c-Cbl induced podocin ubiquitination contributes to the podocytes injury in diabetic nephropathy.

The ubiquitination function in diabetic nephropathy (DN) has attracted much attention, but there is a lack of information on its ubiquitylome profile. To examine the differences in protein content and ubiquitination in the kidney between db/db mice and db/m mice, we deployed liquid chromatography-mass spectrometry (LC-MS/MS) to conduct analysis. We determined 145 sites in 86 upregulated modified proteins and 66 sites in 49 downregulated modified proteins at the ubiquitinated level. Moreover, 347 sites among the 319 modified proteins were present only in the db/db mouse kidneys, while 213 sites among the 199 modified proteins were present only in the db/m mouse kidneys. The subcellular localization study indicated that the cytoplasm had the highest proportion of ubiquitinated proteins (31.87%), followed by the nucleus (30.24%) and the plasma membrane (20.33%). The enrichment analysis revealed that the ubiquitinated proteins are mostly linked to tight junctions, oxidative phosphorylation, and thermogenesis. Podocin, as a typical protein of slit diaphragm, whose loss is a crucial cause of proteinuria in DN. Consistent with the results of ubiquitination omics, the K261R mutant of podocin induced the weakest ubiquitination compared with the K301R and K370R mutants. As an E3 ligase, c-Cbl binds to podocin, and the regulation of c-Cbl can impact the ubiquitination of podocin. In conclusion, in DN, podocin ubiquitination contributes to podocyte injury, and K261R is the most significant site. c-Cbl participates in podocin ubiquitination and may be a direct target for preserving the integrity of the slit diaphragm structure, hence reducing proteinuria in DN.

Oleanolic acid attenuates hydrogen peroxide-induced apoptosis of IPEC-J2 cells through suppressing c-Jun and MAPK pathway.

Oleanolic acid (OA) is a natural triterpenoid with therapeutic potential for a multitude of diseases. However, the precise mechanism by which OA influences stress-induced apoptosis of intestinal epithelial cells remains elusive. Therefore, the effect of OA on intestinal diseases under stressful conditions and its possible mechanisms have been investigated. In a hydrogen peroxide (H2 O2 )-induced oxidative stress model, OA attenuated H2 O2 -induced apoptosis in a concentration-dependent manner. To investigate the underlying mechanisms, the gene expression profile of OA on IPEC-J2 cells was analyzed using an RNA sequencing system. Results from gene ontology and Kyoto encyclopedia of genes and genomes analysis confirmed that OA may mitigate the cytotoxic effects of H2 O2 by downregulating gene expression through the MAPK signaling pathway. Furthermore, Quantitative real-time polymerase chain reaction results validated the differentially expressed genes data. Western blot analysis further demonstrated that OA effectively suppressed the expression level of c-Jun protein induced by H2 O2 in IPEC-J2 cells. Collectively, our results indicate that OA pretreatment significantly attenuated H2 O2 -induced apoptosis in intestinal epithelial cells through suppressing c-Jun and MAPK pathway.

Engineered domain-inlaid Nme2Cas9 adenine base editors with increased on-target DNA editing and targeting scope.

BACKGROUND: Nme2ABE8e has been constructed and characterized as a compact, accurate adenine base editor with a less restrictive dinucleotide protospacer-adjacent motif (PAM: N4CC) but low editing efficiency at challenging loci in human cells. Here, we engineered a subset of domain-inlaid Nme2Cas9 base editors to bring the deaminase domain closer to the nontarget strand to improve editing efficiency. RESULTS: Our results demonstrated that Nme2ABE8e-797 with adenine deaminase inserted between amino acids 797 and 798 has a significantly increased editing efficiency with a wide editing window ranging from 4 to 18 bases in mammalian cells, especially at the sites that were difficult to edit by Nme2ABE8e. In addition, by swapping the PAM-interacting domain of Nme2ABE8e-797 with that of SmuCas9 or introducing point mutations of eNme2-C in Nme2ABE8e-797, we created Nme2ABE8e-797Smu and Nme2ABE8e-797-C, respectively, which exhibited robust activities at a wide range of sites with N4CN PAMs in human cells. Moreover, the modified domain-inlaid Nme2ABE8e can efficiently restore or install disease-related loci in Neuro-2a cells and mice. CONCLUSIONS: These novel Nme2ABE8es with increased on-target DNA editing and expanded PAM compatibility will expand the base editing toolset for efficient gene modification and therapeutic applications.

Epigenomics analysis of miRNA cis-regulatory elements in pig muscle and fat tissues.

Although large-scale and accurate identification of cis-regulatory elements on pig protein-coding and long non-coding genes has been reported, similar study on pig miRNAs is still lacking. Here, we systematically characterized the cis-regulatory elements of pig miRNAs in muscle and fat by adopting miRNAomes, ChIP-seq, ATAC-seq, RNA-seq and Hi-C data. In total, the cis-regulatory elements of 257 (85.95%) expressed miRNAs including 226 known and 31 novel miRNAs were identified. Especially, the miRNAs associated with super-enhancers, active promoters, and "A" compartment were significantly higher than those associated by typical enhancers, prompters without H3K27ac, and "B" compartment, respectively. The tissue specific transcription factors were the primary determination of core miRNA expression pattern in muscle and fat. Moreover, the miRNA promoters are more evolutionarily conserved than miRNA enhancers, like other type genes. Our study adds additional important information to existing pig epigenetic data and provides essential resource for future in-depth investigation of pig epigenetics.

HIF-1α and Caspase-3 expression in aggressive papillary thyroid carcinoma.

BACKGROUND: Tumor cells adapt to hypoxia by regulating transcription factors that involved in regulation of metabolism, angiogenesis, cell proliferation, and apoptosis. Under hypoxic conditions, hypoxia-inducible factor-1 (HIF-1), consisting of HIF-1α and HIF-1ß subunits, acts as a key transcription factor mediating the adaptive cellular responses. Caspase-3 is a key apoptosis-related protease that plays a role in tumor growth and development. Studies have shown that caspase-3 could be regulated by HIF-1α under pathological conditions. Therefore, HIF-1α and caspase-3 expression may be related to the poor prognosis of tumors. In this study, we analyzed the possible relationships between these two signaling factors in correlation with the clinical behavior of PTC. METHODS: We detected the expression levels of HIF-1α and caspase-3 in 70 samples of PTC and para-cancerous tissues (control group) by immunohistochemistry (IHC). Furthermore, various clinicopathological parameters were assessed to determine their correlations with HIF-1α and caspase-3 expressions. RESULTS: First, HIF-1α and caspase-3 expressions (60% and 37.1%, respectively) increased significantly in the PTC samples as compared to normal tissues (2.9% for both HIF-1α and caspase-3) (p < 0.05) as determined by IHC. Second, although there was no significant difference between the expression of HIF-1α and caspase-3 in regard to gender, age distribution, tumor size, lymph node metastasis, and BRAFV600E mutation (all p > 0.05), HIF-1α and caspase-3 expressions were associated with capsule invasion and cell subtypes of PTC (p < 0.05). The percent positivity of caspase-3 expression in tall-cell variant (TCV) was the highest (63.6%). Third, HIF-1α expression was positively correlated with that of caspase-3 (rs = 0.326; p < 0.05). CONCLUSIONS: Overexpression of HIF-1α and caspase-3 is associated with carcinogenesis. These factors might serve as promising predictors of aggressive PTC. These findings also suggest their potential as therapeutic targets.

Peroxyacetic Acid Pretreatment: A Potentially Promising Strategy towards Lignocellulose Biorefinery.

The stubborn and complex structure of lignocellulose hinders the valorization of each component of cellulose, hemicellulose, and lignin in the biorefinery industries. Therefore, efficient pretreatment is an essential and prerequisite step for lignocellulose biorefinery. Recently, a considerable number of studies have focused on peroxyacetic acid (PAA) pretreatment in lignocellulose fractionation and some breakthroughs have been achieved in recent decades. In this article, we aim to highlight the challenges of PAA pretreatment and propose a roadmap towards lignocellulose fractionation by PAA for future research. As a novel promising pretreatment method towards lignocellulosic fractionation, PAA is a strong oxidizing agent that can selectively remove lignin and hemicellulose from lignocellulose, retaining intact cellulose for downstream upgrading. PAA in lignocellulose pretreatment can be divided into commercial PAA, chemical activation PAA, and enzymatic in-situ generation of PAA. Each PAA for lignocellulose fractionation shows its own advantages and disadvantages. To meet the theme of green chemistry, enzymatic in-situ generation of PAA has aroused a great deal of enthusiasm in lignocellulose fractionation. Furthermore, mass balance and techno-economic analyses are discussed in order to evaluate the feasibility of PAA pretreatment in lignocellulose fractionation. Ultimately, some perspectives and opportunities are proposed to address the existing limitations in PAA pretreatment towards biomass biorefinery valorization. In summary, from the views of green chemistry, enzymatic in-situ generation of PAA will become a cutting-edge topic research in the lignocellulose fractionation in future.

Structure-activity relationship of Garcinia xanthones analogues: Potent Hsp90 inhibitors with cytotoxicity and antiangiogenesis activity.

Hsp90 has long been recognized as an attractive and crucial molecular target for cancer therapy. Gambogic acid (GA), the main active compound of Gamboge hanburyi, has been reported as a natural inhibitor of Hsp90. Here, we present the structure-activity relationship of Garcinia xanthones analogues as Hsp90 inhibitors and identify that compound 25, with a simplified skeleton, had an improved inhibitory effect toward Hsp90. Compound 25 inhibited the ATPase activity of Hsp90 with an IC50 value of 3.68±0.18µM. It also exhibited potent antiproliferative activities in some solid tumor cells. In SK-BR-3 cells with high Hsp90 expression, compound 25 induced the degradation of Hsp90 client proteins including Akt and Erk1/2 without causing the heat shock response. Additionally, compound 25 inhibited angiogenesis in HUVEC cells through Hsp90 regulation of the HIF-1α pathway. These results demonstrate that compound 25 as an Hsp90 inhibitor with a new structure could be further studied for the development of tumor therapy.

Novel natural-product-like caged xanthones with improved druglike properties and in vivo antitumor potency.

DDO-6101, a natural-product-like caged xanthone discovered previously in our laboratory based on the pharmacophoric scaffold of Garcinia natural product gambogic acid (GA), shows potent cytotoxicity in vitro but poor efficacy in vivo due to its poor druglike properties. In order to improve the druglike properties and in vivo cytotoxic potency, a novel series of 19 prenyl group-modified derivatives of DDO-6101 was synthesized and evaluated for their in vitro antitumor activity and druglike properties. The SAR and SPR information of these compounds was also obtained. In the light of the in vitro antitumor activity and druglike properties such as aqueous solubility and permeability, compound 6f (named as DDO-6306) was advanced into in vivo efficacy experiment. The results showed that DDO-6306 is more potent than DDO-6101 in vivo and is a promising antitumor candidate for further evaluation.

Investigating river pollution flowing into Dianchi Lake using a combination of GC-MS analysis and toxicological tests.

Due to the presence of various harmful compounds in polluted water, toxicological tests should be combined to evaluate whether a body of water is polluted. The water quality of four rivers flowing into Dianchi Lake, which is well known for its heavy and lasting pollution, was investigated in this study using a combination of GC-MS analysis and cytotoxicity and mutagenicity tests. GC-MS analysis showed that the rivers investigated contained a variety of chemicals and suggested that severe water pollution existed. In addition, the water obtained from the four rivers induced acute cytotoxicity in CHO cells and dose-dependent mutagenicity in four Salmonella typhimurium strains (TA97, TA98, TA100 and TA102). The integration of GC-MS analysis and short-term in vitro toxicological tests might be a valuable approach that can be used to monitor the health hazards that may result from water pollution.

Structural properties and adsorption performance relationship towards three categories of lignin and their derived biochar.

The growing interest in utilizing lignin for dye removal has gained momentum, but there is limited information on the intricate relationship between lignin structural characteristics and adsorption efficacy, especially for its biochar derivatives. This study focused on three types of lignin and their corresponding biochar derivatives. Among them, ZnCl2-activated acidic/alkali densified lignin preparation of lignin-derived active carbon exhibited superior adsorption performance, achieving 526.32 mg/g for methylene blue and 2156.77 mg/g for congo red. Its exceptional adsorption capacity was attributed to its unique structural properties, including low alkyl and O-alkyl group content and high aromatic carbon levels. Furthermore, the adsorption mechanisms adhered to pseudo-second-order kinetics and the Langmuir model, signifying a spontaneous process. Intriguingly, lignin-derived active carbon also demonstrated remarkable recovery capabilities. These findings provide valuable insights into the impact of structural attributes on lignin and its biochar's adsorption performance.

The competitive and selective adsorption of heavy metals by struvite in the Pb(II)-Cd(II)-Zn(II) composite system and its environmental significance.

The prevalence of struvite and other phosphate minerals in eutrophic environments has a significant effect on the transport and transformation of environmental heavy metals, but their competitive immobilization characteristics and mechanisms for heavy metals remain unclear. Three different sources of struvite (BS, CSHS, and CSS) were obtained respectively by biosynthesis and chemical synthesis with or without humic acid to investigate their competitive immobilization characteristics and mechanism of heavy metals in the Pb(II)-Cd(II)-Zn(II) composite system. The results showed that the immobilization of heavy metals by struvite is physico-chemical adsorption and the affinity (in descending order) is Pb(II) >> Cd(II)/Zn(II). Cd(II) promotes the immobilization of Pb(II)/Zn(II) by BS. The order of the selective strength by struvite for Pb(II) is BS >> CSS ≈ CSHS. The study indicates that the difference between struvite holding heavy metal ions is related to the material composition and heavy metal types, and BS shows best selective immobilization for Pb(II) in the Pb(II)-Cd(II)-Zn(II) composite system. This study provides a theoretical basis for understanding the environmental geochemical role and eco-environmental effects of struvite.

Heterologous expression of the novel dimeric antimicrobial peptide LIG in Pichia pastoris.

The antimicrobial peptide (AMP) LI is a fusion product of antimicrobial peptide LL37 produced by human neutrophils and Indolicidin secreted by bovine neutrophils. LI retained the antimicrobial activity of the parental peptides and showed high cell selectivity. In this study, the flexible linker Gly-Ser-Gly (G-S-G) was used to ligate LI into dimeric LIG, and constructed the Pichia pastoris (P. pastoris) expression vector pPIC9K-6×His-3×FLAG-LIG. The total protein expression of P. pastoris GS115 reached the highest level (189.6 mg/L) after 96 h induction with 3 % methanol at the initial pH value of 7.0. Finally, 5.9 mg/L of recombinant LIG (rLIG) was obtained after enterokinase digestion and purification. The rLIG had high antimicrobial activity and low hemolytic activity. Compared with monomer LI, GSG linked dimeric LIG, which had no significant change in antimicrobial activity and had good salt ions stability. In this study, the dimeric antimicrobial peptide LIG was successfully expressed, which provided a new idea for the expression of AMPs in the P. pastoris expression system, and had important significance for the application of AMPs.

Precise large-fragment deletions in mammalian cells and mice generated by dCas9-controlled CRISPR/Cas3.

Currently, the Cas9 and Cas12a systems are widely used for genome editing, but their ability to precisely generate large chromosome fragment deletions is limited. Type I-E CRISPR mediates broad and unidirectional DNA degradation, but controlling the size of Cas3-mediated DNA deletions has proven elusive thus far. Here, we demonstrate that the endonuclease deactivation of Cas9 (dCas9) can precisely control Cas3-mediated large-fragment deletions in mammalian cells. In addition, we report the elimination of the Y chromosome and precise retention of the Sry gene in mice using CRISPR/Cas3 and dCas9-controlled CRISPR/Cas3, respectively. In conclusion, dCas9-controlled CRISPR/Cas3-mediated precise large-fragment deletion provides an approach for establishing animal models by chromosome elimination. This method also holds promise as a potential therapeutic strategy for treating fragment mutations or human aneuploidy diseases that involve additional chromosomes.

Determining the bending modulus of a lipid membrane by simulating buckling.

The force needed to buckle a thin elastic surface is proportional to its bending rigidity. This fact suggests using a buckling setup to measure the bending modulus of lipid membranes. Extending the work of Noguchi [Phys. Rev. E 83, 061919 (2011)], we systematically derive highly accurate analytical expressions for the forces along and perpendicular to the buckle, and we elucidate some of their counterintuitive properties using the framework of a surface stress tensor. Furthermore, we estimate the corrections to buckling forces due to thermal fluctuations and find them significant only for stresses along the ridges. We then apply this buckling protocol to four different lipid membrane models, which widely differ in their level of resolution and the treatment of solvent, and show that in all cases buckling is a reliable and accurate means for measuring their rigidity. Finally, we show that monitoring both stresses and energies during a simulation offers additional insights into the thermodynamics of curvature elasticity and permits one to predict the bending rigidity for a range of temperatures around the actual simulation temperature.

Application of transabdominal ultrasonography in the diagnosis of absent contractility - a case report.

INTRODUCTION: Absent contractility is a kind of esophageal motility disorder. Patients are often diagnosed by endoscopic ultrasonography or high-resolution manometry (HRM). In this paper, we report two cases of absent esophageal contractility first discovered by transabdominal ultrasonography. CASE PRESENTATION: The main symptom of both cases was acid reflux, and the main diagnosis was absent esophageal contractility. They were all discovered by transabdominal ultrasonography. After the treatment of surgery or drugs, the symptoms relieved during follow-up, without any other discomforts. CONCLUSION: Transabdominal ultrasound as a primary screening method for absent contractility is proposed in this paper, which is non-invasive, real-time, and fast. Ultrasound is expected to improve the diagnostic efficiency of peristalsis and patient experience in combination with the above invasive examinations. The use of sonography in the diagnosis of absent contractility has seldom been studied. Further investigation is required to determine whether this technique may better assess absent contractility.

Ammonia fiber expansion-assisted deep eutectic solvent treatment for wheat straw fraction separation and bioconversion.

In this study, an ammonia fiber expansion (AFEX)-assisted deep eutectic solvent (DES) pretreatment method was developed for the rapid separation of wheat straw fractions, which reduced the pretreatment time for DES and improved the pretreatment efficiency. This study describes the feasibility of the AFEX-assisted DES pretreatment in terms of both progressive and parallel relationships and analyzes the subsequent enzymatic effect in generating glucose from cellulose. Ammonia fiber expansion-assisted DES one-pot pretreatment at 120 °C, for 1.5 h resulted in an enzymatic efficiency of 98.0 ± 3.1 %. Moreover, the enzyme efficiency remained greater than 85 % after three recovery cycle experiments. The comparison between regenerated-lignin (d-lignin) and alkaline-lignin showed that regenerated lignin has a lower molecular weight and belongs to para-hydroxy-phenyl-guaiacyl-syringyl (H-G-S) type lignin. This study developed is a green and efficient pretreatment process with great potential in the separation and utilization of biomass fractions.

EcAGL enhances cadmium tolerance in transgenic Arabidopsis thaliana through inhibits cadmium transport and ethylene synthesis pathway.

Cadmium (Cd) is a highly toxic heavy metal with severe impacts on plant growth and development. Although a multitude of plants have acquired strong tolerance to Cd stress, the underlying molecular mechanism has not been fully elucidated. Here, we identified a Agamous-like MADS-box gene (EcAGL) from Erigeron canadensis. The expression of EcAGL was obviously raised under Cd stress and subcellular localization indicated EcAGL was localized in the nucleus. Overexpression of EcAGL in Arabidopsis thaliana showed marked alleviation of the Cd-induced reduction; Compared to wild-type lines, the antioxidant enzymes activities were increased in EcAGL overexpressing lines under Cd stress. The roots Cd content of transgenic lines was not different with the control plants, whereas significant reduction in shoots Cd content was detected in the transgenic lines, indicating that this gene can enhance Cd tolerance by reducing Cd accumulation in Arabidopsis. Moreover, the expression levels of heavy metal ATPase (AtHMA2 and AtHMA3) and natural resistance-associated macrophage protein (AtNRAMP5) genes in the root of transgenic lines decreased under Cd stress, indicating that EcAGL likely hampered the Cd transport pathway. Gene expression profiles in shoot showed that EcAGL likely modulates the expression of 1-aminocyclopropane-1-carboxylic acid synthase gene (AtACS2), which is involved in the ethylene synthesis pathway, to strengthen the tolerance to Cd. Collectively, these results indicate that EcAGL plays a significant role in regulating Cd tolerance in E. canadensis by alleviating oxidative stress, Cd transport and affecting the ethylene biosynthesis pathway, providing new insight into the molecular mechanism underlying plant tolerance to Cd stress.

Colonization and development of the gut microbiome in calves.

Colonization and development of the gut microbiome are crucial for the growth and health of calves. In this review, we summarized the colonization, beneficial nutrition, immune function of gut microbiota, function of the gut barrier, and the evolution of core microbiota in the gut of calves of different ages. Homeostasis of gut microbiome is beneficial for nutritional and immune system development of calves. Disruption of the gut microbiome leads to digestive diseases in calves, such as diarrhea and intestinal inflammation. Microbiota already exists in the gut of calf fetuses, and the colonization of microbiota continues to change dynamically under the influence of various factors, which include probiotics, diet, age, and genotype. Colonization depends on the interaction between the gut microbiota and the immune system of calves. The abundance and diversity of these commensal microbiota stabilize and play a critical role in the health of calves.

Modulating gastrointestinal microbiota to alleviate diarrhea in calves.

The calf stage is a critical period for the development of heifers. Newborn calves have low gastrointestinal barrier function and immunity before weaning, making them highly susceptible to infection by various intestinal pathogens. Diarrhea in calves poses a significant threat to the health of young ruminants and may cause serious economic losses to livestock farms. Antibiotics are commonly used to treat diarrhea and promote calf growth, leading to bacterial resistance and increasing antibiotic residues in meat. Therefore, finding new technologies to improve the diarrhea of newborn calves is a challenge for livestock production and public health. The operation of the gut microbiota in the early stages after birth is crucial for optimizing immune function and body growth. Microbiota colonization of newborn animals is crucial for healthy development. Early intervention of the calf gastrointestinal microbiota, such as oral probiotics, fecal microbiota transplantation and rumen microbiota transplantation can effectively relieve calf diarrhea. This review focuses on the role and mechanisms of oral probiotics such as Lactobacillus, Bifidobacterium and Faecalibacterium in relieving calf diarrhea. The aim is to develop appropriate antibiotic alternatives to improve calf health in a sustainable and responsible manner, while addressing public health issues related to the use of antibiotics in livestock.

Identification and Genome-Wide Gene Expression Perturbation of a Trisomy in Chinese Kale (Brassica oleracea var. alboglabra).

Trisomy harbouring an extra copy of the chromosome generally causes a variety of physical and intellectual disabilities in mammals but is an extremely rare and important genetic stock in plants. In this study, a spontaneous trisomy plant in a Chinese kale accession (Brassica oleracea var. alboglabra, CC, 2n = 18) that showed significantly smaller plant architecture when compared to other normal plants was found and subsequently confirmed by cytological analysis in which the chromosome set of 2n = 19 and abnormal chromosome behaviour were observed. Then, based on the gene expression deviation determined by RNA-seq, the extra chromosome copy in this trisomy was identified as chromosome C2 (TC2). Compared to normal plants, TC2 not only showed generally upregulated differentially expressed genes (DEGs) on chromosome C2 (97.21% of 573 DEGs in chromosome C2) but also exhibited a whole-genome expression perturbation, in which 1329 DEGs (69.87% of total DEGs) were observed along two-copy chromosomes (trans-effect). The genes in the high (gene expression value > 100) and medium (100 > gene expression value > 10) groups were more prone to decreased gene expression, but the genes in the low group (10 > gene expression value > 0.1) showed upregulated expression deviation. In addition, GO (Gene ontology) annotation analysis revealed that the upregulated DEGs in the trans-effect group were overrepresented by the genes involved in the response to stress category, while the downregulated DEGs in the trans-effect group were mostly enriched in pathways related to DNA synthesis. In conclusion, we think our results can provide important resources for genetic analysis in B. oleracea and show some novel insights for understanding trisomy plant biology.