Author index for volume 219

Proteinase inhibitors I and II were purified to electrophoretic homogeneity from leaves of tomato plants induced by either wounding intact plants or by supplying excised plants with the proteinase inhibitor inducing factor. Affinity chromatography with chymotrypsin-Sepharose was employed as a final purification step for each inhibitor. The tomato leaf inhibitors are very similar to potato tuber inhibitors I and II in subunit molecular weight, composition, and inhibitory activities against chymotrypsin, trypsin, and subtilisin. However, unlike the potato tuber which contains multiple isoinhibitors by isoelectric focusing, the tomato leaf exhibits only two isoinhibitor forms of inhibitor I and a single form of inhibitor II. The molecular weight of native potato inhibitor I was reevaluated by rigorous ultracentrifugal analysis and compared with data from previous analyses. The data confirm that native inhibitor I has a native M_r of about 41,000 and is a pentamer. Inhibitor II has a molecular weight of near 23,000 and is a dimer.     

Balancing Detection and Eradication for Control of Epidemics: Sudden Oak Death in Mixed-Species Stands

Culling of infected individuals is a widely used measure for the control of several plant and animal pathogens but culling first requires detection of often cryptically-infected hosts. In this paper, we address the problem of how to allocate resources between detection and culling when the budget for disease management is limited. The results are generic but we motivate the problem for the control of a botanical epidemic in a natural ecosystem: sudden oak death in mixed evergreen forests in coastal California, in which species composition is generally dominated by a spreader species (bay laurel) and a second host species (coast live oak) that is an epidemiological dead-end in that it does not transmit infection but which is frequently a target for preservation. Using a combination of an epidemiological model for two host species with a common pathogen together with optimal control theory we address the problem of how to balance the allocation of resources for detection and epidemic control in order to preserve both host species in the ecosystem. Contrary to simple expectations our results show that an intermediate level of detection is optimal. Low levels of detection, characteristic of low effort expended on searching and detection of diseased trees, and high detection levels, exemplified by the deployment of large amounts of resources to identify diseased trees, fail to bring the epidemic under control. Importantly, we show that a slight change in the balance between the resources allocated to detection and those allocated to control may lead to drastic inefficiencies in control strategies. The results hold when quarantine is introduced to reduce the ingress of infected material into the region of interest.     

Drugs,genes and screens: The ethics of preventing and treating spinal muscular atrophy

Spinal muscular atrophy (SMA) is the most common genetic disease that causes infant mortality. Its treatment and prevention represent the paradigmatic example of the ethical dilemmas of 21st-century medicine. New therapies (nusinersen and AVXS-101) hold the promise of being able to treat, but not cure, the condition. Alternatively, genomic analysis could identify carriers, and carriers could be offered in vitro fertilization and preimplantation genetic diagnosis. In the future, gene editing could prevent the condition at the embryonic stage. How should these different options be evaluated and compared within a health system? In this paper, we discuss the ethical considerations that bear on the question of how to prioritize the different treatments and preventive options for SMA, at a policy level. We argue that despite the tremendous value of what we call ‘ex-post’ approaches to treating SMA (such as using pharmacological agents or gene therapy), there is a moral imperative to pursue ‘ex-ante’ interventions (such as carrier screening in combination with prenatal testing and preimplantation genetic diagnosis, or gene editing) to reduce the incidence of SMA. There are moral reasons relating to autonomy, beneficence and justice to prioritize ex-ante methods over ex-post methods.     

Postcolonial Identities in Africa

Postcolonial Identities in Africa. Richard Werbner and Terence Ranger. eds. London: Zed Books, 1996. 292 pp.     

High-Throughput Nonlinear Optical Microscopy

High-resolution microscopy methods based on different nonlinear optical (NLO) contrast mechanisms are finding numerous applications in biology and medicine. While the basic implementations of these microscopy methods are relatively mature, an important direction of continuing technological innovation lies in improving the throughput of these systems. Throughput improvement is expected to be important for studying fast kinetic processes, for enabling clinical diagnosis and treatment, and for extending the field of image informatics. This review will provide an overview of the fundamental limitations on NLO microscopy throughput. We will further cover several important classes of high-throughput NLO microscope designs with discussions on their strengths and weaknesses and their key biomedical applications. Finally, this review will close with a perspective of potential future technological improvements in this field.     

Solution Structure of the HIV-1 Intron Splicing Silencer and Its Interactions with the UP1 Domain of Heterogeneous Nuclear Ribonucleoprotein (hnRNP) A1

Splicing patterns in human immunodeficiency virus type 1 (HIV-1) are maintained through cis regulatory elements that recruit antagonistic host RNA-binding proteins. The activity of the 3′ acceptor site A7 is tightly regulated through a complex network of an intronic splicing silencer (ISS), a bipartite exonic splicing silencer (ESS3a/b), and an exonic splicing enhancer (ESE3). Because HIV-1 splicing depends on protein-RNA interactions, it is important to know the tertiary structures surrounding the splice sites. Herein, we present the NMR solution structure of the phylogenetically conserved ISS stem loop. ISS adopts a stable structure consisting of conserved UG wobble pairs, a folded 2X2 (GU/UA) internal loop, a UU bulge, and a flexible AGUGA apical loop. Calorimetric and biochemical titrations indicate that the UP1 domain of heterogeneous nuclear ribonucleoprotein A1 binds the ISS apical loop site-specifically and with nanomolar affinity. Collectively, this work provides additional insights into how HIV-1 uses a conserved RNA structure to commandeer a host RNA-binding protein.     

Effects of urbanization on streams of the Melbourne region, Victoria, Australia. I. Benthic macroinvertebrate communities

1. Macroinvertebrate community composition was assessed in small streams of the Melbourne region to test the effects of (a) urban density (catchment imperviousness 0–51%) and (b) stormwater drainage intensity (comparing the intensively drained metropolitan area with urban areas of the hinterland, which had open drains and some localized stormwater drainage).
2. Hinterland communities separated into two groups of sites correlating strongly with patterns of electrical conductivity (EC), basalt geology and annual rainfall. Community composition varied little in the high-EC, western group (imperviousness 0.2–1.2%), but in the eastern group it was strongly correlated with catchment imperviousness (0–12%), with lower taxon richness in more impervious catchments.
3. Metropolitan communities (imperviousness 1–51%) were all severely degraded, with high abundances of a few tolerant taxa. Community composition was poorly correlated with patterns of geology, rainfall or imperviousness. Differences between metropolitan and hinterland communities were well explained by patterns of biochemical oxygen demand and electrical conductivity, which were postulated to indicate the more efficient transport of pollutants to receiving streams by the metropolitan stormwater drainage system.
4. Degradation of macroinvertebrate community composition was well explained by urban density but intensive urban drainage increased degradation severely at even low urban densities. Quantification of relationships between imperviousness, drainage intensity and stream degradation can better inform the assessment, conservation and restoration of urban streams.