Mechanism of DNA flexibility enhancement by HMGB proteins

The mechanism by which sequence non-specific DNA-binding proteins enhance DNA flexibility is studied by examining complexes of double-stranded DNA with the high mobility group type B proteins HMGB2 (Box A) and HMGB1 (Box A+B) using atomic force microscopy. DNA end-to-end distances and local DNA bend angle distributions are analyzed for protein complexes deposited on a mica surface. For HMGB2 (Box A) binding we find a mean induced DNA bend angle of 78°, with a standard error of 1.3° and a SD of 23°, while HMGB1 (Box A+B) binding gives a mean bend angle of 67°, with a standard error of 1.3° and a SD of 21°. These results are consistent with analysis of the observed global persistence length changes derived from end-to-end distance measurements, and with results of DNA-stretching experiments. The moderately broad distributions of bend angles induced by both proteins are inconsistent with either a static kink model, or a purely flexible hinge model for DNA distortion by protein binding. Therefore, the mechanism by which HMGB proteins enhance the flexibility of DNA must differ from that of the Escherichia coli HU protein, which in previous studies showed a flat angle distribution consistent with a flexible hinge model.     

Evaluating molecular support for and against the monophyly of the Peritrichia and phylogenetic relationships within the Mobilida (Ciliophora,Oligohymenophorea)

Zhan, Z., Xu, K. & Dunthorn, M. (2012). Evaluating molecular support for and against the monophyly of the Peritrichia and phylogenetic relationships within the Mobilida (Ciliophora, Oligohymenophorea). —Zoologica Scripta,00, 000–000. An ongoing debate in ciliate molecular phylogenetic analyses is whether the Peritrichia – composed of the Sessilida and the Mobilida – are monophyletic. To further investigate this group, here we increase taxon sampling with four further mobilids: Trichodinella sp., Trichodina pectenis, Urceolaria serpularum and Urceolaria korschelti. Results show that support for and against monophyly of the peritrichs depends on different methods of alignment, and different methods of masking ambiguously aligned nucleotide positions. Results from constrained analyses also are dependent on different alignment and masking methods. We propose that there is no well‐supported SSU‐rDNA evidence supporting for and against the removal of the mobilids from the peritrichs. Within the Mobilida, we find that Trichodinella nest within Trichodina, Urceolaria branch basally, and Trichodina are non‐monophyletic, and suggest that Leiotrocha be formally transferred into Urceolaria. In addition, the data support that Urceolaria‐like denticles and Urceolaria‐/Trichodina‐like adoral ciliary spiral are plesiomorphic conditions within the mobilids.     

The paradox of black patriotism: double consciousness

This study explores the double consciousness of black American patriotism in the modern era marked by publicized police killings of blacks, widespread antiracism protests, and concern for racially motivated violence. This analysis provides timely ethnographic insights into black identities that vividly captures black voices; fuses classical and contemporary race theories and extends them into the literature on patriotism; and proposes a model for understanding how double consciousness is negotiated in personal identity construction. I conducted twenty-two in-depth interviews of black Americans. I explored three questions: (1) how they interpret patriotism; (2) whether their interpretations affirm or defy their black identity; and (3) how tensions between race and nation manifest in their patriotic identity development. Many denounced hegemonic patriotism and constructed alternative patriotic brands. These brands are situated on an “Axis of Identities”, which is comprised of four profiles: the bystander, the sycophant, the subverter, and the conscious patriot.