Interaction of the non-phosphorylated peptide G7-18NATE with Grb7-SH2 domain requires phosphate for enhanced affinity and specificity

Src‐homology (SH2) domains are an attractive target for the inhibition of specific signalling pathways but pose the challenge of developing a truly specific inhibitor. The G7‐18NATE cyclic peptide is reported to specifically inhibit the growth factor receptor bound protein 7 (Grb7) adapter protein, implicated in the progression of several cancer types, via interactions with its SH2 domain. G7‐18NATE effectively inhibits the interaction of Grb7 with ErbB3 and focal adhesion kinase in cell lysates and, with the addition of a cell permeability sequence, inhibits the growth and migration of a number of breast cancer cell lines. It is thus a promising lead in the development of therapeutics targeted to Grb7. Here we investigate the degree to which G7‐18NATE is specific for the Grb7‐SH2 domain compared with closely related SH2 domains including those of Grb10, Grb14, and Grb2 using surface plasmon resonance. We demonstrate that G7‐18NATE binds with micromolar binding affinity to Grb7‐SH2 domain (K_D = 4–6 μm ) compared with 50–200 times lower affinity for Grb10, Grb14, and Grb2 but that this specificity depends critically on the presence of phosphate in millimolar concentrations. Other differences in buffer composition, including use of Tris or 2‐(N‐Morpholino)ethanesulfonic acid or varying the pH, do not impact on the interaction. This suggests that under cellular conditions, G7‐18NATE binds with highest affinity to Grb7. In addition, our findings demonstrate that the basis of specificity of G7‐18NATE binding to the Grb7‐SH2 domain is via other than intrinsic structural features of the protein, representing an unexpected mode of molecular recognition. Copyright © 2011 John Wiley & Sons, Ltd.     

A Simple Novel Agar Diffusion Method for Isolation of Indigenous Microalgae Chlamydomonas sp. CRP7 and Chlorella sp. CB4 from Operational Swampy Top Soil

A simple agar diffusion method is developed where pure colony of Chlamydomonas sp. CRP7 was isolated from Chlorella sp. CB4 mixtures by passing through agar migration with a light exposure of 6,000 lux for 7 h. The main concept behind it is that Chlamydomonas has flagella and the rhodopsin pigment is attracted towards light. Thus the above two microalgae species can be separated from the mixtures as eye spot serves as a navigator and flagella serves as a propeller for Chlamydomonas spp. Further the genomic DNA was isolated and purified from the above mentioned two species after the separation from the mixtures. PCR amplification was carried out for ITS1, 5.8S and ITS2 regions. The amplified products were sequenced and the sequence analysis confirmed that they belong to Chlamydomonas sp. and Chlorella sp. This is an important augmentation for isolation and separation of microalgae.     

A New Secondary Model Developed for the Growth Rate of <Emphasis Type="Italic">Escherichia coli</Emphasis> O157:H7 in Broth

This study was attempted to develop a new exponential sum model to describe the effect of temperature on growth rate (GR) of Escherichia coli O157:H7 in broth. The growth rates of E. coli O157:H7 at different storage temperatures (4, 10, 15, 20, 25, 30, and 35°C) estimated by fitting with the modified Gompertz model were used to develop secondary models such as square root model, Ratkowsky model and exponential sum model. Measures of coefficient of determination (R ²), root mean square error (RMSE) and the sum of squares due to error (SSE) were employed to compare the performances of these three secondary models. Based on these criteria, the developed exponential sum model showed the better goodness-of-fit and performance.     

The sugar,biomass and biofuel potential of temperate by tropical maize hybrids

The demand for biofuels has created a market for feedstocks to meet future energy requirements. Temperate × tropical maize (Zea mays L.) hybrids, which combine high biomass and fermentable stalk sugars, have yet to be considered as a biomass feedstock. Our objective was to evaluate biological potential, genetic variability and impact of nitrogen (N) on biomass, stalk sugar, and biofuel potential of temperate × tropical maize (TTM) hybrids. Twelve TTM hybrids, two grain and silage hybrids were grown in 2008, followed in 2009 by seven earshoot‐bagged TTM hybrids. In both years, they were grown with and without supplemental N (202 kg ha^?1) in Champaign, IL. Plants were sampled for total and partitioned biomass, and analyzed for concentration and content of sugar. The TTM hybrids were 40% taller, exhibited later reproductive maturity, greater flowering asynchrony, and remained green longer. All hybrids responded to supplemental N by producing more biomass and grain, a lower percent of biomass partitioned to stalk and leaf, whereas TTM also had a decreased concentration of sugar. Total average biomass yields were 24 Mg ha^?1 for both the TTM and grain hybrids. However, TTM partitioned 50% more biomass to the stalk and produced 50% more sugar, and had less than half the grain of the commercial hybrids, indicating grain production and sugar accumulation are inversely related. When grain formation was prevented by earshoot bagging, TTM hybrids produced, without supplemental N fertilizer, an average of 4024 kg ha^?1 of sugar, which was three‐ to four‐fold greater than the non earshoot‐bagged TTM and ear removed hybrid. Calculated estimates for ethanol production, considering the potential from sugar, stover and grain, indicate TTM can yield nearly the amount of ethanol per hectare as modern grain hybrids, but with a decreased requirement for supplemental fertilizer N.     

Analysis of the MMP-dependent and independent functions of tissue inhibitor of metalloproteinase-2 on the invasiveness of breast cancer cells

Matrix metalloproteinases (MMPs) are secreted endopeptidases that play an essential role in remodeling the extracellular matrix (ECM). MMPs are primarily active during development, when the majority of ECM remodeling events occurs. In adults, elevated MMP activity has been observed in many pathological conditions such as cancer and osteoarthritis. The proteolytic activity of MMPs is controlled by their natural inhibitors - the tissue inhibitor of metalloproteinases (TIMPs). In addition to blocking MMP-mediated proteolysis, TIMPs have a number of MMP-independent functions including binding to cell surface proteins thereby stimulating signaling cascades. TIMP-2, the most studied member of the family, can both inhibit and activate MMPs directly, as well as inhibit MMP activity indirectly by upregulating expression of RECK, a membrane anchored MMP regulator. While TIMP-2 has been shown to play important roles in breast cancer, we describe how the MMP-independent effects of TIMP-2 can modulate the invasiveness of MCF-7, T47D and MDA-MB-231 breast cancer cells. Using an ALA + TIMP-2 mutant which is devoid of MMP inhibition, but still capable of initiating specific cell signaling cascades, we show that TIMP-2 can differentially affect MMP activity and cellular invasiveness in both an MMP dependent and independent manner. More specifically, MMP activity and invasiveness is increased with the addition of exogenous TIMP-2 in poorly invasive cell lines whereas it is decreased in highly invasive cells lines (MDA-MB-231). Conversely, the addition of ALA + TIMP-2 resulted in decreased invasiveness regardless of cell line.     

Analysis of proteomic changes in roots of soybean seedlings during recovery after flooding

A proteomic approach was used to identify proteins involved in post-flooding recovery in soybean roots. Two-day-old soybean seedlings were flooded with water for up to 3 days. After the flooding treatment, seedlings were grown until 7 days after sowing and root proteins were then extracted and separated using two-dimensional polyacrylamide gel electrophoresis (2-DE). Comparative analysis of 2-D gels of control and 3 day flooding-experienced soybean root samples revealed 70 differentially expressed protein spots, from which 80 proteins were identified. Many of the differentially expressed proteins are involved in protein destination/storage and metabolic processes. Clustering analysis based on the expression profiles of the 70 differentially expressed protein spots revealed that 3 days of flooding causes significant changes in protein expression, even during post-flooding recovery. Three days of flooding resulted in downregulation of ion transport-related proteins and upregulation of proteins involved in cytoskeletal reorganization, cell expansion, and programmed cell death. Furthermore, 7 proteins involved in cell wall modification and S-adenosylmethionine synthesis were identified in roots from seedlings recovering from 1 day of flooding. These results suggest that alteration of cell structure through changes in cell wall metabolism and cytoskeletal organization may be involved in post-flooding recovery processes in soybean seedlings.     

Kidney proteome responses in the teleost fish Paralichthys olivaceus indicate a putative immune response against Streptococcus parauberis

The proteomic response to bacterial infection in a teleost fish (Paralichthys olivaceus) infected with Streptococcus parauberis was analyzed using label-free protein quantitation coupled with LC-MS(E) tandem mass spectrometry. A total of 82 proteins from whole kidney, a major lymphoid organ in this fish, were found to be differentially expressed between healthy and diseased fish analyzed 6, 24, 72 and 120 h post-infection. Among the differentially expressed proteins, those involved in mediating immune responses (e.g., heat shock proteins, cathepsins, goose-type lysozyme and complement components) were most significantly up-regulated by infection. In addition, cell division cycle 48 (CDC48) and calreticulin, which are associated with cellular recovery and glycoprotein synthesis, were up-regulated in the universal protein group, whereas the other proteins in that group were down-regulated. There was continuous activation of expression of immune-associated proteins during infection, but there was also loss of expression of proteins not involved in immune function. We expect that our findings regarding immune response at the protein level would offer new insight into the systemic response to bacterial infection of a major immune organ in teleost fish.     

Effect of the myosin light chain kinase inhibitor ML-7 on the proteome of hearts subjected to ischemia-reperfusion injury

In the development of ischemia/reperfusion (I/R) injury, the role of the myosin light chain (MLC) phosphorylation has been given increased consideration. ML-7, a MLC kinase inhibitor, has been shown to protect cardiac function from I/R, however the exact mechanism remains unclear. Isolated rat hearts were perfused under aerobic conditions (controls) or subjected to I/R in the presence or absence of ML-7. Continuous administration of ML-7 (5 μM) from 10 min before onset of ischemia to the first 10 min of reperfusion resulted in significant recovery of heart contractility. Analysis of gels from two-dimensional electrophoresis revealed eight proteins with decreased levels in I/R hearts. Six proteins are involved in energy metabolism:ATP synthase beta subunit, cytochrome b-c1 complex subunit 1, 24-kDa mitochondrial NADH dehydrogenase, NADH dehydrogenase [ubiquinone] iron-sulfur protein 8, cytochrome c oxidase subunit, and succinyl-CoA ligase subunit. The other two proteins with decreased levels in I/R hearts are: peroxiredoxin-2 and tubulin. Administration of ML-7 increased level of succinyl-CoA ligase, key enzyme involved in the citric acid cycle. The increased level of succinyl-CoA ligase in I/R hearts perfused with ML-7 suggests that the cardioprotective effect of ML-7, at least partially, also may involve increase of energy production.