Local sequential minimization of double stranded B-DNA using Monte Carlo annealing

A software algorithm has been developed to investigate the folding process in B-DNA structures in vacuum under a simple and accurate force field. This algorithm models linear double stranded B-DNA sequences based on a local, sequential minimization procedure. The original B-DNA structures were modeled using initial nucleotide structures taken from the Brookhaven database. The models contain information at the atomic level allowing one to investigate as accurately as possible the structure and characteristics of the resulting DNA structures. A variety of DNA sequences and sizes were investigated containing coding and non-coding, random and real, homogeneous or heterogeneous sequences in the range of 2 to 40 base pairs. The force field contains terms such as angle bend, Lennard-Jones, electrostatic interactions and hydrogen bonding which are set up using the Dreiding II force field and defined to account for the helical parameters such as twist, tilt and rise. A close comparison was made between this local minimization algorithm and a global one (previously published) in order to find out advantages and disadvantages of the different methods. From the comparison, this algorithm gives better and faster results than the previous method, allowing one to minimize larger DNA segments. DNA segments with a length of 40 bases need approximately 4 h, while 2.5 weeks are needed with the previous method. After each minimization the angles between phosphate–oxygen-carbon A₁, the oxygen–phosphate–oxygen A₂ and the average helical twists were calculated. From the generated fragments it was found that the bond angles are A₁=150°±2°and A₂=130°±10°, while the helical twist is 36.6°±2° in the A strand and A₁=150°±6° and A₂=130±6° with helical twist 39.6°±2° in the B strand for the DNA segment with the same sequence as the Dickerson dodecamer.Figure The final minimized DNA segment of the Dickerson dodecamer sequence represented by ball drawings and viewed (left) perpendicular and (right) down the helical axis     

Production of C<Subscript>35</Subscript> isoprenoids depends on H<Subscript>2</Subscript> availability during cultivation of the hyperthermophile<Emphasis Type="Italic"> Methanococcus jannaschii</Emphasis>

A series of five progressively saturated C₃₅ isoprenoids has been identified in cell-free extracts of the deep-sea methanogen Methanococcus jannaschii. Production and relative abundance of the isoprenoids were dependent on culture conditions; significant production occurred in a 16-l fermentor (12-l working volume) and a 2.5-l fermentor (2-l working volume) but could not be duplicated in serum bottles. Several factors were investigated and shown not to account for the different production levels, including medium composition, pH, and temperature. However, the interphase mass transfer rate was shown to significantly affect the production of C₃₅ isoprenoids in a fermentor. The structures of the novel isoprenoids were confirmed by hydrogenation reactions and mass spectra of the isoprenoids. Indirect evidence based on genomics and mass spectrometry data implicates head-to-head condensation of farnesyl pyrophosphate (C₁₅) with geranylgeranyl pyrophosphate (C₂₀) as the mechanism for C₃₅ synthesis.Communicated by J. WiegelB.P. Manquin and J.A. Morgan contributed equally to this work.     

Motion-sensitive neurones in V5/MT modulate perceived spatial position

Until recently, it was widely believed that object position and object motion were represented independently in the visual cortex. However, several studies have shown that adaptation to motion produces substantial shifts in the perceived position of subsequently viewed stationary objects. Two stages of motion adaptation have been proposed: an initial stage at the level of V1 and a secondary stage thought to be located in V5/MT. Indeed, selective adaptation can be demonstrated at each of these levels of motion analysis. What remains unknown is which of these cortical sites are involved in modulating the positional representation of subsequently viewed objects. To answer this question directly, we disrupted cortical activity by using transcranial magnetic stimulation (TMS) immediately after motion adaptation. When TMS was delivered to V5/MT after motion adaptation, the perceived offset of the test stimulus was greatly reduced. In marked contrast, TMS of V1 had no effect on the changes that normally occur in perceived position after motion adaptation. This result demonstrates that the anatomical locus at which motion and positional information interact is area V5/MT rather than V1/V2.     

Tuberous sclerosis complex gene products,Tuberin and Hamartin,control mTOR signaling by acting as a GTPase-activating protein complex toward Rheb

BACKGROUND: Tuberous Sclerosis Complex (TSC) is a genetic disorder that occurs through the loss of heterozygosity of either TSC1 or TSC2, which encode Hamartin or Tuberin, respectively. Tuberin and Hamartin form a tumor suppressor heterodimer that inhibits the mammalian target of rapamycin (mTOR) nutrient signaling input, but how this occurs is unclear. RESULTS: We show that the small G protein Rheb (Ras homolog enriched in brain) is a molecular target of TSC1/TSC2 that regulates mTOR signaling. Overexpression of Rheb activates 40S ribosomal protein S6 kinase 1 (S6K1) but not p90 ribosomal S6 kinase 1 (RSK1) or Akt. Furthermore, Rheb induces phosphorylation of eukaryotic initiation factor 4E binding protein 1 (4E-BP1) and causes 4E-BP1 to dissociate from eIF4E. This dissociation is completely sensitive to rapamycin (an mTOR inhibitor) but not wortmannin (a phosphoinositide 3-kinase [PI3K] inhibitor). Rheb also activates S6K1 during amino acid insufficiency via a rapamycin-sensitive mechanism, suggesting that Rheb participates in nutrient signaling through mTOR. Moreover, Rheb does not activate a S6K1 mutant that is unresponsive to mTOR-mediated signals, confirming that Rheb functions upstream of mTOR. Overexpression of the Tuberin-Hamartin heterodimer inhibits Rheb-mediated S6K1 activation, suggesting that Tuberin functions as a Rheb GTPase activating protein (GAP). Supporting this notion, TSC patient-derived Tuberin GAP domain mutants were unable to inactivate Rheb in vivo. Moreover, in vitro studies reveal that Tuberin, when associated with Hamartin, acts as a Rheb GTPase-activating protein. Finally, we show that membrane localization of Rheb is important for its biological activity because a farnesylation-defective mutant of Rheb stimulated S6K1 activation less efficiently. CONCLUSIONS: We show that Rheb acts as a novel mediator of the nutrient signaling input to mTOR and is the molecular target of TSC1 and TSC2 within mammalian cells.     

Fitness reduction and potential extinction of wild populations of Atlantic salmon, Salmo salar, as a result of interactions with escaped farm salmon

The high level of escapes from Atlantic salmon farms, up to two million fishes per year in the North Atlantic, has raised concern about the potential impact on wild populations. We report on a two-generation experiment examining the estimated lifetime successes, relative to wild natives, of farm, F(1) and F(2) hybrids and BC(1) backcrosses to wild and farm salmon. Offspring of farm and "hybrids" (i.e. all F(1), F(2) and BC(1) groups) showed reduced survival compared with wild salmon but grew faster as juveniles and displaced wild parr, which as a group were significantly smaller. Where suitable habitat for these emigrant parr is absent, this competition would result in reduced wild smolt production. In the experimental conditions, where emigrants survived downstream, the relative estimated lifetime success ranged from 2% (farm) to 89% (BC(1) wild) of that of wild salmon, indicating additive genetic variation for survival. Wild salmon primarily returned to fresh water after one sea winter (1SW) but farm and 'hybrids' produced proportionately more 2SW salmon. However, lower overall survival means that this would result in reduced recruitment despite increased 2SW fecundity. We thus demonstrate that interaction of farm with wild salmon results in lowered fitness, with repeated escapes causing cumulative fitness depression and potentially an extinction vortex in vulnerable populations.     

O-glycan sialylation and the structure of the stalk-like region of the T cell co-receptor CD8

Studies of mucins suggest that the structural effects of O-glycans are restricted to steric interactions between peptide-linked GalNAc residues and adjacent polypeptide residues. It has been proposed, however, that differential O-glycan sialylation alters the structure of the stalk-like region of the T cell co-receptor, CD8, and that this, in turn, modulates ligand binding (Daniels, M. A., Devine, L., Miller, J. D., Moser, J. M., Lukacher, A. E., Altman, J. D., Kavathas, P., Hogquist, K. A., and Jameson, S. C. (2001) Immunity 15, 1051-1061; Moody, A. M., Chui, D., Reche, P. A., Priatel, J. J., Marth, J. D., and Reinherz, E. L. (2001) Cell 107, 501-512). We characterize the glycosylation of soluble, chimeric forms of the alphaalpha- and alphabeta-isoforms of murine CD8 containing the O-glycosylated stalk of rat CD8alphaalpha, and we show that the stalk O-glycans are differentially sialylated in CHO K1 versus Lec3.2.8.1 cells (82 versus approximately 6%, respectively). Sedimentation analysis indicates that the Perrin functions, Pexp, which reflect overall molecular shape, are very similar (1.61 versus 1.54), whereas the sedimentation coefficients (s) of the CHO K1- and Lec3.2.8.1-derived proteins differ considerably (3.73 versus 3.13 S). The hydrodynamic properties of molecular models also strongly imply that the sialylated and non-sialylated forms of the chimera have parallel, equally highly extended stalks ( approximately 2.6 A/residue). Our analysis indicates that, as in the case of mucins, the overall structure of O-glycosylated stalk-like peptides is sialylation-independent and that the functional effects of differential CD8 O-glycan sialylation need careful interpretation.     

Teleost fish spermatozoa contain a cytosolic protein factor that induces calcium release in sea urchin egg homogenates and triggers calcium oscillations when injected into mouse oocytes

Established studies in a variety of organisms including amphibians, fish, ascidians, nemerteans, echinoderms, mammals, and even a species of flowering plant, clearly demonstrate that an increase in intracellular egg calcium is crucial to the process of egg activation at fertilization. In echinoderms, egg activation appears to involve an egg phospholipase C gamma (PLCgamma). However, numerous studies in mammalian species suggest that calcium is released from internal egg stores at fertilization by a sperm-derived cytosolic protein factor. Recent studies in the mouse have identified this sperm-derived factor as being a novel sperm-specific PLC isoform with distinctive properties (PLCzeta). Homologues of PLCzeta have since been isolated from human and cynomolgus monkey sperm. In addition, sperm factor activity has been detected in non-mammalian species such as chicken, Xenopus, and a flowering plant. Here we report evidence for the existence of a similar sperm-derived factor in a commercially important species of teleost fish, the Nile tilapia Oreochromis niloticus (L). Using an established bioassay for calcium release, the sea urchin egg homogenate, we demonstrate that protein extracts obtained from tilapia spermatozoa exhibit PLC activity similar to that seen in mammalian sperm extracts, and also induce calcium release when added directly to the homogenate. Further, tilapia sperm extracts induced calcium oscillations when injected into mouse oocytes.     

Endogenous neurokinins facilitate synaptic transmission in guinea pig airway parasympathetic ganglia

Neurokinin-containing nerve fibers were localized to guinea pig airway parasympathetic ganglia in control tissues but not in tissues pretreated with capsaicin. The purpose of the present study was to determine whether neurokinins, released during axonal reflexes or after antidromic afferent nerve stimulation, modulate ganglionic synaptic neurotransmission. The neurokinin type 3 (NK(3)) receptor antagonists SB-223412 and SR-142801 inhibited vagally mediated cholinergic contractions of bronchi in vitro at stimulation voltages threshold for preganglionic nerve activation but had no effect on vagally mediated contractions evoked at optimal voltage or field stimulation-induced contractions. Intracellular recordings from the ganglia neurons revealed that capsaicin-sensitive nerve stimulation potentiated subsequent preganglionic nerve-evoked fast excitatory postsynaptic potentials. This effect was mimicked by the NK(3) receptor agonist senktide analog and blocked by SB-223412. In situ, senktide analog markedly increased baseline tracheal cholinergic tone, an effect that was reversed by atropine and prevented by vagotomy or SB-223412. Comparable effects of intravenous senktide analog on pulmonary insufflation pressure were observed. These data highlight the important integrative role played by parasympathetic ganglia and indicate that activation of NK(3) receptors in airway ganglia by endogenous neurokinins facilitates synaptic neurotransmission.     

Melanophore appearance in wild and red tilapia embryos

Red tilapia has aroused interest in many countries for its commercial potential. This tilapia strain combines a desirable coloration and appearance with other advantageous farming characteristics. To study the early appearance of melanophore pigmentation in tilapia, a red tilapia strain originating from Thailand and a wild type coloration of Oreochromis niloticus were used as broodstock to produce artificially wild x wild and red x red progenies. The larvae were assessed periodically up to the first feeding and were recorded. Wild type fish showed a regular appearance of stellate melanophores. In the red strain, the pattern of chromatophores varies from total absence of black spotting to different degrees of macromelanophore distribution. Comparison between red and wild types showed that these two tilapia can be easily scored at day 7. Further, we present indications that the pigmentation over the body develops independently of the initial degree of pigmentation.