Optimal design for the maximization of Penicillium cyclopium lipase production

Penicillium cyclopium triacylglycerol lipase production was maximized in stationary batch culture. We used a surface response methodology based on a Doehlert experimental design to study the effect on the lipase activity released in the culture medium of the three most important factors: substrate concentration, pH and inoculum. Besides reducing the number of experiments required for optimization, this technique allowed us to quantify the lipase activity in any part of the experimental domain.We determined an optimal set of conditions for high lipase production: 1% substrate (corn steep), pH 5.5 and an inoculum of 10(4) spores/ml. Between conditions giving the minimum and the maximum lipase production, we observed a nine-fold increase of both the predicted and measured values.     

Enhancement in leghemoglobin content of root nodules by exclusion of solar UV-A and UV-B radiation in soybean

The impact of exclusion of solar UV-B (280–320 nm) and UV-A+B (280–400 nm) radiation on the root nodules was studied in soybean(Glycine max var. MACS 330). Soybean plants were grown in the tropical region of Indore (Latitude-22.4°N), India under field conditions in metal cages covered with polyester exclusion filters that specifically cut off UV-B (<320 nm) and UV-A+B (<400 nm) radiation; control plants were grown under ambient solar radiation. Leghemoglobin content was analyzed in the root nodules on the 50^th day after emergence of seedlings. Exclusion of UV radiations significantly enhanced the leghemoglobin content in the nodules on fresh weight basis; 25% and 45% higher amount of leghemoglobin were present in the nodules after the exclusion of UV-B and UV-A+B radiation respectively. Analysis by native and SDS-PAGE showed high intense bands of leghemoglobin after the exclusion of UV-A+B as compared to control. Exclusion of UV radiation also enhanced the growth of roots as well as aerial parts of the plants. UV Exclusion increased nodulation by increase in the number and size of nodules. The results are discussed in the light of advantage of exclusion for enhancing protein/nitrogen content in the plants.     

Enhanced toxic metal accumulation in engineered bacterial cells expressing Arabidopsis thaliana phytochelatin synthase

Phytochelatins (PCs) are metal-binding cysteine-rich peptides, enzymatically synthesized in plants and yeasts from glutathione in response to heavy metal stress by PC synthase (EC 2.3.2.15). In an attempt to increase the ability of bacterial cells to accumulate heavy metals, the Arabidopsis thaliana gene encoding PC synthase (AtPCS) was expressed in Escherichia coli. A marked accumulation of PCs was observed in vivo together with a decrease in the glutathione cellular content. When bacterial cells expressing AtPCS were placed in the presence of heavy metals such as cadmium or the metalloid arsenic, cellular metal contents were increased 20- and 50-fold, respectively. We discuss the possibility of using genes of the PC biosynthetic pathway to design bacterial strains or higher plants with increased abilities to accumulate toxic metals, and also arsenic, for use in bioremediation and/or phytoremediation processes.     

Nitrilotriacetate stimulation of anaerobic Fe(III) respiration by mobilization of humic materials in soil

An enrichment culture capable of naphthalene mineralization reduced Fe(III) oxides without direct contact in anaerobic soil microcosms when the Fe(III) was placed in dialysis membranes or entrapped within alginate beads. Both techniques demonstrated that a component in soil, possibly humic materials, facilitated Fe(III) reduction when direct contact between cells and Fe(III) was not possible. The addition of the synthetic Fe(III) chelator, nitrilotriacetic acid (NTA), to soil enhanced Fe(III) reduction across the dialysis membrane and alginate beads, with the medium changing from clear to a dark brown color. An NTA-soil extract was more effective in Fe(III) reduction than the extracted soil itself. Characteristics of the NTA extract were consistent with that of humic substances. The results indicate that NTA improved Fe(III) reduction not by Fe(III) solubilization but by extraction of humic substances from soil into the aqueous medium. This is the first study in which stimulation of Fe(III) reduction through the addition of chemical chelators is shown to be due to the extraction of electron-shuttling compounds from the soil and not to solubilization of the Fe(III) and indicates that mobilization of humic materials could be an important component of anaerobic biostimulation.     

Maximizing production of Penicillium cyclopium partial acylglycerol lipase

Penicillium cyclopium partial acylglycerol lipase production was maximized in shaken batch culture. The effect of inoculum size and substrate concentration on the lipase activity released in the culture medium was visualized using a surface response methodology based on a Doehlert experimental design. The main advantage of this approach is the low number of experiments required to construct a predictive model of the experimental domain. Substrate percentage (corn steep, w/v) ranged from 0.1% to 1.9% and inoculum from 100 spores/ml to 3,200 spores/ml. We determined that an optimal set of experimental conditions for high lipase production was 1.0% substrate and 3,200 spores/ml, with initial pH 5.0, temperature 25 degrees C and shaking speed 120 rpm. Between the conditions giving the minimum and the maximum lipase production, we observed a three-fold increase in both the predicted and the measured values.     

Assessing unmodified 70-mer oligonucleotide probe performance on glass-slide microarrays

Background

Long oligonucleotide microarrays are potentially more cost- and management-efficient than cDNA microarrays, but there is little information on the relative performance of these two probe types. The feasibility of using unmodified oligonucleotides to accurately measure changes in gene expression is also unclear.

Results

Unmodified sense and antisense 70-mer oligonucleotides representing 75 known rat genes and 10 Arabidopsis control genes were synthesized, printed and UV cross-linked onto glass slides. Printed alongside were PCR-amplified cDNA clones corresponding to the same genes, enabling us to compare the two probe types simultaneously. Our study was designed to evaluate the mRNA profiles of heart and brain, along with Arabidopsis cRNA spiked into the labeling reaction at different relative copy number. Hybridization signal intensity did not correlate with probe type but depended on the extent of UV irradiation. To determine the effect of oligonucleotide concentration on hybridization signal, 70-mers were serially diluted. No significant change in gene-expression ratio or loss in hybridization signal was detected, even at the lowest concentration tested (6.25 μm). In many instances, signal intensity actually increased with decreasing concentration. The correlation coefficient between oligonucleotide and cDNA probes for identifying differentially expressed genes was 0.80, with an average coefficient of variation of 13.4%. Approximately 8% of the genes showed discordant results with the two probe types, and in each case the cDNA results were more accurate, as determined by real-time PCR.

Conclusions

Microarrays of UV cross-linked unmodified oligonucleotides provided sensitive and specific measurements for most of the genes studied.     

Carbon starvation survival of Listeria monocytogenes in planktonic state and in biofilm: a proteomic study

The proteomes of Listeria monocytogenes expressed in suspension and biofilm state, in the presence and absence of a carbon source, were analysed by two-dimensional electrophoresis with the help of computer software. The up-regulated proteins in each case were identified by peptide sequencing using electrospray ionisation tandem mass spectrometry and a database search against the Listeria genome was performed. Relevant functions could be attributed to a number of the induced proteins which contribute to the understanding of the mechanisms of starvation survival of L. monocytogenes in planktonic state and in biofilm.     

A novel Arnt-interacting protein Ainp2 enhances the aryl hydrocarbon receptor signalling

In an effort to better understand the Ah receptor nuclear translocator (Arnt)-dependent signaling mechanisms, we employed a phage display system to identify Arnt-interacting peptides. Human liver cDNA library was utilized to screen for Arnt-interacting peptides using an Arnt construct fused to thioredoxin (TH-ArntCDelta418). Two clones, namely Ainp1 and Ainp2 (Arnt-interacting peptide), were identified and subsequently Ainp2 was further characterized. Ainp2 interacts with TH-ArntCDelta418 in the GST pull-down and mammalian two-hybrid assays. Northern blot results revealed that Ainp2 is predominantly expressed in human liver. The putative full-length Ainp2 cDNA sequence was subsequently cloned using RACE PCR. Endogenous expression of Ainp2 was found in Jurkat cells at the mRNA and protein levels. Results from the transient transfection studies using a DRE-driven reporter plasmid and the real-time QPCR experiments examining the endogenous CYP1A1 expression showed that Ainp2 enhances the 3-methylchloranthrene-induced activity in HepG2 cells, suggesting that Ainp2 plays a role in the Arnt-dependent function     

Inhibitor of DNA binding/differentiation helix-loop-helix proteins mediate bone morphogenetic protein-induced osteoblast differentiation of mesenchymal stem cells

Bone morphogenetic proteins (BMPs) belong to the TGF-beta superfamily and play an important role in development and in many cellular processes. We have found that BMP-2, BMP-6, and BMP-9 induce the most potent osteogenic differentiation of mesenchymal stem cells. Expression profiling analysis has revealed that the Inhibitors of DNA binding/differentiation (Id)-1, Id-2, and Id-3 are among the most significantly up-regulated genes upon BMP-2, BMP-6, or BMP-9 stimulation. Here, we sought to determine the functional role of these Id proteins in BMP-induced osteoblast differentiation. We demonstrated that the expression of Id-1, Id-2, and Id-3 genes was significantly induced at the early stage of BMP-9 stimulation and returned to basal levels at 3 days after stimulation. RNA interference-mediated knockdown of Id expression significantly diminished the BMP-9-induced osteogenic differentiation of mesenchymal progenitor cells. Surprisingly, a constitutive overexpression of these Id genes also inhibited osteoblast differentiation initiated by BMP-9. Furthermore, we demonstrated that BMP-9-regulated Id expression is Smad4-dependent. Overexpression of the three Id genes was shown to promote cell proliferation that was coupled with an inhibition of osteogenic differentiation. Thus, our findings suggest that the Id helix-loop-helix proteins may play an important role in promoting the proliferation of early osteoblast progenitor cells and that Id expression must be down-regulated during the terminal differentiation of committed osteoblasts, suggesting that a balanced regulation of Id expression may be critical to BMP-induced osteoblast lineage-specific differentiation of mesenchymal stem cells.     

Characterization of AtCHX17, a member of the cation/H+ exchangers, CHX family, from Arabidopsis thaliana suggests a role in K+ homeostasis

The Arabidopsis genome contains many sequences annotated as encoding H(+)-coupled cotransporters. Among those are the members of the cation:proton antiporter-2 (CPA2) family (or CHX family), predicted to encode Na(+),K(+)/H(+) antiporters. AtCHX17, a member of the CPA2 family, was selected for expression studies, and phenotypic analysis of knockout mutants was performed. AtCHX17 expression was only detected in roots. The gene was strongly induced by salt stress, potassium starvation, abscisic acid (ABA) and external acidic pH. Using the beta-glucuronidase reporter gene strategy and in situ RT-PCR experiments, we have found that AtCHX17 was expressed preferentially in epidermal and cortical cells of the mature root zones. Knockout mutants accumulated less K(+) in roots in response to salt stress and potassium starvation compared with the wild type. These data support the hypothesis that AtCHX17 is involved in K(+) acquisition and homeostasis.