Structural Evaluation of Distant Homology. A 3-D Model of the Ligand Binding Domain of the Nicotinic Acetylcholine Receptor Based on Acetylcholinesterase: Consistency with Experimental Data

Acetylcholine is a ligand for both acetylcholinesterases and nicotinic acetylcholine receptors. Hence, at least some local sequence and structural similarities between the acetylcholinesterases and the receptors which recognize acetylcholine (ACh) might be expected. Peterson [2] produced an alignment of the ACh binding region between these two types of ACh–binding molecules, featuring a number of well conserved residues. The extent of this region of sequence similarity suggests the possible existence of a common ancenstral ACh binding module. To attempt to further validate Petersons sequence alignment we have built a homology model of the ACh binding domain of the human neuromuscular nicotinic acetylcholine receptor based on the structure of acetylcholinesterase from Torpedo californica. Using this 3–D model we have examined the residues which were previously shown to interact with the endogenous ligand by various methods (mapping, site–directed mutagenesis). The consistency of such data with the model provides further support for a structural similarity and possibly a divergent evolutionary relationship between the ACh–binding domains of these two classes of proteins. Results suggest that this model may be able to contribute to an understanding of the structure and function of the ACh receptor. Using this case as an example, we propose that 3–dimensional computer modeling can be used as a tool to evaluate distant homologies when adequate experimental data (e.g., site–directed mutagenesis) is available.Supplementary material to this paper is available in electronic form at http://dx.doi.org/10.1007/s0089460020046     

Computational genomic analysis of hemorrhagic fever viruses

A number of distinct viruses are known as hemorrhagic fever viruses based on a shared ability to induce hemorrhage by poorly understood mechanisms, typically involving the formation of blood clots (“disseminated intravascular coagulation”). It is well documented that selenium plays a significant role in the regulation of blood clotting via its effects on the thromboxane/prostacyclin ratio, and effects on the complement system. Selenium has an anticlotting effect, whereas selenium deficiency has a proclotting or thrombotic effect. It is also well documented that extreme dietary selenium deficiency, which is almost never seen in humans, has been associated with hemorrhagic effects in animals. Thus, the possibility that viral selenoprotein synthesis might contribute to hemorrhagic symptoms merits further consideration. Computational genomic analysis of certain hemorrhagic fever viruses reveals the presence of potential protein coding regions (PPCRs) containing large numbers of in-frame UGA codons, particularly in the −1 reading frame. In some cases, these clusterings of UGA codons are very unlikely to have arisen by chance, suggesting that these UGAs may have some function other than being a stop codon, such as encoding selenocysteine. For this to be possible, a downstream selenocysteine insertion element (SECIS) is required. Ebola Zaire, the most notorious hemorrhagic fever virus, has a PPCR with 17 UGA codons, and several potential SECIS elements can be identified in the viral genome. One potential viral selenoprotein may contain up to 16 selenium atoms per molecule. Biosynthesis of this protein could impose an unprecedented selenium demand on the host, potentially leading to severe lipid peroxidation and cell membrane destruction, and contributing to hemorrhagic symptoms. Alternatively, even in the absence of programmed selenoprotein synthesis, it is possible that random slippage errors would lead to increased encounters with UGA codons in overlapping reading frames, and thus potentially to nonspecific depletion of SeC in the host.     

Egg production across a 40-week period in the phasmid Sipyloidea sp. (Diapheromeridae) from a tropical rain forest, north Queensland, Australia

Abstract  In this study we report the results from the first long-term (40 weeks) study of stick-insect fecundity and distribution under natural conditions of which we are aware. We used the number of eggs falling into 72 × 0.5 m² traps to ask: 'Was egg production in Sipyloidea sp. uniform across the sample period'? and 'Was there evidence of host plant species preference or avoidance'? We collected a total of 213 Sipyloidea sp. eggs. The number of eggs caught per week was not uniform and an exponential decay model was the best-fit relationship between egg production and time, indicative of a steep decline from high to low (but continuous) egg production across the study period. Continuous egg production differs from other insect species in tropical areas that often show distinct seasonal differences between wet and dry seasons, timed to leaf production in host plants. The distribution of eggs within traps was aggregated, and more traps than expected from Poisson probabilities received no eggs, or six or more eggs. The concentration of eggs within particular traps was not related to the identity of canopy plant species, however. We suggest that continuous egg production in Sipyloidea sp. may be related to the wider range of plant species available as food resources for the polyphagous Sipyloidea , compared with other tropical insect species.     

Common ragweed (Ambrosia artemisiifolia L.): allergenicity and molecular characterization of pollen after plant exposure to elevated NO2

Ragweed pollen is the main cause of allergenic diseases in Northern America, and the weed has become a spreading neophyte in Europe. Climate change and air pollution are speculated to affect the allergenic potential of pollen. The objective of this study was to investigate the effects of NO₂, a major air pollutant, under controlled conditions, on the allergenicity of ragweed pollen. Ragweed was exposed to different levels of NO₂ throughout the entire growing season, and its pollen further analysed. Spectroscopic analysis showed increased outer cell wall polymers and decreased amounts of pectin. Proteome studies using two‐dimensional difference gel electrophoresis and liquid chromatography–tandem mass spectrometry indicated increased amounts of several Amb a 1 isoforms and of another allergen with great homology to enolase Hev b 9 from rubber tree. Analysis of protein S‐nitrosylation identified nitrosylated proteins in pollen from both conditions, including Amb a 1 isoforms. However, elevated NO₂ significantly enhanced the overall nitrosylation. Finally, we demonstrated increased overall pollen allergenicity by immunoblotting using ragweed antisera, showing a significantly higher allergenicity for Amb a 1. The data highlight a direct influence of elevated NO₂ on the increased allergenicity of ragweed pollen and a direct correlation with an increased risk for human health.     

The genetics of shortleaf pine (<Emphasis Type="Italic">Pinus echinata</Emphasis> mill.) with implications for restoration and management

Shortleaf pine (Pinus echinata Mill.) is an important commercial timber resource and forest ecosystem component in the southeastern USA. The species occurs in mainly drier sites as an early- to mid-successional species, is fire-adapted, and it plays an important role in the fire ecology of the region. However, shortleaf pine genetics are not well-studied, especially in this era of molecular genetics and genomics. Most genetics research about the species has focused on provenance testing. Generally, shortleaf pine performs well in colder areas, when compared to loblolly pine (Pinus taeda L.), a close relative, which is faster growing and the most common plantation species in the region. Though not as advanced in genetic improvement as loblolly pine, tree breeders have improved shortleaf pine in one to two generations of selection, and diverse, genetically improved shortleaf pine materials are available to foresters and landowners throughout the southeastern USA. Researchers have also studied the genetic variation of shortleaf pine using various molecular markers and have found that shortleaf pine is generally a prolific outcrosser, a trait it shares with other non-isolated members of the family Pinaceae. In recent years, however, it has shared less genetic material across long ranges, probably because of habitat fragmentation. Various anthropogenic factors also affect shortleaf pine’s future, as recent studies show that shortleaf pine introgression with loblolly pine puts the species—and the resiliency of southeastern forests—at risk. Importantly, fire exclusion is a likely cause of the increase in introgression. Herein, we provide further details and up-to-date genetic information and resources for foresters and ecologists interested in the restoration and management of shortleaf pine.     

Diel Surface Temperature Range Scales with Lake Size

Ecological and biogeochemical processes in lakes are strongly dependent upon water temperature. Long-term surface warming of many lakes is unequivocal, but little is known about the comparative magnitude of temperature variation at diel timescales, due to a lack of appropriately resolved data. Here we quantify the pattern and magnitude of diel temperature variability of surface waters using high-frequency data from 100 lakes. We show that the near-surface diel temperature range can be substantial in summer relative to long-term change and, for lakes smaller than 3 km², increases sharply and predictably with decreasing lake area. Most small lakes included in this study experience average summer diel ranges in their near-surface temperatures of between 4 and 7°C. Large diel temperature fluctuations in the majority of lakes undoubtedly influence their structure, function and role in biogeochemical cycles, but the full implications remain largely unexplored.     

The priming potential of environmentally weathered pyrogenic carbon during land‐use transition to biomass crop production

Since land‐use change (LUC) to lignocellulosic biomass crops often causes a loss of soil organic carbon (SOC), at least in the short term, this study investigated the potential for pyrogenic carbon (PyC) to ameliorate this effect. Although negative priming has been observed in many studies, most of these are long‐term incubation experiments which do not account for the interactions between environmentally weathered PyC and native SOC. Here, the aim was to assess the impact of environmentally weathered PyC on native SOC mineralization at different time points in LUC from arable crops to short rotation coppice (SRC) willow. At eight SRC willow plantations in England, with ages of 3–22 years, soil amended 18–22 months previously with PyC was compared with unamended control soil. Cumulative CO₂ flux was measured weekly from incubated soil at 0–5 cm depth, and soil‐surface CO₂ flux was also measured in the field. For the incubated soil, cumulative CO₂ flux was significantly higher from soil containing weathered PyC than the control soil for seven of the eight sites. Across all sites, the mean cumulative CO₂ flux was 21% higher from soil incubated with weathered PyC than the control soil. These results indicate the potential for positive priming in the surface 5 cm of soil independent of changes in soil properties following LUC to SRC willow production. However, no net effect on CO₂ flux was observed in the field, suggesting this increase in CO₂ is offset by a contrasting PyC‐induced effect at a different soil depth or that different effects were observed under laboratory and field conditions. Although the mechanisms for these contrasting effects remain unclear, results presented here suggest that PyC does not reduce LUC‐induced SOC losses through negative priming, at least for this PyC type and application rate.     

Inherited susceptibility of cattle to high-altitude pulmonary hypertension.

This study examines the hypothesis that susceptibility of cattle to high-altitude pulmonary hypertension and heart failure (high mountain disease) is genetically transmitted. Eight offspring of cattle recovered from high mountain disease were considered "susceptible." Eleven offspring of healthy cattle residing at high altitude were considered "resistant." At the resident altitude of 1,524 m, 10-day-old susceptible calves had higher pulmonary arterial pressures than did resistant calves (34 vs.21 mmHg), but at 90 days of age the pressures for the two groups were similar (26 vs. 24 mmHg). After 64 days of exposure to an altitude of 3,048 m, the susceptible calves (87 +/- 7 (SE) vs. 40 +/- 3 mmHg). By 124 days at 3,048 m, all susceptible but none of the resistant calves had developed heart failure. The results indicated that susceptibility to pulmonary hypertension at high altitude was inherited. Susceptible cattle may provide a useful model of human hypoxic pulmonary hypertension.