BackgroundSmall RNAs are critical components in regulating various cellular pathways. These molecules may be tissue-associated or circulating in bodily fluids and have been shown to associate with different tumors. Next generation sequencing (NGS) on small RNAs is a powerful tool for profiling and discovery of microRNAs (miRNAs).ResultsIn this study, we isolated total RNA from various bodily fluids: blood, leukocytes, serum, plasma, saliva, cell-free saliva, urine and cell-free urine. Next, we used Illumina’s NGS platform and intensive bioinformatics analysis to investigate the distribution and signature of small RNAs in the various fluids. Successful NGS was accomplished despite the variations in RNA concentrations among the different fluids. Among the fluids studied, blood and plasma were found to be the most promising fluids for small RNA profiling as well as novel miRNA prediction. Saliva and urine yielded lower numbers of identifiable molecules and therefore were less reliable in small RNA profiling and less useful in predicting novel molecules. In addition, all fluids shared many molecules, including 139 miRNAs, the most abundant tRNAs, and the most abundant piwi-interacting RNAs (piRNAs). Fluids of similar origin (blood, urine or saliva) displayed closer clustering, while each fluid still retains its own characteristic signature based on its unique molecules and its levels of the common molecules. Donor urine samples showed sex-dependent differential clustering, which may prove useful for future studies.ConclusionsThis study shows the successful clustering and unique signatures of bodily fluids based on their miRNA, tRNA and piRNA content. With this information, cohorts may be differentiated based on multiple molecules from each small RNA class by a multidimensional assessment of the overall molecular signature.Electronic supplementary materialThe online version of this article (10.1186/s12864-018-4785-8) contains supplementary material, which is available to authorized users.
Cucurbit powdery mildew caused by the obligate parasite Podosphaera xanthii occurs commonly on foliage, petioles, and stems of most cucurbit crops grown in the United States. (3). However, in the field, fruit infection on cucurbits including watermelon (Citrullus lanatus), is rarely, if ever, observed (2). Consequently, it was atypical when severe powdery mildew-like symptoms were observed on seedless and seeded watermelon fruit on several commercial farms in southwestern Florida during November and December 2010. Severe powdery mildew was also observed on ‘Tri-X 313’ and ‘Mickey Lee’ fruit grown at SWFREC, Immokalee, FL. Infected fruit developed poorly and were not marketable. Powdery mildew symptoms were mainly observed on young immature fruit, but not on mature older fruit. Abundant powdery mildew conidia occurred on fruit surface, but not on the leaves. Conidia were produced in chains and averaged 35 × 21 μm. Observation of conidia in 3% KOH indicated the presence of fibrosin bodies commonly found in the cucurbit powdery mildew genus Podosphaera (3). Orange-to-dark brown chasmothecia (formerly cleisthothecia) containing a single ascus were detected on the surface of some fruit samples. Conidial DNA was subjected to PCR using specific primers designed to amplify the internal transcribed spacer (ITS) region of Podosphaera (4). The resulting amplicons were sequenced and found to be 100% identical to the ITS sequences of P. xanthii in the NCBI database (D84387, EU367960, AY450961, AB040322, AB040315). Sequences from the watermelon fruit isolate were also identical to several P. fusca (synonym P. xanthii), P. phaseoli (GQ927253), and P. balsaminae (AB462803) sequences. On the basis of morphological characteristics and ITS sequence analysis, the pathogen infecting watermelon fruit can be considered as P. xanthii (1,3,4). The powdery mildew isolate from watermelon fruit was maintained on cotyledons of squash (Cucurbita pepo, ‘Early Prolific Straight Neck’). Cotyledons and leaves of five plants each of various cucurbits and beans were inoculated with 10 μl of a conidial suspension (105conidia/ml) in water (0.02% Tween 20). Two weeks after inoculation, abundant conidia were observed on cucumber (Cucumis sativus, ‘SMR-58’) and melon (Cucumis melo) powdery mildew race differentials ‘Iran H’ and ‘Vedrantais’. However, no growth was observed on melon differentials ‘PI 414723’, ‘Edisto 47’, ‘PMR 5’, ‘PMR 45’, ‘MR 1’, and ‘WMR 29’ (2,3). The powdery mildew isolate from watermelon fruit behaved as melon race 1 (3). Mycelium and conidia were also observed on fruit surface of watermelon ‘Sugar Baby’ and a susceptible U.S. plant introduction (PI 538888) 3 weeks after inoculation. However, the disease was not as severe as what was observed in the fields in fall 2010. The pathogen did not grow on plants of Impatiens balsamina or on select bean (Phaseolus vulgaris) cultivars (‘Red Kidney’, ‘Kentucky Blue’, and ‘Derby Bush’), but did grow and produce abundant conidia on ‘Pinto bush bean’. Powdery mildew on watermelon fruit in production fields can be considered as a potentially new and serious threat requiring further studies to develop management strategies. References: (1) U. Braun and S. Takamatsu. Schlechtendalia 4:1, 2000. (2) A. R. Davis et al. J. Am. Soc. Hortic. Sci. 132:790, 2007. (3) M. T. McGrath and C. E. Thomas. In: Compendium of Cucurbit Diseases. American Phytopathological Society, St. Paul, MN, 1996. (4) S. Takamatsu and Y. Kano. Mycoscience 42:135, 2001.
A current trend in Florida agriculture to conserve water is to irrigate with surface runoff water (tailwater) recovered in retention ponds and canals. Water fi ltration and lemon leaf baiting recovered Phytophthora capsici and other plant pathogenic Oomycetes in runoff water from ponds and canals. A total of 196 isolates of Phytophthora spp. and 471 isolates of Pythium spp. were recovered. Phytophthora spp. included P. capsici, P. cinnamomi, P. lateralis, P. nicotianae, P. citricola, P. cryptogea and P. erythroseptica. Species of Pythium were P. aphanidermatum, P. catenulatum, P. helicoides, P. irregulare, P. myriotylum, and Pythium 'group F'. Isolates of P. aphanidermatum, P. irregulare, P. myriotylum, and Pythium 'group F' were pathogenic on pepper and tomato. Recovery of P. capsici propagules was related to soil moisture-holding capacity and time interval but not temperature. Recovery of P. capsici propagules at 100% soil moisture-holding capacity and 30°C was 57 days. In tailwater, recovery of propagules of P. capsici was 63 days at 24°C to 25°C. The potential exists to reintroduce and disseminate species of Phytophthora and Pythium when using tailwater for irrigation or other practices.
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