Search

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).

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).

Xin Li, Bo Liu, Peng Cui, Xingxing Zhao, Zhao Liu, Yanxiang Qi, Gangling Zhang Department of Thoracic Oncology, Baotou Cancer Hospital, Baotou, Inner Mongolia, People’s Republic of ChinaCorrespondence: Gangling Zhang, Department of Thoracic Oncology, Baotou Cancer Hospital, Baotou, Inner Mongolia, 014030, People’s Republic of China, Tel +86-138-4827-8198, Email zhanggangling@sohu.comPurpose: 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.Keywords: renal cell carcinoma, renal sinus invasion, machine learning algorithms, peripheral blood indices, prediction model

Banana (Musa acuminate L.) is an important tropical fruit in China. During 2019-2020, a new leaf spot disease was observed on banana (M. acuminate L. AAA Cavendish, cv. Formosana) at two orchards o...

Fusarium mangiferae is a major causal agent of mango malformation disease (MMD) worldwide. Rapid and accurate detection of the causal pathogen is the cornerstone of integrated disease management. In this paper, a real-time fluorescence loop-mediated isothermal amplification assay (RealAmp) was developed for quantitative detection of F. mangiferae in China. The LAMP primer set was designed based on a RAPD marker sequence and positive products were amplified only from F. mangiferae isolates, but not from any other species tested, showing a high specificity of the primer sets. The detection limit was approximately 2.26 × 10−4 ng/μl plasmid DNA when mixed with extracted mango DNA. Quantification of the pathogen DNA of MMD in naturally collected samples was no significant difference compared to classic real-time PCR Additionally, RealAmp assay was visual with an improved closed-tube visual detection system making the assay more convenient in diagnostics.

Fusarium wilt, caused by the soil-borne fungal pathogen Fusarium oxysporum f.sp. cubense tropical race 4 (TR 4), is regarded as a major yield-reducing factor in the banana industry worldwide. Not all the varieties of banana have the same level of resistance to TR 4, and understanding the molecular interactions in banana defense responses is an important tool to reveal the unexplained processes that underlie banana resistance to TR 4. A proteomic approach was used to explore how a susceptible variety (Williams) and a resistant variety (GCTCV-119) respond to TR 4 during infestation. Sixteen proteins spots were subjected to MALDI-TOF-MS. All of the proteins identified were related to metabolism, energy, immunity and defense, and unknown function. In the resistant variety, eight spots were more abundance, and six spots were less abundance relative to control. Of these, a total of five protein spots showed a-fold change in at least two time points. In the susceptible variety, five spots were more abundance and three spots were less abundance compared with the control. Of these, six spots changed significantly after challenge with TR 4. Chitinase, beta-1,3-glucanase and superoxide dismutase were further investigated using quantitative real time polymerase chain reaction (qRT-PCR) to determine whether the observed proteome changes are associated with changes in the mRNA levels or are due to post-transcriptional regulation. In the study, beta-1,3-glucanase and chitinase were found only in pathogen-challenged plants of the resistance variety compared with the control plants at 6, 12, 24, 48 and 72 hpi, but shown by qRT-PCR beta-1,3-glucanase and chitinase were expressed both in the resistance and susceptible variety in the roots of TR 4-infected bananas.

During 2009–2011, a dieback disease of mango (Mangifera indica) has recently emerged on mango trees in Panzhihua City, Sichuan province of China. The disease is characterized by large irregular brown-coloured speckles on the petioles and twigs, vascular necrosis and dry leaves and complete twig mortality. Fusarium species were isolated repeatedly from the infected petioles and twigs. The species was identified as Fusarium decemcellulare Brick based on morphology and sequence analysis of Translation Elongation Factor-1alpha (TEF-1α) gene. Koch's postulates were fulfilled by pathogenicity tests on potted mango seedlings. To our knowledge, this is the first record of dieback on mango caused by F. decemcellulare in China.

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.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.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.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.

Twenty-two isolates of Corynespora cassiicola obtained from cucumber, papaya, eggplant, tomato, bean, Vigna, sesame and Hevea rubber (Hevea brasiliensis) were analysed by morphological features, the differences of the ribosomal DNA internal transcribed spacer (rDNA-ITS) region sequence and the inter simple sequence repeat (ISSR) technique. Variability of morphological features was observed among the isolates. Pathogenicity tests showed that isolates from different hosts attacked Hevea rubber. Sequences of two outgroup taxa, C. proliferata and C. citricola, were downloaded from GenBank. The phylogenetic trees were constructed by using the rDNA-ITS region sequences from 24 Corynespora spp. isolates. In this analysis, the 24 sequences grouped into two clusters (A and B). Cluster A consists of sequences from all isolates of C. cassiicola; whereas cluster B consists of the two outgroup taxa, C. proliferata and C. citricola. However, the ITS region is conservative, and is not fit for studying differences among isolates. A total of 114 DNA fragments was amplified with 16 ISSR primers, among which 102 were polymorphic (89.5%). A dendrogram was created by the unweighted pair-group method with arithmetic averaging (UPGMA) analysis, and 22 isolates grouped into three clusters (C, D and E). Cluster C is composed of all of the Hevea rubber isolates, whereas cluster D is composed of nine isolates: four from papaya, five from cucumber, eggplant, bean, vigna and sesame. Cluster E is composed of two isolates from cucumber and tomato. These analyses showed that the genetic diversity was very rich among the tested isolates. There are no correlations between the morphological characteristics or rDNA-ITS region sequences of the 22 isolates and their host or geographical origin, but there is a link between ISSR clusters and their host origins. ISSR markers appear to be useful for intra-species population study in C. cassiicola.

Corynespora leaf fall (CLF) disease, caused by the fungal pathogen Corynespora cassiicola, is a major disease of rubber tree (Hevea brasiliensis) that affects the production of natural rubber. To study its pathogenesis, we developed a C. cassiicola transformant tagged with green fluorescent protein and studied it using fluorescence and confocal laser scanning microscopy. The transformed isolate retained its pathogenicity and grew similarly to the wild-type. Conidia germinated and produced germ tubes 4 h after inoculation, after which the fungus infected leaves through wounds; extended into veins, cells, and intercellular spaces within 24 h; produced abundant mycelia on the surfaces of diseased leaves within 48 h; and began to form conidiophores and conidia within 72 h. The infection process of C. cassiicola on H. brasiliensis was complete within 72 h. Our findings may be useful for predicting the path of CLF disease and evaluating H. brasiliensis resistance to C. cassiicola via leaf colonization studies.

Mango (Mangifera indica L.) is an important economical crop in South China. In 2014, a stem-end rot disease was observed on mangoes 10 days after harvest from Sanya city（18.2° N and 106.5° E）, Ledong county（18.5° N and 109.1° E） and Lingshui county（18.5° N and 110.0° E）, Hainan province, China. Initial symptoms were dark brown small spots, quickly darkened and expanded into large spots with irregular margin and internal rotten flesh. Signs of the disease could be observed as fungal mycelium and pycnidia developing on the fruit surface. Twelve diseased fruits collected from 4 places weresurface disinfested using 75% ethanol, segments were dissected from the border between symptomatic and visually healthy peel and placed on potato dextrose agar (PDA) at 25 °C. Four representative isolates ACCC 39317, ACCC 39318, ACCC 39320, and ACCC 39321 were purified using the single spore method and submitted to the Agricultural Culture Collection of China（ACCC）. The initial color of the colonies was translucent white, e...

Multiple funding organizations and grants were incorrectly omitted from the Funding Statement. The Funding Statement should read: "The work was supported by the Earmarked Fund for China Agriculture Research System (Project No. CARS-32-04), Keystone Science and Technology Plan of Hainan Province (ZDXM20130044), the National Natural Science Foundation of China (31301628) and the Central Nonprofit Scientific Research Institutes for Basic Scientific Research Special Fund (1630042013021). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript."

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.

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.

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.