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Genes encoding toxin–antitoxin (TA) systems are near ubiquitous in bacterial genomes and they play key roles in important aspects of bacterial physiology, including genomic stability, formation of persister cells under antibiotic stress, and resistance to phage infection. The CptIN locus from Eubacterium rectale is a member of the recently-discovered Type III class of TA systems, defined by a protein toxin suppressed by direct interaction with a structured RNA antitoxin. Here, we present the crystal structure of the CptIN protein–RNA complex to 2.2 Å resolution. The structure reveals a new heterotetrameric quaternary organization for the Type III TA class, and the RNA antitoxin bears a novel structural feature of an extended A-twist motif within the pseudoknot fold. The retention of a conserved ribonuclease active site as well as traits normally associated with TA systems, such as plasmid maintenance, implicates a wider functional role for Type III TA systems. We present evidence for the co-variation of the Type III component pair, highlighting a distinctive evolutionary process in which an enzyme and its substrate co-evolve.

Tulp1 plays a critical role in protein transport from the photoreceptor inner segment (IS) to the outer segment (OS). To dissect which OS protein transport pathways are affected in the absence of Tulp1, we surveyed the localization of proteins destined for the OS in tulp1−/− mice. Immunohistochemistry was used to examine the localization of several classes of OS proteins as well as proteins involved in OS protein transport in young tulp1−/− mice prior to retinal degeneration. Comparisons were made to wild-type littermates. The absence of Tulp1 did not affect the transport of several phototransduction and OS structural proteins including phosphodiesterase, rhodopsin kinase, ROM-1, peripherin/RDS, and the cation channel. However, other phototransduction proteins such as rhodopsin, cone opsins, guanylate cyclase 1, and guanylate cyclase-activating proteins 1 and 2 were mislocalized to additional photoreceptor compartments. Two proteins that translocate in response to light stimulation were affected differently in tulp1−/− retinas; transducin translocated correctly whereas arrestin did not. In addition, chaperone proteins critical in the transport of rhodopsin-containing post-Golgi vesicles, Rab6, Rab8, and Rab11, were severely disrupted in tulp1−/− retinas. We conclude that Tulp1 is required for the correct transport of specific integral membrane proteins and their respective binding partners. Other classes of OS resident proteins do not appear to be affected. These differences support the hypothesis that Tulp1 plays a specific, critical role in photoreceptor OS protein transport pathways.

In this paper we investigate the nature and structure of the relation between imposed classifications and real clustering in a particular case of a scale-free network given by the on-line encyclopedia Wikipedia. We find a statistical similarity in the distributions of community sizes both by using the top-down approach of the categories division present in the archive and in the bottom-up procedure of community detection given by an algorithm based on the spectral properties of the graph. Regardless the statistically similar behaviour the two methods provide a rather different division of the articles, thereby signaling that the nature and presence of power laws is a general feature for these systems and cannot be used as a benchmark to evaluate the suitability of a clustering method., Comment: 5 pages, 3 figures, epl2 style

This thesis deals with advancements made in the field of Electron Paramagnetic Resonance (EPR) for biophysical dosimetry with tooth enamel for accident, emergency and retrospective radiation dose reconstruction. A methodology has been developed to measure retrospective radiation exposures in human tooth enamel. This entails novel sample preparation procedures with minimum mechanical treatment to reduce the preparation induced uncertainties, establish optimum measurement conditions inside the EPR cavity, post process the measured spectrum with functional simulation of dosimetric and other interfering signals, and reconstruct dose. By using this technique, retrospective gamma radiation exposures as low as 80 ± 30 mGy have been successfully deciphered. The notion of dose modifier was introduced in EPR biodosimetry for low dose measurements. It has been demonstrated that by using the modified zero added dose (MZAD) technique for low radiation exposures, doses in the 100 mGy range can be easily reconstructed in teeth which were previously thought useless for EPR dosimetry. Also the use of a dose modifier makes robust dose reconstruction possible for higher radiation exposures. The EPR dosimetry technique was also developed for tooth samples extracted from rodents, which represent small tooth sizing. EPR doses in the molars, extracted from mice irradiated with whole body exposures, were reassessed and shown to be correct within the experimental uncertainty. The sensitivity of human tooth enamel for neutron irradiation, obtained from the 3 MV McMaster K. N. Van de Graaff accelerator, was also studied. For the first time this work has shown that the neutron sensitivity of the tooth enamel is approximately 1/10th of the equivalent gamma sensitivity. Parametric studies for neutron dose rate and neutron energy within the available range of the accelerator, showed no impact on the sensitivity of the tooth enamel. Therefore, tooth enamel can be used as a dosimeter for both neutrons as well as gamma radiation. We will continue experiments to develop this endpoint as a sensitive accident or emergency tool for our response capabilities. Doctor of Philosophy (PhD)