A sensitive and specific multiplex PCR approach for sex identification of ursine and tremarctine bears suitable for non‐invasive samples

We report a new approach for molecular sex identification of extant Ursinae and Tremarctinae bears. Two Y‐specific fragments (SMCY and 318.2) and one X‐specific fragment (ZFX) are amplified in a multiplex PCR, yielding a double test for male‐specific amplification and an internal positive control. The primers were designed and tested to be bear‐specific, thereby minimizing the risk of cross‐amplification in other species including humans. The high sensitivity and small amplicon sizes (100, 124, 160 base pairs) facilitate analysis of non‐invasively obtained DNA material. DNA from tissue and blood as well as from 30 non‐invasively collected hair and faeces yielded clear and easily interpretable results. The fragments were detected both by standard gel electrophoresis and automated capillary electrophoresis.     

Distribution and Ecophysiology of Calanoid Copepods in Relation to the Oxygen Minimum Zone in the Eastern Tropical Atlantic

Oxygen minimum zones (OMZs) affect distribution patterns, community structure and metabolic processes of marine organisms. Due to the prominent role of zooplankton, especially copepods, in the marine carbon cycle and the predicted intensification and expansion of OMZs, it is essential to understand the effects of hypoxia on zooplankton distribution and ecophysiology. For this study, calanoid copepods were sampled from different depths (0–1800 m) at eight stations in the eastern tropical Atlantic (3°47′N to 18°S) during three expeditions in 2010 and 2011. Their horizontal and vertical distribution was determined and related to the extent and intensity of the OMZ, which increased from north to south with minimum O₂ concentrations (12.7 µmol kg⁻¹) in the southern Angola Gyre. Calanoid copepod abundance was highest in the northeastern Angola Basin and decreased towards equatorial regions as well as with increasing depth. Maximum copepod biodiversity was observed in the deep waters of the central Angola Basin. Respiration rates and enzyme activities were measured to reveal species-specific physiological adaptations. Enzyme activities of the electron transport system (ETS) and lactate dehydrogenase (LDH) served as proxies for aerobic and anaerobic metabolic activity, respectively. Mass-specific respiration rates and ETS activities decreased with depth of occurrence, consistent with vertical changes in copepod body mass and ambient temperature. Copepods of the families Eucalanidae and Metridinidae dominated within the OMZ. Several of these species showed adaptive characteristics such as lower metabolic rates, additional anaerobic activity and diel vertical migration that enable them to successfully inhabit hypoxic zones.     

Changes in odor quality discrimination following recovery from olfactory nerve transection

Following recovery from olfactory nerve transection, animals regain their ability to discriminate between odors. Odor discrimination is restored after new neurons establish connections with the olfactory bulb. However, it is not known if the new connections alter odor quality perception. To address this question, 20 adult hamsters were first trained to discriminate between cinnamon and strawberry odors. After reaching criterion (> or = 90% correct response), half of the animals received a bilateral nerve transection (BTX) and half a surgical sham procedure. Animals were not tested again until day 40, a point in recovery when connections are re-established with the bulb. When BTX animals were tested without food reinforcement, they could not perform the odor discrimination task. Sham animals, however, could discriminate, demonstrating that the behavioral response had not been extinguished during the 40 day period. When reinforcement was resumed, BTX animals were able to discriminate between cinnamon and strawberry after four test sessions. In addition, their ability to discriminate between these two familiar odors was no different than that of BTX and sham animals tested with two novel odors, baby powder and coffee. These findings suggest that, after recovery from nerve transection, there are alterations in sensory perception and that restoration of odor quality discrimination requires that the animal must again learn to associate individual odor sensations with a behavioral response.      

Plasma proteome analysis in HTLV-1-associated myelopathy/tropical spastic paraparesis

Background

A new subgroup of HIV-1, designated Group P, was recently detected in two unrelated patients of Cameroonian origin. HIV-1 Group P phylogenetically clusters with SIVgor suggesting that it is the result of a cross-species transmission from gorillas. Until today, HIV-1 Group P has only been detected in two patients, and its degree of adaptation to the human host is largely unknown. Previous data have shown that pandemic HIV-1 Group M, but not non-pandemic Group O or rare Group N viruses, efficiently antagonize the human orthologue of the restriction factor tetherin (BST-2, HM1.24, CD317) suggesting that primate lentiviruses may have to gain anti-tetherin activity for efficient spread in the human population. Thus far, three SIV/HIV gene products (vpu, nef and env) are known to have the potential to counteract primate tetherin proteins, often in a species-specific manner. Here, we examined how long Group P may have been circulating in humans and determined its capability to antagonize human tetherin as an indicator of adaptation to humans.

Results

Our data suggest that HIV-1 Group P entered the human population between 1845 and 1989. Vpu, Env and Nef proteins from both Group P viruses failed to counteract human or gorilla tetherin to promote efficient release of HIV-1 virions, although both Group P Nef proteins moderately downmodulated gorilla tetherin from the cell surface. Notably, Vpu, Env and Nef alleles from the two HIV-1 P strains were all able to reduce CD4 cell surface expression.

Conclusions

Our analyses of the two reported HIV-1 Group P viruses suggest that zoonosis occurred in the last 170 years and further support that pandemic HIV-1 Group M strains are better adapted to humans than non-pandemic or rare Group O, N and P viruses. The inability to antagonize human tetherin may potentially explain the limited spread of HIV-1 Group P in the human population.     

The strategy concept and John Maynard Smith’s influence on theoretical biology

Here we argue that the concept of strategies, as it was introduced into biology by John Maynard Smith, is a prime illustration of the four dimensions of theoretical biology in the post-genomic era. These four dimensions are: data analysis and management, mathematical and computational model building and simulation, concept formation and analysis, and theory integration. We argue that all four dimensions of theoretical biology are crucial to future interactions between theoretical and empirical biologists as well as with philosophers of biology.     

The unique cyanobacterial protein OpcA is an allosteric effector of glucose-6-phosphate dehydrogenase in Nostoc punctiforme ATCC 29133

Glucose-6-phosphate dehydrogenase (G6PD), encoded by zwf, is essential for nitrogen fixation and dark heterotrophic growth of the cyanobacterium Nostoc punctiforme ATCC 29133. In N. punctiforme, zwf is part of a four-gene operon transcribed in the order fbp-tal-zwf-opcA. Genetic analyses indicated that opcA is required for G6PD activity. To define the role of opcA, the synthesis, aggregation state, and activity of G6PD in N. punctiforme strains expressing different amounts of G6PD and/or OpcA were examined. A single tetrameric form of G6PD was consistently observed for all strains, as well as for recombinant N. punctiforme His-G6PD purified from Escherichia coli, regardless of the quantity of OpcA present. However, His-G6PD and the G6PD of strain UCD 351, which lacks OpcA, had low affinities for glucose 6-phosphate (G6P) substrate (K(m)(app) = 65 and 85 mm, respectively) relative to wild-type N. punctiforme G6PD (K(m)(app) = 0.5 mm). Near wild-type affinities for G6P were observed for these enzymes when saturating amounts of His-OpcA- or OpcA-containing extract were added. Kinetic studies were consistent with OpcA acting as an allosteric activator of G6PD. A role in redox modulation of G6PD activity was also indicated, because thioredoxin-mediated inactivation and reactivation of His-G6PD occurred only when His-OpcA was present.     

Trans-Atlantic dispersal and phylogeography of Cerastium arcticum (Caryophyllaceae) inferred from RAPD and SCAR markers

Cerastium arcticum is an autogamous pioneer species with a distribution limited to the North Atlantic region. It has been suggested that such species must have survived in ice-free refugia on both sides of the Atlantic throughout the last, or even several, of the Pleistocene glaciations, because they lack special adaptations for long-distance dispersal. To address the possibility for recent trans-Atlantic dispersal of C. arcticum, we analyzed random amplified polymorphic DNA (RAPD) and sequence characterized amplified region (SCAR) differentiation among 26 populations of this high-polyploid species. Three SCAR markers were obtained that verified the main patterns identified in the RAPD analysis. Eighty-four multilocus RAPD phenotypes were observed in the 126 plants analyzed, based on 35 polymorphic markers. Multivariate analyses and analyses of molecular variance (AMOVAs) identified two highly divergent groups of populations: one arctic group (western and eastern Greenland, and the archipelagos of Svalbard and Franz Josef Land) and one nonarctic group (southern and northern Norway, and Iceland), indicating that C. arcticum is composed of two lineages with different evolutionary histories. However, there was little geographic structuring within each lineage, in spite of the fact that both lineages are disjunctly distributed across the Atlantic. Occurrence of very similar, in some cases even identical RAPD multilocus phenotypes on both sides of the Atlantic in this autogamous allopolyploid is most probably caused by postglacial dispersal. The present geographic distribution of C. arcticum may thus have been established after trans-Atlantic expansion from two Weichselian refugia, one for each evolutionary lineage. Unexpectedly, the level of intrapopulational variation increased towards the north. This may reflect that interpopulational migration is most extensive in the treeless arctic environment, where the species has a more continuous distribution than in the more southerly areas.