Spontaneous Quaternary and Tertiary T-R Transitions of Human Hemoglobin in Molecular Dynamics Simulation

We present molecular dynamics simulations of unliganded human hemoglobin (Hb) A under physiological conditions, starting from the R, R2, and T state. The simulations were carried out with protonated and deprotonated HC3 histidines His(β)146, and they sum up to a total length of 5.6µs. We observe spontaneous and reproducible T→R quaternary transitions of the Hb tetramer and tertiary transitions of the α and β subunits, as detected from principal component projections, from an RMSD measure, and from rigid body rotation analysis. The simulations reveal a marked asymmetry between the α and β subunits. Using the mutual information as correlation measure, we find that the β subunits are substantially more strongly linked to the quaternary transition than the α subunits. In addition, the tertiary populations of the α and β subunits differ substantially, with the β subunits showing a tendency towards R, and the α subunits showing a tendency towards T. Based on the simulation results, we present a transition pathway for coupled quaternary and tertiary transitions between the R and T conformations of Hb

Feeding of Triportheus angulatus (Spix & Agassiz, 1829) in the Camaleão lake, Manaus, Amazonas state, Brazil

Periodical flooding cause strong modifications in Central Amazonian floodplain. Periodical rising and decreasing of the water level influences abiotic and biotic factors of the aquatic environments. During the flooding season, there is a high feed availability, in contrast with dry season in which feed availability is at the lowest level. Limnological parameters also change seasonally. Oxygen concentrations vary both daily and seasonally, sometimes even showing hypoxic conditions. Despite these alterations, floodplain lakes are inhabited by several fish species, having the most diverse and abundant fish fauna among the Amazonian environments. This study focused on Triportheus angulatus feeding in temporal distribution in order to understand the influences of hydrological changes on individual size, diet composition and feeding even in low oxygen concentrations. In rising waters season, small individuals are predominant while the decreasing and the dry seasons there are mostly larger ones. There is a seasonal change on diet composition and this is related to feed type that is more available: during the rising, fishes eat mainly insects and zooplankton; in the flood season and drying season, seeds and fruits are predominant, and at the dry season they eat mainly insects. Feed ingestion was higher in the rising waters and mostly in the flood, and it was lower in the drying season. Feeding activity was not related with oxygen concentrations.As inundações periódicas na Amazônia Central causam profundas modificações no meio ambiente. A alternância dos períodos de cheias e secas tem influência nos fatores bióticos e abióticos do meio aquático. Na enchente e na cheia é alta a oferta de alimentos, ampliando o espectro alimentar que é restrito na seca. As variáveis limnológicas também sofrem modificações. As concentrações de oxigênio têm variações sazonais e diárias, às vezes com períodos de hipoxia. Apesar dessas alterações, os lagos de várzea são habitados por muitas espécies de peixes e estão entre os ambientes de maior abundância e riqueza de peixes na Amazônia. A distribuição temporal e a alimentação de Triportheus angulatus (Spix & Agassiz, 1829) foi estudada em um lago de várzea da Amazônia Central para entender a influência das modificações hídricas sobre o tamanho dos indivíduos, a composição da dieta e a ingestão dos alimentos mesmo em condições de baixas concentrações de oxigênio. Na enchente predominam os indivíduos menores, enquanto que na cheia, vazante e seca os maiores. Houve mudança sazonal na composição da dieta que foi relacionada com a disponibilidade de alimentos no ambientena enchente os peixes ingerem principalmente insetos e zooplâncton; na cheia e vazante frutos e sementes, e na seca insetos. O consumo de alimento foi alto na enchente e cheia, decrescendo na vazante e atingindo as menores quantidades na seca. A atividade alimentar, no período estudado, não foi influenciada pelas baixas concentrações de oxigênio existentes no lago

Padrão geográfico de diversidade genética em populações naturais de Pau-rosa (Aniba rosaeodora), na Amazônia Central

Rosewood (Aniba rosaeodora Ducke, Lauraceae) is an Amazonian evergreen tree and a source of the purest linalool, the main component of its essential oil, which is very valuable in the international perfumery market. After decades of over-exploitation it is currently considered as threatened. We evaluated the genetic diversity and its distribution in four populations in Central Amazonia. Thirty-five reliable RAPD markers were generated, of which 32 were polymorphic (91.4%). Variation was higher within the populations (76.5%; p < 0.0001) and geographic distribution contributed to population differentiation (23.4%; p < 0.0001). The Amazon River had a small influence on gene flow (3.3%; p < 0.0001), but we identified evidence of gene flow across the river. There were significant differences in marker frequencies (p < 0.05), in agreement with the low gene flow (Nm = 2.02). The correlation between genetic distance and gene flow was - 0.95 (p = 0.06) and between geographic distance and gene flow was -0.78 (p = 0.12). There was a geographic cline of variability across an East-West axis, influenced as well by the Amazon River, suggesting the river could be a barrier to gene flow. Although threatened, these Rosewood populations retain high diversity, with the highest levels in the Manaus population, which has been protected for over 42 years in a Reserve.O Pau-rosa (Aniba rosaeodora Ducke, Lauraceae) é uma árvore amazônica fonte do mais puro linalol, o qual é o principal componente do seu óleo essencial e muito valioso no mercado internacional de perfumaria. Após várias décadas de intensa exploração, a espécie foi levada à categoria de ameaçada de extinção. Quatro populações naturais distribuídas na bacia Amazônia Central foram avaliadas quanto ao nível e a distribuição da diversidade genética. Trinta e cinco marcadores RAPD reprodutíveis foram gerados, dos quais 32 foram polimórficos (91,4%). A diversidade foi maior dentro das populações (76,5%; p < 0,0001) e a distribuição geográfica contribuiu para a diferenciação entre as populações (23,4%; p < 0,0001). A AMOVA indicou que pode haver uma influência parcial do Rio Amazonas no fluxo gênico (3,3%; p < 0,0001), mas foram identificadas evidências de fluxo gênico atravessando o rio. Houve diferenças significativas nas freqüências dos marcadores (p < 0,05) e o fluxo gênico estimado foi relativamente baixo (Nm = 2,02). A correlação entre a distância genética e o fluxo gênico foi de - 0,95 (p = 0,06) e para a distância geográfica e o fluxo gênico foi de - 0,78 (p = 0,12). Houve um padrão geográfico de variabilidade ao longo do eixo Leste - Oeste, influenciado também pelo Rio Amazonas, o que sugere que o rio poderia funcionar como uma barreira para o fluxo gênico. Apesar de ameaçadas, estas populações de Pau-rosa possuem alta diversidade, com o maior valor na população de Manaus, que vem sendo protegida por 42 anos em uma reserva

A taxonomic backbone for the global synthesis of species diversity in the angiosperm order Caryophyllales

The Caryophyllales constitute a major lineage of flowering plants with approximately 12500 species in 39 families. A taxonomic backbone at the genus level is provided that reflects the current state of knowledge and accepts 749 genera for the order. A detailed review of the literature of the past two decades shows that enormous progress has been made in understanding overall phylogenetic relationships in Caryophyllales. The process of re-circumscribing families in order to be monophyletic appears to be largely complete and has led to the recognition of eight new families (Anacampserotaceae, Kewaceae, Limeaceae, Lophiocarpaceae, Macarthuriaceae, Microteaceae, Montiaceae and Talinaceae), while the phylogenetic evaluation of generic concepts is still well underway. As a result of this, the number of genera has increased by more than ten percent in comparison to the last complete treatments in the Families and genera of vascular plants” series. A checklist with all currently accepted genus names in Caryophyllales, as well as nomenclatural references, type names and synonymy is presented. Notes indicate how extensively the respective genera have been studied in a phylogenetic context. The most diverse families at the generic level are Cactaceae and Aizoaceae, but 28 families comprise only one to six genera. This synopsis represents a first step towards the aim of creating a global synthesis of the species diversity in the angiosperm order Caryophyllales integrating the work of numerous specialists around the world

Protein dynamics: From structure to function.

Understanding protein function requires detailed knowledge about protein dynamics, i.e. the different conformational states the system can adopt. Despite substantial experimental progress, simulation techniques such as molecular dynamics (MD) currently provide the only routine means to obtain dynamical information at an atomic level on timescales of nano- to microseconds. Even with the current development of computational power, sampling techniques beyond MD are necessary to enhance conformational sampling of large proteins and assemblies thereof. The use of collective coordinates has proven to be a promising means in this respect, either as a tool for analysis or as part of new sampling algorithms. Starting from MD simulations, several enhanced sampling algorithms for biomolecular simulations are reviewed in this chapter. Examples are given throughout illustrating how consideration of the dynamic properties of a protein sheds light on its function

The Evolutionary History of Pagamea

The flora of the Guiana Shield contains several plant lineages that are restricted to white-sand vegetation, some of which are widespread in tropical South America. Here, the history of diversification of one of these lineages, the genus Pagamea (Rubiaceae), is reconstructed through phylogenetic hypotheses. Data from chloroplast (rps16 and rpl20-rps12) and nuclear (ITS) markers were incongruent, with ITS found to be more consistent with morphological criteria to delimit species. Reconstruction of the ancestral area for the genus was ambiguous, with both the western Guiana Shield and the Atlantic coastal areas containing early divergent lineages, but most speciation events appeared to have happened in the western Guiana Shield where most extant diversity is present. Dispersal events into the western Amazon and the Andes (1.5-4.5 Ma) and the eastern Guiana Shield (0.4-2.2 Ma) were followed by speciation events in these regions. Dispersal events between the Amazon and Atlantic rain forest occurred at least three times independently. However, dispersals into new areas were limited, and most regions were found to be phylogenetically clustered. Altitudinal and habitat shifts happened multiple times independently, but ecological traits were found to be phylogenetically conserved, implying that such shifts were not the cause of lineage divergence. The result that most speciation events happened in the western Guiana Shield, where white-sand habitats predominate in both lowlands and highlands, and which has been less affected by Pleistocene climatic change, coupled with the result that ecological traits are phylogenetically conserved, suggests that the diversification of Pagamea may have been related primarily to the patchy distribution of white-sand vegetation. © 2016 The Association for Tropical Biology and Conservation