Desta Beyene

Diversity of rhizobia associated with Amorpha fruticosa isolated from Chinese soils and description of Mesorhizobium amorphae sp. nov.

Fifty-five Chinese isolates from nodules of Amorpha fruticosa were characterized and compared with the type strains of the species and genera of bacteria which form nitrogen-fixing symbioses with leguminous host plants. A polyphasic approach, which included RFLP of PCR-amplified 16S rRNA genes, multilocus enzyme electrophoresis (MLEE), DNA-DNA hybridization, 16S rRNA gene sequencing, electrophoretic plasmid profiles, cross-nodulation and a phenotypic study, was used in the comparative analysis. The isolates originated from several different sites in China and they varied in their phenotypic and genetic characteristics. The majority of the isolates had moderate to slow growth rates, produced acid on YMA and harboured a 930 kb symbiotic plasmid (pSym). Five different RFLP patterns were identified among the 16S rRNA genes of all the isolates. Isolates grouped by PCR-RFLP of the 16S rRNA genes were also separated into groups by variation in MLEE profiles and by DNA-DNA hybridization. A representative isolate from each of these DNA homology groups had a separate position in a phylogenetic tree as determined from sequencing analysis of the 16S rRNA genes. A new species, Mesorhizobium amorphae, is proposed for the majority of the isolates, which belonged to a moderately slow- to slow-growing, acid-producing group based upon their distinct phylogenetic position, their unique electrophoretic type, their low DNA homology with reference strains representing the species within the genus Mesorhizobium and their distinct phenotypic features. Strain ACCC 19665 was chosen as the type strain for M. amorphae sp. nov.

Phylogenetic Relationships among Rhizobium Species Nodulating the Common Bean (Phaseolus vulgaris L.)

The phylogenetic relationships among Rhizobium species that nodulate Phaseolus vulgaris (common bean) were determined by directly sequencing the amplified 16S ribosomal DNA genes of these organisms. The bean strains formed four separate clusters. One cluster was composed of Rhizobium leguminosarum bv. trifolii, R. leguminosarum bv. viciae, and R. leguminosarum bv. phaseoli. Two other clusters comprised Rhizobium etli and Rhizobium tropici, and the fourth cluster contained a single bean-nodulating strain. Data for species identification were obtained from DNA-DNA reassociation experiments. The levels of DNA relatedness among strains belonging to the three biovars of R. leguminosarum ranged from 58 to 67%. The levels of DNA relatedness between R. leguminosarum bv. phaseoli and R. etli and R. tropici ranged from 43 to 45% and 13 to 16%, respectively. The levels of DNA relatedness between the strain belonging to the fourth cluster and strains of the other three Rhizobium species that nodulate beans were less than 10%.

Rhizobium huautlense sp. nov., a symbiont of Sesbania herbacea that has a close phylogenetic relationship with Rhizobium galegae

The nitrogen-fixing rhizobial symbionts of Sesbania herbacea growing in the nature reserve at the Sierra de Huautla, Mexico, were isolated and characterized. All 104 isolates together with the type strain for Rhizobium galegae, HAMBI 540T, had similar 16S rRNA genes as revealed by PCR-RFLP analysis. Similarity in the sequences of the 16S rRNA genes placed the isolates on a phylogenetic branch shared with R. galegae. Among 66 randomly selected isolates, three closely related electrophoretic alloenzyme types (ETs) were identified, which were distinct from 10 ETs distinguished among 23 strains of R. galegae. A new species Rhizobium huautlense, represented by the Sesbania isolate SO2T, is proposed based upon low estimates of DNA relatedness between our chosen type strain and the type strains for the other species, the dissimilarity of the nucleotide sequence of the 16S rRNA genes, and their distinct ETs compared with R. galegae. The description of R. huautlense is significant because in the reconstruction of the phylogeny at R. huautlense there was a shift in the node of the branch of Agrobacterium vitis relative to that of R. galegae. The revised phylogenetic tree would tend to indicate common ancestry between R. galegae and Rhizobium leguminosarum.

Rhizobium mongolense sp. nov. is one of three rhizobial genotypes identified which nodulate and form nitrogen-fixing symbioses with Medicago ruthenica [(L.) Ledebour]

Medicago ruthenica [(L.) Ledebour] is native to inner Mongolia where rhizosphere samples were collected for the isolation of 106 rhizobial cultures. Besides nodulating the original trap host, the isolates formed nitrogen-fixing symbioses with Phaseolus vulgaris. Only half of the isolates nodulated alfalfa (Medicago sativa), but these did not form nitrogen-fixing symbioses. Rhizobium tropici also formed nitrogen-fixing symbioses with Medicago ruthenica. A total of 56 distinctive multilocus electrophoretic types (ETs) were identified among 94 of the 106 isolates which were analysed for variation in electrophoretic mobility of 12 enzyme loci. One isolate (USDA 1920) possessed a unique ET, while the ETs of the other isolates formed two weakly divergent subgroups approximately equal in size. It was concluded from small subunit rRNA gene sequences of eight isolates of Medicago ruthenica that they belonged to the genus Rhizobium and not to the genus Sinorhizobium which is more commonly associated with Medicago. Genomic similarity, determined from DNA hybridization analysis, between USDA 1920 and the strain representing the remaining isolates (USDA 1844) was lower than 20%. Based upon these observations it was concluded that at least three genomic species of rhizobia form nitrogen-fixing symbioses with Medicago ruthenica. One of these genomic species is R. tropici, another is represented by the single isolate USDA 1920 and the name Rhizobium mongolense is proposed for the third genomic species represented by USDA 1844.

Ethiopian soils harbor natural populations of rhizobia that form symbioses with common bean (Phaseolus vulgaris L.)

AbstractThe diversity and taxonomic relationships of 83 bean-nodulating rhizobia indigenous to Ethiopian soils were characterized by PCR-RFLP of the internally transcribed spacer (ITS) region between the 16S and 23S rRNA genes, 16S rRNA gene sequence analysis, multilocus enzyme electrophoresis (MLEE), and amplified fragment-length polymorphism. The isolates fell into 13 distinct genotypes according to PCR-RFLP analysis of the ITS region. Based on MLEE, the majority of these genotypes (70%) was genetically related to the type strain of Rhizobium leguminosarum. However, from analysis of their 16S rRNA genes, the majority was placed with Rhizobium etli. Transfer and recombination of the 16S rRNA gene from presumptively introduced R. etli to local R. leguminosarum is a possible theory to explain these contrasting results. However, it seems unlikely that bean rhizobia originating from the Americas (or Europe) extensively colonized soils of Ethiopia because Rhizobium tropici, Rhizobium gallicum, and Rhizobium giardinii were not detected and only a single ineffective isolate of R. etli that originated from a remote location was identified. Therefore, Ethiopian R. leguminosarum may have acquired the determinants for nodulation of bean from a low number of introduced bean-nodulating rhizobia that either are poor competitors for nodulation of bean or that failed to survive in the Ethiopian environment. Furthermore, it may be concluded from the genetic data presented here that the evidence for separating R. leguminosarum and R. etli into two separate species is inconclusive.

Risk of prostate cancer in African-American men: Evidence of mixed effects of dietary quercetin by serum vitamin D status

African‐American (AA) men experience higher rates of prostate cancer (PCa) and vitamin D (vitD) deficiency than white men. VitD is promoted for PCa prevention, but there is conflicting data on the association between vitD and PCa. We examined the association between serum vitD and dietary quercetin and their interaction with PCa risk in AA men.

Association of Cumulative Ultraviolet Radiation Exposure with Prostate Cancer Risk in a Case-control Study of African-American Men

It is well established that exposure to ultraviolet (UV) radiation has beneficial effects in reducing prostate cancer risk. To determine if there is a correlation between UV exposure and prostate cancer risk, we assessed sun exposure in a case-control study of 182 African-American men aged 40 years and older residing in the Metropolitan Washington, DC area. Using data on cumulative exposure per year and adult sunbathing scores derived from a validated questionnaire, analysis revealed significant difference in cumulative sun exposure between cases and controls (p=0.003). Additionally, the outdoor and recreation UV exposures were significantly higher in controls when compared to cases (p=0.003; p=0.03 in age-matched cases and controls). Although the results of conditional logistic regression analysis indicate that there was no association between total UV exposure and risk of prostate cancer after adjusting for age (OR=2.04, 95% CI 0.54-7.70, p=0.29), outdoor UV exposure was associated with decreased prostate cancer risk (OR= 0.31, 95% CI 0.14-0.65, p=0.002). Furthermore, a trend for reduced prostate cancer risk was found among men with early life high sun exposure during childhood ages 0-5 years (OR=0.17, 95% CI 0.03-0.74, p=0.02) and 6-11 years (OR= 0.28, 95% CI 0.07-1.05, p=0.06). Interestingly, this inverse association between prostate cancer risk and early life high sun exposure intensity was also observed among young men at ages 12-17 years although not statistically significant (OR=0.41, 95% CI 0.09-1.95, p=0.26). These findings indicate that UV exposure earlier in life may affect susceptibility to prostate cancer.

Differential expression of Annexin 2, SPINK1, and Hsp60 predict progression of prostate cancer through bifurcated WHO Gleason score categories in African American men

Although studies have observed several markers correlate with progression of prostate cancer (PCa), no specific markers have been identified that accurately predict the progression of this disease, even in African American (AA) men who are generally at higher risk than other ethnic groups. The primary goal of this study was to explore whether three markers could predict the progression of PCa.

Correlating blood-based DNA methylation markers and prostate cancer risk in African-American men

The objective of this work was to investigate the clinical significance of promoter gene DNA methylation changes in whole blood from African-American (AA) men with prostate cancer (PCa). We used high throughput pyrosequencing analysis to quantify percentage DNA methylation levels in a panel of 8 genes (RARβ2, TIMP3, SPARC, CDH13, HIN1, LINE1, CYB5R2 and DRD2) in blood DNA obtained from PCa and non-cancerous controls cases. Correlations of methylation status and various clinicopathological features were evaluated. Six genes tested achieved significant difference in DNA methylation levels between the PCa compared to control cases (P < 0.05). The TIMP3 loci demonstrated significant correlation of DNA methylation with age for all cases analyzed (p < 0.05). We observed an inverse correlation between CDH13 methylation (p = 0.045; r = -0.21) and serum vitamin D level whereas TIMP3 methylation (p = 0.021; r = -0.24) and DRD2 methylation (p = 0.056; r = -0.201) showed inverse correlation with supplementary vitamin D in the cancer cases. We also observed a direct correlation between methylation of RARβ2 (p = 0.0036; r = 0.293) and SPARC (p = 0.0134; r = 0.20) loci with PSA level in the controls but not the cancer cases. In addition, alcohol cases significantly correlated with higher RARβ2 methylation (p = 0.0314) in comparison with non-alcohol cases. Furthermore, we observed an inverse correlation of DRD2 methylation (p = 0.0349; r = -0.343) and Gleason score. Our data suggests that promoter methylation occurred more frequently in the blood of AA PCa and is associated with various clinicopathological features in AA men with PCa.

Abstract 3603: Metabolic profiles distinguish breast cancer progression in African American women

Breast cancer (BCa) is one of the most common malignancies in women and the incidence, distribution, clinical outcome and mortality rates vary widely among women of different ethnic backgrounds. Because tissue from African American (AA) women is difficult to obtain for biomarker studies, new population-relevant biomarkers that enable earlier detection and novel therapeutic intervention development are critical. To identify new biomarkers and targets that have the potential to be leveraged for earlier detection, classification of disease progression and development of improved therapeutics for AA patients, plasma and tissue samples were selected from two AA BCa case and control cohorts at the Tissue, Plasma and Clinical Bank at the Howard University Cancer Center (HUCC). Samples were from women either diagnosed with BCa, screened for potential BCa lesions or undergoing reduction mammoplasty surgery at both Howard University and Providence Hospitals. Samples were analyzed by untargeted metabolomics using 1 H nuclear magnetic resonance (NMR) spectroscopy. Multivariate and statistical analyses determined bins important to differentiating BCa by progressive stage and grade from control reduction mammoplasty tissues and fibrocystic fibroadenoma. Significant bins were library-matched to identify corresponding metabolites and distinguish common and unique metabolites between tissue groups and compare tissue profiles to plasma samples. Metabolites from each study group were also correlated with other known clinicopathologic BCa risk factors, including age, BMI, and smoking status, to determine their influence on disease progression. Several metabolites were found to distinguish nonmalignant reduction mammoplasty tissues from fibrocystic fibroadenomas, and from Grade (G) I-II estrogen receptor (ER)-positive or GI-II ER-negative tumors and GIII ER-positive or GIII ER-negative tumors. For example, in three comparisons using orthogonal partial least squares discriminant analyses (OPLS-DA) between reduction mammoplasty, fibrocystic fibroadenomas and the malignant tissues, we found 8 unique metabolites when comparing reduction mammoplasty versus fibrocystic fibroadenomas (4-hydroxybenzoate, dimethylamine, formate, glutamine, glutathione, histidine, methionine and UDP-N-acetylglucosamine); 2 unique metabolites comparing reduction mammoplasty versus GI-II (ER-positive and -negative) tumors (2-phenylpropionate and succinate); and 6 unique metabolites comparing reduction mammoplasty versus GIII (ethanolamine, glycine, hypoxanthine, maltose, sucrose and uridine). Our results demonstrate the continued usefulness of metabolomics-based research and the potential for these findings to identify early detection or disease staging biomarkers in a population that experiences a disparate burden of this disease. Citation Format: Delisha A. Stewart, Wimal W. Pathmasiri, Susan L. McRitchie, Lance Buckley, Tammey J. Naab, Robert L. DeWitty, Vikisha T. Fripp, Estelle Cooke-Sampson, Desta A. Beyene, Luisel Ricks-Santi, Robert L. Copeland, Susan J. Sumner, Yasmine M. Kanaan. Metabolic profiles distinguish breast cancer progression in African American women [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 3603.