Nobiletin attenuates inflammation via modulating proinflammatory and antiinflammatory cytokine expressions in an autoimmune encephalomyelitis mouse model.

The aim of this study is to investigate the potential preventive and therapeutic effects of nobiletin by evaluating the expression of cytokines associated with inflammatory reactions in an autoimmune encephalomyelitis mouse model. A total of 60 male C57BL/6 mice aged between 8 and 10 weeks were used. Mice were divided into six groups (n = 10 mice per group): control, EAE, low-prophylaxis, high-prophylaxis, low-treatment and high-treatment. Experimental autoimmune encephalomyelitis (EAE) was induced by myelin oligodendrocyte glycoprotein (MOG) and pertussis toxin. Nobiletin was administered in low (25 mg/kg) and high (50 mg/kg) doses, intraperitoneally. The prophylactic and therapeutic effects of nobiletin on brain tissue and spinal cord were evaluated by expression of interleukin-1 beta (IL-1ß), tumor necrosis factor-alpha (TNF-α), interferon gamma (IFNγ), IL-6, IL-10 and transforming growth factor-beta (TGF-ß) using immunohistochemistry and real-time polymerase chain reaction (RT-PCR). Prophylactic and therapeutic use of nobiletin inhibited EAE-induced increase of TNF-α, IL-1ß and IL-6 activities to alleviate inflammatory response in brain and spinal cord. Moreover, nobiletin supplement dramatically increased the IL-10, TGF-ß and IFNγ expressions in prophylaxis and treatment groups compared with the EAE group in the brain and spinal cord. The results obtained from this study show that prophylactic and therapeutic nobiletin modulates expressions of proinflammatory and antiinflammatory cytokines in brain and spinal cord dose-dependent manner in EAE model. These data demonstrates that nobiletin has a potential to attenuate inflammation in EAE mouse model. These experimental findings need to be supported by clinical studies.

In vivo evaluation of anti-Leishmania activity of alkyltriazoles and alkylphosphocholines by oral route.

The failures in the treatment of leishmaniasis is an increasing problem around the world, especially related to resistance. Thus, we describe the synthesis and in vivo anti-Leishmania activity of alkylphosphocholine and alkyltriazoles; besides, their likely action mechanisms stem from some eventual inhibition of parasite enzymes using computational tools. These compounds were tested in an in vivo hamster model infected with Leishmania Leishmania infantum chagasi. Fifty days after parasite inoculation, the two compounds 12-azidedodecylphosphocholine (3) and 3-(1-(12-fluorododecyl)-1H-1,2,3-triazol-1-yl)propano-1-ol (9), were separately administered once a day as oral suspensions (25 and 12.5 mg/kg/day, respectively) during ten days, and their efficacy was compared to the reference compound pentavalent antimonial Glucantime (GLU). Compound 3 significantly reduced the number of parasites in the spleen (4.93 × 102 amastigotes/g) and liver (4.52 × 103 amastigotes/g). Compound 9 reduced the number of amastigotes in the spleen to 1.30 × 104 and 1.36 × 103 amastigotes/g in the liver. GLU was the most effective overall treatment (7.50 × 101 and 2.28 × 102 amastigotes/g in the spleen and liver, respectively). The high activity levels of these compounds in vivo may stem from their high in vitro leishmanicidal activity and lipophilicity. The in silico absorption, distribution, metabolism, and excretion studies also showed some anti-Leishmania potential. Compound 9 had more lipophilic characteristics than those of compound 3. In silico studies of the nine enzymes of compounds 3 and 9 showed significant evidence of interactions with nicotimidase and tyrosine aminotransferase, demonstrating possible inhibition enzymes present in L. (L.) infantum chagasi. These compounds could be a promising template for developing a new class of leishmanicidal agents, by oral route, and deserve further investigation to explore different therapeutic regimens.

Investigating the molecular control of deer antler extract on articular cartilage.

BACKGROUND: Deer antler is considered as a precious traditional Chinese medicinal material and has been widely used to reinforce kidney's yang, nourish essence, and strengthen bone function. The most prominent bioactive components in deer antler are water-soluble proteins that play potential roles in bone formation and repair. The aim of this study was to explore the molecular control and therapeutic targets of deer antler extract (DAE) on articular cartilage. METHODS: DAE was prepared as previously described. All rats were randomly divided into Blank group and DAE group (10 rats per group) after 7-day adaptive feeding. The rats in DAE group were orally administrated with DAE at a dose of 0.2 g/kg per day for 3 weeks, and the rats in Blank group were fed with drinking water. Total RNA was isolated from the articular cartilage of knee joints. RNA sequencing (RNA-seq) experiment combined with quantitative real-time polymerase chain reaction (qRT-PCR) verification assay was carried out to explore the molecular control and therapeutic targets of DAE on articular cartilage. RESULTS: We demonstrated that DAE significantly increased the expression levels of functional genes involved in cartilage formation, growth, and repair and decreased the expression levels of susceptibility genes involved in the pathophysiology of osteoarthritis. CONCLUSIONS: DAE might serve as a candidate supplement for maintaining cartilage homeostasis and preventing cartilage degeneration and inflammation. These effects were possibly achieved by accelerating the expression of functional genes involved in chondrocyte commitment, survival, proliferation, and differentiation and suppressing the expression of susceptibility genes involved in the pathophysiology of osteoarthritis. Thus, our findings will contribute towards deepening the knowledge about the molecular control and therapeutic targets of DAE on the treatment of cartilage-related diseases.

Tissue distribution of transcription for 29 lipid metabolism-related genes in Takifugu rubripes, a marine teleost storing lipid predominantly in liver.

The tissue distribution pattern of lipid is highly diverse among different fish species. Tiger puffer has a special lipid storage pattern, storing lipid predominantly in liver. In order to better understand the lipid physiology in fish storing lipid in liver, the present study preliminarily investigated the tissue distribution of transcription for 29 lipid metabolism-related genes in tiger puffer, which are involved in lipogenesis, fatty acid oxidation, biosynthesis and hydrolysis of glycerides, lipid transport, and relevant transcription regulation. Samples of eight tissues, brain, eye, heart, spleen, liver, intestine, skin, and muscle, from fifteen juvenile tiger puffer were used in the qRT-PCR analysis. The intestine and brain had high transcription of lipogenic genes, whereas the liver and muscle had low expression levels. The intestine also had the highest transcription level of most apolipoproteins and lipid metabolism-related transcription factors. The transcription of fatty acid ß-oxidation-related genes was low in the muscle. The peroxisomal fatty acid oxidation may dominate over mitochondrial ß-oxidation in the liver and intestine of tiger puffer, and the MAG pathway probably predominates over the G3P pathway in re-acylation of absorbed lipids in the intestine. The intracellular glyceridases were highly transcribed in the brain, eye, and heart. In conclusion, in tiger puffer, the intestine could be a center of lipid metabolism whereas the liver is more likely a pure storage organ for lipid. The lipid metabolism in the muscle could also be inactive, possibly due to the very low level of intramuscular lipid.

Ileal Transcriptome Profiles of Japanese Quail Divergent in Phosphorus Utilization.

Phosphorus (P) is an essential component for all living beings. Low P diets prompt phenotypic and molecular adaptations to maintain P homeostasis and increase P utilization (PU). Knowledge of the molecular mechanisms of PU is needed to enable targeted approaches to improve PU efficiency and thus lower P excretion in animal husbandry. In a previous population study, Japanese quail were subjected to a low P diet lacking mineral P and exogenous phytase. Individual PU was determined based on total P intake and excretion. A subset of 20 extreme siblings discordant for PU was selected to retrieve gene expression patterns of ileum (n = 10 per PU group). Sequencing reads have been successfully mapped to the current Coturnix japonica reference genome with an average mapping rate of 86%. In total, 640 genes were found to be differentially abundant between the low and high PU groups (false discovery rate ≤ 0.05). Transcriptional patterns suggest a link between improved PU and mitochondrial energy metabolism, accelerated cell proliferation of enterocytes, and gut integrity. In assessing indicators of the efficient use of macro- and micronutrients, further research on turnover and proliferation rates of intestinal cells could provide an approach to improve P efficiency in poultry species.

Synergistic Effects of Selenium Nanoparticles and Vitamin E on Growth, Immune-Related Gene Expression, and Regulation of Antioxidant Status of Nile Tilapia (Oreochromis niloticus).

The present study was conducted to investigate the effects of nano-selenium (Nano Se) or/and vitamin E (VE) on growth performance, blood health, intestinal histomorphology, oxidative status, and immune-related gene expression of Nile tilapia. Nano Se or/and VE at a rate of 0, 1 mg Nano Se/kg, 100 mg VE/kg, and 1 mg Nano Se/kg + 100 mg VE diet were fed to fish for 8 weeks. FBW was significantly (P < 0.05) increased in fish fed with Nano Se and VE, while fish fed with Nano Se or Nano Se and VE diets displayed significantly (P < 0.05) higher WG and SGR than the other groups. The lowest FCR was significantly (P < 0.05) detected in fish fed with Nano Se and VE, while the highest value was observed in fish VE diet. The intestinal morphometry (villi length and width) of fish fed with Nano Se or/and VE reported significantly (P < 0.05) the highest values with high number of goblet cells. Blood hematology and biochemistry parameters of fish fed with Nano Se or/and VE showed normal values with insignificant differences except for the blood total protein increased in fish fed with Nano Se or/and VE (P < 0.05). Dietary Nano Se or Nano Se and VE significantly (P < 0.05) increased the GPX, SOD, CAT, NBT, lysozyme, and phagocytosis values with decreased MDA. Liver and spleen TNF-α and IL-1ß expressions were significantly (P < 0.05) upregulated in fish fed on Nano Se or Nano Se and VE. Thus, Nano Se or/and VE can be used effectively in tilapia diets for improving the growth, intestinal health, blood health, oxidative status, and immune-related gene expression.

Transcriptomic analyses reveal the molecular mechanisms of schisandrin B alleviates CCl4-induced liver fibrosis in rats by RNA-sequencing.

Liver fibrosis is a progression of chronic liver disease with lacks effective therapies at present. Schisandrin B (Sch B), a bioactive compound extracted from the traditional Chinese medicine Schisandra chinensis, was reported to benefit liver diseases. This study aimed to investigate the therapeutic effects and molecular mechanisms of Sch B against CCl4-induced liver fibrosis in rats. RNA sequencing and transcriptome analysis were performed collaboratively, including analysis of differential gene expression, gene ontology (GO) analysis, pathway analysis and pathway-act-network analysis. The results demonstrated that Sch B effectively alleviated CCl4-induced liver damage and fibrosis in rats, as evidenced by improved liver function and decreased extracellular matrix deposition. Furthermore, 4440 (1878 up-regulated, 2562 down-regulated) genes in the model group versus (vs) normal group, 4243 (2584 up-regulated, 1659 down-regulated) genes in Sch B-treated group vs model group were identified as differentially expressed genes (DEGs). Subsequently, GO analysis revealed that DEGs were mainly enriched in metabolism, oxidation-reduction, endoplasmic reticulum stress and apoptosis-related biological processes. Pathway analysis suggested that Sch B up-regulated cytochrome P450 drug metabolism, PPAR signaling pathways, and down-regulated glutathione metabolism pathways. In addition, the regulatory patterns of Sch B on key genes and pathways were also confirmed. In conclusion, our study demonstrated Sch B alleviated CCl4-induced liver fibrosis by multiple modulatory mechanisms, which provide new clues for further pharmacological study of Sch B.

Hepatotoxicity and renal toxicity induced by gamma-radiation and the modulatory protective effect of Ficus carica in male albino rats.

It is well-known that gamma radiation initiates generation of free radicals which prompting serious cellular damages in biological systems. In the present study, we investigated the role of Ficus carica, a natural antioxidant substance, in modulating changes in liver and kidney functions, antioxidant enzyme's gene expression, and apoptosis, in male albino rats exposed to gamma radiation. A total of 40 rats were used in this experiment and divided equally into 4 groups: Group 1, rats administered distilled H2O (Control); Group 2, rats administered F. carica; Group 3, rats irradiated; and Group 4, rats treated with F. carica and irradiated. Groups 3 and 4 were exposed to whole-body gamma radiations at a dose level of 8 Gy and with a dose rate of 0.762 Gy/min. F. carica was administered to rats by gavage, for 3 consecutive weeks, before exposure to radiation. Five rats were sacrificed from each group at intervals of 24 and 72 h after cessation of treatment. The results revealed marked increases in alanine aminotransferase and aspartate aminotransferase levels in liver, a decrease in albumin level and increase in urea level in kidney. Irradiation resulted in cytotoxic effects as indicated by elevation in antioxidant enzyme's gene expression at 24 h, the opposite was observed at 72 h. Immunohistochemical analysis revealed that cytochrome c and p53 expressions significantly increased following exposure to radiation. Oral administration of F. carica pre-irradiation as a natural product plays a modulatory protective and anti-apoptotic role against cells damaged by free radicals induced by whole-body irradiation.

Corn dried distillers grains with solubles (cDDGS) in the diet of pigs change the expression of adipose genes that are potential therapeutic targets in metabolic and cardiovascular diseases.

BACKGROUND: Corn dried distillers grains with solubles (cDDGS) are a byproduct of biofuel and alcohol production. cDDGS have been used in pig feed for many years, because they are readily available and rich in protein, fiber, unsaturated fatty acids and phytosterols. However, feed mixtures too high in cDDGS result in the worsening of backfat quality. We performed RNA-sequencing analysis of backfat from crossbred pigs fed different diets. The diets were isoenergetic but contained different amounts of cDDGS and various sources of fats. The animals were divided into four dietary groups during the two months of experimentation: group I (control (-cDDGS+rapeseed oil)), group II (+cDDGS+rapeseed oil), group III (+cDDGS+beef tallow), and group IV (+cDDGS+coconut oil). The aim of the present experiment was to evaluate changes in the backfat transcriptome of pigs fed isoenergetic diets that differed in cDDGS presence. RESULTS: Via DESeq2 software, we identified 93 differentially expressed genes (DEGs) between groups I and II, 13 between groups I and III, and 125 between groups I and IV. DEGs identified between group I (-cDDGS+rapeseed oil) and group II (+cDDGS+rapeseed oil) were highly overrepresented in several KEGG pathways: metabolic pathways (FDR < 1.21e-06), oxidative phosphorylation (FDR < 0.00189), fatty acid biosynthesis (FDR < 0.00577), Huntington's disease (FDR < 0.00577), fatty acid metabolism (FDR < 0.0112), Parkinson's disease (FDR < 0.0151), non-alcoholic fatty liver disease (NAFLD) (FDR < 0.016), Alzheimer's disease (FDR < 0.0211) and complement and coagulation cascades (FDR < 0.02). CONCLUSIONS: We observed that the addition of cDDGS positively affects the expression of several genes that have been recently proposed as potential targets for the treatment of obesity, diabetes, cardiovascular disease, and Alzheimer's disease (e.g., FASN, AACS, ALAS1, HMGCS1, and VSIG4). Thus, our results support the idea of including cDDGS into the diets of companion animals and humans and encourage research into the bioactive ingredients of cDDGS.

Magnetic nano fluids for isolation of genomic DNA and total RNA from various prokaryote and eukaryote cells.

The correct isolation of nucleic acid from various cells is an important preliminary step before many biochemical and diagnostic processes such as cloning, sequencing, replication, hybridization, and complementary DNA (cDNA) synthesis. In this study, the coated magnetic nanoparticles (MNFs) with Tween 20 and oleic acid because of paramagnetic and bio-compatibility properties used in the extractions of genomic DNA (gDNA) and total RNA from prokaryote and eukaryote cells. The amount and accuracy of gDNA and total RNA extracted were proved via agarose gel electrophoresis, digestion and polymerase chain reaction (PCR) techniques. According to UV-Vis spectrophotometry data and gDNA and ribosomal RNA (rRNA) bands observed on the agarose gel, the results showed that extraction of this nano-kit can be comparable with the existing methods used to purifying nucleic acids such as purification based on the use of Cetyltrimethylammonium bromide (CTAB) and phenol-chloroform methods. Characterization of the particles defines them to be ~34.85 nm in diameter and exhibiting high saturation magnetization (28 emu/g). Elimination of hazardous reagents such as phenol and chloroform from extraction solutions, the replacement for inorganic coating such as silica with organic oil, and reduction of reaction time are some advantages of this method. Therefore, according to the challenges in the nucleic acid purification pathway, the use of these kits can be remarkable.

Comparison of RNA extraction methods for the detection of BNYVV rhizomania virus from roots of sugar beet.

Rhizomania is one of serious threat to sugar beet production in Morocco and in several parts of the world. This disease led to a statistically significant decrease in the quality and yield of sugar beet plantations. Therefore, this study aimed at comparing the efficacy of six commonly used RNA extraction methods for the detection, recovery of RNA of beet necrotic yellow vein virus (BNYVV) and removal of amplification inhibitors by reverse transcription-polymerase chain reaction (RT-PCR). The efficiency of these extraction methods was then compared to that of a commercial isolation kit with high content of phenolic compounds. The results showed that the extraction with the lithium chloride technique, the commercial kit, and direct and membrane spotting crude extract methods were found effective in yielding a higher purity and a higher concentration of RNA when compared to the other tested methods. Extraction with the lithium chloride technique and the Qiagen kit (RNeasy Plant Mini Kit) allowed the most intense band, whereas the CTAB method has generated the least intense band. Furthermore, the silica capture extraction method did not yield any RNA after extraction and electrophoresis. Consequently, it was concluded that, of these six methods, the lithium chloride technique and the Qiagen kit are the most appropriate for the extraction of viral RNA from sugar beet samples prior to RT-PCR for detecting BNYVV.

Fast and reliable dissection of porcine parathyroid glands - A protocol for molecular and histological analyses.

As calcium and phosphorus are of vital importance for life, physiological activity of the parathyroid glands (PTGs) is crucial to maintain mineral homeostasis and bone mineralization. However, PTG-specific molecular routes in response to environmental factors and intrinsic hormonal responses are not yet fully understood. Since nutrient requirements, pathophysiology and functional genomics of pigs are similar to those of humans, pigs might be a suitable model to study the holistic gene expression and physiological aspects of the parathyroid gland, which could be used in both animal sciences and biomedical research. However, due to their small size and hidden location, the dissection of the PTGs, particularly in pigs, is difficult. Therefore, a protocol for untrained dissectors has been established that allows a fast and reliable identification of the PTGs in domestic pigs. Based on their localization within the cranial thymus near the carotid bifurcation, sampling was verified by histological staining and mRNA expression pattern. Analyses revealed the prominence of parathyroid hormone (PTH)-producing chief cells. Moreover, the copy numbers of PTH differed substantially between the PTGs and their surrounding thymus tissue, as PTH was expressed virtually exclusively in the PTGs. The developed protocol will substantially facilitate a fast and reliable dissection of porcine PTGs which is essential for studies characterizing the molecular mechanisms of parathyroid glands, e.g. when applying new feeding strategies in pigs.

Transcriptional profiling of swine mammary gland during the transition from colostrogenesis to lactogenesis using RNA sequencing.

BACKGROUND: Colostrum and milk are essential sources of antibodies and nutrients for the neonate, playing a key role in their survival and growth. Slight abnormalities in the timing of colostrogenesis/lactogenesis potentially threaten piglet survival. To further delineate the genes and transcription regulators implicated in the control of the transition from colostrogenesis to lactogenesis, we applied RNA-seq analysis of swine mammary gland tissue from late-gestation to farrowing. Three 2nd parity sows were used for mammary tissue biopsies on days 14, 10, 6 and 2 before (-) parturition and on day 1 after (+) parturition. A total of 15 mRNA libraries were sequenced on a HiSeq2500 (Illumina Inc.). The Dynamic Impact Approach and the Ingenuity Pathway Analysis were used for pathway analysis and gene network analysis, respectively. RESULTS: A large number of differentially expressed genes were detected very close to parturition (-2d) and at farrowing (+ 1d). The results reflect the extraordinary metabolic changes in the swine mammary gland once it enters into the crucial phases of lactogenesis and underscore a strong transcriptional component in the control of colostrogenesis. There was marked upregulation of genes involved in synthesis of colostrum and main milk components (i.e. proteins, fat, lactose and antimicrobial factors) with a pivotal role of CSN1S2, LALBA, WAP, SAA2, and BTN1A1. The sustained activation of transcription regulators such as SREBP1 and XBP1 suggested they help coordinate these adaptations. CONCLUSIONS: Overall, the precise timing for the transition from colostrogenesis to lactogenesis in swine mammary gland remains uncharacterized. However, our transcriptomic data support the hypothesis that the transition occurs before parturition. This is likely attributable to upregulation of a wide array of genes including those involved in 'Protein and Carbohydrate Metabolism', 'Immune System', 'Lipid Metabolism', 'PPAR signaling pathway' and 'Prolactin signaling pathway' along with the activation of transcription regulators controlling lipid synthesis and endoplasmic reticulum biogenesis and stress response.

Evaluation of the Relationship Between the 18S rRNA/rDNA Ratio and Population Growth in the Marine Diatom Skeletonema tropicum via the Application of an Exogenous Nucleic Acid Standard.

Ribosomal RNA (rRNA) has been regarded as a proxy for metabolic activity and population growth in microbes, but the limitations and assumptions of this approach should be better defined, particularly in eukaryotic microalgae. In this study, the 18S rRNA/rDNA ratio of a marine diatom, Skeletonema tropicum, was examined in batch and semi-continuous cultures subjected to low nitrogen and phosphorus treatments at a temperature of 20 °C. In the semi-continuous cultures, the measured 18S rRNA/rDNA ratio ranged from 4.0 × 102 to 5.0 × 103 , and the logarithmic form of this ratio increased linearly with the population growth rate under both low nitrogen and low phosphorus conditions. In batch cultures grown under low nitrogen or low phosphorus conditions, log (rRNA/rDNA) also increased linearly with growth rate when the latter ranged between -0.4 and 1.5 day-1 . The 18S rRNA/rDNA ratios of Skeletonema sampled from in the southern East China Sea were substantially lower than measured from laboratory cultures. Among the field samples, ratios obtained at a coastal station were higher than those obtained farther offshore. These results imply higher growth rate at the coastal station, but the influences of other factors, such as cell size and temperature, cannot be ruled out.

CSCD: a database for cancer-specific circular RNAs.

Circular RNA (circRNA) is a large group of RNA family extensively existed in cells and tissues. High-throughput sequencing provides a way to view circRNAs across different samples, especially in various diseases. However, there is still no comprehensive database for exploring the cancer-specific circRNAs. We collected 228 total RNA or polyA(-) RNA-seq samples from both cancer and normal cell lines, and identified 272 152 cancer-specific circRNAs. A total of 950 962 circRNAs were identified in normal samples only, and 170 909 circRNAs were identified in both tumor and normal samples, which could be further used as non-tumor background. We constructed a cancer-specific circRNA database (CSCD, http://gb.whu.edu.cn/CSCD). To understand the functional effects of circRNAs, we predicted the microRNA response element sites and RNA binding protein sites for each circRNA. We further predicted potential open reading frames to highlight translatable circRNAs. To understand the association between the linear splicing and the back-splicing, we also predicted the splicing events in linear transcripts of each circRNA. As the first comprehensive cancer-specific circRNA database, we believe CSCD could significantly contribute to the research for the function and regulation of cancer-associated circRNAs.

RNA sequencing and proteomics approaches reveal novel deficits in the cortex of Mecp2-deficient mice, a model for Rett syndrome.

BACKGROUND: Rett syndrome (RTT) is an X-linked neurodevelopmental disorder caused by mutations in the transcriptional regulator MeCP2. Much of our understanding of MeCP2 function is derived from transcriptomic studies with the general assumption that alterations in the transcriptome correlate with proteomic changes. Advances in mass spectrometry-based proteomics have facilitated recent interest in the examination of global protein expression to better understand the biology between transcriptional and translational regulation. METHODS: We therefore performed the first comprehensive transcriptome-proteome comparison in a RTT mouse model to elucidate RTT pathophysiology, identify potential therapeutic targets, and further our understanding of MeCP2 function. The whole cortex of wild-type and symptomatic RTT male littermates (n = 4 per genotype) were analyzed using RNA-sequencing and data-independent acquisition liquid chromatography tandem mass spectrometry. Ingenuity® Pathway Analysis was used to identify significantly affected pathways in the transcriptomic and proteomic data sets. RESULTS: Our results indicate these two "omics" data sets supplement one another. In addition to confirming previous works regarding mRNA expression in Mecp2-deficient animals, the current study identified hundreds of novel protein targets. Several selected protein targets were validated by Western blot analysis. These data indicate RNA metabolism, proteostasis, monoamine metabolism, and cholesterol synthesis are disrupted in the RTT proteome. Hits common to both data sets indicate disrupted cellular metabolism, calcium signaling, protein stability, DNA binding, and cytoskeletal cell structure. Finally, in addition to confirming disrupted pathways and identifying novel hits in neuronal structure and synaptic transmission, our data indicate aberrant myelination, inflammation, and vascular disruption. Intriguingly, there is no evidence of reactive gliosis, but instead, gene, protein, and pathway analysis suggest astrocytic maturation and morphological deficits. CONCLUSIONS: This comparative omics analysis supports previous works indicating widespread CNS dysfunction and may serve as a valuable resource for those interested in cellular dysfunction in RTT.

Hypothalamic control systems show differential gene expression during spontaneous daily torpor and fasting-induced torpor in the Djungarian hamster (Phodopus sungorus).

Djungarian hamsters are able to use spontaneous daily torpor (SDT) during the winter season as well as fasting-induced torpor (FIT) at any time of the year to cope with energetically challenging environmental conditions. Torpor is a state of severely reduced metabolism with a pronounced decrease in body temperature, which enables animals to decrease their individual energy requirements. Despite sharing common characteristics, such as reduced body mass before first torpor expression and depressed metabolism and body temperature during the torpid state, FIT and SDT differ in several physiological properties including torpor bout duration, minimal body temperature, fuel utilization and circadian organization. It remains unclear, whether SDT and FIT reflect the same phenomenon or two different physiological states. The hypothalamus has been suggested to play a key role in regulating energy balance and torpor. To uncover differences in molecular control mechanisms of torpor expression, we set out to investigate hypothalamic gene expression profiles of genes related to orexigenic (Agrp/Npy), circadian clock (Bmal1/Per1) and thyroid hormone (Dio2/Mct8) systems of animals undergoing SDT and FIT during different torpor stages. Orexigenic genes were mainly regulated during FIT and remained largely unaffected by SDT. Expression patterns of clock genes showed disturbed circadian clock rhythmicity in animals undergoing FIT, but not in animals undergoing SDT. During both, SDT and FIT, decreased Dio2 expression was detected, indicating reduced hypothalamic T3 availability in both types of torpor. Taken together, our results provide evidence that SDT and FIT also differ in certain central control mechanisms and support the observation that animals undergoing SDT are in energetical balance, whereas animals undergoing FIT display a negative energy balance. This should be carefully taken into account when interpreting data in torpor research, especially from animal models of fasting-induced hypometabolism such as mice.

Transcriptome analysis reveals molecular anthelmintic effects of procyanidins in C. elegans.

Worldwide, more than 1 billion people are affected by infestations with soil-transmitted helminths and also in veterinary medicine helminthiases are a severe threat to livestock due to emerging resistances against the common anthelmintics. Proanthocyanidins have been increasingly investigated for their anthelmintic properties, however, except for an interaction with certain proteins of the nematodes, not much is known about their mode of action. To investigate the anthelmintic activity on a molecular level, a transcriptome analysis was performed in Caenorhabditis elegans after treatment with purified and fully characterized oligomeric procyanidins (OPC). The OPCs had previously been obtained from a hydro-ethanolic (1:1) extract from the leaves of Combretum mucronatum, a plant which is traditionally used in West Africa for the treatment of helminthiasis, therefore, also the crude extract was included in the study. Significant changes in differential gene expression were observed mainly for proteins related to the intestine, many of which were located extracellularly or within cellular membranes. Among the up-regulated genes, several hitherto undescribed orthologues of structural proteins in humans were identified, but also genes that are potentially involved in the worms' defense against tannins. For example, T22D1.2, an orthologue of human basic salivary proline-rich protein (PRB) 2, and numr-1 (nuclear localized metal responsive) were found to be strongly up-regulated. Down-regulated genes were mainly associated with lysosomal activity, glycoside hydrolysis or the worms' innate immune response. No major differences were found between the groups treated with purified OPCs versus the crude extract. Investigations using GFP reporter gene constructs of T22D1.2 and numr-1 corroborated the intestine as the predominant site of the anthelmintic activity. The current findings support previous hypotheses of OPCs interacting with intestinal surface proteins and provide the first insights into the nematode's response to OPCs on a molecular level as a base for the identification of future drug targets.

Maternal polycyclic aromatic hydrocarbon (PAH) transfer and effects on offspring of copepods exposed to dispersed oil with and without oil droplets.

Copepods of the genus Calanus have the potential for accumulating lipophilic oil components due to their high lipid content and found to filter and ingest oil droplets during exposure. As female copepods produce eggs at the expense of lipid storage, there is a concern for transfer of lipophilic contaminants to offspring. To assess the potential for maternal transfer of oil components, ovigerous female copepods (Calanus finmarchicus) were exposed to filtered and unfiltered oil dispersions for 4 days, collected and eggs maintained in clean seawater and hatching and gene expression examined in hatched nauplii. Oil droplet exposure contributed to polycyclic aromatic hydrocarbon (PAH) uptake in dispersion-treated adult copepods, as displayed through PAH body residue analyses and fluorescence microscopy. Applying the latter methodology, transfer of heavy PAH from copepod mothers to offspring were detected Subtle effects were observed in offspring as evidenced by a temporal reduction in hatching success appear to be occurring only when mothers were exposed to the unfiltered oil dispersions. Offspring reared in clean water through to late naupliar stages were collected for RNA extraction and preparation of libraries for high-throughput transcriptome sequencing. Differentially expressed genes were identified through pairwise comparisons between treatments. Among these, several expressed genes have known roles in responses to chemical stress including xenobiotic metabolism enzymes, antioxidants, chaperones, and components of the inflammatory response. While gene expression results suggest a transgenerational activation of stress responses, the increase in relatively small number of differentially expressed genes suggests a minor long-term effect on offspring following maternal exposure.

A Systems Biology Approach Using Transcriptomic Data Reveals Genes and Pathways in Porcine Skeletal Muscle Affected by Dietary Lysine.

Nine crossbred finishing barrows (body weight 94.4 ± 6.7 kg) randomly assigned to three dietary treatments were used to investigate the effects of dietary lysine on muscle growth related metabolic and signaling pathways. Muscle samples were collected from the longissimus dorsi of individual pigs after feeding the lysine-deficient (4.30 g/kg), lysine-adequate (7.10 g/kg), or lysine-excess (9.80 g/kg) diet for five weeks, and the total RNA was extracted afterwards. Affymetrix Porcine Gene 1.0 ST Array was used to quantify the expression levels of 19,211 genes. Statistical ANOVA analysis of the microarray data showed that 674 transcripts were differentially expressed (at p ≤ 0.05 level); 60 out of 131 transcripts (at p ≤ 0.01 level) were annotated in the NetAffx database. Ingenuity pathway analysis showed that dietary lysine deficiency may lead to: (1) increased muscle protein degradation via the ubiquitination pathway as indicated by the up-regulated DNAJA1, HSP90AB1 and UBE2B mRNA; (2) reduced muscle protein synthesis via the up-regulated RND3 and ZIC1 mRNA; (3) increased serine and glycine synthesis via the up-regulated PHGDH and PSPH mRNA; and (4) increased lipid accumulation via the up-regulated ME1, SCD, and CIDEC mRNA. Dietary lysine excess may lead to: (1) decreased muscle protein degradation via the down-regulated DNAJA1, HSP90AA1, HSPH1, and UBE2D3 mRNA; and (2) reduced lipid biosynthesis via the down-regulated CFD and ME1 mRNA. Collectively, dietary lysine may function as a signaling molecule to regulate protein turnover and lipid metabolism in the skeletal muscle of finishing pigs.