The effect of hillslope angle on pocket gopher (<Emphasis Type="Italic">Thomomys bottae</Emphasis>) burrow geometry

One way for animals to decrease energy expenditures is to minimize the cost of movement. For animals dwelling on slopes, gravity can impart a large energetic cost to movement. For this reason, animals traveling aboveground alter their movement patterns in response to the steepness of terrain (specifically hillslope angle) so as to minimize their energetic costs. Subterranean animals should also benefit from choosing optimum movement paths in relation to hillslopes but concurrently must factor the cost of excavation into their movement decisions. In cases where the excavation costs are much higher than the costs of working against gravity, excavation costs may override the consideration of gravitational costs and movement of subterranean animals may be independent of hillslope angle. To determine the response of a subterranean animal to hillslope angle, we excavated tunnels in the burrow systems of 19 pocket gophers in southern California that occupied hillslopes ranging from 2 to 30°. At each excavation we measured several characteristics of burrow geometry and used these data in a model of pocket gopher energetics to calculate the cost of tunnel construction at the various hillslope angles. We found that the cost of tunnel construction was independent of hillslope angle, and that the costs of shearing soil and pushing soil horizontally through the tunnels were 3 orders of magnitude greater than the costs of lifting the soil against the force of gravity. Accordingly, pocket gopher foraging tunnels were oriented independently of the hillslope. The decoupling of the movement patterns of subterranean animals from the effects of gravity is a distinctive feature of the subterranean habit compared to the movement of aboveground animals. Because of the important effects of tunnel construction on soil processes, this unique biological feature of subterranean animals has implications for basic physical processes, such as soil erosion. We found that the rate of soil flux generated by pocket gopher activity was invariant to hillslope. This relationship is in contrast to the most common model of soil movement generated by purely physical processes. Received: 25 October 1999 / Accepted: 13 April 2000     

Separate Introns Gained within Short and Long Soluble Peridinin-Chlorophyll a-Protein Genes during Radiation of Symbiodinium (Dinophyceae) Clade A and B Lineages

Here we document introns in two Symbiodinium clades that were most likely gained following divergence of this genus from other peridinin-containing dinoflagellate lineages. Soluble peridinin-chlorophyll a-proteins (sPCP) occur in short and long forms in different species. Duplication and fusion of short sPCP genes produced long sPCP genes. All short and long sPCP genes characterized to date, including those from free living species and Symbiodinium sp. 203 (clade C/type C2) are intronless. However, we observed that long sPCP genes from two Caribbean Symbiodinium clade B isolates each contained two introns. To test the hypothesis that introns were gained during radiation of clade B, we compared sPCP genomic and cDNA sequences from 13 additional distinct Caribbean and Pacific Symbiodinium clade A, B, and F isolates. Long sPCP genes from all clade B/B1 and B/B19 descendants contain orthologs of both introns. Short sPCP genes from S. pilosum (A/A2) and S. muscatinei (B/B4) plus long sPCP genes from S. microadriaticum (A/A1) and S. kawagutii (F/F1) are intronless. Short sPCP genes of S. microadriaticum have a third unique intron. Symbiodinium clade B long sPCP sequences are useful for assessing divergence among B1 and B19 descendants. Phylogenetic analyses of coding sequences from four dinoflagellate orders indicate that introns were gained independently during radiation of Symbiodinium clades A and B. Long sPCP introns were present in the most recent common ancestor of Symbiodinium clade B core types B1 and B19, which apparently diverged sometime during the Miocene. The clade A short sPCP intron was either gained by S. microadriaticum or possibly by the ancestor of Symbiodinium types A/A1, A3, A4 and A5. The timing of short sPCP intron gain in Symbiodinium clade A is less certain. But, all sPCP introns were gained after fusion of ancestral short sPCP genes, which we confirm as occurring once in dinoflagellate evolution.     

Putting the pH into phosphatidic acid signaling

Background

Camouflage patterns that hinder detection and/or recognition by antagonists are widely studied in both human and animal contexts. Patterns of contrasting stripes that purportedly degrade an observer's ability to judge the speed and direction of moving prey ('motion dazzle') are, however, rarely investigated. This is despite motion dazzle having been fundamental to the appearance of warships in both world wars and often postulated as the selective agent leading to repeated patterns on many animals (such as zebra and many fish, snake, and invertebrate species). Such patterns often appear conspicuous, suggesting that protection while moving by motion dazzle might impair camouflage when stationary. However, the relationship between motion dazzle and camouflage is unclear because disruptive camouflage relies on high-contrast markings. In this study, we used a computer game with human subjects detecting and capturing either moving or stationary targets with different patterns, in order to provide the first empirical exploration of the interaction of these two protective coloration mechanisms.

Results

Moving targets with stripes were caught significantly less often and missed more often than targets with camouflage patterns. However, when stationary, targets with camouflage markings were captured less often and caused more false detections than those with striped patterns, which were readily detected.

Conclusions

Our study provides the clearest evidence to date that some patterns inhibit the capture of moving targets, but that camouflage and motion dazzle are not complementary strategies. Therefore, the specific coloration that evolves in animals will depend on how the life history and ontogeny of each species influence the trade-off between the costs and benefits of motion dazzle and camouflage.     

Molecular docking analysis of compounds from Justica adhatoda L with the MUC1 oncoprotein

The MUC1 oncoprotein is known to be linked with different types of cancer. Therefore, it is of interest to document the molecular docking analysis of compounds from Justica adhatoda L with the MUC1 oncoprotein. We report the structure based molecular binding features compounds such as amrinone, ethambutol, pyrazinamide and vasicoline the MUC1 oncoprotein for further consideration in drug discovery.     

Separating multiple, short-term, deleterious effects of saline solutions on the growth of cowpea seedlings

? Reductions in plant growth as a result of salinity are of global importance in natural and agricultural landscapes. ? Short-term (48-h) solution culture experiments studied 404 treatments with seedlings of cowpea (Vigna unguiculata cv Caloona) to examine the multiple deleterious effects of calcium (Ca), magnesium (Mg), sodium (Na) or potassium (K). ? Growth was poorly related to the ion activities in the bulk solution, but was closely related to the calculated activities at the outer surface of the plasma membrane, {I(z)}?°. The addition of Mg, Na or K may induce Ca deficiency in roots by driving {Ca2+}?° to < 1.6 mM. Shoots were more sensitive than roots to osmolarity. Specific ion toxicities reduced root elongation in the order Ca2+ > Mg2+ > Na+ > K+. The addition of K and, to a lesser extent, Ca alleviated the toxic effects of Na. Thus, Ca is essential but may also be intoxicating or ameliorative. ? The data demonstrate that the short-term growth of cowpea seedlings in saline solutions may be limited by Ca deficiency, osmotic effects and specific ion toxicities, and K and Ca alleviate Na toxicity. A multiple regression model related root growth to osmolarity and {I(z)}?° (R2=0.924), allowing the quantification of their effects.     

Dynamic basis for one-dimensional DNA scanning by the mismatch repair complex Msh2-Msh6

The ability of proteins to locate specific sites or structures among a vast excess of nonspecific DNA is a fundamental theme in biology. Yet the basic principles that govern these mechanisms remain poorly understood. For example, mismatch repair proteins must scan millions of base pairs to find rare biosynthetic errors, and they then must probe the surrounding region to identify the strand discrimination signals necessary to distinguish the parental and daughter strands. To determine how these proteins might function we used single-molecule optical microscopy to answer the following question: how does the mismatch repair complex Msh2-Msh6 interrogate undamaged DNA? Here we show that Msh2-Msh6 slides along DNA via one-dimensional diffusion. These findings indicate that interactions between Msh2-Msh6 and DNA are dominated by lateral movement of the protein along the helical axis and have implications for how MutS family members travel along DNA at different stages of the repair reaction.     

Meta-analysis identified the TNFA -308G > A promoter polymorphism as a risk factor for disease severity in patients with rheumatoid arthritis

Introduction

The goal of this study is to investigate whether the -308G > A promoter polymorphism in the tumor necrosis factor alpha (TNFA) gene is associated with disease severity and radiologic joint damage in a large cohort of patients with rheumatoid arthritis (RA).

Methods

A long-term observational early RA inception cohort (n = 208) with detailed information about disease activity and radiologic damage after 3, 6 and 9 years of disease was genotyped for the TNFA -308G > A promoter polymorphism (rs1800629). A longitudinal regression analysis was performed to assess the effect of genotype on RA disease severity and joint damage. Subsequently, a meta-analysis, including all publically available data, was performed to further test the association between joint erosions and the TNFA polymorphism. To learn more about the mechanism behind the effect of the polymorphism, RNA isolated from peripheral blood from RA patients (n = 66) was used for TNFA gene expression analysis by quantitative PCR.

Results

Longitudinal regression analysis with correction for gender and disease activity showed a significant difference in total joint damage between GG and GA+AA genotype groups (P = 0.002), which was stable over time. The meta-analysis, which included 2,053 patients, confirmed an association of the genetic variant with the development of erosions (odds ratio 0.78, 95% CI 0.62, 0.98). No significant differences in TNFA gene expression were observed for the different genotypes, confirming earlier findings in healthy individuals.

Conclusions

Our data confirm that the TNFA -308G > A promoter polymorphism is associated with joint damage in patients with RA. This is not mediated by differences in TNFA gene expression between genotypes.     

Simulation of stent deployment in a realistic human coronary artery

Background  

The process of restenosis after a stenting procedure is related to local biomechanical environment. Arterial wall stresses caused by the interaction of the stent with the vascular wall and possibly stress induced stent strut fracture are two important parameters. The knowledge of these parameters after stent deployment in a patient derived 3D reconstruction of a diseased coronary artery might give insights in the understanding of the process of restenosis.     

A Markov model for a clinical episode of recurrent genital herpes

A time-homogeneous Markov process is proposed for modeling the clinical course of recurrent genital herpes and is used to obtain estimators for various characteristics of the disease episode. The model has a finite, discrete time parameter and discrete state space, with six transient states corresponding to the six stages a herpes lesion may enter. The healed condition is represented as an absorbing state. The number of lesions present at the onset of the clinical episode and the number of lesions appearing during the course of the episode are assumed to have negative binomial distributions. Clinical trial data are used to examine the assumptions of the model and to estimate its parameters. Estimates of clinical variables based on the model are computed and are compared with those calculated directly to assess how well the model represents the biological process of the disease.