Capturing Transition Paths and Transition States for Conformational Rearrangements in the Ribosome

To reveal the molecular determinants of biological function, one seeks to characterize the interactions that are formed in conformational and chemical transition states. In other words, what interactions govern the molecule’s energy landscape? To accomplish this, it is necessary to determine which degrees of freedom can unambiguously identify each transition state. Here, we perform simulations of large-scale aminoacyl-transfer RNA (aa-tRNA) rearrangements during accommodation on the ribosome and project the dynamics along experimentally accessible atomic distances. From this analysis, we obtain evidence for which coordinates capture the correct number of barrier-crossing events and accurately indicate when the aa-tRNA is on a transition path. Although a commonly used coordinate in single-molecule experiments performs poorly, this study implicates alternative coordinates along which rearrangements are accurately described as diffusive movements across a one-dimensional free-energy profile. From this, we provide the theoretical foundation required for single-molecule techniques to uncover the energy landscape governing aa-tRNA selection by the ribosome.     

Visitor Influence on the Behavior of Captive Greater Rheas (Rhea americana,Rheidae Aves)

Visitors can affect and reduce the welfare of nonhuman animals. The Belo Horizonte Zoo, Brazil, had a group of greater rheas intended for reintroduction to the wild. Because this group received public visitation, evaluating its effect on the birds' behavior and welfare was important. The study conducted 60 hr of behavioral observations: 30 with, and 30 without, visitors in front of the birds' enclosure. The study, conducted April–December 2009, collected data using scan sampling with instantaneous recording of behavior every minute. The study collected data on public behavior, visitor density, and time spent observing the birds. More than 4,000 persons visited the birds' enclosure: 9.86 s average time spent. Public behaviors most expressed were walking-watching-talking and stopped-watching-talking; visitors or not, greater rheas' most expressed behaviors (inversed between treatments) were foraging and walking alert; defecating/urinating and other behaviors differed statistically between treatments. Walking alert was most expressed in the presence of visitors; defecating/urinating and other behaviors were most expressed in their absence. Greater rheas seemed to habituate to visitors. Birds' behaviors differed little in visitors' presence or absence.     

Methods to detect cyanobacteria and their toxins in the environment

Cyanobacteria blooms are since early times a cause for environmental concern because of their negative impact through the release of odors, water discoloration, and more dangerously through the release of toxic compounds (i.e. the cyanotoxins) that can affect both human and animal welfare. Surveillance of the aquatic ecosystems is therefore obligatory, and methods to achieve such require a prompt answer not only regarding the species that are producing the blooms but also the cyanotoxins that are being produced and/or released. Moreover, besides this well-known source of possible intoxication, it has been demonstrated the existence of several other potential routes of exposure, either for humans or other biota such as through food additives and in terrestrial environments (in plants, lichens, biological soil crusts) and the recognition of their harmful impact on less studied ecosystems (e.g. coral reefs). Nowadays, the most frequent approaches to detect toxic cyanobacteria and/or their toxins are the chemical-, biochemical-, and molecular-based methods. Above their particular characteristics and possible applications, they all bring to the environmental monitoring several aspects that are needed to be discussed and scrutinized. The end outcome of this review will be to provide newer insights and recommendations regarding the methods needed to apply in an environmental risk assessment program. Therefore, a current state of the knowledge concerning the three methodological approaches will be presented, while highlighting positive and negative aspects of each of those methods within the purpose of monitoring or studying cyanobacteria and their toxins in the environment.     

Synthetic polymers and their potential as genetic materials

DNA and RNA are the only known natural genetic materials. Systematic modification of each of their chemical building blocks (nucleobase, sugar, and phosphate) has enabled the study of the key properties that make those nucleic acids genetic materials. All three moieties contribute to replication and, significantly, all three moieties can be replaced by synthetic analogs without loss of function. Synthetic nucleic acid polymers capable of storing and propagating information not only expand the central dogma, but also highlight that DNA and RNA are not unique chemical solutions for genetic information storage. By considering replication as a question of information transfer, we propose that any polymer that can be replicated could serve as a genetic material. Editor's suggested further reading in BioEssays Xenobiology: A new form of life as the ultimate biosafety tool Abstract     

Intriguing Plasmonic and Fluorescence Duality in Copper Nanoparticles

Dendrimeric copper nanoparticles (CuNPs) were prepared by the reduction of [Cu₂(CH₃CO₂)₄] with ascorbic acid at 75 °C in the presence of ranelate ions. The metallic nanoparticles exhibited a strong plasmonic band centered at 581 nm, and their average size distribution was typically in the range of 20–30 nm. By adding polyvinylpyrrolidone to the reaction mixture, the growth of the initial copper nanoparticles was hindered. Their sizes were stabilized around 1.8 nm, leading to spherical agglomerates of about 50 nm. Upon green light excitation, the agglomerates exhibited yellow-orange fluorescence emission, keeping the surface plasmon resonance band at 581 nm. This dual behavior suggested the occurrence of collective plasmonic resonance and efficient energy transfer within the agglomerated nanoparticles, in order to account for the observed fluorescence in the system.

Graphical Abstract

     

Phenological stages of arrowroot (Maranta arundinacea L.) according to the Biologische Bundesanstalt Bundessortenamt und Chemische Industrie scale

The present study aimed to characterise and establish the phenological stages of arrowroot (Maranta arundinacea L.) by employing the extended BBCH (Biologische Bundesanstalt Bundessortenamt und Chemische Industrie) scale system and reporting a detailed biometric evaluation. An experiment with individual plants grown in separate pots was set up in a greenhouse for the identification and characterisation of phenological stages (the phenotypic characterisation and tuberisation process was accompanied by histological analyses every 2 months) and for biometric evaluation (plant height, root volume, dry biomass, leaf area and accumulated starch). We identified 36 secondary stages within eight principal stages of arrowroot growth which comprise: (0) sprouting; (1) leaf development–main stem; (2) formation of lateral stems; (3) elongation–main stem; (4) rhizome formation and tuberisation; (5) inflorescence emergence; (6) flowering, and (9) senescence. Results were categorised and recorded by way of photographs and technical drawings. The total growth cycle in this experiment was 230 days, concluding at the point of harvest. It was possible to observe the phenological events that characterised the changes at each stage (colouration, flag leaf emission, inflorescence and the rhizome tuberisation process). The BBCH system was efficient in identifying arrowroot phenological data. It constitutes a tool for agricultural calendar delineation and contributes to the standardisation of research on the species.     

Surface liming triggers improvements in subsoil fertility and root distribution to boost maize crop physiology,yield and revenue

Plant and Soil - Liming is widely used to alleviate soil acidity worldwide. However, the vast majority of studies with liming are restricted to agricultural systems that incorporate lime into the...