Dietary inflammatory impact on NAFLD development in obese vs. lean individuals: an analysis based on NHANES 2003-2018.

BACKGROUND: Non-alcoholic fatty liver disease (NAFLD), often linked with obesity, can also affect individuals with normal weight, a condition known as "lean NAFLD", imposing comparable burdens and adverse effects. However, the impact of diet on lean NAFLD remains underexplored. The objective of this study is to investigate the correlation between the Dietary Inflammatory Index (DII) and NAFLD among Americans, stratified by waist-to-height ratio (WHtR) and body mass index (BMI). METHODS: Five thousand one hundred fifty-two participants from the National Health and Nutrition Examination Survey (NHANES) 2003-2018 were comprised in the final analysis. NAFLD and advanced liver fibrosis were diagnosed by serological markers. Lean and abdominal lean individuals were identified using BMI and WHtR, separately. DII was determined by assigning scores to 28 distinct food parameters based on their inflammatory potential, obtained from the NAHNES website. Differences across DII quartiles were evaluated using the Kruskal-Wallis H Test, Chi-Square Test along with One-Way ANOVA. The correlation between DII and NAFLD was determined by multiple regression models and subgroup analyses. RESULTS: Among the 5152 subjects, 2503 were diagnosed with NAFLD, including 86 cases of lean NAFLD and 8 cases of abdominal lean NAFLD. DII was positively linked with NAFLD (Odds Ratio (OR) = 1.81 [1.48-2.21], P < 0.001) and advanced liver fibrosis (OR = 1.46 [1.02-2.07], P = 0.037). Further analysis revealed that this association was primarily observed in obese or abdominal obese participants (In BMI ≥ 25.00 kg/m^2, OR = 1.56 [1.23-1.98], P < 0.001. In WHtR> 0.50, OR = 1.48 [1.23-1.79], P < 0.001.), rather than their lean counterparts. Subgroup analyses indicated that female individuals, without a diagnosis of hypertension or diabetes appeared to be more sensitive to the rise in DII. CONCLUSIONS: Our data demonstrated a significant positive correlation between DII and NAFLD in the general population. However, the impact of a pro-inflammatory diet was less prominent in lean individuals compared to obese ones.

Use of lasers in gastrointestinal endoscopy: a review of the literature.

Lasers emit highly directional light with consistent wavelengths, and recent studies have demonstrated their successful applications in gastrointestinal endoscopic therapy. Although argon plasma coagulators (APC) became the preferred treatment option due to improved safety profile and lower costs, advancements in laser and optic fiber manufacturing have reignited interest in laser treatment. Different laser wavelengths have distinct features and applications based on their tissue absorption coefficient. Lasers with shorter wavelengths are effectively absorbed by hemoglobin, resulting in a good coagulation effect. Near-infrared lasers have ability to ablate solid tumors, while far-infrared lasers can make precise mucosal incisions without causing peripheral thermal damage. Lasers have proven to be highly applicable to endoscopy devices such as endoscopes, endoscopic ultrasound (EUS), double-balloon enteroscopes (DBE), and endoscopic retrograde cholangiopancreatography (ERCP), making them a potent tool to enhance the effectiveness of endoscopic treatments with minimal adverse events. This review aims to help readers understand the applications and effectiveness of lasers in gastrointestinal endoscopy, with the potential to promote the development and application of laser technology in the medical field.

Transgenic RFP-RPS-30UbL strain of the nematode Caenorhabditis elegans as a biomonitor for environmental pollutants.

Environmental pollutants are recognized as one of the major concerns for public health. The free-living nematode Caenorhabditis elegans are widely used to evaluate the toxicity of environmental contaminants in biomonitoring researches. In the present study, a new transgenic strain, rps-30-/- ;RFP-RPS-30UbL was generated, with constitutively active rps-30 promoter used to control the expression of RFP-RPS-30UbL fusion protein. We found RFP-RPS-30UbL would accumulate to form 'rod-like' structures, when worms were exposed to environmental contaminants, including Cd, Hg, Pb, As, Paraquat and Dichlorvos. The number of the 'rod-like' structures was induced by environmental contaminants in a concentration- and time-dependent manner. The 'rod-like' structure formation could be detectable in response to the concentration of each contaminant as low as 24-h LC50 × 10-7 , and the detectable time could be within 2 h. Detecting the transcription and expression levels of RFP-RPS-30UbL in worms exposed to different kinds of environmental contaminants showed that the expression level of RFP-RPS-30UbL was not regulated by environmental contaminants, and the number differences of 'rod-like' structures were just due to the morphological change of RFP-RPS-30UbL from dispersion to accumulation induced by environmental contaminants. In addition, this transgenic strain was developed in rps-30-/- homozygous worm, which was a longevity strain. Detection of lifespan and brood size showed that rps-30-/- ;RFP-RPS-30UbL transgenic worm was more suitable to be cultured and used further than N2;GFP-RPS-30UbL , for expressing RPS-30UbL in wild type N2 worms shortened the lifespan and deceased the brood size. Therefore, rps-30-/- ;RFP-RPS-30UbL transgenic worm might play a potential role in versatile environmental biomonitoring, with the advantage of not only the convenient and quick fluorescence-based reporter assay, but also the quantificational evaluation of the toxicities of environmental contaminants using 'rod-like' structures with high sensitivity, off-limited the expression level of the reporter protein.

Heat shock transcription factor (Hsf) gene family in common bean (Phaseolus vulgaris): genome-wide identification, phylogeny, evolutionary expansion and expression analyses at the sprout stage under abiotic stress.

BACKGROUND: Common bean (Phaseolus vulgaris) is an essential crop with high economic value. The growth of this plant is sensitive to environmental stress. Heat shock factor (Hsf) is a family of antiretroviral transcription factors that regulate plant defense system against biotic and abiotic stress. To date, few studies have identified and bio-analyzed Hsfs in common bean. RESULTS: In this study, 30 Hsf transcription factors (PvHsf1-30) were identified from the PFAM database. The PvHsf1-30 belonged to 14 subfamilies with similar motifs, gene structure and cis-acting elements. The Hsf members in Arabidopsis, rice (Oryza sativa), maize (Zea mays) and common bean were classified into 14 subfamilies. Collinearity analysis showed that PvHsfs played a role in the regulation of responses to abiotic stress. The expression of PvHsfs varied across different tissues. Moreover, quantitative real-time PCR (qRT-PCR) revealed that most PvHsfs were differentially expressed under cold, heat, salt and heavy metal stress, indicating that PvHsfs might play different functions depending on the type of abiotic stress. CONCLUSIONS: In this study, we identified 30 Hsf transcription factors and determined their location, motifs, gene structure, cis-elements, collinearity and expression patterns. It was found that PvHsfs regulates responses to abiotic stress in common bean. Thus, this study provides a basis for further analysis of the function of PvHsfs in the regulation of abiotic stress in common bean.

Measurement of bistatic sea surface scattering with a parametric acoustic source.

This work presents the results from a series of bistatic sea surface scattering experiments conducted in shallow water using a parametric acoustic array as a source and a receiver comprising a horizontal linear array. The experiments measured scattering at three frequencies (4, 8, and 15 kHz) and at three incident grazing angles (13º, 20º, and 30º). The measurements were made over a 5 day period during which a variety of environmental conditions were encountered. This paper provides an outline of the experiments and presents some results for the forward scattering strength. The results show that the wave direction has a significant effect on the surface forward scattering. At each incident grazing angle, the fluctuations of scattering strength due to environmental conditions decreases as the frequency increases.

Methods of acoustic gas flux inversion-Investigation into the initial amplitude of bubble excitation.

Passive acoustic inversion techniques for measuring gas flux into the water column have the potential to be a powerful tool for the long-term monitoring and quantification of natural marine seeps and anthropogenic emissions. Prior inversion techniques have had limited precision due to lack of constraints on the initial amplitude of a bubble's excitation following its release into the water column ( R). R is determined by observing the acoustic signal of bubbles released from sediment in a controlled experiment and its use is demonstrated by quantifying the flux from a volcanic CO2 seep offshore Panarea (Italy), improving the precision by 78%.

Identification of an Intermediate Form of Ferredoxin That Binds Only Iron Suggests That Conversion to Holo-Ferredoxin Is Independent of the ISC System in Escherichia coli.

Escherichia coli [2Fe-2S]-ferredoxin and other ISC proteins encoded by the iscRSUA-hscBA-fdx-iscX (isc) operon are responsible for the assembly of iron-sulfur clusters. It is proposed that ferredoxin (Fdx) donates electrons from its reduced [2Fe-2S] center to iron-sulfur cluster biogenesis reactions. However, the underlying mechanisms of the [2Fe-2S] cluster assembly in Fdx remain elusive. Here, we report that Fdx preferentially binds iron, but not the [2Fe-2S] cluster, under cold stress conditions (≤16°C). The iron binding in Fdx is characterized by a unique absorption peak at 320 nm based on UV-visible spectroscopy. In addition, the iron-binding form of Fdx could be converted to the [2Fe-2S] cluster-bound form after transferring cold-stressed cells to normal cultivation temperatures above 25°C. In vitro experiments also revealed that Fdx could utilize bound iron to assemble the [2Fe-2S] cluster by itself. Furthermore, inactivation of the genes encoding IscS, IscU, and IscA did not limit [2Fe-2S] cluster assembly in Fdx, which was also observed by inactivating the isc or suf operon, indicating that iron-sulfur cluster biogenesis in Fdx arose from a unique pathway in E. coli Our results suggest that the intracellular assembly of [2Fe-2S] clusters in Fdx is susceptible to environmental temperatures. The iron binding form of Fdx (Fe-Fdx) is a precursor during its maturation to a cluster binding form ([2Fe-2S]-Fdx), and reassembly of the [2Fe-2S] clusters during temperature increases is not strictly reliant on other specific iron donors and scaffold proteins within the Isc or Suf system.IMPORTANCE Fdx is an electron carrier that is required for the maturation of many other iron-sulfur proteins. Its function strictly depends on its [2Fe-2S] center that bonds with the cysteinyl S atoms of four cysteine residues within Fdx. However, the assembly mechanism of the [2Fe-2S] clusters in Fdx remains controversial. This study reports that Fdx fails to form its [2Fe-2S] cluster under cold stress conditions but instead binds a single Fe atom at the cluster binding site. Moreover, when temperatures increase, Fdx can assemble clusters by itself from its iron-only binding form in E. coli cells. The possibility remains that Fdx can effectively accept clusters from multiple sources. Nevertheless, our results suggest that Fdx has a strong iron binding activity that contributes to the assembly of its own [2Fe-2S] cluster and that Fdx acts as a temperature sensor to regulate Isc system-mediated iron-sulfur cluster biogenesis.

Iron-sulphur cluster biogenesis factor LYRM4 is a novel prognostic biomarker associated with immune infiltrates in hepatocellular carcinoma.

BACKGROUND: LYRM4 is necessary to maintain the stability and activity of the human cysteine desulfurase complex NFS1-LYRM4-ACP. The existing experimental results indicate that cancer cells rely on the high expression of NFS1. However, the role of LYRM4 in liver hepatocellular carcinoma (LIHC) remains unclear. METHODS: In this study, we combined bioinformatics analysis and clinical specimens to evaluate the mRNA, protein expression, and gene regulatory network of LYRM4 in LIHC. Furthermore, we detected the activity of several classical iron-sulphur proteins in LIHC cell lines through UV-vis spectrophotometry. RESULTS: The mRNA and protein levels of LYRM4 were upregulated in LIHC. Subsequent analysis revealed that the LYRM4 mRNA expression was related to various clinical stratifications, prognosis, and survival of LIHC patients. In addition, the mRNA expression of LYRM4 was significantly associated with ALT, tumour thrombus, and encapsulation of HBV-related LIHC patients. IHC results confirmed that LYRM4 was highly expressed in LIHC tissues and showed that the expression of LYRM4 protein in LIHC was significantly correlated with age and serum low-density lipoprotein (LDL) and triglyceride (TG) content. In particular, the mRNA expression of key iron- sulphur proteins POLD1 and PRIM2 was significantly overexpressed and correlated with poor prognosis in LIHC patients. Compared with hepatocytes, the activities of mitochondrial complex I and aconitate hydratase (ACO2) in LIHC cell lines were significantly increased. These results indicated that the iron-sulphur cluster (ISC) biosynthesis was significantly elevated in LIHC, leading to ISC-dependent metabolic reprogramming. Changes in the activity of ISC-dependent proteins may also occur in paracancerous tissues. Further analysis of the biological interaction and gene regulation networks of LYRM4 suggested that these genes were mainly involved in the citric acid cycle and oxidative phosphorylation. Finally, LYRM4 expression in LIHC was significantly positively correlated with the infiltrating levels of six immune cell types, and both factors were strongly associated with prognosis. CONCLUSION: LYRM4 could be a novel prognostic biomarker and molecular target for LIHC therapy. In particular, the potential regulatory networks of LYRM4 overexpression in LIHC provide a scientific basis for future research on the role of the ISC assembly mechanism and LYRM4-mediated sulphur transfer routes in carcinogenesis.

Quercetin prevents primordial follicle loss via suppression of PI3K/Akt/Foxo3a pathway activation in cyclophosphamide-treated mice.

BACKGROUND: Chemotherapy improves the survival rates of patients with various cancers but often causes some adverse effects, including ovarian damage, characterised by a decrease in primordial follicle stockpiles. Recent studies have revealed that chemotherapy may stimulate the PI3K signalling pathway, thereby resulting in accelerated primordial follicle activation and a decreased ovarian reserve. Quercetin is an inhibitor of the PI3K pathway; however, its protective effects against chemotherapy-induced follicle loss in mice have not been established. In this study, the effects of quercetin in a mouse model of cyclophosphamide-induced ovarian dysfunction were investigated. METHODS: C57BL/6 female mice were used for the study. Paraffin sections of mouse ovaries (n = 30 mice) were stained with haematoxylin and eosin for differential follicle counts. Apoptosis (n = 5 mice per group) was evaluated by TUNEL assay. Immunohistochemical staining for ki67 and Foxo3a (n = 5 mice per group) was performed to evaluate the activation of primordial follicles. The role of the PI3K signalling pathway in the ovaries (n = 45 mice) was assessed by western blotting. RESULTS: Quercetin attenuated the cyclophosphamide-induced reduction in dormant primordial follicles. Analysis of the PI3K/Akt/Foxo3a pathway showed that quercetin decreased the phosphorylation of proteins that stimulate follicle activation in cyclophosphamide-induced ovaries. Furthermore, quercetin prevented cyclophosphamide-induced apoptosis in early growing follicles and early antral follicles, maintained anti-Müllerian hormone levels secreted by these follicles, and preserved the quiescence of the primordial follicle pool, as determined by intranuclear Foxo3a staining. CONCLUSIONS: Quercetin attenuates cyclophosphamide-induced follicle loss by preventing the phosphorylation of PI3K/Akt/Foxo3a pathway members and maintaining the anti-Müllerian hormone level through reduced apoptosis in growing follicles. Accordingly, quercetin is expected to improve fertility preservation and the prevention of endocrine-related side effects of chemotherapy.

The effect of storage time after vitrification on pregnancy and neonatal outcomes among 24 698 patients following the first embryo transfer cycles.

STUDY QUESTION: To evaluate the impact of storage time after vitrification on embryo viability, pregnancy outcomes and neonatal outcomes. SUMMARY ANSWER: The prolonged storage time of vitrified embryos negatively affected pregnancy outcomes, including biochemical pregnancy rate, clinical pregnancy and live birth rate; but did not influence neonatal outcomes. WHAT IS KNOWN ALREADY: Although vitrification has been the fundamental tool of ART treatments in recent years, few studies have explored the influence of storage period after vitrification on embryonic and clinical outcomes. STUDY DESIGN, SIZE, DURATION: A retrospective study was performed among 24 698 patients with the first vitrified embryo transfer following a freeze-all strategy during the period from January 2011 to December 2017. PARTICIPANTS/MATERIAL, SETTING, METHODS: A total of 24 698 patients met the inclusion criteria and were grouped according to the storage time (11 330 patients in Group 1 with storage time <3 months, 9614 patients in Group 2 with storage time between 3 and 6 months, 3188 patients in Group 3 with storage time between 6 and 12 months and 566 in Group 4 with storage time between 12 and 24 months). The pregnancy outcomes and neonatal outcomes were compared between different storage time groups. Multivariate logistic regression and linear regression were performed to evaluate the independent effect of storage time on clinical outcomes, adjusting for important confounders. MAIN RESULTS AND THE ROLE OF CHANCE: After adjustment for potential confounding factors, the chance of biochemical pregnancy (Group 1 as reference; Group 2: adjusted odds ratio (aOR) = 0.92, 95% CI 0.87-0.97; Group 3: aOR = 0.83, 95% CI 0.76-0.90; Group 4: aOR = 0.68, 95% CI 0.56-0.81), clinical pregnancy (Group 2: aOR = 0.91, 95% CI 0.86-0.96; Group 3: aOR = 0.80, 95% CI 0.73-0.87; Group 4: aOR = 0.65, 95% CI 0.54-0.79) and live birth (Group 2: aOR = 0.89, 95% CI 0.85-0.95; Group 3: aOR = 0.83, 95% CI 0.76-0.91; Group 4: aOR = 0.59, 95% CI 0.48-0.72) significantly decreased with the increasing storage time, whereas the relationship between miscarriage, ectopic pregnancy and storage time did not reach statistical significance. In addition, there was no evidence of differences in adverse neonatal outcomes (preterm birth, low birthweight, high birthweight, macrosomia or birth defects) between groups. LIMITATION, REASONS FOR CAUTION: Our study was limited by the retrospective design from a single center, the conclusion from our study needs to be verified in further studies. WIDER IMPLICATIONS OF THE FINDINGS: This study provides new findings about the relationship between prolonged storage time of vitrified embryos and clinical outcomes and offers evidence for the safety of using long-stored embryos after vitrification. STUDY FUNDING/COMPETING INTEREST(S): This work was supported by the National Natural Science Foundation of China (grant nos. 81903324, 81771533, 81571397, 81701523), National Key Research and Development Program of China (grant no. SQ2018YFC100163). None of the authors have any conflicts of interest to declare.

The live birth and neonatal outcomes in the subsequent pregnancy among patients with adverse pregnancy outcomes in first frozen embryo transfer cycles.

PURPOSE: To explore whether the adverse pregnancy outcomes in first frozen embryo transfer (FET) cycles affect live birth and neonatal outcomes in the subsequent pregnancy? METHODS: This was a retrospective study. Women with a history of adverse pregnancy outcomes in first FET cycles started their subsequent embryo transfer cycles. The adverse pregnancy outcomes included biochemical pregnancy, ectopic pregnancy, and first-trimester pregnancy loss. The main outcomes of present study were live birth rate and neonatal outcomes. RESULTS: Results showed patients with first-trimester pregnancy loss in first FET cycles had a 95 percent greater chance of live birth in subsequent FET cycles (OR 1.95, 95% CI 1.33-2.88). However, the biochemical pregnancy/ectopic pregnancy in initial FET cycles did not affect the chance of live birth in second cycles (biochemical pregnancy: OR 1.21, 95% CI 0.82-1.77; ectopic pregnancy: OR 1.06, 95% CI 0.55-2.05). The neonatal outcomes of singletons were not affected by the number of embryo transfer cycles. CONCLUSIONS: Patients with first-trimester pregnancy loss in first FET cycle had a greater chance of live birth in second FET cycles, but the biochemical pregnancy/ectopic pregnancy in first FET cycles did not significantly affect the live birth in second FET cycles. The three types of adverse pregnancy outcomes in first FET cycles did not affect neonatal outcomes in the second cycles.

Zinc Toxicity and Iron-Sulfur Cluster Biogenesis in Escherichia coli.

While zinc is an essential trace metal in biology, excess zinc is toxic to organisms. Previous studies have shown that zinc toxicity is associated with disruption of the [4Fe-4S] clusters in various dehydratases in Escherichia coli Here, we report that the intracellular zinc overload in E. coli cells inhibits iron-sulfur cluster biogenesis without affecting the preassembled iron-sulfur clusters in proteins. Among the housekeeping iron-sulfur cluster assembly proteins encoded by the gene cluster iscSUA-hscBA-fdx-iscX in E. coli cells, the scaffold IscU, the iron chaperone IscA, and ferredoxin have strong zinc binding activity in cells, suggesting that intracellular zinc overload inhibits iron-sulfur cluster biogenesis by binding to the iron-sulfur cluster assembly proteins. Mutations of the conserved cysteine residues to serine in IscA, IscU, or ferredoxin completely abolish the zinc binding activity of the proteins, indicating that zinc can compete with iron or iron-sulfur cluster binding in IscA, IscU, and ferredoxin and block iron-sulfur cluster biogenesis. Furthermore, intracellular zinc overload appears to emulate the slow-growth phenotype of the E. coli mutant cells with deletion of the iron-sulfur cluster assembly proteins IscU, IscA, and ferredoxin. Our results suggest that intracellular zinc overload inhibits iron-sulfur cluster biogenesis by targeting the iron-sulfur cluster assembly proteins IscU, IscA, and ferredoxin in E. coli cells.IMPORTANCE Zinc toxicity has been implicated in causing various human diseases. High concentrations of zinc can also inhibit bacterial cell growth. However, the underlying mechanism has not been fully understood. Here, we report that zinc overload in Escherichia coli cells inhibits iron-sulfur cluster biogenesis by targeting specific iron-sulfur cluster assembly proteins. Because iron-sulfur proteins are involved in diverse physiological processes, the zinc-mediated inhibition of iron-sulfur cluster biogenesis could be largely responsible for the zinc-mediated cytotoxicity. Our finding provides new insights on how intracellular zinc overload may inhibit cellular functions in bacteria.

Biodetection and bioremediation of copper ions in environmental water samples using a temperature-controlled, dual-functional Escherichia coli cell.

Although a variety of whole-cell biosensors and biosorbents have been developed for detection and removal of heavy metal contaminants, few whole cells can be applied to both monitoring and remediation of copper pollution in water. In this study, a modified plasmid was constructed by incorporating a copper-sensing element and a copper-adsorbing element into a temperature-inducible plasmid, pBV220. This plasmid was subsequently transformed into an engineered Escherichia coli strain lacking copA and cueO. This dual-functional E. coli cell selectively responded to copper ions with a linear detection range of 0.01-25 µM at 37 °C and could express surface-displayed CueR when treated at 42 °C without any costly chemical inducers. The display of CueR on the cell surface specifically enhanced its copper adsorption capacity and rapidly removed copper ions from aqueous solutions. In addition, the CueR surface-displayed cells could be regenerated by adsorption-desorption cycles via pH regulation. Moreover, by simply using two different temperatures, the detection or adsorption of copper using this dual-functional whole cell was achieved without any cross-interference. Most importantly, it provided highly sensitive, accurate quantification, and effective removal of copper in real environmental water samples. Thus, this E. coli cell can be used for large-scale detection and remediation of copper pollutants.

Underwater radiated noise from hydrofoils in coastal water.

Underwater noise from commercial shipping throughout the oceans has been increasing over the past decades and the environmental impact of this noise remains an area of great uncertainty. This has led to the measurement of noise from commercial vessels in order to understand the impacts that these vessels may engender. Hydrofoils are used by ferries in various locations around the world and locally may be a significant contributing factor of the soundscape. However, the investigation on underwater radiated noise from the activity of hydrofoils in the field has not been widely conducted. This article is an attempt to characterize the noise from hydrofoils in the field. Detailed measurements in the coastal water close to the Panarea port, Italy are reported. The investigation describes the broadband frequency spectrum with the main energy approximately centered on 30-130 Hz but covering frequencies up to tens of kHz. A key result was that the spectrum of the noise varied between the three stages (displacement, transition, and foiling) of the hydrofoils heading into or out of the port.

Anaerobic Copper Toxicity and Iron-Sulfur Cluster Biogenesis in Escherichia coli.

While copper is an essential trace element in biology, pollution of groundwater from copper has become a threat to all living organisms. Cellular mechanisms underlying copper toxicity, however, are still not fully understood. Previous studies have shown that iron-sulfur proteins are among the primary targets of copper toxicity in Escherichia coli under aerobic conditions. Here, we report that, under anaerobic conditions, iron-sulfur proteins in E. coli cells are even more susceptible to copper in medium. Whereas addition of 0.2 mM copper(II) chloride to LB (Luria-Bertani) medium has very little or no effect on iron-sulfur proteins in wild-type E. coli cells under aerobic conditions, the same copper treatment largely inactivates iron-sulfur proteins by blocking iron-sulfur cluster biogenesis in the cells under anaerobic conditions. Importantly, proteins that do not have iron-sulfur clusters (e.g., fumarase C and cysteine desulfurase) in E. coli cells are not significantly affected by copper treatment under aerobic or anaerobic conditions, indicating that copper may specifically target iron-sulfur proteins in cells. Additional studies revealed that E. coli cells accumulate more intracellular copper under anaerobic conditions than under aerobic conditions and that the elevated copper content binds to the iron-sulfur cluster assembly proteins IscU and IscA, which effectively inhibits iron-sulfur cluster biogenesis. The results suggest that the copper-mediated inhibition of iron-sulfur proteins does not require oxygen and that iron-sulfur cluster biogenesis is the primary target of anaerobic copper toxicity in cells.IMPORTANCE Copper contamination in groundwater has become a threat to all living organisms. However, cellular mechanisms underlying copper toxicity have not been fully understood up to now. The work described here reveals that iron-sulfur proteins in Escherichia coli cells are much more susceptible to copper in medium under anaerobic conditions than they are under aerobic conditions. Under anaerobic conditions, E. coli cells accumulate excess intracellular copper, which specifically targets iron-sulfur proteins by blocking iron-sulfur cluster biogenesis. Since iron-sulfur proteins are involved in diverse and vital physiological processes, inhibition of iron-sulfur cluster biogenesis by copper disrupts multiple cellular functions and ultimately inhibits cell growth. The results from this study illustrate a new interplay between intracellular copper toxicity and iron-sulfur cluster biogenesis in bacterial cells under anaerobic conditions.

Copper binding in IscA inhibits iron-sulphur cluster assembly in Escherichia coli.

Among the iron-sulphur cluster assembly proteins encoded by gene cluster iscSUA-hscBA-fdx in Escherichia coli, IscA has a unique and strong iron binding activity and can provide iron for iron-sulphur cluster assembly in proteins in vitro. Deletion of IscA and its paralogue SufA results in an E. coli mutant that fails to assemble [4Fe-4S] clusters in proteins under aerobic conditions, suggesting that IscA has a crucial role for iron-sulphur cluster biogenesis. Here we report that among the iron-sulphur cluster assembly proteins, IscA also has a strong and specific binding activity for Cu(I) in vivo and in vitro. The Cu(I) centre in IscA is stable and resistant to oxidation under aerobic conditions. Mutation of the conserved cysteine residues that are essential for the iron binding in IscA abolishes the copper binding activity, indicating that copper and iron may share the same binding site in the protein. Additional studies reveal that copper can compete with iron for the metal binding site in IscA and effectively inhibits the IscA-mediated [4Fe-4S] cluster assembly in E. coli cells. The results suggest that copper may not only attack the [4Fe-4S] clusters in dehydratases, but also block the [4Fe-4S] cluster assembly in proteins by targeting IscA in cells.

FluPMT: Prediction of Predominant Strains of Influenza A Viruses Via Multi-task Learning.

Seasonal influenza vaccines play a crucial role in saving numerous lives annually. However, the constant evolution of the influenza A virus necessitates frequent vaccine updates to ensure its ongoing effectiveness. The decision to develop a new vaccine strain is generally based on the assessment of the current predominant strains. Nevertheless, the process of vaccine production and distribution is very time-consuming, leaving a window for the emergence of new variants that could decrease vaccine effectiveness, so predictions of influenza A virus evolution can inform vaccine evaluation and selection. Hence, we present FluPMT, a novel sequence prediction model that applies an encoder-decoder architecture to predict the hemagglutinin (HA) protein sequence of the upcoming season's predominant strain by capturing the patterns of evolution of influenza A viruses. Specifically, we employ time series to model the evolution of influenza A viruses, and utilize attention mechanisms to explore dependencies among residues of sequences. Additionally, antigenic distance prediction based on graph network representation learning is incorporated into the sequence prediction as an auxiliary task through a multi-task learning framework. Experimental results on two influenza datasets highlight the exceptional predictive performance of FluPMT, offering valuable insights into virus evolutionary dynamics, as well as vaccine evaluation and production.

Protein lipidation in health and disease: molecular basis, physiological function and pathological implication.

Posttranslational modifications increase the complexity and functional diversity of proteins in response to complex external stimuli and internal changes. Among these, protein lipidations which refer to lipid attachment to proteins are prominent, which primarily encompassing five types including S-palmitoylation, N-myristoylation, S-prenylation, glycosylphosphatidylinositol (GPI) anchor and cholesterylation. Lipid attachment to proteins plays an essential role in the regulation of protein trafficking, localisation, stability, conformation, interactions and signal transduction by enhancing hydrophobicity. Accumulating evidence from genetic, structural, and biomedical studies has consistently shown that protein lipidation is pivotal in the regulation of broad physiological functions and is inextricably linked to a variety of diseases. Decades of dedicated research have driven the development of a wide range of drugs targeting protein lipidation, and several agents have been developed and tested in preclinical and clinical studies, some of which, such as asciminib and lonafarnib are FDA-approved for therapeutic use, indicating that targeting protein lipidations represents a promising therapeutic strategy. Here, we comprehensively review the known regulatory enzymes and catalytic mechanisms of various protein lipidation types, outline the impact of protein lipidations on physiology and disease, and highlight potential therapeutic targets and clinical research progress, aiming to provide a comprehensive reference for future protein lipidation research.