Exploring transcriptomic databases to identify and experimentally validate tissue-specific consensus reference gene for gene expression normalization in BALB/c mice acutely exposed to 2,3,7,8-Tetrachlorodibenzo-p-dioxin.

In VitroMetabolism of 4-Vinylcyclohexene in Rat and Mouse Liver, Lung, and Ovary

Background: Groundwater arsenic affects millions of people in about 20 countries. In West Bengal (India) and Bangladesh alone over 100 million people are exposed. The arsenic concentration in contaminated groundwater in Bangladesh was above the maximum permissible level of 0.05 mg/l as recommended by WHO for developing countries [1]. Drinking water is not the only source of poisoning. In arsenic contaminated areas, crops, vegetables, cereals, poultry, cattle, etc, also contain traces of arsenic. Chronic arsenic intoxication has been associated with several diseases such as melanosis, leuco-melanosis, hyperkeratosis, oedema, skin cancer… 
 Cazin et al [2], have demonstrated the effect of high dilutions of arsenic compounds. They noted increased arsenic elimination from blood through urine and faeces in intoxicated rats. According to these research, the aim of Khuda Buksh studies [3-4-5] was to investigate whether high dilution Arsenicum album have any effect on arsenic accumulation in different tissues and to understand also how this high dilution could produce a protective effect on all the different organs.
 Methodology: Firstly, the effect of Arsenicum album 30 cH on the amount of arsenic accumulation was determined by spectrophotometric analysis in four tissues namely liver, kidney and testis in mice intoxicated by arsenic. The protective effect in chronic and acute arsenic intoxicated mice of Arsenicum Album 6cH, 30cH and 200cH has been evaluated using not only the activities of enzymatic and biomarker toxicity (aspartate amino transferase (AST), alanine amino transferase (ALT), acid phosphatase (AcP), alkaline phosphatase (AlkP), lipid peroxidation (LPO) and reduced glutathione (GSH)) but also the cytogenetical parameters (chromosome aberrations (CA), mitotic index (MI), sperm head anomaly (SHA) etc., ). Because, it is well demonstrated that these enzymes biomarkers reflect the degree of hepatotoxicity and oxidative stress caused by arsenic intoxication.
 Results: Compared to controls, Arsenicum album 30cH induced a significant decrease in accumulation of arsenic in 4 tissues namely liver, spleen, kidney and testis in intoxicated mice. In addition, both Arsenicum album 6cH, 30cH and 200cH reduced chromosome aberrations, sperm head abnormality frequencies and activities of acid and alkaline phosphatases, aspartate and alanine aminotransferases and lipid peroxidation, while mitotic index and activities of glutathione, catalase and succinate dehydrogenase were increased compared to controls. 
 Conclusion: Altogether, theses results provide evidence of protective potentials of the Arsenicum album dilution against acute and chronic arsenic intoxication in mice. They also offer a new hypothesis that the mechanism of the homeopathic dilution could act through regulation of expression of certain genes. This explanation seems to be plausible because all biomarker tests are regulated by specific genetic regulatory mechanisms [6].
 keywords: Arsenicum album, arsenic intoxication, enzymatic and biomarker toxicity.

LKB1 is an upstream activating kinase for the AMP-activated protein kinase (AMPK) and at least 12 other AMPK-related kinases. LKB1 therefore acts as a master kinase regulating the activity of a wide range of downstream kinases, which themselves have diverse physiological roles. Here we identify a second form of LKB1 generated by alternative splicing of the LKB1 gene. The two LKB1 proteins have different C-terminal sequences generating a 50-kDa form (termed LKB1L) and a 48-kDa form (LKB1S). LKB1L is widely expressed in mouse tissues, whereas LKB1S has a restricted tissue distribution with predominant expression in the testis. LKB1S, like LKB1L, forms a complex with MO25 and STRAD, and phosphorylates and activates AMPK both in vitro and in intact cells. A phosphorylation site (serine 431 in mouse) and a farnesylation site (cysteine 433 in mouse) within LKB1L are not conserved in LKB1S raising the possibility that these sites might be involved in differential regulation and/or localization of the two forms of LKB1. However, we show that phosphorylation of serine 431 has no effect on LKB1L activity and that both LKB1L and LKB1S have similar patterns of subcellular localization. These results indicate that the physiological significance of the different forms of LKB1 is not related directly to differences in the C-terminal sequences but may be due to their differential patterns of tissue distribution.

The housekeeping (ubiquitously expressed) genes in the mammal genome were shown here to be on average slightly GC-richer than tissue-specific genes. Both housekeeping and tissue-specific genes occupy similar ranges of GC content, but the former tend to concentrate in the upper part of the range. In the human genome, tissue-specific genes show two maxima, GC-poor and GC-rich. The strictly tissue-specific human genes tend to concentrate in the GC-poor region; their distribution is left-skewed and thus reciprocal to the distribution of housekeeping genes. The intermediately tissue-specific genes show an intermediate GC content and the right-skewed distribution. Both in the human and mouse, genes specific for some tissues (e.g., parts of the central nervous system) have a higher average GC content than housekeeping genes. Since they are not transcribed in the germ line (in contrast to housekeeping genes), and therefore have a lower probability of inheritable gene conversion, this finding contradicts the biased gene conversion (BGC) explanation for elevated GC content in the heavy isochores of mammal genome. Genes specific for germ-line tissues (ovary, testes) show a low average GC content, which is also in contradiction to the BGC explanation. Both for the total data set and for the most part of tissues taken separately, a weak positive correlation was found between gene GC content and expression level. The fraction of ubiquitously expressed genes is nearly 1.5-fold higher in the mouse than in the human. This suggests that mouse tissues are comparatively less differentiated (on the molecular level), which can be related to a less pronounced isochoric structure of the mouse genome. In each separate tissue (in both species), tissue-specific genes do not form a clear-cut frequency peak (in contrast to housekeeping genes), but constitute a continuum with a gradually increasing degree of tissue-specificity, which probably reflects the path of cell differentiation and/or an independent use of the same protein in several unrelated tissues.

Selection of Brain Metastasis-Initiating Breast Cancer Cells Determined by Growth on Hard Agar

Oxidation state specific analysis of arsenic species in tissues of wild-type and arsenic (+ 3 oxidation state) methyltransferase-knockout mice

BackgroundKorean Red Ginseng (KRG) is a traditional herb that has several beneficial properties including anti-aging, anti-inflammatory, and autophagy regulatory effects. However, the mechanisms of these effects are not well understood. In this report, the underlying mechanisms of anti-inflammatory and autophagy-promoting effects were investigated in aged mice treated with KRG-water extract (WE) over a long period. MethodsThe mechanisms of anti-inflammatory and autophagy-promoting activities of KRG-WE were evaluated in kidney, lung, liver, stomach, and colon of aged mice using semi-quantitative reverse transcription polymerase chain reaction (RT-PCR), quantitative RT-PCR (qRT-PCR), and western blot analysis. ResultsKRG-WE significantly suppressed the mRNA expression levels of inflammation-related genes such as interleukin (IL)-1β, IL-8, tumor necrosis factor (TNF)-α, monocyte chemoattractant protein-1 (MCP-1), and IL-6 in kidney, lung, liver, stomach, and colon of the aged mice. Furthermore, KRG-WE downregulated the expression of transcription factors and their protein levels associated with inflammation in lung and kidney of aged mice. KRG-WE also increased the expression of autophagy-related genes and their protein levels in colon, liver, and stomach. ConclusionThe results suggest that KRG can suppress inflammatory responses and recover autophagy activity in aged mice.

Tissue-specific gene expression has been found to be associated with multiple complex diseases including cancer, metabolic disease, aging, etc. However, few studies of brain-tissue-specific gene expression patterns have been reported, especially in psychiatric disorders. In this study, we performed joint analysis on large-scale transcriptome multi-tissue data to investigate tissue-specific expression patterns in major depressive disorder (MDD) and bipolar disorder (BP). We established the strategies of identifying tissues-specific modules, annotated pathways for elucidating biological functions of tissues, and tissue-specific genes based on weighted gene co-expression network analysis (WGCNA) and robust rank aggregation (RRA) with transcriptional profiling data from different human tissues and genome wide association study (GWAS) data, which have been expanded into overlapping tissue-specific modules and genes sharing with MDD and BP. Nine tissue-specific modules were identified and distributed across the four tissues in the MDD and six modules in the BP. In general, the annotated biological functions of differentially expressed genes (DEGs) in blood were mainly involved in MDD and BP progression through immune response, while those in the brain were in neuron and neuroendocrine response. Tissue-specific genes of the prefrontal cortex (PFC) in MDD-, such as IGFBP2 and HTR1A, were involved in disease-related functions, such as response to glucocorticoid, taste transduction, and tissue-specific genes of PFC in BP-, such as CHRM5 and LTB4R2, were involved in neuroactive ligand-receptor interaction. We also found PFC tissue-specific genes including SST and CRHBP were shared in MDD-BP, SST was enriched in neuroactive ligand-receptor interaction, and CRHBP shown was related to the regulation of hormone secretion and hormone transport.

Nocardia pyomyositis in a patient with Granulomatosis with polyangiitis

Effect of dietary clofibrate on epoxide hydrolase activity in tissues of mice

Quantitative real-time reverse transcriptase PCR (qRT-PCR) is a sensitive and powerful technique for measuring differential gene expression; however, changes in gene expression induced by abiotic stresses are complex and multifaceted. Therefore, a set of stably expressed reference genes for data normalization is required. Switchgrass (Panicum virgatum L.) is a prime candidate crop for bioenergy production. The expression stability of reference genes in switchgrass, especially under different experimental conditions, is largely unknown. In order to identify the most suitable reference genes for abiotic stress studies in switchgrass, we evaluated 14 candidate genes for their expression stability under drought, high salinity, cold, heat, and waterlogging treatments using the Delta Ct, geNorm, BestKeeper, and NormFinder approaches. Validation of reference genes indicated that the best reference genes should be selected based on the stress treatment. Actin 2 (ACT2), carotenoid-binding protein 20 (CBP20), and Tubulin (TUB) were found to have the highest expression stability to study drought stress. 18S ribosomal RNA1 (18S rRNA1), ACT2, and TUB were the most stably expressed genes under salt stress. Ubiquitin-conjugating enzyme (UBC), TUB, and cyclophilin2 (CYP2) were the most suitable reference genes across cold treatments. Likewise, 18S rRNA1, UBC, and TUB were good reference genes for studying heat stress, while ACT2, 18S rRNA1, and ubiquitin3 (UBQ3) were the top three reference genes under waterlogging treatment. Considering that reference gene expression may vary across switchgrass tissues, ACT2 and 18S ribosomal RNA2 (18S rRNA2) were shown to be the most stably expressed genes in switchgrass leaves and roots, respectively. The highly ranked reference genes that were identified in this study were shown to be capable of detecting subtle differences in the expression rates of other genes. These differences may have been missed if a less suitable reference gene was used.

The Impact of Gene Expression Regulation on Evolution of Extracellular Signaling Pathways

Lectin‐like oxidized low‐density lipoprotein receptor‐1 (LOX‐1) is recognized as an important cardiovascular cell scavenger receptor for oxidized low‐density lipoproteins (oxLDL). LOX‐1 activation mediates several oxLDL‐stimulated intracellular signaling pathways and tissue processes that lead to oxidative stress, inflammatory cell infiltration in the vessel wall, endothelial dysfunction, and cardiovascular pathophysiology. In the current study, we analyzed the gene expression profiles of LOX‐1 in the aortas, hearts, liver, lungs, and kidneys of male and female C57BL/6J mice. Significant sex differences were observed in LOX‐1 mRNA expression. LOX‐1 mRNA levels were higher in male mouse aortas and hearts compared with female tissues. Conversely, LOX‐1 gene expression was elevated in female versus male kidneys. In mouse liver and lungs, we found LOX‐1 mRNA levels were comparable in males and females. These results clearly suggest that significant sex differences exist in the gene expression profiles of LOX‐1 in mouse tissues, and given the data supporting the tissue‐specific differences in LOX‐1 gene expression between males and females, we speculate these studies will provide new insights into the cellular mechanisms directly responsible for the critical, sex‐linked roles of LOX‐1 in both vascular dysfunction and other disease complications.Support or Funding Information(Supported by 5K12HD043451).

Using differential display reverse transcriptase-polymerase chain reaction (RT-PCR) we have cloned a cDNA that encodes a putative peptide with homology to a recently reported A-kinase anchoring protein-associated protein (ASP) in human sperm. The mouse cDNA was 864 bases in length and encoded for a putative protein of 230 amino acids that had 90% amino acid similarity with the human ASP. The N terminal amino acid sequence had 65% similarity to the rat, mouse, and human protein kinase A regulatory type II sequences. Expression of the gene encoding this ASP was specific to testicular germ cells. Northern blot analysis of testis RNA from 5-, 15-, 25-, and 40-day-old mice showed expression of the ASP gene, but similar analyses of busulfan-treated germ cell-deficient mice failed to detect its expression. In addition, Northern blot analysis did not detect expression of the ASP mRNA in cultured Sertoli cells or cultured interstitial cells. Northern blot and RT-PCR analyses did not detect the ASP mRNA in mouse spleen, brain, liver, lung, heart, kidney, skeletal muscle, ovary, or Sertoli cells. In situ hybridization analysis localized the ASP mRNA to the germ cell compartment of the seminiferous tubules in the testis.

Prostate is a well-known androgen-dependent tissue. By sequencing 4,294,186 serial analysis of gene expression (SAGE) tags, we have investigated the transcriptomes of normal mouse prostate, liver, testis, lung, brain, femur, skin, adipose tissue, skeletal muscle, vagina, ovary, mammary gland, and uterus in order to identify the most abundant and tissue-specific transcripts in the prostate, as well as to target the androgen responsive transcripts specifically regulated in the prostate. Small interference RNA (siRNA) in LNCaP cells was applied to validate the roles of prostate-specific/enriched ARGs in the growth of human prostate cancer cells. The most abundant transcripts were involved in prostatic secretion, energy metabolism and immunity. Previously well-known prostate-specific transcripts, including many transcripts involved in prostatic secretion, polyamine biosynthesis and transport, and immunity were specific/enriched in the prostate. Only 22 transcripts among 114 androgen-regulated genes (ARGs) in the mouse prostate were modulated by dihydrotestosterone (DHT) in two or more tissues. The siRNA results showed that inhibition of HSPA5 and MAT2A gene expression repressed growth of human cancer LNCaP cells. The current study globally assessed the transcriptome of the prostate and revealed the most abundant and tissue-specific transcripts which are responsible for the unique functions of this organ. These prostate-specific ARGs might be used as targets to develop safe and effective gene-based therapy for the prevention and treatment of prostate cancer.