Thermodynamic rules for the design of high affinity HIV-1 protease inhibitors with adaptability to mutations and high selectivity towards unwanted targets

Protease inhibitors are key components in the chemotherapy of HIV-1 infection. However, the long term efficacy of antiretroviral therapies is hampered by issues of patient compliance often associated with the presence of severe side effects, and above all by the appearance of drug resistance. The development of new protease inhibitors with high potency, low susceptibility to mutations and minimal affinity for unwanted targets is an urgent goal. The engineering of these adaptive inhibitors requires identification of the critical determinants of affinity, adaptability, and selectivity. Analysis of the binding database for existing clinical and experimental inhibitors has allowed us to address the following questions in a quantitative fashion: (1) Is there an optimal binding affinity? Or, are the highest affinity inhibitors necessarily the best inhibitors? (2) What is the dependence of optimal affinity on adaptability and selectivity? (3) What are the determinants of adaptability to mutations associated with drug resistance? (4) How selectivity against unwanted targets can be improved? It is shown that the optimal affinity is a function of the effective target concentration and the desired adaptability and selectivity factors. Furthermore, knowledge of the enthalpic and entropic contributions to the binding affinity to the wild type provides a way of anticipating the response of an inhibitor to mutations associated with drug resistance, and therefore, a valuable guideline for optimization.     

Phylogenetic analysis of sexual systems in Inuleae (Asteraceae)

From an ancestor with bisexual flowers, plants with unisexual flowers, or even unisexual individuals have evolved in different lineages of angiosperms. The Asteraceae tribe Inuleae includes hermaphroditic, monoecious, dioecious, and gynomonoecious species. Gynomonoecy, the sexual system in which female and bisexual flowers occur on the same plant, is prevalent in the Asteraceae. We inferred one large gene phylogeny (ndhF) and two supertrees to investigate whether gynomonoecy was a stage in the evolution from hermaphroditism to monoecy. We identified transitions in sexual system evolution using the stochastic character mapping method. From gynomonoecious ancestors, both hermaphroditic and monoecious descendants have evolved. Gynomonoecy was not restricted to a stage in the evolution toward monoecy because the number of transitions and the rate of change from monoecy to gynomonoecy were much higher than the opposite. We also investigated one hypothesized association among female flowers and the development of a petaloid ray as an explanation of gynomonoecy maintenance in Asteraceae. We found that peripheral female flowers and petaloid rays were phylogenetically correlated. However, empirical evidence shows that a causal relationship between these traits is not clear.     

Invasion success depends on invader body size in a size-structured mixed predation–competition community

1.  The size of an individual is an important determinant of its trophic position and the type of interactions it engages in with other heterospecific and conspecific individuals. Consequently an individual's ecological role in a community changes with its body size over ontogeny, leading to that trophic interactions between individuals are a size-dependent and ontogenetically variable mixture of competition and predation.
2.  Because differently sized individuals thus experience different biotic environments, invasion success may be determined by the body size of the invaders. Invasion outcome may also depend on the productivity of the system as productivity influences the biotic environment.
3.  In a laboratory experiment with two poeciliid fishes the body size of the invading individuals and the daily amount of food supplied were manipulated.
4.  Large invaders established persistent populations and drove the resident population to extinction in 10 out of 12 cases, while small invaders failed in 10 out of 12 trials. Stable coexistence was virtually absent. Invasion outcome was independent of productivity.
5.  Further analyses suggest that small invaders experienced a competitive recruitment bottleneck imposed on them by the resident population. In contrast, large invaders preyed on the juveniles of the resident population. This predation allowed the large invaders to establish successfully by decreasing the resident population densities and thus breaking the bottleneck.
6.  The results strongly suggest that the size distribution of invaders affects their ability to invade, an implication so far neglected in life-history omnivory systems. The findings are further in agreement with predictions of life-history omnivory theory, that size-structured interactions demote coexistence along a productivity gradient.     

Unlocking Short Read Sequencing for Metagenomics

Background

Different high-throughput nucleic acid sequencing platforms are currently available but a trade-off currently exists between the cost and number of reads that can be generated versus the read length that can be achieved.

Methodology/Principal Findings

We describe an experimental and computational pipeline yielding millions of reads that can exceed 200 bp with quality scores approaching that of traditional Sanger sequencing. The method combines an automatable gel-less library construction step with paired-end sequencing on a short-read instrument. With appropriately sized library inserts, mate-pair sequences can overlap, and we describe the SHERA software package that joins them to form a longer composite read.

Conclusions/Significance

This strategy is broadly applicable to sequencing applications that benefit from low-cost high-throughput sequencing, but require longer read lengths. We demonstrate that our approach enables metagenomic analyses using the Illumina Genome Analyzer, with low error rates, and at a fraction of the cost of pyrosequencing.     

Origin and history of mitochondrial DNA lineages in domestic horses

Domestic horses represent a genetic paradox: although they have the greatest number of maternal lineages (mtDNA) of all domestic species, their paternal lineages are extremely homogeneous on the Y-chromosome. In order to address their huge mtDNA variation and the origin and history of maternal lineages in domestic horses, we analyzed 1961 partial d-loop sequences from 207 ancient remains and 1754 modern horses. The sample set ranged from Alaska and North East Siberia to the Iberian Peninsula and from the Late Pleistocene to modern times. We found a panmictic Late Pleistocene horse population ranging from Alaska to the Pyrenees. Later, during the Early Holocene and the Copper Age, more or less separated sub-populations are indicated for the Eurasian steppe region and Iberia. Our data suggest multiple domestications and introgressions of females especially during the Iron Age. Although all Eurasian regions contributed to the genetic pedigree of modern breeds, most haplotypes had their roots in Eastern Europe and Siberia. We found 87 ancient haplotypes (Pleistocene to Mediaeval Times); 56 of these haplotypes were also observed in domestic horses, although thus far only 39 haplotypes have been confirmed to survive in modern breeds. Thus, at least seventeen haplotypes of early domestic horses have become extinct during the last 5,500 years. It is concluded that the large diversity of mtDNA lineages is not a product of animal breeding but, in fact, represents ancestral variability.     

Pollen subsidies promote whitefly control through the numerical response of predatory mites

Several studies have shown that biological control of pests can be improved by supplying extra food to natural enemies. This increases population levels of the enemies, resulting in decreases in pest densities. In theory, however, supplying food can also have negative effects on biological control. We specifically tested for such negative effects, using a predator–prey system consisting of the whitefly Bemisia tabaci (Gennadius) and a predatory mite Amblyseius swirskii (Athias-Henriot). This predator attacks eggs and young instars of the whitefly, but also feeds on pollen. We added pollen to populations of predators and whiteflies on isolated cucumber plants. Although the set-up of our experiments would favour the occurrence of a negative effect of the addition of pollen on biological control, we found increased control throughout the experiment. This shows that the control of whiteflies by A. swirskii can be improved by supplementing the predators with pollen.     

The effect of application techniques on field‐scale efficacy: can the use of entomopathogenic nematodes reduce damage by western corn rootworm larvae?

• 1 Field studies on the efficacy of entomopathogenic nematodes as biological pest control agents in field crops and over multiple seasons are rare.
• 2 In the present study, we investigated the efficacy of Heterorhabditis bacteriophora (Rhabditida: Heterorhabditidae) at reducing maize root damage caused by the larvae of the western corn rootworm Diabrotica virgifera virgifera LeConte (Coleoptera: Chrysomelidae). The study consisted of 21 field‐scale experiments in Hungary conducted between 2004 and 2007. Key factors behind successful control, such as application techniques, nematode dosage, soil environment and rainfall, were analyzed.
• 3 Five of the six tested techniques for applying the nematodes using readily available farming machinery resulted in a reduction of root damage, as well as subsequent plant lodging.
• 4 According to damage rating with the Iowa 1–6 scale, damage was reduced by 3–18%. According to the 0.00–3.00 node injury scale, damage was reduced by 14–54%. Approximately 7–62 % of plant lodging, and thus direct yield losses as a result of in‐harvestability, was prevented.
• 5 An increase in nematode dosage and/or an increased rainfall during the period of applications increased the efficacy of H. bacteriophora at reducing root damage. Except for the obvious effect of moisture, the soil environment had little measurable influence on nematode efficacy.
• 6 The present study demonstrates the potential for field‐scale nematode application to significantly reduce damage caused by D. v. virgifera larvae. It is recommended that the method of agent application should be selected on a case‐by‐case basis considering the efficacy data presented here, the available application machinery and its associated costs.