Positioning of mRNA codons with respect to 18S rRNA at the P and E sites of human ribosome

Positioning of each nucleotide of the E site and the P site bound codons with respect to the 18S rRNA on the human ribosome was studied by cross-linking with mRNA analogs, derivatives of the hexaribonucleotide UUUGUU (comprising Phe and Val codons) that carried a perfluorophenylazide group on the second or the third uracil, and a derivative of the dodecaribonucleotide UUAGUAUUUAUU with a similar group on the guanine residue. The location of the modified nucleotides at any mRNA position from -3 to +3 (position +1 corresponds to the 5' nucleotide of the P site bound codon) was adjusted by the cognate tRNAs. A modified uridine at positions from -1 to +3 cross-linked to nucleotide G1207 of the 18S rRNA, and to nucleotide G961 when it was in position -2. A modified guanosine cross-linked to nucleotide G1207 if it was in position -3 of the mRNA. These data indicate that nucleotide G961 of the 18S rRNA is close only to mRNA positions -3 and -2, while G1207 is in the vicinity of positions from -3 to +3. The latter suggests that there is a sharp turn between the P and E site bound codons that brings nucleotide G1207 of the 18S rRNA close to each nucleotide of these codons. This correlates well with X-ray crystallographic data on bacterial ribosomes, indicating existence of a sharp turn between the P site and E site bound codons near a conserved nucleotide G926 of the 16S rRNA (corresponding to G1207 in 18S rRNA) close to helix 23b containing the conserved nucleotide 693 of the 16S rRNA (corresponding exactly to G961 of the 18S rRNA).     

Protein kinase structure and function analysis with chemical tools

Protein kinases are the largest enzyme superfamily involved in cell signal transduction and represent therapeutic targets for a range of diseases. There have been intensive efforts from many labs to understand their catalytic mechanisms, discover inhibitors and discern their cellular functions. In this review, we will describe two approaches developed to analyze protein kinases: bisubstrate analog inhibition and phosphonate analog utilization. Both of these methods have been used in combination with the protein semisynthesis method expressed protein ligation to advance our understanding of kinase-substrate interactions and functional elucidation of phosphorylation. Previous work on the nature of the protein kinase mechanism suggests it follows a dissociative transition state. A bisubstrate analog was designed against the insulin receptor kinase to mimic the geometry of a dissociative transition state reaction coordinate distance. This bisubstrate compound proved to be a potent inhibitor against the insulin receptor kinase and occupied both peptide and nucleotide binding sites. Bisubstrate compounds with altered hydrogen bonding potential as well as varying spacers between the adenine and the peptide demonstrate the importance of the original design features. We have also shown that related bisubstrate analogs can be used to potently block serine/threonine kinases including protein kinase A. Since many protein kinases recognize folded protein substrates for efficient phosphorylation, it was advantageous to incorporate the peptide-ATP conjugates into protein structures. Using expressed protein ligation, a Src-ATP conjugate was produced and shown to be a high affinity ligand for the Csk tyrosine kinase. Nonhydrolyzable mimics of phosphoSer/phosphoTyr can be useful in examining the functionality of phosphorylation events. Using expressed protein ligation, we have employed phosphonomethylene phenylalanine and phosphonomethylene alanine to probe the phosphorylation of Tyr and Ser, respectively. These tools have permitted an analysis of the SH2-phosphatases (SHP1 and SHP2), revealing a novel intramolecular stimulation of catalytic activity mediated by the corresponding phosphorylation events. They have also been used to characterize the cellular regulation of the melatonin rhythm enzyme by phosphorylation.     

Design, synthesis, and characterization of an ATP-peptide conjugate inhibitor of protein kinase A

An ATP-peptide conjugate was synthesized as a bisubstrate analogue inhibitor of the serine/threonine kinase protein kinase A. The compound was found to be a linear, competitive inhibitor with respect to ATP substrate, exhibiting a Ki of 3.8 microM. The compound was noncompetitive with respect to peptide substrate. The inhibitor was shown to be selective for protein kinase A versus the closely related protein kinase C as well as tyrosine kinase Csk. This analysis provides new evidence for the dissociative transition state of protein serine/threonine kinases and illustrates a simple method to convert a low affinity peptide substrate to a selective and moderately potent inhibitor for these enzymes.     

Reintroducing a keystone burrowing rodent to restore an arid North American grassland: challenges and successes

Prairie dogs (Cynomys spp.) are important ecosystem engineers in North America's central grasslands, and are a key prey base for numerous predators. Prairie dogs have declined dramatically across their former range, prompting reintroduction efforts to restore their populations and ecosystem functions, but the success of these reintroductions is rarely monitored rigorously. Here, we reintroduced 2,400 Gunnison's prairie dogs (C. gunnisoni) over a period of 6 years to the Sevilleta National Wildlife Refuge, in central New Mexico, U.S.A., a semi‐arid grassland ecosystem at the southern edge of their range. We evaluated the population dynamics of prairie dogs following their reintroduction, and their consequent effects on grassland vertebrates. We found postrelease survival of prairie dogs stabilized at levels typical for the species (ca. 50%) after approximately 1 month, while average annual recruitment was ca. 0.35 juveniles per female, well below what was required for a self‐sustaining, stable population. Extreme drought conditions during much of the study period may have contributed to low recruitment. However, recruitment increased steadily over time, indicating that the reintroduced colony may simply need more time to establish in this arid system. We also found well‐known associates of prairie dog colonies, such as American badgers (Taxidea taxus) and burrowing owls (Athene cunicularia), were significantly more common on the colonies than off. After 7 years, we have yet to meet our goal of establishing a self‐sustaining population of Gunnison's prairie dogs in this semi‐arid grassland. But despite the uncertainty and challenges, our work shows that reestablishing keystone species can promote ecosystem restoration.     

New Eocene dinoflagellate cysts from the southern edge of the Junggar Basin,Xinjiang, China

The Anjihaihe Formation in the southern edge of the Junggar Basin was previously considered a series of freshwater lacustrine depositions. However, abundant marine dinoflagellate cysts were recently recovered from the middle to upper part of the middle member of the formation. Two new genera, six new species and one new subspecies among the abundant dinoflagellate cysts are described and illustrated, i.e. Circulodinium? laeve sp. nov., Kaiwaradinium abbreviatum sp. nov., Spiniferites adnatus subsp. latispinus subsp. nov., Oligosphaeropsis accreta gen. et. sp. nov., Oligosphaeropsis complex gen. et. sp. nov., Oligosphaeropsis megaprocessa gen. et. sp. nov. and Tianshandinium biconicum gen. et. sp. nov. They are rare to common constituents of the dinoflagellate assemblage in the Anjihaihe Formation and may prove useful for regional biostratigraphic correlation and palaeoenvironment re-establishment.     

Direct colony PCR for rapid identification of varied microalgae from freshwater environment

Molecular identification of microalgal species is vital and involves sequencing of specific markers present in the genome, which are unique to a genus. PCR is a vital tool for identification of microalgae; the preparation of template DNA for PCR by traditional methods requires large amount of algal cells and a time-consuming process. One simple way to reduce these complications is to use the microalgal colonies directly for amplification of required DNA fragments from the genome. In this study, a simple cell-disrupting method, using autoclaved glass powder, has been used for direct colony PCR of microalgae. Four morphologically different microalgal strains were chosen from freshwater samples, and the PCR amplification reaction was evaluated with three different molecular markers (rbcL, internal transcribed spacer 2, and 18S rDNA). PCR amplification was optimized with less number of cells (0.04?×?10⁵), minimal quantity of glass powder (0.5 mg), and in the presence of Milli-Q water for internal transcribed spacer marker. The isolated strains were identified as Desmodesmus sp. JQ782747, Coelastrum proboscideum JQ898144, Chlorella sorokiniana JQ898145, and Scenedesmus sp. JQ782746 based on sequence similarity. This direct microalgal colony PCR proves to be a simple and rapid method for detection of varied microalgal species.     

Analysis of Risk-Structured Vaccination Model for the Dynamics of Oncogenic and Warts-Causing HPV Types

A new deterministic model is designed and used to assess the community-wide impact of mass vaccination of new sexually active individuals on the dynamics of the oncogenic and warts-causing HPV types. Rigorous qualitative analyses of the model, which incorporates the two currently available anti-HPV vaccines, reveal that it undergoes competitive exclusion when the reproduction of one HPV risk type (low/high) exceeds unity, while that of the other HPV risk type is less than unity. For the case when the reproduction numbers of the two HPV risk types (low/high) exceed unity, the two risk types co-exist. It is shown that the sub-model with the low-risk HPV types only has at least one endemic equilibrium whenever the associated reproduction threshold exceeds unity. Furthermore, this sub-model undergoes a re-infection-induced backward bifurcation under certain conditions. In the absence of the re-infection of recovered individuals and cancer-induced mortality in males, the associated disease-free equilibrium of the full (risk-structured) model is shown to be globally asymptotically stable whenever the reproduction number of the model is less than unity (that is, the full model does not undergo backward bifurcation under this setting). It is shown, via numerical simulations, that the use of the Gardasil vaccine could lead to the effective control of HPV in the community if the coverage rate is in the range of 73–95 % (84 %). If 70 % of the new sexually active susceptible females are vaccinated with the Gardasil vaccine, additionally vaccinating 34–56 % (45 %) of the new sexually active susceptible males can lead to the effective community-wide control (or elimination) of the HPV types.     

Characterisation of polymorphic microsatellite markers for skates (Elasmobranchii: Rajidae) from expressed sequence tags

Simple sequence repeat markers (SSRs, microsatellites) were characterised for skates (Elasmobranchii: Rajidae) from published expressed sequence tags (ESTs) of Leucoraja erinacea. These were tested in four European species (Raja clavata, Raja montagui, Dipturus batis, and Leucoraja naevus). Thirteen of the fourteen amplified loci were polymorphic in at least one species. Polymorphic loci possessed on average 4.5–5.9 alleles per species, and expected heterozygosity ranged from 0.05 to 0.88. Possible null alleles were detected at three loci, while one locus showed significant deviation from Hardy–Weinberg Equilibrium proportions. Three locus-pairs exhibited significant linkage disequilibrium in one or more species. This marker set will be valuable for population genetic analyses of the focal taxa, and may prove useful for studies of other skate species.     

Parents’ posthumous use of daughter’s ovarian tissue: Ethical dimensions

In recent years, progress in cancer treatment has greatly increased the chances of recovery. Yet, treatment may have irreversible effects on patients’ fertility. In order to protect future fertility, preservation of ovarian tissue may be offered today even to very young girls, involving a surgical procedure that may be performed by minimally invasive laparoscopy, under general anesthesia. However, in the tragic event of a girl’s death, questions may arise regarding the possible use of the preserved ovarian tissue by her parents. Should posthumous reproductive use of ovarian tissue without the girl’s prior consent (due to her young age) be considered a violation of her rights? On the other hand, can it be argued that it is in the interest of a child who died young to leave a genetic trace through posthumous reproduction, because genetic continuity is in the interest of every human being? After presenting the relevant clinical facts, we explore the ethical dimensions of this possible practice through an analysis of the interests of the deceased, her parents, and the child that may be born posthumously.     

Role of divalent metals in the activation and regulation of insulin receptor tyrosine kinase

Multiple equilibrium equations were solved to separate the individual effects of ionic divalent metals, free nucleotides and their chelated species on insulin receptor tyrosine kinase (IRTK). Basal IRTK is activated by divalent metal cations when present in excess of that required for substrate formation, indicating the presence of a divalent cation-dependent regulatory site on the kinase. The activatory order for basal activity was Mn2+ greater than Co2+ greater than Mg2+ and Ca2+ = 0. The insulin-dependent activation of IRTK was minimal in the absence of excess free divalent metal, even when the concentration of MnATP or MgATP substrate present exceeded the apparent Km of the kinase. The activatory order for insulin-dependent activation of IRTK changed to Mg2+ greater than Mn2+ and Co2+ = 0. The titration of the MnCl2 saturation response at several concentrations of MgCl2 revealed that the insulin-dependent response of IRTK increases as a function of increasing MgCl2, while basal activity was unaffected. This enhancement of the responsiveness to insulin in the presence of both cations was not due to differing affinities of the kinase for substrate, as evidenced by nearly identical apparent Km values for MnATP and MgATP. The Mg2+-dependent increase in the response of the kinase to insulin may be due to Mg2+ inducing a stronger coupling between receptor and kinase than that observed with Mn2+ alone. The plotting of the effect of several concentrations of free divalent metals on substrate saturation curves revealed that an increase in either of the reactants increased the affinity of the insulin-activated kinase for the other respective reactant. Accordingly, free divalent metal and metal-ATP substrate interact with IRTK in a mutually inclusive manner. CaCl2 saturation curves in the presence of constant MnCl2 and increasing MgCl2 showed that the affinity of IRTK for Ca2+ decreases and the affinity for CaATP increased with increasing Mg2+. Our data suggests that IRTK contains three sites for interaction with divalent metal cations: a MeATP (active) site, a regulatory site, and a metal-dependent site acting to couple the receptor with the kinase.