Insights into the effects of saline forage on the meat quality of Tibetan sheep by metabolome and multivariate analysis

This work aimed to investigate how two different types of forage (saline and alkaline) impact the meat quality and muscle metabolism of Tibetan sheep. An integrative multi-omics analysis of meat quality and different metabolites was performed using untargeted and targeted metabolomics approaches. The research results indicated that GG grass (saline and alkaline forage) possessed superior characteristics in terms of apparent quality and secondary metabolite content compared with HG grass (Non saline alkali forage), regardless of the targeted metabolites or non-targeted ones. Simultaneously, under stress conditions, the carbohydrates-rich salt-alkali grass play a significant role in slowing down the decline in pH, increasing the unsaturated fatty acid content and reducing the thawing loss in Tibetan sheep. This study provides an understanding of the impact of different salt-alkali grass on the quality of Tibetan sheep meat, while providing a scientific basis for the future development of salt-alkali livestock industry.

Evidence for an RNAi-independent role of Arabidopsis DICER-LIKE2 in growth inhibition and basal antiviral resistance

Flowering plant genomes encode four or five DICER-LIKE (DCL) enzymes that produce small interfering RNAs (siRNAs) and microRNAs which function in RNA interference (RNAi). Different RNAi pathways in plants effect transposon silencing, antiviral defense and endogenous gene regulation. DCL2 acts genetically redundantly with DCL4 to confer basal antiviral defense. However, DCL2 may also counteract DCL4, since knockout of DCL4 causes growth defects that are suppressed by DCL2 inactivation. Current models maintain that RNAi via DCL2-dependent siRNAs is the biochemical basis of both effects. Here, we report that DCL2-mediated antiviral resistance and growth defects cannot be explained by the silencing effects of DCL2-dependent siRNAs. Both functions are defective in genetic backgrounds that maintain high levels of DCL2-dependent siRNAs, either with specific point mutations in DCL2 or with reduced DCL2 dosage because of heterozygosity for dcl2 knockout alleles. Intriguingly, all DCL2 functions require its catalytic activity, and the penetrance of DCL2-dependent growth phenotypes in dcl4 mutants correlates with DCL2 protein levels, but not with levels of major DCL2-dependent siRNAs. We discuss this requirement and correlation with catalytic activity, but not with resulting siRNAs, in light of other findings that reveal a DCL2 function in innate immunity activation triggered by cytoplasmic double-stranded RNA.

Effects of flora deficiency on the structure and function of the large intestine

The significant anatomical changes in large intestine of germ-free (GF) mice provide excellent material for understanding microbe-host crosstalk. We observed significant differences of GF mice in anatomical and physiological involving in enlarged cecum, thinned mucosal layer and enriched water in cecal content. Furthermore, integration analysis of multi-omics data revealed the associations between the structure of large intestinal mesenchymal cells and the thinning of the mucosal layer. Increased Aqp8 expression in GF mice may contribute to enhanced water secretion or altered hydrodynamics in the cecum. In addition, the proportion of epithelial cells, nutrient absorption capacity, immune function and the metabolome of cecum contents of large intestine were also significantly altered. Together, this is the first systematic study of the transcriptome and metabolome of the cecum and colon of GF mice, and these findings contribute to our understanding of the intricate interactions between microbes and the large intestine.

Integrated metabolome and microbiome analysis reveals the effect of rumen-protected sulfur-containing amino acids on the meat quality of Tibetan sheep meat

Introduction

This study investigated the effects of rumen-protected sulfur-containing amino acids (RPSAA) on the rumen and jejunal microbiota as well as on the metabolites and meat quality of the longissimus lumborum (LL) in Tibetan sheep.

Methods

By combining 16S rDNA sequencing with UHPLC-Q-TOF MS and Pearson correlation analysis, the relationship between gastrointestinal microbiota, muscle metabolites and meat quality was identified.

Results

The results showed that feeding RPSAA can increase the carcass weight, abdominal fat thickness (AP-2 group), and back fat thickness (AP-2 and AP-3 group) of Tibetan sheep. The water holding capacity (WHC), texture, and shear force (SF) of LL in the two groups also increased although the fatty acids content and brightness (L*) value significantly decreased in the AP-2 group. Metabolomics and correlation analysis further showed that RPSAA could significantly influence the metabolites in purine metabolism, thereby affecting L* and SF. In addition, RPSAA was beneficial for the fermentation of the rumen and jejunum. In both groups, the abundance of Prevotella 1, Lachnospiraceae NK3A20 group, Prevotella UCG-003, Lachnospiraceae ND3007 group in the rumen as well as the abundance of Eubacterium nodatum group and Mogibacterium group in the jejunum increased. In contrast, that of Turicibacter pathogens in the jejunum was reduced. The above microorganisms could regulate meat quality by regulating the metabolites (inosine, hypoxanthine, linoleic acid, palmitic acid, etc.) in purine and fatty acids metabolism.

Discussion

Overall, reducing the levels of crude proteins in the diet and feeding RPSAA is likely to improve the carcass quality of Tibetan sheep, with the addition of RPMET (AP-2) yielding the best edible quality, possibly due to its ability to influence the gastrointestinal microbiota to subsequently regulate muscle metabolites.

Production of D -tagatose, bioethanol, and microbial protein from the dairy industry by-product whey powder using an integrated bioprocess

We designed and constructed a green and sustainable bioprocess to efficiently coproduce D -tagatose, bioethanol, and microbial protein from whey powder. First, a one-pot biosynthesis process involving lactose hydrolysis and D -galactose redox reactions for D -tagatose production was established in vitro via a three-enzyme cascade. Second, a nicotinamide adenine dinucleotide phosphate-dependent galactitol dehydrogenase mutant, D36A/I37R, based on the nicotinamide adenine dinucleotide-dependent polyol dehydrogenase from Paracoccus denitrificans was created through rational design and screening. Moreover, an NADPH recycling module was created in the oxidoreductive pathway, and the tagatose yield increased by 3.35-fold compared with that achieved through the pathway without the cofactor cycle. The reaction process was accelerated using an enzyme assembly with a glycine-serine linker, and the tagatose production rate was 9.28-fold higher than the initial yield. Finally, Saccharomyces cerevisiae was introduced into the reaction solution, and 266.5 g of D -tagatose, 162.6 g of bioethanol, and 215.4 g of dry yeast (including 38% protein) were obtained from 1 kg of whey powder (including 810 g lactose). This study provides a promising sustainable process for functional food (D -tagatose) production. Moreover, this process fully utilized whey powder, demonstrating good atom economy.

Insight into the differences of meat quality between Qinghai white Tibetan sheep and black Tibetan sheep from the perspective of metabolomics and rumen microbiota

The purpose of this study was to investigate the differences in meat quality between two local breeds of Tibetan sheep, the White Tibetan sheep and the Black Tibetan sheep in Qinghai, and to search for metabolic mechanisms that produce meat quality differences by analyzing differential metabolites and key rumen microorganisms. The meat quality results showed that one breed, SG73, was superior to the other (WG). Further investigation identified differences in the composition of muscle metabolites and rumen microorganisms between the two Tibetan sheep breeds. It also regulates muscle tenderness, water retention, fat content and the composition and content of AA and FA through two major metabolic pathways, AA metabolism and carbohydrate metabolism. These findings could be beneficial for the development of breeding strategies for Tibetan sheep in Qinghai in the future.

A virus induces alterations in root morphology while exerting minimal effects on the rhizosphere and endosphere microorganisms in rice

The highly destructive southern rice black-streaked dwarf virus (SRBSDV) causes significant losses in rice production. To understand its impact on rice root, we studied fibrous root development and root microbiota variation (rhizosphere and endosphere) after SRBSDV infection. SRBSDV infection reduced the number and length of fibrous roots in rice. Interestingly, the rhizosphere had higher bacterial diversity and abundance at the initial (0 days) and 30-day postinfection stages, while 30-day-old roots showed increased diversity and abundance. However, there were no significant differences in microbiota diversity between infected and noninfected rice plants. The major rhizosphere microbiota included Proteobacteria, Bacteroidota, Acidobacteriota, and Planctomycetota, comprising about 80% of the community. The endosphere was dominated by Proteobacteria and Cyanobacteria, constituting over 90%, with Bacteroidota as the next most prominent group. Further, we identified differentially expressed genes related to plant-pathogen interactions, plant hormone signal, and ABC transporters, potentially affecting root morphology. Notably, specific bacteria (e.g. Inquilinus and Actinoplanes) showed correlations with these pathways. In conclusion, SRBSDV primarily influences root growth through host metabolism, rather than exerting direct effects on the root microbiota. These insights into the interactions among the pathogen, rice plant, and associated microbiota could have implications for managing SRBSDV's detrimental effects on rice production.

CAR-T cells targeting CD38 and LMP1 exhibit robust antitumour activity against NK/T cell lymphoma

BACKGROUND

Natural killer/T cell lymphoma (NKTCL) is an aggressive lymphoma with a poor prognosis. Chimeric antigen receptor-transduced T (CAR-T) cell therapy has become a promising immunotherapeutic strategy against haematologic malignancies.

METHODS

In this study, four CAR-T cell lines (CD38-CAR, LMP1-CAR, CD38-LMP1 tandem CAR 1 and CD38-LMP1 tandem CAR 2) were generated. The effect of CAR-T cells against NKTCL cells was evaluated both in vitro and in vivo. Expression of T cell activation markers and cytokines produced by CAR-T cells were detected by flow cytometry.

RESULTS

The four CAR-T cell lines could effectively eliminate malignant NKTCL cells. They could be activated and produce inflammatory cytokines in a target-dependent manner. In vivo tests showed that the CAR-T cells exhibited significant antitumour effects in a xenotransplanted NKTCL mouse model.

CONCLUSIONS

In summary, four CAR-T cell lines exhibited significant cytotoxicity against NKTCL cells both in vitro and in vivo. These results indicated the effective therapeutic promise of CD38 and LMP1 CAR-T cells in NKTCL.

Exploring the effects of palm kernel meal feeding on the meat quality and rumen microorganisms of Qinghai Tibetan sheep

Palm kernel meal (PKM) has been shown to be a high-quality protein source in ruminant feeds. This study focused on the effects of feed, supplemented with different amounts of PKM (ZL-0 as blank group, and ZL-15, ZL-18, and ZL-21 as treatment group), on the quality and flavor profile of Tibetan sheep meat. Furthermore, the deposition of beneficial metabolites in Tibetan sheep and the composition of rumen microorganisms on underlying regulatory mechanisms of meat quality were studied based on ultra-performance liquid chromatography coupled with quadrupole time-of-flight mass spectrometry as well as 16S rDNA sequencing. The results of the study showed that Tibetan sheep in the ZL-18 group exhibited superior eating quality and flavor profile while depositing more protein and fat relative to the other groups. The ZL-18 group also changed significantly in terms of the concentration and metabolic pathways of meat metabolites, as revealed by metabolomics. Metabolomics and correlation analyses finally showed that PKM feed mainly affected carbohydrate metabolism in muscle, which in turn affects meat pH, tenderness, and flavor. In addition, 18% of PKM increased the abundance of Christensenellaceae R-7 group, Ruminococcaceae UCG-013, Lachnospiraceae UCG-002, and Family XIII AD3011 group in the rumen but decreased the abundance of Prevotella 1; the above bacteria groups regulate meat quality by regulating rumen metabolites (succinic acid, DL-glutamic acid, etc.). Overall, the addition of PKM may improve the quality and flavor of the meat by affecting muscle metabolism and microorganisms in the rumen.

Reprogramming the Metabolic Network in Kluyveromyces lactis with a Transcriptional Switch for De Novo Lacto-N-biose Synthesis

Lacto-N-biose (LNB) is a member of the human milk oligosaccharide (HMO) family and is synthesized via an enzymatic reaction in vitro with N-acetylglucosamine (GlcNAc) and cofactors. In this study, LNB was synthesized using a cell factory for the first time. First, three modules were constructed in Kluyveromyces lactis for producing LNB from lactose and GlcNAc without the addition of cofactors. Second, a de novo pathway was constructed in K. lactis for producing LNB from lactose without adding GlcNAc. Finally, a transcriptional switch was introduced into K. lactis to reprogram its metabolic network for improving the flux from GlcNAc-6-P to GlcNAc in the de novo pathway. Subsequently, a final LNB yield of 10.41 g/L, similar to the salvage pathway yield, was achieved through the de novo pathway. The engineered K. lactis provides a promising technology platform for the industrial scale production of LNB.

Selection of p53 pathway in adaptive evolution and reproductive isolation in incipient sympatric speciation of Drosophila at Evolution Canyon

Sympatric speciation (SS) refers to the origin of new species within a freely breeding population. The ‘Evolution Canyon’ (EC) in Israel is a natural microsite model for SS of species across phylogenies from viruses and bacteria to mammals, adapting to, and speciating in, interslope microclimates. The cosmopolitan Drosophila melanogaster at EC I, Mount Carmel, is undergoing incipient SS in response to sharply divergent interslope microclimate stresses, including solar radiation, temperature, humidity and pathogenicity. We demonstrated here a selective interslope divergence of single nucleotide polymorphism (SNP) distribution in the Drosophila p53 pathway. This involves a total of 71 genes, which are associated with DNA repair, heat response, and fungal and bacterial resistant pathways. This distribution pattern links the previously observed thermotolerance and ageing divergence of D. melanogaster between the opposite canyon slopes: the south-facing slope (SFS, or African slope: tropical, savannoid and dry) and the abutting north-facing slope (NFS, or European slope; temperate, forested, cool and humid). The genes with interslope-significant differential SNPs link the p53 pathway with pathways related to the responses to microclimates through protein-protein interaction. Moreover, for the first time we provide evidence that the p53 pathway is linked to reproductive isolation, and is thus actively participating in incipient SS of D. melanogaster. This is the first demonstration of a link between the p53 pathway and reproductive isolation, thereby contributing to adaptive incipient sympatric speciation.

ATANN3 Is Involved in Extracellular ATP-Regulated Auxin Distribution in Arabidopsis thaliana Seedlings

Extracellular ATP (eATP) plays multiple roles in plant growth and development, and stress responses. It has been revealed that eATP suppresses growth and alters the growth orientation of the root and hypocotyl of Arabidopsis thaliana by affecting auxin transport and localization in these organs. However, the mechanism of the eATP-stimulated auxin distribution remains elusive. Annexins are involved in multiple aspects of plant cellular metabolism, while their role in response to apoplastic signals remains unclear. Here, by using the loss-of-function mutations, we investigated the role of AtANN3 in the eATP-regulated root and hypocotyl growth. Firstly, the inhibitory effects of eATP on root and hypocotyl elongation were weakened or impaired in the AtANN3 null mutants (atann3-1 and atann3-2). Meanwhile, the distribution of DR5-GUS and DR5-GFP indicated that the eATP-induced asymmetric distribution of auxin in the root tips or hypocotyl cells occurred in wild-type control plants, while in atann3-1 mutant seedlings, it was not observed. Further, the eATP-induced asymmetric distribution of PIN2-GFP in root-tip cells or that of PIN3-GFP in hypocotyl cells was reduced in atann3-1 seedlings. Finally, the eATP-induced asymmetric distribution of cytoplasmic vesicles in root-tip cells was impaired in atann3-1 seedlings. Based on these results, we suggest that AtANN3 may be involved in eATP-regulated seedling growth by regulating the distribution of auxin and auxin transporters in vegetative organs.

Metabolome and microbiome analysis revealed the effect mechanism of different feeding modes on the meat quality of Black Tibetan sheep

Introduction

Black Tibetan sheep is one of the primitive sheep breeds in China that is famous for its great eating quality and nutrient value but with little attention to the relationship between feeding regimes and rumen metabolome along with its impact on the muscle metabolism and meat quality.

Methods

This study applies metabolomics-based analyses of muscles and 16S rDNA-based sequencing of rumen fluid to examine how feeding regimes influence the composition of rumen microbiota, muscle metabolism and ultimately the quality of meat from Black Tibetan sheep. Twenty-seven rams were randomly assigned to either indoor feeding conditions (SG, n = 9), pasture grazing with indoor feeding conditions (BG, n = 9) or pasture grazing conditions (CG, n = 9) for 120 days.

Results

The results showed that, compared with BG and CG, SG improved the quality of Black Tibetan sheep mutton by preventing a decline in pH and increasing fat deposition to enhance the color, tenderness and water holding capacity (WHC) of the Longissimus lumborum (LL). Metabolomics and correlation analyses further indicated that the feeding regimes primarily altered amino acid, lipid and carbohydrate metabolism in muscles, thereby influencing the amino acid (AA) and fatty acid (FA) levels as well as the color, tenderness and WHC of the LL. Furthermore, SG increased the abundance of Christensenellaceae R-7 group, [Eubacterium] coprostanoligenes group, Methanobrevibacter, Ruminococcus 2 and Quinella, decreased the abundance of Lactobacillus, Prevotella 1 and Rikenellaceae RC9 gut group, and showed a tendency to decrease the abundance of Succinivibrio and Selenomonas 1. Interestingly, all of these microorganisms participated in the deposition of AAs and FAs and modified the levels of different metabolites involved in the regulation of meat quality (maltotriose, pyruvate, L-ascorbic acid, chenodeoxycholate, D-glucose 6-phosphate, glutathione, etc.).

Discussion

Overall, the results suggest that feeding Black Tibetan sheep indoors with composite forage diet was beneficial to improve the mouthfeel of meat, its color and its nutritional value by altering the abundance of rumen bacteria which influenced muscle metabolism.

The impact of Traditional Chinese Medicine on mouse gut microbiota abundances and interactions based on Granger causality and pathway analysis

Objectives

The intestinal microbiota is essential in absorbing nutrients and defending against pathogens and is associated with various diseases, including obesity, type 2 diabetes, and hypertension. As an alternative medicine, Traditional Chinese Medicine (TCM) has long been used in disease treatment and healthcare, partly because it may mediate gut microbiota. However, the specific effects of TCM on the abundance and interactions of microbiota remain unknown. Moreover, using TCM ingredients and data detailing changes in the abundance of gut microorganisms, we developed bioinformatic methods that decipher the impact of TCM on microorganism interactions.

Methods

The dynamics of gut microorganisms affected by TCM treatments is explored using a mouse model, which provided the abundance of 70 microorganisms over time. The Granger causality analysis was used to measure microorganism interactions. Novel "serial connection" and "diverging connection" models were used to identify molecular mechanisms underlying the impact of TCM on gut microorganism interactions, based on microorganism proteins, TCM chemical ingredients, and KEGG reaction equations.

Results

Codonopsis pilosula (Dangshen), Cassia twig (Gui Zhi), Radices saussureae (Mu Xiang), and Sijunzi Decoction did not cause an increase in the abundance of harmful microorganisms. Most TCMs decreased the abundance of Bifidobacterium pseudolongum, suggesting a Bifidobacterium pseudolongum supplement should be used during TCM treatment. The Granger causality analysis indicated that TCM treatment changes more than half the interactions between the 70 microorganisms, and "serial connection" and "diverging connection" models suggested that changes in interactions may be related to the reaction number connecting species proteins and TCM ingredients. From a species diversity perspective, a TCM decoction is better than a single herb for healthcare. The Sijunzi Decoction only significantly increased the abundance of Bifidobacterium pseudolongum and did not cause a decrease in the abundance of other species but was found to improve the alpha diversity with the lowest replacement rate.

Conclusions

Because most of the nine TCMs are medicinal and edible plants, we expect the methods and results presented can be used to optimize and integrate microbiota and TCMs into healthcare processes. Moreover, as a control study, these results can be combined with future disease mouse models to link variations in species abundance with particular diseases.

Association of the characteristics of the blood metabolome and gut microbiome with the outcome of methotrexate therapy in psoriasis

Metabolic status and gut microecology are implicated in psoriasis. Methotrexate (MTX) is usually the first-line treatment for this disease. However, the relationship between MTX and host metabolic status and the gut microbiota is unclear. This study aimed to characterize the features of blood metabolome and gut microbiome in patients with psoriasis after treatment with MTX. Serum and stool samples were collected from 15 patients with psoriasis. Untargeted liquid chromatography–mass spectrometry and metagenomics sequencing were applied to profile the blood metabolome and gut microbiome, respectively. We found that the response to MTX varied according to metabolomic and metagenomic features at baseline; for example, patients who had high levels of serum nutrient molecular and more enriched gut microbiota had a poor response. After 16 weeks of MTX, we observed a reduction in microbial activity pathways, and patients with a good response showed more microbial activity and less biosynthesis of serum fatty acid. We also found an association between the serum metabolome and the gut microbiome before intervention with MTX. Carbohydrate metabolism, transporter systems, and protein synthesis within microbes were associated with host metabolic clusters of lipids, benzenoids, and organic acids. These findings suggest that the metabolic status of the blood and the gut microbiome is involved in the effectiveness of MTX in psoriasis, and that inhibition of symbiotic intestinal microbiota may be one of the mechanisms of action of MTX. Prospective studies in larger sample sizes are needed to confirm these findings.

Metabolomics approach reveals high energy diet improves the quality and enhances the flavor of black Tibetan sheep meat by altering the composition of rumen microbiota

This study aims to determine the impact of dietary energy levels on rumen microbial composition and its relationship to the quality of Black Tibetan sheep meat by applying metabolomics and Pearson's correlation analyses. For this purpose, UHPLC-QTOF-MS was used to identify the metabolome, whereas 16S rDNA sequencing was used to detect the rumen microbiota. Eventually, we observed that the high energy diet group (HS) improved the carcass quality of Black Tibetan sheep and fat deposition in the longissimus lumborum (LL) compared to the medium energy diet group (MS). However, HS considerably increased the texture, water holding capacity (WHC), and volatile flavor of the LL when compared to that of MS and the low energy diet group (LS). Metabolomics and correlation analyses revealed that dietary energy levels mainly affected the metabolism of carbohydrates and lipids of the LL, which consequently influenced the content of volatile flavor compounds (VOCs) and fats. Furthermore, HS increased the abundance of Quinella, Ruminococcus 2, (Eubacterium) coprostanoligenes, and Succinivibrionaceae UCG-001, all of which participate in the carbohydrate metabolism in rumen and thus influence the metabolite levels (stachyose, isomaltose, etc.) in the LL. Overall, a high-energy diet is desirable for the production of Black Tibetan sheep mutton because it improves the mouthfeel and flavor of meat by altering the composition of rumen microbiota, which influences the metabolism in the LL.

Antibiotic-Induced Primary Biles Inhibit SARS-CoV-2 Endoribonuclease Nsp15 Activity in Mouse Gut

The gut microbiome profile of COVID-19 patients was found to correlate with a viral load of SARS-CoV-2, COVID-19 severity, and dysfunctional immune responses, suggesting that gut microbiota may be involved in anti-infection. In order to investigate the role of gut microbiota in anti-infection against SARS-CoV-2, we established a high-throughput in vitro screening system for COVID-19 therapeutics by targeting the endoribonuclease (Nsp15). We also evaluated the activity inhibition of the target by substances of intestinal origin, using a mouse model in an attempt to explore the interactions between gut microbiota and SARS-CoV-2. The results unexpectedly revealed that antibiotic treatment induced the appearance of substances with Nsp15 activity inhibition in the intestine of mice. Comprehensive analysis based on functional profiling of the fecal metagenomes and endoribonuclease assay of antibiotic-enriched bacteria and metabolites demonstrated that the Nsp15 inhibitors were the primary bile acids that accumulated in the gut as a result of antibiotic-induced deficiency of bile acid metabolizing microbes. This study provides a new perspective on the development of COVID-19 therapeutics using primary bile acids.

Antifungal activity of l-azetidine-2-carboxylic acid isolated from Disporopsis aspera rhizomes against Podosphaera xanthii

BACKGROUND

Powdery mildew is one of the fungal diseases commonly occurring in the process of cucurbits protected and open cultivation. Cucumbers, melons and pumpkins are extremely susceptible. The secondary metabolites produced by plants are important sources of fungicides with low toxicity and environment-friendly characteristics. The aim of this study was to reveal the main active ingredient in the crude extracts of Disporopsis aspera rhizomes that inhibit cucurbits powdery mildew and evaluate its activities.

RESULTS

In this study, the crude extracts of Disporopsis aspera rhizomes were found to exhibit excellent antifungal activity aganist Podosphaera xanthii, a causal agent of cucurbits powdery mildew. Based on the bioassay-guided method, l-azetidine-2-carboxylic acid (l-Aze) was isolated from this genus for the first time. l-Aze showed unique curative and eradicative activity against Podosphaera xanthii in vivo, which has never been reported before. Microscopic observation revealed that the curative spraying of l-Aze could effectively inhibit the mycelial growth, resulting in hollow parts of the mycelia, not forming conidiophores, and interrupting the life cycle of powdery mildew. The eradicative spraying of l-Aze caused the fracture of mycelia and deformity of conidiophores, which could not continue to produce conidia.

CONCLUSION

l-Aze was the main active ingredient of D. aspera against Podosphaera xanthii, which had both curative and eradicative effects. The results provided a strong possibility of using the crude extracts of D. aspera rhizomes and its main effective component, l-Aze as biocontrol agents to control cucurbits powdery mildew.

Alleviating Nonproductive Adsorption of Lignin on CBM through the Addition of Cationic Additives for Lignocellulosic Hydrolysis

The nonproductive adsorption of cellulase onto lignin significantly inhibited the enzymatic hydrolysis of lignocellulosic biomass. In this study, we constructed a rapid fluorescence detection (RFD) system, and using this system, we demonstrated that the addition of cationic additives DTAB or polyDADMAC greatly increased the partition coefficients of cellulose/lignin, reduced nonproductive adsorption, and enhanced the hydrolysis efficiency of lignocellulose compared to those of Tweens or PEGs. Moreover, the addition of polyDADMAC and DTAB increased the glucose yield released from the mixture of Avicel and AICS-lignin (MCL) by 16.9 and 20.6%, respectively, and reduced the inhibition rate of lignin by 16.9 and 20.7%, respectively. Interestingly, polyDADMAC or DTAB treatment performed more effectively for the enzymatic hydrolysis of pretreated lignocellulosic biomass, compared with MCL. We confirmed that the reduced hydrophobicity and increased zeta potential of lignin cocontribute to the dampening nonproductive adsorption of lignin. In particular, the zeta potential values of lignin and the partition coefficients of Avicel/lignin with the addition of additives showed a good correlation, suggesting that electrostatic force also plays a crucial role in the adsorbing of cellulase on lignin. This work will be conducive to decreasing the nonproductive binding of cellulase onto lignin and enhancing cellulose conversion.

AtANN1 and AtANN2 are involved in phototropism of etiolated hypocotyls of Arabidopsis by regulating auxin distribution

Phototropism is an essential response in some plant organs and features several signalling molecules involved in either photo-sensing or post-sensing responses. Annexins are involved in regulating plant growth and its responses to various stimuli. Here, we provide novel data showing that two members of the Annexin family in Arabidopsis thaliana, AtANN1 and AtANN2, may be involved in the phototropism of etiolated hypocotyls. In wild type, unilateral blue light (BL) induced a strong phototropic response, while red light (RL) only induced a weak response. The responses of single- or double-null mutants of the two annexins, including atann1, atann2 and atann1/atann2, were significantly weaker than those observed in wild type, indicating the involvement of AtANN1 and AtANN2 in BL-induced phototropism. Unilateral BL induced asymmetric distribution of DR5-GFP and PIN3-GFP fluorescence in hypocotyls; notably, fluorescent intensity on the shaded side was markedly stronger than that on the illuminated side. In etiolated atann1, atann2 or atann1/atann2 hypocotyls, unilateral BL-induced asymmetric distributions of DR5-GFP and PIN3-GFP were weakened or impaired. Herein, we suggest that during hypocotyls phototropic response, AtANN1 and AtANN2 may be involved in BL-stimulated signalling by regulating PIN3-charged auxin transport.

[Value of radiomics model based on dynamic contrast-enhanced magnetic resonance imaging in differentiation fat-poor angiomyolipoma from alpha-fetoprotein-negative hepatocellular carcinoma in the background of non-cirrhotic liver]

Objective: To explore the value of radiomics model based on dynamic contrast-enhanced magnetic resonance imaging (MRI) in differentiation fat-poor angiomyolipoma (fp-AML) from alpha-fetoprotein-negative hepatocellular carcinoma (n-HCC) in the background of non-cirrhotic liver. Methods: The complete data of 121 patients from Guangdong Provincial People's Hospital, Zhongshan Hospital Affiliated to Fudan University and Sun Yat-sen University Cancer Center with hepatic fp-AML and n-HCC confirmed by pathology from October 2010 to July 2020 were retrospectively analyzed. Among them, 75 were males and 46 were females, aged from 23 to 80 (55±12) years. A total of 93 patients from Zhongshan Hospital Affiliated to Fudan University were divided into the training cohort (n=75) and internal test cohort (n=18) according to entry time, and the patients of other 2 hospitals were divided into external test cohort (n=28). The radiomics features were extracted from the preoperative triple-phase contrast-enhanced images. The feature selection algorithm based on Joint Mutual Information Maximisation (JMIM) was used to extract the optimal feature subset, and support vector machine (SVM) was used to build the radiomics model. The diagnostic performance of radiomics model was evaluated using the receiver operating characteristic (ROC) curve, and was compared with that of two radiologists. Results: In the internal cohort, the area under the curve (AUC) for the differential diagnosis between fp-AML and n-HCC of the radiomics model was 0.819 (with an accuracy of 72.2%), outperforming than radiologist 1 with 10 years of diagnostic experience (AUC=0.542, P=0.029) and radiologist 2 with 2 years of diagnostic experience (AUC=0.375, P=0.004). In the external cohort, the AUC of the radiomics model was 0.772 (with and accuracy of 71.4%), which was comparable to that of radiologist 1 (AUC=0.661, P=0.442) and better than that of radiologist 2 (AUC=0.400, P=0.008). Conclusion: The radiomics model based on dynamic contrast-enhanced MRI is of high accuracy for preoperatively differentiating hepatic fp-AML from n-HCC in the noncirrhotic liver.

Effects of different feeding regimes on muscle metabolism and its association with meat quality of Tibetan sheep

This study aimed to explore the effects of different feeding regimes on muscle metabolism and its association with meat quality of Tibetan sheep through correlation analysis of meat quality and differential metabolites using untargeted and targeted metabolomics. The untargeted metabolome was detected by UHPLC-QTOF-MS, and the targeted metabolome was detected by UHPLC-QQQ-MS (amino acids) and GC-MS (fatty acids). Based on the researched results, the nutritional quality of meat, including the content of protein and fat and the edible quality of meat, including tenderness, water holding capacity (WHC), texture, and flavor of Tibetan sheep were superior in the stall-feeding group (GBZ) than in the traditional grazing group (CBZ). In the GBZ group, the key upregulated metabolites and metabolic pathways were dominated by essential amino acids (EAAs) and amino acid metabolism as well as the key downregulated metabolites and metabolic pathways were dominated by polyunsaturated fatty acids (PUFA) and lipid metabolism. Correlation analysis showed that there was a significant correlation between the results of untargeted metabolomics and some phenotypic data, including shear force, cooking loss, drip loss, chewiness, elasticity, flavor, and the content of protein and fat. Taken together, stall-feeding would be appropriate for the production of Tibetan mutton, offering better mouthfeel and higher nutrition by altering the muscle metabolism and increasing the beneficial compound deposition in the muscle.

CALR frameshift mutations in MPN patient-derived iPSCs accelerate maturation of megakaryocytes

Calreticulin (CALR) mutations are driver mutations in myeloproliferative neoplasms (MPNs), leading to activation of the thrombopoietin receptor and causing abnormal megakaryopoiesis. Here, we generated patient-derived CALRins5- or CALRdel52-positive induced pluripotent stem cells (iPSCs) to establish an MPN disease model for molecular and mechanistic studies. We demonstrated myeloperoxidase deficiency in granulocytic cells derived from homozygous CALR mutant iPSCs, rescued by repairing the mutation using CRISPR/Cas9. iPSC-derived megakaryocytes showed characteristics of primary megakaryocytes such as formation of demarcation membrane system and cytoplasmic pro-platelet protrusions. Importantly, CALR mutations led to enhanced megakaryopoiesis and accelerated megakaryocytic development in a thrombopoietin-independent manner. Mechanistically, our study identified differentially regulated pathways in mutated versus unmutated megakaryocytes, such as hypoxia signaling, which represents a potential target for therapeutic intervention. Altogether, we demonstrate key aspects of mutated CALR-driven pathogenesis dependent on its zygosity, and found novel therapeutic targets, making our model a valuable tool for clinical drug screening in MPNs.

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CALR-mutated iPSCs allow efficient modeling of human MPN disease

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CRISPR-mediated repair of CALR mutations rescues normal iPSC function

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Megakaryopoiesis in CALR-mutated iPSCs is hyperplastic and accelerated

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Transcriptome screen of mutated megakaryocytes identifies novel therapeutic options

Altered metabolome and microbiome features provide clues in understanding irritable bowel syndrome and depression comorbidity

Irritable bowel syndrome (IBS) is one of the functional gastrointestinal disorders characterized by chronic and/or recurrent symptoms of abdominal pain and irregular defecation. Changed gut microbiota has been proposed to mediate IBS; however, contradictory results exist, and IBS-specific microbiota, metabolites, and their interactions remain poorly understood. To address this issue, we performed metabolomic and metagenomic profiling of stool and serum samples based on discovery (n = 330) and validation (n = 101) cohorts. Fecal metagenomic data showed moderate dysbiosis compared with other diseases, in contrast, serum metabolites showed significant differences with greater power to distinguish IBS patients from healthy controls. Specifically, 726 differentially abundant serum metabolites were identified, including a cluster of fatty acyl-CoAs enriched in IBS. We further identified 522 robust associations between differentially abundant gut bacteria and fecal metabolites, of which three species including Odoribacter splanchnicus, Escherichia coli, and Ruminococcus gnavus were strongly associated with the low abundance of dihydropteroic acid. Moreover, dysregulated tryptophan/serotonin metabolism was found to be correlated with the severity of IBS depression in both fecal and serum metabolomes, characterized by a shift in tryptophan metabolism towards kynurenine production. Collectively, our study revealed serum/fecal metabolome alterations and their relationship with gut microbiome, highlighted the massive alterations of serum metabolites, which empower to recognize IBS patients, suggested potential roles of metabolic dysregulation in IBS pathogenesis, and offered new clues to understand IBS depression comorbidity. Our study provided a valuable resource for future studies, and would facilitate potential clinical applications of IBS featured microbiota and/or metabolites.

ELMO1 Regulates RANKL-Stimulated Differentiation and Bone Resorption of Osteoclasts

Bone homeostasis is a metabolic balance between the new bone formation by osteoblasts and old bone resorption by osteoclasts. Excessive osteoclastic bone resorption results in low bone mass, which is the major cause of bone diseases such as rheumatoid arthritis. Small GTPases Rac1 is a key regulator of osteoclast differentiation, but its exact mechanism is not fully understood. ELMO and DOCK proteins form complexes that function as guanine nucleotide exchange factors for Rac activation. Here, we report that ELMO1 plays an important role in differentiation and bone resorption of osteoclasts. Osteoclast precursors derived from bone marrow monocytes (BMMs) of Elmo1^–/– mice display defective adhesion and migration during differentiation. The cells also have a reduced activation of Rac1, p38, JNK, and AKT in response to RANKL stimulation. Importantly, we show that bone erosion is alleviated in Elmo1^–/– mice in a rheumatoid arthritis mouse model. Taken together, our results suggest that ELMO1, as a regulator of Rac1, regulates osteoclast differentiation and bone resorption both in vitro and in vivo.

Efficacy and safety of Lianhuaqingwen for mild or moderate coronavirus disease 2019: A meta-analysis of randomized controlled trials

BACKGROUND

: Coronavirus disease 2019 (COVID-19) is an emerging and rapidly evolving disease, with no recommended effective anti-coronavirus treatments. Traditional Chinese Medicine (TCM) has been widely used to treat COVID-19 in China, and the most used one is Lianhuaqingwen (LH). This study aimed to assess the efficacy and safety of LH combined with usual treatment vs usual treatment alone in treating mild or moderate COVID-19 by a meta-analysis of randomized controlled trials (RCTs).

METHODS AND ANALYSIS

: We systematically searched the Medline (OVID), Embase, the Cochrane Library, and 4 Chinese databases from inception to July 2020 to include the RCTs that evaluated the efficacy and safety of LH in combination with usual treatment vs usual treatment for mild or moderate COVID-19. A meta-analysis was performed to calculate the risk ratio (RR) and 95% confidence interval (CI) for binary outcomes and mean difference (MD) for continuous outcomes.

RESULTS

: A total of 5 RCTs with 824 individuals with mild or moderate COVID 19 were included. Compared with the usual treatment alone, LH in combination with usual treatment significantly improved the overall clinical efficacy (RR = 2.39, 95% CI 1.61-3.55), increased the rate of recovery of chest computed tomographic manifestations (RR = 1.80, 95% CI 1.08-3.01), reduced the rate of conversion to severe cases (RR = 0.47, 95% CI 0.29-0.74), shorten the duration of fever (MD = -1.00, 95% CI -1.17 to -0.84). Moreover, LH in combination with usual treatment did not increase the occurrence of the adverse event compared to usual treatment alone.

CONCLUSION

: Our meta-analysis of RCTs indicated that LH in combination with usual treatment may improve the clinical efficacy in patients with mild or moderate COVID-19 without increasing adverse events. However, given the limitations and poor quality of included trials in this study, further large-sample RCTs or high-quality real-world studies are needed to confirm our conclusions.

Nanoparticle-Mediated Delivery of Emodin via Colonic Irrigation Attenuates Renal Injury in 5/6 Nephrectomized Rats

Our previous study showed that emodin enema modulates gut microbiota and delays CKD progression. However, the poor solubility, limited colonic irrigation retention time, and inadequate colon adhesion of emodin hinder its clinical application. Based on the deficiencies of emodin, we prepared monomethoxy-poly (ethylene glycol)-poly (lactic acid)-chitosan-2-mercaptobenzimidazole nanoparticles with incorporated emodin (emodin-NP) and studied their efficacy in delaying CKD progression. 5/6 nephrectomized Male Sprague Dawley rats were administered via colonic irrigation with emodin-NP every two days for eight weeks. We found that treatment with emodin-NP improved the kidney function of the rats and limited the expansion of tubulointerstitial fibrosis. Treatment with emodin-NP once every two days is comparable to emodin treatment once a day. Furthermore, emodin-NP via colonic irrigation remarkably reduced IL-1β, IL-6, and LPS levels in serum, improved intestinal barrier functions, and downregulated the key proteins (TLR4, MyD88, and NF-κB) expression in intestinal TLR4 signaling pathway. 16S rDNA analyses showed that emodin-NP can regulate microbiota disturbance in CKD. Taken together, these results suggest that emodin-NP alleviates kidney dysfunction and tubulointerstitial fibrosis by mediation through the modification of gut microbiota disorders. Emodin-NP may be a new method to treat CKD.

Preparation and photocatalytic performance of silver-modified and nitrogen-doped TiO2 nanomaterials with oxygen vacancies

A modified hydrothermal method for the synthesis of TiO₂ material to achieve a more efficient visible light response.

Metagenomic Analysis Reveals the Distribution of Antibiotic Resistance Genes in a Large-Scale Population of Healthy Individuals and Patients With Varied Diseases

The human gut microbiome is a reservoir for antibiotic resistance gene (ARG). Therefore, characterizing resistome distribution and potential disease markers can help manage antibiotics at the clinical level. While much population-level research has highlighted the strong effect of donor geographic origin on ARG prevalence in the human gut, little is known regarding the effects of other properties, such as age, sex, and disease. Here we employed 2,037 fecal metagenomes from 12 countries. By quantifying the known resistance genes for 24 types of antibiotics in each community, we showed that tetracycline, aminoglycoside, beta-lactam, macrolide-lincosamide-streptogramin (MLS), and vancomycin resistance genes were the dominant ARG types in the human gut. We then compared the ARG profiles of 1427 healthy individuals from the 2,037 samples and observed significant differences across countries. This was consistent with expectations that regional antibiotic usage and exposure in medical and food production contexts affect distribution. Although no specific uniform pattern of ARG was observed, a significant increase in resistance potential among multiple disease groups implied that the disease condition may be another source of ARG variance. In particular, the co-occurrence pattern of some enriched bacterial species and ARGs that were obtained in type 2 diabetes (T2D) and liver cirrhosis patients implied that some disease-associated species may be potential hosts of enriched ARGs, which could be potential biomarkers for the prediction and intervention of such diseases. Overall, our study identifies factors associated with the human gut resistome, including substantial effects of region and heterogeneous effects of disease status, and highlights the value of ARG analysis in disease research and clinical applications.

A comprehensive investigation of metagenome assembly by linked-read sequencing

BACKGROUND

The human microbiota are complex systems with important roles in our physiological activities and diseases. Sequencing the microbial genomes in the microbiota can help in our interpretation of their activities. The vast majority of the microbes in the microbiota cannot be isolated for individual sequencing. Current metagenomics practices use short-read sequencing to simultaneously sequence a mixture of microbial genomes. However, these results are in ambiguity during genome assembly, leading to unsatisfactory microbial genome completeness and contig continuity. Linked-read sequencing is able to remove some of these ambiguities by attaching the same barcode to the reads from a long DNA fragment (10-100 kb), thus improving metagenome assembly. However, it is not clear how the choices for several parameters in the use of linked-read sequencing affect the assembly quality.

RESULTS

We first examined the effects of read depth (C) on metagenome assembly from linked-reads in simulated data and a mock community. The results showed that C positively correlated with the length of assembled sequences but had little effect on their qualities. The latter observation was corroborated by tests using real data from the human gut microbiome, where C demonstrated minor impact on the sequence quality as well as on the proportion of bins annotated as draft genomes. On the other hand, metagenome assembly quality was susceptible to read depth per fragment (C_R) and DNA fragment physical depth (C_F). For the same C, deeper C_R resulted in more draft genomes while deeper C_F improved the quality of the draft genomes. We also found that average fragment length (μ_FL) had marginal effect on assemblies, while fragments per partition (N_F/P) impacted the off-target reads involved in local assembly, namely, lower N_F/P values would lead to better assemblies by reducing the ambiguities of the off-target reads. In general, the use of linked-reads improved the assembly for contig N50 when compared to Illumina short-reads, but not when compared to PacBio CCS (circular consensus sequencing) long-reads.

CONCLUSIONS

We investigated the influence of linked-read sequencing parameters on metagenome assembly comprehensively. While the quality of genome assembly from linked-reads cannot rival that from PacBio CCS long-reads, the case for using linked-read sequencing remains persuasive due to its low cost and high base-quality. Our study revealed that the probable best practice in using linked-reads for metagenome assembly was to merge the linked-reads from multiple libraries, where each had sufficient C_R but a smaller amount of input DNA. Video Abstract.

Photocatalytic Activity Investigation of α-Zirconium Phosphate Nanoparticles Compositing with C3N4 under Ultraviolet Light

In order to further develop efficient ultraviolet light-driven photocatalysts for environmental application, α-zirconium phosphate (α-ZrP) and carbon nitride (C₃N₄) were synthesized, respectively. Then, C₃N₄-ZrP compositing nanomaterials were prepared by compositing α-ZrP nanocrystals and C₃N₄ with different mass ratios. C₃N₄-ZrP compositing nanomaterials were characterized by X-ray diffraction, scanning electron microscopy, Fourier transform infrared spectroscopy, and X-ray photoelectron spectroscopy. The results illustrated that α-ZrP and C₃N₄ were successfully composited, and the polarization of the compositing nanomaterials was reduced compared with raw materials. The photocatalytic performances of C₃N₄-ZrP compositing nanomaterials with different mass ratios were studied by photodegradation of RhB under ultraviolet irradiation. All of the degradation rates of the C₃N₄-ZrP compositing nanomaterials system were achieved more than 90% after 18 min. When the mass ratio of C₃N₄-ZrP compositing nanomaterials is 2:1, the degradation efficiency achieved 99.95%, which is more efficient than other tested mass ratios. The result indicated the possibility of utilizing C₃N₄-ZrP compositing nanomaterials for environmental pollutants degradation.

Zein-Polyglycerol Conjugates with Enhanced Water Solubility and Stabilization of High Oil Loading Emulsion

To increase the water solubility of zein as a stabilizing agent for oil-in-water (O/W) emulsions, three zein-polyglycerol (Zein-PG) conjugates, Zein-PG-2, Zein-PG-6, and Zein-PG-10, were prepared by dehydration between zein and polyglycerol aldehydes obtained by NaIO₄ oxidation of polyglycerol-2, -6, and -10 and characterized by free amine content, grafting degree, Fourier transform infrared spectroscopy, and fluorescence spectra. All conjugates dispersed in water as nanoparticles were verified by transmission electron microscopy. Conjugation with PG changed the isoelectric point of zein from 6.2 to 6.8 and to 4.0. Zein-PG-6 and Zein-PG-10 showed strong stabilization on the O/W emulsions with 18-fold loading of soybean oil on the basis of conjugate mass, displaying high oil loading capacity. Confocal laser scanning microscopy (CLSM) confirmed the O/W structure of emulsions and that the absorption of Zein-PG-10 on the oil droplet surface offered the driving force to be stable. The present Zein-PG conjugates thus produced an enticing resource for use as nanocarriers or bioemulsifiers in food or pharmaceutical industries.

Synthesis and Insecticidal Activity Evaluation of Virtually Screened Phenylsulfonamides

The fastest and most effective way to control pests is to use pesticides. However, with the accumulation of pesticide resistance and the difficulties of rapidly producing new pesticides, it is of great significance to create new pesticides through new synthetic methods. In this study, we report a computer-aided drug design (CADD)-assisted method to obtain two lead sulfonamides by homology modeling and virtual screening. On this basis, the lead compounds were synthesized from p-chlorocresol by four steps of esterification, sulfonation, sulfonamidation, and amidation. Further, 71 derivatives were synthesized by optimizing the lead compounds, and their insecticidal activities against Mythimna separata were evaluated by the leaf-dipping method. Notably, seven sulfonamides (5a, 5g, 5h, 5m, 6b, 6g, and 6m) with excellent insecticidal activity were obtained, and the possible binding modes between receptors and active groups in sulfonamides were verified by structure-activity relationship and docking simulation, which provided theoretical support for the subsequent development of these novel candidate insecticides.

Exerting Spatial Control During Nanoparticle Occlusion within Calcite Crystals

In principle, nanoparticle occlusion within crystals provides a straightforward and efficient route to make new nanocomposite materials. However, developing a deeper understanding of the design rules underpinning this strategy is highly desirable. In particular, controlling the spatial distribution of the guest nanoparticles within the host crystalline matrix remains a formidable challenge. Herein, we show that the surface chemistry of the guest nanoparticles and the [Ca²⁺ ] concentration play critical roles in determining the precise spatial location of the nanoparticles within calcite crystals. Moreover, in situ studies provide important mechanistic insights regarding surface-confined nanoparticle occlusion. Overall, this study not only provides useful guidelines for efficient nanoparticle occlusion, but also enables the rational design of patterned calcite crystals using model anionic block copolymer vesicles.

Triple Phase Inversion of Emulsions Stabilized by Amphiphilic Graphene Oxide and Cationic Surfactants

Amphiphilic graphene oxide (A-GO) with grafted octylamine was prepared via a one-step method of N,N'-dicyclohexylcarbodiimide coupling and epoxide ring opening at a mild temperature of 40 °C. The phase of oil-water emulsion stabilized by the complexes of A-GO and the cetyltrimethyl ammonium bromide (CTAB) surfactant could invert three times by adding CTAB or A-GO. This process was called triple phase inversion, which was a function of the concentration of A-GO or CTAB surfactants. The conductivity and zeta potential measurements confirmed that CTAB could influence the carboxyl ionization of A-GO. In addition, the turbidity of the A-GO and CTAB mixed dispersion system revealed that the appearance and disappearance of precipitation occurred when CTAB or A-GO concentration was increased. Meanwhile, the emulsion prepared by mixing the dispersion with an equal volume of xylene at a fixed CTAB concentration also showed triple phase inversion as the A-GO concentration varied. Results indicated that the stability of the emulsion and the size of the emulsion droplets had a certain correlation during the phase inversion process, which varied with the concentration of CTAB or A-GO.

Rhubarb Enema Improved Colon Mucosal Barrier Injury in 5/6 Nephrectomy Rats May Associate With Gut Microbiota Modification

Chronic kidney disease (CKD) is often accompanied with colon mucosal barrier damage and gut microbiota disturbance, which strongly associate with up-regulated inflammation and kidney tubulointerstitial fibrosis. However, few interventions could protect the damaged barrier effectively. Rheum palmatum L or rhubarb is a common herbal medicine which is widely used to protect the colon mucosal barrier. In previous studies, we found that rhubarb intervention may reduce renal inflammation and tubulointerstitial fibrosis, via gut microbiota modification. However, whether intestinal barrier function could be improved by rhubarb intervention and the relationship with intestinal flora are still unknown. Therefore, we investigated the effects of rhubarb enema on intestinal barrier, and further analyzed the relationship with gut microbiota in 5/6 nephrectomy rats. Results indicated that rhubarb enema improved the intestinal barrier, regulated gut microbiota dysbiosis, suppressed systemic inflammation, and alleviated renal fibrosis. More specifically, rhubarb enema treatment inhibited the overgrowth of conditional pathogenic gut bacteria, including Akkermansia, Methanosphaera, and Clostridiaceae in CKD. The modification of gut microbiota with rhubarb intervention displayed significant correlation to intestinal barrier markers, TLR4–MyD88–NF-κB inflammatory response, and systemic inflammation. These results revealed that rhubarb enema could restore intestinal barrier by modifying several functional enteric bacteria, which may further explain the renal protection mechanism of the rhubarb enema.

Precision Engineering of the Transcription Factor Cre1 in Hypocrea jecorina (Trichoderma reesei) for Efficient Cellulase Production in the Presence of Glucose

In Trichoderma reesei, carbon catabolite repression (CCR) significantly downregulates the transcription of cellulolytic enzymes, which is usually mediated by the zinc finger protein Cre1. It was found that there is a conserved region at the C-terminus of Cre1/CreA in several cellulase-producing fungi that contains up to three continuous S/T phosphorylation sites. Here, S387, S388, T389, and T390 at the C-terminus of Cre1 in T. reesei were mutated to valine for mimicking an unphosphorylated state, thereby generating the transformants Tr_Cre1S387V, Tr_Cre1S388V, Tr_Cre1T389V, and Tr_Cre1T390V, respectively. Transcription of cel7a in Tr_ Cre1S388V was markedly higher than that of the parent strain when grown in glucose-containing media. Under these conditions, both filter paperase (FPase) and p-nitrophenyl-β-D-cellobioside (pNPCase) activities, as well as soluble proteins from Tr_Cre1S388V were significantly increased by up to 2- to 3-fold compared with that of other transformants and the parent strain. The results suggested that S388 is critical site of phosphorylation for triggering CCR at the terminus of Cre1. To our knowledge, this is the first report demonstrating an improvement of cellulase production in T. reesei under CCR by mimicking dephosphorylation at the C-terminus of Cre1. Taken together, we developed a precision engineering strategy based on the modification of phosphorylation sites of Cre1 transcription factor to enhance the production of cellulase in T. reesei under CCR.

A Clostridia-rich microbiota enhances bile acid excretion in diarrhea-predominant irritable bowel syndrome

An excess of fecal bile acids (BAs) is thought to be one of the mechanisms for diarrhea-predominant irritable bowel syndrome (IBS-D). However, the factors causing excessive BA excretion remain incompletely studied. Given the importance of gut microbiota in BA metabolism, we hypothesized that gut dysbiosis might contribute to excessive BA excretion in IBS-D. By performing BA-related metabolic and metagenomic analyses in 290 IBS-D patients and 89 healthy volunteers, we found that 24.5% of IBS-D patients exhibited excessive excretion of total BAs and alteration of BA-transforming bacteria in feces. Notably, the increase in Clostridia bacteria (e.g., C. scindens) was positively associated with the levels of fecal BAs and serum 7α-hydroxy-4-cholesten-3-one (C4), but negatively correlated with serum fibroblast growth factor 19 (FGF19) concentration. Furthermore, colonization with Clostridia-rich IBS-D fecal microbiota or C. scindens individually enhanced serum C4 and hepatic conjugated BAs but reduced ileal FGF19 expression in mice. Inhibition of Clostridium species with vancomycin yielded opposite results. Clostridia-derived BAs suppressed the intestinal FGF19 expression in vitro and in vivo. In conclusion, this study demonstrates that the Clostridia-rich microbiota contributes to excessive BA excretion in IBS-D patients, which provides a mechanistic hypothesis with testable clinical implications.

Redesigning transcription factor Cre1 for alleviating carbon catabolite repression in Trichoderma reesei

Carbon catabolite repression (CCR), which is mainly mediated by Cre1 and triggered by glucose, leads to a decrease in cellulase production in Trichoderma reesei. Many studies have focused on modifying Cre1 for alleviating CCR. Based on the homologous alignment of CreA from wild-type Penicillium oxalicum 114–2 (Po-0) and cellulase hyperproducer JUA10-1(Po-1), we constructed a C-terminus substitution strain—Po-2—with decreased transcriptional levels of cellulase and enhanced CCR. Results revealed that the C-terminal domain of CreA^Po−1 plays an important role in alleviating CCR. Furthermore, we replaced the C-terminus of Cre1 with that of CreA^Po−1 in T. reesei (Tr-0) and generated Tr-1. As a control, the C-terminus of Cre1 was truncated and Tr-2 was generated. The transcriptional profiles of these transformants revealed that the C-terminal chimera greatly improves cellulase transcription in the presence of glucose and thus upregulates cellulase in the presence of glucose and weakens CCR, consistent with truncating the C-terminus of Cre1 in Tr-0. Therefore, we propose constructing a C-terminal chimera as a new strategy to improve cellulase production and alleviate CCR in the presence of glucose.

(20S)-Protopanaxadiol Ginsenosides Induced Cytotoxicity via Blockade of Autophagic Flux in HGC-27 Cells

(20S)-Protopanaxadiol ginsenosides Rg3, Rh2 and PPD have been demonstrated for their anticancer activity. However, the underlying mechanism of their antitumor activity remains unclear. In the present study, we investigated the role of these three ginsenosides on cell proliferation and death of human gastric cancer cells (HGC-27 cells). The sulforhodamine B (SRB) assay, Western blot analysis, fluorescence microscopy, confocal microscopy, high performance liquid chromatography (HPLC) analysis, flow cytometry, and transmission electron microscopy (TEM) were used to evaluate cell proliferation, apoptosis, and autophagy. The results showed that both Rh2 and PPD were more effective than Rg3 in inhibiting HGC-27 cell proliferation and inducing cytoplasmic vacuolation, while no significant changes in apoptosis were observed. Interestingly, cytoplasmic vacuolation and blockade of autophagy flux were observed after treatment with Rh2 and PPD. Rh2 obviously up-regulated the expression of the LC3II and p62. Furthermore, the increase in lysosomal pH and membrane rupture was observed in Rh2-treated and PPD-treated cells. When HGC-27 cells were pretreated with bafilomycin A1, a specific inhibitor of endosomal acidification, cellular vacuolization was increased, and the cell viability was significantly decreased, which indicated that Rh2-induced lysosome-damage accelerated cell death. Furthermore, data derived from mitochondrial analysis showed that excessive mitochondrial reactive oxygen species (ROS) and dysregulation of mitochondrial energy metabolism were caused by Rh2 and PPD treatment in HGC-27 cells. Taken together, these phenomena indicated that Rh2 and PPD inhibited HCG-27 cells proliferation by inducing mitochondria damage, dysfunction of lysosomes, and blockade of autophagy flux. The number of glycosyl groups at C-3 position could have an important effect on the cytotoxicity of Rg3, Rh2 and PPD.

Hypoxia-inducible factor 1 (HIF-1) is a new therapeutic target in JAK2V617F-positive myeloproliferative neoplasms

Classical Philadelphia chromosome-negative myeloproliferative neoplasms (MPN) are a heterogeneous group of hematopoietic malignancies including polycythemia vera (PV), essential thrombocythemia (ET), and primary myelofibrosis (PMF). The JAK2V617F mutation plays a central role in these disorders and can be found in 90% of PV and ~50-60% of ET and PMF. Hypoxia-inducible factor 1 (HIF-1) is a master transcriptional regulator of the response to decreased oxygen levels. We demonstrate the impact of pharmacological inhibition and shRNA-mediated knockdown (KD) of HIF-1α in JAK2V617F-positive cells. Inhibition of HIF-1 binding to hypoxia response elements (HREs) with echinomycin, verified by ChIP, impaired growth and survival by inducing apoptosis and cell cycle arrest in Jak2V617F-positive 32D cells, but not Jak2WT controls. Echinomycin selectively abrogated clonogenic growth of JAK2V617F cells and decreased growth, survival, and colony formation of bone marrow and peripheral blood mononuclear cells and iPS cell-derived progenitor cells from JAK2V617F-positive patients, while cells from healthy donors were unaffected. We identified HIF-1 target genes involved in the Warburg effect as a possible underlying mechanism, with increased expression of Pdk1, Glut1, and others. That was underlined by transcriptome analysis of primary patient samples. Collectively, our data show that HIF-1 is a new potential therapeutic target in JAK2V617F-positive MPN.

Prevalence, risk factors and prognostic role of anxiety and depression in surgical gastric cancer patients

Background

The present study was conducted to explore the prevalence, risk factors and prognostic role of anxiety and depression in surgical gastric cancer patients.

Methods

Totally 200 gastric cancer patients who underwent surgical resection were enrolled and their Hospital Anxiety and Depression Scale (HADS) scores were assessed before surgery. Besides, 200 healthy controls were enrolled with their HADS scores assessed at enrollment.

Results

The HADS-anxiety score (7.4±3.8 vs. 4.7±2.8, P<0.001), prevalence (42.5% vs. 13.5%, P<0.001) and severity (P=0.002) of anxiety were greatly increased in gastric cancer patients compared with healthy controls. And HADS-depression score (6.9±3.5 vs. 4.2±2.6, P<0.001), prevalence (33.5% vs. 10.0%, P<0.001) and severity (P=0.001) of depression were also dramatically elevated in gastric cancer patients compared with healthy controls. Regarding the factors predicting anxiety/depression risks in gastric cancer patients, gender (female) (P=0.003), diabetes (P<0.001), higher pathological grade (P=0.005), larger tumor size (P=0.044) and higher T stage (P=0.017) were independent predictive factors for higher risk of anxiety, and age (>60 years) (P=0.025), gender (female) (P=0.004), hyperlipidemia (P=0.039), diabetes (P<0.001) and higher TNM stage (P=0.003) were independent predictive factors for higher risk of depression. Most importantly, anxiety/depression and the severity of anxiety/depression were all negatively associated with disease-free survival as well as overall survival (all P<0.05) in surgical gastric cancer patients.

Conclusions

Anxiety/depression are common and severe, which predicts unfavorable prognosis in gastric cancer patients underwent surgery, suggesting the necessity of psychological care post-surgery.

Experimental Investigation of Hydrophobically Modified α-ZrP Nanosheets for Enhancing Oil Recovery in Low-Permeability Sandstone Cores

Highly crystalline α-zirconium phosphate (α-ZrP) nanoparticles were synthesized and exfoliated into nanosheets, and then the hydrophilic nanosheets were modified into hydrophobic nanosheets with octadecyltrichlorosilane (OTS). Scanning electron microscopy, Fourier transform infrared spectroscopy, X-ray diffraction, and thermogravimetric analysis were applied to confirm the morphology and chemical structure of the nanosheets. Contact angle measurement was conducted to explore the wettability alteration of the hydrophobically modified α-ZrP nanosheets, and the result showed that the wettability of the core was changed into hydrophobicity. When ZrP-OTS nanosheets were injected during water-flooding, a Pickering emulsion will be formed. The droplet diameters and viscosities of the Pickering emulsions were measured. The hydrophobically modified α-ZrP nanosheets were applied in low-permeability sandstone cores and various concentrations were tested. The injectivity of the hydrophobically modified α-ZrP nanosheets was also studied and the result indicated that the nanosheets exhibit good injectivity. The mechanisms for enhancing oil recovery by utilizing hydrophobic α-ZrP nanosheets were analyzed: forming Pickering emulsions and increasing the viscosity of the displacing phase. Forming emulsions and increasing the viscosity of the flooding phase can enhance the microdisplacement efficiency, while good injectivity can also enhance the macrodisplacement efficiency. The result indicated the possibility of using hydrophobically modified α-ZrP nanosheets for enhancing oil recovery in a low-permeability reservoir.

Use of fusion transcription factors to reprogram cellulase transcription and enable efficient cellulase production in Trichoderma reesei

BACKGROUND

Trichoderma reesei is widely used for cellulase production and accepted as an example for cellulase research. Cre1-mediated carbon catabolite repression (CCR) can significantly inhibit the transcription of cellulase genes during cellulase fermentation in T. reesei. Early efforts have been undertaken to modify Cre1 for the release of CCR; however, this approach leads to arrested hyphal growth and decreased biomass accumulation, which negatively affects cellulase production.

RESULTS

In this study, novel fusion transcription factors (fTFs) were designed to release or attenuate CCR inhibition in cellulase transcription, while Cre1 was left intact to maintain normal hyphal growth. Four designed fTFs were introduced into the T. reesei genome, which generated several transformants, named Kuace3, Kuclr2, Kuace2, and Kuxyr1. No obvious differences in growth were observed between the parent and transformant strains. However, the transcription levels of cel7a, a major cellulase gene, were significantly elevated in all the transformants, particularly in Kuace2 and Kuxyr1, when grown on lactose as a carbon source. This suggested that CCR inhibition was released or attenuated in the transformant strains. The growth of Kuace2 and Kuxyr1 was approximately equivalent to that of the parent strain in fed-batch fermentation process. However, we observed a 3.2- and 2.1-fold increase in the pNPCase titers of the Kuace2 and Kuxyr1 strains, respectively, compared with that of the parent strain. Moreover, we observed a 6.1- and 3.9-fold increase in the pNPCase titers of the Kuace2 and Kuxyr1 strains, respectively, compared with that of Δcre1 strain.

CONCLUSIONS

A new strategy based on fTFs was successfully established in T. reesei to improve cellulase titers without impairing fungal growth. This study will be valuable for lignocellulosic biorefining and for guiding the development of engineering strategies for producing other important biochemical compounds in fungal species.

Whole-genome sequencing reveals novel tandem-duplication hotspots and a prognostic mutational signature in gastric cancer

Genome-wide analysis of genomic signatures might reveal novel mechanisms for gastric cancer (GC) tumorigenesis. Here, we analysis structural variations (SVs) and mutational signatures via whole-genome sequencing of 168 GCs. Our data demonstrates diverse models of complex SVs operative in GC, which lead to high-level amplification of oncogenes. We find varying proportion of tandem-duplications (TDs) among individuals and identify 24 TD hotspots involving well-established cancer genes such as CCND1, ERBB2 and MYC. Specifically, we nominate a novel hotspot involving the super-enhancer of ZFP36L2 presents in approximately 10% GCs from different cohorts, the oncogenic role of which is further confirmed by experimental data. In addition, our data reveal a mutational signature, specifically occurring in noncoding region, significantly enriched in tumors with cadherin 1 mutations, and associated with poor prognoses. Collectively, our data suggest that TDs might serve as an important mechanism for cancer gene activation and provide a novel signature for stratification.

Structural variations in gastric cancer impact progression. Here, the authors perform whole-genome sequencing on 168 gastric cancer patients and identified tandem-duplications of super-enhancer ZFP36L2 in 10% of gastric cancer, and mutational signatures in tumors with cadherin 1 mutations that associated with poor prognoses.