A gene’s eye view of Darwinian populations

Biologists and philosophers differ on whether selection should be analyzed at the level of the gene or of the individual. In Peter Godfrey-Smith’s book, Darwinian Populations and Natural Selection, he argues that individuals can be good members of Darwinian populations, whereas genes rarely can. I take issue with parts of this view, and suggest that Godfrey-Smith’s scheme for thinking about Darwinian populations is also applicable to populations of genes.     

Indicators for photoreactivation and dark repair studies following ultraviolet disinfection

Repair of DNA in bacteria following ultraviolet (UV) disinfection can cause reactivation of inactivated bacteria and negatively impact the efficiency of the UV disinfection process. In this study, various strains of E. coli (wild-type, UV-resistant and antibiotic-resistant strains) were investigated for their ability to perform dark repair and photoreactivation, and compared based on final repair levels after 4 h of incubation, as well as repair rates. Analysis of the results revealed that the repair abilities of different E. coli strains can differ quite significantly. In photoreactivation, the log repair ranged from 10 to 85%, with slightly lower log repair percentages when medium-pressure (MP) UV disinfection was employed. In dark repair, log repair ranged from 13 to 28% following low-pressure (LP) UV disinfection. E. coli strains ATCC 15597 and ATCC 11229 were found to repair the fastest and to the highest levels for photoreactivation and dark repair, respectively. These strains were also confirmed to repair to higher levels when compared to a pathogenic E. coli O157:H7 strain. Hence, these strains could possibly serve as conservative indicators for future repair studies following UV disinfection. In addition, dimer repair by photoreactivation and dark repair was also confirmed on a molecular level using the endonuclease sensitive site (ESS) assay.     

Host-specific factors determine the persistence of IncP-1 plasmids

Conjugative plasmids play a very important role in bacterial adaptation through the dissemination of useful traits. Incompatibility group P-1 (IncP-1) plasmids exhibit an extreme broad-host-range among Gram-negative bacteria and known to be one of the major agents to disseminate various phenotypic traits such as antibiotic resistance and xenobiotic degradation. Although the plasmids are believed to be very stable in most Gram-negative bacteria, little is known about the factors that affect their stability in various hosts, allowing their persistence in bacterial population. Here we show that the stability of the cryptic IncP-1β plasmid pBP136 differed greatly in four different Escherichia coli K12 host backgrounds (MG1655, DH5α, EC100, and JM109), whereas the closely related plasmid pB10 was stable in all four strains. The supply of the kleF gene, which is involved in the stability of IncP-1 plasmids but absent in pBP136, did not improve the stability of the plasmid. Our findings suggest that persistence of IncP-1 plasmids in the absence of selection is affected by strain-specific factors.     

Computer simulation of synchronization of Na/K pump molecules

The behavior of Na/K pump currents when exposed to an oscillating electric field is studied by computer simulation. The pump current from a single pump molecule was sketched based on previous experimental results. The oscillating electric field is designed as a symmetric, dichotomous waveform varying the membrane potential from −30 to −150 mV around the membrane resting potential of −90 mV. Based on experimental results from skeletal muscle fibers, the energy needed to overcome the electrochemical potentials for the Na and K-transports are calculated in response to the field’s two half-cycles. We found that a specially designed oscillating electric field can eventually synchronize the pump molecules so that all the individual pumps run at the same pumping rate and phase as the field oscillation. They extrude Na ions during the positive half-cycle and pump in K ions during the negative half-cycle. The field can force the two ion-transports into the corresponding half-cycles, respectively, but cannot determine their detailed positions. In other words, the oscillating electric field can synchronize pumps in terms of their pumping loops but not at a specific step in the loop. These results are consistent with our experimental results in measurement of the pump currents.     

The late Holocene palaeoecological sequence of Serranía de las Villuercas (southern Meseta,western Spain)

New pollen results and radiocarbon dating from a valley mire in south-western Spain are presented. This is a region where few palaeoecological records have been preserved and the sequence yields important new palaeobotanical evidence for the late Holocene. The landscape is shown as having been largely open woodland, but more wooded than at present. The vegetation history of the last four millennia in these montane territories of south-western Iberia is discussed in the light of anthropogenic indicators, archaeological and documentary archives; fire incidence and climate change. Alnus is the predominant pollen type, although a decline is noted during the last couple of centuries. Its presence is connected with local topography behaving as a phreatophyte, that is, a plant which obtains a significant amount of water from the zone of saturated soil. A framework is also provided for the age and ecological dynamics of some major woodland taxa—Betula, Corylus, Ilex, evergreen and deciduous oaks, Ericaceae and Pinus. In addition, the natural status of several pollen taxa and local trends in biodiversity are discussed. We consider that the results of our work will have important implications for the understanding of the vegetation history in a floristically very rich area, with a noticeable diversity of woody taxa, and a relatively well preserved ecosystem structure.     

X-ray microdensitometry applied to subfossil tree-rings: growth characteristics of ancient pines from the southern boreal forest zone in Finland at intra-annual to centennial time-scales

A collection of subfossil wood of Pinus sylvestris (Scots pine) was exposed to X-ray densitometry. The collection of 64 samples from the southern boreal forest zone was dendrochronologically cross-dated to a.d. 673-1788. Growth characteristics were determined by performing density profiles including the following parameters: minimum density, earlywood and latewood boundary density, maximum density, earlywood width, earlywood density, latewood width, latewood density, annual ring width and annual ring density. Seven out of the nine parameters were found to contain non-climatic growth trends and six were found to be heteroscedastic in their variance. Tree-specific records were indexed, to remove the non-climatic growth trends and stabilize the variance, and combined into nine parameter-specific tree-ring chronologies. Growth characteristics of the pines changed in parallel with the generally agreed climatic cooling from the Medieval Warm Period to the Little Ice Age: pine tree-rings showed decreasing maximum densities from the period a.d. 975-1150 to a.d. 1450–1625. A concomitant change in the intra-annual growth characteristics was detected between these periods. The findings indicate that not only the trees growing near the species’ distributional limits are sensitive to large-scale climatic variations but also the trees growing in habitats remote from the timberline have noticeably responded to past climate changes.     

A simple non-invasive protocol to establish primary cell lines from tail and toe explants for cytogenetic studies in Australian dragon lizards (Squamata: Agamidae)

Primary cell lines were established from cultures of tail and toe clips of five species of Australian dragon lizards: Tympanocryptis pinguicolla, Tympanocryptis sp., Ctenophorus fordi, Amphibolurus norrisi and Pogona vitticeps. The start of exponential cell growth ranged from 1 to 5 weeks. Cultures from all specimens had fibroblastic morphology. Cell lines were propagated continuously up to ten passages, cryopreserved and recovered successfully. We found no reduction in cell viability after short term (<6 months) storage at −80 °C. Mitotic metaphase chromosomes were harvested from these cell lines and used in differential staining, banding and fluorescent in situ hybridisation. Cell lines maintained normal diploidy in all species. This study reports a simple non-invasive method for establishing primary cell lines from Australian dragon lizards without sacrifice. The method is likely to be applicable to a range of species. Such cell lines provide a virtually unlimited source of material for cytogenetic, evolutionary and genomic studies.     

Plant Conservation in the Caribbean Island Biodiversity Hotspot

While the Caribbean is a recognized “biodiversity hotspot”, plant conservation has not received adequate attention; particularly, given the high levels of endemism in many plant groups. Besides establishing protected areas, there needs to be a sustained effort to study the taxonomy, systematics and ecology of the flora. Recent phylogenetic studies have shown high levels of endemism and conservation studies indicate a large propotion of the flora is threatened with extinction. Eight recommendations are given for plant conservation in the region.     

Allelopathic impact of artificially applied coumarin on <Emphasis Type="Italic">Fusarium oxysporum</Emphasis> f.sp. <Emphasis Type="Italic">niveum</Emphasis>

Watermelon production is threatened by fusarium wilt caused by Fusarium oxysporum f.sp. niveum (FON) in continuous cultivation system. Some elements, mainly allelochemicals, released from living roots or decayed plants might be associated with the disease. The purpose of this work was to evaluate the possible impact of coumarin, one kind of watermelon allelochemical, on FON. Furthermore, possible new mechanisms might be investigated during the ecological interactions of plant-microbe. Results showed that coumarin strongly inhibited growth of FON leading to a decrease in its biomass, dry weight of mycelia of FON in a liquid culture. The dry weight was decreased by 62.9% compared with control. The hyphal growth of FON on plates was stopped at high (>400 mg l⁻¹) concentrations of coumarin. At 320 mg l⁻¹, sporulation and enzyme activities of FON were also severely suppressed by coumarin. The yield of conidia, and the activities of proteinase, cellulase, and amylase were reduced by 98.9%, 79.7%, 29.8% and 15.9% respectively. However, conidial germination and mycotoxin (MT) production of FON were greatly stimulated, being increased by 55.7% and 14.9 fold at 320 mg l⁻¹ respectively. We conclude that coumarin acted as an allelochemical substance to inhibit growth and pathogenic enzyme activities of FON but to stimulate mycotoxin production and conidial germination. It was suggested that coumarin acted as a signal transduction element bridging plant and pathogen in the process of plant-microbe interactions.     

Hydrogen exchange of monomeric alpha-synuclein shows unfolded structure persists at physiological temperature and is independent of molecular crowding in Escherichia coli

Amide proton NMR signals from the N-terminal domain of monomeric α-synuclein (αS) are lost when the sample temperature is raised from 10°C to 35°C at pH 7.4. Although the temperature-induced effects have been attributed to conformational exchange caused by an increase in α-helix structure, we show that the loss of signals is due to fast amide proton exchange. At low ionic strength, hydrogen exchange rates are faster for the N-terminal segment of αS than for the acidic C-terminal domain. When the salt concentration is raised to 300 mM, exchange rates increase throughout the protein and become similar for the N- and C-terminal domains. This indicates that the enhanced protection of amide protons from the C-terminal domain at low salt is electrostatic in nature. Cα chemical shift data point to <10% residual α-helix structure at 10°C and 35°C. Conformational exchange contributions to R2 are negligible at both temperatures. In contrast to the situation in vitro, the majority of amide protons are observed at 37°C in ¹H-¹⁵N HSQC spectra of αS encapsulated within living Escherichia coli cells. Our finding that temperature effects on αS NMR spectra can be explained by hydrogen exchange obviates the need to invoke special cellular factors. The retention of signals is likely due to slowed hydrogen exchange caused by the lowered intracellular pH of high-density E. coli cultures. Taken together, our results emphasize that αS remains predominantly unfolded at physiological temperature and pH—an important conclusion for mechanistic models of the association of αS with membranes and fibrils.