Antibody glycan quality predicted from CHO cell culture media markers and machine learning.

N-glycosylation can have a profound effect on the quality of mAb therapeutics. In biomanufacturing, one of the ways to influence N-glycosylation patterns is by altering the media used to grow mAb cell expression systems. Here, we explore the potential of machine learning (ML) to forecast the abundances of N-glycan types based on variables related to the growth media. The ML models exploit a dataset consisting of detailed glycomic characterisation of Anti-HER fed-batch bioreactor cell cultures measured daily under 12 different culture conditions, such as changes in levels of dissolved oxygen, pH, temperature, and the use of two different commercially available media. By performing spent media quantitation and subsequent calculation of pseudo cell consumption rates (termed media markers) as inputs to the ML model, we were able to demonstrate a small subset of media markers (18 selected out of 167 mass spectrometry peaks) in a Chinese Hamster Ovary (CHO) cell cultures are important to model N-glycan relative abundances (Regression - correlations between 0.80-0.92; Classification - AUC between 75.0-97.2). The performances suggest the ML models can infer N-glycan critical quality attributes from extracellular media as a proxy. Given its accuracy, we envisage its potential applications in biomaufactucuring, especially in areas of process development, downstream and upstream bioprocessing.

Environmental pollution of paraben needs attention: A study of methylparaben and butylparaben co-exposure trigger neurobehavioral toxicity in zebrafish.

Parabens (PBs) are commonly utilized as preservatives in various commodities. Of all the PBs, methylparaben (MeP) and butylparaben (BuP) are usually found together at similar levels in the aqueous environment. Although a few studies have demonstrated that PBs are neurotoxic when present alone, the neurobehavioral toxic effects and mechanisms of coexisting MeP and BuP at environmental levels has not been determined. Neurobehavior is a sensitive indicator for identifying neurotoxicity of environmental pollutants. Therefore, adult female zebrafish (Danio rerio) were chronic co-exposure of MeP and BuP at environmental levels (5, 50, and 500 ng/L) for 60 d to investigate the effects on neurobehavior, histopathology, oxidative stress, mitochondrial function, neurotransmitters and gene expression. The results demonstrated that chronic co-exposure of MeP and BuP interfered with several behaviors (learning-memory, anxiety, fear, aggressive and shoaling behavior) in addition to known mechanisms of producing oxidative stress and disrupting energy. More intriguingly, chronic co-exposure of MeP and BuP caused retinal vacuolization and apoptosis in the optic tectum zone. It even has further effects on the phototransduction pathway, impairing optesthesia and leading to neurotransmitters dysregulation. These are critical underlying mechanisms resulting in neurobehavioral abnormalities. This study confirms that the pollution of multiple PBs by chronic co-exposure in aquatic environments can result neurobehavioral toxicity. It also suggests that the prolonged effects of PBs on aquatic ecosystems and health require close attention.

Direct, Embedded, and Embodied Trade of Arsenic: 1990-2019.

International arsenic trade, physical and virtual, has resulted in considerable transfer of arsenic pollution across regions. However, no study has systematically captured, estimated, and compared physical and virtual arsenic trade and its relevant impacts. This study combines material flow analysis and embodied emission factors to estimate embedded (including direct and indirect trade) and embodied arsenic trade during 1990-2019, encompassing 18 arsenic-containing products among 244 countries. Global embedded arsenic trade increased considerably from 47 ± 7.3 to 450 ± 68 kilotonnes (kt) during this time and was dominated by indirect arsenic trade, contributing 94 and 90% to global arsenic trade in 1990 and 2019, respectively. Since the 1990s, global arsenic trade centers and the main flows have shifted from European and American markets to developing countries. The mass of arsenic involved in embodied trade increased from 87.5 ± 26 kt in 1990 to 800 ± 236 kt in 2019. Direct trade and indirect trade aggravate arsenic environmental emissions in major importing countries, like China, while embodied trade aggravates arsenic environmental emissions in major exporting countries, like Peru and Chile. The trade-related arsenic pollution transfer calls for a rational arsenic emission responsibility-sharing mechanism and corresponding policy recommendations for different trading countries.

Streamlined Synthesis of Varied Heteroarene-Condensed Benzofuran Derivatives via [4 + 2] Annulation of Benzofuran-Derived Azadienes and N-Alkyl Quinolinium Salts.

Herein we have pioneered an innovative synthetic strategy for the efficient assembly of various heteroarene-condensed benzofuran derivatives, utilizing benzofuran-derived azadienes (BDAs) and quinolines as the starting materials. This method functions with transition-metal catalysis and uses cost-effective formic acid as the reducing agent. Mechanistic investigations indicate that this transformation would involve a [4 + 2] annulation cascade process. This approach demonstrates a high tolerance to various functional groups and yields excellent results.

Development of a community intervention combining social media-based health education plus exercise programme (SHEEP) to improve muscle function among young-old adults with possible sarcopenia: Co-design approach.

OBJECTIVES: There is no precedent for the use of social media in preventing sarcopenia. The aim of this study is to develop a social media-based intervention programme for the young-old population in the community in China to improve their awareness and behaviours regarding sarcopenia prevention. STUDY DESIGN: Using guidelines for developing complex interventions, this study was divided into two main phases: a co-development phase and a preliminary test phase. Both were carried out in Changsha, China. The development phase employed co-design methodology with relevant stakeholders, including two rounds of consultation with patient and public involvement (12 members) and two rounds of focus groups (30 participants); this was followed by the three-week preliminary test phase (22 participants). MAIN OUTCOME MEASURES: This study evaluated the consultation with patient and public involvement, and mainly collected qualitative data from the two rounds of focus group interviews and a final semi-structured interview following the preliminary test, so as to explore the participants' experiences, comments, and suggestions for revising the social media-based intervention. Handgrip strength was also evaluated. RESULTS: The health education included seven videos of 4-6 min each related to sarcopenia, including information on the concept, influencing factors, adverse effects, manifestations, screening methods, and preventions. The exercise video consisted of four types of training (warm-up, aerobic, resistance, and flexibility training) and lasted 30 min, with a suggested engagement of at least 3 days/week. The specific contents and "dosage" of the final intervention were unanimously favourable to the diverse stakeholders involved (older adults with possible sarcopenia, experts, researchers). After the preliminary test, an improvement in handgrip strength was observed, from M15.92±SD5.22 kg to M19.13±SD5.44 kg (T = -5.44, P < 0.001). Subgroup analysis revealed that this improvement was evident in both men and women. CONCLUSIONS: The social media-based intervention was universally endorsed by the participants and showed indications of a positive influence on sarcopenia. A feasibility study is now needed.

Efficient Functionalization of Organosulfones via Photoredox Catalysis: Direct Incorporation of α-Carbonyl Alkyl Side Chains into α-Allyl-ß-Ketosulfones.

A novel and efficient method for functionalizing organosulfones has been established, utilizing a visible-light-driven intermolecular radical cascade cyclization of α-allyl-ß-ketosulfones. This process employs fac-Ir(ppy)3 as the photoredox catalyst and α-carbonyl alkyl bromide as the oxidizing agent. Via this approach, the substrates experience intermolecular addition of α-carbonyl alkyl radicals to the alkene bonds, initiating a sequence of C-C bond formations that culminate in the production of organosulfone derivatives. Notably, this technique features gentle reaction conditions and an exceptional compatibility with a wide array of functional groups, making it a versatile and valuable addition to the field of organic synthesis.

Mouse KL2 is a unique MTSE involved in chromosome-based spindle organization and regulated by multiple kinases during female meiosis.

Microtubule-severing enzymes (MTSEs) play important roles in mitosis and meiosis of the primitive organisms. However, no studies have assessed their roles in mammalian meiosis of females, whose abnormality accounts for over 80% of the cases of gamete-originated human reproductive disease. In the current study, we reported that katanin-like 2 (KL2) was the only MTSE concentrating at chromosomes. Furthermore, the knockdown of KL2 significantly reduced chromosome-based increase in the microtubule (MT) polymer, increased aberrant kinetochore-MT (K-MT) attachment, delayed meiosis, and severely affected normal fertility. Importantly, we demonstrated that the inhibition of aurora B, a key kinase for correcting aberrant K-MT attachment, eliminated KL2 from chromosomes completely. KL2 also interacted with phosphorylated eukaryotic elongation factor-2 kinase; they competed for chromosome binding. We also observed that the phosphorylated KL2 was localized at spindle poles, and that KL2 phosphorylation was regulated by extracellular signal-regulated kinase 1/2. In summary, our study reveals a novel function of MTSEs in mammalian female meiosis and demonstrates that multiple kinases coordinate to regulate the levels of KL2 at chromosomes.

Accurate diagnosis of severe coronary stenosis based on resting magnetocardiography: a prospective, single-center, cross-sectional analysis.

OBJECTIVE: To evaluate the role of resting magnetocardiography in identifying severe coronary artery stenosis in patients with suspected coronary artery disease. METHODS: A total of 513 patients with angina symptoms were included and divided into two groups based on the extent of coronary artery disease determined by angiography: the non-severe coronary stenosis group (< 70% stenosis) and the severe coronary stenosis group (≥ 70% stenosis). The diagnostic model was constructed using magnetic field map (MFM) parameters, either individually or in combination with clinical indicators. The performance of the models was evaluated using receiver operating characteristic curves, accuracy, sensitivity, specificity, positive predictive value (PPV) and negative predictive value (NPV). Calibration plots and decision curve analysis were performed to investigate the clinical utility and performance of the models, respectively. RESULTS: In the severe coronary stenosis group, QR_MCTDd, S_MDp, and TT_MAC50 were significantly higher than those in the non-severe coronary stenosis group (10.46 ± 10.66 vs. 5.11 ± 6.07, P < 0.001; 7.2 ± 8.64 vs. 4.68 ± 6.95, P = 0.003; 0.32 ± 57.29 vs. 0.26 ± 57.29, P < 0.001). While, QR_MVamp, R_MA, and T_MA in the severe coronary stenosis group were lower (0.23 ± 0.16 vs. 0.28 ± 0.16, P < 0.001; 55.06 ± 48.68 vs. 59.24 ± 53.01, P < 0.001; 51.67 ± 39.32 vs. 60.45 ± 51.33, P < 0.001). Seven MFM parameters were integrated into the model, resulting in an area under the curve of 0.810 (95% CI: 0.765-0.855). The sensitivity, specificity, PPV, NPV, and accuracy were 71.7%, 80.4%, 93.3%, 42.8%, and 73.5%; respectively. The combined model exhibited an area under the curve of 0.845 (95% CI: 0.798-0.892). The sensitivity, specificity, PPV, NPV, and accuracy were 84.3%, 73.8%, 92.6%, 54.6%, and 82.1%; respectively. Calibration curves demonstrated excellent agreement between the nomogram prediction and actual observation. The decision curve analysis showed that the combined model provided greater net benefit compared to the magnetocardiography model. CONCLUSIONS: The novel quantitative MFM parameters, whether used individually or in combination with clinical indicators, have been shown to effectively predict the risk of severe coronary stenosis in patients presenting with angina-like symptoms. Magnetocardiography, an emerging non-invasive diagnostic tool, warrants further exploration for its potential in diagnosing coronary heart disease.

Retroperitoneal bronchogenic cyst: A case report and review of literature.

BACKGROUND: Bronchogenic cysts are rare developmental anomalies that belong to the category of congenital enterogenous cysts. They arise from lung buds and are present at birth. The embryonic foregut is their origin. Typically, they are located within the chest cavity, particularly in the cavum mediastinale of the thoracic cavity or lodged in the pulmonary parenchyma, and are considered a type of lung bud malformation. CASE SUMMARY: A 49-year-old male patient was admitted to the hospital due to the detection of a retroperitoneal mass during a physical examination. Two weeks before admission, the patient underwent a physical examination and routine laboratory tests, which revealed a space-occupying mass in the retroperitoneal region. The patient did not report any symptoms (such as abdominal pain, flatulence, nausea, vomiting, high fever, or chills). The computed tomography (CT) revealed a retroperitoneal space-occupying lesion with minimal enhancement and a CT value of approximately 36 Hounsfield units. The lesion was not delineated from the boundary of the pancreatic body and was closely related to the retroperitoneum locally. CONCLUSION: Following a series of tests, an abdominal mass was identified, prompting the implementation of a laparoscopic retroperitoneal mass excision procedure. During the investigation, an 8 cm × 7 cm cystic round-shaped mass with a distinct demarcation was identified in the upper posterior region of the pancreas. Subsequently, full resection of the mass was performed. Postoperative pathological examination reveled a cystic mass characterized by a smooth inner wall. The cystic mass was found to contain a white, viscous liquid within its capsule.

Celastrol mediates CAV1 to attenuate pro-tumorigenic effects of senescent cells.

BACKGROUND: Cellular senescence is an emerging hallmark of cancers, primarily fuels cancer progression by expressing senescence-associated secretory phenotype (SASP). Caveolin-1 (CAV1) is a key mediator of cell senescence. Previous studies from our group have evidenced that the expression of CAV1 is downregulated by Celastrol (CeT). PURPOSE: To investigate the impact of CeT on cellular senescence and its subsequent influence on post-senescence-driven invasion, migration, and stemness of clear cell renal cell carcinoma (ccRCC). STUDY DESIGN AND METHODS: The expression levels of CAV1, canonical senescence markers, and markers associated with epithelial-mesenchymal transition (EMT) and stemness in clinical samples were assessed through Pearson correlation analysis. Senescent cell models were induced using DOX, and their impact on migration, invasion, and stemness was evaluated. The effects of CeT treatment on senescent cells and their pro-tumorigenic effects were examined. Subsequently, the underlying mechanism of CeT were explored using lentivirus transfection and CRISPR/Cas9 technology to silence CAV1. RESULTS: In human ccRCC clinical samples, the expression of the canonical senescence markers p53, p21, and p16 are associated with ccRCC progression. Senescent cells facilitated migration, invasion, and enhanced stemness in both ccRCC cells and ccRCC tumor-bearing mice. As expected, CeT treatment reduced senescence markers (p16, p53, p21, SA-ß-gal) and SASP factors (IL6, IL8, CXCL12), alleviating cell cycle arrest. However, it did not restore the proliferation of senescent cells. Additionally, CeT suppressed senescence-driven migration, invasion, and stemness. Further investigations into the underlying mechanism demonstrated that CAV1 is a critical mediator of cell senescence and represents a potential target for CeT to attenuate cellular senescence. CONCLUSIONS: This study presents a pioneering investigation into the intricate interplay between cellular senescence and ccRCC progression. We unveil a novel mechanism of CeT to mitigate cellular senescence by downregulating CAV1, thereby inhibiting the migration, invasion and stemness of ccRCC driven by senescent cells. These findings provide valuable insights into the underlying mechanisms of CeT and its potential as a targeted therapeutic approach for alleviating the aggressive phenotypes associated with senescent cells in ccRCC.

A simple and highly sensitive LC-MS workflow for characterization and quantification of ADC cleavable payloads.

Antibody-drug conjugates (ADC) payloads are cleavable drugs that act as the warhead to exert an ADC's cytotoxic effects on cancer cells intracellularly. A simple and highly sensitive workflow is developed and validated for the simultaneous quantification of six ADC payloads, namely SN-38, MTX, DXd, MMAE, MMAF and Calicheamicin (CM). The workflow consists of a short and simple sample extraction using a methanol-ethanol mixture, followed by a fast liquid chromatography tandem mass spectrometry (LC-MS/MS) analysis. The results showed that well-validated linear response ranges of 0.4-100 nM for SN38, MTX and DXd, 0.04-100 nM for MMAE and MMAF, 0.4-1000 nM for CM were achieved in mouse serum. Recoveries for all six payloads at three different concentrations (low, medium and high) were more than 85%. An ultra-low sample volume of only 5 µL of serum is required due to the high sensitivity of the method. This validated method was successfully applied to a pharmacokinetic study to quantify MMAE in mouse serum samples.

Celastrol Elicits Antitumor Effects through Inducing Immunogenic Cell Death and Downregulating PD-L1 in ccRCC.

BACKGROUND: Targeting immunogenic cell death (ICD) is considered a promising therapeutic strategy for cancer. However, the commonly identified ICD inducers promote the expression of programmed cell death ligand 1 (PD-L1) in tumor cells, thus aiding them to evade the recognition and killing by the immune system. Therefore, the finding of novel ICD inducers to avoid enhanced PD-L1 expression is of vital significance for cancer therapy. Celastrol (CeT), a triterpene isolated from Tripterygium wilfordii Hook. F induces various forms of cell death to exert anti-cancer effects, which may make celastrol an attractive candidate as an inducer of ICD. METHODS: In the present study, bioinformatics analysis was combined with experimental validation to explore the underlying mechanism by which CeT induces ICD and regulates PD-L1 expression in clear cell renal cell carcinoma (ccRCC). RESULTS: The results showed that EGFR, IKBKB, PRKCQ and MAPK1 were the crucial targets for CeT-induced ICD, and only MAPK1 was an independent prognostic factor for the overall survival (OS) of ccRCC patients. In addition, CeT triggered autophagy and up-regulated the expressions of HMGB1 and CRT to induce ICD in 786-O cells in vitro. Importantly, CeT can down-regulate PD-L1 expression through activating autophagy. At the molecular level, CeT suppressed PD-L1 via the inhibition of MAPK1 expression. Immunologically, the core target of celastrol, MAPK1, was tightly correlated with CD8+ T cells and CD4+ T cells in ccRCC. CONCLUSION: These findings indicate that CeT not only induces ICD but also suppresses PD-L1 by down-regulating MAPK1 expression, which will provide an attractive strategy for ccRCC immunotherapy.

Advanced "turn-on" colorimetric uranium platform based on the enhanced nanozyme activity of a donor-acceptor structured covalent organic framework.

BACKGROUND: The increasing uranium containing wastes generated during uranium mining and finishing pose a huge threat to the environment and human health, and thus robust strategies for on-site monitoring of uranium pollutant are of great significance for environmental protection around uranium tailings. RESULTS: Herein, a facile "turn-on" colorimetric platform that can achieve uranium detection by spectrometry and naked eyes was developed based on the uranium-enhanced nanozyme activity of covalent organic framework (JUC-505). Thanks to the extended π-conjugated skeleton and donor-acceptor (D-A) structure, JUC-505 exhibited superior photo-activated nanozyme activity, which would be prohibited when the cyano group in JUC-505 skeleton was transformed to the amidoxime group. Further results elucidated that the coordination of uranium with amidoxime groups led to the electron transfer between uranium and the JUC-505-AO skeleton, and thus significantly restored the nanozymatic activity of JUC-505-AO with the subsequent remarkable color changes. Moreover, the uranium concentrations in uranium tailing wastewater detected by the present "turn-on" colorimetric method were well agreed with those by ICP-MS, demonstrating a high accuracy of the present method in real samples. SIGNIFICANCE: The D-A structured JUC-505 with superior photocatalytic property and nanozymatic activity was applied to facilitate colorimetric detection of uranium, which displays the advantages of low detection limit, excellent selectivity, fast response and simple operation for uranium detection in real samples, and shows a great potential in on-site monitoring of uranium pollutant around uranium tailings as well as nuclear power plant.

Peripapillary atrophy area predicts the decrease of macular choroidal thickness in young adults during myopia progression.

OBJECTIVE: This study aimed to investigate the influence of peripapillary atrophy (PPA) area and axial elongation on the longitudinal changes in macular choroidal thickness (ChT) in young individuals with myopia. METHODS AND ANALYSIS: In this longitudinal investigation, 431 eyes-342 categorised as non-high myopia (non-HM) and 89 as HM-were examined for 2 years. Participants were examined with swept-source optical coherence tomography. The macular ChT, PPA area and axial length (AL) were measured at baseline and follow-up visits. Multiple regression analysis was performed to identify factors associated with ChT changes. The areas under the receiver operating characteristic curves were analysed to ascertain the predictive capacity of the PPA area and axial elongation for the reduction in macular ChT. RESULTS: Initial measurements revealed that the average macular ChT was 240.35±56.15 µm in the non-HM group and 198.43±50.27 µm in the HM group (p<0.001). It was observed that the HM group experienced a significantly greater reduction in average macular ChT (-7.35±11.70 µm) than the non-HM group (-1.85±16.95 µm, p=0.004). Multivariate regression analysis showed that a greater reduction of ChT was associated with baseline PPA area (ß=-26.646, p<0.001) and the change in AL (ß=-35.230, p<0.001). The combination of the baseline PPA area with the change in AL was found to be effective in predicting the decrease in macular ChT, with an area under the curve of 0.741 (95% CI 0.694 to 0.787). CONCLUSION: Over 2 years, eyes with HM exhibit a more significant decrease in ChT than those without HM. Combining the baseline PPA area with the change in AL could be used to predict the decrease of macular ChT.

Harnessing developmental dynamics of spinal cord extracellular matrix improves regenerative potential of spinal cord organoids.

Neonatal spinal cord tissues exhibit remarkable regenerative capabilities as compared to adult spinal cord tissues after injury, but the role of extracellular matrix (ECM) in this process has remained elusive. Here, we found that early developmental spinal cord had higher levels of ECM proteins associated with neural development and axon growth, but fewer inhibitory proteoglycans, compared to those of adult spinal cord. Decellularized spinal cord ECM from neonatal (DNSCM) and adult (DASCM) rabbits preserved these differences. DNSCM promoted proliferation, migration, and neuronal differentiation of neural progenitor cells (NPCs) and facilitated axonal outgrowth and regeneration of spinal cord organoids more effectively than DASCM. Pleiotrophin (PTN) and Tenascin (TNC) in DNSCM were identified as contributors to these abilities. Furthermore, DNSCM demonstrated superior performance as a delivery vehicle for NPCs and organoids in spinal cord injury (SCI) models. This suggests that ECM cues from early development stages might significantly contribute to the prominent regeneration ability in spinal cord.

MdTPR16, an apple tetratricopeptide repeat (TPR)-like superfamily gene, positively regulates drought stress in apple.

The Tetratricopeptide repeat (TPR)-like superfamily with TPR conserved domains is widely involved in the growth and abiotic stress in many plants. In this report, the gene MdTPR16 belongs to the TPR family in apple (Malus domestica). Promoter analysis reveal that MdTPR16 incorporated various stress response elements, including the drought stress response elements. And different abiotic stress treatments, drought especially, significantly induce the response of MdTPR16. Overexpression of MdTPR16 result in better drought tolerance in apple and Arabidopsis by up-regulating the expression levels of drought stress-related genes, achieving a higher chlorophyll content level, more material accumulation, and overall better growth compared to WT in the drought. Under drought stress, the overexpressed MdTPR16 also mitigate the oxidative damage in cells by reducing the electrolyte leakage, malondialdehyde content, and the H2O2 and O2- accumulation in apples and Arabidopsis. In conclusion, MdTPR16 act as a beneficial regulator of drought stress response by regulating the expression of related genes and the cumulation of reactive oxygen species (ROS).

Healthy Diet-Related Knowledge, Attitude, and Practice (KAP) and Related Socio-Demographic Characteristics among Middle-Aged and Older Adults: A Cross-Sectional Survey in Southwest China.

Objective This study aimed to investigate the current status and influencing factors of healthy diet knowledge, attitude, and practice (KAP) among middle-aged and older adults aged 45-75 in Southwest China. Methods A questionnaire survey was conducted among 1822 middle-aged and older adults in Southwest China (including Guizhou, Sichuan, Yunnan, and Chongqing) from February to May 2021. Results The average score of healthy diet knowledge was (4.82 ± 2.98), with a passing rate of 7.6%. The mean score of healthy diet attitude was (21.26 ± 4.18), with a passing rate of 69.5%. The average score of healthy diet practice was (13.76 ± 2.84), with a passing rate of 55.5%. The score for healthy diet KAP was (39.85 ± 7.21), with a passing rate of 41.2%. Univariate analysis showed that the scores of healthy diet KAP were significantly different among participants of different ages, genders, ethnicities, residences, education levels, monthly household incomes, and regions, as well as varying according to whether several generations have lived in the same area (p < 0.05). The results of multiple linear regression showed that the healthy diet KAP of participants was influenced by age, gender, residence, education level, monthly household income, and region (p < 0.05). Conclusion The healthy diet KAP of middle-aged and older adults aged 45-75 in Southwest China shows room for improvement. The knowledge regarding healthy diet was relatively low, and certain specific healthy diet practices were not up to the standard. However, there was a positive trend in the attitude towards a healthy diet. Healthy diet education should be promoted for middle-aged and older adults.

ABC2A: A Straightforward and Fast Method for the Accurate Backmapping of RNA Coarse-Grained Models to All-Atom Structures.

RNAs play crucial roles in various essential biological functions, including catalysis and gene regulation. Despite the widespread use of coarse-grained (CG) models/simulations to study RNA 3D structures and dynamics, their direct application is challenging due to the lack of atomic detail. Therefore, the reconstruction of full atomic structures is desirable. In this study, we introduced a straightforward method called ABC2A for reconstructing all-atom structures from RNA CG models. ABC2A utilizes diverse nucleotide fragments from known structures to assemble full atomic structures based on the CG atoms. The diversification of assembly fragments beyond standard A-form ones, commonly used in other programs, combined with a highly simplified structure refinement process, ensures that ABC2A achieves both high accuracy and rapid speed. Tests on a recent large dataset of 361 RNA experimental structures (30-692 nt) indicate that ABC2A can reconstruct full atomic structures from three-bead CG models with a mean RMSD of ~0.34 Å from experimental structures and an average runtime of ~0.5 s (maximum runtime < 2.5 s). Compared to the state-of-the-art Arena, ABC2A achieves a ~25% improvement in accuracy and is five times faster in speed.

Paris polyphylla ethanol extract and polyphyllin I ameliorate adenomyosis by inhibiting epithelial-mesenchymal transition.

BACKGROUND: The active ingredients of the Chinese medical herb Paris polyphylla, P. polyphylla ethanol extract (PPE) and polyphyllin I (PPI), potentially inhibit epithelial-mesenchymal transition (EMT) in tumors. However, the roles of these ingredients in inhibiting EMT in adenomyosis (AM) remain to be explored. PURPOSE: The primary goal of the study was to uncover the underlying molecular processes through which PPE and PPI suppress EMT in AM, alongside assessing the safety profiles of these substances. METHODS: To assess the suppressive impact of PPE on adenomyosis-derived cells (AMDCs), we employed Transwell and wound healing assays. The polyphyllins (PPI, PPII, PPVII) contained in PPE were characterized using high-performance liquid chromatography (HPLC). Then, bioinformatics techniques were performed to pinpoint potential PPI targets that could be effective in treating AM. Immunoblotting was used to verify the key proteins and pathways identified via bioinformatics. Furthermore, we examined the efficacy of PPE and PPI in treating Institute of Cancer Research (ICR) mice with AM by observing the morphological and pathological features of the uterus and performing immunohistochemistry. In addition, we assessed safety by evaluating liver, kidney and spleen pathologic features and serum test results. RESULTS: Three major polyphyllins of PPE were revealed by HPLC, and PPI had the highest concentration. In vitro experiments indicated that PPE and PPI effectively prevent AMDCs invasion and migration. Bioinformatics revealed that the primary targets E-cadherin, N-cadherin and TGFß1, as well as the EMT biological process, were enriched in PPI-treated AM. Immunoblotting assays corroborated the hypothesis that PPE and PPI suppress the TGFß1/Smad2/3 pathway in AMDCs to prevent EMT from progressing. Additionally, in vivo studies showed that PPE (3 mg/kg and 6 mg/kg) and PPI (3 mg/kg and 6 mg/kg), successfully suppressed the EMT process through targeting the TGFß1/Smad2/3 signaling pathway. Besides, it was observed that lower doses of PPE (3 mg/kg) and PPI (3 mg/kg) exerted minimal effects on the liver, kidneys, and spleen. CONCLUSIONS: PPE and PPI efficiently impede the development of EMT by inhibiting the TGFß1/Smad2/3 pathway, revealing an alternative pathway for the pharmacological treatment of AM.

Triphenyltin induced darker body coloration by disrupting melanocortin system and pteridine metabolic pathway in a reef fish, Amphiprion ocellaris.

Triphenyltin (TPT) is a typical persistent organic pollutant whose occurrence in coral reef ecosystems may threaten the survival of reef fishes. In this study, a brightly colored representative reef fish, Amphiprion ocellaris was used to explore the effects of TPT at environmental levels (1, 10, and 100 ng/L) on skin pigment synthesis. After the fish were exposed to TPT for 60 days, the skin became darker, owing to an increase in the relative area of black stripes, a decrease in orange color values while an increase in brown color values, and an increase in the number of melanocytes in the orange part of the skin tissues. To explore the mechanisms by which TPT induces darker body coloration, the enzymatic activity and gene expression levels of the members of melanocortin system that affect melanin synthesis were evaluated. Leptin levels and lepr expression were found to be increased after TPT exposure, which likely contributed to the increase found in pomc expression and α-melanocyte-stimulating hormone (α-MSH) levels. Then Tyr activity and mc1r, tyr, tyrp1, mitf, and dct were upregulated, ultimately increasing melanin levels. Importantly, RT-qPCR results were consistent with the transcriptome analysis of trends in lepr and pomc expression. Because the orange color values decreased, pterin levels and the pteridine metabolic pathway were also evaluated. The results showed that TPT induced BH4 levels and spr, xdh, and gch1 expression associated with pteridine synthesis decreased, ultimately decreasing the colored pterin content (sepiapterin). We conclude that TPT exposure interferes with the melanocortin system and pteridine metabolic pathway to increase melanin and decrease colored pterin levels, leading to darker body coloration in A. ocellaris. Given the importance of body coloration for the survival and reproduction of reef fishes, studies on the effects of pollutants (others alongside TPT) on body coloration are of high priority.