Integrative omics-analysis of lipid metabolism regulation by peroxisome proliferator-activated receptor a and b agonists in male Atlantic cod

Lipid metabolism is essential in maintaining energy homeostasis in multicellular organisms. In vertebrates, the peroxisome proliferator-activated receptors (PPARs, NR1C) regulate the expression of many genes involved in these processes. Atlantic cod (Gadus morhua) is an important fish species in the North Atlantic ecosystem and in human nutrition, with a highly fatty liver. Here we study the involvement of Atlantic cod Ppar a and b subtypes in systemic regulation of lipid metabolism using two model agonists after in vivo exposure. WY-14,643, a specific PPARA ligand in mammals, activated cod Ppara1 and Ppara2 in vitro. In vivo, WY-14,643 caused a shift in lipid transport both at transcriptional and translational level in cod. However, WY-14,643 induced fewer genes in the fatty acid beta-oxidation pathway compared to that observed in rodents. Although GW501516 serves as a specific PPARB/D ligand in mammals, this compound activated cod Ppara1 and Ppara2 as well as Pparb in vitro. In vivo, it further induced transcription of Ppar target genes and caused changes in lipid composition of liver and plasma. The integrative approach provide a foundation for understanding how Ppars are engaged in regulating lipid metabolism in Atlantic cod physiology. We have shown that WY-14,643 and GW501516 activate Atlantic cod Ppara and Pparb, affect genes in lipid metabolism pathways, and induce changes in the lipid composition in plasma and liver microsomal membranes. Particularly, the combined transcriptomic, proteomics and lipidomics analyses revealed that effects of WY-14,643 on lipid metabolism are similar to what is known in mammalian studies, suggesting conservation of Ppara functions in mediating lipid metabolic processes in fish. The alterations in the lipid profiles observed after Ppar agonist exposure suggest that other chemicals with similar Ppar receptor affinities may cause disturbances in the lipid regulation of fish. Model organism: Atlantic cod (Gadus morhua). LSID: urn:lsid:zoobank.org:act:389BE401-2718-4CF2-BBAE-2E13A97A5E7B. COL Identifier: 6K72F.

Hydrodynamic and Ballistic Transport over Large Length Scales in GaAs/AlGaAs

We study hydrodynamic and ballistic transport regimes through nonlocal resistance measurements and high-resolution kinetic simulations in a mesoscopic structure on a high-mobility two-dimensional electron system in a GaAs/AlGaAs heterostructure. We evince the existence of collective transport phenomena in both regimes and demonstrate that negative nonlocal resistances and current vortices are not exclusive to only the hydrodynamic regime. The combined experiments and simulations highlight the importance of device design, measurement schemes, and one-to-one modeling of experimental devices to demarcate various transport regimes.

ReCodLiver0.9: Overcoming Challenges in Genome-Scale Metabolic Reconstruction of a Non-model Species

The availability of genome sequences, annotations, and knowledge of the biochemistry underlying metabolic transformations has led to the generation of metabolic network reconstructions for a wide range of organisms in bacteria, archaea, and eukaryotes. When modeled using mathematical representations, a reconstruction can simulate underlying genotype-phenotype relationships. Accordingly, genome-scale metabolic models (GEMs) can be used to predict the response of organisms to genetic and environmental variations. A bottom-up reconstruction procedure typically starts by generating a draft model from existing annotation data on a target organism. For model species, this part of the process can be straightforward, due to the abundant organism-specific biochemical data. However, the process becomes complicated for non-model less-annotated species. In this paper, we present a draft liver reconstruction, ReCodLiver0.9, of Atlantic cod (Gadus morhua), a non-model teleost fish, as a practicable guide for cases with comparably few resources. Although the reconstruction is considered a draft version, we show that it already has utility in elucidating metabolic response mechanisms to environmental toxicants by mapping gene expression data of exposure experiments to the resulting model.

New Conceptual Toxicokinetic Model to Assess Synergistic Mixture Effects between the Aromatic Hydrocarbon β-Naphthoflavone and the Azole Nocodazole on the CYP1A Biomarker in a Fish Cell Line

Toxicokinetic interactions with catabolic cytochrome P450 (CYP) enzymes can inhibit chemical elimination pathways and cause synergistic mixture effects. We have created a mathematical bottom-up model for a synergistic mixture effect where we fit a multidimensional function to a given data set using an auxiliary nonadditive approach. The toxicokinetic model is based on the data from a previous study on a fish cell line, where the CYP1A enzyme activity was measured over time after exposure to various combinations of the aromatic hydrocarbon β-naphthoflavone and the azole nocodazole. To describe the toxicokinetic mechanism in this pathway and how that affects the CYP1A biomarker, the model uses ordinary differential equations. Local sensitivity and identifiability analyses revealed that all the 10 parameters estimated in the model were identified uniquely while fitting the model to the data for measuring the CYP1A enzyme activity. The model has a good prediction power and is a promising tool to test the synergistic toxicokinetic interactions between different chemicals.

A comparison of Monte Carlo sampling methods for metabolic network models

Reaction rates (fluxes) in a metabolic network can be analyzed using constraint-based modeling which imposes a steady state assumption on the system. In a deterministic formulation of the problem the steady state assumption has to be fulfilled exactly, and the observed fluxes are included in the model without accounting for experimental noise. One can relax the steady state constraint, and also include experimental noise in the model, through a stochastic formulation of the problem. Uniform sampling of fluxes, feasible in both the deterministic and stochastic formulation, can provide us with statistical properties of the metabolic network, such as marginal flux probability distributions. In this study we give an overview of both the deterministic and stochastic formulation of the problem, and of available Monte Carlo sampling methods for sampling the corresponding solution space. We apply the ACHR, OPTGP, CHRR and Gibbs sampling algorithms to ten metabolic networks and evaluate their convergence, consistency and efficiency. The coordinate hit-and-run with rounding (CHRR) is found to perform best among the algorithms suitable for the deterministic formulation. A desirable property of CHRR is its guaranteed distributional convergence. Among the three other algorithms, ACHR has the largest consistency with CHRR for genome scale models. For the stochastic formulation, the Gibbs sampler is the only method appropriate for sampling at genome scale. However, our analysis ranks it as less efficient than the samplers used for the deterministic formulation.

Evaluating model reduction under parameter uncertainty

BACKGROUND

The dynamics of biochemical networks can be modelled by systems of ordinary differential equations. However, these networks are typically large and contain many parameters. Therefore model reduction procedures, such as lumping, sensitivity analysis and time-scale separation, are used to simplify models. Although there are many different model reduction procedures, the evaluation of reduced models is difficult and depends on the parameter values of the full model. There is a lack of a criteria for evaluating reduced models when the model parameters are uncertain.

RESULTS

We developed a method to compare reduced models and select the model that results in similar dynamics and uncertainty as the original model. We simulated different parameter sets from the assumed parameter distributions. Then, we compared all reduced models for all parameter sets using cluster analysis. The clusters revealed which of the reduced models that were similar to the original model in dynamics and variability. This allowed us to select the smallest reduced model that best approximated the full model. Through examples we showed that when parameter uncertainty was large, the model should be reduced further and when parameter uncertainty was small, models should not be reduced much.

CONCLUSIONS

A method to compare different models under parameter uncertainty is developed. It can be applied to any model reduction method. We also showed that the amount of parameter uncertainty influences the choice of reduced models.

Terminal Deoxynucleotidyl Transferase (TdT) Inhibiti on of Cord Blood Derived B and T Cells Expansion

Purpose: Terminal deoxynucleotidyl transferase(TdT) is a DNA polymerase that is present in immature pre-B and pre-T cells. TdT inserts N-nucleotides to the V (D) J gene segment during rearrangements of genes, therefore, it plays a vital role in the development and variation of the immune system in vertebrates. Here we evaluated the relationship between cytokines like interleukin-2 (IL-2), interleukin-7 (IL-7), and interleukin-15 (IL-15) and TdT expression in cord blood mononuclear cells and also effect of inhibition in the expansion of B and T cells derived from cord blood. Methodes: The cord blood mononuclear cells were cultured with different combination of cytokines for 21days, which they were harvested in definite days (7, 14 and 21) and evaluated by flow cytometry. Results: Our data indicated that TdT expression increased in cord blood mononuclear cells using immune cell key cytokines without being dependent on the type of cytokines. TdT inhibition reduced both the expansion of B and T cells derived from cord blood and also declined the apoptosis and proliferation. Considered together, TdT played an important role in the control of the expansion of B and T cells derived from cord blood. Conclusion: considered together, it was observed that TdT expression was increased by cytokines and TdT inhibition not only reduced B and Tcells derived from cord blood, but it also affected the rate of apoptosis and proliferation.

Evaluation of murine norovirus persistence in environments relevant to food production and processing

Human norovirus (NoV) causes outbreaks of acute gastroenteritis associated with many ready-to-eat foods, including fresh produce. Effective inactivation procedures must consider virus survival under conditions of produce production and processing. This study aimed to investigate the persistence of NoV in a variety of environments, using murine NoV (MNV) as a surrogate for NoV. MNV was incubated for up to 42 days at room temperature on stainless steel disks, on lettuce, on soil, and in potable water and titers determined by plaque assay. A 1-log reduction of MNV infectivity was observed after 29 days in water, 4 days on lettuce, 12 days on soil, and 15 days on stainless steel disks. MNV survived longer in water than in any of the other environments, indicating that drying may contribute to NoV inactivation. MNV genomes were not significantly reduced for up to 42 days, suggesting that genomic detection is not a reliable indicator of viability. Overall, our findings provide valuable information regarding the potential for NoV transmission in the food supply.

Retention of a Flowable Composite Resin in Comparison to a Conventional Resin-Based Sealant: One-year Follow-up

OBJECTIVE

Long-term retention of pit and fissure sealants is crucial for their success. This clinical study evaluated the retention rate of a flowable composite resin (Filtek Supreme XT Flowable Restorative) compared to a conventional resin-based sealant (Concise Light Cure White Sealant) over 12 months.

MATERIALS AND METHODS

Forty subjects aged 6 to 9 years were included in the study. Using a half-mouth design, a total of 80 first permanent molars were sealed with conventional fissure sealant on one side of the mouth and flowable composite on the contralateral side. Clinical evaluation was performed at 3, 6, and 12 months by a single blind examiner and the retention was classified as complete retention, partial loss, or total loss.

RESULTS

For both materials, there was no total loss of sealants over 12 months. Partial loss of both materials was observed in one sealant after 3 months. After 6 months, 36 teeth sealed with conventional fissure sealant were intact compared with 37 sealed with a flowable composite, and after 12 months, 33 teeth sealed with conventional fissure sealant were intact compared with 35 that were sealed with a flowable composite. There were no statistically significant difference (P>0.05) between the two materials regarding the retention rate at each follow-up period.

CONCLUSION

As flowable composite resulted in comparable sealant retention rates, this material could be a good choice for fissure sealant.

Soil decontamination of 2,4,6- trinitrotoluene by alfalfa (Medicago sativa)

Present study investigate the toxicity effect of 2,4,6-trinitrotoluene (TNT) on a terrestrial plant, alfalfa (Medicago sativa) in artificial soils. In this study, TNT toxicity assessment was performed on spiked silica with this nitroaromatic compound by determination of the percent of emergence and shoots and roots biomasses at the concentration range of 3.2-10000 mg kg(-1) Dry Weight (DW). The emergence was reduced by 22-32% after 5 days of exposure at TNT concentrations up to 100 mg kg(-1) DW; shoot and root biomasses were reduced by 48-50 and 63-74%, respectively after 30 days exposure at TNT concentrations < or = 32 mg kg(-1) DW. Concentrations higher than 100 mg kg(-1) DW can not be tolerated at all. Concentrations of TNT and its metabolites in silica, root and shoot were measured by High-Performance Liquid Chromatography (HPLC). Analyses of TNT spiked soil extracts reveal hat during alfalfa cultivation for 30 days, TNT was partially transformed at the extent of 15-27%. This transformation decreased at higher TNT soil concentrations. TNT is taken up and metabolized by plants to its downstream derivatives.

The nature of the onset of rheumatoid arthritis: a reassessment

A total of 300 consecutive patients referred to a tertiary-care center and fulfilling the American Rheumatism Association criteria for definite-classical rheumatoid arthritis, (with a mean disease-duration of 10.3 +/- 9 years) were studied by structured interview and medical record review. The type of onset (rapid or insidious), type of joint involved (small, medium, large or combined joints) and pattern of joint involvement (monarticular, pauciarticular or polyarticular) at onset, and the interval between the first symptom and development of established disease were determined from the interview (based on the patient's memory). The onset was rapid in 46%. Initial involvement occurred in small joints in 31%, medium joints in 16%, large joints in 28% and combined sites in 25%. The pattern of joint involvement at onset was monarticular in 21%, pauciarticular in 44% and polyarticular in 35%. The time for disease to become established was less than 1 month in 25%, 1-6 months in 35%, 6-12 months in 14% and over 1 year in 26%. The monarticular pattern of onset was associated with slower development of established disease than the other patterns of joint involvement; polyarticular disease tended to be associated with polyarticular onset; involvement of large joints was associated with pauciarticular onset.

Small joint involvement: a systematic roentgenographic study in rheumatoid arthritis

Standard hand and foot roentgenograms from 200 consecutively hospitalised patients with definite or classical rheumatoid arthritis (RA) were read for marginal erosions by three independent observers. For each joint or group of joints analysed the degree of symmetry (S = absolute symmetry, U = unilateral, PS = partial symmetry) was determined. The total number of joints affected significantly correlated only with disease duration; symmetry of erosions and number of affected patients were not influenced by seropositivity. Metatarsophalangeal erosions (in 70%) were the most common and were classified as S in 16%, U in 21%, and PS in 63%. Metacarpophalangeal erosions (in 68%) were also common, with a symmetry pattern of S in 19%, U in 21%, and PS in 60%. Proximal finger interphalangeal erosions (in 42%) were unilateral in 42% (S in 8% and PS in 50%). The only site where symmetry was usual (90%) was the wrist, but radiocarpal and intercarpal joints were considered together. Erosions also occurred in about 16% of the finger distal interphalangeal and 28% of the great toe interphalangeal joints. In RA roentgenographic asymmetry is usual and unilateral involvement common.

Penicillamine-induced myositis. Observations and unique features in two patients and review of the literature

Dermatomyositis developed during treatment with penicillamine in two patients with rheumatoid arthritis. Both were male without a history of penicillin allergy. Eosinophilia was present at the start of their illness, and HLA tissue typing showed the presence of HLA-DR2 in one patient. One patient was retreated with penicillamine and remained asymptomatic after three years of therapy, and the other was able to take penicillamine in a reduced dosage.

Coexistence of rheumatoid arthritis and sarcoidosis: difficulties encountered in the differential diagnosis of common manifestations

Two patients with rheumatoid arthritis (RA) and sarcoidosis illustrate the dilemmas posed by their coexistence in the same patient. The first patient with classical RA developed iridocyclitis, interstitial lung disease and cranial neuropathies, initially attributed to extraarticular rheumatoid disease. Subsequent lung and skin biopsy revealed many granulomas consistent with sarcoidosis whereas synovium revealed changes typical for RA. In the second patient with cutaneous and pulmonary sarcoidosis development of persistent erosive polyarthritis and a subcutaneous nodule with typical pathology permitted the diagnosis of coexistent RA. These cases emphasize that uveitis alone or multiple cranial neuropathies are not features of RA and symptomatic interstitial lung disease in patients with RA warrants further investigation.

Rheumatoid myositis. Clinical and histologic features and possible pathogenesis

Thirty-one patients with rheumatoid arthritis were consecutively studied for evidence of muscle involvement, using muscle biopsy and electromyography. The patients were initially separated into 4 clinical categories: inactive peripheral joint disease (6 patients); active peripheral joint disease (10 patients); systemic disease and a disproportionately elevated sedimentation rate for the degree of mild synovitis (SERD) (11 patients); or elevated creatinine phosphokinase level (4 patients). In addition to routine histology, muscle tissue was examined for de novo synthesis of IgM and IgM rheumatoid factor, and by indirect immunofluorescence for the presence of immunoglobulin and complement deposits. Our results indicate that: muscle fiber necrosis occurs frequently in patients with rheumatoid arthritis; rheumatoid myositis, defined as muscle fiber necrosis and mononuclear cell infiltration, is a distinct entity and occurs particularly in patients with SERD or an elevated creatinine phosphokinase level; and only muscle from patients with rheumatoid myositis exhibited de novo synthesis of rheumatoid factor and significant quantities of IgM, indicating that local immune events may be important in the pathogenesis of this entity.

Coexistence of Reiter's syndrome and rheumatoid arthritis in a genetically susceptible individual

A patient is presented who had features of Reiter's syndrome for 10 years before developing features of rheumatoid arthritis. Diagnostic criteria for both diseases are fulfilled, and HLA typing revealed the presence of both B27 and DR4 antigens. The coexistence of Reiter's syndrome and rheumatoid arthritis appears to have occurred in an individual genetically susceptible to both diseases.

Nonreducible rotational head tilt and atlantoaxial lateral mass collapse. Clinical and roentgenographic features in patients with juvenile rheumatoid arthritis and ankylosing spondylitis

Nonreducible rotational head tilt resulting from predominantly unilateral collapse of the lateral mass of the atlas (C1) and/or axis (C2) has been characterized in patients with rheumatoid arthritis. An identical phenomenon is reported in five patients with juvenile rheumatoid arthritis (JRA) and in six with ankylosing spondylitis (AS). Most patients had neck pain and crepitus, all had a fixed head tilt deformity, and most also had a rotational deformity. Roentgenographically, all had predominantly unilateral collapse of the lateral masses of C1 and/or C2, and the head always tilted toward the most collapsed side. The patients with JRA had polyarticular disease of long duration and generally mild neck symptoms, with only one requiring neck surgery for pain. The patients with AS tended to have proximal peripheral joint involvement and long-standing disease with more severe neck symptoms; four underwent posterior cervical fusion for intractable pain. None of the 11 patients had demonstrable neurologic deficits.

Nonreducible rotational head tilt and lateral mass collapse. A prospective study of frequency, radiographic findings, and clinical features in patients with rheumatoid arthritis

Of 126 hospitalized, but otherwise unselected, patients with rheumatoid arthritis, 12 (10%) had a persisting nonreducible rotational head tilt deformity (NRRHT). These 12 were grouped with an additional 12 similar subjects, previously found to have the same condition, and all 24 were compared with the remaining 114 who did not have head tilt. Patients with NRRHT differed significantly from the others in that the former were more likely to have a destructive peripheral arthritis, headache, limited neck motion, and various cervical subluxations. All 24 subjects with NRRHT had predominately unilateral collapse of the lateral masses of the atlas and/or axis, compared with only 2 of the 114 with normal head position. The head always tilted to the side of the lateral mass collapse, which appeared to be the sole or major cause of the abnormal head position.