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The Final Frontier of pH and the Undiscovered Country Beyond
Get PDFThe comparison of volumes of cells and subcellular structures with the pH values reported for them leads to a conflict with
the definition of the pH scale. The pH scale is based on the ionic product of water, Kw = [H+]6[OH2].We used Kw [in a
reversed way] to calculate the number of undissociated H2O molecules required by this equilibrium constant to yield at
least one of its daughter ions, H+ or OH2 at a given pH. In this way we obtained a formula that relates pH to the minimal
volume VpH required to provide a physical meaning to Kw, VpH~10DpH{pKw=2D|
10pKw=2
NA
(where NA is Avogadro’s number).
For example, at pH 7 (neutral at 25uC) VpH = 16.6 aL. Any deviation from neutral pH results in a larger VpH value. Our results indicate that many subcellular structures, including coated vesicles and lysosomes, are too small to contain free H+ ions at equilibrium, thus the definition of pH based on Kw is no longer valid. Larger subcellular structures, such as mitochondria, apparently contain only a few free H+ ions. These results indicate that pH fails to describe intracellular conditions, and that water appears to be dissociated too weakly to provide free H+ ions as a general source for biochemical reactions. Consequences of this finding are discussed
Novel ZnO-binding peptides obtained by the screening of a phage display peptide library
Get PDFZinc oxide (ZnO) is a semiconductor compound with a potential for wide use in various applications, including biomaterials and biosensors, particularly as nanoparticles (the size range of ZnO nanoparticles is from 2 to 100 nm, with an average of about 35 nm). Here, we report isolation of novel ZnO-binding peptides, by using screening of a phage display library. Interestingly, amino acid sequences of the ZnO-binding peptides reported in this paper and those described previously are significantly different. This suggests that there is a high variability in sequences of peptides which can bind particular inorganic molecules, indicating that different approaches may lead to discovery of different peptides of generally the same activity (e.g. binding of ZnO) but having various detailed properties, perhaps crucial under specific conditions of different applications
Oxidatively damaged DNA and its repair in colon carcinogenesis
Get PDFInflammation, high fat, high red meat and low fiber consumption have for long been known as the most important etiological factors of sporadic colorectal cancers (CRC). Colon cancer originates from neoplastic transformation in a single layer of epithelial cells occupying colonic crypts, in which migration and apoptosis program becomes disrupted. This results in the formation of polyps and metastatic cancers. Mutational program in sporadic cancers involves APC gene, in which mutations occur most abundantly in the early phase of the process. This is followed by mutations in RAS, TP53, and other genes. Progression of carcinogenic process in the colon is accompanied by augmentation of the oxidative stress, which manifests in the increased level of oxidatively damaged DNA both in the colon epithelium, and in blood leukocytes and urine, already at the earliest stages of disease development. Defence mechanisms are deregulated in CRC patients: (i) antioxidative vitamins level in blood plasma declines with the development of disease; (ii) mRNA level of base excision repair enzymes in blood leukocytes of CRC patients is significantly increased; however, excision rate is regulated separately, being increased for 8-oxoGua, while decreased for lipid peroxidation derived ethenoadducts, Ade and Cyt; (iii) excision rate of Ade and Cyt in colon tumors is significantly increased in comparison to asymptomatic colon margin, and ethenoadducts level is decreased. This review highlights mechanisms underlying such deregulation, which is the driving force to colon carcinogenesis
RNA degradation in yeast and human mitochondria
Get PDFProper function of mitochondria requires that expression of mitochondrially encoded genes be maintained at the right level for the cell’s present conditions, and changed in response to stimuli. To that end the levels of mitochondrial RNAs must be kept under strict, dynamic control. Since yeast and human mitochondria have limited possibilities to regulate gene expression by altering the transcription initiation rate, posttranscriptional processes, including RNA degradation, are of great importance. In both organisms mitochondrial RNA degradation seems to mostly depend on the RNA helicase Suv3. Yeast Suv3 functions in cooperation with Dss1 ribonuclease by forming a two-subunit complex called the mitochondrial degradosome. The human ortholog of Suv3 (hSuv3, hSuv3p, SUPV3L1) is also indispensable for mitochondrial RNA decay but its ribonucleolitic partner has so far escaped identification. In this review we summarize the current knowledge about RNA degradation in human and yeast mitochondria
Urine proteome of autosomal dominant polycystic kidney disease patients.
Get PDFABSTRACT: BACKGROUND: Autosomal dominant polycystic kidney disease (ADPKD) is responsible for 10% of cases of the end stage renal disease. Early diagnosis, especially of potential fast progressors would be of benefit for efficient planning of therapy. Urine excreted proteome has become a promising field of the search for marker patterns of renal diseases including ADPKD. Up to now however, only the low molecular weight fraction of ADPKD proteomic fingerprint was studied. The aim of our study was to characterize the higher molecular weight fraction of urinary proteome of ADPKD population in comparison to healthy controls as a part of a general effort aiming at exhaustive characterization of human urine proteome in health and disease, preceding establishment of clinically useful disease marker panel. RESULTS: We have analyzed the protein composition of urine retentate (>10 kDa cutoff) from 30 ADPKD patients and an appropriate healthy control group by means of a gel-free relative quantitation of a set of more than 1400 proteins. We have identified an ADPKD-characteristic footprint of 155 proteins significantly up- or downrepresented in the urine of ADPKD patients. We have found changes in proteins of complement system, apolipoproteins, serpins, several growth factors in addition to known collagens and extracellular matrix components. For a subset of these proteins we have confirmed the results using an alternative analytical technique. CONCLUSIONS: Obtained results provide basis for further characterization of pathomechanism underlying the observed differences and establishing the proteomic prognostic marker panel
Applications of spin–spin couplings
Get PDFThe material in this chapter covers the period from 1 June 2009 to 31 May 2010. It has been arranged as was done previously,1i.e. according to (i) the increasing atomic number of the nuclei involved, and (ii) the number of the bonds separating them. We follow the IUPAC2 recommendations with one nota..
Oxidative Stress Level in the Testes ofMice and Rats during Nickel Intoxication
Get PDFThe genotioxic and carcinogenic effect of nickel probably results from its capacity to produce reactive oxygen species (ROS) and
disturb the redox balance. The aim of the study was to find out if rats lacking spermatic protamine 2 are less susceptible to Ni(II)
than mice. Consequently, the levels of malondialdehyde + 4 hydroxynonenal (MDA+4HDA) − markers of lipid peroxidation, as
well as the level of reduced glutathione (GSH) were measured within the rat and mouse testes. Our results showed that the levels
of lipid peroxidation markers were elevated in testicular homogenates of intoxicated mice without any changes in rats. GSH level
was lower in the group of intoxicated mice comparing to the control without statistically significant changes in rats’ homogenates.
Moreover, the level of GSH in the testes of intoxicated mice was lower than in rats. On the basis of our results, it appears that Ni(II)
can initiate oxidative stress in the testes of mice but not of rats and can reduce GSH level. Consequently, the antioxidative defense
of the testes is reduced. Ni(II) that causes oxidative stress in the testes may also contribute to infertility
Ancient DNA reveals kinship burial patterns of a pre-Columbian Andean community.
Get PDFGenetic investigation of the population that inhabited Tompullo 2 site shows continuity between pre-Columbian and modern Native Amerindian populations inhabiting the Arequipa region. This suggests that no major demographic processes have influenced the mitochondrial DNA diversity of these populations during the past five hundred years. The kinship analysis involving uni- and biparental markers suggests that the community that inhabited the Tompullo 2 site was organized into extended family groups that were buried in different graves. This finding is in congruence with known models of social organization of Andean communities
Anti-staphylococcal activities of lysostaphin and LytM catalytic domain
Get PDFBACKGROUND:
Lysostaphin and the catalytic domain of LytM cleave pentaglycine crossbridges of Staphylococcus aureus peptidoglycan. The bacteriocin lysostaphin is secreted by Staphylococcus simulans biovar staphylolyticus and directed against the cell walls of competing S. aureus. LytM is produced by S. aureus as a latent autolysin and can be activated in vitro by the removal of an N-terminal domain and occluding region.
RESULTS:
We compared the efficacies of the lysostaphin and LytM catalytic domains using a newly developed model of chronic S. aureus infected eczema. Lysostaphin was effective, like in other models. In contrast, LytM was not significantly better than control. The different treatment outcomes could be correlated with in vitro properties of the proteins, including proteolytic stability, affinity to cell wall components other than peptidoglycan, and sensitivity to the ionic milieu.
CONCLUSIONS:
Although lysostaphin and LytM cleave the same peptide bond in the peptidoglycan, the two enzymes have very different environmental requirements what is reflected in their contrasting performance in mouse eczema model
Biodiversity in Oscypek, a Traditional Polish Cheese, Determined by Culture-Dependent and -Independent Approaches
Get PDFOscypek is a traditional Polish scalded-smoked cheese, with a protected-designation-of-origin (PDO) status, manufactured from
raw sheep’s milk without starter cultures in the Tatra Mountains region of Poland. This study was undertaken in order to gain
insight into the microbiota that develops and evolves during the manufacture and ripening stages of Oscypek. To this end, we
made use of both culturing and the culture-independent methods of PCR followed by denaturing gradient gel electrophoresis
(PCR-DGGE) and pyrosequencing of 16S rRNA gene amplicons. The culture-dependent technique and PCR-DGGE fingerprinting
detected the predominant microorganisms in traditional Oscypek, whereas the next-generation sequencing technique (454
pyrosequencing) revealed greater bacterial diversity. Besides members of the most abundant bacterial genera in dairy products,
e.g., Lactococcus, Lactobacillus, Leuconostoc, Streptococcus, and Enterococcus, identified by all three methods, other, subdominant
bacteria belonging to the families Bifidobacteriaceae and Moraxellaceae (mostly Enhydrobacter), as well as various minor
bacteria, were identified by pyrosequencing. The presence of bifidobacterial sequences in a cheese system is reported for the first
time. In addition to bacteria, a great diversity of yeast species was demonstrated in Oscypek by the PCR-DGGE method. Culturing
methods enabled the determination of a number of viable microorganisms from different microbial groups and their isolation
for potential future applications in specific cheese starter cultures