Optimization of chemiluminescent detection of mitochondrial RNA-protein interaction by nonradioactive mobility shift

RNA mobility shift is one among many procedures used to study RNA-protein interaction. Yet, there are some limitations for the radioactive RNA mobility shift including; 1) the risk of using radiolabeled nucleotides, 2) the long time to get the results; this could range from days to weeks, and 3) its high cost as compared to nonradioactive techniques. In this study, we optimized a nonradioactive procedure using dig-11-UTP nucleotide and chemiluminescent detection for mitochondrial RNA-protein interaction. The optimizations include the quality limiting steps such as using non-specific competitors of RNA probe, UVcross linking time, electrotransfer to membranes, application with various protein extracts, and the examination for false positive RNA-protein complexes using proteinase K digestion. The results show that the optimizations carried out in the study significantly enhanced the quality of the results obtained with this procedure.Keywords: RNA mobility shift, mitochondria, wheat, RNA-protein interaction, chemiluminescent detection, nonradioactiveAfrican Journal of Biotechnology Vol. 12(16), pp. 1915-192

Sustainable phosphorous management in two different soil series of Pakistan by evaluating dynamics of phosphatic fertilizer source

Phosphorous (P) plays the prominent role to promote the plants storage functions and structural roles, as it is recognized as a vital component of ADP, ATP, Cell wall as well as a part of DNA. Soils acts as the sink to supply P to plants because soil pH and its physical condition are the main factor which regulate the solubility and availability P element. Phosphorus is not deficient in Pakistani soils but its availability to plants is the serious matter of concern. A pot experiment was conducted to evaluate P dynamics in two different soil series of Pakistan (Bahawalpur and Lyallpur) using Maize as test crop. The treatments applied were T0: Control (without any fertilizer), T1: Recommended DAP @648 mg pot−1, T2: Half dose DAP @324 mg pot−1, T3: Recommended rate of TSP @900 mg pot−1, T4: Half dose TSP @450 mg pot−1. Soil analysis showed that Bahawalpur soil has sandy clay loam texture with 33% clay and Lyallpur series has sandy loam texture with 15.5% clay; furthermore, these soils contain 4.6 and 2.12% CaCO3, respectively. Results showed an increase in P concentration in roots (23 mg kg−1) with the application of half dose of TSP in Lyallpur series and lowest in Bahawalpur series (14.6 mg kg−1) at recommended dose of DAP. Concentration of P in shoots responded the same; increase at half dose of TSP (16.7 mg kg−1) and lowest at full dose of DAP in Bahawalpur series as (15.58 mg kg−1). Adsorbed P (17 mg kg−1) was recorded highest in Bahawalpur soil with more clay amount in pot with DAP application but lower in Lyallpur soil series (14 mg kg−1) with the application of applied TSP. The PUE was recorded highest in Lyallpur series with the application of half dose of TSP and it was 61% more than control and was Highest in Bahawalpur series was with the application of recommended dose of DAP is 72% more than control treatment. On estimation, results showed that applied sources made an increase in P availability than control, but TSP gave better P uptake than DAP unless of rates applied. Soil of Lyallpur series showed better uptake of P and response to applied fertilizers than Bahawalpur series which showed more adsorption of P by high clay and CaCO3 amount. Conclusively, the study suggested that soil series play a crucial role in choosing fertilizer source for field application

Quantitative response of wheat to sowing dates and irrigation regimes using ceres-wheat model

An experiment was conducted at Punjab Agricultural University, Ludhiana during 2014–15 and 2015–16, keeping four sowing dates {25th Oct (D1), 10th Nov (D2), 25th Nov (D3) and 10th Dec (D4)} in main plots and five irrigation schedules {irrigation at 15 (FC15), 25 (FC25), 35 (FC35) and 45 (FC45) % depletion of soil moisture from field capacity (FC) and a conventional practice} in sub plots. The objective of the study was to evaluate the performance of CERES-Wheat model for simulating yield and water use under varying planting and soil moisture regimes. The simulated and observed grain yield was higher in D1, with irrigation applied at FC15 as compared to all other sowing date and irrigation regime combinations. Simulated grain yield decreased by 19% with delay in sowing from 25th October to 10th December because of 8% reduction in simulated crop evapotranspiration. Simulated evapotranspiration decreased by 16%, wheat grain yield by 23% and water productivity by 15% in drip irrigation at 45% depletion from field capacity as compared to drip irrigation at 15% of field capacity. It was further revealed that the model performed well in simulating the phenology, water use and yield of wheat

Defens in gene expression in some plant sources of Taif

Plant defensins are promising future strategy as antimicrobial agents; however the number of characterized plant defensins is very low. We isolated and studied the expression of plant defensins in six plants from Taif region. Using RT-PCR and two pairs of common as well as three pairs of specific primers, the defensin gene expression was analyzed. Plants showed differences in defensin gene expression in floral buds and leaves, though floral buds represented higher gene expression. The amino acid sequence of the six isolated cDNA sequences showed high similarity with other defensin accessions from the nucleotide database, especially in the cysteine rich motif. Phylogenetic analysis revealed that the isolated sequences share the common features of plant defensins, especially the 8 conserved cysteines. The results of this study help to detect some valuable Saudi plant sources for the development of natural peptides as a replacement for chemical antibiotics

Transcriptome Analysis of Jojoba (Simmondsia chinensis) during Seed Development and Liquid Wax Ester Biosynthesis

Jojoba is one of the main two known plant source of natural liquid wax ester for use in various applications, including cosmetics, pharmaceuticals, and biofuel. Due to the lack of transcriptomic and genomic data on lipid biosynthesis and accumulation, molecular marker breeding has been used to improve jojoba oil production and quality. In the current study, the transcriptome of developing jojoba seeds was investigated using the Illunina NovaSeq 6000 system, 100 × 106 paired end reads, an average length of 100 bp, and a sequence depth of 12 Gb per sample. A total of 176,106 unigenes were detected with an average contig length of 201 bp. Gene Ontology (GO) showed that the detected unigenes were distributed in the three GO groups biological processes (BP, 5.53%), cellular component (CC, 6.06%), and molecular functions (MF, 5.88%) and distributed in 67 functional groups. The lipid biosynthesis pathway was established based on the expression of lipid biosynthesis genes, fatty acid (FA) biosynthesis, FA desaturation, FA elongation, fatty alcohol biosynthesis, triacylglycerol (TAG) biosynthesis, phospholipid metabolism, wax ester biosynthesis, and lipid transfer and storage genes. The detection of these categories of genes confirms the presence of an efficient lipid biosynthesis and accumulation system in developing jojoba seeds. The results of this study will significantly enhance the current understanding of wax ester biology in jojoba seeds and open new routes for the improvement of jojoba oil production and quality through biotechnology applications

Transcriptome Analysis of Testis from HFD-Induced Obese Rats (Rattus norvigicus) Indicated Predisposition for Male Infertility

Obesity is a worldwide life-threatening metabolic disorder, associated with various chronic diseases, including male infertility. Obesity was induced by high fat diet (HFD), and testis RNA was used for the transcriptome analysis using RNAseq via Illumina NovaSeq 6000 System and NovaSeq 6000 Kit. Gene expression level was estimated as FPKM (Fragments Per Kilobase of transcript per Million mapped reads). Differential expressed genes (DEGs) were annotated against gene ontology (GO) and KEGG databases. More than 63.66 million reads per sample were performed with 100 bp cutoff and 6 Gb sequencing depth. Results of this study revealed that 267 GO terms (245 biological processes (BP), 14 cellular components (CC), eight molecular functions (MF)), and 89 KEGG pathways were significantly enriched. Moreover, total numbers of 136 genes were differentially expressed (107 upregulated, 29 downregulated) with |FC| ≥ 2 and bh adjusted <0.05. Interesting DEGs were detected, including obesity and lipid metabolism-related genes, immune response-related genes, cytochrome P450 genes, including aromatase were upregulated, whereas genes related to male fertility and fertilization, cell adhesion, and olfactory receptors were downregulated. The combined expression pattern of the DEGs in obese animals indicated an increase in cholesterol metabolism. Furthermore, high aromatase activity enhances the testosterone turnover into estradiol and lowers the testosterone/estradiol (T/E) ratio, which ultimately reduces fertility. In addition, downregulation of cadherens junction components genes leads to the pre-mature release of sperm from Sertoli cells resulting in the reduction of fertility. Moreover, the downregulation of olfactory receptor genes reduces the chemotaxis capacity of sperms in tracking the oocyte for fertilization, which reduces male fertility. Furthermore, various obesity molecular markers were detected in our transcriptome. The results of this study will enhance our understanding of the molecular network of obesity development, development of obesity novel molecular diagnosis markers, molecular bases of obesity-induced infertility, and the development of anti-obesity drugs

Dietary Cinnamon Successfully Enhanced the Growth Performance, Growth Hormone, Antibacterial Capacity, and Immunity of European Sea Bass (Dicentrarchus labrax)

Dietary cinnamon has several bioactive compounds with growth-promoting and immunomodulation potential and is suggested for finfish species. This study evaluated the inclusion of cinnamon at 0, 10, 15, and 20 g/kg in European sea bass (Dicentrarchus labrax) diets. After 90 days, the highest final weight, weight gain, specific growth rate, protein efficiency ratio, and the lowest feed conversion ratio were seen in fish treated with 10 g/kg (p < 0.05). Further, the measured growth hormone in the blood indicated that fish treated with 10 g/kg had a higher level than fish 0 and 20 g/kg. After the feeding trial, fish treated with cinnamon at varying levels had higher lipid content than fish before the feeding trial (p < 0.05). Lower Vibrio spp. and Faecal Coliform counts were observed in fish treated with cinnamon than fish fed a cinnamon-free diet (p < 0.05). The hematocrit level was markedly (p < 0.05) increased in fish fed cinnamon at 10 g/kg compared to the control without significant differences with fish fed 15 and 20 g/kg. Hemoglobin was significantly increased in fish treated with cinnamon at 10, 15, and 20 g/kg compared to fish fed a cinnamon-free diet (p < 0.05). Red and white blood cells (RBCs and WBCs) were meaningfully (p < 0.05) increased in fish treated with cinnamon compared with the control. Markedly, fish treated with cinnamon had higher serum total lipids than the control with the highest value in fish treated with 15 g/kg (p < 0.05). The lysozyme activity was markedly higher in fish treated with 15 g cinnamon/kg than fish fed 0, 10, and 20 g/kg (p < 0.05). Moreover, phagocytic activity was significantly higher in fish treated with cinnamon at 10, and 15 g/kg than fish fed 0 and 20 g/kg (p < 0.05). In conclusion, dietary cinnamon is suggested at 10–15 g/kg for achieving the high production and wellbeing of European sea bass

Seed germination ecology of Conyza sumatrensis populations stemming from different habitats and implications for management

Conyza sumatrensis (Retz.) E. H. Walker is an obnoxious weed, emerging as an invasive species globally. Seed germination biology of four populations of the species stemming from arid, semi-arid, temperate, and humid regions was determined in this study. Seed germination was recorded under six different environmental cues (i.e., light/dark periods, constant and alternating day and night temperatures, pH, salinity, and osmotic potential levels) in separate experiment for each cue. Populations were main factor, whereas levels of each environmental cue were considered as sub-factor. The impact of seed burial depths on seedling emergence was inferred in a greenhouse pot experiment. Seed germination was recorded daily and four germination indices, i.e., seed germination percentage, mean germination time, time to reach 50% germination, and mean daily germination were computed. Tested populations and levels of different environmental cues had significant impact on various seed germination indices. Overall, seeds stemming from arid and semi-arid regions had higher seed germination potential under stressful and benign environmental conditions compared to temperate and humid populations. Seed of all populations required a definite light period for germination and 12 hours alternating light and dark period resulted in the highest seed germination. Seed germination of all populations occurred under 5–30°C constant and all tested alternate day and night temperatures. However, the highest seed germination was recorded under 20°C. Seeds of arid and semi-arid populations exhibited higher germination under increased temperature, salinity and osmotic potential levels indicating that maternal environment strongly affected germination traits of the tested populations. The highest seed germination of the tested populations was noted under neutral pH, while higher and lower pH than neutral had negative impact on seed germination. Arid and semi-arid populations exhibited higher seed germination under increased pH compared to temperate and humid populations. Seed burial depth had a significant effect on the seedling emergence of all tested populations. An initial increase was noted in seedling emergence percentage with increasing soil depth. However, a steep decline was recorded after 2 cm seed burial depth. These results indicate that maternal environment strongly mediates germination traits of different populations. Lower emergence from >4 cm seed burial depth warrants that deep burial of seeds and subsequent zero or minimum soil disturbance could aid the management of the species in agricultural habitats. However, management strategies should be developed for other habitats to halt the spread of the species

Characterization of the Impacts of Living at High Altitude in Taif: Oxidative Stress Biomarker Alterations and Immunohistochemical Changes

At high elevations, the human body experiences a number of pathological, physiological, and biochemical changes, all of which have adverse impacts on human health and organ vitality. This study aimed to investigate the alterations in the liver and kidney biomarkers, oxidative stress markers, gene expression, and cellular histology of rats maintained at high altitudes and normal sea level. A total of twenty male Wistar rats at 2 months of age were randomly assigned to two groups. The rats in group A were maintained at normal sea level in Jeddah, whereas rats in group B were maintained in an area in Taif 2600 m above sea level. After 2 months of housing, orbital blood samples were collected for the analysis of significant biochemical indicators of oxidative stress biomarkers of the liver and kidneys. Liver and kidney tissues from both groups were taken to examine the hepatorenal changes occurring at the biochemical, histological, immunohistochemical, and genetic levels. The results revealed substantial increases in the serum levels of liver and kidney biomarkers (GPT, GOT, urea, and creatinine) and decreases in the serum levels of antioxidant biomarkers (SOD, catalase, GSH, and NO). In parallel, the levels of the malondialdehyde (MDA) tissue damage marker and inflammatory cytokines (IL-1β, TNF-α, and IFN-γ) were increased in the high-altitude group compared to the normal sea level group. In addition, there were significant alterations in the oxidative and inflammatory status of rats that lived at high altitude, with considerable upregulation in the expression of hepatic VEGF, type 1 collagen, Cox-2, TNF-α, and iNOS as well as renal EPASI, CMYC, HIF-α, and EGLN-2 genes in the high-altitude group compared with controls housed at normal sea level. In conclusion, living at high altitude induces hepatorenal damage and biochemical and molecular alterations, all of which may serve as critical factors that must be taken into account for organisms living at high altitudes

A Genome-Wide Identification and Expression Pattern of <i>LMCO</i> Gene Family from Turnip (<i>Brassica rapa</i> L.) under Various Abiotic Stresses

Laccase-like multi-copper oxidases (LMCOs) are a group of enzymes involved in the oxidation of numerous substrates. Recently, these enzymes have become extremely popular due to their practical applications in various fields of biology. LMCOs generally oxidize various substrates by linking four-electron reduction of the final acceptor, molecular oxygen (O2), to water. Multi-copper oxidases related to laccase are extensively distributed as multi-gene families in the genome sequences of higher plants. The current study thoroughly investigated the LMCO gene family (Br-Lac) and its expression pattern under various abiotic stresses in B. rapa L. A total of 18 Br-Lac gene family members located on five different chromosomes were identified. Phylogenetic analysis classified the documented Br-Lac genes into seven groups: Group-I (four genes), Group-II (nine genes), Group-III (eight genes), Group-IV (four genes), Group-V (six genes), and Group-VI and Group-VII (one gene each). The key features of gene structure and responsive motifs shared the utmost resemblance within the same groups. Additionally, a divergence study also assessed the evolutionary features of Br-Lac genes. The anticipated period of divergence ranged from 12.365 to 39.250 MYA (million years ago). We also identified the pivotal role of the 18 documented members of the LMCO (Br-lac) gene family using quantitative real-time qRT-PCR. Br-Lac-6, Br-Lac-7, Br-Lac-8, Br-Lac-16, Br-Lac-17, and Br-Lac-22 responded positively to abiotic stresses (i.e., drought, heat, and salinity). These findings set the stage for the functional diversity of the LMCO genes in B. rapa