Locomotion in diving elephant seals: physical and physiological constraints

To better understand how elephant seals (Mirounga angustirostris) use negative buoyancy to reduce energy metabolism and prolong dive duration, we modelled the energetic cost of transit and deep foraging dives in an elephant seal. A numerical integration technique was used to model the effects of swim speed, descent and ascent angles, and modes of locomotion (i.e. stroking and gliding) on diving metabolic rate, aerobic dive limit, vertical displacement (maximum dive depth) and horizontal displacement (maximum horizontal distance along a straight line between the beginning and end locations of the dive) for aerobic transit and foraging dives. Realistic values of the various parameters were taken from previous experimental data. Our results indicate that there is little energetic advantage to transit dives with gliding descent compared with horizontal swimming beneath the surface. Other factors such as feeding and predator avoidance may favour diving to depth during migration. Gliding descent showed variable energy savings for foraging dives. Deep mid-water foraging dives showed the greatest energy savings (approx. 18%) as a result of gliding during descent. In contrast, flat-bottom foraging dives with horizontal swimming at a depth of 400m showed less of an energetic advantage with gliding descent, primarily because more of the dive involved stroking. Additional data are needed before the advantages of gliding descent can be fully understood for male and female elephant seals of different age and body composition. This type of data will require animal-borne instruments that can record the behaviour, three-dimensional movements and locomotory performance of free-ranging animals at depth.     

Chip-based detection of hepatitis C virus using RNA aptamers that specifically bind to HCV core antigen

The development of reagents with high affinity and specificity to the antigens of hepatitis C virus (HCV) is important for the early stage diagnosis of its infection. Aptamers are short, single-stranded oligonucleotides with the ability to specifically recognize target molecules with high affinity. Herein, we report the selection of RNA aptamers that bind to the core antigen of HCV. High affinity aptamers were isolated from a 10(15) random library of 60 mer RNAs using the SELEX procedure. Importantly, the selected aptamers specifically bound to the core antigen, but not to another HCV antigen, NS5, in a protein chip-based assay. Using these aptamers, we developed an aptamer-based biosensor for HCV diagnosis and detected the core antigen from HCV infected patients' sera with good specificity. This novel aptamer-based antigen detection sensor could be applied to the early diagnosis of HCV infection.     

Binding of substrate at the effector site of pyrophosphatase increases the rate of its hydrolysis at the active site

It is shown that in addition to the active site, each subunit of Escherichia coli inorganic pyrophosphatase (E-PPase) contains an extra binding site for the substrate magnesium pyrophosphate or its non-hydrolyzable analog magnesium methylenediphosphonate. The occupancy of the extra site stimulates the substrate conversion. Binding affinity of this site decreased or disappeared upon the conversion of E-PPase into a trimeric form or introduction of point mutations. However, when the slowly hydrolyzed substrate, lanthanum pyrophosphate (LaPP(i)), is used, the extra site was revealed in all enzyme forms of E-PPase and of Y-PPase (Saccharomyces cerevisiae PPase), resulting in about 100-fold activation of hydrolysis. A hypothesis on the localization of the extra site and the mechanism of its effect in E-PPase is presented.     

Application of the principal stratification approach to the Faenza randomized experiment on breast self-examination

In this article we present an extended framework based on the principal stratification approach (Frangakis and Rubin, 2002, Biometrics 58, 21-29), for the analysis of data from randomized experiments which suffer from treatment noncompliance, missing outcomes following treatment noncompliance, and "truncation by death." We are not aware of any previous work that addresses all these complications jointly. This framework is illustrated in the context of a randomized trial of breast self-examination.     

Stepwise formation of patterned cell co-cultures in silicone tubing

Here, we describe a method for producing patterned cell adhesion inside silicone tubing. A platinum (Pt) needle microelectrode was inserted through the wall of the tubing and an oxidizing agent electrochemically generated at the inserted electrode. This agent caused local detachment of the anti-biofouling heparin layer from the inner surface of the tubing. The cell-adhesive protein fibronectin selectively adsorbed onto the newly exposed surface, making it possible to initiate a localized cell culture. The electrode could be readily set in place without breaking the tubular structure and, importantly, almost no culture solution leaked from the electrode insertion site after the electrode was removed. Ionic adsorption of poly-L-lysine at the tubular region retaining a heparin coating was used to switch the heparin surface from cell-repellent to cell-adhesive, thereby facilitating the adhesion of a second cell type. The combination of the electrode-based technique with layer-by-layer deposition enabled the formation of patterned co-cultures within the semi-closed tubular structure. The utility of this approach was demonstrated by patterning co-cultures of hepatocytes or endothelial cells with fibroblasts. The controlled co-cultures inside the elastic tubing should be of value for cell-cell interaction studies following application of chemical or mechanical stimuli and for tissue engineering-based bioreactors.     

Coalescence of phospholipid membranes as a possible origin of anticoagulant effect of serum proteins

Interactions between phospholipid membranes (made of palmitoyloleoylphosphatidylcholine, cardiolipin and cholesterol) after addition of beta2 glycoprotein I (beta2GPI) or anti-beta2GPI antibodies or a mixture of both were studied by observing giant phospholipid vesicles under the phase contrast microscope. Both, negatively charged and neutral vesicles coalesced into complexes and adhered to the bottom of the observation chamber in the presence of beta2GPI in solution. Anti-beta2GPIs alone or previously mixed with beta2GPI caused coalescence of charged but not neutral vesicles, i.e. for neutral membranes the effect of beta2GPI was abolished by the presence of anti-beta2GPIs. Since the presence of the above adhesion mediators can prevent fragmentation of the membrane we propose a (new) possible anticoagulant mechanism for some serum proteins by preventing the release of prothrombogenic microexovesicles into circulation.     

Anthropogenic effects on population genetics of phytophagous insects associated with domesticated plants

The hypothesis of isolation by distance (IBD) predicts that genetic differentiation between populations increases with geographic distance. However, gene flow is governed by numerous factors and the correlation between genetic differentiation and geographic distance is never simply linear. In this study, we analyze the interaction between the effects of geographic distance and of wild or domesticated status of the host plant on genetic differentiation in the bean beetle Acanthoscelides obvelatus. Geographic distance explained most of the among-population genetic differentiation. However, IBD varied depending on the kind of population pairs for which the correlation between genetic differentiation and geographic distance was examined. Whereas pairs of beetle populations associated with wild beans showed significant IBD (P < 10(-4)), no IBD was found when pairs of beetle populations on domesticated beans were examined (P= 0.2992). This latter result can be explained by long-distance migrations of beetles on domesticated plants resulting from human exchanges of bean seeds. Beetle populations associated with wild beans were also significantly more likely than those on domesticated plants to contain rare alleles. However, at the population level, beetles on cultivated beans were similar in allelic richness to those on wild beans. This similarity in allelic richness combined with differences in other aspects of the genetic diversity (i.e., IBD, allelic diversity) is compatible with strongly contrasting effects of migration and drift. This novel indirect effect of human actions on gene flow of a serious pest of a domesticated plant has important implications for the spread of new adaptations such as resistance to pesticides.     

改变景观的力量——德克·西蒙斯教授专访

在今天,我们的生存环境面临着诸多挑战,包括气候变化,生物多样性减少,可用于发展的土地资源接近上限等等。面对这些问题,前荷兰首席国家风景园林师德克·西蒙斯认为我们必须关注那些能够改变景观的力量,不管它们是水利工程、旅游业、农业还是新能源。西蒙斯在文中介绍了他的过程导向方法论的思想起点,并通过几个获奖项目阐释了他如何运用这一方法。同时特别强调对生态系统的保护和修复是这个时代最重要的议题之一,也是我们这一代人最重要的使命之一。作为风景园林师,设计结合研究是我们的有力武器。我们不能仅关注眼前工作,还需要用长远的眼光批判地看待整个城市化进程。     

The effect of Piétrain sire on the performance of the progeny of two commercial dam breeds: a pig intervention study

Genetic evaluation of Piétrain sires in Flanders occurs under standardized conditions, on test stations with fixed dam breeds, standardized diets and uniform management practices. As environmental conditions vary on commercial farms and differ from the test stations, this study aimed at understanding to what extent the sire, the dam breed and the interaction between both affects the translation of breeding values to practice. Dams of two commercial breeds were inseminated with semen from one of five different sires selected for contrasting breeding values (daily gain, feed conversion ratio and carcass quality). For each sire by dam breed combination, six pen replicates (with three gilts and three barrows per pen) were evaluated for growth performance from 9 weeks of age (20 kg) to slaughter (110 kg), and for carcass and meat quality. In our experimental setup, both sire and dam breed affected growth, carcass and meat quality traits. No significant sire×dam breed interactions on performance could be detected. Though a tendency for interaction on average daily feed intake between 20 and 110 kg (P=0.087), and on pork colour (lightness) (P=0.093) was present. In general, offspring of all tested sires behaved similarly in both dam breeds, indicating that estimated breeding values for Piétrain sires determined in one dam breed are representative in other dam breeds as well.