Large-scale discovery and characterization of protein regulatory motifs in eukaryotes

The increasing ability to generate large-scale, quantitative proteomic data has brought with it the challenge of analyzing such data to discover the sequence elements that underlie systems-level protein behavior. Here we show that short, linear protein motifs can be efficiently recovered from proteome-scale datasets such as sub-cellular localization, molecular function, half-life, and protein abundance data using an information theoretic approach. Using this approach, we have identified many known protein motifs, such as phosphorylation sites and localization signals, and discovered a large number of candidate elements. We estimate that ~80% of these are novel predictions in that they do not match a known motif in both sequence and biological context, suggesting that post-translational regulation of protein behavior is still largely unexplored. These predicted motifs, many of which display preferential association with specific biological pathways and non-random positioning in the linear protein sequence, provide focused hypotheses for experimental validation.     

Stereoselective synthesis of a conformationally defined cyclohexyl carnitine analogue that binds CPT-1 with high affinity.

Carnitine (1, 3-hydroxy-4-trimethylammoniobutyrate) is important in mammalian tissue as a carrier of acyl groups. In order to explore the binding requirements of the carnitine acyltransferases for carnitine, we designed conformationally defined cyclohexyl carnitine analogues. These diastereomers contain the required gauche conformation between the trimethylammonium and hydroxy groups but vary the conformation between the hydroxy and carboxylic acid groups. Here we describe the synthesis and biological activity of the all-trans diastereomer (2), which was prepared by the ring opening of trans-methyl 2,3-epoxycylohexanecarboxylate with NaN3. Racemic 2 was a competitive inhibitor of neonatal rat cardiac myocyte CPT-1 (K(i) 0.5 mM for racemic 2; K(m) 0.2 mM for L-carnitine) and a noncompetitive inhibitor of neonatal rat cardiac myocyte CPT-2 (K(i) 0.67 mM). These results suggest that 2 represents the bound conformation of carnitine for CPT-1.     

Cyclotrisiloxan and β-Sitosterol rich Cassia alata (L.) flower inhibit HT-115 human colon cancer cell growth via mitochondrial dependent apoptotic stimulation

Cancer traits dependent chemo and radiotherapy display acute toxicity and long-term side effects. Since last two decades, researchers investigated a new anticancer agents derived from plants. Cassia alata (L.) is a medicinal herb distributed in the tropical and humid regions. In this study, C. alata flower methanol extract (CME) have been prepared using cold percolation method and the phytochemical components were identified using GC–MS analysis. CME have been used to study the antiproliferative and apoptosis properties against human colon cancer HT-115 colon cancer cells, its molecular mechanism have been explored. 0.2 mg/mL dose of CME, inhibited 50% of HT-115 colon cancer cell growth after 48hr was confirmed the significant antiproliferation effect. In normal cells such as Vero cells and hMSCs, 0.2 mg/mL dose of CME shown only 4% and 5% growth inhibition confirmed the HT-115 cell specific cytotoxic effect. This effect might be due to the availability of phytoactive biomolecules in CME such as, cyclotrisiloxan, beta-sitosterol and alpha-tocopherol have been confirmed by GC–MS. Most interestingly, PI and AO/ErBr staining of CME treated HT-115 cells shown early (25%), pro (17%) and late (8%) apoptotic and 3% necrotic cells after 48 hr. Treatment with CME extract showed potential effect on the inhibition of protumorigenic inflammatory and oxidative stress genes. Protumorigenic COX-2/PGE-2 and TNF-α/NF-κB immune axis were normalized after CME treatment. Amounts of both apoptosis related mRNA p53, Bax, caspase 3 and p21 genes were upregulated, whereas it resulted in significant reduction in the anti-apoptotic marker mdm2 and Bcl-2 genes. In conclusion, bioactive compounds present in CME potentially inhibit HT-115 colon cancer cell proliferation via an inhibition of protumorigenic immune axis and stimulation of mitochondria dependent apoptotic pathway without necrotic effect.     

Differential mobilization and metal uptake versus leaching in multimetal soil columns using EDTA and three metal bioaccumulators

Tannery waste is a major environmental concern that needs proper management. Tannery solid waste (TSW) can be added to the soil as an organic amendment but needs metal removal. Chelant-assisted phytoremediation hastens the process of metal removal but also poses risk of leaching at the same time. This research evaluates Ethylenediaminetetraacetic acid (EDTA)-assisted phytoextraction and associated leaching hazard using metal-tolerant plants. Greenhouse trials were carried out with sunflower, spinach, and marigold using columns of uniform diameter packed with field soil and multimetal contamination of TSW (5% and 10%) with four EDTA doses. The amounts of metal absorbed or leached conformed to amounts in the soil amendment and the dose of EDTA. The mobilization of metals by EDTA was however metal-specific. The metals that were extracted in greater amounts by the plants were leached less compared to Cr and Cu. A significant amount of other metals was leached down and thus less amount was phytoextracted by the plants e.g. Cd and Ni. A high correlation was observed between the amount of metal absorbed by the plant and the amount in leachate except for Cr in all the plants. Antioxidant activities like SOD and catalase were also found to be high in sunflower and spinach.     

Therapeutic effects of Typha elephantina leave’s extract against paracetamol induced renal injury in rabbits

Present study focuses on ameliorative potential of Typha elephantina leave’s aqueous (TE.AQ) extract against Paracetamol (PCM) induced toxicity in rabbits. We fed the male rabbits with 300 mg PCM in alone and in combination with TE.AQ at different doses i.e. (100, 200 and 300 mg/kg body weight) or silymarin (100 mg/kg) daily for 21 days. PCM in alone significantly (P < 0.5) increased serum urea, uric acid, creatinine, total protein, albumin, globulin and blood urea nitrogen. Serum sodium, potassium and magnesium level were high. The glutathione, radical scavenging activity and Thiobarbituric acid reactive substances were significantly reduced. Treatment with TE.AQ at dose rate 300 mg/kg body weight and Silymarin significantly ameliorated all the parameters when compared with PCM administered group. The 100 and 200 mg of TE.AQ showed no significant effects. The histopathological examination confirmed the therapeutic potential of TE.AQ. These results established the presence of natural antioxidants in Typha elephantina leaves.     

Study of interactions between DNA and aflatoxin B1 using electrochemical and fluorescence methods

In this study, a carbon paste electrode modified with N-butylpyridinium hexafluorophosphate (BPPF₆) ionic liquid and DNA was introduced as an electrochemical biosensor to study the interaction between DNA and aflatoxin B1 molecules. For this purpose, variations in oxidation peak current of guanine in various concentrations of aflatoxin B1 were measured by using the differential pulse voltammetry (DPV) method. According to this study, the binding constant of DNA–aflatoxin B1 was found to be 3.5 × 10⁶ M⁻¹. This modified electrode was also used for determination of low concentrations of aflatoxin B1 by using differential pulse voltammetry. A linear dynamic range from 8.00 × 10⁻⁸ to 5.91 × 10⁻⁷ M and a limit of detection of 2.00 × 10⁻⁸ M resulted from DPV measurements. To confirm our results, a fluorescence study was also performed. It resulted in a binding constant of 2.8 × 10⁶ M⁻¹, which is in good agreement with that obtained from electrochemical study.     

Oxidative stress elevated DNA damage and homocysteine level in normal pregnant women in a segment of Pakistani population

Maternal oxidative stress during pregnancy may impair fetal growth and help in the development of diseases in adulthood. The aim of current study was to assess total oxidation status (TOS), related parameters and their relationship to DNA damage (%) and homocysteine level in normal pregnant women in low-income participants. In a cross-sectional study healthy women were grouped as normal, while age matched nulliparous and singleton pregnancies were included for first, second and third trimester groups. TOS (P < 0.01), melanodialdehyde (MDA) (P < 0.001), aspartate aminotransferase (AST) (P < 0.01), triiodothyronine (T3) (P < 0.01), thyroxine (T4) (P < 0.01), and homocysteine (P < 0.001), in pregnant women were significantly higher as compared to normal healthy women. While serum total proteins (P < 0.01), albumin (P < 0.01) and total antioxidant status (TAS) (P < 0.001) decreased significantly as compared to normal healthy women. Women in third trimester showed a significantly high level of body temperature (P < 0.01), triglyceride (P < 0.01), LDL-cholesterol (P < 0.05), AST (P < 0.01), T3 (P < 0.01), homocysteine (P < 0.001), TOS (P < 0.01) and MDA (P < 0.001) but a lower concentration of serum proteins, albumin and TAS at the end of the pregnancy. Pearson correlation indicated a positive relationship of homocysteine with triglycerides (P < 0.027), TOS (P < 0.01), MDA (P < 0.035) and had a negative relationship with total protein (P < 0.026). DNA damage was strongly related with T3 (P < 0.008), TOS (P < 0.02), MDA (P < 0.037) and MBI (P < 0.048) profiles of pregnant women. These changes were considered normal for pregnant women having optimum blood pressure and normal child birth. Hormonal influences and hemodilution may contribute towards the observed changes in this study.     

A survey on basal resistance and riboflavin-induced defense responses of sugar beet against Rhizoctonia solani

We examined basal defense responses and cytomolecular aspects of riboflavin-induced resistance (IR) in sugar beet-Rhizoctonia solani pathsystem by investigating H(2)O(2) burst, phenolics accumulation and analyzing the expression of phenylalanine ammonia-lyase (PAL) and peroxidase (cprx1) genes. Riboflavin was capable of priming plant defense responses via timely induction of H(2)O(2) production and phenolics accumulation. A correlation was found between induction of resistance by riboflavin and upregulation of PAL and cprx1 which are involved in phenylpropanoid signaling and phenolics metabolism. Application of peroxidase and PAL inhibitors suppressed not only basal resistance, but also riboflavin-IR of sugar beet to the pathogen. Treatment of the leaves with each inhibitor alone or together with riboflavin reduced phenolics accumulation which was correlated with higher level of disease progress. Together, these results demonstrate the indispensability of rapid H(2)O(2) accumulation, phenylpropanoid pathway and phenolics metabolism in basal defense and riboflavin-IR of sugar beet against R. solani.     

Hematological and serum biochemical analyses in experimental caprine besnoitiosis

This study was undertaken to investigate the hematological and biochemical changes in experimentally infected goats with Besnoitia caprae from the time of infection till 360 days post-infection (PI). Six male goats were inoculated subcutaneously with 13 × 10(7) bradyzoites of B. caprae, and blood samples were collected from the jugular vein. The total erythrocyte and total leukocyte counts, hematocrit value, and differential leukocyte counts were determined. Serum biochemical analysis, including the total protein, albumin, total globulin, cholesterol, triglyceride, chloride, testosterone, calcium (Ca(2+)), inorganic phosphorus, sodium (Na(+)), potassium (K(+)), iron (Fe(2+)), glucose, serum amyloid A (SAA), haptoglobin (Hp), fibrinogen, ceruloplasmin, aspartate aminotransferase, alanine aminotransferase, creatine kinase, lactate dehydrogenase, and alkaline phosphatase, was undertaken. Skin biopsy from the limbs were collected at weekly intervals and histologically examined for Besnoitia cysts. Cysts were present in the skin biopsies of the leg of the infected goats from day 28 PI. There were variations in hematological analyses, but no significant difference was seen. From day 30 to 360 PI, results showed that SAA, Hp, fibrinogen, and ceruloplasmin concentrations increased, whereas testosterone concentrations decreased. Infected goats exhibited decrease of albumin and increase of serum total protein and globulin concentrations. By contrast, there were no significant differences in the remained analyses concentrations.     

Role of the endoplasmic reticulum-associated degradation (ERAD) pathway in degradation of hepatitis C virus envelope proteins and production of virus particles

Viral infections frequently cause endoplasmic reticulum (ER) stress in host cells leading to stimulation of the ER-associated degradation (ERAD) pathway, which subsequently targets unassembled glycoproteins for ubiquitylation and proteasomal degradation. However, the role of the ERAD pathway in the viral life cycle is poorly defined. In this paper, we demonstrate that hepatitis C virus (HCV) infection activates the ERAD pathway, which in turn controls the fate of viral glycoproteins and modulates virus production. ERAD proteins, such as EDEM1 and EDEM3, were found to increase ubiquitylation of HCV envelope proteins via direct physical interaction. Knocking down of EDEM1 and EDEM3 increased the half-life of HCV E2, as well as virus production, whereas exogenous expression of these proteins reduced the production of infectious virus particles. Further investigation revealed that only EDEM1 and EDEM3 bind with SEL1L, an ER membrane adaptor protein involved in translocation of ERAD substrates from the ER to the cytoplasm. When HCV-infected cells were treated with kifunensine, a potent inhibitor of the ERAD pathway, the half-life of HCV E2 increased and so did virus production. Kifunensine inhibited the binding of EDEM1 and EDEM3 with SEL1L, thus blocking the ubiquitylation of HCV E2 protein. Chemical inhibition of the ERAD pathway neither affected production of the Japanese encephalitis virus (JEV) nor stability of the JEV envelope protein. A co-immunoprecipitation assay showed that EDEM orthologs do not bind with JEV envelope protein. These findings highlight the crucial role of the ERAD pathway in the life cycle of specific viruses.