Structural basis for the inactivation of AdoMetDC K12R mutant

S-adenosylmethionine decarboxylase (AdoMetDC) is a key enzyme in the biosynthesis of the polyamines spermidine and spermine. Polyamines are ubiquitous organic cations that are absolutely required for normal cell proliferation and differentiation. AdoMetDC catalyzes decarboxylation of S-adenosylmethionine (AdoMet) which provides aminopropyl groups for spermidine and spermine synthesis. Mammalian AdoMetDC is produced as a proenzyme (38 kDa) which is cleaved to form the alpha (30.7 kDa) and beta (7.7 kDa) subunits of the mature enzyme. It is here shown that the catalytic activity of the enzyme was completely eliminated when lysine 12 was mutated to an arginine residue in the small subunit; however, the proenzyme processing was not affected. On the other hand, mutations of other lysine residues (Lys45-->Arg and Lys56-->Arg) did not affect either the enzyme activity or the proenzyme processing. Structure analysis using Swiss Deep Viewer v3.7 has indicated that Arg in place of Lys12 may eliminate AdoMetDC activity by restricting the mobility of Thr85 through hydrogen bonding. Sequence alignment of various AdoMetDC sequences indicated that Thr85 is in a highly conserved region, suggesting that Thr85 is critical for the decarboxylation reaction.     

Effects of combining microbial and chemical insecticides on mortality of the Pecan Weevil (Coleoptera: Curculionidae)

The pecan weevil, Curculio caryae (Horn), is a key pest of pecan [Carya illinoinensis (Wangenh.) K. Koch]. Current control recommendations are based on chemical insecticide applications. Microbial control agents such as the entomopathogenic nematode, Steinernema carpocapsae (Weiser) and the fungus Beauveria bassiana (Balsamo) Vuillemin occur naturally in southeastern U.S. pecan orchards and have shown promise as alternative control agents for C. caryjae. Conceivably, the chemical and microbial agents occur simultaneously within pecan orchards or might be applied concurrently. The objective of this study was to determine the interactions between two chemical insecticides that are used in commercial C. caryae control (i.e., carbaryl and cypermethrin applied below field rates) and the microbial agents B. bassiana and S. carpocapsae. In laboratory experiments, pecan weevil larval or adult mortality was assessed after application of microbial or chemical treatments applied singly or in combination (microbial + chemical agent). The nature of interactions (antagonism, additivity, or synergy) in terms of weevil mortality was evaluated over 9 d (larvae) or 5 d (adults). Results for B. bassiana indicated synergistic activity with carbaryl and antagonism with cypermethrin in C. caryae larvae and adults. For S. carpocapsae, synergy was detected with both chemicals in C. caryae larvae, but only additive effects were detected in adult weevils. Our results indicate that the chemical-microbial combinations tested are compatible with the exception of B. bassiana and cypermethrin. In addition, combinations that exhibited synergistic interactions may provide enhanced C. caryae control in commercial field applications; thus, their potential merits further exploration.     

Growth and reproduction of the mosquitofish,Gambusia affinis,in relation to temperature and ration level: consequences for life history

The allocation of energy to growth and reproduction, in relation to temperature and food availability, was investigated in laboratory experiments with the mosquitofish,Gambusia affinis. At constant temperature of 20, 25 and 30°C and ad libitum feeding, specific growth rates increased with increasing temperature at 1.7, 3.1 and 3.4% dry mass day⁻¹, respectively. Growth rates in a cycling temperature regime (20–30°C, ) were faster than in a 25°C constant temperature. As temperature increased from 20 to 30°C, mean age at first reproduction decreased from 191 to 56 days and brood size and mass of offspring increased significantly. Interbrood interval was also temperature dependent; estimates at 25 and 30°C for females >1000 mg were 22.6 and 18.6 days, respectively. Interbrood interval could not be calculated at 20°C. Although fitness was highest at 30°C, females at 25°C invested a greater proportion of surplus energy (growth and reproduction) to reproduction (38%) than at 20 (17%) or 30°C (36%) during the 32-week study. Fish at cooler temperatures began reproduction at a smaller size. Where rations were controlled at low, medium, and ad libitum levels, somatic and gonadal growth increased with increasing temperatures and food availability. The proportion of energy invested in reproduction was highest at 25°C for each comparable ration level. Calculated energy budgets indicated that over the 10-week study, 17–22% of the food energy was invested in growth, 0–7% in reproduction, and 75–83% in respiration and excretory losses, depending on feeding and temperature conditions.     

Assessing enzyme activities using stable isotope labeling and mass spectrometry

Activity-based protein profiling has emerged as a valuable technology for labeling, enriching, and assessing protein activities from complex mixtures. This is primarily accomplished via a two-step identification and quantification process. Here we show a highly quantitative and streamlined method, termed catch-and-release activity profiling of enzymes (CAPE), which reduces this procedure to a single step. Furthermore the CAPE approach has the ability to detect small quantitative changes that may have been missed by alternative mass spectrometry-based techniques.     

Riluzole is a radio‐sensitizing agent in an in vivo model of brain metastasis derived from GRM1 expressing human melanoma cells

Approximately 50% of patients having metastatic melanoma develop brain metastases during the course of their illness. Evidence exists that melanoma cells have increased aptitude for the repair of sublethal DNA damage caused by ionizing radiation therapy. To address the radio‐resistance of melanoma, many groups adopted radiotherapy schedules that deliver larger daily fractions of radiation, but due to the risk of neurotoxicity, these large fractions cannot be delivered to the whole brain for patients with brain metastases. Here, we used orthotopic implanted GRM1 expressing human melanoma cell xenografts in mice, to demonstrate that animals receiving concurrent glutamate signaling blockade (riluzole) and radiation led to a decrease in intracranial tumor growth compared to either modality alone. These preclinical results suggest riluzole may cause radio‐sensitization that offers enhanced efficacy for a subset of human melanoma patients undergoing radiotherapy for brain metastasis.     

MONOPHYLY OF ANEUPLOID ASTRAGALUS (FABACEAE): EVIDENCE FROM NUCLEAR RIBOSOMAL DNA INTERNAL TRANSCRIBED SPACER SEQUENCES

Evolutionary relationships within Astragalus L. (Fabaceae) were inferred from nucleotide sequence variation in nuclear ribosomal DNA of both New World and Old World species. The internal transcribed spacer regions (ITS) of 18S–26S nuclear ribosomal DNA from representatives of 26 species of Astragalus, three species of Oxytropis DC., and two outgroup taxa were analyzed by polymerase chain reaction amplification and direct DNA sequencing. The length of the ITS 1 region within these taxa varied from 221 to 231 bp, while ITS 2 varied in length from 207 to 217 bp. Of the aligned, unambiguous positions, approximately 34% were variable in each spacer region. In pairwise comparisons among Astragalus species and outgroup taxa, sequence divergence at these sites ranged from 0 to 18.8% in ITS 1 and from 0 to 21.7% in ITS 2. Parsimony analyses of these sequences resulted in a well-resolved phylogeny that is highly concordant with previous cytogenetic and chloroplast DNA evidence for a major phylogenetic division in the genus. These data suggest that the New World aneuploid species of Astragalus form a monophyletic but morphologically cryptic group derived from euploid species of Old World (Eurasian) origin, which are consequently paraphyletic.     

The inhibition of photosynthesis and photorespiration in isolated mesophyll cells of Phaseolus and Lycopersicon by reduced osmotic potentials

Mesophyll cells isolated from Phaseolus vulgaris and Lycopersicon esculentum show decreasing photosynthetic rates when suspended in media containing increasing concentrations of osmoticum. The photosynthetic activity was sensitive to small changes in osmotic potential over a range of sorbitol concentrations from 0.44 M (−1.08 MPa) to 0.77 M (−1.88 MPa). Photorespiration assayed by ¹⁴CO₂ release in CO₂-free air and by ¹⁴CO₂ release from the oxidation of [1–¹⁴C] glycolate also decreased as the osmotic potential of the incubation medium was reduced. The CO₂ compensation points of the cells increased with increasing concentration of osmoticum from approximately 60 μ I⁻¹1 at −1.08 MPa to 130 μl 1⁻¹ for cells stressed at −1.88 MPa. Changes in photosynthetic and photorespiratory activities occurred at moderate osmotic potentials in these cells suggesting that in whole leaves during a reduction in water potential, non- stomatal inhibition of CO₂ assimilation and glycolate pathway metabolism occurs simultaneously with stomatal closure.     

Paleoceanography of the Gulf of Alaska during the past 15,000 years: Results from diatoms, silicoflagellates, and geochemistry

High-resolution records of diatoms, silicoflagellates, and geochemistry covering the past 15,000 years were studied in three cores from the Gulf of Alaska (GOA). Core EW0408-85JC in an oceanic setting on the Kayak Slope displays a paleoceanographic record similar to that at several locations on the California margin during deglaciation. Biologic productivity as reconstructed using geochemical and microfossil proxies increased abruptly during the Bølling–Alleröd (Bø–Al) warm interval (14.7–12.9 cal ka), declined during the Younger Dryas (YD) cold interval (12.9 to 11.7 cal kyr BP), and rose again during the earliest Holocene. At this site, the record after ~ 11 cal kyr BP is dominated by oceanic diatoms and silicoflagellates, with geochemical proxies displaying more subtle variation.Cores EW0408-66JC in the Yakobi Sea Valley near Cross Sound and EW0408-11JC in the Gulf of Esquibel contain an expanded, composite record along the southeast Alaskan margin. Core 66JC contains a detailed record of the Bø–Al and YD. Diatoms and silicoflagellates indicate that coastal upwelling and biosiliceous productivity were strong during the Bø–Al but declined during the YD. Sea ice-related diatoms increased in abundance during the YD, indicating cooler, but less productive waters.The glacial to biogenic marine sediment transition in core 11JC occurs at 1280 cmbsf (centimeters below sea floor), probably representing rising sea level and deglaciation early in the Bø–Al. Freshwater and sea-ice related diatoms are common in the lower part of the core (Bø–Al and YD), but upwelling-related diatoms and silicoflagellates quickly increased in relative abundance up-core, dominating the record of the past 11,000 years. Low oxygen conditions in the bottom water as reconstructed using geochemical proxies (U and Mo concentration) were most intense between ~ 6.5 and 2.8 cal kyr BP, the beginning of which is coincident with increases in abundance of upwelling-related diatoms.The records from these three cores jointly thus made it possible to reconstruct paleoclimatic and paleoceanographic conditions at high northern Pacific latitudes during the last 15 kyr.     

A novel ensemble-based scoring and search algorithm for protein redesign and its application to modify the substrate specificity of the gramicidin synthetase a phenylalanine adenylation enzyme.

Realization of novel molecular function requires the ability to alter molecular complex formation. Enzymatic function can be altered by changing enzyme-substrate interactions via modification of an enzyme's active site. A redesigned enzyme may either perform a novel reaction on its native substrates or its native reaction on novel substrates. A number of computational approaches have been developed to address the combinatorial nature of the protein redesign problem. These approaches typically search for the global minimum energy conformation among an exponential number of protein conformations. We present a novel algorithm for protein redesign, which combines a statistical mechanics-derived ensemble-based approach to computing the binding constant with the speed and completeness of a branch-and-bound pruning algorithm. In addition, we developed an efficient deterministic approximation algorithm, capable of approximating our scoring function to arbitrary precision. In practice, the approximation algorithm decreases the execution time of the mutation search by a factor of ten. To test our method, we examined the Phe-specific adenylation domain of the nonribosomal peptide synthetase gramicidin synthetase A (GrsA-PheA). Ensemble scoring, using a rotameric approximation to the partition functions of the bound and unbound states for GrsA-PheA, is first used to predict binding of the wildtype protein and a previously described mutant (selective for leucine), and second, to switch the enzyme specificity toward leucine, using two novel active site sequences computationally predicted by searching through the space of possible active site mutations. The top scoring in silico mutants were created in the wetlab and dissociation/binding constants were determined by fluorescence quenching. These tested mutations exhibit the desired change in specificity from Phe to Leu. Our ensemble-based algorithm, which flexibly models both protein and ligand using rotamer-based partition functions, has application in enzyme redesign, the prediction of protein-ligand binding, and computer-aided drug design.