Proteogenomic analysis of Mycobacterium tuberculosis by high resolution mass spectrometry

The genome sequencing of H37Rv strain of Mycobacterium tuberculosis was completed in 1998 followed by the whole genome sequencing of a clinical isolate, CDC1551 in 2002. Since then, the genomic sequences of a number of other strains have become available making it one of the better studied pathogenic bacterial species at the genomic level. However, annotation of its genome remains challenging because of high GC content and dissimilarity to other model prokaryotes. To this end, we carried out an in-depth proteogenomic analysis of the M. tuberculosis H37Rv strain using Fourier transform mass spectrometry with high resolution at both MS and tandem MS levels. In all, we identified 3176 proteins from Mycobacterium tuberculosis representing ~80% of its total predicted gene count. In addition to protein database search, we carried out a genome database search, which led to identification of ~250 novel peptides. Based on these novel genome search-specific peptides, we discovered 41 novel protein coding genes in the H37Rv genome. Using peptide evidence and alternative gene prediction tools, we also corrected 79 gene models. Finally, mass spectrometric data from N terminus-derived peptides confirmed 727 existing annotations for translational start sites while correcting those for 33 proteins. We report creation of a high confidence set of protein coding regions in Mycobacterium tuberculosis genome obtained by high resolution tandem mass-spectrometry at both precursor and fragment detection steps for the first time. This proteogenomic approach should be generally applicable to other organisms whose genomes have already been sequenced for obtaining a more accurate catalogue of protein-coding genes.     

Effects of Hydroponic Solution EC,Substrates, PPF and Nutrient Scheduling on Growth and Photosynthetic Competence During Acclimatization of Micropropagated <Emphasis Type="Italic">Spathiphyllum</Emphasis> plantlets

In vitro regenerated shoots of Spathiphyllum from bioreactor were hydroponically cultured for 30 days. The response of plant growth and photosynthesis to different substrates, photosynthetic photon flux (PPF), nutrient scheduling and electrical conductivity (EC) of hydroponic solution were studied. The best plant growth response was observed in perlite based substrates with moderate PFF (70–100μmol m⁻² s⁻¹). Highest fresh weight, dry weight, shoot length, root length, root number and photosynthetic characteristics (chlorophyll, carotenoids and Fv/Fm) was observed in continuous immersion system. Plant growth responses, photosynthetic rate, stomatal conductance and transpiration rate were also found to be affected by EC levels. The optimum EC of a balanced nutrient solution was recorded as 1.2 dS m⁻¹. Photosynthetic activity was also characterized in terms of photochemical efficiency using measurements of chlorophyll fluorescence. Fv/Fm (it is a measure of the intrinsic or maximum efficiency of PSII i.e. the quantum efficiency if all PSII centers were open) also decreased significantly in plants grown under higher EC level; a decrease in this parameter indicates down regulation of photosynthesis or photoinhibition. Antioxidant defense enzymes such as catalase (CAT), ascorbate peroxidase (APX), peroxidase (POD), glutathione reductase (GR) and monodehydroascorbate reductase (MDHAR) significantly elevated in the leaves and roots of plantlets at higher EC levels. This increase could reflect a defense response to the cellular damage provoked by higher EC levels in the nutrient solution.     

Proanthocyanidin exposure to B6C3F1 mice significantly attenuates dimethylnitrosamine-induced liver tumor induction and mortality by differentially modulating programmed and unprogrammed cell deaths

Proanthocyanidins are of current interest as chemopreventive agents. The potential of the pre-, post- and co-exposure of proanthocyanidin-rich grape seed extract (GSPE) in preventing, reducing and/or delaying dimethylnitrosamine (N-nitrosodimethylamine, DMN)-induced liver tumorigenesis, carcinogenesis and mortality in male B6C3F1 mice was determined. Animals were divided into six groups: I—control, II—GSPE alone, III—DMN alone, IV—GSPE + DMN, V—DMN exposure (3 months) followed by GSPE diet (9 months) and VI—GSPE diet (3 months) + DMN (3 months) + control diet (6 months). DMN exposure (0–8 weeks: 5 mg/kg; 8–12 weeks: 10 mg/kg, i.p.) was limited to a total period of 3 months. GSPE was incorporated in laboratory chow (ADI: 100 mg/kg b.w.). Animals were sacrificed at 3 month intervals, and serum chemistry, liver histopathology, integrity of hepatic genomic DNA, antioxidant status, and rates of apoptotic and necrotic cell deaths were determined. DMN-induced liver tumor formation (85%) and animal lethality (38%) were powerfully antagonized by co-administration of GSPE + DMN (tumor positive: 45%; death: 11%). More than 75% of the DMN-treated animals had numerous tumors (five or more), which were significantly reduced in the GSPE + DMN group (35%). GSPE also negatively influenced other protocols specifically designed to test initiation and progression phases. Thus, GSPE was instrumental in modulating metabolic cascades and regulated orchestration of cell death processes involved during the multistage tumorigenic process. These results unraveled that long-term exposure to proanthocyanidin-rich grape seed extract may serve as a potent barrier to all three stages of DMN-induced liver carcinogenesis and tumorigenesis by selectively altering oxidative stress, genomic integrity and cell death patterns in vivo.     

Sufficient progesterone-priming prior to estradiol stimulation is required for optimal induction of the cervical prostaglandin system in pregnant sheep at 0.7 gestations

The purposes of this study were to determine the separate and interactive functions of progesterone and estradiol in regulating the cervical prostaglandin (PG) system in pregnant sheep at 0.7 gestations. At 106-108 days of gestational age (dGA), ewes were treated with vehicle for 14 days (n = 5) or vehicle for 12 days followed by estradiol 5 mg twice a day, intramuscularly for 2 days (n = 5) or progesterone 100 mg, twice a day, intramuscularly for 14 days (n = 5) or progesterone 100 mg twice a day, intramuscularly for 10 days and then 2 days vehicle followed by estradiol 5 mg twice a day intramuscularly for 2 days (n = 5). At 121-123 dGA, cervical tissues were obtained under halothane anesthesia. Cervical RNA and protein were extracted and analyzed for prostaglandin-endoperoxide synthase 2 (COX2), two PGE(2) receptors, PTGER2 and PTGER4, and estrogen receptor alpha (ESR1) by Northern and Western blot analysis. Immunocytochemistry and in situ hybridization were applied to localize cellular distribution of COX2, PTGER2, and PTGER4 in the cervix. Data were analyzed by ANOVA. COX2 and PTGER4 mRNAs and proteins were increased (P < 0.05) in ewes treated with combined estradiol and progesterone but not in ewes treated with estradiol or progesterone alone compared with controls. ESR1 mRNA was increased in ewes treated with progesterone and estradiol plus progesterone. In contrast, PTGER2 mRNA and protein remained the same after all treatments. COX2 mRNA and protein were localized only in cervical glandular epithelial cells, whereas PTGER2 and PTGER4 were localized in both cervical glandular epithelial and smooth muscle cells. In conclusion, these data suggest that additional progesterone priming at 0.7 gestations synergizes with estradiol to induce cervical COX2, PTGER4, and ESR1 and support our hypothesis that stimulation of the cervical PG system by estradiol is optimized by sufficient progesterone priming in the pregnant sheep cervix.     

Effect of water stress and heavy metals on induction of somatic embryogenesis in wheat leaf base cultures

In vitro cultures of plant tissues are known to mimic the response of field-grown plants when subjected to stress treatments. This investigation on Triticum aestivum explores the effect of drought stress on somatic embryogenesis and endogenous proline content. Leaf bases were cultured on MS medium supplemented with 2,4-D (10 microM) and different concentrations of PEG (2.5, 5, 7.5%) or mannitol (0.25 and 0.5 M) and also subjected to different periods of aerial drying in the laminar flow for one-day and subsequently transferred to MS basal medium. PEG treatment induced a high percentage (up to 50%) of embryoid formation. However, with mannitol and aerial drying, percentage of embryoid formation decreased with increasing concentrations and duration. After ten days, the endogenous proline content of explants treated with different concentrations of PEG, mannitol and different durations of aerial drying increased with increasing concentration and increasing duration of the treatment, thus, corroborating the role of proline as an osmolyte during stress conditions. Similarly, addition of metals such as cadmium and cobalt caused a reduction in percentage explants depicting embryogenesis. However, when cadmium was employed alone, 22% explants displayed somatic embryogenesis as compared to 54% in 2,4-D treated cultures.     

Use of common carp (Cyprinus carpio L.) in increasing the fertilizer value of phospate rock

Thirty-two glass jars (3 L each) in the laboratory and outdoor tanks (300 L) were used to examine the influence of common carp ( Cyprinus carpio L. ) in increasing the fertilizer value of phoshate rock in eight treatment combinations in quadruplicate. Input of water soluble hosphate was determined to quantify the effects of bioturbation, fish excrements and soil. The level of orthophosphate in water was always lowest in the control series. Introduction of common carp fry resulted in a net increase of 0.1 to 0.114 mg. L^-1 of orthophosphate attributable to the effect of fish excrement. Bioturbation caused by common carp resulted in as high as a 72 to 100 % influx of phosphate from bottom soil in the presence of phosphate rock but only about 7 to 8 % in the absence of phosphate rock.

Zusammenfassung

Die Bedeutung eingesetzter Karpfen (Cyprinus carpio L.) zur Steigerung des Düngerwertes von Phosphatgestein
32 Glasgefäße (3 L Volumen) wurden im Labor und 4 Behälter (300 L) im Freien aufgestellt urn den Einfluß zunehmender Düngung durch Phosphatgestein auf Karpfen ( Cyprinus carpio L. ) in 8 unterschiedlichen Applikationen mit jeweils 4 Replikaten zu testen. Der Eintrag wasserloslichen Phosphats wurde bestimmt, urn die Wirkung von Bioturbation, Fischexkrementen und Bodensubstrat zu prüfen. Die Konzentration an Orthophosphat war in den Kontrollen am niedrigsten. Das Einsetzen von Karpfen-Jungfischen erhöhte die Nertozunahme des Orrhophosphats auf 0,1 bis 0,114 mg. ^-1 und diese Zunahme muß den Ausscheidungen der Fische zugeschrieben werden. Die durch die Karpfen verursachte Bioturbation resultiene in einer 72 bis 100% igen Zunahme des Influx des Phosphats aus dem Bodensubstrat wenn Phosphatgestein dem Boden zugegeben wurde, wahrend dieser Wert nur 7–8%) ohne Phosphatgestein betrug.     

Crystal structures of HbA2 and HbE and modeling of hemoglobin delta 4: interpretation of the thermal stability and the antisickling effect of HbA2 and identification of the ferrocyanide binding site in Hb

Hemoglobin A(2) (alpha(2)delta(2)) is an important hemoglobin variant which is a minor component (2-3%) in the circulating red blood cells, and its elevated concentration in beta-thalassemia is a useful clinical diagnostic. In beta-thalassemia major, where there is beta-chain production failure, HbA(2) acts as the predominant oxygen deliverer. HbA(2) has two more important features. (1) It is more resistant to thermal denaturation than HbA, and (2) it inhibits the polymerization of deoxy sickle hemoglobin (HbS). Hemoglobin E (E26K(beta)), formed as a result of the splice site mutation on exon 1 of the beta-globin gene, is another important hemoglobin variant which is known to be unstable at high temperatures. Both heterozygous HbE (HbAE) and homozygous HbE (HbEE) are benign disorders, but when HbE combines with beta-thalassemia, it causes E/beta-thalassemia which has severe clinical consequences. In this paper, we present the crystal structures of HbA(2) and HbE at 2.20 and 1.74 A resolution, respectively, in their R2 states, which have been used here to provide the probable explanations of the thermal stability and instability of HbA(2) and HbE. Using the coordinates of R2 state HbA(2), we modeled the structure of T state HbA(2) which allowed us to address the structural basis of the antisickling property of HbA(2). Using the coordinates of the delta-chain of HbA(2) (R2 state), we also modeled the structure of hemoglobin homotetramer delta(4) that occurs in the case of rare HbH disease. From the differences in intersubunit contacts among beta(4), gamma(4), and delta(4), we formed a hypothesis regarding the possible tetramerization pathway of delta(4). The crystal structure of a ferrocyanide-bound HbA(2) at 1.88 A resolution is also presented here, which throws light on the location and the mode of binding of ferrocyanide anion with hemoglobin, predominantly using the residues involved in DPG binding. The pH dependence of ferrocyanide binding with hemoglobin has also been investigated.