Population genetics in nonmodel organisms: II. natural selection in marginal habitats revealed by deep sequencing on dual platforms

Population genetics of species living in marginal habitats could be particularly informative about the genetics of adaptation, but such analyses have not been readily feasible until recently. Sonneratia alba, a mangrove species widely distributed in the Indo-West Pacific, provides a very suitable system for the study of local adaptation. In this study, we analyzed DNA variation by pooling 71 genes from 85-100 individuals for DNA sequencing. For each of the two nearby S. alba populations, we obtained ~2,500 × coverage on the Illumina GA platform and for the Sanya population, an additional 5,400 × coverage on the AB SOLiD platform. For the Sanya sample, although each sequencing method called many putative single nucleotide polymorphisms, the two sets of calls did not overlap, suggesting platform-dependent errors. Conventional sequencing corroborated that each population is monomorphic. The two populations differ by 54 bp of 79,000 sites, but 90% of the variants are found in 10% of the genes. Strong local adaptation and high migration may help to explain the extensive monomorphism shared by the two populations in the presence of a small number of highly differentiated loci.     

Analysis of thirteen populations of black cohosh for formononetin.

Black cohosh (Actaea racemosa L. syn. Cimicifuga racemosa (L.) Nutt.), a North American perennial plant, is a promising natural alternative to hormone replacement therapy for treating menopausal symptoms, but the mechanism of action is not understood. The clinical actions of this plant have been attributed to the isoflavonone formononetin since 1985, when its presence was reported in a black cohosh extract. Others have since looked for formononetin, but have not detected it. We looked for formononetin in extracts of black cohosh roots and rhizomes collected in thirteen locations in the eastern United States, including Maryland, New Jersey, New York, North Carolina, Pennsylvania, Virginia, and Tennessee. The rhizome samples were extracted using 80% methanol, and the extracts were partially purified using solid-phase extraction to concentrate any isoflavonoids that might be present. We tested for formononetin in these partially purified samples using thin-layer chromatography and high-performance liquid chromatography with a photodiode array detector and a mass spectrometer. Formononetin was not detected in any of the thirteen plant populations examined. Remifemin, a German product now on the United States market, and CimiPure, a commercially available black cohosh rhizome extract, were also analyzed. We did not detect formononetin, or ononin (formononetin-7-glucoside), in any sample tested by the above-mentioned chemical analyses. Therefore, the clinically observed estrogen-like actions of black cohosh, such as reduction of hot flashes, are likely due to a compound, or combination of compounds, other than formononetin.     

Post-Discharge Mortality in Children with Severe Malnutrition and Pneumonia in Bangladesh

Background

Post-discharge mortality among children with severe illness in resource-limited settings is under-recognized and there are limited data. We evaluated post-discharge mortality in a recently reported cohort of children with severe malnutrition and pneumonia, and identified characteristics associated with an increased risk of death.

Methods

Young children (<5 years of age) with severe malnutrition (WHO criteria) and radiographic pneumonia on admission to Dhaka Hospital of icddr,b over a 15-month period were managed according to standard protocols. Those discharged were followed-up and survival status at 12 weeks post-discharge was determined. Verbal autopsy was requested from families of those that died.

Results

Of 405 children hospitalized with severe malnutrition and pneumonia, 369 (median age, 10 months) were discharged alive with a follow-up plan. Of these, 32 (8.7%) died in the community within 3 months of discharge: median 22 (IQR 9–35) days from discharge to death. Most deaths were reportedly associated with acute onset of new respiratory or gastrointestinal symptoms. Those that died following discharge were significantly younger (median 6 [IQR 3,12] months) and more severely malnourished, on admission and on discharge, than those that survived. Bivariate analysis found that severe wasting on admission (OR 3.64, 95% CI 1.66–7.97) and age <12 months (OR 2.54, 95% CI 1.1–8.8) were significantly associated with post-discharge death. Of those that died in the community, none had attended a scheduled follow-up and care-seeking from a traditional healer was more common (p<0.001) compared to those who survived.

Conclusion and Significance

Post-discharge mortality was common in Bangladeshi children following inpatient care for severe malnutrition and pneumonia. The underlying contributing factors require a better understanding to inform the potential of interventions that could improve survival.     

Inhibition of the Cardiac Na+ Channel Nav1.5 by Carbon Monoxide

Sublethal carbon monoxide (CO) exposure is frequently associated with myocardial arrhythmias, and our recent studies have demonstrated that these may be attributable to modulation of cardiac Na⁺ channels, causing an increase in the late current and an inhibition of the peak current. Using a recombinant expression system, we demonstrate that CO inhibits peak human Nav1.5 current amplitude without activation of the late Na⁺ current observed in native tissue. Inhibition was associated with a hyperpolarizing shift in the steady-state inactivation properties of the channels and was unaffected by modification of channel gating induced by anemone toxin (rATX-II). Systematic pharmacological assessment indicated that no recognized CO-sensitive intracellular signaling pathways appeared to mediate CO inhibition of Nav1.5. Inhibition was, however, markedly suppressed by inhibition of NO formation, but NO donors did not mimic or occlude channel inhibition by CO, indicating that NO alone did not account for the actions of CO. Exposure of cells to DTT immediately before CO exposure also dramatically reduced the magnitude of current inhibition. Similarly, l-cysteine and N-ethylmaleimide significantly attenuated the inhibition caused by CO. In the presence of DTT and the NO inhibitor N^ω-nitro-l-arginine methyl ester hydrochloride, the ability of CO to inhibit Nav1.5 was almost fully prevented. Our data indicate that inhibition of peak Na⁺ current (which can lead to Brugada syndrome-like arrhythmias) occurs via a mechanism distinct from induction of the late current, requires NO formation, and is dependent on channel redox state.     

Function of polyphenol oxidase in higher plants

Recent evidence has supported the folllowing views:
1. Polyphenol oxidase (PPO) is a plastidic enzyme that is unclear-coded, but is inactive until incorporated into the plastid.
2. In healthy green tissues PPO exists in a latent form on the thylakoid membrane and is not involved in synthesis of phenolic compounds. In leucoplasts, proplastids, or amyloplasts PPO is often present in a latent form in rudimentary thylakoids.
3. PPO normally functions as a phenol oxidase in vivo only in sencent or damaged cells.
4. In the functional chloroplast, PPO may be involved in some aspect of oxygen chemistry – pherhaps mediation of pseudocyclic photophosphorylation.     

Gas exchange and habitat selection in the aquatic salamanders Necturus maculosus and Cryptobranchus alleganiensis

Summary The standard metabolic rate (SMR) and critical O₂ tension (P_c) of water-breathing mudpuppies and hellbenders were determined at 20° C using open-system respirometry. Both species are metabolic O₂ regulators, although the P_c of hellbenders (90 mmHg) is much higher than that of mudpuppies (40 mmHg). The SMR of the two species in water saturated with air was similar (19.5 and 20.0 l O₂/g·h for Cryptobranchus and Necturus, respectively) and not different from that of salamanders in general. Both species were able to survive for at least 5–11 days in severely hypoxic water (9–10 mmHg) by breathing air, indicating that the lungs are functional accessory respiratory structures.We conclude that hellbenders are restricted to relatively cool and flowing waters because of their limited gas exchange capabilities, particularly with regard to their limited aerobic scope for activity and slow recovery from exercise. Necturus maculosus is much more tolerant of hypoxia, but it is not known if they can inhabit areas were hypoxia is combined with hypercarbia.     

Purification and Characterization of Pea Epicotyl beta-Amylase

The most abundant β-amylase (EC 3.2.1.2) in pea (Pisum sativum L.) was purified greater than 880-fold from epicotyls of etiolated germinating seedlings by anion exchange and gel filtration chromatography, glycogen precipitation, and preparative electrophoresis. The electrophoretic mobility and relative abundance of this β-amylase are the same as that of an exoamylase previously reported to be primarily vacuolar. The enzyme was determined to be a β-amylase by end product analysis and by its inability to hydrolyze β-limit dextrin and to release dye from starch azure. Pea β-amylase is an approximate 55 to 57 kilodalton monomer with a pl of 4.35, a pH optimum of 6.0 (soluble starch substrate), an Arrhenius energy of activation of 6.28 kilocalories per mole, and a K_m of 1.67 milligrams per milliliter (soluble starch). The enzyme is strongly inhibited by heavy metals, p-chloromer-curiphenylsulfonic acid and N-ethylmaleimide, but much less strongly by iodoacetamide and iodoacetic acid, indicating cysteinyl sulfhydryls are not directly involved in catalysis. Pea β-amylase is competitively inhibited by its end product, maltose, with a K_i of 11.5 millimolar. The enzyme is partially inhibited by Schardinger maltodextrins, with α-cyclohexaamylose being a stronger inhibitor than β-cycloheptaamylose. Moderately branched glucans (e.g. amylopectin) were better substrates for pea β-amylase than less branched or non-branched (amyloses) or highly branched (glycogens) glucans. The enzyme failed to hydrolyze native starch grains from pea and glucans smaller than maltotetraose. The mechanism of pea β-amylase is the multichain type. Possible roles of pea β-amylase in cellular glucan metabolism are discussed.     

Extremely low genetic diversity across mangrove taxa reflects past sea level changes and hints at poor future responses

The projected increases in sea levels are expected to affect coastal ecosystems. Tropical communities, anchored by mangrove trees and having experienced frequent past sea level changes, appear to be vibrant at present. However, any optimism about the resilience of these ecosystems is premature because the impact of past climate events may not be reflected in the current abundance. To assess the impact of historical sea level changes, we conducted an extensive genetic diversity survey on the Indo‐Malayan coast, a hotspot with a large global mangrove distribution. A survey of 26 populations in six species reveals extremely low genome‐wide nucleotide diversity and hence very small effective population sizes (N_e) in all populations. Whole‐genome sequencing of three mangrove species further shows the decline in N_e to be strongly associated with the speed of past changes in sea level. We also used a recent series of flooding events in Yalong Bay, southern China, to test the robustness of mangroves to sea level changes in relation to their genetic diversity. The events resulted in the death of half of the mangrove trees in this area. Significantly, less genetically diverse mangrove species suffered much greater destruction. The dieback was accompanied by a drastic reduction in local invertebrate biodiversity. We thus predict that tropical coastal communities will be seriously endangered as the global sea level rises. Well‐planned coastal development near mangrove forests will be essential to avert this crisis.