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.

Green mold disease (causal agent, Trichoderma) has resulted in severe crop losses on mushroom farms worldwide in recent years. We analyzed 160 isolates of Trichoderma from mushroom farms for morphological, cultural, and molecular characteristics and classified these isolates into phenotypic groups. The most common group comprised approximately 40% of the isolates and was identified as a strain of Trichoderma harzianum. This group was consistently recovered from farms with severe green mold disease but not from farms with little or no problem. In addition, the strain identified as the major cause of green mold disease in Ireland and the United Kingdom grouped with these North American isolates in having very similar randomly amplified polymorphic DNA patterns.

No abstract

Bovine adenovirus type 3 (BAV3) is a DNA virus that causes respiratory and gastrointestinal disorders in cattle. We have sequenced the extreme left end of BAV3 genome (0–11.7 map units). Partial analysis of the nucleotide sequence revealed 19 potential open reading frames (ORFs) that could encode for polypeptides of 50 or more amino acids. Four of these ORFs show homology to known adenovirus polypeptides. The four BAV3 ORFs are located in approximately the same area as the Ad5 Ela, Elb, and pIX ORFs. ORF 1 has the potential to code for a 208 amino acid long polypeptide that is 75.5% homologous to the Ela conserved region III of Ad5. ORFs 2 and 3 encode 157 and 420 amino acid long polypeptide, respectively. The 157 amino acid polypeptides exhibits 69.3% homology to the Ad5 small T antigen, and the 420 amino acid polypeptide exhibits 73% homology to the large T antigen of Ad5. ORF 4 has the potential to code for a 125 amino acid long polypeptide that has 73% homology to the hexon-associated pIX of Ad7.

No abstract