RNA-Seq Transcriptome Analysis of the Liver and Brain of the Black Carp (Mylopharyngodon piceus) During Fasting.

The black carp (Mylopharyngodon piceus) is an important carnivorous freshwater-cultured species. To understand the molecular basis underlying the response of black carp to fasting, we used RNA-Seq to analyze the liver and brain transcriptome of fasting fish. Annotation to the NCBI database identified 66,609 unigenes, of which 22,841 were classified into the Gene Ontology database and 15,925 were identified in the Kyoto Encyclopedia of Genes and Genomes (KEGG) database. Comparative analysis of the expression profile between fasting and normal feeding fish revealed 13,737 differentially expressed genes (P < 0.05), of which 12,480 were found in liver tissue and 1257 were found in brain tissue. The KEGG pathway analysis showed significant differences in expression of genes involved in metabolic and immune pathways, such as the insulin signaling pathway, PI3K-Akt signaling pathway, cAMP signaling pathway, FoxO signaling pathway, AMPK signaling pathway, endocytosis, and apoptosis. Quantitative real-time PCR analysis confirmed that expression of the genes encoding the factors involved in those pathways differed between fasting and feeding fish. These results provide valuable information about the molecular response mechanism of black carp under fasting conditions.

Complete mitochondrial genome of gray black carp (Mylopharyngodon piceus).

The black carp (Mylopharyngodon piceus), native to eastern Asian, is a large, commercially valuable fish, and has been widely introduced to other countries. In this study, the mitochondrial gene sequence of gray black carp (M. piceus MT084757) in Foshan, Guangdong Province was first determined using the Sanger sequencing method. The mitochondrial DNA genome was 16,616 bp in length, including 13 protein-coding genes (PCGs), two rRNA genes, 22 transfer RNA genes, and a non-coding control region (D-loop). The overall nucleotide composition of the mitochondrial DNA is 32.04% A, 24.52% T, 15.68% C, 27.76% G, with 56.56% AT, respectively. Phylogenetic tree analysis suggests that the gray black carp (M. piceus MT 084757) is closely related to Elopichthys bambus and Squaliobarbus curriculus. The complete mitochondrial genome of the gray black carp (M. piceus MT 084757) would be useful for researching the causes of changes in body color.

Cloning and transcriptional activity analysis of the porcine cofilin 2 gene promoter.

Cofilins (CFL), including CFL1 and CFL2, are members of the family of actin-binding proteins in eukaryote. CFL2 is predominantly expressed in mammalian skeletal muscle and heart and is important to muscle fiber formation and muscular regeneration. To study transcriptional regulation of porcine CFL2, a 2.5 kb upstream sequence starting from the major CFL2 transcriptional start site was cloned by genome walking. Twelve DNA fragments of the 5' flank region of the porcine CFL2 gene were further isolated from porcine genomic DNA via PCR and inserted into the luciferase reporter vector pGL4.10 to make 12 CFL2 reporter constructs. All reporter vectors were transfected into C2C12, NIH3T3, or Hela cells and their relative luciferase activity measured after 48 h, respectively. Bioinformatics analysis suggested that there were two TATA-boxes at the -508 bp and -453 bp, as well as a GC-box and a CAAT-box in this sequence. Additional transcription factor binding sites including SP1, AP1, AP2, and GATA-1 sites were also predicted. The transcriptional activity of pGL4.10-1554 (1502 bp to +51 bp) was the strongest, and the promoter's active region was mapped to a region from -1502 bp to -1317 bp. Our data provide a foundation for future studies into transcriptional regulation of CFL2.

Single-nucleotide polymorphisms and activity analysis of the promoter and enhancer of the pig lactase gene.

Lactose intolerance in northern Europeans is strongly associated with a single-nucleotide polymorphism (SNP) located 14 kb upstream of the human lactase gene: -13,910 C/T. We examined whether SNPs in the 5' flanking region of the pig lactase gene are similar to those in the human gene and whether these polymorphisms play a functional role in regulating pig lactase gene expression. The 5' flanking region of the lactase gene from several different breeds of pigs was cloned and analyzed for gene regulatory activity of a luciferase reporter gene. One SNP was found in the enhancer region (-797 G/A) and two were found in the promoter region (-308G/C and -301 A/G). The promoter C-308,G-301(Pro-CG) strongly promotes the expression of the lactase gene, but the promoter G-308,A-301(Pro-GA) does not. The enhancer A-797(Enh-A) genotype for Pro-GA can significantly enhance promoter activity, but has an inhibitory effect on Pro-CG. The Enhancer G-797(Enh-G) has a significant inhibitory effect on both promoters. In conclusion, the order of effectiveness on the pig lactase gene is Enh-A+Pro-GA>Enh-A/G+Pro-CG>Enh-G+Pro-GA.

Impact of reclaimed water irrigation on antibiotic resistance in public parks, Beijing, China.

The abundance and distribution of antibiotics and antibiotic resistance genes (ARGs) in soils from six parks using reclaimed water in Beijing, China, were characterized. Three classes of commonly used antibiotics (tetracycles, quinolones, and sulfonamides) were analyzed by liquid chromatography-tandem mass spectrometry (LC-MS/MS). The highest concentrations of tetracyclines and quinolones were 145.2 µg kg(-1) and 79.2 µg kg(-1), respectively. Detected tetG, tetW, sulI, and sulII genes were quantified by quantitative PCR. ARGs exhibited various abundances for different park soils. The integrase gene (intI1) as an indicator of horizontal gene transfer potential was also detected in high abundance, and had significant positive correlation with tetG, sulI, and sulII genes, suggesting that intI1 may be involved in ARGs dissemination. Both sulII and intI1 clones had high homology with some classes of pathogenic bacteria, such as Klebsiella oxytoca, Acinetobacter baumannii, Shigella flexneri, which could trigger potential public health concern.

The role of the rice aquaporin Lsi1 in arsenite efflux from roots.

*When supplied with arsenate (As(V)), plant roots extrude a substantial amount of arsenite (As(III)) to the external medium through as yet unidentified pathways. The rice (Oryza sativa) silicon transporter Lsi1 (OsNIP2;1, an aquaporin channel) is the major entry route of arsenite into rice roots. Whether Lsi1 also mediates arsenite efflux was investigated. *Expression of Lsi1 in Xenopus laevis oocytes enhanced arsenite efflux, indicating that Lsi1 facilitates arsenite transport bidirectionally. *Arsenite was the predominant arsenic species in arsenate-exposed rice plants. During 24-h exposure to 5 mum arsenate, rice roots extruded arsenite to the external medium rapidly, accounting for 60-90% of the arsenate uptake. A rice mutant defective in Lsi1 (lsi1) extruded significantly less arsenite than the wild-type rice and, as a result, accumulated more arsenite in the roots. By contrast, Lsi2 mutation had little effect on arsenite efflux to the external medium. *We conclude that Lsi1 plays a role in arsenite efflux in rice roots exposed to arsenate. However, this pathway accounts for only 15-20% of the total efflux, suggesting the existence of other efflux transporters.

[Genetic polymorphism of 15 STR loci in Tibetan population].

The polymorphism distributions of 15 STR loci (D8S1179, D21S11, D7S820, CSF1PO, D3S1358, TH01, D13S317, D16S539, D2S1338, D19S433, VWA, TPOX, D18S51, D5S818, and FGA) were investigated in a Tibetan population by multiplex PCR amplification using five fluorochromes (6FAM, VIC, NED, PET, LIZ). Gene frequency, discrimination power (DP), heterozygosity (H), polymorphism information content (PIC) and probability of paternity exclusion (EPP) were calculated, and all loci were tested for Hardy-Weinberg equilibrium. Results indicate that the gene frequency of these 15 STR loci is in Hardy-Weinberg equilibrium. The DP is at 0.7555-0.9602, H is at 0.5651-0.8530, PIC is at 0.5528-0.8456, and EPP is at 0.3811-0.8549. Cumulative DP of the 15 STR is 0.99999999, and cumulative EPP is 0.999999997. Therefore, these 15 STR loci can be used as genetic markers of Tibetan populations in anthropological studies, linkage analysis of genetic diseases, individual identification and paternity testing in forensic medicine.

Transporters of arsenite in rice and their role in arsenic accumulation in rice grain.

Arsenic poisoning affects millions of people worldwide. Human arsenic intake from rice consumption can be substantial because rice is particularly efficient in assimilating arsenic from paddy soils, although the mechanism has not been elucidated. Here we report that two different types of transporters mediate transport of arsenite, the predominant form of arsenic in paddy soil, from the external medium to the xylem. Transporters belonging to the NIP subfamily of aquaporins in rice are permeable to arsenite but not to arsenate. Mutation in OsNIP2;1 (Lsi1, a silicon influx transporter) significantly decreases arsenite uptake. Furthermore, in the rice mutants defective in the silicon efflux transporter Lsi2, arsenite transport to the xylem and accumulation in shoots and grain decreased greatly. Mutation in Lsi2 had a much greater impact on arsenic accumulation in shoots and grain in field-grown rice than Lsi1. Arsenite transport in rice roots therefore shares the same highly efficient pathway as silicon, which explains why rice is efficient in arsenic accumulation. Our results provide insight into the uptake mechanism of arsenite in rice and strategies for reducing arsenic accumulation in grain for enhanced food safety.

Uptake of selected PAHs from contaminated soils by rice seedlings (Oryza sativa) and influence of rhizosphere on PAH distribution.

The uptake of selected polycyclic aromatic hydrocarbons (PAHs) by rice (Oryza sativa) seedlings from spiked aged soils was investigated. When applied to soils aged for 4 months, naphthalene, phenanthrene, and pyrene exhibited volatilization loss of 98, 95, and 30%, respectively, with the remaining fraction being fixed by soil organic matter and/or degraded by soil microbes. In general, concentrations of the three PAHs in rice roots were greater than those in the shoots. The concentrations of root associated PHN and PYR increased proportionally with both soil solution and rhizosphere concentrations. PAH concentrations in shoots were largely independent of those in soil solution, rice roots, or rhizosphere soil. The relative contributions of plant uptake and plant-promoted rhizosphere microbial biodegradation to the total mass balance were 0.24 and 14%, respectively, based on PYR concentrations in rhizosphere and non-rhizosphere soils, the biomass of rice roots, and the dry soil weight.

delta-Opioid receptor stimulation enhances the growth of neonatal rat ventricular myocytes via the extracellular signal-regulated kinase pathway.

1. The aims of the present study were to determine whether delta-opioid receptor stimulation enhanced proliferation of and to investigate the role of the extracellular signal-regulated kinase (ERK) pathway in ventricular myocytes from neonatal rats. 2. At concentratins ranging from 10 nmol/L to 10 micromol/L, [D-Ala2,D-Leu5]enkephalin (DADLE) concentration-dependently promoted myocardial growth and DNA synthesis and altered the cytoskeleton. 3. At 1 micromol/L, DADLE also increased the expression and phosphorylation of ERK. 4. These effects of 1 micromol/L DADLE were abolished by 10 micromol/L naltrindole, a selective delta-opioid receptor antagonist, 10 nmol/L U0126, a selective ERK antagonist, 1 micromol/L staurosporine, an inhibitor of protein kinase (PK) C, and 100 micromol/L Rp-adenosine 3',5'-cyclic monophosphorothioate triethylammonium salt hydrate (Rp-cAMPS), an inhibitor of PKA. 5. In conclusion, delta-opioid receptor stimulation enhances the proliferation and development of the ventricular myocytes of neonatal rats. The ERK pathway and related signalling mechanisms, namely PKC and PKA, are involved.

[Chemical fixation of metals in soil using bone char and assessment of the soil genotoxicity].

We evaluate the effects of soil in situ remediation by application of bone char as a soil amendment based on chemical and biological assessment. The application of bone char decreased the Pb in the in the water soluble (WS), exchangeable (EX), carbonate-bound (CAR) and Fe-Mn oxides-Bound (Fe-Mn) fraction but increased the Pb in organic-bound (ORG) fraction indicating the decreased bioavailability of Pb. The application of bone char decreased the Cd, Cu and Zn in water soluble, exchangeable, carbonate-bound fraction by increasing substantial amounts of heavy metals in the ORG fraction or Residual (RES) fraction. The soil genotoxicity was evaluated using plant comet assay of root tip cells of Allium cepa L. and the results indicated that bone char application reduced genotoxcity of heavy metals, decreasing the DNA damages in plants which was consistent with the changes of the chemical forms of Pb, Cd, Cu and Zn indicating the changes of the chemical forms of heavy metals may be one of the reasons for decreased soil genotoxicity.

[Progress in animal models for inherited cataract].

Cataract is a serious public health problem. It is usually inherited as an autosomal dominant trait, although autosomal recessive and X-linked inheritance are seen less commonly. With the development of molecular biology techniques, a large number of inherited cataract models are produced, which will reveal the pathogenesis of cataracts and provide a new view for the development and physiology of the lens. In addition, these models also facilitate our understanding of the manner of inheritance, the effect of the environment and nutrition on the lens and provide clues for the diagnosis and treatment of cataracts. Here we presented the relative genes of the animal models for inherited cataract, mutation forms and its progress.

Transport mechanisms for the uptake of organic compounds by rice (Oryza sativa) roots.

Uptake of six organic compounds, dinitrobenzene (DNB), dinitrotoluene (DNT), lindan (LIN), 1,2,3-triclorobenzene (TCB), phenanthrene (PHN) and pyrene (PYR) by freshly excised rice roots and dead rice roots (heated for 40min at 105 degrees C) were investigated. Results indicated that the uptake by the two types of roots did not increase proportionally with those in external solution. There appears to be some special chemical function of root cells other than simple absorption by the cells. The contribution of this special function can be roughly estimated by deducting the partition uptake into cells from the total uptake. Both time-dependent uptake data and concentration-dependent uptake curves demonstrate that, DNT and DNB transport is achieved presumably mainly via the symplastic pathway, while PHN and PYR transport mainly via the apoplastic pathway. For LIN and TCB, apoplastic transport pathway plays major roles in the first 2h of uptake, then symplastic transport pathway dominates uptake.

Effects of exposure time and co-existing organic compounds on uptake of atrazine from nutrient solution by rice seedlings (Oryza sativa L.).

Root uptake of atrazine (ATR) by rice seedlings (Oryza sativa L.) from nutrient solution was investigated with exposure periods of 48, 96, and 240h. A similar ATR uptake was carried out with two co-existing organic compounds (o-chlorophenol (CP) and 2,4-dichlorophenol (DCP)) with 48h exposure. In contact with the seedlings, the ATR level in nutrient solution decreased sharply during the early exposure and then reached relatively steady levels after 48h. It was observed that the ATR levels within whole seedlings approached the estimated equilibrium partition limits in about 48h, according to the partition-limited model utilizing the measured plant water and organic matter contents and the ATR partition coefficients with whole seedlings. However, when roots and shoots were consisted separately, the detected ATR levels in roots were lower than estimated equilibrium limit while the levels in shoots exceeded the equilibrium limit. The data with roots suggested the occurrence of rapid ATR degradation in roots. The results with shoots are intrinsically consistent with the suggested complex formation of ATR with free metal ions in shoots. The ATR levels in roots and shoots varied to a moderate extent when the seedlings were exposed to different levels of ATR-CP-DCP mixtures. The variation results presumably from the interference of coexisting CP and DCP and the phytotoxicity of the mixed chemicals.

Linear adsorption of nonionic organic compounds from water onto hydrophilic minerals: silica and alumina.

To characterize the linear adsorption phenomena in aqueous nonionic organic solute-mineral systems, the adsorption isotherms of some low-molecular-weight nonpolar nonionic solutes (1,2,3-trichlorobenzene, lindane, phenanthrene, and pyrene) and polar nonionic solutes (1,3-dinitrobenzene and 2,4-dinitrotoluene) from single- and binary-solute solutions on hydrophilic silica and alumina were established. Toward this objective, the influences of temperature, ionic strength, and pH on adsorption were also determined. It is found that linear adsorption exhibits low exothermic heats and practically no adsorptive competition. The solute-solid configuration and the adsorptive force consistent with these effects were hypothesized. For nonpolar solutes, the adsorption occurs presumably by London (dispersion) forces onto a water film above the mineral surface. For polar solutes, the adsorption is also assisted by polar-group interactions. The reduced adsorptive forces of solutes with hydrophilic minerals due to physical separation by the water film and the low fractions of the water-film surface covered by solutes offer a theoretical basis for linear solute adsorption, low exothermic heats, and no adsorptive competition. The postulated adsorptive forces are supported by observations that ionic strength or pH poses no effect on the adsorption of nonpolar solutes while it exhibits a significant effect on the uptake of polar solutes.

[Genetic polymorphism of 15 STR loci in a Lhasa Tibetan population].

The polymorphism distributions of 15 STR loci (D8S1179, D21S11, D7S820, CSF1PO, D3S1358, TH01, D13S317, D16S539, D2S1338, D19S433, VWA, TPOX, D18S51, D5S818 and FGA) were investigated in a Lhasa Tibetan population by multiplex PCR amplification using five fluorochromes (6FAM, VIC, NED, PET, LIZ). Gene frequency, discrimination power (DP), heterozygosity (H), polymorphism information content (PIC) and probability of paternity exclusion (EPP) were calculated, and all loci were tested for Hardy-Weinberg equilibrium. Results indicate that the gene frequency of these 15 STR loci is in Hardy-Weinberg equilibrium. The DP is at 0.7515 - 0.9599, H is at 0.5576 - 0.8538, PIC is at 0.5455 - 0.8458, and EPP is at 0.37550.8520. Cumulative DP of the 15 STR is 0.99999999, and cumulative EPP is 0.999999997. Therefore, these 15 STR loci can be used as genetic markers of in Lhasa Tibetan populations in anthropological studies, linkage analysis of genetic diseases, individual identification and paternity testing in forensic medicine.

[Relationship between MC4R gene polymorphyism and body weight trait in beagle dogs].

The relationship between MC4R gene polymorphism and body weight in beagle dogs was analyzed. Using gene-specific primers based on canine MC4R exonic sequences a gene fragment was PCR amplified, cloned and sequenced to identify potential polymorphisms. The relationship between a MC4R gene polymorphism detected by PCR-RFLP and canine body weight was analyzed. Three variants were found in beagle dog MC4R DNA sequence, of which two were deletions and one was a transversion which created a PshA I site that could be detected by PCR-RFLP. A statistically significant relationship between this polymorphism and body weight was found. MC4R gene could be a candidate modifier gene for canine body weight.

[DNA damages and apoptosis induced by cd in the leaves of horsebean Vicia faba].

DNA damages and programmed cell death in leaves of Vicia faba induced by Cd were studied with methods including alkaline/alkaline, alkaline/neutral, neutral/neutral comet assay and DAPI staining. Types of DNA damages induced by Cd were different detected by three types of comet assay. Single strand breakage and alkali labile sites were detected in the leaves of Vicia faba with 5 mg x L(-1) Cd treatment by alkaline/alkaline comet assay. With 10 mg x L(-1) Cd treatments, double strand breakages began to be detected by neutral/neutral comet assay. However, single strand breakages and alkali labile sites were still the main types of DNA damages. Three types of DNA damages increased significantly with 20 mg x L(-1) Cd treatment especially double strand breakages. These results indicated that DNA damages increased with increasing of Cd concentration, which was consistent with the programmed cell death induced by Cd. The result of apoptosis detected by DAPI staining indicated that there existed a relationship between apoptosis and DNA damage. These results indicated that Cd was an element with high genotoxicity and DNA damage was one of the mechanisms of cell apoptosis induced by Cd.

Bioconcentration of atrazine and chlorophenols into roots and shoots of rice seedlings.

Accumulation of o-chlorophenol (CP), 2,4-dichlorophenol (DCP), and atrazine (ATR), as single and mixed contaminants, from hydroponic solutions into roots and shoots of rice seedlings was studied following 48-h exposure of the plant roots. As single contaminants at low levels, the observed bioconcentration factors (BCFs) of CP and DCP with roots approximated the equilibrium values according to the partition-limited model. The BCF of atrazine with roots was about half the partition limit for unknown reasons. The BCFs of CP and ATR with shoots also approximated the partition limits, while the BCF for more lipophilic DCP with shoots was about half the estimated limit, due to insufficient water transport into plants for DCP. As mixed contaminants at low levels, the BCFs with both roots and shoots were comparable with those for the single contaminants; at high levels, the BCFs generally decreased because of the enhanced mixed-contaminant phytotoxicity, as manifested by the greatly reduced plant transpiration rate.

Interaction between cadmium and atrazine during uptake by rice seedlings (Oryza sativa L.).

The uptake of atrazine by rice seedlings (Oryza sativa L.) through plant roots from nutrient solution was investigated in the presence and absence of Cd2+ over an exposure period of four weeks. It was found that both atrazine and Cd2+ were toxic to rice seedlings. Both shoot and root biomasses decreased when the seedlings were exposed to increasing atrazine or Cd2+ concentrations in nutrient solutions. In the absence of Cd2+, a linear relationship was observed between atrazine concentrations in roots/shoots and in external solution, and more atrazine is concentrated in roots than in shoots. When atrazine and Cd2+ concentrations in solution were maintained at mole ratio of 1:1, the accumulation of atrazine by seedlings was less and the seedling biomass was greater than found with other ratios, such as 1:2 or 2:1. Therefore, the formation of the complex between atrazine and Cd2+ reduced the individual toxicities. Analyses of data with the quasi-equilibrium partition model indicated that the atrazine concentrations in rice seedlings and external water were close to equilibrium. In the presence of Cd2+, however, the measured bioconcentration factor (BCF) of atrazine with roots and shoots were considerably greater. The latter findings resulted presumably from the atrazine-Cd2+ complex formation that led to a large apparent BCF.