assays resulted in the identification of eleven residues that contribute significantly to LuxO regulatory function.

Deciphering the cytotoxicity of micro- and nanoplastics in Caco-2 cells through meta-analysis and machine learning

Plastic pollution, driven by micro- and nanoplastics (MNPs), poses a major environmental threat, exposing humans through various routes. Despite human colorectal adenocarcinoma Caco-2 cells being used as an in vitro model for studying the intestinal epithelium, uncertainties linger about MNPs harming these cells and the factors influencing adverse effects. Addressing this lacuna, our study aimed to elucidate the pivotal MNP parameters influencing cytotoxicity in Caco-2 cells, employing meta-analysis and machine learning techniques for quantitative assessment. Initial scrutiny of 95 publications yielded 17 that met the inclusion criteria, generating a dataset of 320 data points. This dataset underwent meticulous stratification based on polymer type, exposure time, polymer size, MNP concentration, and biological assays utilised. Subsequent dose-response curve analysis revealed moderate correlations for selected subgroups, such as the (3-[4,5-dimethylthiazol-2-yl]-2,5 diphenyl tetrazolium bromide) MTT biological assay and exposure time exceeding 24 h, with coefficient of determination (R2) values of 0.50 (p-value: 0.0065) and 0.60 (p-value: 0.0018) respectively. For the aforementioned two subgroups, the MNP concentrations surpassing 10 μg/mL led to diminished viability of Caco-2 cells. Notably, we observed challenges in employing meta-analysis to navigate this multidimensional MNP dataset. Leveraging a random forest model, we achieved improved predictive performance, with R2 values of 0.79 and a root mean square error (RMSE) of 0.14 for the prediction of the Log Response Ratio on the test set. Model interpretation indicated that size and concentration are the principal drivers influencing Caco-2 cell cytotoxicity. Additionally, the partial dependence plot illustrating the relationship between the size of MNPs and predicted cytotoxicity reveals a complex pattern. Our study provides crucial insights into the health impacts of plastic pollution, informing policymakers for targeted interventions, thus contributing to a comprehensive understanding of its human health consequences.

Design and synthesis of novel 8-(azaindolyl)-benzoazepinones as potent and selective ROCK inhibitors.

We report the characterization of potent and selective ROCK inhibitors identified through a core-hopping strategy. A virtual screening workflow, combining ligand- and structure-based methods, was applied on a known series of ROCK inhibitors bearing an acetamido-thiazole scaffold. The most promising replacement of the central core was represented by a benzoazepinone ring, which was selected as a starting point for a subsequent chemical exploration. The overall design approach exploited previous SARs available for congeneric series and crystallographic information to optimize the hinge-binding group as well as the terminal aromatic moiety interacting with the glycine-rich loop. The introduction of elongated and flexible charged groups led to compound 15, which exhibited sub-nanomolar potencies in biochemical and cellular assays, as well as a remarkable selectivity over PKA. HDX studies not only supported the postulated binding mode of compound 15 but also confirmed the crucial role of specific ROCK peptide segments in driving ligand selectivity.

Long-term changes in phospholipids and free fatty acids and the possible subcellular origins for phospholipid degradation in kainic acid-damaged mouse hippocampus

Kainic acid (KA)-induced excitotoxicity induces acute degradation of phospholipids and release of free fatty acids (FFAs) in rodent hippocampus, but the long-term changes in phospholipids or the subcellular origins of liberated FFAs remain unclarified. Phospholipids and FFAs were determined in KA-damaged mouse hippocampus by enzyme-coupled biochemical assays. The evolution of membrane injuries in the hippocampus was examined by a series of morphological techniques. The levels of phospholipids in the hippocampus decreased shortly after KA injection but recovered close to the control levels at 24 h. The decline in phospholipids was accelerated again from 72 to 120 after KA treatment. The levels of FFAs were negatively related to those of phospholipids, exhibiting a similar but opposite trend of changes. KA treatment caused progressively severe damage to vulnerable neurons, which was accompanied by increased permeability in the cell membrane and increased staining of membrane-bound dyes in the cytoplasm. Double fluorescence staining showed that the latter was partially overlapped with abnormally increased endocytic and autophagic components in damaged neurons. Our results revealed intricate and biphasic changes in phospholipid and FFA levels in KA-damaged hippocampus. Disrupted endomembrane system may be one of the major origins for KA-induced FFA release.

ACL1-ROC4/5 complex reveals a common mechanism in rice response to brown planthopper infestation and drought

Brown planthopper (BPH) is the most destructive insect pest of rice. Drought is the most detrimental environmental stress. BPH infestation causes adaxial leaf-rolling and bulliform cells (BCs) shrinkage similar to drought. The BC-related abaxially curled leaf1 (ACL1) gene negatively regulates BPH resistance and drought tolerance, with decreased cuticular wax in the gain-of-function mutant ACL1-D. ACL1 shows an epidermis-specific expression. The TurboID system and multiple biochemical assays reveal that ACL1 interacts with the epidermal-characteristic rice outermost cell-specific (ROC) proteins. ROC4 and ROC5 positively regulate BPH resistance and drought tolerance through modulating cuticular wax and BCs, respectively. Overexpression of ROC4 and ROC5 both rescue ACL1-D mutant in various related phenotypes. ACL1 competes with ROC4/ROC5 in homo-dimer and hetero-dimer formation, and interacts with the repressive TOPLESS-related proteins. Altogether, we illustrate that ACL1–ROC4/5 complexes synergistically mediate drought tolerance and BPH resistance through regulating cuticular wax content and BC development in rice, a mechanism that might facilitate BPH-resistant breeding.

Abstract B089: Identification of novel drivers of gemcitabine resistance in pancreatic cancer

Abstract Pancreatic cancer is an aggressive disease with limited therapeutic options. Gemcitabine is a clinically used chemotherapy for pancreatic cancer treatment but has limited efficacy. The molecular mechanisms responsible for gemcitabine resistance in pancreatic cancer are still unclear. Here, we analyzed the genomics of drug sensitivity in cancer dataset and identified various pancreatic cancer cells with distinct sensitivity to gemcitabine. Validation with proliferation and clonogenic assays confirmed that while CFPAC1 and PANC0327 are highly gemcitabine-sensitive, ASPC1 and PANC1 display intrinsic gemcitabine resistance. Analysis of the gene expression profile of these cells identified several genes that are differentially upregulated in resistant versus sensitive cells. Pathway enrichment analysis using the differential genes revealed the upregulation of Hippo, Wnt, MAPK signaling pathways as well as autophagy and glutathione metabolism in the resistant cells. Using quantitative PCR, immunoblotting and biochemical assays, and extracellular flux analysis methods, we have characterized the molecular distinctions between gemcitabine sensitive and resistant cells. Our results provide insight on the molecular mechanisms driving gemcitabine resistance in pancreatic cancer and could lead to novel therapeutic strategies to overcome resistance and improve patients’ treatment. Citation Format: Amina D Bilalbegovic, Bowen Fu, Zeribe Nwosu. Identification of novel drivers of gemcitabine resistance in pancreatic cancer [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Advances in Pancreatic Cancer Research; 2024 Sep 15-18; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2024;84(17 Suppl_2):Abstract nr B089.

Assessment of the biological activities of Azolla pinnata growing in the North-West of Algeri

Many plants' phytochemical composition and pharmacological activities offer medicinal potential for sci-entific research. This work aims to assess the bioactivities of Azolla pinnata extracts by evaluating their antioxidant, anticancer, antibacterial, and antifungal properties. Ultrasonic pretreatment of the samples was carried out to increase the yield of extracts. Two methods were chosen for extraction (maceration and de-coction), using five solvents of different polarities: water, methanol, water/methanol (20:80; v/v), wa-ter/acetone (10:90; v/v) and chloroform. The phytochemical contents were determined using chemical as-says and HPLC analysis. The antioxidants, anticancer, and antimicrobial capacities of the different extracts were evaluated. The results revealed that the ultrasonic treatment enhanced the extraction yield; the highest rate was noted for the methanolic extract (27.3±1.18%), while the lowest values were reported for those obtained by chloroform (5.8±1.04%). The phytochemical screening has shown that extracts are rich in fla-vonoids, tannins, and phenolic compounds. The assessment of the bioactivities of extracts reveals that A. pinnata possesses a wide range of pharmacological properties, including antioxidant, anticancer, antibac-terial, and antifungal. Despite the substantial correlation identified between bioactivity and bioactive con-tents in the extracts, the specific components accountable for each activity remain unknown. Keywords: Azolla pinnata, bioactive compounds, Ultrasonic treatment, phytochemicals, bioactivities as-sessment.

SCRATCH: A programmable, open-hardware, benchtop robot that automatically scratches cultured tissues to investigate cell migration, healing, and tissue sculpting.

Despite the widespread popularity of the ' scratch assay', where a pipette is dragged through cultured tissue to create an injury gap to study cell migration and healing, the manual nature of the assay carries significant drawbacks. So much of the process depends on individual manual technique, which can complicate quantification, reduce throughput, and limit the versatility and reproducibility of the approach. Here, we present a truly open-source, low-cost, accessible, and robotic scratching platform that addresses all of the core issues. Compatible with nearly all standard cell culture dishes and usable directly in a sterile culture hood, our robot makes highly reproducible scratches in a variety of complex cultured tissues with high throughput. Moreover, we demonstrate how scratching can be programmed to precisely remove areas of tissue to sculpt arbitrary tissue and wound shapes, as well as enable truly complex co-culture experiments. This system significantly improves the usefulness of the conventional scratch assay, and opens up new possibilities in complex tissue engineering and cell biological assays for realistic wound healing and migration research.

Protein kinase C iota promotes glycolysis via PI3K/AKT/mTOR signalling in high grade serous ovarian cancer.

Epithelial ovarian cancer, especially high grade serous ovarian cancer (HGSOC) is by far, the most lethal gynecological malignancy with poor prognosis and high relapse rate. Despite of availability of several therapeutic interventions including poly-ADP ribose polymerase (PARP) inhibitors, HGSOC remains unmanageable and identification of early detection biomarkers and therapeutic targets for this lethal malady is highly warranted. Aberrant expression of protein kinase C iota (PKCί) is implicated in many cellular and physiological functions involved in tumorigenesis including cell proliferation and cell cycle deregulation. Two high grade serous ovarian cancer cells SKOV3 and COV362 were employed in this study. PKCί was genetically knocked down or pharmacologically inhibited and several functional and biochemical assays were performed. We report that PKCί is overexpressed in HGSOC cells and patient tissue samples with a significant prognostic value. Pharmacological inhibition of PKCί by Na-aurothiomalate or its shRNA-mediated genetic knockdown suppressed HGSOC cell proliferation, EMT and induced apoptosis. Moreover, PKCί positively regulated GLUT1 and several other glycolytic genes including HK1, HK2, PGK1, ENO1 and LDHA to promote elevated glucose uptake and glycolysis in HGSOC cells. Mechanistically, PKCί drove glycolysis via PI3K/AKT/mTOR signalling. Na-aurothiomalate and highly selective, dual PI3K/mTOR inhibitor dactolisib could serve as novel anti-glycolytic drugs in HGSOC. Taken together, our results indicate PKCί/PI3K/AKT/mTOR signalling cascade could be a novel therapeutic target in a lethal pathology like HGSOC.

PPP2R5E: New gene potentially involved in specific learning disorders and myopathy

Protein phosphatase 2A (PP2A) is a family of multifunctional enzymatic complexes crucial for cellular signalling, playing a pivotal role in brain function and development. Mutations in specific genes encoding PP2A complexes have been associated with neurodevelopmental disorders with hypotonia and high risk of seizures. In the current work, we present an individual with specific learning problems, motor coordination disorders, hypotonia and behavioural issues. Although whole exome sequencing (WES) did not unveil pathogenic variants in known genes related to these symptoms, a de novo heterozygous variant Glu191Lys was identified within PPP2R5E, encoding the PP2A regulatory subunit B56ε. The novel variant was not observed in the four healthy brothers and was not detected as parental somatic mosaicism. The mutation predicted a change of charge of the mutated amino acid within a conserved LFDSEDPRER motif common to all PPP2R5 B-subunits. Biochemical assays demonstrated a decreased interaction with the PP2A A and C subunits, leading to disturbances in holoenzyme formation, and thus likely, function. For the first time, we report a potential causal link between the observed variant within the PPP2R5E gene and the symptoms manifested in the subject, spanning specific learning problems and motor coordination disorders potentially associated with myopathy.

Evaluation of an Enzyme-Linked Magnetic Electrochemical Assay for Hepatitis a Virus Detection in Drinking and Vegetable Processing Water

Globally, waterborne viral infections significantly threaten public health. While current European Union regulations stipulate that drinking water must be devoid of harmful pathogens, they do not specifically address the presence of enteric viruses in water used for irrigation or food production. Traditional virus detection methods rely on molecular biology assays, requiring specialized personnel and laboratory facilities. Here, we describe an electrochemical sandwich enzyme-linked immunomagnetic assay (ELIME) for the detection of the hepatitis A virus (HAV) in water matrices. This method employed screen-printed electrodes as the sensing platform and utilized commercially available pre-activated magnetic beads to provide a robust foundation for the immunological reaction. The ELIME assay demonstrated exceptional analytical performance in only 185 min achieving a detection limit of 0.5 genomic copies per milliliter (g.c./mL) and exhibiting good reproducibility with a relative standard deviation (RSD) of 7% in HAV-spiked drinking and processing water samples. Compared with the real-time RT-qPCR method described in ISO 15216-1, the ELIME assay demonstrated higher sensitivity, although the overall linearity of the method was moderate. These analytical attributes highlight the potential of the ELIME assay as a rapid and viable alternative for HAV detection in water used for agriculture and food processing.

Peptides as modulators of FPPS enzyme: A multifaceted evaluation from the design to the mechanism of action

Bone diseases are medical conditions caused by the loss of bone homeostasis consecutive to increased osteoclast activity and diminished osteoblast activity. The mevalonate pathway (MVA) is crucial for maintaining this balance since it drives the post-translational prenylation of small guanosine triphosphatases (GTPases) proteins. Farnesyl pyrophosphate synthase (FPPS) plays a crucial role in the MVA pathway. Consequently, in the treatment of bone-related diseases, FPPS is the target of FDA-approved nitrogen-containing bisphosphonates (N-BPs), which have tropism mainly for bone tissue due to their poor penetration in soft tissues. The development of inhibitors targeting the FPPS enzyme has garnered significant interest in recent decades due to FPPS's role in the biosynthesis of cholesterol and other isoprenoids, which are implicated in cancer, bone diseases, and other conditions. In this study, we describe a multidisciplinary approach to designing novel FPPS inhibitors, combining computational modeling, biochemical assays, and biophysical techniques. A series of peptides and phosphopeptides were designed, synthesized, and evaluated for their ability to inhibit FPPS activity. Molecular docking was employed to predict the binding modes of these compounds to FPPS, while Surface Plasmon Resonance (SPR) and Nuclear Magnetic Resonance (NMR) spectroscopy experiments – based on Saturation Transfer Difference (STD) and an enzymatic NMR assay – were used to measure their binding affinities and kinetics. The biological activity of the most promising compounds was further assessed in cellular assays using murine colorectal cancer (CRC) cells. Additionally, genomics and metabolomics profiling allowed to unravel the possible mechanisms underlying the activity of the peptides, confirming their involvement in the modulation of the MVA pathway. Our findings demonstrate that the designed peptides and phosphopeptides exhibit significant inhibitory activity against FPPS and possess antiproliferative effects on CRC cells, suggesting their potential as therapeutic agents for cancer.

A FAPα-activated MRI nanoprobe for precise grading diagnosis of clinical liver fibrosis

Molecular imaging holds the potential for noninvasive and accurate grading of liver fibrosis. It is limited by the lack of biomarkers that strongly correlate with liver fibrosis grade. Here, we discover the grading potential of fibroblast activation protein alpha (FAPα) for liver fibrosis through transcriptional analysis and biological assays on clinical liver samples. The protein and mRNA expression of FAPα are linearly correlated with fibrosis grade (R2 = 0.89 and 0.91, respectively). A FAPα-responsive MRI molecular nanoprobe is prepared for quantitatively grading liver fibrosis. The nanoprobe is composed of superparamagnetic amorphous iron nanoparticles (AFeNPs) and paramagnetic gadoteric acid (Gd-DOTA) connected by FAPα-responsive peptide chains (ASGPAGPA). As liver fibrosis worsens, the increased FAPα cut off more ASGPAGPA, restoring a higher T1-MRI signal of Gd-DOTA. Otherwise, the signal remains quenched due to the distance-dependent magnetic resonance tuning (MRET) effect between AFeNPs and Gd-DOTA. The nanoprobe identifies F1, F2, F3, and F4 fibrosis, with area under the curve of 99.8%, 66.7%, 70.4%, and 96.3% in patients’ samples, respectively. This strategy exhibits potential in utilizing molecular imaging for the early detection and grading of liver fibrosis in the clinic.

Leukocyte classification using relative-relationship-guided contrastive learning

Hematologic diseases and blood disorders can be studied through microscopic examination of blood smear images or chemical assays. Many researchers are focused on utilizing deep learning (DL) to identify, quantify, and classify various types of blood cells, which is crucial for addressing theoretical and practical challenges in disease diagnosis and treatment planning. However, there is a significant deficiency in annotations for leukocyte classification, limiting the effectiveness of current DL methods. Contrastive learning (CL) facilitates the extraction of prior knowledge from unlabeled data, reducing the dependency on manual annotations. While CL demonstrates remarkable achievements in classifying natural images, the direct application to leukocyte classification presents certain defects. We observe that standard data augmentation techniques in CL exhibit varying sensitivity to different categories of white blood cell images. Employing a uniform augmentation strategy may lead the network into an optimization trap, acquiring inadequate representations from erroneous sample relationships. To address this issue, we propose a Relative-Relationship-Guided Contrastive Learning Representation (ReCLR) framework for the leukocyte classification. ReCLR mines positive and negative samples based on relative distance knowledge. Specifically, we provide adversarial guidance for the positive sample, restricting the distance between the positive sample and the original sample less than but as close as possible to the distance between the original sample and the farthest negative sample. Then, we utilize the entropy constraint to regulate the relative distance relationship between the negative and original samples. Finally, the guided positive and negative samples are employed for contrastive learning in leukocyte classification. The extensive experiments, including linear evaluation, domain transfer, and fine-tuning, demonstrate the effectiveness of the proposed method. Our ReCLR achieves accuracies of 92.07%, 65.36%, and 92.49% on three real-world leukocyte datasets, respectively, outperforming several state-of-the-art methods. The source code is released at https://github.com/AlchemyEmperor/ReCLR.

Determination of antioxidant capacity and phenolic content of haskap berries (Lonicera caerulea L.) by attenuated total reflectance-Fourier transformed-infrared spectroscopy

The total phenolic content (TPC) and antioxidant capacity (TAC) of haskap berries cultivated in various locations across Alberta were analyzed using attenuated total reflectance-Fourier transform infrared (ATR-FTIR) spectroscopy. The Folin–Ciocalteu assay was used to determine TPC, while TAC was quantified by 2,2-diphenyl-1-picrylhydrazl radicals (DPPH) assay and oxygen radical absorbance capacity (ORAC) assay. Three tenfold cross-validated partial least-squares regression (PLSR) models and three fivefold cross-validated deep learning models were developed separately based on FT-IR spectra collected from 22 haskap berry samples and their corresponding reference values determined through Folin-Ciocalteu, DPPH, and ORAC assays. The deep learning models (R2 = 0.95, 0.93, and 0.90 for Folin-Ciocalteu, DPPH, and ORAC assays, respectively) demonstrated better prediction capability compared to the PLSR models (R2 = 0.74, 0.72, and 0.66 for Folin-Ciocalteu, DPPH, and ORAC assays, respectively). In addition, PLS loading plots indicated that phenolic contents and polysaccharides in haskap berries could contribute to their antioxidant capacity. Using ATR-FTIR to estimate the TPC and TAC of fruits offers a rapid alternative to the conventional chemical assays.