Premature refutation of a human-mediated marine species introduction: the case history of the marine snail <Emphasis Type="Italic">Littorina littorea</Emphasis> in the Northwestern Atlantic

The closely documented spread of the European periwinkle snail, Littorina littorea from Pictou, Nova Scotia in 1840 to New Jersey by 1870, its near absence in pre-European fossil deposits, and its close association with human mechanisms of transport from Europe, are among the clearest evidence of a human-mediated marine introduction ever reported. Genetic data were recently proposed as evidence that North American L. littorea predate European contact and thus, are not introduced. Review of these genetic data and all other data reveals that the simplest explanation of the modern occurrence of this snail in North America is by human introduction.     

Estrogenic effect on swelling and monocytic receptor expression in an arthritic temporomandibular joint model

Clinical presentation of temporomandibular joint (TMJ) disorders are more common in women and changes in the female hormone estrogen affect the level of swelling, pro-inflammatory cytokine release and pain in animal models of TMJ arthritis. Estrogen also modulates the expression of the CD16 receptor in vitro. This alters pro-inflammatory cytokine release in monocytes/macrophages when auto-antigens and arthritic factors bind the CD16 receptor. This study investigated the effects of various levels of estrogen on the intensity of inflammation and CD16 expression in a TMJ arthritic animal model. The experiments included rats that were intact or ovariectomized (OVX), eliminating the major source of estrogen output. A portion of the OVX animals had estrogen replaced with 17-beta estradiol (E2) using Alzet pumps. In OVX animals E2 levels were administered for 10 days to create an artificial estrus cycle or to simulate pregnancy. Following E2 treatment the rats were given an intra-articular TMJ injection of saline or complete Freund's adjuvant (CFA). CFA injection significantly increased TMJ swelling, stress induced chromodacryorrhea and attenuated food intake, thus indicating the adjuvant induced TMJ pain/inflammation. Removing endogenous E2 through OVX reduced CFA induced TMJ inflammation, whereas CFA increased the number of TMJ monocytes expressing the CD14 receptor equally in all groups irrespective of plasma E2 levels. Paradoxically, higher levels of E2 reduced the number of TNF-alpha positive, CD16+ and double labeled CD14+/CD16+ cells. The findings indicate that reduced plasma E2 levels attenuated CFA induced TMJ inflammation, whereas increasing E2 levels enhanced TMJ swelling in a dose dependent manner. Estrogenic group differences in CFA induced swelling were independent of TMJ CD14+, CD14+/CD16+ or CD16+ cell numbers suggesting E2 action on the CFA immune response primarily excluded CD16 receptor action.     

<Emphasis Type="Italic">Scoredist</Emphasis>: A simple and robust protein sequence distance estimator

Background  

Distance-based methods are popular for reconstructing evolutionary trees thanks to their speed and generality. A number of methods exist for estimating distances from sequence alignments, which often involves some sort of correction for multiple substitutions. The problem is to accurately estimate the number of true substitutions given an observed alignment. So far, the most accurate protein distance estimators have looked for the optimal matrix in a series of transition probability matrices, e.g. the Dayhoff series. The evolutionary distance between two aligned sequences is here estimated as the evolutionary distance of the optimal matrix. The optimal matrix can be found either by an iterative search for the Maximum Likelihood matrix, or by integration to find the Expected Distance. As a consequence, these methods are more complex to implement and computationally heavier than correction-based methods. Another problem is that the result may vary substantially depending on the evolutionary model used for the matrices. An ideal distance estimator should produce consistent and accurate distances independent of the evolutionary model used.     

Improved profile HMM performance by assessment of critical algorithmic features in SAM and HMMER

Background  

Profile hidden Markov model (HMM) techniques are among the most powerful methods for protein homology detection. Yet, the critical features for successful modelling are not fully known. In the present work we approached this by using two of the most popular HMM packages: SAM and HMMER. The programs' abilities to build models and score sequences were compared on a SCOP/Pfam based test set. The comparison was done separately for local and global HMM scoring.     

Intermittent nicotine administration modulates food intake in rats by acting on nicotine receptors localized to the brainstem

Previous studies have shown nicotine (NIC) administration leads to decreased food intake, while other investigations have reported that NIC stimulates c-Fos expression in the brainstem. Whether there is a causal relationship between NIC effects on ingestion and its effect on brainstem neurons is uncertain, however we hypothesized that blocking NIC action in the brainstem would prevent, to some extent, the hypophagic effects of NIC. In the present study, cannulas were placed in the fourth ventricle of rats. A dose of NIC or saline was injected i.p. in four equal injections during the dark phase for four days. At the start of the second day of injections the NIC receptor antagonist mecamylamine (MEC) or artificial cerebrospinal fluid (a-CSF) was infused intracerebroventricularly (i.c.v.). Thus, four experimental groups were examined: a-CSF + SAL; a-CSF + NIC; MEC + SAL; MEC + NIC. Meal patterns were recorded using a computerized system and water intake and body weight were measured daily. Peripheral NIC injections suppressed food intake by decreasing meal size, whereas infusion of the NIC receptor antagonist MEC (4 microg) into the fourth ventricle blocked the NIC suppression of food intake. Moreover, the MEC effect was due primarily to an increase in dark phase meal size, which suggests neurons localized to the brainstem transmit NIC signals that regulate feeding behavior by affecting meal size.     

COMPOSITION OF EXTRACELLULAR POLYMERIC SUBSTANCES FROM PERIPHYTON ASSEMBLAGES IN THE FLORIDA EVERGLADES1

In wetland habitats, periphyton is a common component of open‐water areas with species assemblage determined by local water quality. Extracellular polymeric substances (EPS) secreted by algae and bacteria give structure to periphyton, and differences in EPS chemistry affect the functional roles of these polymers. The Florida Everglades provide a unique opportunity to study compositional differences of EPS from distinctive algal assemblages that characterize areas of differing water chemistry. Water conservation area (WCA)‐1 is a soft‐water impoundment; periphyton was loosely associated with Utricularia stems and amorphous in structure, with a diverse desmid and diatom assemblage, and varying cyanobacterial abundance. Extracellular polymers were abundant and were loosely cell‐associated sheaths and slime layers in addition to tightly cell‐associated capsules. The EPS were complex heteropolysaccharides with significant saccharide residues of glucose, xylose, arabinose, and fucose. Carboxylic acids were also prominent, while ester sulfates and proteins were small components. Structured, cohesive cyanobacteria‐dominated periphyton was observed in WCA‐2A, a minerotrophic impoundment, and filaments were heavily encrusted with calcium carbonate and detrital matter. EPS were primarily cell‐associated sheaths, and polymer residues were dominated by glucose, xylose, fucose, and galactose, with uronic acids also a significant component of the polymers. Principal components analysis revealed that periphyton community assemblage determined the monosaccharide composition of EPS, which ultimately determines a range of biogeochemical processes within the periphyton.     

Detrital Floc and Surface Soil Microbial Biomarker Responses to Active Management of the Nutrient Impacted Florida Everglades

Alterations in microbial community composition, biomass, and function in the Florida Everglades impacted by cultural eutrophication reflect a new physicochemical environment associated with monotypic stands of Typha domingensis. Phospholipid fatty acid (PLFA) biomarkers were used to quantify microbial responses in detritus and surface soils in an active management experiment in the eutrophic Everglades. Creation of open plots through removal of Typha altered the physical and chemical characteristics of the region. Mass of PLFA biomarkers increased in open plots, but magnitude of changes differed among microbial groups. Biomarkers indicative of Gram-negative bacteria and fungi were significantly greater in open plots, reflective of the improved oxic environment. Reduction in the proportion of cyclopropyl lipids and the ratio of Gram-positive to Gram-negative bacteria in open plots further suggested an altered oxygen environment and conditions for the rapid growth of Gram-negative bacteria. Changes in the PLFA composition were greater in floc relative to soils, reflective of rapid inputs of new organic matter and direct interaction with the new physicochemical environment. Created open plot microbial mass and composition were significantly different from the oligotrophic Everglades due to differences in phosphorus availability, plant community structure, and a shift to organic peat from marl-peat soils. PLFA analysis also captured the dynamic inter-annual hydrologic variability, notably in PLFA concentrations, but to a lesser degree content. Recently, use of concentration has been advocated over content in studies of soil biogeochemistry, and our results highlight the differential response of these two quantitative measures to similar pressures.