Reproducibility and Reliability Assays of the Gene

Background Reliability and reproducibility are key metrics for gene expression assays. This report assesses the utility of the correlation coefficient in the analysis of reproducibility and reliability of gene expression data. Results The correlation coefficient alone is not sufficient to assess equality among sample replicates but when coupled with slope and scatter plots expression data equality can be better assessed. Narrow-intervals of scatter plots should be shown as a tool to inspect the actual level of noise within the data. Here we propose a method to examine expression data reproducibility, which is based on the ratios of both the means and the standard deviations for the inter-treatment expression ratios of genes. In addition, we introduce a fold-change threshold with an inter-replicate occurrence likelihood lower than 5% to perform analysis even when reproducibility is not acceptable. There is no possibility to find a perfect correlation between transcript and protein levels even when there is not any post-transcriptional regulatory mechanism. We therefore propose an adjustment for protein abundance with that of transcript abundance based on open reading frame length. Conclusions Here, we introduce a very efficient reproducibility approach. Our method detects very small changes in large datasets which was not possible through regular correlation analysis. We also introduce a correction on protein quantities which allows us to examine the post-transcriptional regulatory effects with a higher accuracy

Identification of circular RNAs from the parental genes involved in multiple aspects of cellular metabolism in barley

RNA circularization made by head-to-tail back-splicing events is involved in the regulation of gene expression from transcriptional to post-translational levels. By exploiting RNA-Seq data and down-stream analysis, we shed light on the importance of circular RNAs in plants. The results introduce circular RNAs as novel interactors in the regulation of gene expression in plants and imply the comprehensiveness of this regulatory pathway by identifying circular RNAs for a diverse set of genes. These genes are involved in several aspects of cellular metabolism as hormonal signaling, intracellular protein sorting, carbohydrate metabolism and cell-wall biogenesis, respiration, amino acid biosynthesis, transcription and translation, and protein ubiquitination. Additionally, these parental loci of circular RNAs, from both nuclear and mitochondrial genomes, encode for different transcript classes including protein coding transcripts, microRNA, rRNA, and long non-coding/microprotein coding RNAs. The results shed light on the mitochondrial exonic circular RNAs and imply the importance of circular RNAs for regulation of mitochondrial genes. Importantly, we introduce circular RNAs in barley and elucidate their cellular-level alterations across tissues and in response to micronutrients iron and zinc. In further support of circular RNAs' functional roles in plants, we report several cases where fluctuations of circRNAs do not correlate with the levels of their parental-loci encoded linear transcripts.Keywords: circular RNAs, coding and non-coding transcripts, leaves, seeds, transfer cells, micronutrients, mitochondri

Gaming Platform vs. Traditional Text-only Stated-Preference Survey of Neighborhood Choice

This research explores the influence of representational methods as they are used in stated-preference (SP) surveys of neighbourhood choice. These types of surveys have traditionally been administered in text-only format, by asking subjects which alternative they prefer based on written descriptions of neighbourhoods. It has been argued, alternately, that the visual presentation of attributes can either dominate in SP surveys, or that it can be used to help improve the realism of choice tasks, and/or increase the number of attributes that can be included in such surveys. A few studies have tested the difference between multimedia and text-only SP surveys of housing choice. While these studies have been informative, they have drawn conflicting conclusions, and have been based on small sample sizes. The research presented here sought to take advantage of the capabilities made available by gaming engines to compare the results of SP surveys of neighbourhood choice administered either on a gaming platform, or as a traditional text-only survey. A sample of 368 (184 for each survey) respondents was used to compare neighbourhood choice model parameter estimates drawn from data administered with the two different survey methodologies. We found that while both surveys result in similar models, the model estimated using data obtained from the gaming platform show slightly better performance; providing 3D simulations appears to better focus respondent attention. At the same time, these 3D simulations have the unfortunate drawback of decreasing the generalizability of some visual parameter estimates, as they need to provide precise visual representations of their characteristics

Development of a Procedure to Measure the Effectiveness of Electret N-95 Respirator Filter Media for Capturing Nano-Particles

The phenomenal growth of the nano-technological products and their impacts on our society led government organizations and scientists to consider the risks related to human exposure to nano-particles (NPs). As a precautionary approach, respiratory protection is suggested for workers to reduce their exposure to NPs. Thus, it is important to characterize the performance of these respirators to capture NPs. In this study, the performance of one model of N95 respirators was characterized against poly and mono-disperse NPs. With poly-disperse NPs, a methodology was developed to measure the performance of the N95 respirators against NaCl aerosols in the size range of 15 to 200 nm in three scenarios. The N95 respirator performance was also characterized at 85 liters/min against twelve mono-size aerosols with size ranging from 20 to 200 nm. Using poly-disperse aerosols test (PAT) method; the results demonstrated that the initial penetration was significantly enhanced with the increased airflows and a shift toward small particle size was observed for the most penetrating particle size (MPPS). For particles below 100 nm, the penetration decreased with further loading. The MPPS was also found to shift toward the large sized particles. In addition, the penetration augmented slightly as the (RH) increased. Using mono-disperse aerosol test (MAT) method; the results revealed the initial particle penetration is less than 5% NIOSH certification criterion. However, it was found that the initial value, measured with (MAT) method, is not related with the initial penetration measured with (PAT) method at each corresponding particle size at 85 liters/min

Identification and characterisation of two high-affinity glucose transporters from the spoilage yeast Brettanomyces bruxellensis

The yeast Brettanomyces bruxellensis (syn. Dekkera bruxellensis) is an emerging and undesirable contaminant in industrial low-sugar ethanol fermentations that employ the yeast Saccharomyces cerevisiae. High-affinity glucose import in B. bruxellensis has been proposed to be the mechanism by which this yeast can outcompete S. cerevisiae. The present study describes the characterization of two B. bruxellensis genes (BHT1 and BHT3) believed to encode putative high-affinity glucose transporters. In vitro-generated transcripts of both genes as well as the S. cerevisiae HXT7 high-affinity glucose transporter were injected into Xenopus laevis oocytes and subsequent glucose uptake rates were assayed using 14C-labelled glucose. At 0.1 mM glucose, Bht1p was shown to transport glucose five times faster than Hxt7p. pH affected the rate of glucose transport by Bht1p and Bht3p, indicating an active glucose transport mechanism that involves proton symport. These results suggest a possible role for BHT1 and BHT3 in the competitive ability of B. bruxellensis

The biosynthetic gene cluster for the cyanogenic glucoside dhurrin in <i>Sorghum bicolor</i> contains its co-expressed vacuolar MATE transporter

Genomic gene clusters for the biosynthesis of chemical defence compounds are increasingly identified in plant genomes. We previously reported the independent evolution of biosynthetic gene clusters for cyanogenic glucoside biosynthesis in three plant lineages. Here we report that the gene cluster for the cyanogenic glucoside dhurrin in Sorghum bicolor additionally contains a gene, SbMATE2, encoding a transporter of the multidrug and toxic compound extrusion (MATE) family, which is co-expressed with the biosynthetic genes. The predicted localisation of SbMATE2 to the vacuolar membrane was demonstrated experimentally by transient expression of a SbMATE2-YFP fusion protein and confocal microscopy. Transport studies in Xenopus laevis oocytes demonstrate that SbMATE2 is able to transport dhurrin. In addition, SbMATE2 was able to transport non-endogenous cyanogenic glucosides, but not the anthocyanin cyanidin 3-O-glucoside or the glucosinolate indol-3-yl-methyl glucosinolate. The genomic co-localisation of a transporter gene with the biosynthetic genes producing the transported compound is discussed in relation to the role self-toxicity of chemical defence compounds may play in the formation of gene clusters

Coupling engineering of Saccharomyces cerevisiae with medium optimization for the production of ergothioneine

Ergothioneine (ERG) is a naturally occurring, exogenous antioxidant that is nonetheless abundant in the human body. It has been shown both to reduce oxidative damage and to be involved in several diseases in vivo1,2. Therefore, ergothioneine is poised to take a place in the dietary supplement industry. Here we describe the engineering of the yeast Saccharomyces cerevisiae and subsequent medium optimization to produce ergothioneine by fermentation. After integrating combinations of biosynthetic pathways from different organisms, we screened yeast strains for their production of ERG. Next, the highest producing strain was engineered with ergothioneine transporters, and its amino acid metabolism was altered by knock-out of Tor1 or Yih1. The bottleneck for ergothioneine production was determined by integration of a second copy of the pathway enzymes. We also optimized the media composition for production of ergothioneine using yeast S. cerevisiae. Following these manipulations, we obtained a titer of 630 mg/l in fed-batch cultivation in bioreactors. This work shows that with further engineering of the strain, current chemical synthesis of ergothioneine could be replaced with a sustainable alternative. 1. Cheah, I. K. & Halliwell, B. Ergothioneine; antioxidant potential, physiological function and role in disease. Biochim. Biophys. Acta - Mol. Basis Dis. 1822, 784–793 (2012). 2. Halliwell, B., Cheah, I. K. & Tang, R. M. Y. Ergothioneine - a diet-derived antioxidant with therapeutic potential. FEBS Lett. (2018). doi:10.1002/1873-3468.1312

A survey on some biological aspects of spiny lobster Panulirus homarus for optimizing fishing season in Sistan - o – Baluchestan province

Research project was conducted on some biological aspects of lobster in Oman Sea in the years1385-86. During the project some parameters such as length distribution, spawning peak, length (Carapace) at first maturity, the length at which 50% of the lobsters were found to be mature sexually, sex ratio, relative frequency index and population dynamics parameters were examined. Quantitative factors and catch composition of lobster including the amount of catch in terms of weight and number of ovigerous-female, under-sized specimens and so were compared by monthly. According to the results of present study caught specimens were male with carapace length of 22 and 110 mm respectively. The smallest ovigerous female was taken as 46mm CL when length at first maturity was estimated to be 69-70mm. the male: female ratio was 0.7: 1.3 for the whole year. A closed fishing season for the species is proposed during spring and September and October in Oman Sea. A large amount of the catches for the all sampling months came from the under-sized specimens, consist of 50 to 85% of the total catch. Therefore, presence of these small length groups have direct effects on time of closing season. Population dynamics parameters were calculated as follows: K=0.57 year, L∞= 103mm and Ǿ = 8.69. Total mortality (Z), natural mortality (M) and fishing mortality (F) coefficients were calculated as 2.73, 0.87 and 1.86, respectively. Exploitation ratio for the whole population was 0.681, indicating an overexploitation of the species. Based on the available data, the recruitment pattern for lobster was obtained for two season including spring (major) and autumn (minor). Catch per unite effort (CPUE) was calculated as 0.908 kg/Cage/day which was higher in comparison with two other areas including Ramin and Chabahar. Examination of CPUE for a 10-year period showed a decreased trend and the reduction for the year 1386 was about 30% when compared to the data from the year 1375. Moreover, the mean length during 1369-70 to 1385-86 (present study) decreased for the three areas including Pozm, Ramin and Chabahar, so that the carapas length decreased up to 10 mm in length. This sudden decrease in mean length during the 10-year period should be considered as a serious precariousness for sustainable exploitation of lobster in Oman Sea along Sistan and Baluchistan province

Temperature effect on the optical emission intensity in laser induced breakdown spectroscopy of super alloys

In this paper, the influence of heating and cooling samples on the optical emission spectra and plasma parameters of laser-induced breakdown spectroscopy for Titanium 64, Inconel 718 super alloys, and Aluminum 6061 alloy is investigated. Samples are uniformly heated up to approximately 200°C and cooled down to -78°C by an external heater and liquid nitrogen, respectively. Variations of plasma parameters like electron temperature and electron density with sample temperature are determined by using Boltzmann plot and Stark broadening methods, respectively. Heating the samples improves LIBS signal strength and broadens the width of the spectrum. On the other hand, cooling alloys causes fluctuations in the LIBS signal and decrease it to some extent, and some of the spectral peaks diminish. In addition, our results show that electron temperature and electron density depend on the sample temperature variations