Differential expression of proteins associated with seasonal bud dormancy at four critical stages in Japanese apricot

Dormancy is of great significance in the growth and development of deciduous fruit trees. We used a combination of two-dimensional gel electrophoresis (2-DE) and matrix-assisted laser desorption/ionisation time of flight/time of flight mass spectrometry (MALDI-TOF/TOF MS) to identify the differentially expressed proteome of Japanese apricot flower buds at four critical stages, from paradormancy before leaf fall to dormancy release. More than 400 highly reproducible protein spots (P < 0.05) were detected: 34 protein spots showed a greater than twofold difference in expression values, of which 32 protein spots were confidently identified from databases. Identified proteins were classified into six functional categories: stress response and defence (11), energy metabolism (ten), protein metabolism (five), cell structure (three), transcription (one) and unclassified (two). The glyoxalase I homologue could help Japanese apricot survival under various abiotic and biotic stresses, greatly contributing to its dormancy. Enolase, thioredoxin family proteins and triose phosphate isomerase provide adequate energy to complete consecutive dormancy release and bud break in Japanese apricot. Cinnamyl alcohol dehydrogenase 9 and arginase enhance the resilience of plants, enabling them to complete dormancy safely. Analysis of functions of identified proteins and related metabolic pathways will increase our knowledge of dormancy in woody plants.

First Report of Phytophthora palmivora Causing Root Rot of Cassava in China

Cassava (Manihot esculenta) is an economically important crop grown widely in South China. Seventy percent of the cassava grown is used for starch and ethanol production and it has become the foundation of local food and bioenergy systems. In November 2010, a new root rot disease was found on cv. HuaNan205 from a cassava plantation in Danzhou, Hainan Province. Disease occurred on 30% or less of the plants. Initially, the upper leaves wilted at noon and recovered in the evening. Eventually, infected plants no longer recovered and the whole plant wilted and died. Root rot symptoms consisting of irregular brown patches occurred on the tuberous roots. Symptomatic root rot tissue was cut into 1-cm pieces, washed in distilled water, and soaked in a solution of 1% sodium hypochlorite for 3 min. A subsection was cut from each sterilized piece, placed on a plate of V8 agar medium, and incubated at 28°C for 7 days. Pathogenicity was established by following Koch's postulates. In July 2011, 10 plants of cassava cv. HuaNan205 were selected from a disease-free plantation in Danzhou. The pathogen was cultivated on V8 agar at 28°C for 14 days. Four holes were established 15 cm from the base of the cassava plants. Five plants were inoculated with 100 mL of the mycelial suspension in each of the four spots and covered by soil. The other five plants were treated with sterile water as control. Plants were maintained for 4 months. All five of the inoculated plants wilted and two died, while the control plants grew normally. Symptoms similar to the original root lesions were observed on tuberous roots of inoculated plants, while only scars formed on tuberous roots of control plants. The pathogen was reisolated from the lesions of inoculated plants. Microscopic examination showed the sporangia as papillate and ovoid with the widest part close to the base. They were easily washed off and each detached sporangium contained a short pedicel 1.2 to 6.9 μm long, average 2.9 μm. Chlamydospores were readily observed on diseased roots and observed in pure cultures on V8 agar. Morphological characteristics of the specimen were similar to the descriptions for Phytophthora palmivora (2). Genomic DNA of this isolate was extracted with a cetyltrimethylammoniumbromide protocol (3) from mycelium and used as a template for amplification of the internal transcribed spacer (ITS) region of rDNA with primer pair ITS1/ITS4 (1). The sequence (GenBank Accession No. HE580279) exactly matched several sequences (e.g., GenBank Accession Nos. HQ237481.1, AY745750, and AY745751) of P. palmivora. To our knowledge, this is the first report of root rot caused by P. palmivora on cassava in China. References: (1) D. E. L. Cooke et al. Fungal Genet. Biol. 30:17, 2000. (2) D. C. Erwin and O. K. Ribeiro. Phytophthora Diseases Worldwide. The American Phytopathological Society, St. Paul, MN, 1996. (3) J. R. Xu et al. Genetics 143:175, 1996.

Correlation between Thyroid Nodule Calcification Morphology on Ultrasound and Thyroid Carcinoma

OBJECTIVE: This study investigated the detection of thyroid nodule calcifications on ultrasound and their relationship to thyroid carcinoma. METHODS: Microcalcifications (≤ 2 mm) and macrocalcifications (> 2 mm) on preoperative ultrasound examination of thyroid and lymph nodes were compared with postoperative pathological diagnoses in 4186 patients undergoing thyroid surgery. RESULTS: Higher incidences of micro- and macrocalcifications were found in patients with thyroid carcinoma than in those with benign disease. The incidence of malignant disease was significantly higher in patients with microcalcifications than those with macrocalcifications, suggesting that the presence of microcalcifications is a better predictor of malignant thyroid carcinoma than other calcification types. The specificity of microcalcifications for a diagnosis of malignant thyroid carcinoma was 96.5%. Microcalcifications were significantly more frequent in patients aged ≤ 45 years, but there was no difference between genders. The incidence of malignancy was significantly higher in patients with single nodule calcifications than in those with multiple nodule calcifications. Lymph node calcifications were seen in 12 patients, all of whom had papillary carcinoma. CONCLUSIONS: Thyroid microcalcifications are strongly associated with thyroid carcinoma, especially micropapillary carcinoma. When cervical lymph node calcification is present, immediate surgery is required.

Differential effects of down-regulated steroidogenic factor-1 on basal and angiotensin II-induced aldosterone secretion

Aldosterone synthase (CYP11B2) is responsible for the final step in aldosterone synthesis and is importantly regulated by angiotensin-II (Ang II) through diverse pathways. However, under pathological conditions, such as in hyperaldosteronism, the regulation becomes disordered. The transcription factor steroidogenic factor-1 (SF-1) is important in regulating the endocrine system and is overexpressed in aldosterone-producing adenoma (APA), a common cause of hyperaldosteronism. Overexpression of SF-1 has been extensively studied, but little in-depth information is available regarding the effects of inhibitory SF-1 on CYP11B2 and Ang II. In this paper, we have investigated the roles of down-regulated SF-1 in basal and Ang II-induced CYP11B2 expression using SF-1-specific short hairpin RNA. Inhibitory SF-1 was found to decrease the sensitivity of CYP11B2 and aldosterone to Ang II stimulation, whereas a down-regulation of SF-1 enhanced basal CYP11B2 expression and aldosterone production in H295R cells. Considering these differential effects of SF-1 on aldosterone production, these results might provide a new insight into the understanding of hyperaldosteronism.

Expression (Exp) of FIP200 and Rb in breast cancer (BreastCA) metastasis (met) to the brain

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Background: BreastCA is the 2nd leading cause of cancer deaths in women in the US. Although the outcome for BreastCA with brain met remains poor, there is significant variation in overall survival (OS). Yet, there are no markers or models to predict OS. FIP200 regulates several pathways. In the nucleus, it inhibits cell proliferation by promoting Rb-1 and p21, and in the cytoplasm it promotes cell survival by inhibiting Pyk2 and regulating autophagy. It has been reported that FIP200 gene is deleted or mutated in 20% of primary BreastCAs, and its Exp is correlated with Rb1 levels. FIP200 Exp, its cellular localization, and gene alterations have not been examined in brain met of any cancer.

Methods: Brain met tissues of 21 BreastCA patients (pts) biopsied in our institution between 8/2000 and 3/2010 were obtained and Exp of FIP200 and Rb1 were analyzed. Biopsies were selected based on tissue adequacy and prior diagnosis (Dx) of invasive intra-ductal BreastCA. Immunohistochemistry (IHC) was used to evaluate the localization and Exp levels of FIP200 and Rb1 which in turn were tested as predictors of OS. Genetic alterations in FIP200 and Rb1 were examined after DNA extraction.

Results: Median time from Dx to met was 23 (range 0-245) months (mos), and median OS from Dx was 43 (range 6-264) mos. Nuclear Exp of Rb1 in < 30% vs. ≥ 30% of cells were seen in 11 vs. 10 pts. Median OS was 39 (range 6-264) mos for Rb1 Exp < 30% and 47 (range 20-190) mo for Rb1 Exp ≥ 30%. Nuclear Exp of FIP200 in <20% vs. ≥ 20% of cells were seen in 13 vs. 8 pts. Median OS was 39 (range 6-264) mo for FIP200 nuclear Exp <20% and 45 (range 43-122) mo for FIP200 Exp ≥ 20%. DNA analysis of 11 pts for copy number variations and loss of heterozygocity (LOH) showed no deletion mutations in FIP200 or Rb1, loss of p53 in 4 of 11, ErbB2 (Her-2) amplification in 4 of 11, and no EGFR gene mutations.

Conclusions: The nuclear Exp of Rb1 in brain met from invasive intra-ductal BreastCA may be linked OS. An expanded study is underway to define whether nuclear FIP200 in >20% of cells correlates with nuclear Rb and OS in BreastCA.

Functional analysis of multiple genomic signatures demonstrates that classification algorithms choose phenotype-related genes

Gene expression signatures of toxicity and clinical response benefit both safety assessment and clinical practice; however, difficulties in connecting signature genes with the predicted end points have limited their application. The Microarray Quality Control Consortium II (MAQCII) project generated 262 signatures for ten clinical and three toxicological end points from six gene expression data sets, an unprecedented collection of diverse signatures that has permitted a wide-ranging analysis on the nature of such predictive models. A comprehensive analysis of the genes of these signatures and their nonredundant unions using ontology enrichment, biological network building and interactome connectivity analyses demonstrated the link between gene signatures and the biological basis of their predictive power. Different signatures for a given end point were more similar at the level of biological properties and transcriptional control than at the gene level. Signatures tended to be enriched in function and pathway in an end point and model-specific manner, and showed a topological bias for incoming interactions. Importantly, the level of biological similarity between different signatures for a given end point correlated positively with the accuracy of the signature predictions. These findings will aid the understanding, and application of predictive genomic signatures, and support their broader application in predictive medicine.

A comparison of batch effect removal methods for enhancement of prediction performance using MAQC-II microarray gene expression data

Batch effects are the systematic non-biological differences between batches (groups) of samples in microarray experiments due to various causes such as differences in sample preparation and hybridization protocols. Previous work focused mainly on the development of methods for effective batch effects removal. However, their impact on cross-batch prediction performance, which is one of the most important goals in microarray-based applications, has not been addressed. This paper uses a broad selection of data sets from the Microarray Quality Control Phase II (MAQC-II) effort, generated on three microarray platforms with different causes of batch effects to assess the efficacy of their removal. Two data sets from cross-tissue and cross-platform experiments are also included. Of the 120 cases studied using Support vector machines (SVM) and K nearest neighbors (KNN) as classifiers and Matthews correlation coefficient (MCC) as performance metric, we find that Ratio-G, Ratio-A, EJLR, mean-centering and standardization methods perform better or equivalent to no batch effect removal in 89, 85, 83, 79 and 75% of the cases, respectively, suggesting that the application of these methods is generally advisable and ratio-based methods are preferred.

Tumour necrosis factor-alpha polymorphisms and hepatocellular carcinoma: a meta-analysis

The genetic basis of susceptibility to hepatocellular carcinoma (HCC) is poorly understood. To summarize the quantitative association between polymorphisms of the tumour necrosis factor-alpha (TNFA) gene and HCC, a meta-analysis of relevant studies was performed. Ten case-control studies involving 1421 HCC cases were identified from the Medline, Embase and Current Contents databases. Combined results based on all studies showed that patients with HCC had a significantly lower frequency of the TNFA gene polymorphism -308GG than healthy controls. When stratifying for race, results were similar among Asians and Caucasians. When comparing with hepatitis B virus infection cases, no statistical association was found. This meta-analysis suggests that TNFA -308GG gene polymorphism is associated with a modest decrease in the risk of HCC.

First Report of Leaf Spot Caused by Bipolaris setariae on Cassava in China

Cassava (Manihot esculenta Crantz) is an important food crop in tropical regions of China. Seventy percent of the cassava output is used for starch and ethanol production and it has become the base of food and bioenergy industries. In July 2009, a new leaf spot disease was found on cv. HuaNan205 from a cassava plantation in Danzhou, Hainan Province. Disease occurred on 50% or less of the plants. Initial symptoms were elliptical, chlorotic, and water-immersion lesions of 2 to 4 mm in diameter. These lesions became dry and yellow due to the progress of the disease. A brown halo was around the lesions, and in wet conditions, a dark gray mildew often appeared in the middle of the lesion. Diseased leaves turned yellow and the plants eventually became defoliated. The pathogen was isolated and pathogenicity was established by following Koch's postulates. Young, healthy, and fully expanded green leaves of Cassava cv. HuaNan205 were surface sterilized and then inoculated by spraying them with a suspension of conidia (1 × 10⁵ conidia per ml) of the isolate. Sterile water was used as a control. The leaves were kept in a humid chamber at 28°C for 4 days, at which time similar symptoms to those described above were observed on the leaves. The pathogen was reisolated from inoculated leaves. Microscopic examination showed the conidiophores were fasciculate and brown, septate and straight, and the basal cell was enlarged and hemispherical. Well-developed conidia were long-obclavate, obtuse at both ends, straight, brown, with five to eight transverse septa, and measured 49.7 to 117.1 × 13.3 to 17.2 μm. Genomic DNA of this isolate was extracted with a cetyltrimethylammoniumbromide protocol, and amplification and sequencing of the internal transcribed spacer (ITS) region of rDNA was performed with procedures outlined by Cooke et al. (2). The sequence of the region was deposited in GenBank (Accession No. GU290228). Comparison of the sequences available in the GenBank database revealed that the current ITS sequence differs by three base pairs from two Bipolaris setariae isolates (EF452444 and FJ606786). Morphological identification and sequence analysis of ITS rDNA showed that the pathogen was B. setariae. B. setariae is one of the most important pathogens of lawn grass, gramineous crops, and other plants (1,3). However, no leaf spot disease caused by B. setariae has been recorded previously on cassava in China or elsewhere. References: (1) P. Busey. Crop Sci. 43:1899, 2003. (2) D. E. L. Cooke et al. Fungal Genet. Biol. 30:17, 2000. (3) H. D. Wells and W. W. Hanna. Phytopathology 78:1179, 1988.

First Report of Corynespora cassiicola Causing Leaf Spot of Cassava in China

Cassava (Manihot esculenta) is an important economic crop in the tropical area of China. During a survey of diseases in July and September of 2009, leaf spots were observed on cassava plants at three separate plantations in Guangxi (Yunfu and Wuming) and Hainan (Baisha) provinces. Circular or irregular-shaped leaf spots were present on more than one-third of the plants. Spots were dark brown or had white papery centers delimited by dark brown rims and surrounded by a yellow halo. Usually, the main vein or small veinlets adjacent to the spots were dark. Some defoliation of plants was evident at the Wuming location. A fungus was isolated from symptomatic leaves from each of the three locations and designated CCCGX01, CCCGX02, and CCCHN01. Single-spore cultures of these isolates were incubated on potato dextrose agar (PDA) for 7 days with a 12-h light/dark cycle at a temperature of 28 ± 1°C. Conidiophores were straight to slightly curved, unbranched, and pale to light brown. Conidia were formed singly or in chains, obclavate to cylindrical, straight or curved, subhyaline-to-pale olivaceous brown, 19.6 to 150.3 μm long and 5.5 to 10.7 μm wide at the base, with 4 to 13 pseudosepta. Morphological characteristics of the specimen and their conidia were similar to the descriptions for Corynespora cassiicola (2). The isolate CCCGX01 was selected as a representative for molecular identification. Genomic DNA was extracted by the cetyltrimethylammoniumbromide protocol (3) from mycelia and used as a template for amplification of the internal transcribed spacer (ITS) region of rDNA with primer pair ITS1/ITS4. The sequence (GenBank Accession No. GU138988) exactly matched several sequences (e.g., GenBank Accession Nos. FJ852715, EF198117, and AY238606) of C. cassiicola (1). Young, healthy, and fully expanded green leaves of cassava cv. SC205 were surface sterilized. Ten leaves were inoculated with 10-μl drops of 10⁴ ml suspension of conidia and five leaves were inoculated with the same volume of sterile water to serve as controls. After inoculation, leaves were placed in a dew and dark chamber for 36 h at 25°C and subsequently transferred to the light for 5 days. All inoculated leaves with isolates showed symptoms similar to those observed in natural conditions, whereas the controls remained symptom free. The morphological characteristics of reisolated conidia that formed on the diseased parts were identical with the nature isolates. To our knowledge, this is the first report of leaf spot caused by C. cassiicola on cassava in China. References: (1) L. J. Dixon et al. Phytopathology 99:1015, 2009. (2) M. B. Ellis et al. Corynespora cassiicola. No. 303 in: CMI Description of Pathogenic Fungi and Bacteria. Commonwealth Mycological Institute, Kew, UK 1971. (3) J. R. Xu et al. Genetics 143:175, 1996.

Establishment and evaluation of a model of a community health service in an underdeveloped area of China

OBJECTIVES

To develop and evaluate an applicable model for a community health service (CHS) in an underdeveloped area of China that ensures efficient, convenient and affordable primary healthcare access for all residents.

STUDY DESIGN

The current study was carried out in Puyang, a typical medium-sized city in central-eastern China. Based on the healthcare requirements of the residents in Puyang, a CHS network was set up and its operation was evaluated from 1999 to 2006. The system is characterized by its focus on community health education (CHE).

METHODS

Firstly, 8231 residents, selected at random, were surveyed to investigate the healthcare requirements of the local residents. Meanwhile, the operation of the pre-existing healthcare resources was investigated in Puyang. Based on the information gained, a network-based CHS system was proposed and established, with CHE as the major focus. This study compared CHS operation prior to and after establishment of the network. Finally, an analytic hierarchy process based evaluation model was applied to evaluate the operation of the CHS network.

RESULTS

There was a high prevalence (86.98 per thousand) of chronic diseases among the residents who participated in this investigation. The majority (84.39%) of the residents who had healthcare requirements resorted to professional health care; the other residents did not have access to health services. Among those residents who sought professional treatment, 71.3% visited primary healthcare institutions. This information reflects the enormous requirement for a CHS in primary health care but the lack of accessibility among the residents; this motivated the authors to establish a system to solve the problem. The improvement in CHS operation after the network was established suggests the importance of a network for optimizing the primary healthcare system. The improvement was indicated by better understanding of the residents regarding the CHS, and enhanced capability of self-monitoring for chronic diseases such as hypertension after the network was established. Moreover, the residents' knowledge of health care was significantly increased and, accordingly, the incidence of health risk behaviour was reduced after the network was established. Furthermore, the CHE index between 1999 and 2006 showed good correlation (r=0.988, p<0.005) with the CHS index, suggesting the important role of CHE in CHS development.

CONCLUSIONS

A network-characterized CHS system was established in Puyang, and improved the primary healthcare situation. This study provides a feasible model for the development of a CHS in medium and small cities in underdeveloped parts of China.

CCDC134, a novel secretory protein, inhibits activation of ERK and JNK, but not p38 MAPK

In this study, we report a novel gene, CCDC134 (coiled-coil domain containing 134), that encodes a secretory protein that can inhibit the MAPK pathway as a novel human MAPK-regulating protein. The CCDC134 mRNA contains 1280 nucleotides, encoding a protein of 229 amino acids. CCDC134 is a classical secretory protein. Expression profile analysis by Northern blot, RT-PCR, immunohistochemistry and Western blot reveals that CCDC134 is widely expressed in normal adult tissues, tumor tissues and cell lines. Functional investigation reveals that overexpression of CCDC134 and its purified protein significantly inhibit transcriptional activity of Elk1 and phosphorylation of Erk and JNK/SAPK but not p38 MAPK. Conversely, specific siRNA against CCDC134 activates Elk1 transcriptional activity and promotes Erk and JNK/SAPK phosphorylation. These results clearly indicate that CCDC134 is a novel member of the secretory family and down-regulates the Raf-1/MEK/ERK and JNK/ SAPK pathways.

Insulin growth factor-binding protein 2 is a candidate biomarker for PTEN status and PI3K/Akt pathway activation in glioblastoma and prostate cancer

PTEN is an important tumor-suppressor gene associated with many cancers. Through expression profiling of glioblastoma tissue samples and prostate cancer xenografts, we identified a molecular signature for loss of the PTEN tumor suppressor in glioblastoma and prostate tumors. The PTEN signature consists of a minimum of nine genes, several of which are involved in various pathways already implicated in tumor formation. Among these signature genes, the most significant was an increase in insulin growth factor-binding protein 2 (IGFBP-2) mRNA. Up-regulation of IGFBP-2 was confirmed at the protein level by Western blot analysis and validated in samples not included in the microarray analysis. The link between IGFBP-2 and PTEN was of particular interest because elevated serum IGFBP-2 levels have been reported in patients with prostate and brain tumors. To further investigate this link, we determined that IGFBP-2 expression is negatively regulated by PTEN and positively regulated by phosphatidylinositol 3-kinase (PI3K) and Akt activation. In addition, Akt-driven transformation is impaired in IGFBP2(-/-) mouse embryo fibroblasts, implicating a functional role for IGFBP-2 in PTEN signaling. Collectively, these studies establish that PTEN and IGFBP-2 expression are inversely correlated in human brain and prostate cancers and implicate serum IGFBP-2 levels as a potential serum biomarker of PTEN status and PI3K Akt pathway activation in cancer patients.

Pathogenic role of anti-beta 2-glycoprotein I antibodies in antiphospholipid associated fetal loss: characterisation of beta 2-glycoprotein I binding to trophoblast cells and functional effects of anti-beta 2-glycoprotein I antibodies in vitro

BACKGROUND

Antiphospholipid antibodies reacting with beta2-glycoprotein I (beta 2GPI) have been associated with recurrent fetal loss and pregnancy complications.

OBJECTIVE

To investigate whether specific mutations in the phospholipid binding site of beta 2GPI might affect its binding to trophoblast and in turn the anti-beta 2GPI antibody induced functional effects.

METHODS

beta 2GPI adhesion to trophoblast was evaluated as human monoclonal IgM or polyclonal IgG anti-beta 2GPI antibody binding to trophoblast monolayers cultured (1) in complete medium; (2) in serum-free medium; (3) after serum starvation in the presence of purified human beta 2GPI; or (4) in the presence of beta 2GPI with single or multiple mutations in the amino acid loop Cys(281)-Lys-Asn-Lys-Glu-Lys-Lys-Cys(288). The effect of anti-beta 2GPI binding to trophoblast was evaluated as chorionic gonadotropin (hCG) mRNA expression, and protein release by RT-PCR and radioimmunoassay, respectively.

RESULTS

beta 2GPI adhesion to trophoblast and its consequent recognition by the specific antibodies were inversely proportional to the mutation number in the phospholipid binding site. Anti-beta 2GPI antibodies reduced gonadotropin release, hormone dependent hCG mRNA expression, and protein synthesis in the presence of beta 2GPI, while the addition of the mutants or the absence of beta 2GPI had no effect.

CONCLUSIONS

beta 2GPI binds to trophoblast in vitro through its fifth domain, as reported for endothelial cells, and can be recognised by anti-beta 2GPI antibodies; the antibody binding downregulates trophoblast hCG synthesis and secretion. Such a mechanism might contribute to defective placentation in women with fetal loss associated with the antiphospholipid syndrome.