Next Generation Sequencing in Aquatic Models

The most valuable application of next generation sequencing (NGS) technology is genome sequencing. Genomes of several aquatic models had been sequenced in the past few years due to their importance in genomics, development biology, toxicology, pathology, and cancer research. NGS technology is greatly advanced in sequencing length and accuracy, which facilitate the sequencing process, but sequence assembly, especially for the species with complicated genomes, is still the biggest challenge for bench-top scientists

Genome level analysis of rice mRNA 3′-end processing signals and alternative polyadenylation

The position of a poly(A) site of eukaryotic mRNA is determined by sequence signals in pre-mRNA and a group of polyadenylation factors. To reveal rice poly(A) signals at a genome level, we constructed a dataset of 55 742 authenticated poly(A) sites and characterized the poly(A) signals. This resulted in identifying the typical tripartite cis-elements, including FUE, NUE and CE, as previously observed in Arabidopsis. The average size of the 3′-UTR was 289 nucleotides. When mapped to the genome, however, 15% of these poly(A) sites were found to be located in the currently annotated intergenic regions. Moreover, an extensive alternative polyadenylation profile was evident where 50% of the genes analyzed had more than one unique poly(A) site (excluding microheterogeneity sites), and 13% had four or more poly(A) sites. About 4% of the analyzed genes possessed alternative poly(A) sites at their introns, 5′-UTRs, or protein coding regions. The authenticity of these alternative poly(A) sites was partially confirmed using MPSS data. Analysis of nucleotide profile and signal patterns indicated that there may be a different set of poly(A) signals for those poly(A) sites found in the coding regions. Based on the features of rice poly(A) signals, an updated algorithm termed PASS-Rice was designed to predict poly(A) sites

Simultaneous Determination of Selegiline, Desmethylselegiline, R/S-methamphetamine, and R/S-amphetamine on Dried Urine Spots by LC/MS/MS: Application to a Pharmacokinetic Study in Urine

Objective: Chiral analysis is a crucial method to differentiate selegiline intake from drug abuse. A dried urine spot (DUS) analytical method based on spotting urine samples (10 μL) onto dried spot collection cards, and followed by air-drying and extraction, was developed and validated for the determination of selegiline, desmethylselegiline, R/S-methamphetamine, and R/S-amphetamine.Methods: Methanol (0.5 mL) was found to be the ideal extraction solvent for target extraction from DUSs under orbital-horizontal stirring on a lateral shaker at 1,450 rpm for 30 min. Determinations were performed by direct electrospray ionization tandem mass spectrometry (ESI-MS/MS) under positive electrospray ionization conditions using multiple reaction monitoring mode. The chromatographic system consisted of a ChirobioticTM V2 column (2.1 × 250 mm, 5 μm) and a mobile phase of methanol containing 0.1% (v/v) glacial acetic acid and 0.02% (v/v) ammonium hydroxide.Results and conclusions: The calibration curves were linear from 50 to 5,000 ng/mL, with r > 0.995 for all analytes, imprecisions ≤ 15% and accuracies between −11.4 and 11.7%. Extraction recoveries ranged from 48.6 to 105.4% with coefficients of variation (CV) ≤ 13.7%, and matrix effects ranged from 45.4 to 104.1% with CV ≤ 10.3%. The lower limit of quantification was 50 ng/mL for each analyte. The present method is simple, rapid (accomplished in 12 min), sensitive, and validated by a pharmacokinetic study in human urine collected after a single oral administration of SG

X. couchianus and X. hellerii genome models provide genomic variation insight among Xiphophorus species

4 inter-chromosomal rearrangement events between X. hellerii and X. maculatus. (XLSX 40 kb

Rapid Visual Detection of Pathogenic Streptococcus suis Type 2 through a Recombinase Polymerase Amplification Assay Coupled with Lateral Flow Test

Streptococcus suis serotype 2 (SS2) is an important zoonotic pathogen causing serious disease and even death in pigs and humans. Public health events and economic losses caused by SS2 have prompted widespread concern. Because of the unavailability of vaccines, the development of rapid detection methods for timely diagnosis of SS2 infection or contaminated products, and monitoring of its prevalence in susceptible animals and populations, is required to aid in the prevention and control of SS2 infections. Several sets of primers and one probe for a recombinase polymerase amplification (RPA) assay targeting the cpsJ2 gene were designed and synthesized. Lateral flow (LF) tests in combination with RPA were used to provide visual results. Primers with high amplification efficiency were screened, and the reaction system was optimized. Indicators of detection effectiveness were evaluated. The established method had a detection limit of 100 copies/reaction for recognizing SS2 rather than other organisms. The sensitivity was 100%, as evaluated in infected animal samples. The detection could be completed within 20 min and required only constant temperature equipment. The established rapid, visual, sensitive and specific RPA-LF assay showed superior detection performance and is expected to be widely applied to fight SS2 infection in resource-limited areas

Predictive modeling of plant messenger RNA polyadenylation sites

BACKGROUND: One of the essential processing events during pre-mRNA maturation is the post-transcriptional addition of a polyadenine [poly(A)] tail. The 3'-end poly(A) track protects mRNA from unregulated degradation, and indicates the integrity of mRNA through recognition by mRNA export and translation machinery. The position of a poly(A) site is predetermined by signals in the pre-mRNA sequence that are recognized by a complex of polyadenylation factors. These signals are generally tri-part sequence patterns around the cleavage site that serves as the future poly(A) site. In plants, there is little sequence conservation among these signal elements, which makes it difficult to develop an accurate algorithm to predict the poly(A) site of a given gene. We attempted to solve this problem. RESULTS: Based on our current working model and the profile of nucleotide sequence distribution of the poly(A) signals and around poly(A) sites in Arabidopsis, we have devised a Generalized Hidden Markov Model based algorithm to predict potential poly(A) sites. The high specificity and sensitivity of the algorithm were demonstrated by testing several datasets, and at the best combinations, both reach 97%. The accuracy of the program, called poly(A) site sleuth or PASS, has been demonstrated by the prediction of many validated poly(A) sites. PASS also predicted the changes of poly(A) site efficiency in poly(A) signal mutants that were constructed and characterized by traditional genetic experiments. The efficacy of PASS was demonstrated by predicting poly(A) sites within long genomic sequences. CONCLUSION: Based on the features of plant poly(A) signals, a computational model was built to effectively predict the poly(A) sites in Arabidopsis genes. The algorithm will be useful in gene annotation because a poly(A) site signifies the end of the transcript. This algorithm can also be used to predict alternative poly(A) sites in known genes, and will be useful in the design of transgenes for crop genetic engineering by predicting and eliminating undesirable poly(A) sites

Ratio-Based Analysis of Differential mRNA Processing and Expression of a Polyadenylation Factor Mutant pcfs4 Using Arabidopsis Tiling Microarray

US National Institutes of Health [1R15GM07719201A1]; US National Science Foundation [IOS-0817818]; Ohio Plant Biotech Consortium; National Natural Science Foundation of China [60774033]; Specialized Research Fund for the Doctoral Program of Higher EducatiBackground: Alternative polyadenylation as a mechanism in gene expression regulation has been widely recognized in recent years. Arabidopsis polyadenylation factor PCFS4 was shown to function in leaf development and in flowering time control. The function of PCFS4 in controlling flowering time was correlated with the alternative polyadenylation of FCA, a flowering time regulator. However, genetic evidence suggested additional targets of PCFS4 that may mediate its function in both flowering time and leaf development. Methodology/Principal Findings: To identify further targets, we investigated the whole transcriptome of a PCFS4 mutant using Affymetrix Arabidopsis genomic tiling 1.0R array and developed a data analysis pipeline, termed RADPRE (Ratio-based Analysis of Differential mRNA Processing and Expression). In RADPRE, ratios of normalized probe intensities between wild type Columbia and a pcfs4 mutant were first generated. By doing so, one of the major problems of tiling array data-variations caused by differential probe affinity-was significantly alleviated. With the probe ratios as inputs, a hierarchy of statistical tests was carried out to identify differentially processed genes (DPG) and differentially expressed genes (DEG). The false discovery rate (FDR) of this analysis was estimated by using the balanced random combinations of Col/pcfs4 and pcfs4/Col ratios as inputs. Gene Ontology (GO) analysis of the DPGs and DEGs revealed potential new roles of PCFS4 in stress responses besides flowering time regulation. Conclusion/Significance: We identified 68 DPGs and 114 DEGs with FDR at 1% and 2%, respectively. Most of the 68 DPGs were subjected to alternative polyadenylation, splicing or transcription initiation. Quantitative PCR analysis of a set of DPGs confirmed that most of these genes were truly differentially processed in pcfs4 mutant plants. The enriched GO term "regulation of flower development'' among PCFS4 targets further indicated the efficacy of the RADPRE pipeline. This simple but effective program is available upon request

Transgenerational Effects of Hexavalent Chromium on Marine Medaka (<i>Oryzias melastigma</i>) Reveal Complex Transgenerational Adaptation in Offspring

Hexavalent chromium [Cr(VI)] pollution is one of most serious heavy metal pollutants in the coastal area and posed serious threats to marine organisms and human beings. Many studies have been conducted on its toxicological effects on living organisms from morphological to physiological aspects. However, there are few studies about the transgenerational toxicological of Cr(VI). In this study, we exposed adult marine medaka fishes with Cr(VI) and their offspring with Cr(VI) to examine transgenerational effects of Cr(VI). We found that there were mechanisms such as changing reproduction modes in males to compensate for impacts on the reproduction. There were differences and similarities between the parental effect and the environmental effect, with the former one causing more serious adverse effects on the offspring of Cr(VI)-exposed fish. It was noteworthy that there was an interaction between the parental and offspring treatment which leads to the attenuation of the parental effects on offspring when the offspring also underwent the same treatment. In addition, physiological adaptation has also been observed in fish to improve their fitness. Overall, effects of Cr(VI) on fish and their offspring were studied to pave a way to study the of mechanisms of adaptation

Transgenerational Effects of Hexavalent Chromium on Marine Medaka (Oryzias melastigma) Reveal Complex Transgenerational Adaptation in Offspring

Hexavalent chromium [Cr(VI)] pollution is one of most serious heavy metal pollutants in the coastal area and posed serious threats to marine organisms and human beings. Many studies have been conducted on its toxicological effects on living organisms from morphological to physiological aspects. However, there are few studies about the transgenerational toxicological of Cr(VI). In this study, we exposed adult marine medaka fishes with Cr(VI) and their offspring with Cr(VI) to examine transgenerational effects of Cr(VI). We found that there were mechanisms such as changing reproduction modes in males to compensate for impacts on the reproduction. There were differences and similarities between the parental effect and the environmental effect, with the former one causing more serious adverse effects on the offspring of Cr(VI)-exposed fish. It was noteworthy that there was an interaction between the parental and offspring treatment which leads to the attenuation of the parental effects on offspring when the offspring also underwent the same treatment. In addition, physiological adaptation has also been observed in fish to improve their fitness. Overall, effects of Cr(VI) on fish and their offspring were studied to pave a way to study the of mechanisms of adaptation