Copper homeostasis in chronic kidney disease and its crosstalk with ferroptosis.

Chronic kidney disease (CKD) has become a global public health problem with high morbidity and mortality. Renal fibrosis can lead to end-stage renal disease (ESRD). However, there is still no effective treatment to prevent or delay the progression of CKD into ESRD. Therefore, exploring the pathogenesis of CKD is essential for preventing and treating CKD. There are a variety of trace elements in the human body that interact with each other within a complex regulatory network. Iron and copper are both vital trace elements in the body. They are critical for maintaining bodily functions, and the dysregulation of their metabolism can cause many diseases, including kidney disease. Ferroptosis is a new form of cell death characterized by iron accumulation and lipid peroxidation. Studies have shown that ferroptosis is closely related to kidney disease. However, the role of abnormal copper metabolism in kidney disease and its relationship with ferroptosis remains unclear. Here, our current knowledge regarding copper metabolism, its regulatory mechanism, and the role of abnormal copper metabolism in kidney diseases is summarized. In addition, we discuss the relationship between abnormal copper metabolism and ferroptosis to explore the possible pathogenesis and provide a potential therapeutic target for CKD.

Stimulation of lipopolysaccharide from Pseudomonas aeruginosa following H9N2 IAV infection exacerbates inflammatory responses of alveolar macrophages and decreases virus replication.

H9N2 IAV infection contributed to P. aeruginosa coinfection, causing severe hemorrhagic pneumonia in mink. In this study, the in vitro alveolar macrophage models were developed to investigate the innate immune responses to P. aeruginosa LPS stimulation following H9N2 IAV infection, using MH-S cells. The cytokine levels, apoptosis levels and the viral nucleic acid levels were detected and analyzed. As a result, the levels of IFN-α, IL-1ß, TNF-α, and IL-10 in MH-S cells with P. aeruginosa LPS stimulation following H9N2 IAV infection were significantly higher than those in MH-S cells with single H9N2 IAV infection and single LPS stimulation (P < 0.05), exacerbating inflammatory responses. LPS stimulation aggravated the apoptosis of MH-S cells with H9N2 IAV infection. Interestingly, LPS stimulation influences H9N2 IAV replication and indirectly reduced H9N2 IAV replications in in vitro AMs. It implied that LPS should play an important role in the pathogenesis of H9N2 IAV and P. aeruginosa coinfection.

TBK1-medicated DRP1 phosphorylation orchestrates mitochondrial dynamics and autophagy activation in osteoarthritis.

Mitochondrial dynamics, including mitochondrial fission and fusion, are critical for maintaining mitochondrial functions. Evidence shows that TANK-binding kinase 1 (TBK1) regulates mitochondrial fusion and fission and then mitophagy. Since a previous study demonstrates a strong correlation between mitophagy and osteoarthritis (OA), we herein investigated the potential role of TBK1 in OA process and mitochondrial functions. We demonstrated a strong correlation between TBK1 and OA, evidenced by significantly downregulated expression of TBK1 in cartilage tissue samples of OA patients and in the chondrocytes of aged mice, as well as TNF-α-stimulated phosphorylation of TBK1 in primary mouse chondrocytes. TBK1 overexpression significantly attenuated TNF-α-induced apoptosis and abnormal mitochondrial function in primary mouse chondrocytes. Furthermore, TBK1 overexpression induced remodeling of mitochondrial morphology by directly phosphorylating dynamin-related protein 1 (DRP1) at Ser637, abolishing the fission of DRP1 and preventing its fragmentation function. Moreover, TBK1 recruitment and DRP1 phosphorylation at Ser637 was necessary for engulfing damaged mitochondria by autophagosomal membranes during mitophagy. Moreover, we demonstrated that APMK/ULK1 signaling contributed to TBK1 activation. In OA mouse models established by surgical destabilization of the medial meniscus, intraarticular injection of lentivirus-TBK1 significantly ameliorated cartilage degradation via regulation of autophagy and alleviation of cell apoptosis. In conclusion, our results suggest that the TBK1/DRP1 pathway is involved in OA and pharmacological targeting of the TBK1-DRP1 cascade provides prospective therapeutic benefits for the treatment of OA.

Peri-treatment adverse events of primary mediastinal non-seminomatous germ cell tumors.

Primary mediastinal non-seminomatous germ cell tumors (PMNSGCT) are rare but life-threatening thoracic cancers. We report our experience from eight patients with peri-treatment adverse events. By analyzing changes in tumor extent, serum tumor markers, and pathologies between diagnosis and transfer, those events could be attributed to postbiopsy respiratory insufficiency, growing teratoma syndrome, secondary histiocytic malignancy, and PMNSGCT progression. Subjecting patients to respiratory therapy, conventional or high-dose chemotherapy, and surgery controlled the disease, with five of the eight patients surviving disease free. These outcomes indicate that integrated appropriate and timely approaches are important in tackling peri-treatment adverse events.

Non-numerical strategies used by bees to solve numerical cognition tasks.

We examined how bees solve a visual discrimination task with stimuli commonly used in numerical cognition studies. Bees performed well on the task, but additional tests showed that they had learned continuous (non-numerical) cues. A network model using biologically plausible visual feature filtering and a simple associative rule was capable of learning the task using only continuous cues inherent in the training stimuli, with no numerical processing. This model was also able to reproduce behaviours that have been considered in other studies indicative of numerical cognition. Our results support the idea that a sense of magnitude may be more primitive and basic than a sense of number. Our findings highlight how problematic inadvertent continuous cues can be for studies of numerical cognition. This remains a deep issue within the field that requires increased vigilance and cleverness from the experimenter. We suggest ways of better assessing numerical cognition in non-speaking animals, including assessing the use of all alternative cues in one test, using cross-modal cues, analysing behavioural responses to detect underlying strategies, and finding the neural substrate.

GREMA: modelling of emulated gene regulatory networks with confidence levels based on evolutionary intelligence to cope with the underdetermined problem.

MOTIVATION: Non-linear ordinary differential equation (ODE) models that contain numerous parameters are suitable for inferring an emulated gene regulatory network (eGRN). However, the number of experimental measurements is usually far smaller than the number of parameters of the eGRN model that leads to an underdetermined problem. There is no unique solution to the inference problem for an eGRN using insufficient measurements. RESULTS: This work proposes an evolutionary modelling algorithm (EMA) that is based on evolutionary intelligence to cope with the underdetermined problem. EMA uses an intelligent genetic algorithm to solve the large-scale parameter optimization problem. An EMA-based method, GREMA, infers a novel type of gene regulatory network with confidence levels for every inferred regulation. The higher the confidence level is, the more accurate the inferred regulation is. GREMA gradually determines the regulations of an eGRN with confidence levels in descending order using either an S-system or a Hill function-based ODE model. The experimental results showed that the regulations with high-confidence levels are more accurate and robust than regulations with low-confidence levels. Evolutionary intelligence enhanced the mean accuracy of GREMA by 19.2% when using the S-system model with benchmark datasets. An increase in the number of experimental measurements may increase the mean confidence level of the inferred regulations. GREMA performed well compared with existing methods that have been previously applied to the same S-system, DREAM4 challenge and SOS DNA repair benchmark datasets. AVAILABILITY AND IMPLEMENTATION: All of the datasets that were used and the GREMA-based tool are freely available at https://nctuiclab.github.io/GREMA. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Clinical, genetic, and structural basis of congenital adrenal hyperplasia due to 11ß-hydroxylase deficiency.

Congenital adrenal hyperplasia (CAH), resulting from mutations in CYP11B1, a gene encoding 11ß-hydroxylase, represents a rare autosomal recessive Mendelian disorder of aberrant sex steroid production. Unlike CAH caused by 21-hydroxylase deficiency, the disease is far more common in the Middle East and North Africa, where consanguinity is common often resulting in identical mutations. Clinically, affected female newborns are profoundly virilized (Prader score of 4/5), and both genders display significantly advanced bone ages and are oftentimes hypertensive. We find that 11-deoxycortisol, not frequently measured, is the most robust biochemical marker for diagnosing 11ß-hydroxylase deficiency. Finally, computational modeling of 25 missense mutations of CYP11B1 revealed that specific modifications in the heme-binding (R374W and R448C) or substrate-binding (W116C) site of 11ß-hydroxylase, or alterations in its stability (L299P and G267S), may predict severe disease. Thus, we report clinical, genetic, hormonal, and structural effects of CYP11B1 gene mutations in the largest international cohort of 108 patients with steroid 11ß-hydroxylase deficiency CAH.

Mechanisms of fibronectin-binding protein A (FnBPA110-263) vaccine efficacy in Staphylococcus aureus sepsis versus skin infection.

Increasing rates of life-threatening infections and decreasing susceptibility to antibiotics urge an effective vaccine targeting Staphylococcus aureus. Here we investigate the role of cellular immunity in FnBPA110-263 mediated protection in Staphylococcus aureus infection. This study revealed FnBPA110-263 broadly protected mice from seven FnBPA isotypes strains in the sepsis model. FnBPA110-263 immunized B-cell deficient mice were protected against lethal challenge, while T-cell deficient mice were not. Reconstituting mice with FnBPA110-263 specific CD4+ T-cells conferred antigen specific protection. In vitro assays indicated that isolated FnBPA110-263 specific splenocytes from immunized mice produced abundant IL-17A. IL-17A deficient mice were not protected from a lethal challenge by FnBPA110-263 vaccination. Moreover, neutralizing IL-17A, but not IFN-γ,reverses FnBPA110-263-induced protective efficacy in sepsis and skin infection model. These findings suggest that IL-17A producing Th17 cells play an essential role in FnBPA110-263 vaccine-mediated defense against S. aureus sepsis and skin infection in mice.

Highly Enantioselective Kinetic Resolution of Michael Adducts through N-Heterocyclic Carbene Catalysis: An Efficient Asymmetric Route to Cyclohexenes.

A highly efficient strategy for the kinetic resolution of Michael adducts was realized using a chiral N-heterocyclic carbene catalyst. The kinetic resolution provides a new convenient route to single diastereomers of cyclohexenes and Michael adducts in good yields with high enantiomeric excesses (up to 99 % ee with a selectivity factor of up to 458). This "two flies with one swat" concept allows the synthesis of these two synthetically valuable compound classes at the same time by a single transformation.

Ultrasound-Assisted Extraction of Polysaccharides from Volvariella volvacea: Process Optimization and Structural Characterization.

The aims of the present study were to optimize the operational parameters to maximize the yield of ultrasound-assisted polysaccharide extraction from Volvariella volvacea (straw mushroom) fruiting bodies by using for the first time one-factor-at-a-time and three-level Box-Behnken factorial designs. A maximum polysaccharide yield of 8.28 ± 0.23% was obtained under the optimized conditions of ultrasound power of 175 W, extraction temperature of 57 °C, extraction time of 33 min, and the ratio of liquid to raw material of 25:1, respectively. Compared to the hot-water extraction, the ultrasound-assistance favored the extraction of polysaccharides from V. volvacea for its higher polysaccharide yield and efficiency. Further preliminary polysaccharide structural characterization indicated that ultrasound treatment affected the monosaccharide compositions and ratios, and molecular weight range of polysaccharides extracted from V. volvacea.

Asymmetric Synthesis of Spirocyclic ß-Lactams through Copper-Catalyzed Kinugasa/Michael Domino Reactions.

The first copper-catalyzed highly chemo-, regio-, diastereo-, and enantioselective Kinugasa/Michael domino reaction for the desymmetrization of prochiral cyclohexadienones is described. In the presence of a chiral copper catalyst, alkyne-tethered cyclohexadienones couple with nitrones to generate the chiral spirocyclic lactams with excellent stereoselectivity (up to 97 % ee, >20:1 dr). The new method provides direct access to versatile highly functionalized spirocyclic ß-lactams possessing four contiguous stereocenters, including one quaternary and one tetra-substituted stereocenter.

Control of N-Heterocyclic Carbene Catalyzed Reactions of Enals: Asymmetric Synthesis of Oxindole-γ-Amino Acid Derivatives.

A strategy to control the switch between a non-cycloaddition reaction and a cycloaddition reaction of enals, using N-heterocyclic carbene (NHC) catalyisis, has been developed. The new scalable protocol leads to γ-amino-acid esters bearing a tetrasubstituted stereocenter in good yields and high stereoselectivities by homo-Mannich reactions of enals and isatin-derived ketimines. By simply changing the N-ketimine substituent to an ortho-hydroxy phenyl group, the corresponding spirocyclic oxindolo-γ-lactams are obtained.

N-Heterocyclic Carbene Catalyzed [3+2] Cycloaddition of Enals with Masked Cinnamates for the Asymmetric One-Pot Synthesis of Adipic Acid Derivatives.

A novel short entry to 3,4-disubstituted adipic acids has been developed by employing an asymmetric NHC-catalyzed [3+2] cycloaddition of enals with masked cinnammates in moderate to good yields and high stereoselectivities. The synthetic utility of the protocol was demonstrated by the basic conversion of the masked cyclopentanone intermediates to 3S,4S-disubstituted adipic acid precursors of pharmaceutically important gababutins.

Switchable Access to Different Spirocyclopentane Oxindoles by N-Heterocyclic Carbene Catalyzed Reactions of Isatin-Derived Enals and N-Sulfonyl Ketimines.

A novel NHC-catalyzed annulation protocol for the asymmetric synthesis of biologically important ß-lactam fused spirocyclopentane oxindoles with four contiguous stereocenters, including two quaternary carbon centers, was developed. Alternatively, spirocyclopentane oxindoles containing an enaminone moiety can be achieved using the same starting materials, isatin-derived enals, and N-sulfonyl ketimines, in the presence of a slightly different NHC catalytic system. This switchable annulation strategy enables the selective assembly of both heterocyclic scaffolds with good yields and excellent enantioselectivities for a broad range of substrates.

N-Heterocyclic Carbene Catalyzed [4+2] Annulation of Enals via a Double Vinylogous Michael Addition: Asymmetric Synthesis of 3,5-Diaryl Cyclohexenones.

A strategy for the N-heterocyclic carbene (NHC) catalyzed asymmetric synthesis of 3,5-diaryl substituted cyclohexenones has been developed via oxidative [4+2] annulation of enals and alkenylisoxazoles. It is the first example of using NHC organocatalysis in a double vinylogous Michael type reaction, a challenging but highly desirable topic. This unprecedented protocol affords good yields as well as high to excellent diastereo- and enantioselectivities.

Asymmetric, Three-Component, One-Pot Synthesis of Spiropyrazolones and 2,5-Chromenediones from Aldol Condensation/NHC-Catalyzed Annulation Reactions.

A novel one-pot, three-component diastereo- and enantioselective synthesis of spiropyrazolones has been developed involving the aldol condensation of an enal to generate α,ß-unsaturated pyrazolones, which react with a second equivalent of enal through an N-heterocyclic carbene (NHC)-catalyzed [3+2] annulation. The desired spirocyclopentane pyrazolones are obtained in moderate to good yields and good to excellent stereoselectivities. Alternatively, starting from cyclic 1,3-diketones, 2,5-chromenediones are available through [2+4] annulation.

[Contents and the Correlations of the Total Anthocyanins and Saponins of the Vegetative Organs of Panax notoginseng with Purple and Green Aerial Stems at Different Growth Stages].

Objective: To study the accumulation characteristics of total anthocyanins and saponins in the vegetative organ of Panax notoginseng with purple and green aerial stems at different growth stages. Methods: The contents of the total anthocyanins and saponins of the leaves, aerial stems, rhizomes and the adventitious roots of one-, two- and three-year-old Panax notoginseng with purple and green aerial stems were determined by spectrophotometry. Results: From one-year-old to three-year-old Panax notoginseng, the total anthocyanin contents (TACs) of the leaves, aerial stems and all vegetative organs and the percentages of the aerial stems TACs to those of all vegetative organs of purple aerial stemmed Panax notoginseng plants, the percentages of the total saponin contents (TSCs) of the leaves and aerial stems to those of all vegetative organs of the purple and green aerial stemmed plants and the percentages of the leaves TACs to those of vegetative organs of the green aerial stemmed plants all decreased. The TACs of the leaves and all vegetative organs of the green aerial stemmed plants, the TACs of the rhizomes and their adventitious roots, the vegetative organ TSCs and the percentages of the TSCs of the rhizomes and their adventitious roots to those of all vegetative organs of the purple and green aerial stemmed plants, and the percentages of the TACs of the rhizomes and their adventitious roots to those of all vegetative organs of the purple aerial stemmed plants were increased. The increasing rates of the TACs of the aerial stems and all vegetative organs and the TSCs of the aerial stems, rhizomes and their adventitious roots and all vegetative organs of the purple aerial stemmed plants were always higher than those of the green aeria stemmed plants, but the increasing rates of the leaves TSCs were lower than those of the green aerial stemmed plants, and the content changes of the vegetative organ TACs and TSCs of the purple and green aerial stemmed plants exhibited different correlations. Additionally, the three-years-old plants, the TSCs of the vegetative organs of the purple aerial stemmed plants were all higher than those of the green aerial stemmed plants, but the TACs of the leaves and rhizomes and their adventitious roots were lower than those of the green aerial stemmed plants. Conclusion: The saponin-accumulating capacity of the vegetative organs of purple aerial stemmed Panax notoginseng plants is stronger than that of green aerial stemmed Panax notoginseng.

Asymmetric Synthesis of Spirobenzazepinones with Atroposelectivity and Spiro-1,2-Diazepinones by NHC-Catalyzed [3+4] Annulation Reactions.

A strategy for the NHC-catalyzed asymmetric synthesis of spirobenzazepinones, spiro-1,2-diazepinones, and spiro-1,2-oxazepinones has been developed via [3+4]-cycloaddition reactions of isatin-derived enals (3C component) with in-situ-generated aza-o-quinone methides, azoalkenes, and nitrosoalkenes (4atom components). The [3+4] annulation strategy leads to the seven-membered target spiro heterocycles bearing an oxindole moiety in high yields and excellent enantioselectivities with a wide variety of substrates. Notably, the benzazepinone synthesis is atroposelective and an all-carbon spiro stereocenter is generated.

SCMMTP: identifying and characterizing membrane transport proteins using propensity scores of dipeptides.

BACKGROUND: Identifying putative membrane transport proteins (MTPs) and understanding the transport mechanisms involved remain important challenges for the advancement of structural and functional genomics. However, the transporter characters are mainly acquired from MTP crystal structures which are hard to crystalize. Therefore, it is desirable to develop bioinformatics tools for the effective large-scale analysis of available sequences to identify novel transporters and characterize such transporters. RESULTS: This work proposes a novel method (SCMMTP) based on the scoring card method (SCM) using dipeptide composition to identify and characterize MTPs from an existing dataset containing 900 MTPs and 660 non-MTPs which are separated into a training dataset consisting 1,380 proteins and an independent dataset consisting 180 proteins. The SCMMTP produced estimating propensity scores for amino acids and dipeptides as MTPs. The SCMMTP training and test accuracy levels respectively reached 83.81% and 76.11%. The test accuracy of support vector machine (SVM) using a complicated classification method with a low possibility for biological interpretation and position-specific substitution matrix (PSSM) as a protein feature is 80.56%, thus SCMMTP is comparable to SVM-PSSM. To identify MTPs, SCMMTP is applied to three datasets including: 1) human transmembrane proteins, 2) a photosynthetic protein dataset, and 3) a human protein database. MTPs showing α-helix rich structure is agreed with previous studies. The MTPs used residues with low hydration energy. It is hypothesized that, after filtering substrates, the hydrated water molecules need to be released from the pore regions. CONCLUSIONS: SCMMTP yields estimating propensity scores for amino acids and dipeptides as MTPs, which can be used to identify novel MTPs and characterize transport mechanisms for use in further experiments. AVAILABILITY: http://iclab.life.nctu.edu.tw/iclab_webtools/SCMMTP/.

Relationship between thrombus vWF and NETs with clinical severity and peripheral blood immunocytes' indicators in patients with acute ischemic stroke.

OBJECTIVE: To investigate the association between von Willebrand factor (vWF) and neutrophil extracellular traps (NETs) in thrombus with clinical severity and peripheral blood immunocytes' indicators in patients with early-stage acute ischemic stroke (AIS). METHODS: A retrospective study was conducted using the clinical data of 66 patients with AIS who underwent endovascular mechanical thrombectomy and had their thrombus samples collected. The concentrations of vWF and NETs in the thrombus samples were quantitatively assessed. Peripheral blood samples taken in the early stages of the disease were analyzed for total white blood cell counts (WBC), ratios of neutrophils (NEU%), lymphocytes (LYM%), eosinophils (EOS%), and monocytes (MONO%). The severity of clinical symptoms in these patients was evaluated using the modified Rankin Scale (mRS), Essen Stroke Risk Score (ESRS), Barthel Index (BI), and National Institute of Health Stroke Scale (NIHSS). RESULTS: Higher vWF levels in thrombus were associated with lower NIHSS scores, while higher NETs levels were associated with higher initial NIHSS scores. In the early stages of AIS, WBC count and vWF levels were negatively correlated, as well as NEU%. LYM% was positively correlated with vWF level; however, it was negatively correlated with NETs. EOS% was positively correlated with vWF levels. CONCLUSION: In the early stages of AIS, a higher peripheral WBC count and NEU%, combined with decreased EOS% and LYM%, were significantly correlated with a lower vWF level in the thrombus, potentially indicating more severe symptoms. Consequently, the timely administration of vWF-targeted medications is recommended for such patients. Reduced LYM% is indicative of elevated NETs levels and correlated with more severe clinical symptoms. Therefore, the prompt initiation of NETs-targeted medication is warranted for these patients.