Adsorption of ethylenediaminetetraacetic dianhydride modified oxalate decarboxylase on calcium oxalate

We used ethylenediaminetetraacetic acid dianhydride (EDTAD) to modify oxalate decarboxylase (OXDC) to improve its adsorption on calcium oxalate stones. The modified sites were identified by Ultra performance liquid chromatography-mass spectrometry (UPLC-MS) and the adsorption mechanism of the EDTAD-modified OXDC on calcium oxalate (CaOx) was investigated. We investigated adsorption time, initial enzyme concentration, temperature and solution pH on the adsorption process. Data were analyzed using kinetics, thermodynamics and isotherm adsorption models. UPLC-MS showed that EDTAD was attached to OXDC covalently and suggested that the chemical modification occurred at both the free amino of the side chain and the α-NH₂ of the peptide. The adsorption capacity of the EDTAD-OXDC on calcium oxalate was 53.37% greater than that of OXDC at the initial enzyme concentration of 5 mg/ml, pH = 7.0, at 37° C. The modified enzyme (EDTAD-OXDC) demonstrated improved oxalate degradation activity at pH 4.5?6.0. Kinetic data fitting analysis suggested a pseudo second order kinetic model. Estimates of the thermodynamic parameters including ΔG⁰, ΔH⁰ and ΔS⁰ of the adsorption process showed it to be feasible, spontaneous and endothermic. Isotherm data fitting analysis indicated that the adsorption process is reduced to monolayer adsorption at a low enzyme concentration and to multilayer adsorption at a high enzyme concentration. It may be possible to apply OXDC to degradation of calcium oxalate stones.     

Delayed blockade of the kinin B1 receptor reduces renal inflammation and fibrosis in obstructive nephropathy

Renal fibrosis is the common histological feature of advanced glomerular and tubulointerstitial disease leading to end-stage renal disease (ESRD). However, specific antifibrotic therapies to slow down the evolution to ESRD are still absent. Because persistent inflammation is a key event in the development of fibrosis, we hypothesized that the proinflammatory kinin B1 receptor (B1R) could be such a new target. Here we show that, in the unilateral ureteral obstruction model of renal fibrosis, the B1R is overexpressed and that delayed treatment with an orally active nonpeptide B1R antagonist blocks macrophage infiltration, leading to a reversal of the level of renal fibrosis. In vivo bone marrow transplantation studies as well as in vitro studies on renal cells show that part of this antifibrotic mechanism of B1R blockade involves a direct effect on resident renal cells by inhibiting chemokine CCL2 and CCL7 expression. These findings suggest that blocking the B1R is a promising antifibrotic therapy.     

Identification of novel DNA repair proteins via primary sequence, secondary structure, and homology

Background  

DNA repair is the general term for the collection of critical mechanisms which repair many forms of DNA damage such as methylation or ionizing radiation. DNA repair has mainly been studied in experimental and clinical situations, and relatively few information-based approaches to new extracting DNA repair knowledge exist. As a first step, automatic detection of DNA repair proteins in genomes via informatics techniques is desirable; however, there are many forms of DNA repair and it is not a straightforward process to identify and classify repair proteins with a single optimal method. We perform a study of the ability of homology and machine learning-based methods to identify and classify DNA repair proteins, as well as scan vertebrate genomes for the presence of novel repair proteins. Combinations of primary sequence polypeptide frequency, secondary structure, and homology information are used as feature information for input to a Support Vector Machine (SVM).     

Quantification of angiogenesis in estrogen receptor-positive and negative breast carcinoma

Background

The objective of this study was to evaluate angiogenesis according to CD34 antigen expression in estrogen receptor (ER)-positive and negative breast carcinomas.

Methods

This study comprised 64 cases of infiltrating ductal carcinoma in postmenopausal women divided into two groups: Group A: ER-positive, n = 35; and Group B: ER-negative, n = 29. The anti-CD34 monoclonal antibody was used as a marker for endothelial cells. Microvessel count was carried out in 10 fields per slide using a 40× objective lens (magnification 400×). Statistical analysis of the data was performed using Student's t-test (p < 0.05).

Results

The mean number of vessels stained with the anti-CD34 antibody in the estrogen receptor-positive and negative tumors was 23.51 ± 1.15 and 40.24 ± 0.42, respectively. The number of microvessels was significantly greater in the estrogen receptor-negative tumors (p < 0.001).

Conclusion

ER-negative tumors have significantly greater CD34 antigen expression compared to ER-positive tumors.

     

Substitution bias, rapid saturation, and the use of mtDNA for nematode systematics

Only relatively recently have researchers turned to molecular methods for nematode phylogeny reconstruction. Thus, we lack the extensive literature on evolutionary patterns and phylogenetic usefulness of different DNA regions for nematodes that exists for other taxa. Here, we examine the usefulness of mtDNA for nematode phylogeny reconstruction and provide data that can be used for a priori character weighting or for parameter specification in models of sequence evolution. We estimated the substitution pattern for the mitochondrial ND4 gene from intraspecific comparisons in four species of parasitic nematodes from the family Trichostrongylidae (38-50 sequences per species). The resulting pattern suggests a strong mutational bias toward A and T, and a lower transition/transversion ratio than is typically observed in other taxa. We also present information on the relative rates of substitution at first, second, and third codon positions and on relative rates of saturation of different types of substitutions in comparisons ranging from intraspecific to interordinal. Silent sites saturate extremely quickly, presumably owing to the substitution bias and, perhaps, to an accelerated mutation rate. Results emphasize the importance of using only the most closely related sequences in order to infer patterns of substitution accurately for nematodes or for other taxa having strongly composition-biased DNA. ND4 also shows high amino acid polymorphism at both the intra- and interspecific levels, and in higher level comparisons, there is evidence of saturation at variable amino acid sites. In general, we recommend using mtDNA coding genes only for phylogenetics of relatively closely related nematode species and, even then, using only nonsynonymous substitutions and the more conserved mitochondrial genes (e.g., cytochrome oxidases). On the other hand, the high substitution rate in genes such as ND4 should make them excellent for population genetics studies, identifying cryptic species, and resolving relationships among closely related congeners when other markers show insufficient variation.      

Phylogeny of the Drosophila saltans species group based on combined analysis of nuclear and mitochondrial DNA sequences

Nucleotide sequences from two nuclear loci, alcohol dehydrogenase and internal transcribed spacer-1 of the nuclear ribosomal DNA repeats, and two mitochondrial genes, cytochrome oxidase I and cytochrome oxidase II, were determined from nine species in the Drosophila saltans species group. The partition homogeneity test and partitioned Bremer support were used to measure incongruence between phylogenetic hypotheses generated from individual partitions. Individual loci were generally congruent with each other and consistent with the previously proposed morphological hypothesis, although they differed in level of resolution. Since extreme conflict between partitions did not exist, the data were combined and analyzed simultaneously. The total evidence method gave a more resolved and highly supported phylogeny, as indicated by bootstrap proportions and decay indices, than did any of the individual analyses. The cordata and elliptica subgroups, considered to have diverged early in the history of the D. saltans group, were sister taxa to the remainder of the saltans group. The sturtevanti subgroup, represented by D. milleri and D. sturtevanti, occupies an intermediate position in this phylogeny. The saltans and parasaltans subgroups are sister clades and occupy the most recently derived portion of the phylogeny. As with previous morphological studies, phylogenetic relationships within the saltans subgroup were not satisfactorily resolved by the molecular data.      

Phylogenetic analysis supports horizontal transfer of P transposable elements

Nucleotide sequence comparisons were used to investigate the evolution of P transposable elements and the possibility that horizontal transfer has played a role in their occurrence in natural populations of Drosophila and other Diptera. The phylogeny of P elements was examined using published sequences from eight dipteran taxa and a new, partial sequence from Scaptomyza elmoi. The results from a number of different analyses are highly consistent and reveal a P-element phylogeny that contradicts the phylogeny of the species. At least three instances of horizontal transfer are necessary to explain this incongruence, but other explanations cannot be ruled out at this time.      

Toxicity, Histopathological Alterations and Immunohistochemical CYP1A Induction in the Early Life Stages of the Seabream, Sparus aurata, Following Waterborne Exposure to B(a)P and TCDD

In this paper, the toxicity (percentage of hatching and LC50) and histopathological alterations induced by benzo(a)pyrene (B(a)P; 0.032, 0.056, 0.1, 0.32, 0.56 and 0.1 microg l(-1)) and 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD; 0.025, 0.05, 0.1, 1.5 and 5 pg l(-1)) have been studied in the early life stages of the seabream, Sparus aurata, from 0 to 15 days post-hatching (dph). Toxicity assays showed that the percentage of hatching decreased with increasing the contaminant concentration. Moreover, the number of hatched larvae was lower for TCDD-exposed eggs in comparison with the B(a)P exposed ones. The sensitivity of the larvae, in terms of LC50, towards B(a)P and TCDD increased with age of the larvae. The LC50 were 0.81 microg l(-1) for B(a)P and 4.37 pg l(-1) for TCDD in neonate larvae and 0.11 microg l(-1) for B(a)P and 1.45 pg l(-1) for TCDD in 5 dph larvae. For histopathological examination, samples from LC50 experiments were taken at different concentrations of B(a)P (between 0.032 and 0.1 microg l(-1)) and TCDD (between 0.025 and 5 pg l(-1)). In both, B(a)P- and TCDD-exposed larvae, a concentration-dependency of the histopathological alterations was detected. In contrast, an age-dependency was not clearly detected, possibly due to the lack of development of mostly the organs in the early life stages. Cytoplasmic vacuolization of hepatocytes, as well as subcutaneous edema and necrosis of the trunk musculature, were the most common histopathological disorders detected in both B(a)P- and TCDD-exposed larvae. On the other hand, there were differences in histopathology on exposure to B(a)P and TCDD. Epithelial desquamation in gills, lack of inflation of the swim bladder, as well as lesions in the nervous system were specific for TCDD, while hepatic, vascular and muscular alterations were common for both toxicants. In parallel to the histopathological examinations, immunohistochemical analyses on cytochrome P450-1A isoenzyme (CYP1A) expression were performed on the same samples. The basal/constitutive distribution of CYP1A and its induction was also analysed in similar stages of larval development of the seabream under control conditions and after sublethal exposure to B(a)P (between 0.032 and 0.1 microg l(-1)) and TCDD (between 0.025 and 5 pg l(-1)). During the endogenous nutrition period (from hatching until 4 dph), constitutive CYP1A immunoreactivity was observed in the syncytium and in the matrix of the yolk sac. On the other hand, during exogenous feeding (between 4 and 10 dph), basal CYP1A immunoreactivity was detected in vascular hepatic system, whereas exocrine pancreas showed no reactivity. In gut, basal CYP1A immunoreactivity was restricted to the intestinal brush border and the apical cytoplasm of some enterocytes. Induced CYP1A immunoreactivity in B(a)P-exposed larvae was detected within cytoplasm of hepatocytes, intestinal enterocytes and endothelial cells of the heart. Finally, in TCDD-exposed larvae, CYP1A induction was also detected in pancreatic acinar cells, as well as in renal epithelial cells. The results of this study provided preliminary evidence that constitutive and inducible CYP1A organ distribution in S. aurata larvae was similar to that existing in adult fish. Moreover, exposure to TCDD was more toxic for the larvae and induced more CYP1A that exposure to B(a)P.     

Larval organogenesis of Pagrus pagrus L., 1758 with special attention to the digestive system development

Organogenesis of the red porgy (Pagrus pagrus L., 1758) was examined from hatching until 63 days post-hatching (dph) using histological and histochemical techniques. At hatching, the heart appeared as a tubular structure which progressively developed into four differentiated regions at 2 dph: bulbus arteriosus, atrium, ventricle and sinus venosus. First ventricle and atrium trabeculae were appreciated at 6 and 26 dph, respectively. Primordial gill arches were evident at 2 dph. Primordial filaments and first lamellae were observed at 6 and 15 dph, respectively. At mouth opening (3dph), larvae exhausted their yolk-sac reserves. The pancreatic zymogen granules appeared at 6 dph. Glycogen granules, proteins and neutral lipids (vacuoles in paraffin sections) were detected in the cytoplasm of the hepatocytes from 4-6 dph. Hepatic sinusoids could be observed from 9 dph. Pharyngeal and buccal teeth were observed at 9 and 15 dph, respectively. Oesophageal goblet cells appeared around 6 dph, containing neutral and acid mucosubstances. An incipient stomach could be distinguished at 2 dph. The first signs of gastric gland development were detected at 26 dph, increasing in number and size by 35-40 dph. Gastric glands were concentrated in the cardiac stomach region and presented a high content of protein rich in tyrosine, arginine and tryptophan. The intestinal mucous cells appeared at 15 dph and contained neutral and acid glycoconjugates, the carboxylated mucins being more abundant than the sulphated ones. Acidophilic supranuclear inclusions in the intestinal cells of the posterior intestine, related to pynocitosis of proteins, were observed at 4-6 dph.