Mathematical modeling and comparison of protein size distribution in different plant, animal, fungal and microbial species reveals a negative correlation between protein size and protein number, thus providing insight into the evolution of proteomes

<p>Abstract</p> <p>Background</p> <p>The sizes of proteins are relevant to their biochemical structure and for their biological function. The statistical distribution of protein lengths across a diverse set of taxa can provide hints about the evolution of proteomes.</p> <p>Results</p> <p>Using the full genomic sequences of over 1,302 prokaryotic and 140 eukaryotic species two datasets containing 1.2 and 6.1 million proteins were generated and analyzed statistically. The lengthwise distribution of proteins can be roughly described with a gamma type or log-normal model, depending on the species. However the shape parameter of the gamma model has not a fixed value of 2, as previously suggested, but varies between 1.5 and 3 in different species. A gamma model with unrestricted shape parameter described best the distributions in ~48% of the species, whereas the log-normal distribution described better the observed protein sizes in 42% of the species. The gamma restricted function and the sum of exponentials distribution had a better fitting in only ~5% of the species. Eukaryotic proteins have an average size of 472 aa, whereas bacterial (320 aa) and archaeal (283 aa) proteins are significantly smaller (33-40% on average). Average protein sizes in different phylogenetic groups were: Alveolata (628 aa), Amoebozoa (533 aa), Fornicata (543 aa), Placozoa (453 aa), Eumetazoa (486 aa), Fungi (487 aa), Stramenopila (486 aa), Viridiplantae (392 aa). Amino acid composition is biased according to protein size. Protein length correlated negatively with %C, %M, %K, %F, %R, %W, %Y and positively with %D, %E, %Q, %S and %T. Prokaryotic proteins had a different protein size bias for %E, %G, %K and %M as compared to eukaryotes.</p> <p>Conclusions</p> <p>Mathematical modeling of protein length empirical distributions can be used to asses the quality of small ORFs annotation in genomic releases (detection of too many false positive small ORFs). There is a negative correlation between average protein size and total number of proteins among eukaryotes but not in prokaryotes. The %GC content is positively correlated to total protein number and protein size in prokaryotes but not in eukaryotes. Small proteins have a different amino acid bias than larger proteins. Compared to prokaryotic species, the evolution of eukaryotic proteomes was characterized by increased protein number (massive gene duplication) and substantial changes of protein size (domain addition/subtraction).</p

Stigma Diversity in Tropical Legumes with Considerations on Stigma Classification

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)The great stigma diversity in angiosperms implies a choice of criteria for stigma classification, which nowadays is characterized as dry (= little or no secretory surface and exudate retained by the cuticle and/or protein pellicle), wet (= conspicuous secretory surface, abundant in fluid exudate) and semidry (exudate retained by cuticle and/or protein pellicle). Despite being a very species-rich family, whose representatives exhibit a wide floral variation, no comparative studies of stigma diversity have been done for the whole Leguminosae. In order to assess the stigma morphological diversity in legumes and to evaluate the criteria used in the main classifications of the stigma, we compared the stigma morphology in 15 distinct legume lineages. In addition, we evaluated the stigma classification in other 152 legume species whose morphology was already described in the literature. Stigmas were removed from floral buds and flowers and processed for analyses under scanning electron and light microscopes. The stigma of the study legumes exhibits quite variable morphology, mainly concerning the diameter, the occurrence of an orifice or a furrow, the coating, the cellular composition, and the occurrence, chemical nature and release mechanism of the exudate. This diversity appears to be related mainly to the evolutionary history of the group and also to the selective pressures exerted by different types of pollen and pollinator. More conflicting criteria for stigma classification lie in defining the semidry type, found mostly in papilionoids. For better stigma classification we suggest that stigma morphology be evaluated at the time prior to anthesis, when the cuticle is not yet broken and the exudate is not exposed or drained. In addition, several techniques should be employed for a better classification.801129Fundacao de Amparao a Pesquisa do Estado de Sao Paulo [2002/11834-5, 2008/57487-0, 2009/01057-0]Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)Fundacao de Amparao a Pesquisa do Estado de Sao Paulo [2002/11834-5, 2008/57487-0, 2009/01057-0]CNPq [142876/2008-9, 301960/2009-7, 152759/2010-7

Histopathological analysis of corticosteroid-antibiotic preparation and propolis paste formulation as intracanal medication after pulpectomy: an in vivo study

Intracanal medication in pulpectomy therapy is used between appointments with the objective of reducing pain and inflammatory processes in pulp and periapical tissues. Propolis has been known as a natural antibiotic and has been subject of medical and dental research due to its therapeutic properties such as antibiotic, analgesic and anti-inflammatory effects. OBJECTIVE: The aim was to carry out an in vivo evaluation of the periapical tissue response to propolis paste when used as an intracanal medication in the teeth of dogs after pulpectomy. MATERIAL AND METHODS: 72 dog's incisors were selected for the experiment. After biomechanical preparation the root canal was filled with a corticosteroid-antibiotic preparation, experimental propolis paste, non-medicament (negative control) or non-pulpectomy at all (positive control). The medications were left inside the root canal for 7, 14 or 28 days. At the end of the experimental period histological sections were prepared and all laboratories processes for Harris hematoxylin and eosin staining was proceeded followed by the analysis using an optical microscope. Sections were classified according to a score representing the inflammatory events observed: the presence of polymorphonuclear neutrophils, polymorphonuclear eosinophils, lymphocytes and plasma cells, macrophages and/or giant cells, fibrous condensation and abscesses. RESULTS: There were statistically significant differences between the tissue reactions caused by the two substances being tested, after different experimental periods, with the periapical tissue that was in contact with propolis paste exhibiting fewer inflammatory reactions in comparison to corticosteroid-antibiotic preparation. CONCLUSIONS: The low tissue responses from propolis paste suggest that this material could be considered as an option for root canal medication after pulpectomy

The effect of cyclic torsion on the dislocation structure of drawn mild steel

Cold forming is usually associated with the "work hardening" of the material being formed. The work hardening behavior of metals subject to complex processing paths is different from that in monotonic deformation. The results show that, after some initial hardening, there is a possibility that further deformation will cause softening in the material ("work softening"). Recent work showed that cyclic torsion applied to drawn products causes changes in the subsequent tensile behavior of low carbon steel, and that the effect will depend on the previous "history" of the material. For annealed samples, the cyclic torsion leads to an increase in the yield strength, but does not affect the tensile strength and elongation. For the case of previously drawn bars, the cyclic deformation caused a decrease in the yield and tensile strength and an increase in the total elongation. The present paper discusses the dislocation structure changes associated with different strain paths in mild steel