Tissue Distribution Research Articles

Determination of doxorubicin in plasma and tissues of mice by UPLC-MS/MS and its application to pharmacokinetic study

A rapid and sensitive ultra-high performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS) method was established for the simultaneous determination of doxorubicin (DOX) in mouse plasma and tissues, including the heart, liver, spleen, lung, kidney and tumor, and to investigate the pharmacokinetics and distribution in mice. In this study, daunorubicin (DNR) was used as an internal standard, and the mobile phase consisted of ammonium formate 2 mM containing 0.1 % formic acid (A) and acetonitrile (B), the chromatographic column was ACQUITY UPLC BEHTM C18 with a gradient elution at a flow rate of 0.2 mL/min. Electrospray ionization (ESI) in positive ion pattern was utilized for the ion separation of DOX, with the ions used for quantitative analysis being DOX m/z 544.28 → 397.10 and DNR m/z 528.35 → 321.08, respectively. The results showed that a good linear relationship in the calibration curve range of 1–800 ng/mL in mouse plasma and 1–2500 ng/g in tissues (R2 > 0.99) with the limits of quantification of 1 ng/mL in plasma and tissues. The method exhibited good matrix effect and extraction recovery, with the intra-day and inter-day precision of plasma and tissue were less than 10.3 % and 15.4 %, and the relative error (RE) were both less than ±14.8 % and ±18.9 %, respectively. The stability results under different conditions were found to be accurate. It also revealed the distribution of DOX in various tissues of mice, with the concentration ranking as liver > heart > kidney > spleen > lung > tumor. This method was successfully used to the study for the pharmacokinetics in plasma and drug distribution in tissues of BALB/c mice.

First-in-human evaluation of 6-bromo-7-[11C]methylpurine, a PET tracer for assessing the function of multidrug resistance-associated proteins in different tissues.

Multidrug resistance-associated protein 1 (MRP1) is a transport protein with a widespread tissue distribution, which has been implicated in the pathophysiology of Alzheimer's and chronic respiratory disease. PET with 6-bromo-7-[11C]methylpurine ([11C]BMP) has been used to measure MRP1 function in rodents. In this study, [11C]BMP was for the first time characterised in humans to assess the function of MRP1 and other MRP subtypes in different tissues. Thirteen healthy volunteers (7 men, 6 women) underwent dynamic whole-body PET scans on a long axial field-of-view (LAFOV) PET/CT system after intravenous injection of [11C]BMP. Three subjects of each sex were scanned a second time to assess reproducibility. Volumes of interest were outlined for MRP-expressing tissues (cerebral cortex, cerebellum, choroid plexus, retina, lungs, myocardium, kidneys, and liver). From the time-activity curves, the elimination rate constant (kE, h- 1) was derived as a parameter for tissue MRP function and its test-retest variability (TRTV, %) was calculated. Radiation dosimetry was calculated using the Medical Internal Radiation Dose (MIRD) methodology. Mean kE and corresponding TRTV values were: cerebral cortex: 0.055 ± 0.010h- 1 (- 4 ± 24%), cerebellum: 0.033 ± 0.009h- 1 (1 ± 39%), choroid plexus: 0.292 ± 0.059h- 1 (0.1 ± 16%), retina: 0.234 ± 0.045h- 1 (30 ± 38%), lungs: 0.875 ± 0.095h- 1 (- 3 ± 11%), myocardium: 0.641 ± 0.105h- 1 (11 ± 25%), kidneys: 1.378 ± 0.266h- 1 (14 ± 16%), and liver: 0.685 ± 0.072h- 1 (7 ± 9%). Significant sex differences were found for kE in the cerebellum, lungs and kidneys. Effective dose was 4.67 ± 0.18 µSv/MBq for men and 4.55 ± 0.18 µSv/MBq for women. LAFOV PET/CT with [11C]BMP potentially allows for simultaneous assessment of MRP function in multiple human tissues. Mean TRTV of kE in different tissues was in an acceptable range, except for the retina. The radiation dosimetry of [11C]BMP was in the typical range of 11C-tracers. LAFOV PET/CT holds great potential to assess at a whole-body, multi-tissue level molecular targets relevant for drug disposition in humans. EudraCT 2021-006348-29. Registered 15 December 2021.

Spillover of highly pathogenic avian influenza H5N1 virus to dairy cattle.

Highly pathogenic avian influenza (HPAI) H5N1 clade 2.3.4.4b virus has caused the death of millions of domestic birds and thousands of wild birds in the U.S. since January, 20221-4 Throughout this outbreak, spillovers to mammals have been frequently documented5-12. We report spillover of HPAI H5N1 virus in dairy cattle herds across several states in the U.S. The affected cows displayed clinical signs encompassing decreased feed intake, altered fecal consistency, respiratory distress, and decreased milk production with abnormal milk. Infectious virus and viral RNA were consistently detected in milk from affected cows. Viral distribution in tissues via immunohistochemistry and in situ hybridization revealed a distinct tropism of the virus for the epithelial cells lining the alveoli of the mammary gland in cows. Whole viral genome sequences recovered from dairy cows, birds, domestic cats, and a raccoon from affected farms indicated multidirectional interspecies transmissions. Epidemiologic and genomic data revealed efficient cow-to-cow transmission after apparently healthy cows from an affected farm were transported to a premise in a different state. These results demonstrate the transmission of HPAI H5N1 clade 2.3.4.4b virus at a non-traditional interface underscoring the ability of the virus to cross species barriers.

Gene expression and protein localization of Cl− transporters, Slc26a6 and Cftr, in the gill ionocytes of rainbow trout

AbstractEuryhaline fishes acclimate to various osmotic environments by changing the direction of water and ion transport between body fluids and environmental waters. Ionocytes in the gills are one of the most important cells for the active ion transport. This study aimed to identify the molecules responsible for apical Cl− transport in rainbow trout ionocytes. Tissue distribution and time-course changes after seawater transfer were analyzed for mRNA expression of slc26a6, cftr1, and cftr2. slc26a6 was specifically expressed in the freshwater gills and decreased after seawater transfer. Both cftr genes were expressed in the gills and higher in seawater; however, the magnitude of expression increase after seawater transfer was greater in cftr1 than in cftr2. These results suggest that Cftr1 is mainly functioned in hypo-osmoregulation and that Cftr2 may also be involved in ion transport under freshwater conditions, such as acid–base regulation. Slc26a6 was localized at the apical membrane of Nkcc1-negative ionocytes only in freshwater-acclimated trout. Apical Cftr1 localization was also identified in most of ionocytes in seawater-acclimated fish. These results indicate that Slc26a6 in freshwater and Cftr1 in seawater contribute to osmoregulatory Cl− transport across the apical membrane of ionocytes in rainbow trout.

Long-Circulating and Brain-Targeted Liposomes Loaded with Isoliquiritigenin: Formation, Characterization, Pharmacokinetics, and Distribution.

Isoliquiritigenin (ISL) has excellent neuroprotective effects. However, its limitations, including poor solubility, low bioavailability, and low accumulation in the brain, restrict its clinical promotion. In this study, a novel type of ISL-loaded liposome (ISL-LP) modified with the brain-targeting polypeptide angiopep-2 was prepared to improve these properties. The zeta potential, morphology, particle size, encapsulation efficiency, drug loading, and in vitro release of ISL-LP were evaluated. The pharmacokinetics and tissue distribution of ISL and ISL-LP were also investigated. The results demonstrated that ISL-LP had an average particle size of 89.36 ± 5.04 nm, a polymer dispersity index of 0.17 ± 0.03, a zeta potential of -20.27 ± 2.18 mV, and an encapsulation efficiency of 75.04 ± 3.28%. The in vitro release experiments indicate that ISL-LP is a desirable sustained-release system. After intravenous administration, LPC-LP prolonged the circulation time of ISL in vivo and enhanced its relative brain uptake. In conclusion, ISL-LP could serve as a promising brain-targeting system for the treatment and prevention of central nervous system (CNS) disorders.

What matters for drug delivery to tumor by nanoparticles: Gaining insights from PBPK/PD simulation of drug nanocrystals

Background and purpose: In our previous studies, drug nanocrystals were directly prepared by solution crystallization, possessing uniform particle size and morphology suitable for intravenous (IV) injection. These nanocrystals accumulated in a small percentage of their injected dose in tumor-bearing mice but showed similar anti-tumor effectiveness and much-reduced side effects compared with current commercial solubilized and encapsulated delivery systems. Experimental approach: In this study, we aimed to delineate possible controlling factors for the pharmacokinetics (PK) and biodistribution behaviors of paclitaxel (PTX) nanocrystals tested in mice by applying physiologically based pharmacokinetics (PBPK) modeling, coupled with pharmacodynamics (PD) simulation, to the data. Key Results: Our results show that clearance of the drug plays a significant, if not the most important, role in determining tissue distribution, including tumor accumulation of PTX nanocrystals. Surface treatment of drug nanocrystals with polymeric surfactants also appeared to affect PK profiles and PD outcomes. Importantly, when scaled to model human parameters, our PK/PD simulations suggest that drug distribution in humans, as opposed to animal models, was significantly influenced by tissue partitioning rather than drug clearance. This finding could facilitate the design and development of future drug delivery systems. Conclusion: Drug nanocrystals deposited in tissues, including tumors, could therefore act as depots, releasing the drug back into the circulation, possibly contributing to extended treatment, as well as any detrimental effects.

The influence of body fat content and distribution on bone mass in healthy Chinese adults.

Previous studies have reported a close relationship between body mass index (BMI) and bone mineral density (BMD). However, the effects of fat on bone mass remain controversial, particularly for fat tissue distribution. The aim of this study was to evaluate the association between regional fat percentage and BMD using a population-based database. This study included participants who were referred to the Department of Radio Diagnosis for dual-energy X-ray absorptiometry (DEXA) scan from January 2018 to December 2020. The relationships between BMI and regional fat percentage with BMD were assessed using multiple linear regression and generalized additive models. The risk of low bone mass was determined using logistic regression. There was a negative relationship between the regional fat percentage and femoral neck BMD (FN BMD) or lumbar spine BMD (LS BMD) in both genders (p < 0.05). In females, an inverted U-shaped relationship was observed between regional fat percentage and BMD at both the femoral neck and lumbar spine. The impact of trunk fat percentage on LS BMD was associated with the highest OR of low bone mass in females (OR 3.1, 95% CI 2.6 to 3.7, p for trend <0.001), while the impact of abdomen fat percentage on FN BMD was associated with the highest OR of low bone mass in males (OR 2.2, 95% CI 1.8 to 2.7, p for trend <0.001). There was an inverted U-shaped relationship between regional fat percentage and BMD. Excessive regional fat percentage may be harmful to bone health in both genders. To promote bone health, males should restrict their abdomen circumference and avoid abdominal adiposity, while females should control their trunk circumference.

Effect of nitrogen fertilization and shading on morphogenesis, structure and leaf anatomy of Megathyrsus maximus genotypes.

The use of exotic grasses of African origin for pastures in Brazil has been a major advancement in livestock production, but little is known about the responses of these grasses to nitrogen fertilizers associated with shading. In this study, the morphogenetic, structural, and leaf anatomical characteristics of Megathyrsus maximus cultivars' Tamani and Quênia were investigated as a function of N dose and shade. Morphogenetic and structural characteristics and leaf anatomy were studied under three shading levels (0, 30, and 50 %) and four N doses (0, 100, 200, and 300 kg N ha-1) to simulate growth in a silvopastoral system. When comparing the cultivars, Quênia was more efficient in terms of phyllochron up to fertilization with 100 kg N ha-1. The leaf senescence rate of Tamani was higher than that of Quênia at the 30 and 50 % shade levels. The total area (TA) occupied by leaf tissues decreased in Quênia as a function of the increase in N fertilization, whereas the TA of Tamani did not change. The thickness of the adaxial epidermis was greater in Quênia (0.68 µm) than in Tamani (0.50 µm) when not fertilized. The area occupied by the mesophyll was greater in both cultivars when they received fertilization equivalent to 300 kg N ha-1. Quênia grass has a smaller phyllochron than Tamani grass, due to the rapid reconstruction of its photosynthetic apparatus, especially when it receives higher levels of nitrogen fertilization. However, Tamani grass has a greater distribution of plant tissues. The mesophyll area is larger in Tamani grass due to the greater presence of chloroplasts, which facilitates digestion by animals. The Tamani modified the leaf anatomical tissues more significantly in relation to shading, whereas the Quênia modified them in relation to N fertilization, which reinforces the suggestion of a more appropriate use of Tamani in silvopastoral systems.

Assessment of the Ferroptosis Regulators: Glutathione Peroxidase 4, Acyl-Coenzyme A Synthetase Long-Chain Family Member 4, and Transferrin Receptor 1 in Patient-Derived Endometriosis Tissue.

Ferroptosis, an iron-dependent form of non-apoptotic cell death, plays a pivotal role in various diseases and is gaining considerable attention in the realm of endometriosis. Considering the classical pathomechanism theories, we hypothesized that ferroptosis, potentially driven by increased iron content at ectopic sites, may contribute to the progression of endometriosis. This retrospective case-control study provides a comprehensive immunohistochemical assessment of the expression and tissue distribution of established ferroptosis markers: GPX4, ACSL4, and TfR1 in endometriosis patients. The case group consisted of 38 women with laparoscopically and histologically confirmed endometriosis and the control group consisted of 18 women with other gynecological conditions. Our study revealed a significant downregulation of GPX4 in stromal cells of endometriosis patients (M = 59.7% ± 42.4 versus 90.0% ± 17.5 in the control group, t (54) = -2.90, p = 0.005). This finding aligned with slightly, but not significantly, higher iron levels detected in the blood of endometriosis patients, using hemoglobin as an indirect predictor (Hb 12.8 (12.2-13.5) g/dL versus 12.5 (12.2-13.4) g/dL in the control group; t (54) = -0.897, p = 0.374). Interestingly, there was no concurrent upregulation of TfR1 (M = 0.7 ± 1.2 versus 0.2 ± 0.4 for EM, t (54) = 2.552, p = 0.014), responsible for iron uptake into cells. Our empirical findings provide support for the involvement of ferroptosis in the context of endometriosis. However, variances in expression patterns within stromal and epithelial cellular subsets call for further in-depth investigations.

Preparation, characterization, and liver targeting evaluation of a novel sustained-release brucine self-assembled micelle mediated by glycyrrhetinic acid.

Background: Cancer is a serious threat to human life, health and social development. In recent years, nanomicelles, as an emerging drug carrier material, have gradually entered people's field of vision because of their advantages of improving bioavailability, maintaining drug levels, reducing systemic side effects and increasing drug accumulation at target sites. Methods: In this study, B-GPSG nano-micelles were prepared by film dispersion hydration method using brucine as model drug and glycyrrhetinic acid-polyethylene glycol-3-methylene glycol-dithiodipropionic acid-glycerol monostearate polymer as nano-carrier. The preparation process, characterization, drug release in vitro, pharmacokinetics and liver targeting were investigated. Results: The results showed that the range of particle size, polydispersion index and Zeta potential were 102.7 ± 1.09nm, 0.201 ± 0.02 and -24.5 ± 0.19mV respectively. The entrapment efficiency and drug loading were 83.79 ± 2.13% and 12.56 ± 0.09%, respectively. The drug release experiments in vitro and pharmacokinetic experiments showed that it had obvious sustained release effect. For pharmacokinetics study, it shows that both the B-GPSG solution group and the B-PSG solution group changed the metabolic kinetic parameters of brucine, but the B-GPSG solution group had a better effect. Compared with the B-PSG solution group, the drug was more prolonged in rats. The half-life in the body and the retention time in the body of B-GPSG are more helpful to improve the bioavailability of the drug and play a long-term effect. The tail vein injection results of mice indicate that B-GPSG can target and accumulate brucine in the liver without affecting other key organs. Cell uptake experiments and tissue distribution experiments in vivo show that glycyrrhetinic acid modified nano-micelles can increase the accumulation of brucine in hepatocytes, has a good liver targeting effect, and can be used as a new preparation for the treatment of liver cancer. Conclusion: The B-SPSG prepared in this experiment can provide a new treatment method and research idea for the treatment of liver cancer.

Detection and genetic characterization of chicken astrovirus and avian nephritis virus from hatchery to farm

ABSTRACT Astroviruses are an emerging hazard in hatchery management, and they are responsible for great economic losses in poultry farms worldwide. Chicken astrovirus (CAstV) and avian nephritis virus (ANV) are involved in decreased hatching rate, mainly due to embryo deaths, and pale and runted chicks too weak to hatch. Hatchery diseases occur through direct egg infection or vertical transmission. However, the specific role of astroviruses in these diseases is still largely unknown. To elucidate this a high-quality Piedmont hatchery (Italy) was selected based on farm clinical signs and the astrovirus serological positivity in the breeder farm. The viral dynamics were followed from the hatchery to the farm. The presence of both CAstV and ANV was monitored by evaluating the viral load in environmental and bird samples. Interestingly, both viruses were detected in chick yolk sacs at 18 days of incubation, and in the gut contents of 1-day chicks, whereas in the hatchery environmental samples, the eggs' external surfaces and the embryos’ intestinal contents were negative. The CAstV copy number was higher in bird tissues from the hatchery, while a greater ANV load was detected in bird tissues from the farm. Moreover, our data suggest vertical transmission of both viruses. Frequent co-infection was also observed in samples from both the hatchery and the farm. Lastly, the first Italian full-length genome and molecular characterization of ANV was obtained. RESEARCH HIGHLIGHTS Identified the role of the hatchery in astrovirus transmission. Sequenced the avian nephritis virus complete genome. Investigated tissue distribution of astrovirus from egg to chicks. Demonstrated co-infection of ANV/CAstV.

Tissue distribution and exposure risk assessment of dioxins, dioxin-like polychlorinated biphenyls and perfluoroalkyl substances in red swamp crayfish

Significant attention has been paid to the adverse effects of dioxins, dioxin-like polychlorobiphenyls (DL-PCBs) and per-and polyfluoroalkyl substances (PFAS) in environment and food on ecosystem and human health. However, limited information exists regarding the occurrence, tissue distribution and exposure risk of these pollutants in crayfish. This study investigated tissue-specific distribution characteristics, influence factors and exposure risk of dioxins, DL-PCBs and PFAS in crayfish. Dioxins, DL-PCBs, and PFAS were detected in crayfish samples, with concentrations ranging from 0.361 to 1.91 pg TEQ g−1 for sum dioxins and DL-PCBs, and 1.54–21.2 ng g−1 for sum PFAS. The highest concentrations of dioxins, DL-PCBs TEQ and total PFAS were found in crayfish viscera and accounting for over 69% of the relative body burden (RBBs) of these pollutants. The specific-tissue distribution of these pollutants linked to tissue fat and protein content and log Kow and molecular weights of homologues. The consumption of crayfish edible tissue posed no health risks from exposure to dioxins and DL-PCBs as well as sum 4 PFAS in adults. However, consumption of crayfish viscera significantly increased exposure risk. This study can provide valuable insights into the tissue-specific distribution and human exposure risks associated with dioxins, DL-PCBs and PFAS in crayfish.

Vasorin-deficient mice display disturbed vitamin D and mineral homeostasis in combination with a low bone mass phenotype

Vasorin (Vasn) is a pleiotropic molecule involved in various physiological and pathological conditions, including cancer. Vasn has also been detected in bone cells of developing skeletal tissues but no function for Vasn in bone metabolism has been implicated yet. Therefore, this study aimed to investigate if Vasn plays a significant role in bone biology. First, we investigated tissue distribution of Vasn expression, using lacZ knock-in reporter mice. We detected clear Vasn expression in skeletal elements of postnatal mice. In particular, osteocytes and bone forming osteoblasts showed high expression of Vasn, while the bone marrow was devoid of signal. Vasn knockout mice (Vasn−/−) displayed postnatal growth retardation and died after four weeks. MicroCT analysis of femurs from 22- to 25-day-old Vasn−/−mice demonstrated reduced trabecular and cortical bone volume corresponding to a low bone mass phenotype. Ex vivo bone marrow cultures demonstrated that osteoclast differentiation and activity were not affected by Vasn deficiency. However, osteogenesis of Vasn−/− bone marrow cultures was disturbed, resulting in lower numbers of alkaline phosphate positive colonies, impaired mineralization and lower expression of osteoblast marker genes. In addition to the bone phenotype, these mice developed a vitamin D3-related phenotype with a strongly reduced circulating 25-hydroxyvitamin D3 and 1,25-dihydroxyvitamin D3 and urinary loss of vitamin D binding protein. In conclusion, Vasn-deficient mice suffer from severe disturbances in bone metabolism and mineral homeostasis.

Calixarene‐Guest Complexes: The Next Innovation in Delivery of Drugs and Biologics

AbstractCalixarenes are third generation of macrocyclic molecules with excellent biocompatibility currently being researched extensively for their diverse potential as therapeutic candidates and for delivery of drugs and biologics. This review discusses the unique structural features which allow them to selectively bind to a wide variety of guest molecules within their hydrophobic cavity, as well as complex with other molecules on their upper and lower rims to enable their application for encapsulation of drugs for targeted and controlled release, molecular carriers for antigens and nucleic acids, and as biomedical sensors. The calixarenes’ unique host–guest chemistry enables encapsulation of lipophilic drugs in the latter's cavity, while the head groups and side chains on the upper and lower rim can be functionalized readily with various targeting moieties as peptides and biological ligands which specifically recognize and bind to cancer cells via surface receptors. The design of calixarene constructs help incorporation of multiple functionalities into a single platform. This active targeting approach enhances the accumulation of the drug at the tumor site while reducing its distribution in healthy tissues, thereby minimizing side effects. Ongoing research in exploration and optimization of calixarenes for application as targeted drug and gene delivery agents has been discussed.

The Comparison of the Clinical Efficacy and Drug Tissue Distribution of Furazolidone and Tetracycline-quadruple Therapy in Helicobacter pylori Eradication: A Randomized Controlled Trial.

Helicobacter pylori (H. Pylori) is considered a main causative organism of gastric ulcers, gastric cancer and duodenal ulcers. The current treatment relies on a combination of antimicrobial agents and acid suppressant agents, but the eradication effect is not satisfactory. To clarify the concentration of antibiotics at the lesion site, we investigate the clinical efficacy and drug tissue distribution of the combination therapy of furazolidone and tetracycline in eradicating H. Pylori. Patients with H. pylori infection (n = 60) were randomized to either group A or B. Bismuth potassium citrate capsules 220mg, omeprazole enteric-coated capsules 20mg, amoxicillin capsules 1000mg, each twice per day, and furazolidone tablets 500mg were administered to group A. Group B was treated with bismuth potassium citrate capsules 220mg, omeprazole enteric-coated capsules 20mg, amoxicillin capsules 1000mg, and tetracycline tablets 500mg each twice per day for 2 weeks. The serum and gastric juice, gastric antrum, gastric horn, and gastric body samples were taken under a gastroscope on the 14th day. The antimicrobial concentrations in serum and tissue samples were determined by high-performance liquid chromatography. In the negative group of furazolidone, the concentrations of gastric antrum, gastric body, and gastric angle were significantly higher than those in the positive group (P = 0.017, 0.015, and 0.028). The concentrations of furazolidone in gastric fluid, gastric antrum, gastric angle, and gastric body were ∼421 times, 82 times, 17 times, and 51 times higher than those in serum, respectively. The concentrations of tetracycline in the serum and gastric angle of the tetracycline negative group were significantly higher than those in the positive group (P = 0.036 and 0.042), and the tetracycline concentrations in the gastric horn and gastric body were about 4 and 6 times higher than those in the serum, respectively. The concentration of amoxicillin in group B was higher than that in group A, especially in serum, gastric juice, gastric angle, and gastric body (P < 0.05). Furazolidone is mainly concentrated and sequentially distributed in gastric juice, gastric antrum, and gastric body tissue, and tetracycline is mainly distributed in serum, gastric angle, and gastric body, whereas amoxicillin is mainly distributed in serum, gastric juice, gastric angle, and gastric body. Improving the concentration and tissue distribution of antibacterial drugs in the human gastric mucosa is the key to ensuring the ideal eradication rate of quadruple therapy.

Unraveling Spatial Domain Characterization in Spatially Resolved Transcriptomics with Robust Graph Contrastive Clustering.

Spatial transcriptomics can quantify gene expression and its spatial distribution in tissues, thus revealing molecular mechanisms of cellular interactions underlying tissue heterogeneity, tissue regeneration, and spatially localized disease mechanisms. However, existing spatial clustering methods often fail to exploit the full potential of spatial information, resulting in inaccurate identification of spatial domains. In this paper, we develop a deep graph contrastive clustering framework, stDGCC, that accurately uncovers underlying spatial domains via explicitly modeling spatial information and gene expression profiles from spatial transcriptomics data. The stDGCC framework proposes a spatially informed graph node embedding model to preserve the topological information of spots and to learn the informative and discriminative characterization of spatial transcriptomics data through self-supervised contrastive learning. By simultaneously optimizing the contrastive learning loss, reconstruction loss, and Kullback-Leibler (KL) divergence loss, stDGCC achieves joint optimization of feature learning and topology structure preservation in an end-to-end manner. We validate the effectiveness of stDGCC on various spatial transcriptomics datasets acquired from different platforms, each with varying spatial resolutions. Our extensive experiments demonstrate the superiority of stDGCC over various state-of-the-art clustering methods in accurately identifying cellular-level biological structures. Code and data are available from https://github.com/TimE9527/stDGCC and https://figshare.com/projects/stDGCC/186525. Supplementary data are available at Bioinformatics online.

Network pharmacology and molecular dynamics study of the effect of the Astragalus-Coptis drug pair on diabetic kidney disease.

Diabetic kidney disease (DKD) is the primary cause of end-stage renal disease. The Astragalus-Coptis drug pair is frequently employed in the management of DKD. However, the precise molecular mechanism underlying its therapeutic effect remains elusive. To investigate the synergistic effects of multiple active ingredients in the Astragalus-Coptis drug pair on DKD through multiple targets and pathways. The ingredients of the Astragalus-Coptis drug pair were collected and screened using the TCMSP database and the SwissADME platform. The targets were predicted using the SwissTargetPrediction database, while the DKD differential gene expression analysis was obtained from the Gene Expression Omnibus database. DKD targets were acquired from the GeneCards, Online Mendelian Inheritance in Man database, and DisGeNET databases, with common targets identified through the Venny platform. The protein-protein interaction network and the "disease-active ingredient-target" network of the common targets were constructed utilizing the STRING database and Cytoscape software, followed by the analysis of the interaction relationships and further screening of key targets and core active ingredients. Gene Ontology (GO) function and Kyoto Ency-clopedia of Genes and Genomes (KEGG) pathway enrichments were performed using the DAVID database. The tissue and organ distributions of key targets were evaluated. PyMOL and AutoDock software validate the molecular docking between the core ingredients and key targets. Finally, molecular dynamics (MD) simulations were conducted to simulate the optimal complex formed by interactions between core ingredients and key target proteins. A total of 27 active ingredients and 512 potential targets of the Astragalus-Coptis drug pair were identified. There were 273 common targets between DKD and the Astragalus-Coptis drug pair. Through protein-protein interaction network topology analysis, we identified 9 core active ingredients and 10 key targets. GO and KEGG pathway enrichment analyses revealed that Astragalus-Coptis drug pair treatment for DKD involves various biological processes, including protein phosphorylation, negative regulation of apoptosis, inflammatory response, and endoplasmic reticulum unfolded protein response. These pathways are mainly associated with the advanced glycation end products (AGE)-receptor for AGE products signaling pathway in diabetic complications, as well as the Lipid and atherosclerosis. Molecular docking and MD simulations demonstrated high affinity and stability between the core active ingredients and key targets. Notably, the quercetin-AKT serine/threonine kinase 1 (AKT1) and quercetin-tumor necrosis factor (TNF) protein complexes exhibited exceptional stability. This study demonstrated that DKD treatment with the Astragalus-Coptis drug pair involves multiple ingredients, targets, and signaling pathways. We propose a novel approach for investigating the molecular mechanism underlying the therapeutic effects of the Astragalus-Coptis drug pair on DKD. Furthermore, we suggest that quercetin is the most potent active ingredient and specifically targets AKT1 and TNF, providing a theoretical foundation for further exploration of pharmacologically active ingredients and elucidating their molecular mechanisms in DKD treatment.

The challenges of assessing adiposity in a clinical setting.

To tackle the burden of obesity-induced cardiometabolic disease, the scientific community relies on accurate and reproducible adiposity measurements in the clinic. These measurements guide our understanding of underlying biological mechanisms and clinical outcomes of human trials. However, measuring adiposity and adipose tissue distribution in a clinical setting can be challenging, and different measurement methods pose important limitations. BMI is a simple and high-throughput measurement, but it is associated relatively poorly with clinical outcomes when compared with waist-to-hip and sagittal abdominal diameter measurements. Body composition measurements by dual energy X-ray absorptiometry or MRI scans would be ideal due to their high accuracy, but are not high-throughput. Another important consideration is that adiposity measurements vary between men and women, between adults and children, and between people of different ethnic backgrounds. In this Perspective article, we discuss how these critical challenges can affect our interpretation of research data in the field of obesity and the design and implementation of clinical guidelines.

In silico identification and functional study of long non-coding RNA involved in acute hepatopancreatic necrosis disease caused by Vibrio parahaemolyticus infection in white shrimp, Litopenaeus vannamei

Acute hepatopancreatic necrosis disease (AHPND) caused by toxin-producing Vibrio parahaemolyticus (VpAHPND) has severely affected shrimp production. Long non-coding RNA (lncRNA), a regulatory non-coding RNA, which can play important function in shrimp disease responses. This study aimed to identify and investigate the role of lncRNA involved in VpAHPND infection in Pacific white shrimp, Litopenaeus vannamei. From a total of 368,736 de novo assembled transcripts, 67,559 were identified as putative lncRNAs, and only 72 putative lncRNAs showed differential expression between VpAHPND-infected and normal shrimp. The six candidate lncRNAs were validated for their expression profiles during VpAHPND infection and tissue distribution using RT-qPCR. The role of lnc2088 in response to VpAHPND infection was investigated through RNA interference. The result indicated that the suppression of lnc2088 expression led to an increase in shrimp mortality after VpAHPND infection. To explore the set of genes involved in lnc2088 knockdown, RNA sequencing was performed. A total of 275 differentially expressed transcripts were identified in the hepatopancreas of lnc2088 knockdown shrimp. The expression profiles of five candidate metabolic and immune-related genes were validated in lnc2088 knockdown and VpAHPND-infected shrimp. The result showed that the expression of ChiNAG was significantly increased, while that of NCBP1, WIPF2, and NFKB1 was significantly downregulated in ds2088-injected shrimp. Additionally, the expression of NFKB1, NCBP1 and WIPF2 was significantly increased, whereas that of ChiNAG and CUL5 were significantly decreased after infection with VpAHPND. Our work identified putative lncRNA profiles in L. vannamei in response to VpAHPND infection and investigated the role of lncRNA in shrimp immunity.

Sensitive quantification of mevalonate pathway intermediates and prediction of relative novel analogs by chemical derivatization-based LC-MS/MS

The mevalonate (MVA) pathway plays a crucial role in the occurrence and progression of various diseases, such as osteoporosis, breast cancer, and lung cancer, etc. However, determining all the MVA pathway intermediates is still challenging due to their high polarity, low concentration, chelation effect with metal compartments, and poor mass spectrometric response. In this study, we established a liquid chromatography-tandem mass spectrometry (LC-MS/MS) method coupled with N2, N2, N4, N4-tetramethyl-6-(4-(piperazin-1-ylsulfonyl) phenyl)-1,3,5-triazine-2,4-diamine (Tmt-PP) labeling for the simultaneous analysis of all MVA intermediates in biospecimens. Chemical derivatization significantly improved the chromatographic retention, peak shape, and detection sensitivity of the analytes. Moreover, we employed a method named mass spectrum calculation to achieve the absolute quantification of the isomers, i.e., isopentenyl pyrophosphate (IPP) and dimethylallyl pyrophosphate (DMAPP). The established method was fully qualified and applied to explore the difference of these metabolites in cisplatin-resistant non-small cell lung cancer (NSCLC) cells. Additionally, several MVA intermediate analogs, including isopentenyl monophosphate or dimethylallyl monophosphate (IMP/DMAMP), geranyl monophosphate (GMP), 5-triphosphomevalonate (MTP), and isopentenyl triphosphate or dimethylallyl triphosphate (ITP/DMATP), were identified for the first time using a knowledge-driven prediction strategy. We further explored the tissue distribution of these novel metabolites. Overall, this work developed a sensitive quantification method for all MVA intermediates, which will enhance our understanding of the role of this pathway in various health and disease conditions. The novel metabolites we discovered warrant further investigations into their biosynthesis and biological functions.