Analysis of gene expression and DNA methylation in a cognitive phenotype model of schizophrenia

<p>The underpinning hypothesis of this study is that the environmental insults implicated in schizophrenia cause epigenetic changes that trigger deleterious gene expression, resulting in deviations from normal neurodevelopment. The behavioural abnormalities in schizophrenia can be grouped into the three common classes of symptoms: positive, negative, and cognitive. Cognitive symptoms are symptoms that impair cognitive processing and have detrimental effects on individuals with schizophrenia. Maternal immune activation refers to a rat model that stimulates a maternal immune system with an infection or infectious-like stimulus resulting in adverse phenotypes. A cognitive phenotype, maternal immune activation (MIA) model of schizophrenia was employed to use epigenetic markers to discover what deleterious genes drive the cognitive deficits phenotype. Previous work has discerned many changes in gene expression that are implicated in schizophrenia. A hypothesis-driven approach was utilized to determine whether previously studied candidate genes are relevant in the cognitive symptoms of schizophrenia in this cognitive-phenotype model. It was found that prenatal treatment of lipopolysaccharide (LPS) (which is the major outer membrane component of gram-negative bacteria and mimics bacterial infection) on prenatal day 10 and 11 led to changes in mRNA levels in the prefrontal cortex of adolescent rats. Typically, an increase in the amount of transcript in the LPS condition compared to the saline condition, or a greater variability in the amount of transcript between replicates in the LPS condition than the saline condition, was observed. Statistical analysis revealed that these changes did not met statistical significance. To build towards a whole genome DNA methylation analysis, two discrete approaches were used. The first utilized bisulfite modification and investigated changes in candidate genes as a precursor to genome-wide BS-sequencing. DNA methylation was measured across CpG rich regions and an absence of DNA methylation was detected in these regions in both the LPS and saline conditions in the candidate genes. The second approach utilized a long-read sequencing platform to establish the feasibility of a bisulfite conversion-free method for whole-genome DNA methylation approach within our lab. Through the establishment of this method factors that affect the reliability, quality, and accuracy of the final sequencing product were explored. Many of which were in the downstream-from-sequencing, data analysis component of the process. Discoveries were also made regarding how much data would be needed to make direct DNA methylation detection feasible. The data presented here demonstrated that the cognitive-phenotype MIA model had altered gene expression correlating with previously measured behavioural cognitive deficits in the prefrontal cortex in genes that were known to be associated with schizophrenia. To extend this further, a whole genome approach would be needed to discover novel drivers of the phenotype. In the current study, headway was made towards the development and establishment of a whole genome DNA methylation detection method to further this continued aim.</p>

Analysis of gene expression and DNA methylation in a cognitive phenotype model of schizophrenia

<p>The underpinning hypothesis of this study is that the environmental insults implicated in schizophrenia cause epigenetic changes that trigger deleterious gene expression, resulting in deviations from normal neurodevelopment. The behavioural abnormalities in schizophrenia can be grouped into the three common classes of symptoms: positive, negative, and cognitive. Cognitive symptoms are symptoms that impair cognitive processing and have detrimental effects on individuals with schizophrenia. Maternal immune activation refers to a rat model that stimulates a maternal immune system with an infection or infectious-like stimulus resulting in adverse phenotypes. A cognitive phenotype, maternal immune activation (MIA) model of schizophrenia was employed to use epigenetic markers to discover what deleterious genes drive the cognitive deficits phenotype. Previous work has discerned many changes in gene expression that are implicated in schizophrenia. A hypothesis-driven approach was utilized to determine whether previously studied candidate genes are relevant in the cognitive symptoms of schizophrenia in this cognitive-phenotype model. It was found that prenatal treatment of lipopolysaccharide (LPS) (which is the major outer membrane component of gram-negative bacteria and mimics bacterial infection) on prenatal day 10 and 11 led to changes in mRNA levels in the prefrontal cortex of adolescent rats. Typically, an increase in the amount of transcript in the LPS condition compared to the saline condition, or a greater variability in the amount of transcript between replicates in the LPS condition than the saline condition, was observed. Statistical analysis revealed that these changes did not met statistical significance. To build towards a whole genome DNA methylation analysis, two discrete approaches were used. The first utilized bisulfite modification and investigated changes in candidate genes as a precursor to genome-wide BS-sequencing. DNA methylation was measured across CpG rich regions and an absence of DNA methylation was detected in these regions in both the LPS and saline conditions in the candidate genes. The second approach utilized a long-read sequencing platform to establish the feasibility of a bisulfite conversion-free method for whole-genome DNA methylation approach within our lab. Through the establishment of this method factors that affect the reliability, quality, and accuracy of the final sequencing product were explored. Many of which were in the downstream-from-sequencing, data analysis component of the process. Discoveries were also made regarding how much data would be needed to make direct DNA methylation detection feasible. The data presented here demonstrated that the cognitive-phenotype MIA model had altered gene expression correlating with previously measured behavioural cognitive deficits in the prefrontal cortex in genes that were known to be associated with schizophrenia. To extend this further, a whole genome approach would be needed to discover novel drivers of the phenotype. In the current study, headway was made towards the development and establishment of a whole genome DNA methylation detection method to further this continued aim.</p>

Relaxation behavior in low-frequency complex conductivity of sands caused by bacterial growth and biofilm formation by Shewanella oneidensis under a high-salinity condition

Complex electrical conductivity is increasingly used to monitor subsurface processes associated with microbial activities because microbial cells mostly have surface charges and thus electrical double layers. Although highly saline environments are frequently encountered in coastal and marine sediments, there are limited data available on the complex conductivity associated with microbial activities under a high-salinity condition. Therefore, we have developed the spectral responses of complex conductivity of sand associated with bacterial growth and biofilm formation under a highly saline condition of approximately 1% salinity and approximately 2 S/m pore water conductivity with an emphasis on relaxation behavior. A column test is performed, in which the model bacteria Shewanella oneidensis MR-1 are stimulated for cell growth and biofilm formation in a sand pack, whereas the complex conductivity is monitored from 0.01 Hz to 10 kHz. The test results indicate that the real conductivity increases in the early stage due to the microbial metabolites and the increased surface conduction with cell growth but soon begin to decrease because of the reduction of charge passages due to bioclogging. However, the imaginary conductivity significantly increases with time, and clear bell-shaped relaxation behaviors are observed with the peak frequency of 0.1–1 Hz, associated with the double-layer polarization of cells and electrically conductive pili and biofilms. The Cole-Cole relaxation model appears to capture such relaxation behaviors well, and the modeling results indicate gradual increases in normalized chargeability and decreases in relaxation time during bacterial growth and biofilm formation in the highly saline condition. Comparison with previous literature confirms that the high-salinity condition further increases the normalized chargeability, whereas it suppresses the phase shift and thus the imaginary conductivity. Our results suggest that the complex conductivity can effectively capture microbial biomass formation in sands under a highly saline condition.

EC Sensitivity of Hydroponically-Grown Lettuce (Lactuca sativa L.) Types in Terms of Nitrate Accumulation

The goal of this research was to investigate the effect of electrical conductivity (EC) levels of the nutrient solution on the fresh weight, chlorophyll, and nitrate content of hydroponic-system-grown lettuce. The selected cultivars are the most representative commercial varieties grown for European markets. Seven cultivars (‘Sintia,’ ‘Limeira,’ ‘Corentine,’ ‘Cencibel,’ ‘Kiber,’ ‘Attiraï,’ and ‘Rouxaï’) of three Lactuca sativa L. types’ (butterhead, loose leaf, and oak leaf) were grown in a phytotron in rockwool, meanwhile the EC level of the nutrient solutions were different: normal (<1.3 dS/m) and high (10 dS/m). The plants in the saline condition had a lower yield but elevated chlorophyll content and nitrate level, although the ‘Limeira’ and ‘Cencibel’ cultivars had reduced nitrate levels. The results and the special characteristic of the lollo-type cultivars showed that the nitrate level could be very different due to salinity (‘Limeira’ had the lowest (684 µg/g fresh weight (FW)) and ‘Cencibel’ had the highest (4396 µg/g FW)). There was a moderately strong negative correlation (−0.542) in the reverse ratio among the chlorophyll and nitrate contents in plants treated with a normal EC value, while this relationship was not shown in the saline condition. Under the saline condition, cultivars acted differently, and all examined cultivars stayed under the permitted total nitrate level (5000 µg/g FW).

Evaluation of Salinitys Induced Modification in Growth, Biochemical and Yield Characteristics of Spring Wheat (Triticum aestivum L.) Cultivars

Salt stress impact was appraised on different antioxidative enzymes, MDA and H2O2 in ten spring wheat cultivars i.e., S-24, Lasani, Fsd-2008, Saher-2006, Inqlab-91, AARI-10, P.B-18, S.H-20, M.P-65, and G.A-20 when salinity applied at the seedling stage. The wheat cultivars were grown under saline (150 mM) and non-saline regimes (0 mM) in pots filled with sand. Diverse response in all wheat cultivars was observed in different studied attributes. Saline stress markedly decline SOD, CAT and POD conc. in different wheat cultivars. While some cultivars (S-24, Lasani, AARI-10 and GA-20) showed increase in these attributes under saline condition as compared to control. MDA and H2O2 content were increased in different wheat cultivars due to imposition of salt stress at the seedling stage. Whereas decrease in some cultivars was recorded in these attributes under saline regime than in non-saline conditions. Of all wheat cultivars, S-24, Lasani, AARI-10 and GA-20 showed high antioxidative activity, less lipid peroxidation and H2O2 content in plant shoot when salt stress applied at the seedling stage. On the basis of higher antioxidative activity and less MDA and H2O2 content, these four cultivars (S-24, Lasani, AARI-10 and GA-20) could be categorized as salt tolerant as compared to others