Klee sets and Chebyshev centers for the right Bregman distance

We systematically investigate the farthest distance function, farthest points, Klee sets, and Chebyshev centers, with respect to Bregman distances induced by Legendre functions. These objects are of considerable interest in Information Geometry and Machine Learning; when the Legendre function is specialized to the energy, one obtains classical notions from Approximation Theory and Convex Analysis. The contribution of this paper is twofold. First, we provide an affirmative answer to a recently-posed question on whether or not every Klee set with respect to the right Bregman distance is a singleton. Second, we prove uniqueness of the Chebyshev center and we present a characterization that relates to previous works by Garkavi, by Klee, and by Nielsen and Nock.Comment: 23 pages, 2 figures, 14 image

Three-dimensional structure of a type III glutamine synthetase by single-particle reconstruction

GlnN, the type III glutamine synthetase (GSIII) from the medically important, anaerobic, opportunistic pathogen Bacteroides fragilis, has 82.8 kDa subunits that share only 9% sequence identity with the type I glutamine synthetases (GSI), the only family for which a structure is known. Active GlnN was found predominantly in a single peak that eluted from a calibrated gel-filtration chromatography column at a position equaivalent to 0.86(±0.08) MDa. Negative-stain electron microscopy enabled the identification of double-ringed particles and single hexameric rings (“pinwheels”) resulting from partial staining. A 2D average of these pinwheels showed marked similarity to the corresponding structures found in preparations of GSI, except that the arms of the subunits were 40% longer. Reconstructions from particles embedded in vitreous ice showed that GlnN has a double-ringed, dodecameric structure with a 6-fold dihedral space group (D6) symmetry and dimensions of 17.0 nm parallel with the 6-fold axis and 18.3 nm parallel with the 2-fold axes. The structures, combined with a sequence alignment based on structural principles, showed how many aspects of the structure of GSI, and most notably the α/β barrel fold active site were preserved. There was evidence for the presence of this structure in the reconstructed volume, thus, identifying the indentations between the pinwheel spokes as putative active sites and suggesting conservation of the overall molecular geometry found in GSI despite their low level of global homology. Furthermore, docking of GSI into the reconstruction left sufficient plausibly located unoccupied density to account for the additional residues in GSIII, thus validating the structure

Probing an Interfacial Surface in the Cyanide Dihydratase from Bacillus pumilus, A Spiral Forming Nitrilase

Nitrilases are of significant interest both due to their potential for industrial production of valuable products as well as degradation of hazardous nitrile-containing wastes. All known functional members of the nitrilase superfamily have an underlying dimer structure. The true nitrilases expand upon this basic dimer and form large spiral or helical homo-oligomers. The formation of this larger structure is linked to both the activity and substrate specificity of these nitrilases. The sequences of the spiral nitrilases differ from the non-spiral forming homologs by the presence of two insertion regions. Homology modeling suggests that these regions are responsible for associating the nitrilase dimers into the oligomer. Here we used cysteine scanning across these two regions, in the spiral forming nitrilase cyanide dihydratase from Bacillus pumilus (CynD), to identify residues altering the oligomeric state or activity of the nitrilase. Several mutations were found to cause changes to the size of the oligomer as well as reduction in activity. Additionally one mutation, R67C, caused a partial defect in oligomerization with the accumulation of smaller oligomer variants. These results support the hypothesis that these insertion regions contribute to the unique quaternary structure of the spiral microbial nitrilases

Probing C-terminal interactions of the Pseudomonas stutzeri cyanide-degrading CynD protein

The cyanide dihydratases from Bacillus pumilus and Pseudomonas stutzeri share high amino acid sequence similarity throughout except for their highly divergent C-termini. However, deletion or exchange of the C-termini had different effects upon each enzyme. Here we extended previous studies and investigated how the C-terminus affects the activity and stability of three nitrilases, the cyanide dihydratases from B. pumilus (CynDpum) and P. stutzeri (CynDstut) and the cyanide hydratase from Neurospora crassa. Enzymes in which the C-terminal residues were deleted decreased in both activity and thermostability with increasing deletion lengths. However, CynDstut was more sensitive to such truncation than the other two enzymes. A domain of the P. stutzeri CynDstut C-terminus not found in the other enzymes, 306GERDST311, was shown to be necessary for functionality and explains the inactivity of the previously described CynDstut-pum hybrid. This suggests that the B. pumilus C-terminus, which lacks this motif, may have specific interactions elsewhere in the protein, preventing it from acting in trans on a heterologous CynD protein. We identify the dimerization interface A-surface region 195–206 (A2) from CynDpum as this interaction site. However, this A2 region did not rescue activity in C-terminally truncated CynDstutΔ302 or enhance the activity of full-length CynDstut and therefore does not act as a general stability motif

Fate of haem iron in the malaria parasite Plasmodium falciparum.

Chemical analysis has shown that Plasmodium falciparum trophozoites contain 61+/-2% of the iron within parasitized erythrocytes, of which 92+/-6% is located within the food vacuole. Of this, 88+/-9% is in the form of haemozoin. (57)Fe-Mössbauer spectroscopy shows that haemozoin is the only detectable iron species in trophozoites. Electron spectroscopic imaging confirms this conclusion

Reproducibly sampling SARS-CoV-2 genomes across time, geography, and viral diversity

The COVID-19 pandemic has led to a rapid accumulation of SARS-CoV-2 genomes, enabling genomic epidemiology on local and global scales. Collections of genomes from resources such as GISAID must be subsampled to enable computationally feasible phylogenetic and other analyses. We present genome-sampler, a software package that supports sampling collections of viral genomes across multiple axes including time of genome isolation, location of genome isolation, and viral diversity. The software is modular in design so that these or future sampling approaches can be applied independently and combined (or replaced with a random sampling approach) to facilitate custom workflows and benchmarking. genome-sampler is written as a QIIME 2 plugin, ensuring that its application is fully reproducible through QIIME 2’s unique retrospective data provenance tracking system. genome-sampler can be installed in a conda environment on macOS or Linux systems. A complete default pipeline is available through a Snakemake workflow, so subsampling can be achieved using a single command. genome-sampler is open source, free for all to use, and available at https://caporasolab.us/genome-sampler. We hope that this will facilitate SARS-CoV-2 research and support evaluation of viral genome sampling approaches for genomic epidemiology.ISSN:2046-140

Subjetividade e crítica cultural

Nos muitos trabalhos que tentam resgatar "o ator" em algum sentido, existe uma tendência a evitar questões de subjetividade, ou seja, "estruturas de sentimento" complexas (na expressão de Raymond Williams). Este artigo retorna ao trabalho de Max Weber e Clifford Geertz para considerar várias questões de subjetividade, incluindo tanto ansiedades existenciais fundamentais como construções sociais e históricas específicas de "consciência". O artigo conclui com uma releitura de vários textos recentes sobre a consciência pós-moderna como uma configuração específica de ansiedades, ligadas a formações do "capitalismo tardio".<br>In the many works that try to bring back 'the actor' in some sense, there is a tendency to avoid questions of subjectivity, that is, complex 'structures of feeling' (in Raymond Williams's phrase). This article returns to the work of Max Weber and Clifford Geertz to consider various issues of subjectivity, including both fundamental existential anxieties, and specific cultural and historical constructions of 'consciousness'. The article concludes with a rereading of several recent texts on postmodern consciousness as a specific configuration of anxieties, tied in turn to formations of 'late capitalism'