Going rogue

The problem of ‘rogue taxa’ explored by Buenaventura et al. (2017, Cladistics 33 : 109–133) is due to complementary patterns of missing data in their matrix, which are evident from perusal of their supplementary table S1.     

Capturing pluripotency

In this Essay, we argue that pluripotent epiblast founder cells in the embryo and embryonic stem (ES) cells in culture represent the ground state for a mammalian cell, signified by freedom from developmental specification or epigenetic restriction and capacity for autonomous self-replication. We speculate that cell-to-cell variation may be integral to the ES cell condition, safe-guarding self-renewal while continually presenting opportunities for lineage specification.     

Comments on detecting rogue taxa using RogueNaRok

Rogues are relatively unstable taxa in phylogenetic analyses that are of concern if they obfuscate relationships, or support for relationships, of interest among more stable taxa. RogueNaRok is a recently developed heuristic solution to the problem of identifying rogue taxa. We illustrate the performance of RogueNaRok with simple examples designed to clarify its behaviour. We argue that the optimality criterion currently used by RogueNaRok may sometimes be poorly suited to the task of detecting rogues and that the scores reported by RogueNaRok should not be interpreted as measures of taxon instability. We suggest how RogueNaRok might be enhanced and recommend that it not be relied upon exclusively for detecting rogues.     

Capturing Nature's Diversity

Natural products are universally recognized to contribute valuable chemical diversity to the design of molecular screening libraries. The analysis undertaken in this work, provides a foundation for the generation of fragment screening libraries that capture the diverse range of molecular recognition building blocks embedded within natural products. Physicochemical properties were used to select fragment-sized natural products from a database of known natural products (Dictionary of Natural Products). PCA analysis was used to illustrate the positioning of the fragment subset within the property space of the non-fragment sized natural products in the dataset. Structural diversity was analysed by three distinct methods: atom function analysis, using pharmacophore fingerprints, atom type analysis, using radial fingerprints, and scaffold analysis. Small pharmacophore triplets, representing the range of chemical features present in natural products that are capable of engaging in molecular interactions with small, contiguous areas of protein binding surfaces, were analysed. We demonstrate that fragment-sized natural products capture more than half of the small pharmacophore triplet diversity observed in non fragment-sized natural product datasets. Atom type analysis using radial fingerprints was represented by a self-organizing map. We examined the structural diversity of non-flat fragment-sized natural product scaffolds, rich in sp3 configured centres. From these results we demonstrate that 2-ring fragment-sized natural products effectively balance the opposing characteristics of minimal complexity and broad structural diversity when compared to the larger, more complex fragment-like natural products. These naturally-derived fragments could be used as the starting point for the generation of a highly diverse library with the scope for further medicinal chemistry elaboration due to their minimal structural complexity. This study highlights the possibility to capture a high proportion of the individual molecular interaction motifs embedded within natural products using a fragment screening library spanning 422 structural clusters and comprised of approximately 2800 natural products.     

Capturing the uncultivated majority

The metagenomic analysis of environmental microbial communities continues to be a rapidly developing area of study. DNA isolation, the first step in capturing the uncultivated majority, has seen many advances in recent years. Protocols have been developed to distinguish DNA from live versus dead cells and to separate extracellular from intracellular DNA. Looking to increase our understanding of the role that members of a microbial community play in ecological processes, several techniques have been developed that are enabling greater in-depth analysis of environmental metagenomes. These include the development of environmental gene tags and the serial analysis of 16S rRNA gene sequence tags. In addition, new screening methods have been designed to select for specific functional genes within metagenomic libraries. Finally, new cultivation methods continue to be developed to improve our ability to capture a greater diversity of microorganisms within the environment.     

Capturing Cardiogenesis in Gastruloids

1. Download : Download high-res image (146KB)
2. Download : Download full-size image

     

Capturing ER calcium dynamics

The lumen of the endoplasmic reticulum (ER) contributes to the dynamics of Ca(2+) signaling by acting as a source or sink of signal Ca(2+). Despite its relevance for the understanding of the cell biology and pathophysiology of the luminal calcium store, the direct measurement of luminal Ca(2+) release and uptake is still critical when Ca(2+) homeostasis is analyzed in neural cells. For the analysis of Ca(2+)-dependent signaling, synthetic Ca(2+) indicators have become popular. The properties of these indicators allow only limited targeting to subcellular structures such as the ER. Recently, we introduced a new strategy for the targeting of synthetic Ca(2+) indicators to the lumen of the ER. The method, termed Targeted-Esterase-induced Dye loading (TED) is based on the targeted recombinant expression of a high carboxylesterase (CES) activity in the lumen of the ER, which is needed to trap synthetic indicators. The method combines the selectivity of protein targeting with the biochemical advantages of low-affinity synthetic Ca(2+) indicators. TED permits direct and non-disruptive measurement and imaging of Ca(2+)-store dynamics. Here, we summarize major topics in the cell biology of ER Ca(2+) signaling and discuss the perspectives of the TED method for the morphological and physiological analysis of temporal and spatial Ca(2+)-dynamics in neural cells.     

Capturing intrinsic nanomechanics of allostery

The Hsp70 chaperone exploits allosteric communication between its substrate binding domain and its nucleotide binding domain to regulate the loading and release of misfolded polypeptides in an ATP-hydrolysis-dependent manner. In this issue of Biophysical Journal, Singh, Rief, and ?oldák report an exquisitely detailed study of the nanomechanical aspects of the allosteric mechanism in DnaK, an Escherichia coli heat shock protein 70 chaperone.     

Capturing a Flavivirus Pre-Fusion Intermediate

During cell entry of flaviviruses, low endosomal pH triggers the rearrangement of the viral surface glycoproteins to a fusion-active state that allows the release of the infectious RNA into the cytoplasm. In this work, West Nile virus was complexed with Fab fragments of the neutralizing mAb E16 and was subsequently exposed to low pH, trapping the virions in a pre-fusion intermediate state. The structure of the complex was studied by cryo-electron microscopy and provides the first structural glimpse of a flavivirus fusion intermediate near physiological conditions. A radial expansion of the outer protein layer of the virion was observed compared to the structure at pH 8. The resulting ∼60 Å-wide shell of low density between lipid bilayer and outer protein layer is likely traversed by the stem region of the E glycoprotein. By using antibody fragments, we have captured a structural intermediate of a virus that likely occurs during cell entry. The trapping of structural transition states by antibody fragments will be applicable for other processes in the flavivirus life cycle and delineating other cellular events that involve conformational rearrangements.     

Ensuring an exit strategy: RTEL1 restricts rogue recombination

Success of homologous recombination-based DNA repair depends not only on recombinases, which promote invasion of the homologous DNA duplex that serves as a template for repair, but also on antirecombinases, which dismantle recombination intermediates to allow completion of repair. In this issue, Barber et al. (2008) identify a previously elusive antirecombinase activity important for maintaining genome stability in animals.     

Capturing biological information with class-responsibility-collaboration cards

SUMMARY: Class-responsibility-collaboration (CRC) cards have been used extensively in the software industry for defining complex object-oriented software requirements. We have adapted this tool to capture information about biological components, collaborators and responsibilities within these collaborations, which is not captured by current annotation tools. CRC cards should provide a common ground that will facilitate communication between biologist and computer scientists. AVAILABILITY: A CRC card template, XML representation and XML schema are freely available at http://people.musc.edu/~zhengw/CRCCard/CRC_Card_Index.html SUPPLEMENTARY INFORMATION: Supplemental Figures 1-4.