Cell wall-targeting domain of glycylglycine endopeptidase distinguishes among peptidoglycan cross-bridges

ALE-1, a homologue of lysostaphin, is a peptidoglycan hydrolase that specifically lyses Staphylococcus aureus cell walls by cleaving the pentaglycine linkage between the peptidoglycan chains. Binding of ALE-1 to S. aureus cells through its C-terminal 92 residues, known as the targeting domain, is functionally important for staphylolytic activity. The ALE-1-targeting domain belongs to the SH3b domain family, the prokaryotic counterpart of the eukaryotic SH3 domains. The 1.75 angstroms crystal structure of the targeting domain shows an all-beta fold similar to typical SH3s but with unique features. The structure reveals patches of conserved residues among orthologous targeting domains, forming surface regions that can potentially interact with some common features of the Gram-positive cell wall. ALE-1-targeting domain binding studies employing various bacterial peptidoglycans demonstrate that the length of the interpeptide bridge, as well as the amino acid composition of the peptide, confers the maximum binding of the targeting domain to the staphylococcal peptidoglycan. Truncation of the highly conserved first 9 N-terminal residues results in loss of specificity to S. aureus cell wall-targeting, suggesting that these residues confer specificity to S. aureus cell wall.     

Effect of corn hybrids expressing the coleopteran-specific cry3Bb1 protein for corn rootworm control on aboveground insect predators

Field and laboratory studies were conducted to determine the effect of transgenic Bacillus thuringiensis (Bt) corn, Zea mays L. (YieldGard Rootworm), expressing the Cry3Bb1 protein on aboveground nontarget insect predators (minute pirate bug, ladybird beetles, and carabids). Visual counts of adult and immature Orius insidiosus (Say), Coleomegilla maculata (DeGeer), Hippodamia convergens Gurin-Meneville, and Scymnus spp. occurring in Bt corn and its non-Bt isoline were made at Manhattan, KS, in 2002 and at Manhattan and Scandia, KS, in 2003. No significant differences were found between the Bt corn and non-Bt isoline plots in the abundance (number per plant) of O. insidiosus, C. maculata, H. convergens, and Scymnus spp. Field predation on Ostrinia nubilalis (Hübner) (Lepidoptera: Crambidae) egg masses was also observed during the silking stage of corn at Manhattan and Scandia in 2003. No significant differences were observed among treatments in predation rate for predators with chewing versus sucking mouthparts. Two laboratory studies determined the effect of Cry3Bb1 protein expressed in Bt corn pollen on C. maculata and carabids. The larvae of C. maculata were reared on Bt pollen, non-Bt pollen, or greenbugs, Schizaphis graminum (Rondani). The duration of larval and pupal stages, developmental time from egg hatch to adult emergence, percentage of survival, and elytra length were compared among treatments. There were no significant differences in developmental time of larvae fed pollen or greenbugs during their first two instars. However, significantly prolonged development of the third (1 d) and fourth instars (2 d) was observed for larvae fed greenbugs only. Total time for larval development was significantly longer for larvae that fed on greenbugs versus larvae fed on pollen. No significant differences were observed among treatments in the percentage of larvae that pupated or pupal stage duration. Larvae that fed on greenbugs had higher pupal and adult weights compared with pollen-fed larvae. However, pupal and adult weights did not vary between the Bt and non-Bt pollen treatments. No significant differences occurred in longevity and elytra length of beetles among all treatments. Two carabid species, Harpalus caliginosus F. and Harpalus pensylvanicus DeGeer, were reared on moistened dog food sprinkled with Bt or non-Bt corn pollen. No significant differences in mortality of H. caliginosus and H. pensylvanicus were detected among any of the treatments. There was no significant effect of Bt pollen on fecundity and egg viability of H. caliginosus. Our studies showed that YieldGard Rootworm had no effect on the selected coleopteran predators; therefore, this Bt corn hybrid could be used in an integrated pest management system.     

The soft-bottom macrobenthos of Gray's Reef National Marine Sanctuary and nearby shelf waters off the coast of Georgia, USA

As part of an ongoing ecological assessment of the Gray's Reef National Marine Sanctuary (GRNMS), a 58-km² marine protected area 32 km off the coast of Georgia, USA, surveys of benthic macroinfaunal communities, contaminant levels in sediments and biota, and general habitat conditions were conducted during 2000-2002 at 20 stations within the sanctuary and along three cross-shelf transects in nearby shelf waters. Macroinfaunal community structure and composition exhibited distinct cross-shelf patterns associated with sediment granulometry, depth and possibly other factors related to shoreline proximity (e.g., erosional effects, recruitment of estuarine species). Finer-scale spatial patterns of benthic fauna among stations within the sanctuary appear to be related to proximity to live-bottom habitat and other features of seafloor structure (e.g., rippled vs. flat sand). Population densities of dominant fauna within the sanctuary also varied considerably among years, resulting in shifts in the ranking of dominants at most stations. Chemical contaminants generally were at low background concentrations below probable bioeffect levels and thus are not a likely cause of the observed spatial patterns of benthic fauna. However, trace concentrations of pesticides, PCBs, and PAHs were detectable in sediments and biota throughout the study area, demonstrating that chemicals originating from human activities are capable of reaching the offshore sanctuary environment, possibly from atmospheric deposition or cross-shelf transport of materials outwelled through coastal sounds. Highly diverse infaunal assemblages also were observed within the sanctuary and nearby sites of similar depth, suggesting that the sanctuary is an important reservoir of marine biodiversity. Results of this study should be useful in addressing long-term science and management needs of the GRNMS and in furthering our understanding of broader ecological patterns and dynamics of the surrounding South Atlantic Bight (SAB) ecosystem.     

Mechanism of the inhibition of Ca2+-activated Cl- currents by phosphorylation in pulmonary arterial smooth muscle cells

The aim of the present study was to provide a mechanistic insight into how phosphatase activity influences calcium-activated chloride channels in rabbit pulmonary artery myocytes. Calcium-dependent Cl- currents (I(ClCa)) were evoked by pipette solutions containing concentrations between 20 and 1000 nM Ca2+ and the calcium and voltage dependence was determined. Under control conditions with pipette solutions containing ATP and 500 nM Ca2+, I(ClCa) was evoked immediately upon membrane rupture but then exhibited marked rundown to approximately 20% of initial values. In contrast, when phosphorylation was prohibited by using pipette solutions containing adenosine 5'-(beta,gamma-imido)-triphosphate (AMP-PNP) or with ATP omitted, the rundown was severely impaired, and after 20 min dialysis, I(ClCa) was approximately 100% of initial levels. I(ClCa) recorded with AMP-PNP-containing pipette solutions were significantly larger than control currents and had faster kinetics at positive potentials and slower deactivation kinetics at negative potentials. The marked increase in I(ClCa) was due to a negative shift in the voltage dependence of activation and not due to an increase in the apparent binding affinity for Ca2+. Mathematical simulations were carried out based on gating schemes involving voltage-independent binding of three Ca2+, each binding step resulting in channel opening at fixed calcium but progressively greater "on" rates, and voltage-dependent closing steps ("off" rates). Our model reproduced well the Ca2+ and voltage dependence of I(ClCa) as well as its kinetic properties. The impact of global phosphorylation could be well mimicked by alterations in the magnitude, voltage dependence, and state of the gating variable of the channel closure rates. These data reveal that the phosphorylation status of the Ca2+-activated Cl- channel complex influences current generation dramatically through one or more critical voltage-dependent steps.     

Conformational study of Met-enkephalin based on the ECEPP force fields

We report a computational study of the small peptide Met-enkephalin based on the ECEPP/2 and ECEPP/3 force fields using the basin paving method. We have located a new global minimum when using the ECEPP/3 force field with peptide angles omega fixed at 180 degrees. With this new result, we can conclude that the lowest energy configurations of Met-enkephalin predicted based on all four versions of ECEPP have a classic gamma-turn centered at residue Gly3 and a beta-turn at residues Gly3-Phe4. However, minor differences between the structures also exist.     

Effective temperature in stochastic kinetics and gene networks

The fluctuation-dissipation theorem, one of the central theorems in thermal dynamics, breaks down in out-of-equilibrium systems. The idea of effective temperature coming from the extensions of that theorem has been recently introduced to study glasses and has proved to be a key concept for out-of-equilibrium systems. Gene networks involve stochastic chemical kinetics and are far from equilibrium. This leads us to try to use the notion of effective temperature to study them. To develop this idea, we study a simple birth-death process and a general two-species interacting process using the language of effective temperature. Furthermore, a model of a nonregulatory gene is studied as an example. The effective temperature may serves as an alternative and somewhat more fundamental language to describe the intrinsic-extrinsic noise distinction that has already provided a tool for qualifying gene networks.     

Quantitative trait loci with age-specific effects on fecundity in Drosophila melanogaster

Life-history theory and evolutionary theories of aging assume the existence of alleles with age-specific effects on fitness. While various studies have documented age-related changes in the genetic contribution to variation in fitness components, we know very little about the underlying genetic architecture of such changes. We used a set of recombinant inbred lines to map and characterize the effects of quantitative trait loci (QTL) affecting fecundity of Drosophila melanogaster females at 1 and 4 weeks of age. We identified one QTL on the second chromosome and one or two QTL affecting fecundity on the third chromosome, but these QTL affected fecundity only at 1 week of age. There was more genetic variation for fecundity at 4 weeks of age than at 1 week of age and there was no genetic correlation between early and late-age fecundity. These results suggest that different loci contribute to the variation in fecundity as the organism ages. Our data provide support for the mutation accumulation theory of aging as applied to reproductive senescence. Comparing the results from this study with our previous work on life-span QTL, we also find evidence that antagonistic pleiotropy may contribute to the genetic basis of senescence in these lines as well.     

Inflammation induces myeloid-derived suppressor cells that facilitate tumor progression

Epidemiological and experimental observations support the hypothesis that chronic inflammation contributes to cancer development and progression; however, the mechanisms underlying the relationship between inflammation and cancer are poorly understood. To study these mechanisms, we have transfected the mouse 4T1 mammary carcinoma with the proinflammatory cytokine IL-1beta to produce a chronic inflammatory microenvironment at the tumor site. Mice with 4T1/IL-1beta tumors have a decreased survival time and elevated levels of immature splenic Gr1+CD11b+ myeloid-derived cells. These myeloid suppressor cells (MSC) are present in many patients with cancer and inhibit the activation of CD4+ and CD8+ T lymphocytes. 4T1/IL-1beta-induced MSC do not express the IL-1R, suggesting that the cytokine does not directly activate MSC. Neither T or B cells nor NKT cells are involved in the IL-1beta-induced increase of MSC because RAG2-/- mice and nude mice with 4T1/IL-1beta tumors also have elevated MSC levels. MSC levels remain elevated in mice inoculated with 4T1/IL-1beta even after the primary tumor is surgically removed, indicating that the IL-1beta effect is long lived. Collectively, these findings suggest that inflammation promotes malignancy via proinflammatory cytokines, such as IL-1beta, which enhance immune suppression through the induction of MSC, thereby counteracting immune surveillance and allowing the outgrowth and proliferation of malignant cells.     

Response of hatchling wood turtles (Glyptemys insculpta) to an aquatic thermal gradient

Effective thermoregulation and the ability to select preferred temperature is an important factor influencing fitness in hatchling and juvenile turtles. Six-month-old Glyptemys insculpta acclimated to 20 °C selected the warmest temperature available and avoided the coldest temperature available in a gradient of 12–27 °C. Turtles visited fewer chambers and switched chambers in the gradient tank less frequently when the gradient was present than during control tests. Mean selection of chambers differed between control and gradient tests across all temperatures except at 21 °C, the temperature closest to the acclimation and control temperature (20 °C).     

Oxidation and haem loss kinetics of poly(ethylene glycol)-conjugated haemoglobin (MP4): dissociation between in vitro and in vivo oxidation rates

Haemoglobin-based oxygen carriers can undergo oxidation of ferrous haemoglobin into a non-functional ferric form with enhanced rates of haem loss. A recently developed human haemoglobin conjugated to maleimide-activated poly(ethylene glycol), termed MP4, has unique physicochemical properties (increased molecular radius, high oxygen affinity and low cooperativity) and lacks the typical hypertensive response observed with most cell-free haemoglobin solutions. The rate of in vitro MP4 autoxidation is higher compared with the rate for unmodified SFHb (stroma-free haemoglobin), both at room temperature (20-22 degrees C) and at 37 degrees C (P<0.001). This appears to be attributable to residual catalase activity in SFHb but not MP4. In contrast, MP4 and SFHb showed the same susceptibility to oxidation by reactive oxygen species generated by a xanthine-xanthine oxidase system. Once fully oxidized to methaemoglobin, the rate of in vitro haem loss was five times higher in MP4 compared with SFHb in the fast phase, which we assign to the beta subunits, whereas the slow phase (i.e. haem loss from alpha chains) showed similar rates for the two haemoglobins. Formation of MP4 methaemoglobin in vivo following transfusion in rats and humans was slower than predicted by its first-order in vitro autoxidation rate, and there was no appreciable accumulation of MP4 methaemoglobin in plasma before disappearing from the circulation. These results show that MP4 oxidation and haem loss characteristics observed in vitro provide information regarding the effect of poly(ethylene glycol) conjugation on the stability of the haemoglobin molecule, but do not correspond to the oxidation behaviour of MP4 in vivo.