Proteomic Analysis of Zebrafish Protein Recoding via mRNA Editing by ADAR Enzymes.

RNA editing by adenosine deaminases of the ADAR family can lead to protein recoding, since inosine formed from adenosine in mRNA is complementary to cytosine; the resulting codon editing might introduce amino acid substitutions into translated proteins. Proteome recoding can have functional consequences which have been described in many animals including humans. Using protein recoding database derived from publicly available transcriptome data, we identified for the first time the recoding sites in the zebrafish shotgun proteomes. Out of more than a hundred predicted recoding events, ten substitutions were found in six used datasets. Seven of them were in the AMPA glutamate receptor subunits, whose recoding has been well described, and are conserved among vertebrates. Three sites were specific for zebrafish proteins and were found in the transmembrane receptors astrotactin 1 and neuregulin 3b (proteins involved in the neuronal adhesion and signaling) and in the rims2b gene product (presynaptic membrane protein participating in the neurotransmitter release), respectively. Further studies are needed to elucidate the role of recoding of the said three proteins in the zebrafish.

Evaluation of coagulation factor activity and sterility of thawed fresh frozen plasma during storage up to 5 days at 4°C.

INTRODUCTION: Fresh frozen plasma (FFP) is a blood component containing functional quantities of all coagulation factors stored at -18°C or below. FFP has to be thawed and transfused as soon as possible to prevent the loss of certain coagulation factor activities and to minimise microbial contamination. MATERIALS AND METHODS: Thirty units of FFP kept at -20°C were thawed using a 37°C water bath and immediately sampled for baseline Factor II (FII), Factor VIII (FVIII) and fibrinogen activity levels and sterility testing. Each unit was then divided into two smaller bags (i.e. Bag I and Bag II) and kept at 4°C. At 6 hours and Day 3, representative samples were taken from Bag I for coagulation factor activity assays, while at Day 5 representative samples were taken from Bag II for coagulation factor activity assays and sterility testing. RESULTS: FII activities at the four time points were 73.43%, 73.73%, 71% and 69.8%, respectively, while FVIII activities were 177.63%, 144.37%, 80.8% and 70.97%, respectively. Fibrinogen levels at the four time points were 3.24 g/L, 3.24 g/L, 3.21 g/L and 3.20 g/L, respectively. All samples were free from microbial contamination even at Day 5. CONCLUSION: The mean reduction in FII and fibrinogen activities on Day 5 was 5% and 1%, respectively. However, FVIII activity declined significantly by approximately 60% at Day 5. Despite these reductions, thawed plasma stored for up to 5 days at 4°C is still suitable for use as the coagulation factor activity levels still exceed the minimum release criteria recommended in quality assurance regulations.

Proteogenomics of Adenosine-to-Inosine RNA Editing in the Fruit Fly.

Adenosine-to-inosine RNA editing is one of the most common types of RNA editing, a posttranscriptional modification made by special enzymes. We present a proteomic study on this phenomenon for Drosophila melanogaster. Three proteome data sets were used in the study: two taken from public repository and the third one obtained here. A customized protein sequence database was generated using results of genome-wide adenosine-to-inosine RNA studies and applied for identifying the edited proteins. The total number of 68 edited peptides belonging to 59 proteins was identified in all data sets. Eight of them being shared between the whole insect, head, and brain proteomes. Seven edited sites belonging to synaptic vesicle and membrane trafficking proteins were selected for validation by orthogonal analysis by Multiple Reaction Monitoring. Five editing events in cpx, Syx1A, Cadps, CG4587, and EndoA were validated in fruit fly brain tissue at the proteome level using isotopically labeled standards. Ratios of unedited-to-edited proteoforms varied from 35:1 ( Syx1A) to 1:2 ( EndoA). Lys-137 to Glu editing of endophilin A may have functional consequences for its interaction to membrane. The work demonstrates the feasibility to identify the RNA editing event at the proteome level using shotgun proteomics and customized edited protein database.

Multivariate analysis of PRISMA optimized TLC image for predicting antioxidant activity and identification of contributing compounds from Pereskia bleo.

Multivariate analysis of thin-layer chromatography (TLC) images was modeled to predict antioxidant activity of Pereskia bleo leaves and to identify the contributing compounds of the activity. TLC was developed in optimized mobile phase using the 'PRISMA' optimization method and the image was then converted to wavelet signals and imported for multivariate analysis. An orthogonal partial least square (OPLS) model was developed consisting of a wavelet-converted TLC image and 2,2-diphynyl-picrylhydrazyl free radical scavenging activity of 24 different preparations of P. bleo as the x- and y-variables, respectively. The quality of the constructed OPLS model (1 + 1 + 0) with one predictive and one orthogonal component was evaluated by internal and external validity tests. The validated model was then used to identify the contributing spot from the TLC plate that was then analyzed by GC-MS after trimethylsilyl derivatization. Glycerol and amine compounds were mainly found to contribute to the antioxidant activity of the sample. An alternative method to predict the antioxidant activity of a new sample of P. bleo leaves has been developed.

AliNA - a deep learning program for RNA secondary structure prediction.

Nowadays there are numerous discovered natural RNA variations participating in different cellular processes and artificial RNA, e. g., aptamers, riboswitches. One of the required tasks in the investigation of their functions and mechanism of influence on cells and interaction with targets is the prediction of RNA secondary structures. The classic thermodynamic-based prediction algorithms do not consider the specificity of biological folding and deep learning methods that were designed to resolve this issue suffer from homology-based methods problems. Herein, we present a method for RNA secondary structure prediction based on deep learning - AliNA (ALIgned Nucleic Acids). Our method successfully predicts secondary structures for non-homologous to train-data RNA families thanks to usage of the data augmentation techniques. Augmentation extends existing datasets with easily-accessible simulated data. The proposed method shows a high quality of prediction across different benchmarks including pseudoknots. The method is available on GitHub for free (https://github.com/Arty40m/AliNA).

Optimisation of self-healing of bio-foamed concrete bricks pores using Bacillus tequilensis under different temperature and CO2 curing conditions.

The self-healing of bio-concrete cracks and pores have been utilised worldwide to improve the properties of bio-concrete using different types of bacteria. Meanwhile, no published research was conducted to heal bio-foamed concrete bricks (B-FCB) pores using Bacillus tequilensis. Previous studies focused on the concentration of bacteria and neglect other factors that could affect the healing process. This research aimed to optimise the healing ratio of B-FCB pores using four factors: B. tequilensis concentration, concrete density, temperature and CO2 concentration. Initial water absorption (IWA) and water absorption (WA) were used as responses in statistical methods, namely, factorial and response surface methodology (RSM). B. tequilensis species was isolated from cement kiln dust, produced in a powder form, then subjected to simulate test using a special medium consisting of foamed concrete materials to check the survival ability in B-FCB. SEM, EDX, and XRD were used to investigate the healing process of B-FCB pores. The results revealed that the decrement ratios of IWA and WA of B-FCB were 52.8% and 29.1% compared to FCB, respectively. SEM results reflect the healing that occurred in B-FCB pores, mostly healed via precipitation of CaCO3 as demonstrated on the XRD results.

Optimization of Bio-Foamed Concrete Brick Strength via Bacteria Based Self-Healing and Bio-Sequestration of CO2.

This research aimed to optimize the compressive strength of bio-foamed concrete brick (B-FCB) via a combination of the natural sequestration of CO2 and the bio-reaction of B. tequilensis enzymes. The experiments were guided by two optimization methods, namely, 2k factorial and response surface methodology (RSM). The 2k factorial analysis was carried out to screen the important factors; then, RSM analysis was performed to optimize the compressive strength of B-FCB. Four factors, namely, density (D), B. tequilensis concentration (B), temperature (T), and CO2 concentration, were selectively varied during the study. The optimum compressive strength of B-FCB was 8.22 MPa, as deduced from the following conditions: 10% CO2, 3 × 107 cell/mL of B, 27 °C of T and 1800 kg/m3 of D after 28 days. The use of B. tequilensis in B-FCB improved the compressive strength by 35.5% compared to the foamed concrete brick (FCB) after 28 days. A microstructure analysis by scanning electronic microscopy (SEM), energy dispersive X-ray (EDX) and X-ray diffraction analysis (XRD) reflected the changes in chemical element levels and calcium carbonate (CaCO3) precipitation in the B-FCB pores. This was due to the B. tequilensis surface reactions of carbonic anhydrase (CA) and urease enzyme with calcium in cement and sequestered CO2 during the curing time.

Blood lead levels of urban and rural Malaysian primary school children.

The objective of this article is to study the influence of exposure and socio-economic variables on the blood lead level of Malaysian school children. Data on respirable lead and blood lead of 346 school children were obtained from Kuala Lumpur (urban), Kemaman (semi-urban) and Setiu (rural). Respirable lead and blood lead were highest for Kuala Lumpur (95 ng/m3 and 5.26 micrograms/dL) followed by Kemaman (27 ng/m3 and 2.81 micrograms/dL) and Setiu (15 ng/m3 and 2.49 micrograms/dL), and the differences were statistically significant. The percentage of school children with excessive blood lead of 10 micrograms/dL or greater was 6.36% overall, and highest for Kuala Lumpur (11.73%). Regression analyses show that urban children are at higher risk of exhibiting excessive blood lead levels. Kuala Lumpur's school children have a 25 times greater risk of having excessive blood lead levels when compared to Kemaman's and Setiu's school children. Respirable and blood lead were correlated (r = 0.999, p = 0.021). Urban school children acquire higher blood lead levels than their rural and semi-urban counterparts, even after controlling for age, sex, parents' education and income levels. In conclusion, it is time that lead in the Malaysian environment and population be monitored closely, especially its temporal and spatial variability. Only then can a comprehensive preventive strategy be implemented.