Transcriptome and anatomical analysis of Stipa breviflora in response to different grazing intensities in desert steppe.

Stipa breviflora is a dominant species in the desert steppe of Northern China. Grazing is the main land use pattern of grassland, which could cause a variety of adaptive evolutionary mechanisms in plant community composition as well as individual plant growth and morphological characteristics. However, very little is known about the morphological structure and transcriptional regulation response to different grazing intensities in S. breviflora. In this study, transcriptome and anatomical analyses of S. breviflora under different grazing intensities, including no grazing, moderate grazing, and heavy grazing, were performed. The anatomical analysis results showed that epidermis cells and xylems significantly thicken with grazing intensity, suggesting that grazing results in increasing lignification. Furthermore, the components of cell walls such as lignin, cellulose, hemicellulose, and pectin were all increased dramatically and significantly under both moderate and heavy grazing. Transcriptome analysis showed that the differentially expressed genes related to different grazing intensities were also engaged in plant cell wall formation and in photosynthesis and respiration. In addition, the activities of ATP synthase and Rubisco-activating enzyme increased significantly with enhanced grazing intensity and differed significantly between moderate and heavy grazing intensities. The trends in transcriptome and plant phenotype changes are consistent. Taken together, these results indicated that S. breviflora has evolved a grazing tolerance strategy under long-term grazing conditions, influencing photosynthesis and respiration in terms of its own structure and enzyme activities in the body, to maintain normal life activities under different grazing conditions.

Exposure to polymetallic contaminated sites induced toxicological effects on chicken lungs: A multi-level analysis.

Heavy metal pollution is an important environmental issue causing several hazards to organisms. In the present study, we investigated the uptake and accumulation of heavy metals (Pb, Cd, Cu, and Zn) in chicken lungs after six months of breeding on polymetallic-contaminated area in Jebel Ressas village. Genotoxicity in term of micronuclei frequency as well as oxidative stress in term of enzymatic activities of Catalase (CAT), Glutathion-S-Transferase (GST) and malondialdehydes accumulation (MDA) were performed. In addition, gene expression levels involved in oxidative stress genes (cat, sod and gst), metal homeostasis (mt1 and mt4) and DNA metabolism (p53, bcl2, caspase 3 and DNA ligase) were detected. Exposed chicken lungs revealed an important heavy metal accumulation of Cd and Zn co-occurring with oxidative status modulation. Transcriptomic results unveiled an upregulation of oxidative stress and homeostasis genes. On the other hand, genes involved in DNA metabolism indicated cellular functioning towards cells death and apoptosis modulation. Moreover, the histopathological examination revealed lung lesions in the chickens exposed to heavy metal contamination. Our study highlights the hazardous effects of heavy metal pollution on chicken respiratory system.

The relationship between protein modified folding molecular network and Alzheimer's disease pathogenesis based on BAG2-HSC70-STUB1-MAPT expression patterns analysis.

Background: Alzheimer's disease (AD) is the most common cause of dementia and cognitive decline, while its pathological mechanism remains unclear. Tauopathies is one of the most widely accepted hypotheses. In this study, the molecular network was established and the expression pattern of the core gene was analyzed, confirming that the dysfunction of protein folding and degradation is one of the critical factors for AD. Methods: This study analyzed 9 normal people and 22 AD patients' microarray data obtained from GSE1297 in Gene Expression Omnibus (GEO) database. The matrix decomposition analysis was used to identify the correlation between the molecular network and AD. The mathematics of the relationship between the Mini-Mental State Examination (MMSE) and the expression level of the genes involved in the molecular network was found by Neural Network (NN). Furthermore, the Support Vector Machine (SVM) model was for classification according to the expression value of genes. Results: The difference of eigenvalues is small in first three stages and increases dramatically in the severe stage. For example, the maximum eigenvalue changed to 0.79 in the severe group from 0.56 in the normal group. The sign of the elements in the eigenvectors of biggest eigenvalue reversed. The linear function of the relationship between clinical MMSE and gene expression values was observed. Then, the model of Neural Network (NN) is designed to predict the value of MMSE based on the linear function, and the predicted accuracy is up to 0.93. For the SVM classification, the accuracy of the model is 0.72. Conclusion: This study shows that the molecular network of protein folding and degradation represented by "BAG2-HSC70-STUB1-MAPT" has a strong relationship with the occurrence and progression of AD, and this degree of correlation of the four genes gradually weakens with the progression of AD. The mathematical mapping of the relationship between gene expression and clinical MMSE was found, and it can be used in predicting MMSE or classification with high accuracy. These genes are expected to be potential biomarkers for early diagnosis and treatment of AD.

Chloroplast gene expression level is negatively correlated with evolutionary rates and selective pressure while positively with codon usage bias in Ophioglossum vulgatum L.

BACKGROUND: Characterization of the key factors determining gene expression level has been of significant interest. Previous studies on the relationship among evolutionary rates, codon usage bias, and expression level mostly focused on either nuclear genes or unicellular/multicellular organisms but few in chloroplast (cp) genes. Ophioglossum vulgatum is a unique fern and has important scientific and medicinal values. In this study, we sequenced its cp genome and transcriptome to estimate the evolutionary rates (dN and dS), selective pressure (dN/dS), gene expression level, codon usage bias, and their correlations. RESULTS: The correlation coefficients between dN, dS, and dN/dS, and Transcripts Per Million (TPM) average values were -0.278 (P = 0.027 < 0.05), -0.331 (P = 0.008 < 0.05), and -0.311 (P = 0.013 < 0.05), respectively. The codon adaptation index (CAI) and tRNA adaptation index (tAI) were significantly positively correlated with TPM average values (P < 0.05). CONCLUSIONS: Our results indicated that when the gene expression level was higher, the evolutionary rates and selective pressure were lower, but the codon usage bias was stronger. We provided evidence from cp gene data which supported the E-R (E stands for gene expression level and R stands for evolutionary rate) anti-correlation.

Effect of maternal lactoferrin supplementation on iron contents and anti-oxidant capacity in Dahe black Pig neonates.

Iron levels are closely related to animals' growth performance and anti-oxidant function. Lactoferrin (LF) is an iron-binding glycoprotein, which can promote the absorption of iron and regulate immune function. This study aimed to clarify the effect of maternal LF supplementation on the iron metabolism of Dahe piglets. Sixty sows (Dahe black, parity 3-4, no significant differences in body weight) were randomly assigned to five groups: control (basal diet with no iron supplementation), supplemented 100 (LF1 group), 200 (LF2 group), or 300 (LF3 group) mg LF/kg in the basal diet, and the basal diet supplemented with 100 (Fe-Gly group) mg Fe/kg as ferrous glycine (Fe-Gly). The serum anti-oxidant parameters of the sows and neonatal piglets were determined. The iron contents, anti-oxidant gene expression levels, and Fe-acquisition genes were detected in the liver, heart, spleen, and other neonatal organs. The results indicated that (1) the LF3 group of sows had the highest serum and colostrum iron contents (P < 0.05). The maternal LF significantly promoted the iron stores in the heart, liver, spleen, and lung of piglets compared with Fe-Gly. (2) The maternal LF increased serum glutathione peroxidase (GSH-Px) and total superoxide dismutase (T-SOD) activities of sows. Compared with other groups, the total anti-oxidant capacity (T-AOC) activity of LF2 groups increased significantly (P < 0.05). (3) LF significantly increased piglet serum GSH-Px, T-SOD, and T-AOC activities (P < 0.05). (4) Gene expression levels of GSH-Px, and SOD in the duodenum and jejunum of the LF2 group were significantly higher than in the Fe-Gly group (P < 0.05), while the expression levels in the liver and heart were lower (P < 0.05). (5) The expression levels of hepcidin and LF in the liver and duodenum of the LF2 group were significantly higher than in the Fe-Gly group (P < 0.05). In conclusion, maternal LF supplementation showed remarkable effects on iron storage in neonatal piglets, and exhibited strong antioxidant activities, it is helpful to prevent the occurrence of iron deficiency, and improves the immune function of animals.

RUNX1 and RUNX3 Genes Expression Level in Adult Acute Lymphoblastic Leukemia-A Case Control Study.

The genetic factors of adult acute lymphoblastic leukemia (ALL) development are only partially understood. The Runt-Related Transcription Factor (RUNX) gene family play a crucial role in hematological malignancies, serving both a tumor suppressor and promoter function. The aim of this study was the assessment of relative RUNX1 and RUNX3 genes expression level among adult ALL cases and a geographically and ethnically matched control group. The relative RUNX1 and RUNX3 genes expression level was assessed by qPCR. The investigated group comprised 60 adult patients newly diagnosed with ALL. The obtained results were compared with a group of 40 healthy individuals, as well as clinical and hematological parameters of patients, and submitted for statistical analysis. ALL patients tend to have significantly higher RUNX1 gene expression level compared with controls. This observation is also true for risk group stratification where high-risk (HR) patients presented higher levels of RUNX1. A higher RUNX1 transcript level correlates with greater leukocytosis while RUNX3 expression is reduced in Philadelphia chromosome bearers. The conducted study sustains the hypothesis that both a reduction and increase in the transcript level of RUNX family genes may be involved in leukemia pathogenesis, although their interaction is complex. In this context, overexpression of the RUNX1 gene in adult ALL cases in particular seems interesting. Obtained results should be interpreted with caution. Further analysis in this research field is needed.

Downregulation of EHT1 and EEB1 in Saccharomyces cerevisiae Alters the Ester Profile of Wine during Fermentation.

EHT1 and EEB1 are the key Saccharomyces cerevisiae genes involved in the synthesis of ethyl esters during wine fermentation. We constructed single (Δeht1, Δeeb1) and double (Δeht1Δeeb1) heterogenous mutant strains of the industrial diploid wine yeast EC1118 by disrupting one allele of EHT1 and/or EEB1. In addition, the aromatic profile of wine produced during fermentation of simulated grape juice by these mutant strains was also analyzed. The expression levels of EHT1 and/or EEB1 in the relevant mutants were less than 50% of the wild-type strain when grown in YPD medium and simulated grape juice medium. Compared to the wild-type strain, all mutants produced lower amounts of ethyl esters in the fermented grape juice and also resulted in distinct ethyl ester profiles. ATF2, a gene involved in acetate ester synthesis, was expressed at higher levels in the EEB1 downregulation mutants compared to the wild-type and Δeht1 strains during fermentation, which was consistent with the content of acetate esters. In addition, the production of higher alcohols was also markedly affected by the decrease in EEB1 levels. Compared to EHT1, EEB1 downregulation had a greater impact on the production of acetate esters and higher alcohols, suggesting that controlling EEB1 expression could be an effective means to regulate the content of these aromatic metabolites in wine. Taken together, the synthesis of ethyl esters can be decreased by deleting one allele of EHT1 and EEB1 in the diploid EC1118 strain, which may modify the ester profile of wine more subtly compared to the complete deletion of target genes.

Combined Analysis of the Metabolome and Transcriptome to Explore Heat Stress Responses and Adaptation Mechanisms in Celery (Apium graveolens L.).

Celery is an important leafy vegetable that can grow during the cool season and does not tolerate high temperatures. Heat stress is widely acknowledged as one of the main abiotic stresses affecting the growth and yield of celery. The morphological and physiological indices of celery were investigated in the present study to explore the physiological mechanisms in response to high temperatures. Results showed that the antioxidant enzyme activity, proline, relative conductivity, and malondialdehyde were increased, while chlorophyll and the water content of leaves decreased under high-temperature conditions. Short-term heat treatment increased the stomatal conductance to cool off the leaves by transpiration; however, long-term heat treatment led to stomatal closure to prevent leaf dehydration. In addition, high temperature caused a disordered arrangement of palisade tissue and a loose arrangement of spongy tissue in celery leaves. Combined metabolomic and transcriptomic analyses were further used to reveal the regulatory mechanisms in response to heat stress at the molecular level in celery. A total of 1003 differential metabolites were identified and significantly enriched in amino acid metabolism and the tricarboxilic acid (TCA) cycle. Transcriptome sequencing detected 24,264 different genes, including multiple transcription factor families such as HSF, WRKY, MYB, AP2, bZIP, and bHLH family members that were significantly upregulated in response to heat stress, suggesting that these genes were involved in the response to heat stress. In addition, transcriptional and metabolic pathway analyses showed that heat stress inhibited the glycolysis pathway and delayed the TCA cycle but increased the expression of most amino acid synthesis pathways such as proline, arginine, and serine, consistent with the results of physiological indicators. qRT-PCR further showed that the expression pattern was similar to the expression abundance in the transcriptome. The important metabolites and genes in celery that significantly contributed to the response to high temperatures were identified in the present study, which provided the theoretical basis for breeding heat-resistant celery.

The guppy (Poecilia reticulata) is a useful model for analyzing age-dependent changes in metabolism, motor function, and gene expression.

Aging is a major risk factor for many chronic diseases, causing a general decline in physiological function and loss of homeostasis. Recently, small teleost fish have been used as animal models of aging research because their genetic structures and organs closely resemble those of humans. Guppy (Poecilia reticulata), a small teleost fish, has a shorter lifespan than zebrafish. However, the age-dependent changes in physiology and genetics in guppies are not well understood. Here, we investigated the age-associated changes in metabolic rate, physical activity, and gene expression in guppies. Our results indicated that the resting metabolic rate and spontaneous motor activity in guppies decreased from an earlier age than those in mice. Moreover, the mRNA expression level of ppargc1a and the accumulation of lipofuscin were affected by age in the guppy livers; however, these changes were species-specific. On the other hand, in aged guppy brains, the mRNA expression changes of some genes were partly consistent with aged mammals. Although the process of senescence of the liver in guppies might vary from mammals, our findings suggest that guppy could be a useful animal model for age-related changes in physiological functions.

The impact of gene-body H3K36me3 patterns on gene expression level changes in chronic myelogenous leukemia.

Chronic myelogenous leukemia (CML) is a malignant clonal disease of hematopoietic stem cells. Researches have exhibited that the progression of CML is related to histone modifications. Here, we perform the systematic analyses of H3K36me3 patterns and gene expression level changes. We observe that the genes with higher gene-body H3K36me3 levels in normal cells show fewer expression changes during leukemogenesis, while the genes with lower gene-body H3K36me3 levels in normal cells yield obvious expression changes during leukemogenesis (ρ = -0.98, P = 9.30 × 10-8). These findings are conserved in human lung/breast cancers and mouse CML, regardless of gene expression levels and gene lengths. Regulatory element analysis and Random Forest regression display that Hoxd13, Rara, Scl, Smad3, Smad4 and Tgif1 induce the up-regulation of genes with lower H3K36me3 levels (ρ = 0.97, P = 2.35 × 10-56). Enrichment analysis shows that the differentially expressed genes with lower H3K36me3 levels are involved in leukemia-related pathways, such as leukocyte migration and regulation of leukocyte activation. Finally, six driver genes (Tp53, Wt1, Dnmt3a, Cacna1b, Phactr1 and Gbp4) with lower H3K36me3 levels are identified. Our analyses indicate that lower gene-body H3K36me3 levels may serve as a biomarker for the progression of CML.

Genes Common in Primary Immunodeficiencies and Cancer Display Overrepresentation of Codon CTG and Dominant Role of Selection Pressure in Shaping Codon Usage.

Primary immunodeficiencies (PIDs) are disorders of the immune system that involve faulty cellular, humoral, or both cellular and humoral functions. PIDs are present at the crossroad between infections, immune dysregulation, and cancers. A panel encompassing 42 genes involved in both PIDs and cancer has been investigated for the genes' compositional properties, codon usage patterns, various forces affecting codon choice, protein properties, and gene expression profiles. In the present study, the codon choice of genes was found to be dependent upon the richness of the nucleotide; the viz AT nucleotide rich genome preferred AT ending codons. The dinucleotide TpA adversely affected protein expression, while CpG did not. The CTG codon was the most overrepresented codon in 80.95% of genes. Analysis of various protein properties, including GRAVY, AROMA, isoelectric point, aliphatic index, hydrophobicity, instability index, and numbers of acidic, basic, and neutral amino acid residues revealed that the hydrophobicity index, instability index, and numbers of acidic and basic amino acid residues are the factors affecting gene expression. Based on neutrality analysis, parity analysis, ENc-GC3 analysis, and regression analysis of nucleotides present at the first and third positions of the codon, it was determined that selection pressure, mutation pressure, and compositional constraints all participated in shaping codon usage. The study will help determine the various evolutionary forces acting on genes common to both PIDs and cancer. Codon usage analysis might be helpful in the future to augment both diseases simultaneously. The research also indicates a peculiar pattern adapted by a set of genes involved in any disease.

The Differential Growth Inhibition of Phytophthora spp. Caused by the Rare Sugar Tagatose Is Associated With Species-Specific Metabolic and Transcriptional Changes.

Tagatose is a rare sugar with no negative impacts on human health and selective inhibitory effects on plant-associated microorganisms. Tagatose inhibited mycelial growth and negatively affected mitochondrial processes in Phytophthora infestans, but not in Phytophthora cinnamomi. The aim of this study was to elucidate metabolic changes and transcriptional reprogramming activated by P. infestans and P. cinnamomi in response to tagatose, in order to clarify the differential inhibitory mechanisms of tagatose and the species-specific reactions to this rare sugar. Phytophthora infestans and P. cinnamomi activated distinct metabolic and transcriptional changes in response to the rare sugar. Tagatose negatively affected mycelial growth, sugar content and amino acid content in P. infestans with a severe transcriptional reprogramming that included the downregulation of genes involved in transport, sugar metabolism, signal transduction, and growth-related process. Conversely, tagatose incubation upregulated genes related to transport, energy metabolism, sugar metabolism and oxidative stress in P. cinnamomi with no negative effects on mycelial growth, sugar content and amino acid content. Differential inhibitory effects of tagatose on Phytophthora spp. were associated with an attempted reaction of P. infestans, which was not sufficient to attenuate the negative impacts of the rare sugar and with an efficient response of P. cinnamomi with the reprogramming of multiple metabolic processes, such as genes related to glucose transport, pentose metabolism, tricarboxylic acid cycle, reactive oxygen species detoxification, mitochondrial and alternative respiration processes. Knowledge on the differential response of Phytophthora spp. to tagatose represent a step forward in the understanding functional roles of rare sugars.

The Missing Expression Level-Evolutionary Rate Anticorrelation in Viruses Does Not Support Protein Function as a Main Constraint on Sequence Evolution.

One of the central goals in molecular evolutionary biology is to determine the sources of variation in the rate of sequence evolution among proteins. Gene expression level is widely accepted as the primary determinant of protein evolutionary rate, because it scales with the extent of selective constraints imposed on a protein, leading to the well-known negative correlation between expression level and protein evolutionary rate (the E-R anticorrelation). Selective constraints have been hypothesized to entail the maintenance of protein function, the avoidance of cytotoxicity caused by protein misfolding or nonspecific protein-protein interactions, or both. However, empirical tests evaluating the relative importance of these hypotheses remain scarce, likely due to the nontrivial difficulties in distinguishing the effect of a deleterious mutation on a protein's function versus its cytotoxicity. We realized that examining the sequence evolution of viral proteins could overcome this hurdle. It is because purifying selection against mutations in a viral protein that result in cytotoxicity per se is likely relaxed, whereas purifying selection against mutations that impair viral protein function persists. Multiple analyses of SARS-CoV-2 and nine other virus species revealed a complete absence of any E-R anticorrelation. As a control, the E-R anticorrelation does exist in human endogenous retroviruses where purifying selection against cytotoxicity is present. Taken together, these observations do not support the maintenance of protein function as the main constraint on protein sequence evolution in cellular organisms.

Analysis of microRNA Regulation in Single Cells.

MicroRNAs (miRNAs) regulate gene expression by binding to mRNAs. Consequently, they reduce target gene expression levels and expression variability, also known as "noise." Single-cell RNA sequencing (scRNA-seq) technology has been used to study miRNA and mRNA expression in single cells, and has demonstrated its strength in quantifying cell-to-cell variation. Here we describe how to investigate miRNA regulation using data with both mRNA and miRNA expression in single cell format. We show that miRNAs reduce the expression levels and also expression noise of target genes in single cells. Finally, we also discuss potential improvements in experimental design and computational analysis of scRNA-seq in order to reduce or partition the technical noise.

Analysis of synonymous codon usage of transcriptome database in Rheum palmatum.

BACKGROUND: Rheum palmatum is an endangered and important medicinal plant in Asian countries, especially in China. However, there is little knowledge about the codon usage bias for R. palmatum CDSs. In this project, codon usage bias was determined based on the R. palmatum 2,626 predicted CDSs from R. palmatum transcriptome. METHODS: In this study, all codon usage bias parameters and nucleotide compositions were calculated by Python script, Codon W, DNA Star, CUSP of EMBOSS. RESULTS: The average GC and GC3 content are 46.57% and 46.6%, respectively, the results suggested that there exists a little more AT than GC in the R. palmatum genes, and the codon bias of R. palmatum genes preferred to end with A/T. We concluded that the codon bias in R. palmatum was affect by nucleotide composition, mutation pressure, natural selection, gene expression levels, and the mutation pressure is the prominent factor. In addition, we figured out 28 optimal codons and most of them ended with A or U. The project here can offer important information for further studies on enhancing the gene expression using codon optimization in heterogeneous expression system, predicting the genetic and evolutionary mechanisms in R. palmatum.

New novel non-MHC genes were identified for cervical cancer with an integrative analysis approach of transcriptome-wide association study.

Although genome-wide association studies (GWAS) have successfully identified multiple genetic variants associated with cervical cancer, the functional role of those variants is not well understood. To bridge such gap, we integrated the largest cervical cancer GWAS (N = 9,347) with gene expression measured in six human tissues to perform a multi-tissue transcriptome-wide association study (TWAS). We identified a total of 20 associated genes in the European population, especially four novel non-MHC genes (i.e. WDR19, RP11-384K6.2, RP11-384K6.6 and ITSN1). Further, we attempted to validate our results in another independent cervical cancer GWAS from the East Asian population (N = 3,314) and re-discovered four genes including WDR19, HLA-DOB, MICB and OR2B8P. In our subsequent co-expression analysis, we discovered SLAMF7 and LTA were co-expressed in TCGA tumor samples and showed both WDR19 and ITSN1 were enriched in "plasma membrane". Using the protein-protein interaction analysis we observed strong interactions between the proteins produced by genes that are associated with cervical cancer. Overall, our study identified multiple candidate genes, especially four non-MHC genes, which may be causally associated with the risk of cervical cancer. However, further investigations with larger sample size are warranted to validate our findings in diverse populations.

Molecular Mechanisms of Hemoglobin Adaptation to High Altitude Hypoxia in Pseudopodoces humilis / 中国生物化学与分子生物学报

As the main carrier of oxygen delivery in the blood circulation system, hemoglobin (Hb) plays a key role in the adaptation of animals to high altitude hypoxia.In this paper, we combined analysis of genome, transcriptome, molecular evolution, homology modeling and molecular dynamics simulation, and explored the molecular mechanisms of increased blood oxygen affinity of Pseudopodoces humilis.Our results showed that the prenatal expressed p gene was highly expressed in the adult Pseudopodoces humilis (RPKM = 32.22) compared to Parus major (RPKM = 0), and this may result in the presence of two additional p-type Hbs with high oxygen affinity in the blood of P.humilis, i.e.(al>p)2 and (aAp)2.The PA25G-A and pA55L-I mutations may increase the van der Waals force between the B and D helices, which might eventually make the entire Pv subunit more compact and finally reduce the number of hydrogen bonds between a dimers, hence the transition from T state to R state is prone to occur.The two mutations of (3a43A-S and pA44S-N could change the conformation and polarity of the heme pocket opening, thus making the solution easier to flow into/out of the heme pocket and therefore facilitating the gas exchange.The pA90E-K mutation in P.humilis has undergone strong positive selection, which could increase the basicity of pA-type Hb, thereby offsetting the decrease in Hb-02 affinity caused by the Bohr effect.In addition, we also found that aA44P-S and pA43A-S mutations may increase the hydrophilicity of otA and pv type Hbs, which is beneficial to the accumulation of Hb to a higher concentration in red blood cells.Collectively, the prenatal Hb genes highly expressed in the adult together with the genetic based changes in intrinsic 0, affinity and physicochemical property of aA and pA Hb could be the main causes for the increase in blood oxygen affinity of P.humilus.

Association between the CEBPA and c-MYC genes expression levels and acute myeloid leukemia pathogenesis and development.

CEBPA and c-MYC genes belong to TF and play an essential role in hematologic malignancies development. Furthermore, these genes also co-regulate with RUNX1 and lead to bone marrow differentiation and may contribute to the leukemic transformation. Understanding the function and full characteristics of selected genes in the group of patients with AML can be helpful in assessing prognosis, and their usefulness as prognostic factors can be revealed. The aim of the study was to evaluate CEBPA and c-MYC mRNA expression level and to seek their association with demographical and clinical features of AML patients such as: age, gender, FAB classification, mortality or leukemia cell karyotype. Obtained results were also correlated with the expression level of the RUNX gene family. To assess of relative gene expression level the qPCR method was used. The expression levels of CEBPA and c-MYC gene varied among patients. Neither CEBPA nor c-MYC expression levels differed significantly between women and men (p=0.8325 and p=0.1698, respectively). No statistically significant correlation between age at the time of diagnosis and expression of CEBPA (p=0.4314) or c-MYC (p=0.9524) was stated. There were no significant associations between relative CEBPA (p=0.4247) or c-MYC (p=0.4655) expression level and FAB subtype and mortality among the enrolled patients (p=0.5858 and p=0.8437, respectively). However, it was observed that c-MYC and RUNX1 expression levels were significantly positively correlated (rS=0.328, p=0.0411). Overall, AML pathogenesis involves a complex interaction among CEBPA, c-MYC and RUNX family genes.

Compositional Features and Codon Usage Pattern of Genes Associated with Anxiety in Human.

Codon usage bias (CUB) is the unequal usage of synonymous codon; some codons are more preferred than others. CUB analysis has applications in understanding the molecular organization of genome, genetics, gene expression, and molecular evolution. Bioinformatic approach was used to analyze the protein-coding sequences of genes involved in the anxiety to understand the patterns of codon usage as no work was reported yet. The improved effective number of codons (Nc) values ranged from 43.55 to 55.06, with a mean of 44.57, suggested that the overall CUB was low for genes associated with anxiety. The overall GC and AT content was 54.76 and 45.24, respectively. Relative synonymous codon usage (RSCU) analysis revealed that most frequently used codon ended mostly with C or G. The over-represented codons in genes associated with anxiety were CTG, ATC, GTG, AGC, ACC, and GCC, while under-represented codons were TTA, CTT, CTA, ATA, GTT, GTA, TCG, CCG, GCG, CAA, and CGT. Correlation analysis was performed between overall nucleotide composition and its 3rd codon positions, and observed highly significant (p < 0.01) correlation between them suggested that both mutation pressure and natural selection might affect the pattern of CUB. The highly significant correlation (0.598**, p < 0.01) was also observed between GC12 with GC3 suggested that directional mutation pressure might acted on all codon positions for genes associated with anxiety.