Antigenic Properties of the Human Immunodeficiency Virus Envelope Glycoprotein Gp120 on Virions Bound to Target Cells

The HIV-1 envelope glycoprotein, gp120, undergoes multiple molecular interactions and structural rearrangements during the course of host cell attachment and viral entry, which are being increasingly defined at the atomic level using isolated proteins. In comparison, antigenic markers of these dynamic changes are essentially unknown for single HIV-1 particles bound to target cells. Such markers should indicate how neutralizing and/or non-neutralizing antibodies might interdict infection by either blocking infection or sensitizing host cells for elimination by Fc-mediated effector function. Here we address this deficit by imaging fluorescently labeled CCR5-tropic HIV-1 pseudoviruses using confocal and superresolution microscopy to track the exposure of neutralizing and non-neutralizing epitopes as they appear on single HIV-1 particles bound to target cells. Epitope exposure was followed under conditions permissive or non-permissive for viral entry to delimit changes associated with virion binding from those associated with post-attachment events. We find that a previously unexpected array of gp120 epitopes is exposed rapidly upon target cell binding. This array comprises both neutralizing and non-neutralizing epitopes, the latter being hidden on free virions yet capable of serving as potent targets for Fc-mediated effector function. Under non-permissive conditions for viral entry, both neutralizing and non-neutralizing epitope exposures were relatively static over time for the majority of bound virions. Under entry-permissive conditions, epitope exposure patterns changed over time on subsets of virions that exhibited concurrent variations in virion contents. These studies reveal that bound virions are distinguished by a broad array of both neutralizing and non-neutralizing gp120 epitopes that potentially sensitize a freshly engaged target cell for destruction by Fc-mediated effector function and/or for direct neutralization at a post-binding step. The elucidation of these epitope exposure patterns during viral entry will help clarify antibody-mediated inhibition of HIV-1 as it is measured in vitro and in vivo.     

The Evolutionary Origins of Hierarchy

Hierarchical organization—the recursive composition of sub-modules—is ubiquitous in biological networks, including neural, metabolic, ecological, and genetic regulatory networks, and in human-made systems, such as large organizations and the Internet. To date, most research on hierarchy in networks has been limited to quantifying this property. However, an open, important question in evolutionary biology is why hierarchical organization evolves in the first place. It has recently been shown that modularity evolves because of the presence of a cost for network connections. Here we investigate whether such connection costs also tend to cause a hierarchical organization of such modules. In computational simulations, we find that networks without a connection cost do not evolve to be hierarchical, even when the task has a hierarchical structure. However, with a connection cost, networks evolve to be both modular and hierarchical, and these networks exhibit higher overall performance and evolvability (i.e. faster adaptation to new environments). Additional analyses confirm that hierarchy independently improves adaptability after controlling for modularity. Overall, our results suggest that the same force–the cost of connections–promotes the evolution of both hierarchy and modularity, and that these properties are important drivers of network performance and adaptability. In addition to shedding light on the emergence of hierarchy across the many domains in which it appears, these findings will also accelerate future research into evolving more complex, intelligent computational brains in the fields of artificial intelligence and robotics.     

Evaluation of different botanical for the management of cowpea bruchid (Callosobruchus maculatus) in north-eastern Ethiopia

The pesticide efficacy of locally available seven botanicals “Gime” (Chenopodium ambrosioides), “Ayderke” (Jatropha curcas), Neem (Azadirachta indica), Melia (Melia azadirach), “Chobe” (Cisus rotonifolia), “Kelewa” (Maesa lanceolata) and “Antharfa” at a rate of 4% weight by weight was evaluated for the control of cowpea bruchid using 200?g cowpea seeds in 500?cm³ volume jar in 2010 and 2011 under laboratory condition at Sirinka Agricultural Research Centre. The combined analysis showed that “Gime” (both leaf and seed) had high speed of pesticide effect as it showed significantly higher per cent of parent adult mortality (84 and 71%, respectively) as to the standard check Malathion 5% dust (100%) in the first day of adult mortality count. “Antharfa” and “Ayderke” also have shown significantly higher per cent of parent adult mortality as to Malathion in the third and fifth day of adult mortality count, respectively. In the seventh day, all botanicals showed significantly higher per cent of adult mortality as compared to untreated check. “Gime” leaf and seed powder, “Ayderke” seed, Neem seed and “Antharfa” leaf powders significantly reduced the number of progeny emergence per day as compared to all other treatments. Moreover, these botanicals were effective in reducing per cent seed damage (0.00, 0.00, 0.57, 5.86 and 10.86%, respectively) and storage loss (0.00, 0.00, 0.073, 1.02 and 2.27%, respectively). Gime (both leaf and seed powder), “Ayderke” seed and Neem seed are locally available, simple for preparation and environmentally friendly. Therefore, these three botanicals can be recommended to satisfy the demand for organic food and save the seed damage and yield loss of cowpea caused by Callosobruchus maculates and bean bruchid (Zabrotes subfasciatus) which has similar biology with Callosobruchus maculatus.     

A New Assemblage of Mid-Pliocene Proboscideans from the Woranso-Mille Area, Afar Region, Ethiopia: Taxonomic, Evolutionary, and Paleoecological Considerations

Recent fieldwork at Woranso-Mille, Ethiopia led to the recovery of an abundant, diverse mammalian fauna that includes remains of the early hominid Australopithecus afarensis. Proboscideans are among the taxa well sampled at the site, primarily by gnathodental specimens, dated to the mid-Pliocene interval of 3.8–3.6 Ma. These fossils document traces of the last anancine gomphotheres (Anancus ultimus) in eastern Africa and several elephant taxa. Comparative study of the elephant fossils indicates the presence of cf. Mammuthus sp. “Hadar-type,” cf. Elephas ekorensis, E. recki brumpti, and cf. Loxodonta adaurora adaurora. Proboscidean evolution in the mid-Pliocene is interesting because during this time archaic elephants were completely replaced by basal members of crown elephant lineages, taxonomic diversity was high (multiple elephant species, anancine gomphotheres, stegodonts, and deinotheres), and elephants were undergoing substantial reorganization of the craniodental masticatory apparatus, presumably in response to the spread of more open habitats and greater competition for grazing resources. The Woranso-Mille sample is important because this interval is only represented elsewhere in eastern Africa by a small number of sites, and because adaptive diversification among early crown elephants requires greater clarification. Morphometric contrasts among the fossil dentition from Woranso-Mille presage the differential success of elephant lineages in eastern Africa during the Pleistocene, providing hints about the beginnings of competitive displacement. Differences between E. recki brumpti from Woranso-Mille and the slightly younger Sidi Hakoma Member of the Hadar Formation reveal the beginnings of continuous, directional morphometric change that characterized the lineage. Reconsideration of E. recki subspecies indicates that they are arbitrary lineage divisions tied to geochronological boundaries (with utility for biochronological correlation at well sampled sites) rather than real phylogenetic entities, but does not reject monophyly or anagenetic evolution of the lineage.     

Does avian malaria infection affect feather stable isotope signatures?

It is widely accepted that stable isotope ratios in inert tissues such as feather keratin reflect the dietary isotopic signature at the time of the tissue synthesis. However, some elements such as stable nitrogen isotopes can be affected by individual physiological state and nutritional stress. Using malaria infection experiment protocols, we estimated the possible effect of malaria parasite infections on feather carbon (δ¹³C) and nitrogen (δ¹⁵N) isotope signatures in juvenile common crossbills Loxia curvirostra. The birds were experimentally infected with Plasmodium relictum (lineage SGS1) and P. ashfordi (GRW2), two widespread parasites of passerines. Experimental birds developed heavy parasitemia of both parasites and maintained high levels throughout the experiment (33 days). We found no significant difference between experimental and control birds in both δ¹³C and δ¹⁵N values of feathers re-grown. The study shows that even heavy primary infections of malaria parasites do not affect feather δ¹³C and δ¹⁵N isotopic signatures. The results of this experiment demonstrate that feather isotope values of wild-caught birds accurately reflect the dietary isotopic sources at the time of tissue synthesis even when the animal’s immune system might be challenged due to parasitic infection.     

Differential interaction of dicarboxylates with human sodium-dicarboxylate cotransporter 3 and organic anion transporters 1 and 3

Organic anions are taken up from the blood into proximal tubule cells by organic anion transporters 1 and 3 (OAT1 and OAT3) in exchange for dicarboxylates. The released dicarboxylates are recycled by the sodium dicarboxylate cotransporter 3 (NaDC3). In this study, we tested the substrate specificities of human NaDC3, OAT1, and OAT3 to identify those dicarboxylates for which the three cooperating transporters have common high affinities. All transporters were stably expressed in HEK293 cells, and extracellularly added dicarboxylates were used as inhibitors of [(14)C]succinate (NaDC3), p-[(3)H]aminohippurate (OAT1), or [(3)H]estrone-3-sulfate (OAT3) uptake. Human NaDC3 was stably expressed as proven by immunochemical methods and by sodium-dependent uptake of succinate (K(0.5) for sodium activation, 44.6 mM; Hill coefficient, 2.1; K(m) for succinate, 18 μM). NaDC3 was best inhibited by succinate (IC(50) 25.5 μM) and less by α-ketoglutarate (IC(50) 69.2 μM) and fumarate (IC(50) 95.2 μM). Dicarboxylates with longer carbon backbones (adipate, pimelate, suberate) had low or no affinity for NaDC3. OAT1 exhibited the highest affinity for glutarate, α-ketoglutarate, and adipate (IC(50) between 3.3 and 6.2 μM), followed by pimelate (18.6 μM) and suberate (19.3 μM). The affinity of OAT1 to succinate and fumarate was low. OAT3 showed the same dicarboxylate selectivity with ～13-fold higher IC(50) values compared with OAT1. The data 1) reveal α-ketoglutarate as a common high-affinity substrate of NaDC3, OAT1, and OAT3 and 2) suggest potentially similar molecular structures of the binding sites in OAT1 and OAT3 for dicarboxylates.     

Ancient DNA from Nubian and Somali wild ass provides insights into donkey ancestry and domestication

Genetic data from extant donkeys (Equus asinus) have revealed two distinct mitochondrial DNA haplogroups, suggestive of two separate domestication events in northeast Africa about 5000 years ago. Without distinct phylogeographic structure in domestic donkey haplogroups and with little information on the genetic makeup of the ancestral African wild ass, however, it has been difficult to identify wild ancestors and geographical origins for the domestic mitochondrial clades. Our analysis of ancient archaeological and historic museum samples provides the first genetic information on the historic Nubian wild ass (Equus africanus africanus), Somali wild ass (Equus africanus somaliensis) and ancient donkey. The results demonstrate that the Nubian wild ass was an ancestor of the first donkey haplogroup. In contrast, the Somali wild ass has considerable mitochondrial divergence from the Nubian wild ass and domestic donkeys. These findings resolve the long-standing issue of the role of the Nubian wild ass in the domestication of the donkey, but raise new questions regarding the second ancestor for the donkey. Our results illustrate the complexity of animal domestication, and have conservation implications for critically endangered Nubian and Somali wild ass.     

Comparison of epigenetic profiles of human oral epithelial cells from HIV-positive (on HAART) and HIV-negative subjects

HIV-infected subjects on highly active antiretroviral therapy (HAART) are susceptible to comorbid microbial infections in the oral cavity. We observed that primary oral epithelial cells (POECs) isolated from HIV+ subjects on HAART grow more slowly and are less innate immune responsive to microbial challenge when compared with POECs from normal subjects. These aberrant cells also demonstrate epigenetic differences that include reduction in histone deacetylase 1 (HDAC-1) levels and reduced total DNA methyltransferase (DNMT) activity specific to enzymes DNMT1 and DNMT3A. The DNMT activity correlates well with global DNA methylation, indicating that aberrant DNMT activity in HIV+ (on HAART) POECs leads to an aberrantly methylated epithelial cell phenotype. Overall, our results lead us to hypothesize that, in patients with chronic HIV infection on HAART, epigenetic changes in key genes result in increased vulnerability to microbial infection in the oral cavity.     

Formation of Spatially Discordant Alternans Due to Fluctuations and Diffusion of Calcium

Spatially discordant alternans (SDA) of action potential duration (APD) is a phenomenon where different regions of cardiac tissue exhibit an alternating sequence of APD that are out-of-phase. SDA is arrhythmogenic since it can induce spatial heterogeneity of refractoriness, which can cause wavebreak and reentry. However, the underlying mechanisms for the formation of SDA are not completely understood. In this paper, we present a novel mechanism for the formation of SDA in the case where the cellular instability leading to alternans is caused by intracellular calcium (Ca) cycling, and where Ca transient and APD alternans are electromechanically concordant. In particular, we show that SDA is formed when rapidly paced cardiac tissue develops alternans over many beats due to Ca accumulation in the sarcoplasmic reticulum (SR). The mechanism presented here relies on the observation that Ca cycling fluctuations dictate Ca alternans phase since the amplitude of Ca alternans is small during the early stages of pacing. Thus, different regions of a cardiac myocyte will typically develop Ca alternans which are opposite in phase at the early stages of pacing. These subcellular patterns then gradually coarsen due to interactions with membrane voltage to form steady state SDA of voltage and Ca on the tissue scale. This mechanism for SDA is distinct from well-known mechanisms that rely on conduction velocity restitution, and a Turing-like mechanism known to apply only in the case where APD and Ca alternans are electromechanically discordant. Furthermore, we argue that this mechanism is robust, and is likely to underlie a wide range of experimentally observed patterns of SDA.