A SAXS-based ensemble model of the native and phosphorylated regulatory domain of the CFTR

The cystic fibrosis transmembrane conductance regulator (CFTR), the defective protein in cystic fibrosis, is an anion channel activated by protein kinase A phosphorylation. The regulatory domain (RD) of CFTR has multiple phosphorylation sites, and is responsible for channel activation. This domain is intrinsically disordered, rendering the structural analysis a difficult task, as high-resolution techniques are barely applicable. In this work, we obtained a biophysical characterization of the native and phosphorylated RD in solution by employing complementary structural methods. The native RD has a gyration radius of 3.25 nm, and a maximum molecular dimension of 11.4 nm, larger than expected for a globular protein of the same molecular mass. Phosphorylation causes compaction of the structure, yielding a significant reduction of the gyration radius, to 2.92 nm, and on the maximum molecular dimension to 10.2 nm. Using an ensemble optimization method, we were able to generate a low-resolution, three-dimensional model of the native and the phosphorylated RD based on small-angle X-ray scattering data. We have obtained the first experiment-based model of the CFTR regulatory domain, which will be useful to understand the molecular mechanisms of normal and pathological CFTR functioning.     

The gating of the CFTR channel

Cystic fibrosis transmembrane conductance regulator (CFTR) is an anion channel expressed in the apical membrane of epithelia. Mutations in the CFTR gene are the cause of cystsic fibrosis. CFTR is the only ABC-protein that constitutes an ion channel pore forming subunit. CFTR gating is regulated in complex manner as phosphorylation is mandatory for channel activity and gating is directly regulated by binding of ATP to specific intracellular sites on the CFTR protein. This review covers our current understanding on the gating mechanism in CFTR and illustrates the relevance of alteration of these mechanisms in the onset of cystic fibrosis.     

Valveless Thermally-Driven Phase-Change Micropump

A dynamic model with moving heat sources was developed to analyze the pumping mechanism of a valveless thermally-driven phase-change micropump. The coupled equations were solved to determine the pumping characteristics. The numerical results agree with experimental data from micropumps with different diameter microtubes. The maximum flow rate reached 33 μL / min and the maximum pump pressure was over 20 kPa for a 200-μm diameter microtube. Analysis of the pumping mechanism shows that the main factors affecting the flow come from the large density difference between the liquid and vapor phases and the choking effect of the vapor region.     

Functional metagenomic profiling of nine biomes

Microbial activities shape the biogeochemistry of the planet and macroorganism health. Determining the metabolic processes performed by microbes is important both for understanding and for manipulating ecosystems (for example, disruption of key processes that lead to disease, conservation of environmental services, and so on). Describing microbial function is hampered by the inability to culture most microbes and by high levels of genomic plasticity. Metagenomic approaches analyse microbial communities to determine the metabolic processes that are important for growth and survival in any given environment. Here we conduct a metagenomic comparison of almost 15 million sequences from 45 distinct microbiomes and, for the first time, 42 distinct viromes and show that there are strongly discriminatory metabolic profiles across environments. Most of the functional diversity was maintained in all of the communities, but the relative occurrence of metabolisms varied, and the differences between metagenomes predicted the biogeochemical conditions of each environment. The magnitude of the microbial metabolic capabilities encoded by the viromes was extensive, suggesting that they serve as a repository for storing and sharing genes among their microbial hosts and influence global evolutionary and metabolic processes.     

Hermeneutical contributions to the history of science: Gadamer on ‘presentism’

This article examines how Hans G. Gadamer’s philosophical hermeneutics can contribute to contemporary debates on the concept of ‘presentism’. In the field of the history of science, this term is usually employed in two ways. First, ‘presentism’ refers to the kind of historiography which judges the past to legitimate the present. Second, this concept designates the inevitable influence of the present in the interpretation of the past. In this paper, I argue that both dimensions of the relationship between the present and the past are explored by Hans G. Gadamer in Truth and Method and other texts. In the first place, Gadamer’s critique of historicism calls into question the anti-presentist ideal of studying the past for ‘its own sake’. In the second place, Gadamer’s thesis that all understanding inevitably involves some prejudice poses the question of the inherent “present-centredness” of historical interpretations. By examining Gadamer’s hermeneutics, I seek to provide historians with new arguments and perspectives on the question of ‘presentism’.     

NLRP10 is a NOD-like receptor essential to initiate adaptive immunity by dendritic cells

NLRs (nucleotide-binding domain leucine-rich-repeat-containing receptors; NOD-like receptors) are a class of pattern recognition receptor (PRR) that respond to host perturbation from either infectious agents or cellular stress. The function of most NLR family members has not been characterized and their role in instructing adaptive immune responses remains unclear. NLRP10 (also known as PYNOD, NALP10, PAN5 and NOD8) is the only NLR lacking the putative ligand-binding leucine-rich-repeat domain, and has been postulated to be a negative regulator of other NLR members, including NLRP3 (refs 4-6). We did not find evidence that NLRP10 functions through an inflammasome to regulate caspase-1 activity nor that it regulates other inflammasomes. Instead, Nlrp10(-/-) mice had a profound defect in helper T-cell-driven immune responses to a diverse array of adjuvants, including lipopolysaccharide, aluminium hydroxide and complete Freund's adjuvant. Adaptive immunity was impaired in the absence of NLRP10 because of a dendritic cell (DC) intrinsic defect in emigration from inflamed tissues, whereas upregulation of DC costimulatory molecules and chemotaxis to CCR7-dependent and -independent ligands remained intact. The loss of antigen transport to the draining lymph nodes by a subset of migratory DCs resulted in an almost absolute loss in naive CD4(+) T-cell priming, highlighting the critical link between diverse innate immune stimulation, NLRP10 activity and the immune function of mature DCs.     

International trade drives biodiversity threats in developing nations

Human activities are causing Earth's sixth major extinction event-an accelerating decline of the world's stocks of biological diversity at rates 100 to 1,000 times pre-human levels. Historically, low-impact intrusion into species habitats arose from local demands for food, fuel and living space. However, in today's increasingly globalized economy, international trade chains accelerate habitat degradation far removed from the place of consumption. Although adverse effects of economic prosperity and economic inequality have been confirmed, the importance of international trade as a driver of threats to species is poorly understood. Here we show that a significant number of species are threatened as a result of international trade along complex routes, and that, in particular, consumers in developed countries cause threats to species through their demand of commodities that are ultimately produced in developing countries. We linked 25,000 Animalia species threat records from the International Union for Conservation of Nature Red List to more than 15,000 commodities produced in 187 countries and evaluated more than 5?billion supply chains in terms of their biodiversity impacts. Excluding invasive species, we found that 30% of global species threats are due to international trade. In many developed countries, the consumption of imported coffee, tea, sugar, textiles, fish and other manufactured items causes a biodiversity footprint that is larger abroad than at home. Our results emphasize the importance of examining biodiversity loss as a global systemic phenomenon, instead of looking at the degrading or polluting producers in isolation. We anticipate that our findings will facilitate better regulation, sustainable supply-chain certification and consumer product labelling.     

A mechanical explanation of RNA pseudoknot function in programmed ribosomal frameshifting

The triplet-based genetic code requires that translating ribosomes maintain the reading frame of a messenger RNA faithfully to ensure correct protein synthesis. However, in programmed -1 ribosomal frameshifting, a specific subversion of frame maintenance takes place, wherein the ribosome is forced to shift one nucleotide backwards into an overlapping reading frame and to translate an entirely new sequence of amino acids. This process is indispensable in the replication of numerous viral pathogens, including HIV and the coronavirus associated with severe acute respiratory syndrome, and is also exploited in the expression of several cellular genes. Frameshifting is promoted by an mRNA signal composed of two essential elements: a heptanucleotide 'slippery' sequence and an adjacent mRNA secondary structure, most often an mRNA pseudoknot. How these components operate together to manipulate the ribosome is unknown. Here we describe the observation of a ribosome-mRNA pseudoknot complex that is stalled in the process of -1 frameshifting. Cryoelectron microscopic imaging of purified mammalian 80S ribosomes from rabbit reticulocytes paused at a coronavirus pseudoknot reveals an intermediate of the frameshifting process. From this it can be seen how the pseudoknot interacts with the ribosome to block the mRNA entrance channel, compromising the translocation process and leading to a spring-like deformation of the P-site transfer RNA. In addition, we identify movements of the likely eukaryotic ribosomal helicase and confirm a direct interaction between the translocase eEF2 and the P-site tRNA. Together, the structural changes provide a mechanical explanation of how the pseudoknot manipulates the ribosome into a different reading frame.