Structural insights into the allosteric effects of 4EBP1 on the eukaryotic translation initiation factor eIF4E

The eukaryotic translation initiation factor eIF4E plays key roles in cap-dependent translation and mRNA export. These functions rely on binding the 7-methyl-guanosine moiety (5'cap) on the 5'-end of all mRNAs. eIF4E is regulated by proteins such as eIF4G and eIF4E binding proteins (4EBPs) that bind the dorsal surface of eIF4E, distal to the cap binding site, and modulate cap binding activity. Both proteins increase the affinity of eIF4E for 5'cap. Our understanding of the allosteric effects and structural underpinnings of 4EBP1 or eIF4G binding can be advanced by obtaining structural data on cap-free eIF4E bound to one of these proteins. Here, we report the crystal structure of apo-eIF4E and cap-free eIF4E in complex with a 4EBP1 peptide. We also monitored 4EBP1 binding to cap-free eIF4E in solution using NMR. Together, these studies suggest that 4EBP1 transforms eIF4E into a cap-receptive state. NMR methods were also used to compare the allosteric routes activated by 4EBP1, eIF4G, and the arenavirus Z protein, a negative regulator of cap binding. We observed chemical shift perturbation at the dorsal binding site leading to alterations in the core of the protein, which were ultimately communicated to the unoccupied cap binding site of eIF4E. There were notable similarities between the routes taken by 4EBP1 and eIF4G and differences from the negative regulator Z. Thus, binding of 4EBP1 or eIF4G allosterically drives alterations throughout the protein that increase the affinity of eIF4E for the 5'cap.     

Genetic variants in interferon gamma (<Emphasis Type="Italic">IFN-γ</Emphasis>) gene are associated with resistance against ticks in <Emphasis Type="Italic">Bos taurus</Emphasis> and <Emphasis Type="Italic">Bos indicus</Emphasis>

In tropical and subtropical regions of the world, parasitic diseases are major obstacle in the health and ultimately overall performance of animals. Cattle express heritable, contrasting phenotypes when exposed to ticks depicting genetic nature of trait. IFN-γ is one of the most reported genes critical for innate and adaptive immunity against viral and intracellular infections. To identify its role in resistance for ectoparasite especially tick, genetic characterization of this gene was done in resistant and susceptible animals of Sahiwal cattle (n = 95) and Friesian (n = 92). Nine Polymorphisms were identified, three of them were found in exonic region. One out of nine variants was being reported previously (ss82716193) and was confirmed in Pakistani Sahiwal cattle population as well. Single site analysis of each variant depicted their significance in tick resistant and tick susceptible groups (P < 0.05). The associations using haplotypes were more informative than for single markers. Eighteen different haplotypes resulting from nine polymorphic sites were used in construction of maximum parsimony tree which categorized resistant and susceptible animals in two clades. Genetic markers identified in this study can be useful in future breeding selection programs against tick resistance.     

Novel mutations of endothelin-B receptor gene in Pakistani patients with Waardenburg syndrome

Mutations in EDNRB gene have been reported to cause Waardenburg-Shah syndrome (WS4) in humans. We investigated 17 patients with WS4 for identification of mutations in EDNRB gene using PCR and direct sequencing technique. Four genomic mutations were detected in four patients; a G to C transversion in codon 335 (S335C) in exon 5 and a transition of T to C in codon (S361L) in exon 5, a transition of A to G in codon 277 (L277L) in exon 4, a non coding transversion of T to A at −30 nucleotide position of exon 5. None of these mutations were found in controls. One of the patients harbored two novel mutations (S335C, S361L) in exon 5 and one in Intronic region (−30exon5 A>G). All of the mutations were homozygous and novel except the mutation observed in exon 4. In this study, we have identified 3 novel mutations in EDNRB gene associated with WS4 in Pakistani patients.     

Exogenous salicylic acid stimulates physiological and biochemical changes to improve growth, yield and active constituents of fennel essential oil

Fennel (Foeniculum vulgare Mill) is a high-value medicinal and essential oil bearing plant used extensively in pharmaceutical, food and cosmetic industries. A pot experiment was carried out in the natural conditions of net house to resolve whether the foliar application of salicylic acid (SA) might enhance the growth, yield and essential oil production of fennel. Plants were sprayed three times with SA. The first spray was carried out at 40?days after sowing (DAS); the second and third sprays were applied one and 2?weeks later, the plants were sprayed with deionised water (control) and different concentrations of SA (10^?5, 10^?4 and 10^?3?M). The foliar spray of SA at 10^?4?M significantly enhanced the vegetative growth (shoot and root lengths, fresh and dry weights), physiological and biochemical characteristics (chl ??a??, chl ??b??, total chlorophyll and carotenoids contents, nitrate reductase activity, carbonic anhydrase activity, leaf-N, -P and -K contents), yield characteristics (number of umbels and fruits, 1,000-seed weight and seed yield) and essential oil yield of fennel. GLC analysis revealed the significant increase in the components of essential oil, viz. trans-anethole (80.4?C84.7?%), methyl chavicol (2.3?C2.5?%) and fenchone (5.6?C7.9?%). It was concluded that foliar spray of SA at 10^?4?M might be employed for enhancing the plant growth as well as yield and quality of essential oil of fennel.     

Plant Growth-Promoting Rhizobacteria Associated with Ancient Clones of Creosote Bush (Larrea tridentata)

Plant growth-promoting rhizobacteria (PGPR) are common components of the rhizosphere, but their role in adaptation of plants to extreme environments is not yet understood. Here, we examined rhizobacteria associated with ancient clones of Larrea tridentata in the Mohave desert, including the 11,700-year-old King Clone, which is oldest known specimen of this species. Analysis of unculturable and culturable bacterial community by PCR-DGGE revealed taxa that have previously been described on agricultural plants. These taxa included species of Proteobacteria, Bacteroidetes, and Firmicutes that commonly carry traits associated with plant growth promotion, including genes encoding aminocyclopropane carboxylate deaminase and β–propeller phytase. The PGPR activities of three representative isolates from L. tridentata were further confirmed using cucumber plants to screen for plant growth promotion. This study provides an intriguing first view of the mutualistic bacteria that are associated with some of the world’s oldest living plants and suggests that PGPR likely contribute to the adaptation of L. tridentata and other plant species to harsh environmental conditions in desert habitats.     

Characterization of 1064 nm Nd:YAG laser-produced cu plasma

The plasma was produced by focusing Nd:YAG laser pulses of 1064 nm wavelength on to a copper target at laser fluences of 5.35, 6.95, and 9.33 J/cm². An ion collector placed along the target surface normal was used to record the time-of-flight (TOF) ion signal during plasma expansion in vacuum. The TOF ion pulses were deconvoluted using the Coulomb-Boltzmann-shifted function to estimate the available Cu ion charge states, equivalent plasma ion temperature, and accelerating potential in the nonequilibrium plasma. The maximum available ion charge state, equivalent plasma ion temperature, and accelerating potential are found to increase with laser fluence. In the local thermal equilibrium conditions, the accelerating potential can be supposed to apply across a distance of the order of the Debye length. The Debye length and, hence, the electric field in the laser produced plasma at three laser fluences values were estimated. The electric field was in the range of 1 MV/cm and increased with laser fluence. In the laser fluence range used in this work, the sum of thermal and adiabatic energy of the ion was slightly higher than its Coulomb energy.     

Development of genetic markers for Ochradenus arabicus (Resedaceae), an endemic medicinal plant of Saudi Arabia

Some species of the genus Ochradenus are difficult to identify based on morphological markers. Similar limitations are found for biochemical markers. We developed genetic markers based on DNA sequences for Ochradenus arabicus, which is an endemic plant to Saudi Arabia, locally utilized as a medicinal shrub. The internal transcribed spacer sequence of nuclear ribosomal DNA and chloroplast (rpoB and rpoC1) markers were more informative than other chloroplast DNA markers. Based on these markers, we were able to discriminate this species from another species of the same genus (O. baccatus) that is widely distributed in Saudi Arabia, despite a high degree of morphological similarity. These genetic markers facilitate its identification, even when acquired in a dried state from local markets.     

Expression and identification of folate-sensitive fragile sites in British Suffolk sheep (<Emphasis Type="Italic">Ovis aries</Emphasis>)

An investigation to understand the dynamics and biological significance of fragile site expression, and identification of 5-fluorodeoxyuridine (FUdR) induced chromosomal gaps/breaks, were carried out in an experimental flock of 45 Suffolk sheep. The statistical comparison revealed, highly significant variation in the frequency of chromosomal fragile site expression between control and FUdR cultures. Mean (± S.D.) values for cells with gaps and breaks, or aberrant cell count (AC), and the number of aberrations (NoA) per animal were 2.02 ± 0.34, 2.42 ± 0.48, 13.26 ± 0.85 and 21.87 ± 1.88 (P < 0.01) in control and FUdR cultures, respectively. The comparison of age revealed nonsignificant variation between control and FUdR cultures. The G-band analysis of fragile site data revealed gaps in 29 autosomal and two X-chromosomal bands in the control cultures, whereas FUdR treated cultures scored 78 unstable bands in autosomes of which 56 were significantly fragile. X-chromosomes expressed breaks and gaps in six G-negative bands and five of them (Xq13, Xq15, Xq17, Xq24 and Xq26) were significantly fragile. The distribution comparison of autosomal fragile sites between sex groups did not reveal any significant variation. Female X-chromosomes were significantly more fragile than the male X-chromosomes. The distribution comparison for age groups (lambs versus adults) revealed significantly higher number of fragile bands in adults. Comparison of published data on reciprocal translocations in sheep with the fragile-site data obtained in this study indicated that the break sites of both phenomena were correlated. Similarities were also found between fragile sites and breakpoints of evolutionary significance in family Bovidae.     

Binding of bilirubin with albumin-coupled liposomes: implications in the treatment of jaundice

In the present study, we demonstrated the suitability of liposomes as a method of removing plasma bilirubin in hyperbilirubinemic rats. The liposomes have innate tendency to bind with bilirubin through hydrophobic interaction. Among different types of liposomes, the positively charged liposomes were found to have maximum affinity to free bilirubin. However, the entrapment or coupling of serum albumin on the surface of egg phosphatidylcholine liposomes can render a several-fold increase in their bilirubin binding capacity. The proteoliposomes were able to preferentially bind with bilirubin even in the presence of erythrocytes. Interestingly, these liposomes were found to displace bilirubin bound on the surface of erythrocytes as well. The results of the present study further demonstrate that albumin-bearing liposomes were equally effective in removing plasma bilirubin in experimental jaundiced animals. These observations indicate that liposome-mediated selective homing of excess plasma bilirubin to the liver cells (cf. hepatocytes) may help in the development of safer strategy for the treatment of hyperbilirubinemic conditions in the model animals.     

GA3 induced flowering in Podophyllum hexandrum Royle: A rare alpine medicinal herb

Podophyllum hexandrum Royle, an important alpine herb, is the source of highly valued podophyllotoxin. The effect of some plant growth substances (GA₃, BAP & ABA), uniconazole (an inhibitor of GA biosynthesis), and a combination of GA₃ and uniconazole were examined in respect to influence on sprouting in rhizomes of P. hexandrum and on induction of flowering at a lower altitude. Amongst the various chemicals tested, GA₃ had a marked effect resulting in uniform sprouting and also induced flowering in about half of the treated rhizomes. While BAP also promoted early sprouting, delayed sprouting was seen in rhizomes treated with ABA. Uniconazole treatment, either alone or with GA₃ was found to inhibit flowering and also resulted in reduced plant height. GA₃ treatment of rhizomes from plants that was maintained for up to 30 months at a lower altitude also induced flowering thus replacing the normal chilling requirement of plants. These results suggest that treatment of GA₃ could be effectively used for inducing uniform sprouting and flowering in rhizomes of P. hexandrum grown at lower altitudes.