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Application of next-generation sequencing method to decode potato genome/Wykorzystanie sekwencjonowania nowej generacji do poznania genomu ziemniaka
Get PDFThe last years have been a time of exponential progress of sequencing methods. The beginning of the 21st century closed a thirty-year domination of sequencing by the Sanger’s method. Next generation technology resulted in a mass sequencing of the successive genomes. The time necessary to discover full genomes, as occurred for potato, was dramatically reduced
Systematic bioinformatics and experimental validation of yeast complexes reduces the rate of attrition during structural investigations.
Get PDFFor high-throughput structural studies of protein complexes of composition inferred from proteomics data, it is crucial that candidate complexes are selected accurately. Herein, we exemplify a procedure that combines a bioinformatics tool for complex selection with in vivo validation, to deliver structural results in a medium-throughout manner. We have selected a set of 20 yeast complexes, which were predicted to be feasible by either an automated bioinformatics algorithm, by manual inspection of primary data, or by literature searches. These complexes were validated with two straightforward and efficient biochemical assays, and heterologous expression technologies of complex components were then used to produce the complexes to assess their feasibility experimentally. Approximately one-half of the selected complexes were useful for structural studies, and we detail one particular success story. Our results underscore the importance of accurate target selection and validation in avoiding transient, unstable, or simply nonexistent complexes from the outset
Is annexin 1 a multifunctional protein during stress responses?
Get PDFAccumulating evidence suggest that certain annexins can play a role in abiotic stress responses in plants. We found that for one member of the Arabidopsis annexin gene family, annexin 1 (AnnAt1), loss-of-function mutants are more sensitive to drought stress and gain-of-function mutants are more tolerant1. We also found that AnnAt1 is able to regulate accumulation of H2O2 in vivo in Arabidopsis cells based on the observation that the level of ROS accumulation following induction by ABA correlates with the level of AnnAt1 protein in transgenic Arabidopsis plants. Here we provide more commentary on the antioxidant activity of AnnAt1, critically assess the evidence that AnnAt1 and other annexins possess peroxidase activity, emphasize a redox-induced post-translational modification which occurs to AnnAt1 during ABA signaling, and discuss ways this annexin’s membrane associations could mediate stress signaling while addressing the potential that AnnAt1 is a multifunctional protein in plants
SYNTHESIS, BIOLOGICAL PROPERTIES AND ANTI-HIV-1 ACTIVITY OF NEW PYRIMIDINE P1,P2-DINUCLEOTIDES
Get PDFNew homo- and hetero-P1,P2-dinucleotides were prepared with the use of multistep procedures starting from the monophosphates of 3'-fluoro-2-thiothymidine, 3'-fluoro-4-thiothymidine, AZT and 1-[(2-hydroxyethoxy)-methyl-5-propyl-6-phenylselenenyl]uracil. Anti-HIV properties of the synthesized P1,P2-dinucleotides were evaluated against laboratory syncytia inducing strain HIV-1 in CEM-T4 cells. Anti-HIV activities were in the range of 5–45 nM, and therapeutic indexes were higher than 4666–14000. Interactions of the above mentioned compounds with recombinant HIV-1
reverse transcriptase were also investigated. The obtained results point to reverse transcriptase inhibition,
with somewhat lower inhibitory activity than that of their parental nucleoside-5'-triphosphates.
Compound 6 may be regarded as a potent anti-HIV/AIDS drug
Can a fermentation gas mainly produced by rumen Isotrichidae ciliates be a potential source of biohydrogen and a fuel for a chemical fuel cell?
Get PDFABSTRACT
Bacteria, fungi and protozoa inhabiting the rumen – the largest chamber of the ruminants’ stomach, release large quantities of hydrogen during the fermentation of carbohydrates. The hydrogen is used by coexisting methanogens to produce methane in energy-yielding processes. This work shows, for the first time, a fundamental possibility of using a hydrogen-rich fermentation gas produced by selected rumen ciliates to feed a low-temperature hydrogen fuel cell. A biohydrogen fuel cell (BHFC) was constructed consisting of (i) a bioreactor, in which a hydrogen-rich gas was produced from glucose by rumen ciliates, mainly of the Isotrichidae family, deprived of intra- and extracellular bacteria, methanogens, and fungi, and (ii) a chemical fuel cell of the polymer-electrolyte type (PEFC). The fuel cell was used as a tester of the technical applicability of the fermentation gas produced by the rumen ciliates for power generation. The average estimated hydrogen yield was ca. 1.15 mol H2 per mol of fermented glucose. The BHFC performance was equal to the performance of the PEFC running on pure hydrogen. No fuel cell poisoning effects were detected. A maximum power density of 1.66 kW/m2 (PEFC geometric area) was obtained at room temperature. The maximum volumetric power density was 128 W/m3 but the coulombic efficiency was only ca. 3.8%. The configuration of the bioreactor limited the continuous operation time of this BHFC to ca. 14 hours
A direct determination of the dissociation constant for the Cu(II) complex of amyloid beta 1-40 peptide.
No full textInteractions of amyloid beta (Abeta) peptides with Cu(II) are believed to play a crucial role in the molecular mechanisms of neurotoxicity of Alzheimer's disease. There is, however, a serious disagreement regarding the strength of Cu(II) binding to these peptides. We used recombinant amyloid beta peptide 1-40 (Abeta40) to determine the stoichiometry and dissociation constants of Cu(II)-Abeta40 complexes using fluorescence spectroscopy. A single Cu(Abeta40) complex, characterized with the conditional dissociation constant K(d)(cond) = 57 +/- 5 nM was identified. This complex does not bind Hepes buffer molecules, as indicated by the total lack of relationship between K(d)(cond) values and Hepes concentration. The differences between this and other determinations of this constant and its relevance for the understanding of Cu(II) interaction with Abeta peptides are discussed
The effect of oxidative stress on nucleotide-excision repair in colon tissue of newborn piglets.
Get PDFNucleotide-excision repair (NER) is important for the maintenance of genomic integrity and to prevent the onset of carcinogenesis. Oxidative stress was previously found to inhibit NER in vitro, and dietary antioxidants could thus protect DNA not only by reducing levels of oxidative DNA damage, but also by protecting NER against oxidative stress-induced inhibition. To obtain further insight in the relation between oxidative stress and NER activity in vivo, oxidative stress was induced in newborn piglets by means of intra-muscular injection of iron (200mg) at day 3 after birth. Indeed, injection of iron significantly increased several markers of oxidative stress, such as 8-oxo-7,8-dihydro-2'-deoxyguanosine (8-oxodG) levels in colon DNA and urinary excretion of 8-oxo-7,8-dihydroguanine (8-oxoGua). In parallel, the influence of maternal supplementation with an antioxidant-enriched diet was investigated in their offspring. Supplementation resulted in reduced iron concentrations in the colon (P=0.004) at day 7 and a 40% reduction of 8-oxodG in colon DNA (P=0.044) at day 14 after birth. NER capacity in animals that did not receive antioxidants was significantly reduced to 32% at day 7 compared with the initial NER capacity on day 1 after birth. This reduction in NER capacity was less pronounced in antioxidant-supplemented piglets (69%). Overall, these data indicate that NER can be reduced by oxidative stress in vivo, which can be compensated for by antioxidant supplementation
Aberrant repair of etheno-DNA adducts in leukocytes and colon tissue of colon cancer patients.
Get PDFTo assess the role of lipid peroxidation-induced DNA damage and repair in colon carcinogenesis, the excision rates and levels of 1,N(6)-etheno-2'-deoxyadenosine (epsilondA), 3,N(4)-etheno-2'-deoxycytidine (epsilondC), and 1,N(2)-etheno-2'-deoxyguanosine (1,N(2)-epsilondG) were analyzed in polymorphic blood leukocytes (PBL) and resected colon tissues of 54 colorectal carcinoma (CRC) patients and PBL of 56 healthy individuals. In PBL the excision rates of 1,N(6)-ethenoadenine (epsilonAde) and 3,N(4)-ethenocytosine (epsilonCyt), measured by the nicking of oligodeoxynucleotide duplexes with single lesions, and unexpectedly also the levels of epsilondA and 1,N(2)-epsilondG, measured by LC/MS/MS, were lower in CRC patients than in controls. In contrast the mRNA levels of repair enzymes, alkylpurine- and thymine-DNA glycosylases and abasic site endonuclease (APE1), were higher in PBL of CRC patients than in those of controls, as measured by QPCR. In the target colon tissues epsilonAde and epsilonCyt excision rates were higher, whereas the epsilondA and epsilondC levels in DNA, measured by (32)P-postlabeling, were lower in tumor than in adjacent colon tissue, although a higher mRNA level was observed only for APE1. This suggests that during the onset of carcinogenesis, etheno adduct repair in the colon seems to be under a complex transcriptional and posttranscriptional control, whereby deregulation may act as a driving force for malignancy
The effects of temperature and salinity on vital biological functions of the Antarctic crustacean Serolis polita
Get PDFEffects of temperature rise (from 0 to +5°C) and salinity decline (from 34 to 30psu) on vital biological functions of the Antarctic isopod Serolis polita were studied in laboratory experiments. Behavioural reactions to food odour, as well as righting responses and reburying in the sediments, were measured. Both temperature increase and salinity decline impaired the ability of S. polita to perform these biological functions critical for their long-term survival, by lowering the number of isopods able to right and rebury in the sediment, increasing time-to-right, reducing locomotory activity and weakening isopod reaction to food odour. Significant interactive effects between temperature and salinity on time-to-right and time spent swimming were observed, with isopods being more vulnerable to lower salinities when exposed to higher temperatures. Some biological functions (righting, reburying) were more sensitive to temperature and salinity changes than others (swimming). In conclusion, our findings strongly suggest that Antarctic isopods are vulnerable to environmental changes, and their ability to cope with them is limited
Control of RNA polymerases I and III by the TOR signaling pathway
Get PDFComment on: Sch9 partially mediates TORC1 signaling to control ribosomal RNA synthesis. Wei Y, et al. Cell Cycle 2009; 8