Silencing, Positive Selection and Parallel Evolution: Busy History of Primate Cytochromes c

Cytochrome c (cyt c) participates in two crucial cellular processes, energy production and apoptosis, and unsurprisingly is a highly conserved protein. However, previous studies have reported for the primate lineage (i) loss of the paralogous testis isoform, (ii) an acceleration and then a deceleration of the amino acid replacement rate of the cyt c somatic isoform, and (iii) atypical biochemical behavior of human cyt c. To gain insight into the cause of these major evolutionary events, we have retraced the history of cyt c loci among primates. For testis cyt c, all primate sequences examined carry the same nonsense mutation, which suggests that silencing occurred before the primates diversified. For somatic cyt c, maximum parsimony, maximum likelihood, and Bayesian phylogenetic analyses yielded the same tree topology. The evolutionary analyses show that a fast accumulation of non-synonymous mutations (suggesting positive selection) occurred specifically on the anthropoid lineage root and then continued in parallel on the early catarrhini and platyrrhini stems. Analysis of evolutionary changes using the 3D structure suggests they are focused on the respiratory chain rather than on apoptosis or other cyt c functions. In agreement with previous biochemical studies, our results suggest that silencing of the cyt c testis isoform could be linked with the decrease of primate reproduction rate. Finally, the evolution of cyt c in the two sister anthropoid groups leads us to propose that somatic cyt c evolution may be related both to COX evolution and to the convergent brain and body mass enlargement in these two anthropoid clades

Probabilistic Reconstruction of Ancestral Protein Sequences

Using a maximum-likelihood formalism, we have developed a method with which to reconstruct the sequences of ancestral proteins. Our approach allows the calculation of not only the most probable ancestral sequence but also of the probability of any amino acid at any given node in the evolutionary tree. Because we consider evolution on the amino acid level, we are better able to include effects of evolutionary pressure and take advantage of structural information about the protein through the use of mutation matrices that depend on secondary structure and surface accessibility. The computational complexity of this method scales linearly with the number of homologous proteins used to reconstruct the ancestral sequence.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/42365/1/239-42-2-313_42n2p313.pd

Synthesis, characterization, and hydrolytic degradation of polylactide-functionalized polyoxanorbornenes

This paper describes the synthesis of polylactide-functionalized polyoxanorbornenes and their hydrolytic degradation behavior. Macromonomers with one or two exo-PLA chains as well with two endo,exo chains were prepared using tin(II) 2-ethylhexanoate as a catalyst in the presence of mono- or dialcohol derivatives of oxanorbornene. The well-characterized macromonomers were then subjected to ROMP by first, second, and modified second generation Grubbs ruthenium initiators. Investigation of these graft copolymers by SEC and NMR spectroscopy showed the presence of some uncapped PLA homopolymer, formed as a side product during the ROP of lactide. The degradation behavior showed that the presence of PLA homopolymer impurities in the graft copolymers significantly increases the rate of degradation of the final material. Therefore, a convenient procedure of graft copolymers purification to remove PLA homopolymer from the samples was developed. The degradation studies of graft copolymers with the same oxanorbornyl backbone length and different length of PLA grafts indicated that the degradation rate increased with increasing length of PLA grafts. The degradation behavior of material depends also on configuration of PLA side chains on polyoxanorbornene backbone chain. The fastest degradation was observed in the case of graft copolymers with one exo-PLA side chain

Electrophoretic polymorphisms and their taxonomic implications in Callitrichini (Primates, Platyrrhini)

Wayne State University. School of Medicine. Department of Anatomy and Cell Biology. Detroit, Michigan, US.Wayne State University. School of Medicine. Department of Anatomy and Cell Biology. Detroit, Michigan, US.Universidade Federal do Pará. Departamento de Genetica. Belém, PA, Brazil.Universidade Federal do Pará. Departamento de Genetica. Belém, PA, Brazil.Universidade Federal do Pará. Departamento de Genetica. Belém, PA, Brazil.Centro de Primatologia do Rio de Janeiro. Fundação Estadual de Engenharia do Meio Ambiente. Rio de Janeiro, RJ, Brazil.Centro de Primatologia do Rio de Janeiro. Fundação Estadual de Engenharia do Meio Ambiente. Rio de Janeiro, RJ, Brazil.Ministério da Saúde. Fundação Nacional de Saúde. Instituto Evandro Chagas. Centro Nacional de Primatas. Ananindeua, PA, Brasil.Ministério da Saúde. Fundação Nacional de Saúde. Instituto Evandro Chagas. Centro Nacional de Primatas. Ananindeua, PA, Brasil.Universidade Federal do Pará. Departamento de Genetica. Belém, PA, Brazil.Five hundred forty-three blood samples from 15 populations of the four genera of callitrichin primates were studied electrophoretically. Polymorphism and genetic distances were estimated for 20 loci, 13 of which were polymorphic. The lion tamarin (Leontopithecus) studied here exhibited the least variability for these loci, while the monospecific Cebuella showed the most. The genetic distances observed between Callithrix and Cebuella genera support previous evidence indicating a close taxonomic relationship between them. Genetic distance values obtained in this study also support the synonimyzation of the kuhli form with Callithrix jacchus penicillate

MACHINA, the Movable Accelerator for Cultural Heritage In-situ Non-destructive Analysis: project overview

Over the years, transportable instrumentation for cultural heritage (CH) in situ measurements has noticeably widespread, due to logistic, economical and safety reasons. Ion beam analysis, a powerful set of analytical techniques, of great importance for CH, is instead carried out by using fixed instrumentation. To overcome this limit, the Italian national Institute of Nuclear Physics (INFN), CERN (European Centre for Nuclear Research) and the Opificio delle Pietre Dure (OPD), started MACHINA, the “Movable Accelerator for CH In-situ Non-destructive Analysis: the new generation of accelerators for art” to build a transportable accelerator, compact, with strongly reduced weight, absorbed power and cost. MACHINA will be installed at the OPD and dedicated to CH. It will be moved to major conservation centres and museums, when needed. The INFN-CERN proposal, approved in December 2017, became operative in February 2018. 2018 was dedicated to the acquisition of material/instrumentations, to set up both a dummy accelerator (to test the vacuum system) and a vacuum chamber (to test the source). Due to COVID, in 2020 and 2021 the experimental work was slowed down, but we kept developing the control electronics/software and built the second-generation supporting structure. The HF-RFQ power supplies were integrated in October 2021. At the rise of 2022, after conditioning the cavities, we tested the system and in March 2022 we got the first extracted 2-MeV proton beam. In this paper, we present the structure of the MACHINA system, the approach followed and the main solutions adopted, with a special focus on the control system, and finally the first experimental results