Conformational preferences of anticodon 3'-adjacent hypermodified nucleic acid base cis-or trans-zeatin and its 2-methylthio derivative, cis-or trans- ms(2)zeatin

Conformational preferences of the hypermodified nucleic acid bases N6-(Delta(2)-cis-hydroxyisopentenyl)adenine, cis-io(6)Ade also known as cis-zeatin, and N(6)-(Delta(2)-trans-hydroxyisopentenyl)adenine, trans-io(6)ade or trans-zeatin, and 2-methylthio derivatives of these cis-ms(2)io(6)Ade or cis-ms(2)zeatin, and trans-ms(2)io6Ade or trans-ms(2)zeatin have been investigated theoretically by the quantum chemical Perturbative Configuration Interaction with Localized Orbitals (PCILO) method. Automated geometry optimization using quantum chemical MNDO, AM1 and PM3 methods has also been made to compare the salient features. The predicted most stable conformation of cis-io(6)Ade, trans-io(6)Ade, cis-ms(2)io(6)Ade and trans-ms(2)io(6)Ade are such that in each of these molecules the isopentenyl substituent spreads away (has "dista" conformation) from the five membered ring imidazole moiety of the adenine. The atoms N(6), C(10) and C(11) remain coplanar with the adenine ring in the predicted preferred conformation for each of these molecules. In cis-io(6)Ade as well as cis-ms(2)io(6)Ade the hydroxyl oxygen may participate in intramolecular hydrogen bonding with the H-C(10)-H group. In trans-io(6)Ade the hydroxyl group is oriented towards the H-C(2) instead. This orientation is retained in trans-ms(2)io(6)Ade, possible O-H...S hydrogen bonding may be a stabilizing factor. In all these four modified adenines C(11)-H is favourably placed to participate in intramolecular hydrogen bonding with N(1). In cis-ms(2)io(6)Ade as well as trans-ms(2)io(6)Ade the 2-methylthio group preferentially orients on the same side as C(2)-N(3) bond, due to this non-obstrusive placing, orientation of the hydroxyisopentenyl substituent remains unaffected by 2-methylthiolation. Thus the N(1) site remains shielded irrespective of the 2-methylthiolation status in these various cis-and trans-zeatin analogs alike. Firmly held orientation of hydroxyisopentenyl substituent in zeatin isomers and derivatives, in contrast to adaptable orientation of isopentenyl substituent in i(6)Ade and ms(2)i(6)Ade, may account for the increased efficiency of suppressor tRNA and reduced codon context sensitivity accompanied with the occurrence of ms(2)-zeatin (ms(2)io(6)Ade) modification.     

Sample preparation method for tissue based proteomic analysis of <Emphasis Type="Italic">Azolla microphylla</Emphasis>

The nitrogen fixing aquatic pteridophyte Azolla is used as biofertilizer for rice paddy. It is also used as poultry and cattle feed due to high protein content. However, its mass cultivation and exploitation is constrained due to the abiotic stress conditions it is exposed to. The system is interesting due to the presence of symbiotic nitrogen fixing cyanobacteria and its interaction with the carbon fixing host. Therefore these interactions have to be studied at the molecular level using advanced techniques. Proteomics is a technique which can be employed to reveal the mechanism of cross talk between the host and its symbiont as well as its response to abiotc stress. The primary step that contributes to successful proteomic analysis is standardization of sound protocols for protein extraction and sufficient yield to initiate proteomic studies using 2-dimensional electrophoresis. However, reports are not available on the protein extraction procedures in Azolla. Therefore in the present study we attempted to optimize protein extraction protocol in the whole plant, roots and the chloroplast of Azolla microphylla using phenol extraction, TCA-acetone and phosphate buffer methods. Our studies showed the efficacy of phenol extraction method in terms of maximum yield and resolution of proteins in Azolla.     

Improvement in survival after paraquat ingestion following introduction of a new formulation in Sri Lanka

Background

Pesticide ingestion is a common method of self-harm in the rural developing world. In an attempt to reduce the high case fatality seen with the herbicide paraquat, a novel formulation (INTEON) has been developed containing an increased emetic concentration, a purgative, and an alginate that forms a gel under the acid conditions of the stomach, potentially slowing the absorption of paraquat and giving the emetic more time to be effective. We compared the outcome of paraquat self-poisoning with the standard formulation against the new INTEON formulation following its introduction into Sri Lanka.

Methods and Findings

Clinical data were prospectively collected on 586 patients with paraquat ingestion presenting to nine large hospitals across Sri Lanka with survival to 3 mo as the primary outcome. The identity of the formulation ingested after October 2004 was confirmed by assay of blood or urine samples for a marker compound present in INTEON. The proportion of known survivors increased from 76/297 with the standard formulation to 103/289 with INTEON ingestion, and estimated 3-mo survival improved from 27.1% to 36.7% (difference 9.5%; 95% confidence interval [CI] 2.0%–17.1%; p = 0.002, log rank test). Cox proportional hazards regression analyses showed an approximately 2-fold reduction in toxicity for INTEON compared to standard formulation. A higher proportion of patients ingesting INTEON vomited within 15 min (38% with the original formulation to 55% with INTEON, p < 0.001). Median survival time increased from 2.3 d (95% CI 1.2–3.4 d) with the standard formulation to 6.9 d (95% CI 3.3–10.7 d) with INTEON ingestion (p = 0.002, log rank test); however, in patients who did not survive there was a comparatively smaller increase in median time to death from 0.9 d (interquartile range [IQR] 0.5–3.4) to 1.5 d (IQR 0.5–5.5); p = 0.02.

Conclusions

The survey has shown that INTEON technology significantly reduces the mortality of patients following paraquat ingestion and increases survival time, most likely by reducing absorption.     

A study on risk factors for Parkinson?s disease in Indian population

Parkinson׳s disease is the second most common neurodegenerative disorder. The exact cause of selective dopaminergic neurodegeneration is unknown, but it is supposed that etiology of Parkinson׳s disease is multifactorial and consists of an interaction between environmental factors and genetic predisposition. To find out the association between environmental factors and risk of Parkinson׳s disease, a case control study was designed including 97 Parkinson׳s disease patients and 97 controls. Logistic regression analysis was used to determine the risk factors for Parkinson׳s disease. Results from the present study showed that gender, religion, education, place of living, occupation, dietary habits, tobacco chewing, smoking, alcohol intake, and head injury had no association with PD. However, chemical exposure and well water drinking were significantly associated with PD, which concluded that environmental factors could act as a risk factor for PD in some way.     

Metals toxicity and its correlation with the gene expression in Alzheimer's disease

Molecular Biology Reports - Alzheimer's disease is a common neurodegenerative disease in the elderly population and a leading cause of dementia. Genetics and environmental risk factors were...     

A Multi-Exon-Skipping Detection Assay Reveals Surprising Diversity of Splice Isoforms of Spinal Muscular Atrophy Genes

Humans have two near identical copies of Survival Motor Neuron gene: SMN1 and SMN2. Loss of SMN1 coupled with the predominant skipping of SMN2 exon 7 causes spinal muscular atrophy (SMA), a neurodegenerative disease. SMA patient cells devoid of SMN1 provide a powerful system to examine splicing pattern of various SMN2 exons. Until now, similar system to examine splicing of SMN1 exons was unavailable. We have recently screened several patient cell lines derived from various diseases, including SMA, Alzheimer’s disease, Parkinson’s disease and Batten disease. Here we report a Batten disease cell line that lacks functional SMN2, as an ideal system to examine pre-mRNA splicing of SMN1. We employ a multiple-exon-skipping detection assay (MESDA) to capture simultaneously skipping of multiple exons. Our results show surprising diversity of splice isoforms and reveal novel splicing events that include skipping of exon 4 and co-skipping of three adjacent exons of SMN. Contrary to the general belief, MESDA captured oxidative-stress induced skipping of SMN1 exon 5 in several cell types, including non-neuronal cells. We further demonstrate that the predominant SMN2 exon 7 skipping induced by oxidative stress is modulated by a combinatorial control that includes promoter sequence, endogenous context, and the weak splice sites. We also show that an 8-mer antisense oligonucleotide blocking a recently described GC-rich sequence prevents SMN2 exon 7 skipping under the conditions of oxidative stress. Our findings bring new insight into splicing regulation of an essential housekeeping gene linked to neurodegeneration and infant mortality.     

Quantification of isotope encoded proteins in 2-D gels using surface enhanced resonance Raman

A strategy for quantification of multiple protein isoforms from a complex sample background is demonstrated, combining isotopomeric rhodamine 6G (R6G) labels and surface-enhanced Raman in polyacrylamide matrix. The procedure involves isotope-encoding by lysine-labeling with (R6G) active ester reagents, isoform separation by 2-DGE, fluorescence quantification using internal standardization to water, and silver nanoparticle deposition followed by surface-enhanced Raman detection. R6G sample encoding and standardization enabled the determination of total protein concentration and the distribution of specific isoforms using the combined detection approach of water-referenced fluorescence spectral imaging and ratiometric quantification. A detection limit of approximately 13.5 picomolar R6G-labeled protein was determined for the surface-enhanced Raman in a gel matrix (15-fold lower than fluorescence). High quantification accuracies for small differences in protein populations at low nanogram abundance were demonstrated for human GMP synthetase (hGMPS) either as purified protein samples in a single-point determination mode (3% relative standard deviation, RSD%) or as HCT116 human cancer cellular lysate in an imaging application (with 16% RSD%). These results represent a prototype for future applications of isotopic surface-enhanced resonance Raman scatter to quantification of protein distributions.     

MODULATION OF P‐GLYCOPROTEIN ATPASE OF HELICOVERPA ARMIGERA BY CHOLESTEROL: EFFECTS ON ATPASE ACTIVITY AND INTERACTION OF INSECTICIDES

Purified P‐glycoprotein ATPase from Helicoverpa armigera (Ha‐Pgp), reconstituted in proteoliposomes composed of phospholipids and cholesterol, shows higher ATPase activity in the presence of cholesterol than in its absence. The Ha‐Pgp ATPase activity was increased 30–40% with cholesterol. The K_M for ATP was found to be 1 and 0.8 mM in the absence and presence of cholesterol, respectively. The insecticide‐stimulated Ha‐Pgp ATPase activity was increased by 10–20% for all the insecticides in the reconstituted proteoliposomes containing cholesterol compared to those with no cholesterol. The effects of cholesterol on K_M and V_max values of insecticide‐stimulated Ha‐Pgp ATPase activity were unrelated to the size of the insecticide. Ha‐Pgp tryptophan fluorescence displayed a red shift of 3 and 8 nm in emission spectra upon binding of insecticides. Cholesterol enhances the interaction of insecticides with Ha‐Pgp. K_d values of different insecticides for binding to Ha‐Pgp were found to be lower in the presence of cholesterol in the proteoliposomes compared to its absence. Results suggest that cholesterol plays a role in the recognition and interaction of insecticides by modulating Ha‐Pgp ATPase and may be involved in efflux of insecticides from cells by the transporter.     

Bioactive molecules from Nocardia: diversity,bioactivities and biosynthesis

Journal of Industrial Microbiology & Biotechnology - Nocardia spp. are catalase positive, aerobic, and non-motile Gram-positive filamentous bacteria. Many Nocarida spp. have been reported as...