Development and Validation of a Clinic Machine Learning Classifier for the Prediction of Risk Stratifications of Prostate Cancer Bone Metastasis Progression to Castration Resistance.

Objective: To explore the predictive factors and predictive model construction for the progression of prostate cancer bone metastasis to castration resistance. Methods: Clinical data of 286 patients diagnosed with prostate cancer with bone metastasis, initially treated with endocrine therapy, and progressing to metastatic castration resistant prostate cancer (mCRPC) were collected. By comparing the differences in various factors between different groups with fast and slow occurrence of castration-resistant prostate cancer (CRPC). Kaplan-Meier survival analysis and COX multivariate risk proportional regression model were used to compare the differences in the time to progression to CRPC in different groups. The COX multivariate risk proportional regression model was used to evaluate the impact of candidate factors on the time to progression to CRPC and establish a predictive model. The accuracy of the model was then tested using receiver operating characteristic (ROC) curves and decision curve analysis (DCA). Results: The median time for 286 mCRPC patients to progress to CRPC was 17 (9.5-28.0) months. Multivariate analysis showed that the lowest value of PSA (PSA nadir), the time when PSA dropped to its lowest value (timePSA), and the number of BM, and LDH were independent risk factors for rapid progression to CRPC. Based on the four independent risk factors mentioned above, a prediction model was established, with the optimal prediction model being a random forest with area under curve (AUC) of 0.946[95% CI: 0.901-0.991] and 0.927[95% CI: 0.864-0.990] in the training and validation cohort, respectively. Conclusion: After endocrine therapy, the PSA nadir, timePSA, the number of BM, and LDH are the main risk factors for rapid progression to mCRPC in patients with prostate cancer bone metastases. Establishing a CRPC prediction model is helpful for early clinical intervention decision-making.

TRPA1 promotes the maturation of embryonic stem cell-derived cardiomyocytes by regulating mitochondrial biogenesis and dynamics.

BACKGROUND: Cardiomyocytes derived from pluripotent stem cells (PSC-CMs) have been widely accepted as a promising cell source for cardiac drug screening and heart regeneration therapies. However, unlike adult cardiomyocytes, the underdeveloped structure, the immature electrophysiological properties and metabolic phenotype of PSC-CMs limit their application. This project aimed to study the role of the transient receptor potential ankyrin 1 (TRPA1) channel in regulating the maturation of embryonic stem cell-derived cardiomyocytes (ESC-CMs). METHODS: The activity and expression of TRPA1 in ESC-CMs were modulated by pharmacological or molecular approaches. Knockdown or overexpression of genes was done by infection of cells with adenoviral vectors carrying the gene of interest as a gene delivery tool. Immunostaining followed by confocal microscopy was used to reveal cellular structure such as sarcomere. Staining of mitochondria was performed by MitoTracker staining followed by confocal microscopy. Calcium imaging was performed by fluo-4 staining followed by confocal microscopy. Electrophysiological measurement was performed by whole-cell patch clamping. Gene expression was measured at mRNA level by qPCR and at protein level by Western blot. Oxygen consumption rates were measured by a Seahorse Analyzer. RESULTS: TRPA1 was found to positively regulate the maturation of CMs. TRPA1 knockdown caused nascent cell structure, impaired Ca2+ handling and electrophysiological properties, and reduced metabolic capacity in ESC-CMs. The immaturity of ESC-CMs induced by TRPA1 knockdown was accompanied by reduced mitochondrial biogenesis and fusion. Mechanistically, we found that peroxisome proliferator-activated receptor gamma coactivator-1α (PGC-1α), the key transcriptional coactivator related to mitochondrial biogenesis and metabolism, was downregulated by TRPA1 knockdown. Interestingly, overexpression of PGC-1α ameliorated the halted maturation induced by TRPA1 knockdown. Notably, phosphorylated p38 MAPK was upregulated, while MAPK phosphatase-1 (MKP-1), a calcium-sensitive MAPK inhibitor, was downregulated in TRPA1 knockdown cells, suggesting that TRPA1 may regulate the maturation of ESC-CMs through MKP-1-p38 MAPK-PGC-1α pathway. CONCLUSIONS: Taken together, our study reveals the novel function of TRPA1 in promoting the maturation of CMs. As multiple stimuli have been known to activate TRPA1, and TRPA1-specific activators are also available, this study provides a novel and straightforward strategy for improving the maturation of PSC-CMs by activating TRPA1. Since a major limitation for the successful application of PSC-CMs for research and medicine lies in their immature phenotypes, the present study takes a big step closer to the practical use of PSC-CMs.

First report of Neopestalotiopsis clavispora causing leaf spot disease on banana (Musa acuminate L.) in China.

Banana (Musa acuminate L.) is an important tropical fruit in China. In October 2020, a new leaf spot disease was observed on banana plants at an orchard of Zhenkang county (23°45'23.46″ N, 98°48'46.52″ E), Lincang city, Yunnan province, China. The disease incidence was about 1%. The leaf spots occurred sporadically and the percentage of the leaf area covered by lesions was less than 5%. Symptoms on the leaves were initially small, irregular, reddish-brown spots that gradually expanded to fusiform-shaped lesions with a yellow halo and eventually become necrotic, dry, and cracked. To isolate the pathogen, thirty symptomatic leaves (15 mm2) from five plants were surface disinfected in 70% ethanol (10 s) and 0.8% NaClO (2 min), rinsed in sterile water three times, and transferred to potato dextrose agar (PDA) at 28°C for 5 days. Twenty-five colonies formed on the PDA plates were white with cottony aerial mycelium, round with a light orange underside. Abundant black globular acervuli semi-immersed on PDA were observed after a week. Conidia were straight or slightly curved, clavate to spindle, five cells, four septa with dimensions of 17.49 to 34.51 µm × 4.24 to 7.28 µm (avg. 23.83 × 5.62 µm; n=50). The apical and basal cells were hyaline, whereas the three median cells were dark brown. Conidia had a single basal appendage with lengths of 2.95 to 17.7 µm (avg. 7.18 µm; n=50) and two to three apical appendages with lengths of 10.7 to 53.84 µm (avg. 17.36 µm; n=50). These morphological characteristics are consistent with those of Neopestalotiopsis spp. (Maharachchikumbura et al. 2014). To confirm species, single-spore cultures of two representative isolates CATAS-102001 and CATAS-102002 were selected for further identification. The internal transcribed spacer (ITS) region, translation elongation factor 1-α (TEF1-α) and ß-tubulin (TUB2) genes of the two isolates were amplified with primers ITS1/ITS4 (White et al. 1990), EF1-728/EF2 (O'Donnell et al. 1998; Carbone and Kohn, 1999) and T1/Bt2b (Glass and Donaldson, 1995; O'Donnell and Cigelnik, 1997), respectively, and sequenced. The sequences were deposited in GenBank (ITS: OM281005 and OM281006; TEF1-α: OM328820 and OM328821; TUB2: OM328818 and OM328819). A maximum likelihood phylogenetic tree was constructed using the MEGA 7.0 (Kumar et al. 2016) based on the concatenated sequences ITS region, EF1-α and TUB2 gene, and the cluster analysis placed the representative isolates CATAS-102001 and CATAS-102002 within a clade comprising Neopestalotiopsis clavispora. The pathogenicity of two isolates was conducted on six 7-leaf-old banana seedlings. Two leaves from each potted plants were stab inoculated by puncturing into 1-mm using a sterilized needle, and stabbing three points at both sides of leaf midrib, and then placing 10 µl conidial suspension (1×106 conidia/ml) on one side of wounded points and the other side of wounded points were inoculated with sterile water as control. Inoculated plants were kept inside a plastic bag for 72 h and maintained in the greenhouse (12 h/12 h light/dark, 28°C, 90% relative humidity). The experiments were repeated twice. Irregular necrotic lesions on inoculated leaves appeared 7 days after inoculation, whereas controls were asymptomatic. The fungus was recovered from inoculated leaves, and its taxonomy was confirmed morphologically and molecularly, fulfilling Koch's postulates. Neopestalotiopsis clavispora has been reported to cause leaf spot on Mangifera indica (Shu et al. 2020), Macadamia integrifolia (Santos et al. 2019) and Ligustrum lucidum (Chen et al. 2020). To our knowledge, this is the first report of N. clavispora on banana in China. The identification of N. clavispora as the causal agent of the observed leaf spot disease on banana is critical to the prevention and control of this disease in the future.

Integrative Analysis of Peripheral Blood Indices for the Renal Sinus Invasion Prediction of T1 Renal Cell Carcinoma: An Ensemble Study Using Machine Learning-Assisted Decision-Support Models.

PURPOSE: Renal sinus invasion is an attributive factor affecting the prognosis of renal cell carcinoma (RCC). This study aimed to construct a risk prediction model that could stratify patients with RCC and predict renal sinus invasion with the help of a machine learning (ML) algorithm. PATIENTS AND METHODS: We retrospectively recruited 1229 patients diagnosed with T1 stage RCC at the Baotou Cancer Hospital between November 2013 and August 2021. Iterative analysis was used to screen out predictors related to renal sinus invasion, after which ML-based models were developed to predict renal sinus invasion in patients with T1 stage RCC. The receiver operating characteristic curve (ROC), decision curve analysis (DCA), and clinical impact curve (CIC) were performed to evaluate the robustness and clinical practicability of each model. RESULTS: A total of 21 candidate variables were shortlisted for model building. Iterative analysis screened that neutrophil to albumin ratio (NAR), hemoglobin level * albumin level * lymphocyte count/platelet count ratio (HALP), prognostic nutrition index (PNI), body mass index*serum albumin/neutrophil-lymphocyte ratio (AKI), NAR, and fibrinogen (FIB) concentration (NARFIB), platelet to lymphocyte ratio (PLR), and R.E.N.A.L score was related to renal sinus invasion and contributed significantly to ML-based algorithm. The areas under the ROC curve (AUCs) of the random forest classifier (RFC) model, support vector machine (SVM), eXtreme gradient boosting (XGBoost), artificial neural network (ANN), and decision tree (DT) ranged from 0.797 to 0.924. The optimal risk probability of renal sinus invasion predicted was RFC (AUC = 0.924, 95% confidence interval [CI]: 0.414-1.434), which showed robust discrimination for identifying high-risk patients. CONCLUSION: We successfully develop practical models for renal sinus invasion prediction, particularly the RFC, which could contribute to early detection via integrating systemic inflammatory factors and nutritional parameters.

Rheinheimera lutimaris sp. nov., a marine bacterium isolated from coastal sediment.

A Gram-stain-negative, aerobic, rod-shaped bacterium, designated strain YQF-2T, was isolated from coastal sediment sampled in Jiangsu Province and characterized phylogenetically and phenotypically. Optimal bacterial growth occurred at 28 °C (range 4-38 °C) and pH 7 (pH 6-10). Phylogenetic analysis based on 16S rRNA gene sequences showed that strain YQF-2T was related to members of the genus Rheinheimera and shared the highest sequence identities with Rheinheimera pacifica KMM 1406T (98.6%), followed by Rheinheimera aestuarii H29T (98.4%), Rheinheimera japonica KMM 9513T (98.3%), Rheinheimera aquimaris SW-353T (98.3%), Rheinheimera hassiensis E48T (97.8%) and Rheinheimera muenzenbergensis E49T (97.7%). The 16S rRNA gene sequence identities between strain YQF-2T and other members of the genus Rheinheimera were below 97.2%. The digital DNA-DNA hybridization value between strain YQF-2T and R. pacifica KMM 1406T was 23.3±2.3%. The average nucleotide identity value between strain YQF-2T and R. pacifica KMM 1406T was 79.7%. The unique respiratory quinone was ubiquinone-8. Phosphatidylethanolamine and phosphatidylglycerol were identified as the major polar lipids. The strain had summed feature 3 (C16:1 ω7c and/or C16:1 ω6c), summed feature 8 (C18:1 ω7c and/or C18:1 ω6c), C16:0, C12:0 3-OH and iso-C17:0 3-OH as major fatty acids. The G+C content of the genomic DNA was 50.0 mol%. On the basis of phenotypic, genotypic and phylogenetic evidence, strain YQF-2T represents a novel species of the genus Rheinheimera, for which the name Rheinheimera lutimaris sp. nov. is proposed, with the type strain YQF-2T (=KCTC 72184T=MCCC 1K03663T).

Mitochondrial Biogenesis, Mitochondrial Dynamics, and Mitophagy in the Maturation of Cardiomyocytes.

Pluripotent stem cells (PSCs) can undergo unlimited self-renewal and can differentiate into all the cell types present in our body, including cardiomyocytes. Therefore, PSCs can be an excellent source of cardiomyocytes for future regenerative medicine and medical research studies. However, cardiomyocytes obtained from PSC differentiation culture are regarded as immature structurally, electrophysiologically, metabolically, and functionally. Mitochondria are organelles responsible for various cellular functions such as energy metabolism, different catabolic and anabolic processes, calcium fluxes, and various signaling pathways. Cells can respond to cellular needs to increase the mitochondrial mass by mitochondrial biogenesis. On the other hand, cells can also degrade mitochondria through mitophagy. Mitochondria are also dynamic organelles that undergo continuous fusion and fission events. In this review, we aim to summarize previous findings on the changes of mitochondrial biogenesis, mitophagy, and mitochondrial dynamics during the maturation of cardiomyocytes. In addition, we intend to summarize whether changes in these processes would affect the maturation of cardiomyocytes. Lastly, we aim to discuss unanswered questions in the field and to provide insights for the possible strategies of enhancing the maturation of PSC-derived cardiomyocytes.

Rheinheimera sediminis sp. nov., a marine bacterium isolated from coastal sediment.

A Gram-stain-negative, aerobic, rod-shaped bacterium, designated strain YQF-1T, was isolated from coastal sediment in Jiangsu Province (PR China) and characterized phylogenetically and phenotypically. Bacterial optimal growth occurred at 28 °C (range 4-40 °C) and pH 7 (range pH 6-11). Phylogenetic analysis based on 16S rRNA gene sequence indicated that YQF-1T was related to members of the genus Rheinheimera and shared the highest sequence identities with Rheinheimera mesophila DSM 29723T (98.5 %), followed by Rheinheimera tangshanensis DSM 19460T (98.4 %), Rheinheimera tilapiae Ruye-90T (97.9 %), Rheinheimera soli BD-d46T (97.9 %), Rheinheimera aquatica GR5T (97.4 %), Rheinheimera coerulea TAPG2T (97.3 %) and Rheinheimera texasensis A62-14BT (97.1 %). The 16S rRNA gene sequence identities between YQF-1T and other members of the genus Rheinheimera were below 97.0 %. The digital DNA-DNA hybridization value between YQF-1T and Rheinheimera mesophila DSM 29723T was 25.1±2.3 %. The average nucleotide identity (ANI) value between YQF-1T and Rheinheimera mesophila DSM 29723T was 81.4 %. The major respiratory quinone was Q-8. The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol, phospholipid, two unidentified aminolipids and three unidentified lipids. The strain had summed feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c), C16 : 0, summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c), iso-C15 : 0, and anteiso-C17 : 1 ω9c as the major fatty acids. The G+C content of the genomic DNA was 46.2 mol%. On the basis of phenotypic, genotypic and phylogenetic evidence, strain YQF-1T represents a novel species of the genus Rheinheimera, for which the name Rheinheimera sediminis sp. nov. is proposed, with the type strain YQF-1T (=KCTC 72183T=MCCC 1K03646T).

TRPC3 Regulates the Proliferation and Apoptosis Resistance of Triple Negative Breast Cancer Cells through the TRPC3/RASA4/MAPK Pathway.

Currently, there is no effective molecular-based therapy for triple-negative breast cancer (TNBC). Canonical transient receptor potential isoform 3 (TRPC3) was previously shown to be upregulated in breast cancer biopsy tissues when compared to normal breast tissues. However, the biological role of TRPC3 in breast cancer still remains to be elucidated. In this study, subcellular fractionation followed by Western blot and immunocytochemistry showed that TRPC3 was over-expressed on the plasma membrane of TNBC line MDA-MB-231 when compared to an estrogen receptor-positive cell line MCF-7. TRPC3 blocker Pyr3 and dominant negative of TRPC3 attenuated proliferation, induced apoptosis and sensitized cell death to chemotherapeutic agents in MDA-MB-231 as measured by proliferation assays. Interestingly, Ras GTPase-activating protein 4 (RASA4), a Ca2+-promoted Ras-MAPK pathway suppressor, was found to be located on the plasma membrane of MDA-MB-231. Blocking TRPC3 decreased the amount of RASA4 located on the plasma membrane, with concomitant activation of MAPK pathways. Our results suggest that, in TNBC MDA-MB-231 cells, Ca2+ influx through TRPC3 channel sustains the presence of RASA4 on the plasma membrane where it inhibits the Ras-MAPK pathway, leading to proliferation and apoptosis resistance. Our study reveals the novel TRPC3-RASA4-MAPK signaling cascade in TNBC cells and suggests that TRPC3 may be exploited as a potential therapeutic target for TNBC.

Genome-wide identification and expression profile analysis of the NAC transcription factor family during abiotic and biotic stress in woodland strawberry.

The NAC transcription factors involved plant development and response to various stress stimuli. However, little information is available concerning the NAC family in the woodland strawberry. Herein, 37 NAC genes were identified from the woodland strawberry genome and were classified into 13 groups based on phylogenetic analysis. And further analyses of gene structure and conserved motifs showed closer relationship of them in every subgroup. Quantitative real-time PCR evaluation different tissues revealed distinct spatial expression profiles of the FvNAC genes. The comprehensive expression of FvNAC genes revealed under abiotic stress (cold, heat, drought, salt), signal molecule treatments (H2O2, ABA, melatonin, rapamycin), biotic stress (Colletotrichum gloeosporioides and Ralstonia solanacearum). Expression profiles derived from quantitative real-time PCR suggested that 5 FvNAC genes responded dramatically to the various abiotic and biotic stresses, indicating their contribution to abiotic and biotic stresses resistance in woodland strawberry. Interestingly, FvNAC genes showed greater extent responded to the cold treatment than other abiotic stress, and H2O2 exhibited a greater response than ABA, melatonin, and rapamycin. For biotic stresses, 3 FvNAC genes were up-regulated during infection with C. gloeosporioides, while 6 FvNAC genes were down-regulated during infection with R. solanacearum. In conclusion, this study identified candidate FvNAC genes to be used for the genetic improvement of abiotic and biotic stress tolerance in woodland strawberry.

[Genetic diversity analysis of Fusarium oxysporum f. sp. cubense populations from China using Inter-Simple Sequence Repeats-PCR (ISSR-PCR) technique].

OBJECTIVE: We used Inter-Simple Sequence Repeats (ISSR) markers to reveal the genetic diversity of 95 Fusarium oxysporum f. sp. cubense ( FOC ) isolates from banana in China, for the rational control of the disease. METHODS: Eight primers were chosen for analyzing FOC isolates to study their genetic diversity by ISSR-PCR. All isolates were clustered using Unweighted Pair-Group Method with Arithmetic means (UPGMA) analysis by NTSYSpc v2.10e software. RESULTS: A total of 52 sites were generated, among them 92.3% were polymorphic. Genetic distance was 0.57 to 1.00 based on the Nei's standard. Isolates were grouped into six distinct clusters (A, B, C, D, E and F) based on ISSR analysis using a genetic distance threshold of 0.68, the proportion of 51.06%, 39.58%, 5.20%, 2.08%, 1.04%, and 1.04%, respectively. CONCLUSION: There were high levels of genetic variation among the FOC isolates, and the ISSR clustering groups had obvious correlation with hosts and races of the pathogen.

Development of a real-time fluorescence loop-mediated isothermal amplification assay for rapid and quantitative detection of Fusarium oxysporum f. sp. cubense tropical race 4 in soil.

Fusarium oxysporum f. sp. cubense (Foc), the causal agent of Fusarium wilt (Panama disease), is one of the most devastating diseases of banana (Musa spp.). The Foc tropical race 4 (TR4) is currently known as a major concern in global banana production. No effective resistance is known in Musa to Foc, and no effective measures for controlling Foc once banana plants have been infected in place. Early and accurate detection of Foc TR4 is essential to protect banana industry and guide banana planting. A real-time fluorescence loop-mediated isothermal amplification assay (RealAmp) was developed for the rapid and quantitative detection of Foc TR4 in soil. The detection limit of the RealAmp assay was approximately 0.4 pg/µl plasmid DNA when mixed with extracted soil DNA or 10(3) spores/g of artificial infested soil, and no cross-reaction with other relative pathogens were observed. The RealAmp assay for quantifying genomic DNA of TR4 was confirmed by testing both artificially and naturally infested samples. Quantification of the soil-borne pathogen DNA of Foc TR4 in naturally infested samples was no significant difference compared to classic real-time PCR (P>0.05). Additionally, RealAmp assay was visual with an improved closed-tube visual detection system by adding SYBR Green I fluorescent dye to the inside of the lid prior to amplification, which avoided the inhibitory effects of the stain on DNA amplification and makes the assay more convenient in the field and could thus become a simple, rapid and effective technique that has potential as an alternative tool for the detection and monitoring of Foc TR4 in field, which would be a routine DNA-based testing service for the soil-borne pathogen in South China.

Molecular and pathogenic variation identified among isolates of Corynespora cassiicola.

Pathogenicity tests and inter simple sequence repeat (ISSR) molecular fingerprinting markers were utilized to analyze 24 Corynespora cassiicola isolates obtained from a lot of Hevea clones grown in most rubber nurseries and a few plantations in China. The C. cassiicola isolates were collected from Hainan and Yunnan provinces, China, from 2006 to 2008. The assay of 24 C. cassiicola isolates on detached leaves of four different Hevea rubber clones (genotypes PR 107, Dafeng 95, RRIM 600, and Reyan 7-33-97) indicated that 23 of the isolates were susceptible to RRIM 600, and were therefore considered race 1 except for CC-023. ISSR analysis grouped 24 C. cassiicola isolates into four clusters (A, B, C, and D). Unweighted pair-group method with arithmetic averaging (UPGMA) analysis based on Nei and Li's coefficient (calculated from the binary matrix data of 103 DNA fragments generated from 16 ISSR primers) indicated that cluster A included 19 isolates from Hainan and Yunnan (this cluster was further divided into two sub clusters (I, II), sub cluster II contained isolate CC-023); clusters B and C comprised of 1 isolates from Hainan, respectively; while cluster D encompassed 3 isolates from Hainan and Yunnan. Pathogenicity tests and ISSR analysis showed that there was no correlation between race structure, the geographical origin of the pathogen and their ISSR clusters because 23 of the isolates belonging to four distinct clusters were considered race 1 except for isolate CC-023. However, most of the isolates with different pathogenicity levels shared the same clades, and furthermore, the ISSR clusters and cology color had an exact correlation. These results should facilitate the development of rubber clones with enhanced resistance against all genetic clusters of C. cassiicola.

[Detection and identification of Xanthomonas oryzae pv. oryzae and Xanthomonas oryzae pv. oryzicola by real-time fluorescent PCR].

A novel and sensitive real time PCR was developed to detection Xanthomonas oryzae pv. oryzae and Xanthomonas oryzae pv. oryzicola, which cause the bacteria leaf blight (BLB) and leaf streak respectively, Universal and specific TaqMan probes, which were designed based on the sequence of Putative siderophore receptor gene cds were used to detect 13 bacteria and one phytoplasmas, only in X. oryzae pv. oryzae and X. oryzae pv. oryzicola, fluorescent signal can be collected with their specific probes respectively. The level of detection of the probe was 30.6fg plasmid, roughly equaling to one cell and 100 times sensitive than PCR gel electrophoresis detection. X. oryzae pv. oryzae and X. oryzae pv oryzicola were detected from seed washes and DNA extracted from the seed washes of naturally infected seeds and infected leaves as small as 10g naturally infected seeds or 0.3g leaf. This method is little time consumption (only 2h) and without contamination from PCR product.