On the Photosynthetic Potential in the Very Early Archean Oceans

In this work we apply a mathematical model of photosynthesis to quantify the potential for photosynthetic life in the very Early Archean oceans. We assume the presence of oceanic blockers of ultraviolet radiation, specifically ferrous ions. For this scenario, our results suggest a potential for photosynthetic life greater than or similar to that in later eras/eons, such as the Late Archean and the current Phanerozoic eon.     

A molecular dynamics study of a model built Pro-36-Gly mutant derived from the potato carboxypeptidase A inhibitor protein

A 120ps molecular dynamics (MD) trajectory was calculated and analyzed for a putative Pro-36-Gly mutant of the potato carboxypeptidase A (CPA) protein inhibitor (PCIm). The mutant protein's fold shows a large degree of stability, judged from its low alpha-carbon r.m.s. deviation from the X-ray structure of the wild type PCI (PCIw). The N-terminal tail of PCIm differs slightly less from the X-ray structure than it does in PCIw, while the mutant's C-terminal tail (the primary contact site with CPA) and residues 13-17 present deviations as they approach each other. Differences in fluctuation pattern exist between PCIm and PCIw in residues 2-4 (the N-terminal tail), 13-17, 22-23, 28-31 (the secondary contact site with CPA) and 37-38 (the C-terminal tail); the latter region is rigidified in PCIm. Results show that the MD method is able to sense local perturbative effects produced by amino acid substitutions in flexible regions of protein molecules. The simulation suggests that the conformation of the C-terminal tail is less favorable for interaction with the target protein in the mutant than it is in the wild type protein. The Pro-36-Gly mutant is predicted to be a less potent inhibitor.     

The effects of lubrol WX on brain membrane Ca2+/Mg2+ ATPase and ATP-dependent Ca2+ uptake activity following acute and chronic ethanol

Acute administration of ethanol (2.5 gm/kg, i.p.) to rats inhibits the cytosolic buffering of Ca2+ in nerve terminals. Ca2+ ATPase and ATP-dependent Ca2+ uptake are both inhibited 30 min after a single dose of ethanol. Chronic ethanol administration (6%, 14 days) did not inhibit Ca2+ ATPase but significantly stimulated ATP-dependent Ca2+ uptake. Lubrol WX treatment of acute ethanolic membranes reverses the inhibition of Ca2+ ATPase seen following ethanol. Lubrol WX treatment of chronic ethanolic membranes prevents the increase in ATP-dependent Ca2+ uptake seen in ethanolic membranes. Both acute and chronic ethanol-induced changes in Ca2+ transport within nerve terminals may involve lipid-dependent parameters of the membrane which may underlie neuronal adaptation.     

Effect of exercise-induced hyperventilation on airway resistance and cycling endurance

The purpose of the present study was to investigate the effect of exercise induced hyperventilation and hypocapnia on airway resistance (R _aw), and to try to answer the question whether a reduction of R _aw is a mechanism contributing to the increase of endurance time associated with a reduction of exercise induced hyperventilation as for example has been observed after respiratory training. Eight healthy volunteers of both sexes participated in the study. Cycling endurance tests (CET) at 223 (SD 47) W, i.e. at 74 (SD 5)% of the subject's peak exercise intensity, breathing endurance tests and body plethysmograph measurements of pre- and postexercise R _aw were carried out before and after a 4-week period of respiratory training. In one of the two CET before the respiratory training CO₂ was added to the inspired air to keep its end-tidal concentration at 5.4% to avoid hyperventilatory hypocapnia (CO₂-test); the other test was the control. The pre-exercise values of specific expiratory R _aw were 8.1 (SD 2.8), 6.8 (SD 2.6) and 8.0 (SD 2.1) cm H₂O · s and the postexercise values were 8.5 (SD 2.6), 7.4 (SD 1.9) and 8.0 (SD 2.7) cm H₂O · s for control CET, CO₂-CET and CET after respiratory training, respectively, all differences between these tests being nonsignificant. The respiratory training significantly increased the respiratory endurance time during breathing of 70% of maximal voluntary ventilation from 5.8 (SD 2.9) min to 26.7 (SD 12.5) min. Mean values of the cycling endurance time (t _cend) were 22.7 (SD 6.5) min in the control, 19.4 (SD 5.4) min in the CO₂-test and 18.4 (SD 6.0) min after respiratory training. Mean values of ventilation ( _E) during the last 3␣min of CET were 123 (SD 35.8) l · min⁻¹ in the control, 133.5 (SD 35.1) l · min⁻¹ in the CO₂-test and 130.9 (SD 29.1) l · min⁻¹ after respiratory training. In fact, six subjects ventilated more and cycled for a shorter time, whereas two subjects ventilated less and cycled for a longer time after the respiratory training than in the control CET. In general, the subjects cycled longer the lower the _E, if all three CET are compared. It is concluded that R _aw measured immediately after exercise is independent of exercise-induced hyperventilation and hypocapnia and is probably not involved in limiting t _cend, and that t _cend at a given exercise intensity is shorter when _E is higher, no matter whether the higher _E occurs before or after respiratory training or after CO₂ inhalation. Accepted: 11 September 1996     

Using Complete Genome Comparisons to Identify Sequences Whose Presence Accurately Predicts Clinically Important Phenotypes

In clinical settings it is often important to know not just the identity of a microorganism, but also the danger posed by that particular strain. For instance, Escherichia coli can range from being a harmless commensal to being a very dangerous enterohemorrhagic (EHEC) strain. Determining pathogenic phenotypes can be both time consuming and expensive. Here we propose a simple, rapid, and inexpensive method of predicting pathogenic phenotypes on the basis of the presence or absence of short homologous DNA segments in an isolate. Our method compares completely sequenced genomes without the necessity of genome alignments in order to identify the presence or absence of the segments to produce an automatic alignment of the binary string that describes each genome. Analysis of the segment alignment allows identification of those segments whose presence strongly predicts a phenotype. Clinical application of the method requires nothing more that PCR amplification of each of the set of predictive segments. Here we apply the method to identifying EHEC strains of E. coli and to distinguishing E. coli from Shigella. We show in silico that with as few as 8 predictive sequences, if even three of those predictive sequences are amplified the probability of being EHEC or Shigella is >0.99. The method is thus very robust to the occasional amplification failure for spurious reasons. Experimentally, we apply the method to screening a set of 98 isolates to distinguishing E. coli from Shigella, and EHEC from non-EHEC E. coli strains and show that all isolates are correctly identified.     

The Contribution of Agriculture,Forestry and other Land Use activities to Global Warming, 1990–2012

We refine the information available through the IPCC AR5 with regard to recent trends in global GHG emissions from agriculture, forestry and other land uses (AFOLU), including global emission updates to 2012. Using all three available AFOLU datasets employed for analysis in the IPCC AR5, rather than just one as done in the IPCC AR5 WGIII Summary for Policy Makers, our analyses point to a down‐revision of global AFOLU shares of total anthropogenic emissions, while providing important additional information on subsectoral trends. Our findings confirm that the share of AFOLU emissions to the anthropogenic total declined over time. They indicate a decadal average of 28.7 ± 1.5% in the 1990s and 23.6 ± 2.1% in the 2000s and an annual value of 21.2 ± 1.5% in 2010. The IPCC AR5 had indicated a 24% share in 2010. In contrast to previous decades, when emissions from land use (land use, land use change and forestry, including deforestation) were significantly larger than those from agriculture (crop and livestock production), in 2010 agriculture was the larger component, contributing 11.2 ± 0.4% of total GHG emissions, compared to 10.0 ± 1.2% of the land use sector. Deforestation was responsible for only 8% of total anthropogenic emissions in 2010, compared to 12% in the 1990s. Since 2010, the last year assessed by the IPCC AR5, new FAO estimates indicate that land use emissions have remained stable, at about 4.8 Gt CO₂ eq yr^?1 in 2012. Emissions minus removals have also remained stable, at 3.2 Gt CO₂ eq yr^?1 in 2012. By contrast, agriculture emissions have continued to grow, at roughly 1% annually, and remained larger than the land use sector, reaching 5.4 Gt CO₂ eq yr^?1 in 2012. These results are useful to further inform the current climate policy debate on land use, suggesting that more efforts and resources should be directed to further explore options for mitigation in agriculture, much in line with the large efforts devoted to REDD+ in the past decade.     

Minimizing the biodiversity impact of Neotropical oil palm development

Oil palm agriculture is rapidly expanding in the Neotropics, at the expense of a range of natural and seminatural habitats. A key question is how this expansion should be managed to reduce negative impacts on biodiversity. Focusing on the Llanos of Colombia, a mixed grassland–forest system identified as a priority zone for future oil palm development, we survey communities of ants, dung beetles, birds and herpetofauna occurring in oil palm plantations and the other principal form of agriculture in the region – improved cattle pasture – together with those of surrounding natural forests. We show that oil palm plantations have similar or higher species richness across all four taxonomic groups than improved pasture. For dung beetles, species richness in oil palm was equal to that of forest, whereas the other three taxa had highest species richness in forests. Hierarchical modelling of species occupancy probabilities indicated that oil palm plantations supported a higher proportion of species characteristic of forests than did cattle pastures. Across the bird community, occupancy probabilities within oil palm were positively influenced by increasing forest cover in a surrounding 250 m radius, whereas surrounding forest cover did not strongly influence the occurrence of other taxonomic groups in oil palm. Overall, our results suggest that the conversion of existing improved pastures to oil palm has limited negative impacts on biodiversity. As such, existing cattle pastures of the Colombian Llanos could offer a key opportunity to meet governmental targets for oil palm development without incurring significant biodiversity costs. Our results also highlight the value of preserving remnant forests within these agricultural landscapes, protecting high biodiversity and exporting avian ‘spill‐over’ effects into oil palm plantations.     

Evidence of incipient speciation in the Neotropical mangrove Pelliciera rhizophorae (Tetrameristaceae) as revealed by molecular,morphological, physiological and climatic characteristics

Two variants of the Neotropical mangrove species Pelliciera rhizophorae distributed along both sides of the Isthmus of Panama were detected by different colouration of the floral bracts and the size of the floral and vegetative structures. These findings raised questions concerning a possible speciation event in P. rhizophorae, for which a series of macro‐ and microscopic morphological traits (reproductive and vegetative structures), molecular markers from plastid DNA and climatic profiles were analyzed. Samples of P. rhizophorae were collected in three localities from the Panamanian Caribbean and Pacific coasts. The data obtained from molecular markers and morphological traits showed significant differences between the variants. The climatic profiles showed contrasting characteristics of rainfall and temperature in their habitats: variant A is found in wetter zones and variant B occupies drier zones. Evidence suggesting that a process of incipient speciation has occurred in P. rhizophorae in response to ecogeographical isolation due to climatic factors is presented. The presence of two geographically separate genetic‐morphological groups, adapted to contrasting climatic conditions, will be the basis for suggesting the existence of incipient lineages in Pelliciera. © 2015 The Linnean Society of London, Botanical Journal of the Linnean Society, 2015, 179 , 499–510.