Zebrafish model of photochemical thrombosis for translational research and thrombolytic screening in vivo

Acute thromboembolic diseases remain the major global cause of death or disability. Although an array of thrombolytic and antithrombotic drugs has been approved to treat or prevent thromboembolic diseases, many more drugs that target specific clotting mechanisms are under development. Here a novel zebrafish model of photochemical thrombosis is reported and its prospective application for the screening and preclinical testing of thrombolytic agents in vivo is demonstrated. Through photochemical excitation, a thrombus was induced to form at a selected section of the dorsal aorta of larval zebrafish, which had been injected with photosensitizers. Such photochemical thrombosis can be consistently controlled to occlude partially or completely the targeted blood vessel. Detailed mechanistic tests indicate that the zebrafish model of photochemical thrombosis exhibits essential features of classical coagulation and a thrombolytic pathway. For demonstration, tissue plasminogen activator (tPA), a clinically feasible thrombolytic agent, was shown to effectively dissolve photochemically induced blood clots. In light of the numerous unique advantages of zebrafish as a model organism, our approach is expected to benefit not only the development of novel thrombolytic and antithrombotic strategies but also the fundamental or translational research targeting hereditary thrombotic or coagulation disorders.

     

The effects of simulated nitrogen deposition on extracellular enzyme activities of litter and soil among different-aged stands of larch

Aims Nitrogen (N) addition could affect the rate of forest litter and soil organic matter decomposition by regulating extracellular enzyme activity (EEA). The impact of N addition on EEA may differ across different age stands with different organic matter quality. We were interested in whether the impact of N addition on EEA in litter and mineral soil during the growing season was dependent on stand age of a larch plantation in North China.Methods We added three levels of N (0, 20 and 50kg N ha^-1 year^-1) in three age stands (11, 20 and 45 years old) of Larix principis-rupprechtii plantation in North China. We measured potential activities of β-1,4-glucosidase (BG), cellobiohydrolase (CB), β-1,4-N-acetyl-glucosaminidase (NAG) and phenol oxidase (PO) in litter (organic horizon) and mineral soil (0–10cm) during the second growing season after N amendment. We also measured C and N concentrations, microbial biomass C and N, and KCl-extractable ammonium and nitrate in both litter and mineral soil.Important findings We observed unimodal patterns of EEA during the growing season in all three stands, consistent with the seasonal variations of soil temperature. Stand age had a strong effect on EEA in both litter and mineral soil, and this effect differed between litter and mineral soil as well as between different enzymes. N addition did not significantly affect the activities of BG or CB but significantly suppressed the activity of NAG in litter. We also found stand age-specific responses of PO activity to N addition in both litter and mineral soil. N addition suppressed PO activity of the high C:N ratio litters in 20- and 45-year-old stands but had no significant effect on PO activity of the low C:N ratio litter in 11-year-old stand. Moreover, N addition inhibited PO activity of the high C:N ratio soil in 20-year-old stand but had no significant impact on PO activity of the low C:N ratio soils in 11- and 45-year-old stands. Overall, stand age had a greater effect on EEA in litter and mineral soil compared to 2 years of N addition. Moreover, the effect of N addition on PO activity is stand age dependent, which may affect the long-term soil carbon storage in this forest.     

Change in Vascular Adhesion Protein‐1 and Metabolic Phenotypes after Vertical Banded Gastroplasty for Morbid Obesity

Objective: The association between circulating vascular adhesion protein‐1 (VAP‐1) and metabolic phenotypes has been shown to be inconsistent. The current study explored whether the changes in serum VAP‐1 levels correlate with the changes in metabolic phenotypes after weight reduction surgery. Research Methods and Procedures: Clinical characteristics and serum VAP‐1 levels in 20 morbidly obese subjects (mean BMI 38.84 kg/m²) were measured before and after vertical banded gastroplasty. Results: Before surgery, serum VAP‐1 levels correlated positively with fasting plasma glucose (γ = 0.56, p = 0.01) and negatively with insulin levels (γ = ?0.51, p = 0.021). After surgery, the changes in serum VAP‐1 levels were negatively correlated with the changes in waist circumference (γ = ?0.57, p = 0.011), diastolic blood pressure (DBP) (γ = ?0.56, p = 0.015), and mean arterial pressure (γ = ?0.46, p = 0.055). In multivariate regression, serum VAP‐1 levels were negatively correlated with waist circumference (β = ?2.36, p = 0.014) and DBP (β = ?3.02, p = 0.017) after adjusting for age and gender. The change in DBP was negatively correlated with the change in VAP‐1 levels after adjusting for age, gender, and steady‐state plasma glucose. Discussion: The results suggest that VAP‐1 levels are correlated with fasting glucose and insulin levels in morbidly obese subjects. After surgery, the changes in VAP‐1 levels were associated with changes in visceral adiposity and DBP. Serum VAP‐1 might modulate DBP independently from the changes in insulin resistance in morbidly obese people.     

Reconstruction of a rabbit corneal epithelium on a lyophilized amniotic membrane using tilting air-liquid interface culture followed by tilting submerged culture

Herein, we reconstructed a rabbit corneal epithelium on a lyophilized amniotic membrane (LAM) using a modified version of two Teflon rings (the Ahn’s supporter). We compared the corneal epithelial cells we had differentiated in vitro using air-liquid interface (6 days, 12 days) and submerged (6 days, 12 days) cultures and followed a six-day tilting dynamic air-liquid interface culture with a six-day tilting submerged culture. We characterized the reconstructed corneal epithelium using digital photography, histological imaging, and transmission electron microscopy. The reconstructed corneal epithelium created under air-liquid interface culture exhibited a healthier basal corneal epithelial layer than that created under submerged culture. The reconstructed corneal epithelium on the LAM that was produced using the tilting dymanic culture exhibited a healthy basal layer. We therefore proposed that tilting submerged culture not only supplied nutrients from the medium to the corneal epithelial cells on the LAM, but it also removed the horny layer in the upper part of the reconstructed corneal epithelium, presumably by mimicking the effects of blinking. This study demonstrated that corneal epithelium reconstruction on a LAM using a tilting submerged culture after a tilting air-liquid interface culture may be useful not only for allogeneic or autologous transplantation, but also for in vitro toxicological test kits.     

The nonsteroidal anti-inflammatory drug NS398 reactivates SPARC expression via promoter demethylation to attenuate invasiveness of lung cancer cells

Nonsteroidal anti-inflammatory drugs (NSAIDs) have been shown to exhibit potent anticancer effects in vitro and in vivo. One of the mechanisms by which NSAIDs suppress tumorigenesis is inhibition of angiogenesis and metastasis. In this study, we used a microarray system to study the change of expression profile of metastasis-related genes regulated by NS398, a NSAID and a cyclooxygenase-2 (COX-2) inhibitor. We found that several negative regulators of cell invasion, including secreted protein acidic and rich in cysteine (SPARC), thrombospondin 1 (TSP-1), thrombospondin 3 (TSP-3), and tissue inhibitors of matrix metalloproteinase-2 (TIMP-2) are upregulated by NS398. In addition, we demonstrated that upregulation of SPARC expression by NS398 in human lung cancer cells is mediated by promoter demethylation and associated with a decrease in DNA methyltransferase (DNMT) expression. This is the first report to show that NS398 can inhibit the expression of DNMT1 and 3b. Functional assay indicated that SPARC is a critical mediator for NS398 to inhibit cell invasion. Our results provide new insights for the understanding of the anticancer actions of NSAIDs.     

New structures help the modeling of toxic amyloidbeta ion channels

The mechanism of amyloid toxicity is poorly understood and there are two schools of thought in this hotly debated field: the first favors membrane destabilization by intermediate-to-large amyloid oligomers, with consequent thinning and non-specific ion leakage; the second favors ion-specific permeable channels lined by small amyloid oligomers. Published results currently support both mechanisms. However, the amyloidbeta (Abeta) peptide has recently been shown to form a U-shaped 'beta-strand-turn-beta-strand' structure. This structure and the available physiological data present a challenge for computational biology--to provide candidate models consistent with the experimental data. Modeling based on small Abeta oligomers containing extramembranous N-termini predicts channels with shapes and dimensions consistent with experimentally derived channel structures. These results support the hypothesis that small Abeta oligomers can form ion channels. Molecular dynamics modeling can provide blueprints of 3D structural conformations for many other amyloids whose membrane association is key to their toxicity.     

Total HLA class I loss in a sarcomatoid renal carcinoma cell line caused by the coexistence of distinct mutations in the two encoding β<Subscript>2</Subscript>-microglobulin genes

In renal cell carcinoma (RCC), HLA class I downregulation has been found in about 40% of the lesions examined. Since only scanty information is available about the molecular basis of these defects, we have investigated the mechanism(s) underlying HLA class I antigen downregulation or loss in six RCC cell lines. Five of them express HLA class I antigens although at various levels; on the other hand, HLA class I antigens are not detectable on the remaining cell line, the RCC52 cell line, belonging to a sarcomatoid subtype, even following incubation with IFN-γ. β₂-microglobulin (β₂ m) was not detected in RCC52 cells. Surprisingly, RCC52 cells harbor two mutations in the β ₂ m genes in exon 1: a single G deletion (delG) in codon 6, which introduces a premature stop at codon 7, and a CT dinucleotide deletion (delCT), which leads to a premature stop at codon 55. Analysis of eight clonal sublines isolated from the RCC52 cell line showed that the two β ₂ m gene mutations are carried separately by RCC52 cell subpopulations. The delG/delCT double mutations were detected in two sublines with a fibroblast-like morphology, while the delCT mutation was detected in the remaining six sublines with an epithelial cell morphology. Furthermore, loss of heterozygosity (LOH) of the β ₂ m gene at STR D15S-209 was found only in the epithelioid subpopulation, indicating loss of one copy of chromosome 15. Immunostaining results of the tumor lesion from which the cell line RCC52 was originated were consistent with the phenotyping/molecular findings of the cultured cells. This is the first example of the coexistence of distinct β ₂ m defects in two different tumor subpopulations of a RCC, where loss of one copy of chromosome 15 occurs in one of the subpopulations with total HLA class I antigen loss. Chin-Hsuan Hsieh, Ya-Jan Hsu and Cheng-Keng Chuang contributed equally to the work.     

Fermentative Production of Thymidine by a Metabolically Engineered Escherichia coli Strain

Thymidine is an important precursor in the production of various antiviral drugs, including azidothymidine for the treatment of AIDS. Since thymidine-containing nucleotides are synthesized only by the de novo pathway during DNA synthesis, it is not easy to produce a large amount of thymidine biologically. In order to develop a host strain to produce thymidine, thymidine phosphorylase, thymidine kinase, and uridine phosphorylase genes were deleted from an Escherichia coli BL21 strain to develop BLdtu. Since the genes coding for the enzymes related to the nucleotide salvage pathway were disrupted, BLdtu was unable to utilize thymidine or thymine, and thymidine degradation activity was completely abrogated. We additionally expressed T4 thymidylate synthase, T4 nucleotide diphosphate reductase, bacteriophage PBS2 TMP phosphohydrolase, E. coli dCTP deaminase, and E. coli uridine kinase in the BLdtu strain to develop a thymidine-producing strain (BLdtu24). BLdtu24 produced 649.3 mg liter⁻¹ of thymidine in a 7-liter batch fermenter for 24 h, and neither thymine nor uridine was detected. However, the dUTP/dTTP ratio was increased in BLdtu24, which could lead to increased double-strand breakages and eventually to cell deaths during fermentation. To enhance thymidine production and to prevent cell deaths during fermentation, we disrupted a gene (encoding uracil-DNA N-glycosylase) involved in DNA excision repair to suppress the consumption of dTTP and developed BLdtug24. Compared with the thymidine production in BLdtu24, the thymidine production in BLdtug24 was increased by ∼1.2-fold (740.3 mg liter⁻¹). Here, we show that a thymidine-producing strain with a relatively high yield can be developed using a metabolic engineering approach.Thymidine, which is composed of 2-deoxyribose and a thymine base, is a commercially useful precursor in the chemical synthesis of various antiviral drugs, including stavudine and zidovudine (azidothymidine), the active ingredient in a formulation for the treatment of AIDS (18, 19). Because thymidine is required only in DNA synthesis, intracellular thymidine levels are very low and are tightly controlled (40). For the production of precursors for antiviral drugs, thymidine is either biologically produced in a low yield by a few modified microorganisms or chemically synthesized through a very costly process (17, 33, 48, 49). Thus, there is a need for developing a more efficient strain for thymidine production on a large scale.In nature, there are two distinct pathways for dTTP synthesis, the salvage and de novo pathways. The salvage pathway enables the cells to utilize preformed nucleobases and nucleosides for nucleotide synthesis, using thymidine phosphorylase (deoA), uridine phosphorylase (udp), and thymidine kinase (tdk) (Fig. ​(Fig.1)1) (40).Open in a separate windowFIG. 1.Thymidine biosynthetic pathway. The steps engineered in this study are indicated by the bold arrows and lines. Components of the catabolism are as follows: pyrA, carbamoylphosphate synthase; pyrBI, aspartate-carbamoyl transferase; pyrC, dihydroorotase; pyrD, dihydroorotate oxidase; pyrE, orotate phosphoribosyltransferase; pyrF, OMP decarboxylase; pyrG, CTP synthetase; pyrH, UMP kinase; TMPase, TMP phosphohydrolase; nrd, nucleotide diphosphate reductase; tdΔI, T4 thymidylate synthase (intron deleted); thyA, thymidylate synthase; dcd, dCTP deaminase; udk, uridine kinase; deoA, thymidine phosphorylase; tdk, thymidine kinase; udp, uridine phosphorylase; dut, deoxyribonucleotide triphosphatase; ndk, nucleotide diphosphate kinase; tmk, TMP kinase; ung, uracil-DNA N-glycosylase; upp, uracil phosphoribosyl-transferase; cdd, cytidine deaminase; codA, cytosine deaminase.As the name indicates, the de novo pathway enables the cells to synthesize nucleobases de novo. The de novo pathway leading to thymidine biosynthesis starts with the condensation of aspartate and carbamoylphosphate, synthesized by carbamoylphosphate synthase (pyrA) (41). This condensation reaction is catalyzed by aspartate-carbamoyl transferase (pyrBI) to produce carbamoyl aspartate, which undergoes several reactions to produce UMP, the common precursor for the synthesis of the pyrimidine ribonucleoside and deoxynucleosides (Fig. ​(Fig.1)1) (39-41). For thymidine biosynthesis, UMP is converted to UDP in a reaction catalyzed by UMP kinase (pyrH), and UDP is converted to dUDP by ribonucleoside diphosphate reductase (nrdAB), which is regulated by NTP effectors through binding to specific allosteric sites on ribonucleotide diphosphate reductase (nrdA). Escherichia coli can synthesize dUMP from both dCDP and dUDP. The major pathway involves phosphorylation of dCDP to dCTP, deamination of dCTP to dUTP, and hydrolysis of dUTP to dUMP. Only 20 to 30% of the cellular dUMP is supplied by hydrolysis of dUTP (29, 37). The deamination of dCTP (dcd) is located at a branch point in the pyrimidine metabolic pathway. Because of its importance, dcd is regulated by a positive homotropic cooperativity toward dCTP and by a feedback inhibition by dTTP (29, 31, 40).Deoxyuridine triphosphatase (dUTPase [dut]) is a pyrophosphatase that contains zinc ions (42). dUTPase catalyzes the hydrolysis of dUTP to PP_i and dUMP, a substrate for thymidylate synthase (thyA). Generally, the intracellular concentration of dUTP is <10 nmol per 1 g dry cell weight (DCW), and that of dTTP exceeds 500 nmol per 1 g DCW (5, 39, 52). The intracellular dUTP-to-dTTP ratio is increased in dut-deficient mutants, leading to an increased frequency of misincorporation of uracil for thymine in DNA (34). This incorporation is transient only because uracil is removed from DNA via a subsequent excision repair initiated by uracil-DNA N-glycosylase, which is encoded by ung (15, 50). Attempted repair of deoxyuridine residues from DNA without adequate dTTP available to complete the repair reaction can result in multiple single-strand breaks, eventually leading to double-strand breaks (15). Indeed, single- and double-strand breaks accumulate in thymidine-deprived cells (16). In such cells, the loss of uracil glycosylase activity should decrease DNA breaks arising from attempted repair and thereby decrease the toxicity of thymidine depletion.The synthesis of dTMP from dUMP involves the transfer of a methylene group and two reducing equivalents from 5,10-methylenetetrahydrofolate to dUMP, catalyzed by the dimeric enzyme thymidylate synthase (thyA). Even though ThyA catalyzes the committed step for de novo synthesis of dTTP, neither the activity of the enzyme nor the expression of the thyA gene seems to be regulated (2, 3).The general strategy used for the development of a thymidine-overproducing strain involves the alleviation of control mechanisms in key pathways. Several different microorganisms have been modified for thymidine production, including E. coli, Brevibacterium helvolum, and Corynebacterium ammoniagenes, by classical mutagenesis methods, and they were selected based on their capacity to grow on toxic thymidine analogues (30, 33, 48, 49). In these studies, feedback inhibition-resistant variants of thymidine biosynthetic enzymes were obtained by random mutation, and high-producing variants were selected. The most optimum B. helvolum strain obtained by this procedure produced 500 mg liter⁻¹ of thymidine by batch fermentation (33). However, engineered B. helvolum and E. coli mutants also produced thymine, deoxyuridine, and uracil, which are unfavorable for thymidine production since it increases costs during the purification process (30, 33, 48, 49). Furthermore, these thymidine-producing strains have residual thymidine degradation activities, resulting in decreased productivities.Thus, we tried to develop a more efficient thymidine-producing strain by enhancing the de novo pathway leading to thymidine biosynthesis and by disrupting the thymidine salvage pathway. The strategy reported here is based on disrupting genes which encode enzymes involved in thymidine degradation and on expressing foreign genes in the de novo pathway leading to thymidine biosynthesis which encode enzymes that are expected to be less sensitive to feedback inhibition by thymidine than the original enzymes in the host strain. The T4 ribonucleotide diphosphate reductase (nrdAB) operon, T4 thioredoxin (nrdC), T4 thymidylate synthase (td), and PBS2 TMP phosphohydrolase (TMPase) were expressed in an E. coli mutant strain which was modified to block the salvage pathway (deoA, tdk, and udp). In order to increase the influx of dUMP, E. coli dCTP deaminase (dcd), deoxyuridine triphosphatase (dut), and uridine kinase (udk) were expressed with phage-derived genes. We found that the dUTP/dTTP ratio was increased by increasing the level of dUTP in our mutant, leading to the frequent misincorporation of dUTP in DNA. In order to prevent frequent temporary DNA breaks and gaps by excision repair caused by the increased intracellular dUTP/dTTP ratio, uracil-DNA N-glycosylase (ung) was additionally disrupted.