Chemotaxis of a Ralstonia sp. SJ98 toward co-metabolizable nitroaromatic compounds

We have earlier reported chemotaxis of a Gram-negative, motile Ralstonia sp. SJ98 towards p-nitrophenol (PNP), 4-nitrocatechol (NC), o-nitrobenzoate (ONB), p-nitrobenzoate (PNB), and 3-methyl-4-nitrophenol (MNP) that also served as sole source of carbon and energy to the strain [S.K. Samanta, B. Bhushan, A. Chauhan, R.K. Jain, Biochem. Biophy. Res. Commun. 269 (2000) 117; B. Bhushan, S.K. Samanta, A. Chauhan, A.K. Chakraborti, R.K. Jain, Biochem. Biophy. Res. Commun. 275 (2000) 129]. In this paper, we report chemotaxis of a Ralstonia sp. SJ98 toward seven different nitroaromatic compounds (NACs) by drop assay, swarm plate assay, and capillary assay. These NACs do not serve as sole carbon and energy source to strain SJ98 but are partially transformed in the presence of an alternate carbon source such as succinate. This is the first report showing chemotaxis of a bacterial strain toward co-metabolizable NACs.     

EGFR kinase activity is required for TLR4 signaling and the septic shock response

Mammalian Toll-like receptors (TLR) recognize microbial products and elicit transient immune responses that protect the infected host from disease. TLR4—which signals from both plasma and endosomal membranes—is activated by bacterial lipopolysaccharides (LPS) and induces many cytokine genes, the prolonged expression of which causes septic shock in mice. We report here that the expression of some TLR4-induced genes in myeloid cells requires the protein kinase activity of the epidermal growth factor receptor (EGFR). EGFR inhibition affects TLR4-induced responses differently depending on the target gene. The induction of interferon-β (IFN-β) and IFN-inducible genes is strongly inhibited, whereas TNF-α induction is enhanced. Inhibition is specific to the IFN-regulatory factor (IRF)-driven genes because EGFR is required for IRF activation downstream of TLR—as is IRF co-activator β-catenin—through the PI3 kinase/AKT pathway. Administration of an EGFR inhibitor to mice protects them from LPS-induced septic shock and death by selectively blocking the IFN branch of TLR4 signaling. These results demonstrate a selective regulation of TLR4 signaling by EGFR and highlight the potential use of EGFR inhibitors to treat septic shock syndrome.     

Molecular interaction of bZIP domains of GBF1, HY5 and HYH in Arabidopsis seedling development

The bZIP proteins, GBF1, HY5 and HYH, play important regulatory roles in Arabidopsis seedling development. Whereas GBF1 plays a dual regulatory role, HY5 and HYH act as positive regulators of photomorphogenesis. The molecular and functional relations of GBF1 with HY5 and HYH in photomorphogenesis have recently been demonstrated. However, the possible interaction of bZIP domain of each of these proteins remains to be investigated. In this study, our results suggest that bZIP domains of HY5 and HYH are able to interact with the bZIP domain of GBF1. Taken together with the earlier study,⁹ these results suggest that the N-terminal domain of GBF1 has an inhibitory effect on its interaction with HY5 and HYH.     

Characterization of the structures and dynamics of phosphoric acid doped benzimidazole mixtures: a molecular dynamics study

Benzimidazole-based polymer membranes like poly(2,5-benzimidazole) (ABPBI) doped with phosphoric acid (PA) are electrolytes that exhibit high proton conductivity in fuel cells at elevated temperatures. The benzimidazole (BI) moiety is an important constituent of these membranes, so the present work was performed in order to achieve a molecular understanding of the BI–PA interactions in the presence of varying levels of the PA dopant, using classical molecular dynamics (MD) simulations. The various hydrogen-bonding interactions, as characterized based on structural properties and hydrogen-bond lifetime calculations, show that both BI and PA molecules exhibit dual proton-acceptor/donor functionality. An examination of diffusion coefficients showed that the diffusion of BI decreases with increasing PA uptake, whereas the diffusion of PA slightly increases. The hydrogen-bond lifetime calculations pointed to the existence of competitive hydrogen bonding between various sites in BI and PA.

Responses to Light Intensity in a Genome-Scale Model of Rice Metabolism

We describe the construction and analysis of a genome-scale metabolic model representing a developing leaf cell of rice (Oryza sativa) primarily derived from the annotations in the RiceCyc database. We used flux balance analysis to determine that the model represents a network capable of producing biomass precursors (amino acids, nucleotides, lipid, starch, cellulose, and lignin) in experimentally reported proportions, using carbon dioxide as the sole carbon source. We then repeated the analysis over a range of photon flux values to examine responses in the solutions. The resulting flux distributions show that (1) redox shuttles between the chloroplast, cytosol, and mitochondrion may play a significant role at low light levels, (2) photorespiration can act to dissipate excess energy at high light levels, and (3) the role of mitochondrial metabolism is likely to vary considerably according to the balance between energy demand and availability. It is notable that these organelle interactions, consistent with many experimental observations, arise solely as a result of the need for mass and energy balancing without any explicit assumptions concerning kinetic or other regulatory mechanisms.Rice (Oryza sativa) makes up nearly 20% of the total caloric intake for the human population as a whole; the income of more than 100 million households in developing countries depends on rice cultivation. Although rice yield has increased, though gradually more slowly, during the last four decades, the world population continues to grow, while the land and water resources for cultivation are declining, leading to a need for high-yielding, stress-tolerant, nutrient-rich rice cultivars (Nguyen and Ferrero, 2006).Researchers are trying to meet the challenges of improving production in different ways. Some of the efforts include (1) identifying the stress-tolerant rice varieties and stress-responsive genes (Xiang et al., 2007), (2) producing a “Green Super Rice” combining, in a single plant, many different favorable characteristics from the large number of available strains and cultivars, guided by molecular marker-based selection (Zhang, 2007), (3) introducing the genes of C₄ plant to change the leaf anatomy of rice and hence improving the photosynthesis (Kajala et al., 2011), and (4) producing vitamin A-enriched golden rice (Al-Babili and Beyer, 2005). In addition, current research on the genetic basis of signaling between nitrogen-fixing soil bacteria and legumes (Xie et al., 2012) has the potential to allow the engineering of nodule formation in cereal crops such as rice and wheat (Triticum aestivum).Here, we present a genome-scale model of rice metabolism and examine its responses to changing light availability. Because rice is also a model organism for other cereal crops, such as wheat, this effort should help researchers to understand the biochemistry of a photosynthetic crop plant as well as to compare it with other plants. In addition, the metabolic model of rice, which is the second metabolic model of a crop plant, can be used as a template for comparing the metabolism of different varieties of rice that are pathogen tolerant, drought tolerant, lower or higher yield, etc., and thus, it may also help in identifying characteristics of individual varieties that may assist rice biotechnologists to breed the desired rice crop.     

Inactivation of the mitochondrial carrier SLC25A25 (ATP-Mg2+/Pi transporter) reduces physical endurance and metabolic efficiency in mice

An ATP-Mg(2+/)P(i) inner mitochondrial membrane solute transporter (SLC25A25), which is induced during adaptation to cold stress in the skeletal muscle of mice with defective UCP1/brown adipose tissue thermogenesis, has been evaluated for its role in metabolic efficiency. SLC25A25 is thought to control ATP homeostasis by functioning as a Ca(2+)-regulated shuttle of ATP-Mg(2+) and P(i) across the inner mitochondrial membrane. Mice with an inactivated Slc25a25 gene have reduced metabolic efficiency as evidenced by enhanced resistance to diet-induced obesity and impaired exercise performance on a treadmill. Mouse embryo fibroblasts from Slc25a25(-/-) mice have reduced Ca(2+) flux across the endoplasmic reticulum, basal mitochondrial respiration, and ATP content. Although Slc25a25(-/-) mice are metabolically inefficient, the source of the inefficiency is not from a primary function in thermogenesis, because Slc25a25(-/-) mice maintain body temperature upon acute exposure to the cold (4 °C). Rather, the role of SLC25A25 in metabolic efficiency is most likely linked to muscle function as evidenced from the physical endurance test of mutant mice on a treadmill. Consequently, in the absence of SLC25A25 the efficiency of ATP production required for skeletal muscle function is diminished with secondary effects on adiposity. However, in the absence of UCP1-based thermogenesis, induction of Slc25a25 in mice with an intact gene may contribute to an alternative thermogenic pathway for the maintenance of body temperature during cold stress.     

Novel fluorescence detection technique for non-contact temperature sensing in microchip PCR

DNA amplification using Polymerase Chain Reaction (PCR) in a small volume is used in Lab-on-a-chip systems involving DNA manipulation. For few microliters of volume of liquid, it becomes difficult to measure and monitor the thermal profile accurately and reproducibly, which is an essential requirement for successful amplification. Conventional temperature sensors are either not biocompatible or too large and hence positioned away from the liquid leading to calibration errors. In this work we present a fluorescence based detection technique that is completely biocompatible and measures directly the liquid temperature. PCR is demonstrated in a 3 muL silicon-glass microfabricated device using non-contact induction heating whose temperature is controlled using fluorescence feedback from SYBR green I dye molecules intercalated within sensor DNA. The performance is compared with temperature feedback using a thermocouple sensor. Melting curve followed by gel electrophoresis is used to confirm product specificity after the PCR cycles.     

Evaluation of rapid molecular diagnostics for differentiating medicinal Kaempferia species from its adulterants

Accurate detection of unique herbs is crucial for herbal medicine preparation. Zingiberaceae species, which are important in Ayurvedic medicine of India, are often misidentified in Northeast (NE) Indian herbal markets. Kaempferia galanga (Zingiberaceae) is one of the major components of popular Ayurvedic drugs used for rheumatic diseases (i.e.,“Gandha Thailam” and “Rasnairandadi Kashayam”), contusions, fractures, and sprains. In NE India, herbal healers often misidentify plants from the Marantaceae family (e.g., Calathea bachemiana and Maranta leuconeura) as Kaempferia, which leads to adulteration of the medicinal herb. This misidentification of herbs occurs in NE India because Zingiberaceae plant barcoding information is inadequate. As a consequence, herbal medicine is not only therapeutically less effective but may also cause adverse reactions that range from mild to life-threatening. In this study, we used eight barcoding loci to develop “fingerprints” for four Kaempferia species and two species frequently mistaken for Kaempferia. The PCR and sequencing success of the loci matK, rbcL and trnH-psbA were found to be 100%;the combination of matK, rbcL, and trnH-psbA proved to be the ideal locus for discriminating the Kaempferia species from their adulterants because the combined loci showed greater variability than individual loci. This reliable tool was therefore developed in the current study for accurate identification of Kaempferia plants which can effectively resolve identification issues for herbal healers.