On the Breeds of Cattle—Historic and Current Classifications

Classification of cattle breeds contributes to our understanding of the history of cattle and is essential for an effective conservation of genetic diversity. Here we review the various classifications over the last two centuries and compare the most recent classifications with genetic data. The classifications devised during the 19th to the late 20th century were in line with the Linnaean taxonomy and emphasized cranial or horn morphology. Subsequent classifications were based on coat color, geographic origin or molecular markers. Several theories were developed that linked breed characteristics either to a supposed ancestral aurochs subspecies or to a presumed ethnic origin. Most of the older classifications have now been discarded, but have introduced several Latin terms that are still in use. The most consistent classification was proposed in 1995 by Felius and emphasizes the geographic origin of breeds. This is largely in agreement with the breed clusters indicated by a biochemical and molecular genetic analysis, which reflect either groups of breeds with a common geographic origin or single breeds that have expanded by export and/or crossbreeding. We propose that this information is also relevant for managing the genetic diversity of cattl

Come back Marshall, all is forgiven? : Complexity, evolution, mathematics and Marshallian exceptionalism

Marshall was the great synthesiser of neoclassical economics. Yet with his qualified assumption of self-interest, his emphasis on variation in economic evolution and his cautious attitude to the use of mathematics, Marshall differs fundamentally from other leading neoclassical contemporaries. Metaphors inspire more specific analogies and ontological assumptions, and Marshall used the guiding metaphor of Spencerian evolution. But unfortunately, the further development of a Marshallian evolutionary approach was undermined in part by theoretical problems within Spencer's theory. Yet some things can be salvaged from the Marshallian evolutionary vision. They may even be placed in a more viable Darwinian framework.Peer reviewedFinal Accepted Versio

Identification of fossil worm tubes from Phanerozoic hydrothermal vents and cold seeps

One of the main limitations to understanding the evolutionary history of hydrothermal vent and cold seep communities is the identification of tube fossils from ancient deposits. Tube-dwelling annelids are some of the most conspicuous inhabitants of modern vent and seep ecosystems, and ancient vent and seep tubular fossils are usually considered to have been made by annelids. However, the taxonomic affinities of many tube fossils from vents and seeps are contentious, or have remained largely undetermined due to difficulties in identification. In this study, we make a detailed chemical (Fourier-transform infrared spectroscopy and pyrolysis gas-chromatography mass-spectrometry) and morphological assessment of modern annelid tubes from six families, and fossil tubes (seven tube types from the Cenozoic, 12 Mesozoic and four Palaeozoic) from hydrothermal vent and cold seep environments. Characters identified from these investigations were used to explore for the first time the systematics of ancient vent and seep tubes within a cladistic framework. Results reveal details of the compositions and ultrastructures of modern tubes, and also suggest that two types of tubes from ancient vent localities were made by the annelid family Siboglinidae, which often dominates modern vents and seeps. Our results also highlight that several vent and seep tube fossils formerly thought to have been made by annelids cannot be assigned an annelid affiliation with any certainty. The findings overall improve the level of quality control with regard to interpretations of fossil tubes, and, most importantly, suggest that siboglinids likely occupied Mesozoic vents and seeps, greatly increasing the minimum age of the clade relative to earlier molecular estimates

Taxonomic surrogacy in biodiversity assessments, and the meaning of Linnaean ranks

Copyright © 2006 The Natural History MuseumThe majority of biodiversity assessments use species as the base unit. Recently, a series of studies have suggested replacing numbers of species with higher ranked taxa (genera, families, etc.); a method known as taxonomic surrogacy that has an important potential to save time and resources in assesments of biological diversity. We examine the relationships between taxa and ranks, and suggest that species/higher taxon exchanges are founded on misconceptions about the properties of Linnaean classification. Rank allocations in current classifications constitute a heterogeneous mixture of various historical and contemporary views. Even if all taxa were monophyletic, those referred to the same rank would simply denote separate clades without further equivalence. We conclude that they are no more comparable than any other, non-nested taxa, such as, for example, the genus Rattus and the phylum Arthropoda, and that taxonomic surrogacy lacks justification. These problems are also illustrated with data of polychaetous annelid worms from a broad-scale study of benthic biodiversity and species distributions in the Irish Sea. A recent consensus phylogeny for polychaetes is used to provide three different family-level classifications of polychaetes. We use families as a surrogate for species, and present Shannon–Wiener diversity indices for the different sites and the three different classifications, showing how the diversity measures rely on subjective rank allocations.Y. Bertrand, F. Pleijel and G. W. Rous

Polyphyly and hidden species among Hawaiʻi’s dominant mesophotic coral genera, Leptoseris and Pavona (Scleractinia: Agariciidae)

Widespread polyphyly in stony corals (order Scleractinia) has prompted efforts to revise their systematics through approaches that integrate molecular and micromorphological evidence. To date, these approaches have not been comprehensively applied to the dominant genera in mesophotic coral ecosystems (MCEs) because several species in these genera occur primarily at depths that are poorly explored and from which sample collections are limited. This study is the first integrated morphological and molecular systematic analysis of the genera Leptoseris and Pavona to examine material both from shallow-water reefs (<30 m) and from mid- to lower-MCEs (>60 m). Skeletal and tissue samples were collected throughout the Hawaiian Archipelago between 2–127 m. A novel mitochondrial marker (cox1-1-rRNA intron) was sequenced for 70 colonies, and the micromorphologies of 94 skeletons, plus selected type material, were analyzed. The cox1-1-rRNA intron resolved 8 clades, yet Leptoseris and Pavona were polyphyletic. Skeletal micromorphology, especially costal ornamentation, showed strong correspondence and discrete differences between mitochondrial groups. One putative new Leptoseris species was identified and the global depth range of the genus Pavona was extended to 89 m, suggesting that the diversity of mesophotic scleractinians has been underestimated. Examination of species’ depth distributions revealed a pattern of depth zonation: Species common in shallow-water were absent or rare >40 m, whereas others occurred only >60 m. These patterns emphasize the importance of integrated systematic analyses and more comprehensive sampling by depth in assessing the connectivity and diversity of MCEs

Estudo fitoquímico e atividade leishmanicida in vitro do extrato bruto de Arrabidaea chica (Humb. & Bonpl.) Verlot

73 f. Dissertação (Mestrado em Ciência Animal) – Universidade Estadual do Maranhão, São Luís, 2012. Orientadora: Profa. D. Sc. Ana Lucia Abreu Silva.O tratamento para as leishmanioses instituído há mais de cem anos dispõe de poucas drogas, e estas devem ser avaliadas quanto à toxicidade e efeitos adversos ao paciente, com alguns casos de resistência já relatados. A diversidade química e a imensa gama de bioagentes derivados de plantas levou à criação de centenas de drogas farmacêuticas, muitas, inclusive, possuem atividade leishmanicida. A Arrabidaea chica, conhecida como pariri possui diversos metabólitos ativos com propriedades antiinflamatórias, adstringentes e terapêuticas. Este trabalho realizou o estudo fitoquímico e a avaliação atividade leishmanicida in vitro do extrato bruto de Arrabidaea chica. Os extratos brutos das folhas e do caule de Arrabidaea chica (Humb. & Bonpl.) Verlot tiveram rendimento de 59,2% e 3,33%, respectivamente. A prospecção fitoquímica preliminar mostrou que os extratos possuem flavonóides, compostos fenólicos, taninos, antocianinas e chalconas. O extrato das folhas da Arrabidaea chica (Humb. & Bonpl.) Verlot demonstrou atividade contra formas promastigota na dosagem de 500 μg/ml. O extrato bruto de Arrabidaea chica (Humb. & Bonpl.) Verlot apresentou citotoxicidade na concentração de 189,9 μg/mL. O extrato bruto das folhas da Arrabidaea chica é ativo contra formas promastigotas de L amazonensis em modelo in vitro e promissor para novas pesquisas de opções terapêuticas para leishmaniose

Study of clinical, histopathological profile and search for protein markers associated with the progression from Proliferative Verrucous Leukoplakia to Squamous Cell Carcinoma

Orientadores: Adriana Franco Paes Leme, Márcio Ajudarte LopesDissertação (mestrado) - Universidade Estadual de Campinas, Faculdade de Odontologia de PiracicabaResumo: Segundo a Organização Mundial da Saúde (OMS), as leucoplasias orais (LO) são definidas clinicamente como placas brancas não removíveis à raspagem e que não podem ser definidas como qualquer outra doença. Já a leucoplasia verrucosa proliferativa (LVP), um subtipo de LO, apresenta um perfil epidemiológico diferente, não ligado a hábitos de fumo ou etilismo e apresenta altos índices de recorrência. A progressão de LO e LVP para carcinoma espinocelular (CEC) é de aproximadamente 2% e maior que 70%, respectivamente. A grande preocupação da progressão é que o CEC apresenta taxa de sobrevida de casos avançados de aproximadamente 50% em 5 anos após o diagnóstico, e corresponde a 90% dos tumores malignos de cavidade oral. Além disso, de acordo com o GLOBOCAN 2018, o CEC está entre os 10 tumores com maior incidência no mundo. Dessa forma, torna-se fundamental conhecer os marcadores que possam ajudar predizer a transformação maligna na prática clínica. Para isso, nesse estudo avaliou a abundância das proteínas na saliva por proteômica baseada em descoberta, cujo fluido é promissor como fonte de marcadores por não ser invasivo e estar em contato direto com as lesões. Foi realizada a coleta de saliva dos pacientes, divididos em quatro condições de acordo com o tipo de lesão, LO (N=16), LVP (N=13) e CEC (N=14) e, grupo controle (CO, N=15). Em resumo, as proteínas de cada amostra foram submetidas aos passos de i) quantificação, ii) precipitação, iii) redução, alquilação e digestão com tripsina e LysC, iv) marcação dos peptídeos com etiquetas contendo 10 diferentes reagentes isóbaros que permitem a quantificação relativa por meio de íons repórteres únicos e v) injeção e aquisição dos dados no equipamento Q Exactive HF-X acoplado ao sistema de cromatografia líquida. Os arquivos brutos foram submetidos às buscas no programa Proteome Discoverer 2.2 e analisados no programa Scaffold 4.8.7. As análises estatísticas foram realizadas no Perseus 1.6, o enriquecimento dos processos biológicos no Enrichr e a correlação com dados clínicos públicos no PROGgeneV2. Os resultados indicam a identificação e quantificação de 319 proteínas na saliva. Trinta e sete proteínas são estatisticamente significantes entre todas as condições, sendo 13 proteínas diferencialmente abundantes entre CO e CEC e 18 entre LO e CEC, três proteínas foram exclusivas do grupo CO e quatro exclusivas entre LVP e CEC. Das 37 proteínas, doze proteínas tiveram associação entre a expressão gênica em carcinoma de cabeça e pescoço com o baixo prognóstico em sobrevida geral, sobrevida livre de metástase e sobrevida livre de recorrência. Em conclusão, esse estudo indica que proteínas da saliva apresentam potencial de predizer a transformação maligna. Destaca-se as proteínas alfa-2-macroglobulina, moesina e receptor polimérico de imunoglobulina (CO e CEC) como candidatas a marcadoras de malignização, pois são diferencialmente abundantes entre CO e CEC e nos grupos LO e LVP apresentam uma abundância intermediária. O próximo passo desse projeto é a verificação dos candidatos em saliva por proteômica dirigida e em imunohistoquímica das lesões em um coorte independente de pacientesAbstract: According to the World Health Organization (WHO), Oral Leukoplakias (OL) are clinically defined as irremovable onto scraping white plaques, which cannot be defined as any other lesion. Proliferative Verrucous Leukoplakia (PVL) is a subtype of OL which has a different epidemiological profile, not related to smoking or drinking habits and presents high rates of recurrence. The progression of OL and PVL into Oral Squamous Cell Carcinoma (OSCC) are about 2% and higher than 70%, respectively. The major concern from this progression is that the OSCC survival rate is still about 50% in 5 years after the diagnosis for advanced cases, and corresponds to 90% of malignant tumors of oral cavity. According to GLOBOCAN 2018, it is amongst the 10 most incident tumors in the world. Thus, the knowledge of potential markers that can anticipate the malignant transformation in the clinical routine is needed. For that, this study analyzed the abundance of proteins in saliva through discovery-based proteomics, this fluid is a promising source of markers for not being invasive and having direct contact with the lesions. The saliva was collected from the patients divided in four conditions according to each lesion, OL (N=16), PVL (N=13), OSCC (N=14) and control group (CO), (N=15). Briefly, the proteins of each group were submitted to: i) quantification, ii) precipitation, iii) reduction, alkylation and digestion with trypsin and LysC, iv) peptide tagging with 10 different isobaric tags that allows relative quantification through unique reporter ions and v) injection and data acquisition on a Q Exactive HF-X coupled to liquid chromatography system. Raw files were submitted to Proteome Discoverer 2.2 and Scaffold 4.8.7. This statistical analysis was performed in Perseus 1.6, the enrichment of biological processes in Enrichr and the correlation with public clinical data in PROGgeneV2. Results show the identification and quantification of 319 proteins in saliva. Thirdy-seven proteins are statistically significant amongst all conditions and 3 are exclusive of CO group and 4 are exclusive between PVL and OSCC, 13 proteins were differentially abundant between CO and OSCC and 18 between OL and OSCC. From 37 proteins, twelve showed association between the gene expression in HNSCC and poor prognosis in overall survival rate, metastasis free survival rate and relapse free survival rate. In conclusion, this study indicates that saliva proteins have potential to predict malignant transformation. We highlight the proteins alfa-2-macroglobulin, moesin and polymeric imunoglobulin receptor as candidate markers in malignant transformation, considering they are diferentially abundant in CO and OSCC and have an intermediary abundancy in OL and PVL. The next step of this project will be to verify these candidates in saliva through targeted proteomics and immunohistochemistry of lesions in an independent patient cohortMestradoPatologiaMestra em EstomatopatologiaCAPE

Contemplating an evolutionary approach to entrepreneurship

This paper explores that application of evolutionary approaches to the study of entrepreneurship. It is argued an evolutionary theory of entrepreneurship must give as much concern to the foundations of evolutionary thought as it does the nature entrepreneurship. The central point being that we must move beyond a debate or preference of the natural selection and adaptationist viewpoints. Only then can the interrelationships between individuals, firms, populations and the environments within which they interact be better appreciated