Structural basis of the differential binding of the SH3 domains of Grb2 adaptor to the guanine nucleotide exchange factor Sos1

Grb2-Sos1 interaction, mediated by the canonical binding of N-terminal SH3 (nSH3) and C-terminal SH3 (cSH3) domains of Grb2 to a proline-rich sequence in Sos1, provides a key regulatory switch that relays signaling from activated receptor tyrosine kinases to downstream effector molecules such as Ras. Here, using isothermal titration calorimetry in combination with site-directed mutagenesis, we show that the nSH3 domain binds to a Sos1-derived peptide containing the proline-rich consensus motif PPVPPR with an affinity that is nearly threefold greater than that observed for the binding of cSH3 domain. We further demonstrate that such differential binding of nSH3 domain relative to the cSH3 domain is largely due to the requirement of a specific acidic residue in the RT loop of the β-barrel fold to engage in the formation of a salt bridge with the arginine residue in the consensus motif PPVPPR. While this role is fulfilled by an optimally positioned D15 in the nSH3 domain, the chemically distinct and structurally non-equivalent E171 substitutes in the case of the cSH3 domain. Additionally, our data suggest that salt tightly modulates the binding of both SH3 domains to Sos1 in a thermodynamically distinct manner. Our data further reveal that, while binding of both SH3 domains to Sos1 is under enthalpic control, the nSH3 binding suffers from entropic penalty in contrast to entropic gain accompanying the binding of cSH3, implying that the two domains employ differential thermodynamic mechanisms for Sos1 recognition. Our new findings are rationalized in the context of 3D structural models of SH3 domains in complex with the Sos1 peptide. Taken together, our study provides structural basis of the differential binding of SH3 domains of Grb2 to Sos1 and a detailed thermodynamic profile of this key protein-protein interaction pertinent to cellular signaling and cancer.     

Time dependent effects of gentamicin on the enzymes of carbohydrate metabolism, brush border membrane and oxidative stress in rat kidney tissues

Gentamicin (GM), an antibiotic against life threatening bacterial infection, induces remarkable toxicity in the kidney. Histological studies have indicated that mitochondria, microsomes, lysosomes and plasma membranes of renal proximal convoluted tubules in particular are major GM targets. Despite numerous investigations, the biochemical/cellular basis of GM nephrotoxicity is not well understood. Recently reactive oxygen species (ROS) are considered to be important mediators of GM-induced nephrotoxicity. We hypothesize that GM causes damage to intracellular organelles and affects their structural integrity and alters metabolic and other functional capabilities. To address above hypothesis a long-term, time-dependent effect of GM has been studied on blood/urine parameters, enzymes of carbohydrate metabolism, brush border membrane (BBM) and basolateral (BLM), lysosomes and oxidative stress in renal tissues. A nephrotoxic dose of GM (80 mg/kg body weight) was administered to rats daily for 15 days. The long-term treatment with GM induced a significant increase in serum creatinine, blood urea nitrogen followed by massive proteinuria, glucosuria, enzymuria along with loss of electrolytes in the urine. The activities of the enzymes of carbohydrate metabolism, plasma membranes, lysosomes significantly declined. The activities of antioxidant enzymes e.g. superoxide dismutase, catalase and glutathione peroxidase were severely depressed and lipid peroxidation was significantly increased in the renal cortex and medulla. We conclude that GM administration induced oxidative damage to renal tissues that resulted in impaired carbohydrate metabolism and decreased activities of BBM, BLM and lysosomes associated with increased lipid peroxides.     

Role of ghrelin axis in colorectal cancer: a novel association

Recently discovered orexigenic peptide, ghrelin, which is primarily produced by gastrointestinal tract, has been implicated in the malignant cell proliferation and invasion, presumably through an autocrine/paracrine mechanism. This study was aimed to identify the role of endogenously produced ghrelin in colorectal cancer progression. Malignant intestinal epithelial cells differentially over-express ghrelin receptors and produce more ghrelin as compared to normal human colonocytes, leading to their enhanced proliferative and invasive behavior. Though, systemically available endocrine ghrelin levels in patients with colorectal cancer do not exhibit significant correlation with any tumor stage or grade, however, locally produced autocrine tissue ghrelin strongly correlates both with advancing colorectal malignancy in a stage-dependent manner and BMI of the colorectal patients. We conclude that ghrelin might play an important role in promoting colorectal malignancy.     

Studies on the protective effect of dietary fish oil on gentamicin-induced nephrotoxicity and oxidative damage in rat kidney

Gentamicin (GM)-induced nephrotoxicity limits its long-term clinical use. Several agents/strategies were attempted to prevent GM nephrotoxicity but were not found suitable for clinical practice. Dietary fish oil (FO) retard the progression of certain types of cancers, cardiovascular and renal disorders. We aimed to evaluate protective effect of FO on GM-induced renal proximal tubular damage. The rats were pre-fed experimental diets for 10 days and then received GM (80 mg/kg body weight/day) treatment for 10 days while still on diet. Serum/urine parameters, enzymes of carbohydrate metabolism, brush border membrane (BBM), oxidative stress and phosphate transport in rat kidney were analyzed. GM nephrotoxicity was recorded by increased serum creatinine and blood urea nitrogen. GM increased the activities of lactate and glucose-6-phosphate dehydrogenases whereas decreased malate, isocitrate dehydrogenases; glucose-6 and fructose-1,6-bisphosphatases; superoxide dismutase, catalase, glutathione peroxidase and BBM enzymes. In contrast, FO alone increased enzyme activities of carbohydrate metabolism, BBM and oxidative stress. FO feeding to GM treated rats markedly enhanced resistance to GM elicited deleterious effects and prevented GM-induced decrease in 32Pi uptake across BBM. Dietary FO supplementation ameliorated GM-induced specific metabolic alterations and oxidative damage due to its intrinsic biochemical/antioxidant properties.     

Cultivation and ecosystem role of a marine roseobacter clade-affiliated cluster bacterium

Isolation and cultivation are a crucial step in elucidating the physiology, biogeochemistry, and ecosystem role of microorganisms. Many abundant marine bacteria, including the widespread Roseobacter clade-affiliated (RCA) cluster group, have not been cultured with traditional methods. Using novel techniques of cocultivation with algal cultures, we have accomplished successful isolation and propagation of a strain of the RCA cluster. Our experiments revealed that, in addition to growing on alga-excreted organic matter, additions of washed bacterial cells led to significant biomass decrease of dinoflagellate cultures as measured by in vivo fluorescence. Bacterial filtrate did not adversely affect the algal cultures, suggesting attachment-mediated activity. Using an RCA cluster-specific rRNA probe, we documented increasing attachment of these algicidal bacteria during a dinoflagellate bloom, with a maximum of 70% of the algal cells colonized just prior to bloom termination. Cross-correlation analyses between algal abundances and RCA bacterial colonization were statistically significant, in agreement with predator-prey models suggesting that RCA cluster bacteria caused algal bloom decline. Further investigation of molecular databases revealed that RCA cluster bacteria were numerically abundant during algal blooms sampled worldwide. Our findings suggest that the widespread RCA cluster bacteria may exert significant control over phytoplankton biomass and community structure in the oceans. We also suggest that coculture with phytoplankton may be a useful strategy to isolate and successfully grow previously uncultured but ecologically abundant marine heterotrophs.     

Ethnopharmacological studies of indigenous plants in Kel village,Neelum Valley,Azad Kashmir,Pakistan

Background

This explorative study was undertaken for the first time in Kel village located in the Upper Neelum Valley, Azad Kashmir, Pakistan. The purpose was to document the indigenous knowledge of the native people used in the preparation of herbal medicines.

Methods

To get the data on traditional uses of medicinal plants, 20 informants were interviewed. Quantitative ethnobotanical indices, i.e., use value (UV), relative frequencies of citation (RFC), informant consensus factor (Fic), fidelity level (FL), data matrix ranking (DMR), preference ranking (PR), and jaccard index (JI), were calculated for the recorded medicinal plants.

Results

A total of 50 medicinal plants belonging to 33 families used in 13 disease categories were documented. Leaves were the frequently used plant parts, and decoction was the commonly used method for herbal medicine. Plants with high use value were Berberis lycium (2.05), Impatiens glandulifera (1.95), Artemisia scoparia (1.75), Ageratum conozoides (1.75), and Achillea millefolium (1.7). The highest RFC value was calculated for Berberis lycium (0.75), Cynoglossum lanceolatum (0.65), and Impatiens glandulifera and Achillea millefolium (0.60 each). The maximum informant consensus factor was for urinary system, cardiac diseases, baldness, and abortion and miscarriage (1.00). Berberis lyceum (95%) used in jaundice, hepatitis, typhoid, fever, and tuberculosis disorders. Plants with maximum fidelity level (FL) were Berberis lycium (95%) followed by Dioscorea bulbifera, Impatiens glandulifera, and Artemisia vulgaris (90%). Olea ferruginea was the most multipurpose plant and exports (21.2%) was the leading threat in the area. The pearson correlation coefficient (0.500) showed a positive correlation between the use value and relative frequency of citation.

Conclusion

The present study provides useful information about traditional uses of medicinal plants used by local communities in different ailments. The plants with the highest use values could be employed in pharmacological research and biotechnological approaches in order to achieve adequate revenue. Some of the plants in the study area are facing high threats of becoming rare, and conservation initiatives are needed to conserve them for sustainable management in the region.

     

Growth of Vibrio cholerae O1 in Red Tide Waters off California

Vibrio cholerae serotype O1 is autochthonous to estuarine and coastal waters. However, its population dynamics in such environments are not well understood. We tested the proliferation of V. cholerae N16961 during a Lingulodinium polyedrum bloom, as well as other seawater conditions. Microcosms containing 100-kDa-filtered seawater were inoculated with V. cholerae or the 0.6-μm-pore-size filterable fraction of seawater assemblages. These cultures were diluted 10-fold with fresh 100-kDa-filtered seawater every 48 h for four cycles. Growth rates ranged from 0.3 to 14.3 day⁻¹ (4.2 day⁻¹ ± 3.9) for V. cholerae and 0.1 to 9.7 day⁻¹ (2.2 ± 2.8 day⁻¹) for bacterial assemblage. Our results suggest that dissolved organic matter during intense phytoplankton blooms has the potential to support explosive growth of V. cholerae in seawater. Under the conditions tested, free-living V. cholerae was able to reach concentrations per milliliter that were up to 3 orders of magnitude higher than the known minimum infectious dose (10⁴ cell ml⁻¹) and remained viable under many conditions. If applicable to the complex conditions in marine ecosystems, our results suggest an important role of the growth of free-living V. cholerae in disease propagation and prevention during phytoplankton blooms.     

Distribution of AB0 and RH blood group alleles in different populations of southern Punjab, Pakistan.

The analysis of a sample of 1632 individuals from patients of the Nishtar Teaching Hospital, Multan, suggests that different ethnic groups (Araeen, Mughals, Syed, Jat, Rajputs, Baloch and Pathan) are not significantly different from another with regard to the distribution of RH blood group alleles (RH*d around 0.30). The distributions of the AB0 blood group alleles suggest that different ethnic groups are not significantly different from the average alele frequencies (AB0*A = 0.23, AB0*B = 0.33, AB0*0 = 0.47) except for the Pathan ethnic group (AB0*A = 0.35, AB0*B = 0.47, AB0*0 = 0.27). The populations of different geographic areas are not significantly different from the average allele frequencies, except for the southern district of Rahim Yar Khan (AB0*A = 0.12) and the northern district of Sahiwal (AB0*A = 0.19). The populations of Sahiwal (RH*d = 0.35) and Muzaffargarh (RH*d = 0.36) yield significantly different allele frequencies at the RH locus. The interpopulation differences can be explained by the geographic distance. There is a significant difference in the frequencies of the AB0 alleles between rural and urban populations, suggesting that rural populations maintain their isolation from urban populations. Rural and urban populations are not significantly different from one another concerning the allele frequencies at the RH locus.