"Living" under the challenge of information decay: the stochastic corrector model vs. hypercycles

The combined problem of having a large genome size when the accuracy of replication was a limiting factor is probably the most difficult transition to explain at the late stages of RNA world. One solution has been to suggest the existence of a cyclically coupled system of autocatalytic and cross-catalytic molecular mutualists, where each member helps the following member and receives help from the preceding one (i.e., a "hypercycle"). However, such a system is evolutionarily unstable when mutations are taken into account because it lacks individuality. In time, the cooperating networks of genes should have been encapsulated in a cell-like structure. But once the cell was invented, it closely aligned genes' common interests and helped to reduce gene selfishness, so there was no need for hypercycles. A simple package of competing genes, described by the "stochastic corrector model" (SCM), could have provided the solution. Until now, there is no clear demonstration that the proposed mechanisms (compartmentalized hypercycles and the stochastic corrector model) do in fact solve the error threshold problem. Here, we present a Monte Carlo model to test the viability of protocell populations that enclose a hypercyclic (HPC) or a non-hypercyclic (SCM) system when faced with realistic mutation rates before the evolution of efficient enzymic machinery for replication. The numerical results indicate that both systems are efficient information integrators and are able to overcome the danger of information decay in the absence of accurate replication. However, a population of SCM protocells can tolerate higher deleterious mutation rates and reaches an equilibrium mutational load lower than that in a population of HPC protocells.     

Genetic dissection of a major Fusarium head blight QTL in tetraploid wheat

The devastating effect of Fusarium head blight (FHB) caused by Fusarium graminearum has led to significant financial losses across the Upper Midwest of the USA. These losses have spurred the need for research in biological, chemical, and genetic control methods for this disease. To date, most of the research on FHB resistance has concentrated on hexaploid wheat (Triticum aestivum L.) lines originating from China. Other sources of resistance to FHB would be desirable. One other source of resistance for both hexaploid wheat and tetraploid durum wheat (T. turgidum L. var. durum) is the wild tetraploid, T. turgidum L. var. dicoccoides (T. dicoccoides). Previous analysis of the `Langdon'-T. dicoccoides chromosome substitution lines, LDN(Dic), indicated that the chromosome 3A substitution line expresses moderate levels of resistance to FHB. LDN(Dic-3A) recombinant inbred chromosome lines (RICL) were used to generate a linkage map of chromosome 3A with 19 molecular markers spanning a distance of 155.2 cM. The individual RICL and controls were screened for their FHB phenotype in two greenhouse seasons. Analysis of 83 RICL identified a single major quantitative trait locus, Qfhs.ndsu-3AS, that explains 37% of the phenotypic or 55% of the genetic variation for FHB resistance. A microsatellite locus, Xgwm2, is tightly linked to the highest point of the QTL peak. A region of the LDN (Dic-3A) chromosome associated with the QTL for FHB resistance encompasses a 29.3 cM region from Xmwg14 to Xbcd828.     

T-kininogen inhibits kinin-mediated activation of ERK in endothelial cells

Serum levels of T-kininogen increase dramatically as rats approach the end of their lifespan. Stable expression of the protein in Balb/c 3T3 fibroblasts leads to a dramatic inhibition of cell proliferation, as well as inhibition of the ERK signaling pathway. T-kininogen is a potent inhibitor of cysteine proteinases, and we have described that the inhibition of ERK activity occurs, at least in part, via stabilization of the MAP kinase phosphatase, MKP-1. Since fibroblasts are not a physiological target of T-kininogen, we have now purified the protein from rat serum, and used it to assess the effect of T-kininogen on endothelial cells. Adding purified T-kininogen to EAhy 926 hybridoma cells resulted in inhibition of basal ERK activity levels, as estimated using appropriate anti-phospho ERK antibodies. Furthermore, exogenously added T-kininogen inhibited the activation of the ERK pathway induced by either bradykinin or T-kinin. We conclude that the age-related increase in hepatic T-kininogen gene expression and serum levels of the protein could have dramatic consequences on endothelial cell physiology, both under steady state conditions, and after activation by cell-specific stimuli. Our results are consistent with T-kininogen being an important modulator of the senescent phenotype in vivo.     

Pig vitreous gel: macromolecular composition with particular reference to hyaluronan-binding proteoglycans

The aim of this study was to examine the macromolecular composition of pig vitreous body with particular emphasis on hyaluronan-binding proteoglycans. The whole pig vitreous gel was found to contain 76 microg of hyaluronan-derived uronic acid, 700 microg of total protein and 150 microg of collagen per ml of gel. The contents of neutral hexoses and sialic acids were 80 and 22 microg/ml of vitreous gel, but only a minor proportion of them were found to be associated with the proteoglycan fraction. As estimated by gel chromatography on Sepharose CL-2B, hyaluronan presents a polydisperse hydrodynamic behavior with a lower molecular mass (M(r)) value of 220 kDa. The existence of low amounts of a hyaluronan-binding proteoglycan population with structural and immunological characteristics similar to a member of the hyalectan family, versican, has also been demonstrated. The concentration of this versican-like proteoglycan in whole vitreous accounts for 50 microg proteoglycan protein per ml of vitreous gel and represents a minor proportion (about 7%) of the total protein content. The proteoglycan has an average M(r) of 360 kDa and is substituted by chondroitin sulphate (CS) side chains. Study of the CS sulphation pattern showed that the chains were composed of both type 4- and 6-sulphated disaccharide units.     

Biosensors for rapid monitoring of primary-source drinking water using naturally occurring photosynthesis

Working with primary-source freshwater drinking samples from the Clinch and Tennessee Rivers, we have developed a tissue-based biosensor detection system that uses naturally occurring aquatic photosynthetic tissue as the sensing material for detection of chemical antagonists in the water. Sensor readout is based on well-known principles of fluorescence induction by living photosynthetic tissue. The Clinch River is the main source of drinking water for Oak Ridge, Tennessee, while the Tennessee River is a major source for the city of Knoxville. We have successfully detected algae in every sample that we examined and readily monitored changes in the characteristic fluorescence induction curves when the samples were exposed to potassium cyanide (KCN), methyl parathion (MPt), N'(3,4-dichlorophenyl)-N,N-dimethylurea (DCMU), and paraquat. The percentage decreases in photochemical yields observed in Tennessee River samples after a 24-min exposure to KCN, MPt, and DCMU were, respectively, 21.89+/-0.76, 3.28+/-0.18, and 14.77+/-1.81. For a site at the Clinch River, the percentage decreases were 22.78+/-1.63, 8.32+/-0.21, and 17.71+/-1.32 (Table 1). The unique aspect of this approach to real-time water quality monitoring is that unlike conventional sensing devices, this sensor material is external to the detecting instrument and is continuously refreshed. These biosensors may be used as continuous rapid-warning sentinels for detection of chemical warfare agents in sunlight-exposed drinking water supplies.     

Synthesis and SAR of N-benzoyl-L-biphenylalanine derivatives: discovery of TR-14035, a dual alpha(4)beta(7)/alpha(4)beta(1) integrin antagonist

alpha(4)beta(1) and alpha(4)beta(7) integrins are key regulators of physiologic and pathologic responses in inflammation and autoimmune disease. The effectiveness of anti-integrin antibodies to attenuate a number of inflammatory/immune conditions provides a strong rationale to target integrins for drug development. Important advances have been made in identifying potent and selective candidates, peptides and peptidomimetics, for further development. Herein, we report the discovery of a series of novel N-benzoyl-L-biphenylalanine derivatives that are potent inhibitors of alpha4 integrins. The potency of the initial lead compound (1: IC(50) alpha(4)beta(7)/alpha(4)beta(1)=5/33 microM) was optimized via sequential manipulation of substituents to generate low nM, orally bioavailable dual alpha(4)beta(1)/alpha(4)beta(7) antagonists. The SAR also led to the identification of several subnanomolar antagonists (134, 142, and 143). Compound 81 (TR-14035; IC(50) alpha(4)beta(7)/alpha(4)beta(1)=7/87 nM) has completed Phase I studies in Europe. The synthesis, SAR and biological evaluation of these compounds are described.     

The role of wetlands in wildlife migration in the Tarangire ecosystem,Tanzania

Twenty-two years of rainfall data from six sites, 5 years of animal migration data and 2 years of water quality at 13 sites were explored to quantify the role of water in the Tarangire ecosystem. Inter-annual fluctuations in rainfall were large and not predictable solely from the Southern Oscillation Index. Seasonal fluctuations of rainfall were pronounced, with marked wet and dry seasons. In the dry season, the only drinking water available for wildlife was the Tarangire River and a number of small, scattered wetland-fringed water holes. Their salinity was often high (>8 ppt) and was higher in dry years than in wet years, as well as at the start of the wet season. Water quantity and quality may control the annual migration of wildebeest, zebra, elephants and buffaloes. These animals aggregate in the dry season in areas with the least salty water. The timing of seasonal variations in rainfall is largely predictable and controls annual migration. All wildebeest and most zebras migrated out of Tarangire National Park and into the wider Tarangire ecosystem at the start of the wet season, and they returned into the park in the dry season. Some elephants and buffaloes also migrated in out of the park and a larger resident population remained, whose size may vary inter-annually depending on surface water quantity and quality. The extent of the migration zone may also vary inter-annually.This revised version wa published online in March 2005 with corrections to the issue cover date.     

Can albuterol help resistance exercise attenuate unloading-induced bone loss?

Hind-limb-suspended rats incur attenuated bone loss with beta(2)-agonists, and humans note similar changes with concurrent resistance exercise. To examine if the beta(2)-agonist albuterol helps resistance exercise reduce unloading-induced bone loss, human subjects performed 40 days of unilateral limb suspension with their left legs, otherwise refraining from normal ambulatory activity. While performing left leg strength training 3 days.week(-1), subjects received a concurrent placebo or albuterol (16 mg.day(-1)) treatment. Left leg muscle and bone changes were analyzed with 2 x 2 analyses of covariance (ANCOVAs). Mechanical loading values were calculated from workouts and compared using a 2 x 5 analysis of variance (ANOVA) and a Tukey post hoc test. The resistance exercise-albuterol assignment evoked significant (p < 0.05) left leg bone mineral content (BMC) gains (+2.24%) after 40 days. During the final unloading days, the resistance exercise-placebo group's mechanical loading data declined (-13.91%) significantly (p < 0.05) versus initial values. A resistance exercise-albuterol assignment likely increased BMC by maintaining the mechanical loading stimulus.     

Tertiary structure of thiopurine methyltransferase from Pseudomonas syringae, a bacterial orthologue of a polymorphic, drug-metabolizing enzyme

In humans, the enzyme thiopurine methyltransferase (TPMT) metabolizes 6-thiopurine (6-TP) medications, including 6-thioguanine, 6-mercaptopurine and azathioprine, commonly used for immune suppression and for the treatment of hematopoietic malignancies. S-Methylation by TPMT prevents the intracellular conversion of these drugs into active 6-thioguanine nucleotides (6-TGNs). Genetic polymorphisms in the TPMT protein sequence have been associated with decreased tissue enzymatic activities and an increased risk of life-threatening myelo-suppression from standard doses of 6-TP medications. Biochemical studies have demonstrated that TPMT deficiency is primarily associated with increased degradation of the polymorphic proteins through an ubiquitylation and proteasomal-dependent pathway. We have now determined the tertiary structure of the bacterial orthologue of TPMT from Pseudomonas syringae using NMR spectroscopy. Bacterial TPMT similarly catalyzes the S-adenosylmethionine (SAM)-dependent transmethylation of 6-TPs and shares 45% similarity (33% identity) with the human enzyme. Initial studies revealed an unstructured N terminus, which was removed for structural studies and subsequently determined to be required for enzymatic activity. Despite lacking sequence similarity to any protein of known three-dimensional structure, the tertiary structure of bacterial TPMT reveals a classical SAM-dependent methyltransferase topology, consisting of a seven-stranded beta-sheet flanked by alpha-helices on both sides. However, some deviations from the consensus topology, along with multiple insertions of structural elements, are evident. A review of the many experimentally determined tertiary structures of SAM-dependent methyltransferases demonstrates that such structural deviations from the consensus topology are common and often functionally important.