MeRIPseqPipe: an integrated analysis pipeline for MeRIP-seq data based on Nextflow.

SUMMARY: MeRIPseqPipe is an integrated and automatic pipeline that can provide users a friendly solution to perform in-depth mining of MeRIP-seq data. It integrates many functional analysis modules, range from basic processing to downstream analysis. All the processes are embedded in Nextflow with Docker support, which ensures high reproducibility and scalability of the analysis. MeRIPseqPipe is particularly suitable for analyzing a large number of samples at once with a simple command. The final output directory is structured based on each step and tool. And visualization reports containing various tables and plots are provided as HTML files. AVAILABILITY AND IMPLEMENTATION: MeRIPseqPipe is freely available at https://github.com/canceromics/MeRIPseqPipe. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Soil chemical quality assessment and spatial distribution of pomelo orchards in acidic red soil hilly regions of China.

BACKGROUND: Soil quality assessment is a critical strategy for determining optimum fertilization in intensive pomelo production. In this study, we evaluated the soil quality status and mapped the spatial distribution of 347 soil samples collected from pomelo orchards in Pinghe County, southern China. We analyzed nine chemical parameters and an altitude indicator. RESULTS: The mean soil quality index (SQI) was 0.355 in the total data set (TDS) and 0.292 in the minimum data set (MDS). Available Ca (Avail-Ca), pH value, organic matter and altitude were selected as indicators of soil quality in the MDS. The SQI in mature orchards (>10 years) was higher than that in young orchards (<10 years), while no differences between soil types and altitude gradients were identified. We detected a significant positive correlation between the SQI based on TDS (SQITDS ) and the SQI based on MDS (SQIMDS ), and the spatial distribution of soil properties and SQITDS showed a uniform pattern, except for Avail-N, Avail-B and SQIMDS . Overall, unfavorable soil quality indicators, including rich in Avail-P, deficient in Avail-Ca, -Mg and -B, soil acidification and high altitude, were considered to be limiting factors for pomelo production. CONCLUSION: The soil chemical quality in pomelo orchards is generally low, indicating that integrated management by controlling acidification, reducing planting altitude, regulating fertilization and monitoring soil properties is required for sustainable pomelo production. © 2021 Society of Chemical Industry.

[From Grid Cells to Place Cells:A Gauss Distribution Activation Function Model].

It has been found that in biological studies,the simple linear superposition mathematical model cannot be used to express the feature mapping relationship from multiple activated grid cells' grid fields to a single place cell's place field output in the hippocampus of the cerebral cortex of rodents.To solve this problem,people introduced the Gauss distribution activation function into the area.We in this paper use the localization properties of the function to deal with the linear superposition output of grid cells' input and the connection weights between grid cells and place cells,which filters out the low activation rate place fields.We then obtained a single place cell field which is consistent with biological studies.Compared to the existing competitive learning algorithm place cell model,independent component analysis method place cell model,Bayesian positon reconstruction method place cell model,our experimental results showed that the model on the neurophysiological basis can not only express the feature mapping relationship between multiple activated grid cells grid fields and a single place cell's place field output in the hippocampus of the cerebral cortex of rodents,but also make the algorithm simpler,the required grid cells input less and the accuracy rate of the output of a single place field higher.

Mechano-growth factor enhances differentiation of bone marrow-derived mesenchymal stem cells.

OBJECTIVES: To investigate the effect of mechano-growth factor (MGF) on the differentiation of human bone marrow-derived mesenchymal stem cells (hBMSCs) in vitro. RESULTS: Flow cytometry assay identified the isolated cells were human bone marrow mesenchymal stem cells, which had differentiation ability when cultured with specific induction culture media. Alizarin Red S, Oil Red O and Alcian Blue staining showed osteogenic, adipogenic and chondrogenic differentiation were significantly increased after hBMSCs were treated with MGF E peptide. Collagen II expression was considerably increased after hBMSCs were induced with chondrogenic induction culture medium supplemented with TGF-ß3 and MGF E peptide. Overexpression of MGF by an expression plasmid further confirmed the MGF could enhance tri-lineage differentiation of hBMSCs. Moreover, we found that hBMSCs proliferation rate was decreased and G1 phase of the cell cycle was lengthened after MGF treatment when compared to the control group. CONCLUSIONS: MGF can enhance differentiation of hBMSCs during specific induction culture media induction by lengthening G1 phase of cell cycle.

In vitro determination of osteo-adipogenic lineage choice of bone marrow stromal/stem cells (BMSCs).

Bone marrow stromal/stem cells (BMSCs) are primitive and heterogeneous cells that can be differentiated into osteoblasts, adipocytes and other subsets. Their bone-fat lineage commitment is responsible for the homeostasis of bone marrow microenvironment. However, there are little effective methods and evidence to simultaneously visualise the lineage commitment of BMSCs. Here we provide a bivalent differentiation medium that can enable BMSCs differentiation into osteoblasts and adipocytes in vitro, and establish a method to simultaneously distinguish osteoblasts or adipocytes from the heterogeneous BMSCs based on Alizarin red S and Oil red O staining, which have been used for detection of specific mineralized nodules and lipid droplets, respectively. This assay provides a specifically simple but effective and low-cost method to evaluate the efficiency of osteo-adipogenic (OA) allocation of BMSCs.►Researchers can utilize the bivalent differentiation medium to evaluate the efficiency of osteogenic and adipogenic differentiation of BMSCs in vitro.

Gene features of tumor-specific T cells relevant to immunotherapy, targeted therapy and chemotherapy in lung cancer.

1 Background: In lung cancer, the use of small-molecule inhibitors, chemotherapy and immunotherapy has led to unprecedented survival benefits in selected patients. Considering most patients will experience a relapse within a short period of time due to single drug resistance, combination therapy is also particularly important to improve patient prognosis. Therefore, more robust biomarkers to predict responses to immunotherapy, targeted therapy, chemotherapy and rationally drug combination therapies may be helpful in clinical treatment choices. 2 Methods: We defined tumor-specific T cells (TSTs) and their features (TSTGs) by single-cell RNA sequencing. We applied LASSO regression to filter out the most survival-relevant TSTGs to form the Tumor-specific T cell score (TSTS). Immunological characteristics, enriched pathways, and mutation were evaluated in high- and low TSTS groups. 3 Results: We identified six clusters of T cells as TSTs in lung cancer, and four most robust genes from 9 feature genes expressed only on tumor-specific T cells were screened to construct a tumor-specific T cells score (TSTS). TSTS was positively correlated with immune infiltration and angiogenesis and negatively correlated with malignant cell proliferation. Moreover, potential vascular-immune crosstalk in lung cancer provides the theoretical basis for combined anti-angiogenic and immunotherapy. Noticeable, patients in high TSTS had better response to ICB and targeted therapy and patients in the low TSTS group often benefit from chemotherapy. 4 Conclusion: The proposed TSTS is a promising indicator to predict immunotherapy, targeted therapy and chemotherapy responses in lung cancer patients for helping clinical treatment choices.

Rejuvenation of BMSCs senescence by pharmacological enhancement of TFEB-mediated autophagy alleviates aged-related bone loss and extends lifespan in middle aged mice.

Bone marrow stromal/stem cells (BMSCs) are generally considered as common progenitors for both osteoblasts and adipocytes in the bone marrow, but show preferential differentiation into adipocytes rather than osteoblasts under aging, thus leading to senile osteoporosis. Accumulated evidences indicate that rejuvenation of BMSCs by autophagic enhancement delays bone aging. Here we synthetized and demonstrated a novel autophagy activator, CXM102 that could induce autophagy in aged BMSCs, resulting in rejuvenation and preferential differentiation into osteoblasts of BMSCs. Furthermore, CXM102 significantly stimulated bone anabolism, reduced marrow adipocytes, and delayed bone loss in middle-age male mice. Mechanistically, CXM102 promoted transcription factor EB (TFEB) nuclear translocation and favored osteoblasts formation both in vitro and in vivo. Moreover, CXM102 decreased serum levels of inflammation and reduced organ fibrosis, leading to a prolonger lifespan in male mice. Our results indicated that CXM102 could be used as an autophagy inducer to rejuvenate BMSCs and shed new lights on strategies for senile osteoporosis and healthyspan improvement.

Rapid Access to Chiral Spiro[2.3] Lactams: Stereoselective Hydroborylation and Hydrosilylation and Remote Control of Axial Chirality by Copper-Catalyzed Desymmetrization of Spirocyclopropenes.

Chiral spirocyclopropyl ß-lactams are common motifs in bioactive compounds and pharmaceuticals. Here we disclose a diastereoselective and enantioselective hydroborylation and hydrosilylation of spirocyclopropenes, via a Cu-catalyzed desymmetrization strategy, for the rapid preparation of enantio-enriched spirocyclopropyl ß-lactams. The efficient desymmetrization strategy allows the remote control of axial chirality, offering the borylated and silylated products bearing central, spiro, and axial chirality. The combination of multichiral elements would provide a novel motif for biological evaluation in potential drug discovery.

[Optimized nutrients management improved citrus yield and fruit quality in China: A meta-analysis]. / å »åˆ†ä¼˜åŒ–ç®¡ç†æé«˜æˆ‘å›½æŸ‘æ©˜äº§é‡å’Œå“è´¨çš„æ•´åˆåˆ†æž.

Clarifying current situation of farmers' fertilization and yield in citrus producing areas and the effects of different fertilization measures can provide a scientific basis for improving the yield and quality of citrus in China. We retrieved 92 literatures on citrus fertilization from the CNKI and Web of Science to examine the impacts of nitrogen (N), phosphorus (P or P2O5), and potassium (K or K2O) fertilizer dosage and partial productivity under farmers' conventional fertilization and experts' optimized fertilization, as well as the effects of optimized fertilization measures on citrus yield and quality by using meta-analysis approach. The average conventional application rates of N, P2O5, and K2O were 507.3, 262.2, and 369.3 kg·hm-2 in citrus production in China. Compared with conventional fertilization, optimized fertilization resulted in a reduction of N and P2O5 by 14.7% and 8.3%, an increase in K2O application by 6.6%, which promoted partial productivity of N, P2O5, and K2O fertilizers by 7.8%, 18.4%, and 14.7%, correspondingly. The optimized fertilization resulted in 11.9% and 2.8% increase in fruit yield and single fruit weight, while improved vitamin C content (Vc, 3.1%), total soluble solids (TSS, 5.9%) and total sugar content (TSC, 8.6%). Additionally, it also led to a reduction in titratable acid (TA, -3.4%) and total acid content (TAC, -3.6%), and consequently elevated the TSS/TA (14.0%) and TSC/TAC (9.5%). Among different optimized fertilization methods, the effect of optimized NPK + medium and/or micro element fertilizer on citrus yield and fruit quality was the best, especially NPK decrement ≤25% between optimized NPK measures. The effect of conventional NPK + organic fertilizer was higher than conventional NPK + medium and/or micro element fertilizer. However, different citrus varieties, including mandarins, pomelos, and oranges, showed different responses to optimized fertilization. Optimized fertilization management could synergistically improve citrus yield, fertilizer use efficiency, and fruit quality. Therefore, the strategy of integrated nutrient management1 with reducing NPK fertilizer, balancing medium and/or micro nutrient fertilizer and improving soil fertility by organic fertilizer should be adopted according to local conditions in citrus producing areas of China.

Excessive boron fertilization-induced toxicity is related to boron transport in field-grown pomelo trees.

Boron (B) is an essential micronutrient for plant growth and development; however, the process of B toxicity in citrus production is still poorly understood. We proposed a hypothesis that B toxicity in citrus trees is related to the characteristics of B transport from soil to leaf or fruit. For this, a field experiment was conducted for two treatments, control (B free or without B) and B fertilizer treatment (100 g Na2B4O7·10H2O plant-1), to investigate the effects on plant growth, nutrient uptake, fruit yield and quality, and B transport in 10-year-old pomelo trees [Citrus grandis (L.) Osbeck cv. Guanximiyou]. Our results showed that excess B fertilization directly led to B toxicity in pomelo trees by dramatically increasing soil total B and water-soluble B contents. B toxicity induced interveinal chlorosis in leaves and decreased leaf biomass and function, resulting in a decreased 45.3% fruit yield by reducing 30.6% fruit load and 21.4% single fruit weight. Also, B toxicity induced changes in mineral elements between leaf positions and fruit parts, in which the concentrations of B, potassium, and magnesium were increased while those of nitrogen and iron were decreased. Under B toxicity conditions, fruit quality parameters of total soluble solids (TSS), TSS/titratable acidity (TA), total soluble sugar, sucrose, pH, vitamin C, and total phenol contents decreased, which were regulated by the lower carbohydrate production in new leaves and the lower transport capacity in old leaves. Moreover, B toxicity significantly increased the transfer factor and bio-concentration factor of B in pomelo plants, with higher levels in leaf organs than in fruit organs. Taken together, excess B fertilization-induced B toxicity in pomelo trees, with induced growth inhibition and nutrient disorder, results in reduced fruit yield and quality, which are related to B transport from soil to organs. The findings of this study highlight the understanding of B toxicity in citrus plants and strengthen B management in pomelo production for high yield and high quality.

Mitigating life-cycle environmental impacts and increasing net ecosystem economic benefits via optimized fertilization combined with lime in pomelo production in Southeast China.

Excessive fertilization is acknowledged as a significant driver of heightened environmental pollution and soil acidification in agricultural production. Combining fertilizer optimization with soil acidity amendment can effectively achieve sustainable crop production in China, especially in Southeast China. However, there is a lack of long-term studies assessing the environmental and economic sustainability of combining fertilizer optimization with soil acidity amendment strategies, especially in fruit production. A four-year field experiment was conducted to explore pomelo yield, fruit quality, and environmental and economic performance in three treatments, e.g., local farmer practices (FP), optimized NPK fertilizer application (OPT), and OPT with lime (OPT+L). The results showed that the OPT+L treatment exhibited the highest pomelo yield and fruit quality among the three treatments. The OPT treatment had the lowest net greenhouse gas (GHG) emissions among the three treatments, which were 90.1 % and 42.6 % lower than those in FP and OPT+L, respectively. It is essential to note that GHG emissions associated with lime production constitute 40.7 % of the total emissions from fertilizer production. The OPT+L treatment reduced reactive nitrogen (Nr) emissions and phosphorus (P) losses, compared to FP and OPT. Moreover, the OPT+L treatment increased the net ecosystem economic benefit by 220.3 % and 20.3 % compared with the FP and OPT treatments, respectively. Overall, the OPT and OPT+L treatments underscore the potential to achieve environmentally friendly and economically sustainable pomelo production. Our study provides science-based evidence to achieve better environmental and economic performance in pomelo production through optimized NPK fertilization and alleviating soil acidification by lime.

Targeted Degradation of SOS1 Exhibits Potent Anticancer Activity and Overcomes Resistance in KRAS-Mutant Tumors and BCR-ABL-Positive Leukemia.

SOS1 is an essential guanine nucleotide exchange factor for RAS that also plays a critical role in the activation of the small GTPase RAC mediated by BCR-ABL in leukemogenesis. Despite this, small molecule inhibitors targeting SOS1 have shown limited efficacy in clinical trials for KRAS mutant cancers, and their potential as a therapeutic approach for chronic myeloid leukemia (CML) remains largely unexplored. In this study, we developed a potent SOS1 PROTAC SIAIS562055, which was designed by connecting a CRBN ligand to an analogue of the SOS1 inhibitor BI-3406. SIAIS562055 exhibited sustained degradation of SOS1 and inhibition of downstream ERK pathways, resulting in superior anti-proliferative activity compared to small molecule inhibitors. SIAIS562055 also potentiated the activity of both KRAS inhibitors in KRAS-mutant cancers and ABL inhibitors in BCR-ABL+ CML. In KRAS-mutant xenografts, SIAIS562055 displayed promising antitumor potency as a monotherapy and enhanced ERK inhibition and tumor regression when combined with KRAS inhibitors, overcoming acquired resistance. In CML cells, SIAIS562055 promoted the active uptake of BCR-ABL inhibitors by upregulating the carnitine/organic cation transporter SLC22A4. SIAIS562055 and BCR-ABL inhibitors synergistically enhanced inhibition of ABL phosphorylation and downstream signaling, demonstrating robust antitumor activities in both mouse xenografts and primary CML patient samples. In summary, this study suggests that PROTAC-mediated SOS1 degradation represents an effective therapeutic strategy for treating not only KRAS-mutant cancers but also BCR-ABL-harboring leukemia.

Palladium-Catalyzed Stereoselective Defluorosilylation of gem-Difluoroalkenes for the Synthesis of Tetrasubstituted Monofluorinated Vinylsilanes.

Stereoselective synthesis of tetrasubstituted vinylsilanes is a challenging task. We herein report a novel palladium(0)-catalyzed defluorosilylation of ß,ß-difluoroacrylates to access tetrasubstituted vinylsilanes containing the monofluoroalkene motif in excellent diastereoselectivities (>99:1). This is our first example of C-heteroatom bond formation from the C-F bond under such a Pd catalytic manifold.

Three-Component Domino Acylation/Trifluoromethylation of Bicyclic Amidines.

We herein describe a three-component reaction involving bicyclic amidines such as DBN/DBU, acyl fluorides, and TMSCF3 for access to a novel class of N-acyl trifluoromethylated bicyclic aminals. Under mild and operationally simple conditions, bicyclic amidines can undergo difunctionalization (acylation/trifluoromethylation) using readily available reagents. Further Lewis acid-promoted nucleophilic ring-opening can lead to diverse products with quaternary carbon centers containing CF3. The corresponding pentafluoroethylation is also achieved by using TMSC2F5.

Palladium-Catalyzed Stereoselective Defluoroborylation of gem-Difluoroalkenes with Unsymmetrical Diboron: Access to Tetrasubstituted Monofluorinated Vinyl-B(dan) Derivatives.

The stereoselective C-F bond borylation of tetrasubstituted ß,ß-difluoroacrylates has been achieved. In contrast to the previously used B2pin2 reagent, which only led to dimerization products, this work employs the unsymmetrical diboron reagent (pin)B-B(dan) under the palladium(0)-catalyzed conditions to access novel boronamides containing the monofluorinated vinyl-B(dan) functionality. These compounds can cross-couple directly with gem-difluoroalkenes without reactivation in Suzuki-Miyaura reactions to afford vincinal difluoro 1,3-dienes with modular control of the substituents.

Copper-Catalyzed Visible-Light-Induced Allylic Difluoromethylation of Unactivated Alkenes Using Difluoroacetic Acid.

We herein describe a straightforward allylic difluoromethylation reaction of unactivated alkenes. Compared to cross-couplings of prefunctionalized allylic substrates for the construction of allylic CF2H bonds, this reaction employs readily available alkenes as substrates under mild conditions. Difluoroacetic acid is used as an inexpensive and easy-to-handle source of CF2H radical under visible light irradiation with PIDA. The copper catalyst plays an important role of diverting the reaction pathway toward allylic difluoromethylation as opposed to previously found hydrodifluoromethylation.

IL16 Regulates Osteoarthritis Progression as a Target Gene of Novel-miR-81.

OBJECTIVE: Functional polymorphisms of interleukin 16 (IL16) have been reported to be closely related to the risk of osteoarthritis (OA). However, how IL16 affects OA remains unclear. In this study, the role of IL16 in OA and the possible mechanisms were examined. METHODS: We established a meniscal/ligament injury (MLI) post-traumatic OA model in Sprague Dawley rats and an IL1ß-induced ADTC5 cells OA model. We detected the expression of IL16, novel-miR-81, MMP3, and MMP13 by quantitative real-time polymerase chain reaction. Western blot was performed to detect the expression of IL16, MMP3, and MMP13. The association between IL16 and novel-miR-81 was confirmed by luciferase reporter assay. Hematoxylin and eosin staining, Safranin O and Fast Green staining, and immunohistochemical staining were performed to clarify the effect of intra-articular injection of novel-miR-81 agomir in rats OA model. RESULTS: IL16 was upregulated in OA model. Knockdown of IL16 and overexpression of novel-miR-81 downregulated the expression of MMP3 and MMP13. Importantly, IL16 was a key target of novel-miR-81. Intra-articular injection of novel-miR-81 agomir could attenuate OA progression in rats OA model. CONCLUSION: Novel-miR-81 targeted IL16 to relieve OA, suggesting that novel-miR-81and IL16 may be new therapeutic targets for OA.

Isotope-coded derivatization with designed Girard-type reagent as charged isobaric mass tags for non-targeted profiling and discovery of natural aldehydes by liquid chromatography-tandem mass spectrometry.

Aldehyde-containing metabolites are reactive electrophiles that have attracted extensive attention due to their widespread occurrence in organisms and natural foods. Herein we described a newly-designed Girard's reagent, 1-(4-hydrazinyl-4-oxobutyl)pyridin-1-ium bromide (HBP), as charged tandem mass (MS/MS) tags to facilitate selective capture, sensitive detection and semi-targeted discovery of aldehyde metabolites via hydrazone formation. After HBP labeling, the detection signals of the test aldehydes were increased by 21-2856 times, with the limits of detection were 2.5-7 nM. Upon isotope-coded derivatization with a pair of labeling reagents, HBP-d0 and its deuterium-labeled counterpart HBP-d5, the aldehyde analytes were converted to hydrazone derivatives, which generated characteristic neutral fragments of 79 Da and 84 Da, respectively. The isobaric HBP-d0/HBP-d5 labeling based LC-MS/MS method was validated by relative quantification of human urinary aldehydes (slope=0.999, R2 > 0.99, RSDs ≤ 8.5%) and discrimination analysis between diabetic and control samples. The unique isotopic doubles (Δm/z = 5 Da) by dual neutral loss scanning (dNLS) provided a generic reactivity-based screening strategy that allowed non-targeted profiling and identification of endogenous aldehydes even amidst noisy data. The LC-dNLS-MS/MS screening of cinnamon extracts led to finding 61 possible natural aldehydes and guided discovery of 10 previously undetected congeners in this medicinal plant.

Atractylodes lancea volatile oils target ADAR2-miR-181a-5p signaling to mesenchymal stem cell chondrogenic differentiation.

Atractylodeslancea Rhizoma (Rhizoma atractylodis [RA]) has long been recommended for the treatment of arthritis in traditional Chinese medicine, but its mechanism of action is still unclear. RA contains a large amount of Atractylodes lancea volatile oils (Atr). In this study, we investigated whether Atr can promote mesenchymal stem cells (MSCs) chondrogenic differentiation. The Atr were extracted from RA by steam distillation method, and the effect of Atr on MSCs was detected by the CCK8 assay. The optimal concentration of Atr for MSCs cultivation was 3 µg/ml. The differentially expressed miR-181a-5p was screened by miRNA microarray assay, and its mimics and inhibitors were transfected into MSCs. It was found that the inhibitor of miR-181a-5p could upregulate cartilage-specific genes such as SOX9, COL2A1, and ACAN. Meanwhile, we also found that the expression of gene editing enzyme ADAR2 was significantly increased in the chondrogenic differentiation of MSCs induced by Atr, and the bases of precursor sequence of miR-181a-5p were changed from A to G. After ADAR2 deletion, the expression of cartilage-specific genes was significantly down-regulated and the precursor sequence bases of miR-181a-5p were not changed. Bioinformatics analysis revealed that the predicted target gene of miR-181a-5p was yingyang1 (YY1), and the targeting relationship was verified by dual-luciferase reporter assay. After deleting YY1, the expression of cartilage-specific genes was significantly down-regulated. In conclusion, our study demonstrated that Atr can promote chondrogenic differentiation of MSC through regulation of the ADAR2-miR-181a-5p signaling pathway. This may provide a new insight into the possible mechanism of traditional Chinese medicine (Atr) in treating inflammatory joint diseases.

TIGER: A Web Portal of Tumor Immunotherapy Gene Expression Resource.

Immunotherapy is a promising cancer treatment method; however, only a few patients benefit from it. The development of new immunotherapy strategies and effective biomarkers of response and resistance is urgently needed. Recently, high-throughput bulk and single-cell gene expression profiling technologies have generated valuable resources. However, these resources are not well organized and systematic analysis is difficult. Here, we present TIGER, a tumor immunotherapy gene expression resource, which contains bulk transcriptome data of 1508 tumor samples with clinical immunotherapy outcomes and 11,057 tumor/normal samples without clinical immunotherapy outcomes, as well as single-cell transcriptome data of 2,116,945 immune cells from 655 samples. TIGER provides many useful modules for analyzing collected and user-provided data. Using the resource in TIGER, we identified a tumor-enriched subset of CD4+ T cells. Patients with melanoma with a higher signature score of this subset have a significantly better response and survival under immunotherapy. We believe that TIGER will be helpful in understanding anti-tumor immunity mechanisms and discovering effective biomarkers. TIGER is freely accessible at http://tiger.canceromics.org/.