Toxicogenomic biomarkers for liver toxicity

Toxicogenomics (TGx) is a widely used technique in the preclinical stage of drug development to investigate the molecular mechanisms of toxicity. A number of candidate TGx biomarkers have now been identified and are utilized for both assessing and predicting toxicities. Further accumulation of novel TGx biomarkers will lead to more efficient, appropriate and cost effective drug risk assessment, reinforcing the paradigm of the conventional toxicology system with a more profound understanding of the molecular mechanisms of drug-induced toxicity. In this paper, we overview some practical strategies as well as obstacles for identifying and utilizing TGx biomarkers based on microarray analysis. Since clinical hepatotoxicity is one of the major causes of drug development attrition, the liver has been the best documented target organ for TGx studies to date, and we therefore focused on information from liver TGx studies. In this review, we summarize the current resources in the literature in regard to TGx studies of the liver, from which toxicologists could extract potential TGx biomarker gene sets for better hepatotoxicity risk assessment.     

Diffusive separation of the lower atmosphere

The separation of atmospheric constituents by gravity has been proposed theoretically for almost two centuries. However, turbulent mixing has prevented the detection of this phenomenon in the lower atmosphere. By using precise measurements of the Ar/N2 ratio of air samples taken under strong nocturnal inversions, we have detected such separation in near-surface layers. The effect is shown to be consistent with combined influence of thermal and gravimetric separation, with the thermal contribution being more important.     

Effects of 5'-uridylic acid feeding on postprandial plasma concentrations of metabolites and metabolic hormones in pre-weaning goats

5'-Uridylic acid (UMP), which is present at high concentrations in cow's colostrum, has been shown to cause a reduction in increased plasma levels of insulin and glucose after ingestion of milk replacer in pre-weaning calves. However, the precise mechanisms of UMP action have not been investigated, and its action has not been investigated in other pre-weaning ruminants. In order to demonstrate whether UMP causes changes in postprandial metabolic and hormonal parameters in pre-weaning goats, 11 Saanen kids were given milk replacer (twice a day) without ( n  = 5) or with ( n  = 6) UMP (1 g for each meal, 2 g/day for each head) for 14 days. Analysis of blood samples taken in the morning of day 14 demonstrated that the feeding of milk replacer with UMP abolished the significant changes in postprandial plasma glucose, NEFA, GH and insulin concentrations induced by feeding of milk replacer alone, and demonstrated a tendency to increase IGF-I levels. However, there was no significant difference between the two groups at any sampling time. We conclude that UMP feeding with milk replacer showed a tendency to blunt the postprandial changes in levels of some plasma metabolites and hormones that are induced by replacer alone in pre-weaning goats.     

Successful interspecific hybridization between Cucumis sativus L. and C. hystrix Chakr.

Interspecific F₁ hybrids were obtained from a cross between Cucumis sativus L. (2n = 2x = 14) and C. hystrix Chakr. (2n = 2x = 24). Controlled crossing resulted in fruit containing embryos which were excised and rescued on a Murashige and Skoog solid medium. A total of 59 vigorous plants were obtained from a fruit containing 159 embryos (37.3% regeneration rate). Hybrid plants were morphologically uniform. The multiple branching habit, densely brown hairs (especially on corolla and pistil), orange-yellow collora, and ovate fruit of F₁ hybrid plants were similar to that of the C. hystrix paternal parent. While appearance of the first pistillate flower was more similar to that of C. sativus maternal parent than to C. hystrix, staminate flower appearance was mid-parent in occurence. The diameter and internode length of stem, shape and size of leaves and flowers were intermediate when compared to the parents. An elongated green, trilobate style/stigma which was not apparent in either parent was observed in staminate flowers of F₁ plants. Similarly, the style/stigma of pistillate flower of F₁ plants were longger when compared to their parents. The brown pubescence observed on pistillate flowers of the F₁ and C. hystrix was not observed on the C. sativus parent. The somatic chromosome number of F₁ plants was 19. Two morphologically distinct groups of chromosomes were observed in the F₁ hybrid; 7 relatively large chromosomes characteristic of C. sativus, and 12 smaller chromosomes characteristic of C. hystrix. Analysis of malate dehydrogenase isozyme banding patterns provided additional comfirmation of hybridity. Reciprocal crossing of F₁ plants to either parent and self-crossing indicated that the hybrids were male and female sterile. This revised version was published online in July 2006 with corrections to the Cover Date.     

A novel black tea pigment and two new oxidation products of epigallocatechin-3-O-gallate

During tea fermentation, oxidation-reduction dismutation of a number of quinone metabolites of tea catechins yields numerous minor products, which make it difficult to separate and purify black tea polyphenols. In this study, epigallocatechin-3-O-gallate was enzymatically oxidized and then the unstable quinone metabolites in the oxidation mixture were hydrogenated with 2-mercaptoethanol to reduce production of inseparable minor dismutation products. As a result, three new oxidation products including a new black tea pigment were isolated, and their structures were determined based on chemical and spectroscopic data. Dehydrotheasinensin AQ is a new reddish-orange pigment with a 1,2-diketone structure, and its presence in commercial black tea was confirmed. In addition, a new quinone dimer with a complex caged structure and a trimer of epigallocatechin-3-O-gallate were also isolated and their production mechanisms are proposed. The presence of this trimer suggested participation of galloyl quinones in production of minor polyphenols in black tea.     

Differential heterosis in a natural population of Asian wild rice (<Emphasis Type="Italic">Oryza rufipogon</Emphasis> Griff.) due to reproductive strategy and edge effect

Asian common wild rice (Oryza rufipogon) is a polycarpic perennial plant with a mixed inbreeder/outbreeder strategy. Seeds and clones are both reproductive components of the population. However, when collected in the flowering stage, the two differ substantially as to whether they have experienced natural selection directly or not. This study is aimed at evaluating mechanisms for the survival of a population by comparing genetic structure among subpopulations that are classified in terms of: (1) reproductive systems (clones or seeds); and also (2) location (fringe or inside). First, the genotypes determined at seven SSR (Simple Sequence Repeat) loci showed that parameters of observed heterozygosity (H_O) and outcrossing rate (t) were clearly higher in clones (H_O = 0.609, t = 82.4%) than in seeds (H_O = 0.346, t = 35.5%), although the two had approximately the same values for the number of alleles (A) and expected heterozygosity (H_E)(A = 4.43 in both clones and seeds, H_E = 0.709, 0.692 in clones and seeds, respectively). This result indicates that the individuals showing heterosis, with high numbers of heterozygous loci and outcrossing rates, are more likely to survive in the natural habitat. Secondly, parameters of observed heterozygosity and outcrossing rates were lower for seeds from the fringe area (H_O = 0.238, t = 24.6%) compared to seeds from the inside area (H_O = 0.443, t = 60.7%), although values were similar in clones of both the fringe and inside areas. This result suggests that the edge effect might be due mainly to the restriction of wind strength in fringe area of the forested swamp.     

Population genetic structure and diversity of the East Balkan Swine (Sus scrofa) in Bulgaria,revealed by mitochondrial DNA and microsatellite analyses

The East Balkan Swine (EBS) is the only indigenous pig breed in Bulgaria. We analyzed the mitochondrial DNA (mtDNA) control region and 21 microsatellite loci for 198 individuals from 11 farms in Bulgaria. Obtained 11 mtDNA haplotypes including three novel ones were grouped to two major clades, European clade E1 (146/198 individuals, 73.7%) and Asian clade A (52/198, 26.3%). The mixture of the two clades may have resulted from historical crossbreeding between the European and Asian pig breeds. Clade A was frequent in southeastern Bulgaria (Burgas Province), but less frequent or absent in northeastern Bulgaria (Varna and Shumen Provinces). The distribution of Europe- and Asia-specific haplotypes relative to EBS farm locations could be attributed to regional differences of breeding systems (e.g., crossbreeding with imported commercial pigs). A microsatellite analysis showed high heterozygosities for all the EBS farms, and negative inbreeding coefficients presumably due to crossing with commercial pigs or wild boars and/or efforts to reduce inbreeding by farmers. Bayesian clustering analyses showed that all farm populations are genetically well distinguishable from one another. Although diversity has been maintained by the efforts of farmers and a breeding association, the effective population size remains small, and conservation efforts should be continued.     

Genetic variation detected with random amplified polymorphicDNA markers among isolates of the red rot disease fungus Pythiumporphyrae isolated from Porphyra yezoensis from Koreaand Japan

ABSTRACT:   Genetic variation of the fungal parasite Pythium porphyrae ,causative organism of red rot disease of Porphyra , isolatedfrom Asan, Mokpo, Pusan and Wando in Korea, and from Aichi, Fukuokaand Miyagi in Japan was investigated by random amplified polymorphicDNA (RAPD) cluster analysis. The total 67 RAPD markers were generatedfrom 38 isolates by RAPD-polymerase chain reaction (PCR) using arbitraryprimers consisting of 10 nucleotide sequences and 33 of them indicatedpolymorphisms. The dissimilarity coefficients calculated from theRAPD banding patterns ranged from 0.0010 to 0.6983. The dendrogramgenerated by the unweighted pair-group method using arithmetic averagesshowed that the 38 isolates were classified into three clusters(Groups 1, 2 and 3). Group 1 consisting of two isolates from Miyagiwas separated from all other isolates by a genetic distance of 0.6983.Groups 2 and 3 containing the majority of the isolates were branchedon genetic distance of 0.3957. These two clusters subdivided intofour and three subclusters, respectively, which were apparentlyassociated with geographic origins of the isolates. Interestingly,the isolates from Asan of Korea were close to Japanese isolatesrather than Korean isolates on genetic diversity. In addition, thegenetic distances of intra-isolates from Japan were higher thanthose from Korea.     

Immunological detection of translation products of type V/XI collagen α1 gene and their degradation products in red sea bream muscle

We previously cloned cDNA of type V/XI collagen α1 chain (ColVa1) gene from cultured cells derived from red sea bream embryo. We raised an antibody against the deduced C-telopeptide of ColVa1 in order to detect the translation products of this cDNA and their degradation products in red sea bream muscle. To improve its specificity, the antibody was purified from rabbit antiserum by use of an affinity column cross-linked with recombinant C-terminal peptide of ColVa1 produced by Epicurian coli. The purified antibody recognized a band corresponding to the α chain of type V/XI collagen in western blot analysis of the extract of cultured cells. The antibody also recognized two bands in acid-soluble and pepsin-solubilized collagens, indicating that the translation products of the ColVa1 gene are present in muscle and that bands correspond to α and β chains of type V/XI collagen. A band corresponding to a molecular weight of approximately 65 k was detected in the NaOH extracts of muscle, suggesting that type V/XI collagen α1 chain is restrictedly digested in red sea bream muscle.     

Time-dependent central compensatory mechanisms of finger dexterity after spinal cord injury

Transection of the direct cortico-motoneuronal pathway at the mid-cervical segment of the spinal cord in the macaque monkey results in a transient impairment of finger movements. Finger dexterity recovers within a few months. Combined brain imaging and reversible pharmacological inactivation of motor cortical regions suggest that the recovery involves the bilateral primary motor cortex during the early recovery stage and more extensive regions of the contralesional primary motor cortex and bilateral premotor cortex during the late recovery stage. These changes in the activation pattern of frontal motor-related areas represent an adaptive strategy for functional compensation after spinal cord injury.