Meat and egg-type chickens have been selected for several generations for different traits. Artificial and natural selection for different phenotypes can change frequency of genetic variants, leaving ...particular genomic footprints throghtout the genome. Thus, the aims of this study were to sequence 28 chickens from two Brazilian lines (meat and white egg-type) and use this information to characterize genome-wide genetic variations, identify putative regions under selection using Fst method, and find putative pathways under selection.
A total of 13.93 million SNPs and 1.36 million INDELs were identified, with more variants detected from the broiler (meat-type) line. Although most were located in non-coding regions, we identified 7255 intolerant non-synonymous SNPs, 512 stopgain/loss SNPs, 1381 frameshift and 1094 non-frameshift INDELs that may alter protein functions. Genes harboring intolerant non-synonymous SNPs affected metabolic pathways related mainly to reproduction and endocrine systems in the white-egg layer line, and lipid metabolism and metabolic diseases in the broiler line. Fst analysis in sliding windows, using SNPs and INDELs separately, identified over 300 putative regions of selection overlapping with more than 250 genes. For the first time in chicken, INDEL variants were considered for selection signature analysis, showing high level of correlation in results between SNP and INDEL data. The putative regions of selection signatures revealed interesting candidate genes and pathways related to important phenotypic traits in chicken, such as lipid metabolism, growth, reproduction, and cardiac development.
In this study, Fst method was applied to identify high confidence putative regions under selection, providing novel insights into selection footprints that can help elucidate the functional mechanisms underlying different phenotypic traits relevant to meat and egg-type chicken lines. In addition, we generated a large catalog of line-specific and common genetic variants from a Brazilian broiler and a white egg layer line that can be used for genomic studies involving association analysis with phenotypes of economic interest to the poultry industry.
Delta VOC is highly diverse with more than 120 sublineages already described as of November 30, 2021. In this study, through active monitoring of circulating severe acute respiratory ...syndrome coronavirus‐2 (SARS‐CoV‐2) variants in the state of São Paulo, southeast Brazil, we identified two emerging sublineages from the ancestral AY.43 strain which were classified as AY.43.1 and AY.43.2. These sublineages were defined by the following characteristic nonsynonymous mutations ORF1ab:A4133V and ORF3a:T14I for the AY.43.1 and ORF1ab:G1155C for the AY.43.2 and our analysis reveals that they might have a likely‐Brazilian origin. Much is still unknown regarding their dissemination in the state of São Paulo and Brazil as well as their potential impact on the ongoing vaccination process. However, the results obtained in this study reinforce the importance of genomic surveillance activity for timely identification of emerging SARS‐CoV‐2 variants which can impact the ongoing SARS‐CoV‐2 vaccination and public health policies.
•The dissemination of Alpha VOC in the São Paulo state was examined.•Alpha VOC sustained transmission was observed in the city of Bauru and metropolitan São Paulo.•The phylogenetic clustering was ...significant of multiple Alpha VOC introductions in the State of São Paulo from other Brazilian locations and abroad.
The SARS-CoV-2 alpha VOC (also known as lineage B.1.1.7) initially described in the autumn, 2020 in UK, rapidly became the dominant lineage across much of Europe. Despite multiple studies reporting molecular evidence suggestive of its circulation in Brazil, much is still unknown about its genomic diversity in the state of São Paulo, the main Brazilian economic and transportation hub. To get more insight regarding its transmission dynamics into the State we performed phylogenetic analysis on all alpha VOC strains obtained between February and August 2021 from the Sao Paulo state Network for Pandemic Alert of Emerging SARS-CoV-2 variants. The performed phylogenetic analysis showed that most of the alpha VOC genomes were interspersed with viral strains sampled from different Brazilian states and other countries suggesting that multiple independent Alpha VOC introductions from Brazil and overseas have occurred in the São Paulo State over time. Nevertheless, large monophyletic clusters were also observed especially from the Central-West part of the São Paulo State (the city of Bauru) and the metropolitan region of the São Paulo city. Our results highlight the Alpha VOC molecular epidemiology in the São Paulo state and reinforce the need for continued genomic surveillance strategies for the real-time monitoring of potential emerging SARS-CoV-2 variants during the ever-growing vaccination process.
São Paulo state has been the epicenter of the Coronavirus Disease 2019 (COVID-19) in Brazil, ranking first by state with over six million reported cases. In February 2021, the P.4 lineage was ...reported in 21 cities across the state by public health authorities due to the L452R mutation. Here, by analyzing 17,304 genome sequences of SARS-CoV-2 sampled between February and August of 2021 in 476 distinct cities in São Paulo, we assess the transmission dynamics of the P.4 lineage and other SARS-CoV-2 variants that were, at the time of the study, co-circulating in the state. Additionally, clinical parameters from the city of Araras, São Paulo (N = 251) were considered to estimate the potential risk and mortality rate associated with the P.4 lineage since its higher prevalence was observed in that city. Our data suggest a low frequency (0.55%) of the P.4 lineage across the state, with the gamma variant being the dominant form in all regions (90%) at that time. Furthermore, no evidence of increased transmissibility and disease severity related to the P.4 lineage was observed. The displacement through the time of different lineages in São Paulo highlights how challenging genomic surveillance appears to track the emergence of new SARS-CoV-2 lineages, which could better guide the implementation of control measures.
The Lambda variants of interest (VOI) (C37/GR/452Q.V1/21G) was initially reported in Lima, Peru but has gained rapid dissemination through other Latin American countries. Nevertheless, the ...dissemination and molecular epidemiology of the Lambda VOI in Brazil is unknown apart from a single case report. In this respect, we characterized the circulation of the SARS‐CoV‐2 Lambda VOI (C37/GR/452Q.V1/21G) in Sao Paulo State, Brazil. From March to June 2021, we identified seven Lambda isolates in a set of approximately 8000 newly sequenced genomes of the Network for Pandemic Alert of Emerging SARS‐CoV‐2 variants from Sao Paulo State. Interestingly, in three of the positive patients, the Lambda VOI infection was probably related to a contact transmission. These individuals were fully vaccinated to COVID‐19 and presented mild symptoms. The remaining positive for Lambda VOI individuals showed different levels of COVID‐19 symptoms and one of them needed hospitalization (score 5, WHO). In our study, we present a low level of Lambda VOI circulation in the Sao Paulo State. This reinforces the essential role of molecular surveillance for the effective SARS‐CoV‐2 pandemic response, especially in regard to circulating variants.
Highlights
Our study shows the low circulation of the Lambda variants of interest (VOI) in the São Paulo State.
Two distinct Lambda VOI introductions may have occurred in the Sao Paulo State.
Epidemiological data revealed Lambda VOI transmission in three cases of fully vaccinated individuals.
The authors hereby request the inclusion of two authors (Olivia Teixeira and Maria Cristina Nonato) in the recently published article in Viruses entitled “Nucleocapsid (N) gene mutations of ...SARS-CoV-2 can affect real-time RT-PCR diagnostic and impact false-negative results” ...
Orientadores: Lucia Helena Innocentini Mei, Elisa Esposito
Dissertação (mestrado) - Universidade Estadual de Campinas, Faculdade de Engenharia Quimica
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Previous issue date: 2005
Resumo: A consciência ambiental crescente, somada às políticas de gerenciamento de resíduos sólidos, tem impulsionado o desenvolvimento de materiais biodegradáveis par a substituição parcial dos plásticos de origem petroquímica em algumas áreas estratégicas como a de embalagens. No presente trabalho, avaliou-se a biodegrabilidade da blenda de PCL/Amido adipatado em solo, se acordo com a norma ASTM D5988-96 e Anderson et al. (1982); e em meio liquido de acordo com a norma ASTM 6691-01e Mergaert et al. (2000). No teste realizado em solo, a biodegradação foi acompanhada pela determinação da porcentagem de mineralização, através da medida da produção do dióxido de carbono e da perda de massa. O acompanhamento das alterações na cristalinidade da blenda foi feito um ambos os testes através de Calorimetria Exploratória Diferencial (DSC). Foi verificado que a blenda atingiu 70% de mineralização após 90 dias de incubação no solo. De acordo com a norma ASTM D 6400, esse valor permite concluir que a blenda é biodegradável. Por sua vez, a perda de massa da blenda incubada no solo foi maior do que no meio liquido, mostrando que a biodegradação no solo é bastante eficiente
Abstract: Increasing environmental concens and the waste management policies in the last decade have prompted the use of natural-based biodegradable materials instead od nonbiodegradable petrochemical - basead plastic. The present work it investigated the biodegradation in soil of a PCL/Starch-adipate blend, a natural ¿ based material, according to the ASTM D5988-96 standart and Anderson (1982). Furthermore, it was investigated the biodegradation of this material in liquid medium, according to the ASTM 6691-01 standart and Megaert et al (2000). During the soil tests,the biodegradation was indicated by 'CO IND. 2¿ evolution and mass loss measurements. In the liquid medium, the biodegradation was indicated by mass loss measurements only. Differential Scanning Calorimetry (DSC) was used to follow the crystallinity change in samples treated in liquid and solid medium. It wa observed that the blend reached 70% of mineralization after 90 days of soil incubation. According to the ASTM D 6400, this is a strong indication that the blend is biodegradable. The mass loss of blend sample incubated in soil was higher than for the sample incubated in liquid, showing that the biodegradation in soil was very efficient
Mestrado
Ciencia e Tecnologia de Materiais
Mestre em Engenharia Química
Orientadores: Lucia Helena Innocentini Mei, Elke Jurandy Bran Nogueira Cardoso
Tese (doutorado) - Universidade Estadual de Campinas, Faculdade de Engenharia Quimica
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Previous issue date: 2010
Resumo: O desenvolvimento de polímeros biodegradáveis tem como objetivo contribuir com a redução do volume de lixo plástico descartado no meio ambiente. Em vista disso, a utilização de polímeros naturais na confecção de blendas tem proporcionado o aproveitamento de recursos de fontes renováveis como e o caso do amido e da soja. Nesse trabalho, dando continuidade as pesquisas realizadas anteriormente no grupo de materiais biodegradáveis da Profa. Lucia H. Innocentini-Mei (FEQ/UNICAMP),foram utilizadas blendas a base de poli (e-caprolactona), amido de milho modificado, proteína isolada de soja (PIS) e sorbitol. As blendas foram preparadas através de extrusão em extrusora mono-rosca e prensagem a quente e as amostras assim obtidas foram submetidas a caracterização e estudo da biodegradação em diferentes solos, com o apoio do Laboratório de Microbiologia do solo da ESALQ/USP, sob a supervisão da Profa. Elke J.B. Cardoso. A caracterização dos materiais obtidos deu enfoque as propriedades térmicas, mecânicas, morfológicas e capacidade de biodegradação em solos de diferentes texturas, e com ou sem a adição de N-fertilizante. Observou-se que a incorporação de amido modificado e proteína isolada de soja foram responsáveis pela redução das propriedades térmicas e mecânicas dos materiais, mas, para muitas aplicações estas propriedades não são requisitos indispensáveis. Com relação à proteína isolada de soja, esta proporcionou a redução da relação carbono/nitrogênio (C/N) da blenda como esperado, atributo que foi decisivo durante o processo de biodegradacao das formulacoes em diferentes solos. A mineralizacao das formulações foi maior em solo de textura arenosa, com maior conversão de carbono a dióxido de carbono (CO2); por outro lado, o solo de textura argilosa não apresentou taxas altas de conversão de carbono a dióxido de carbono para as blendas, mas foi mais eficiente na formação de biomassa microbiana, comparado ao solo arenoso.
Abstract: The development of biodegradable polymers came to reduce the volume of plastic waste discarded in the environment. As a result, the use of natural polymers in the manufacture of blends has provided the use of renewable resources such as starch and soy. In this work, continuing the research done previously in the biodegradable materials group of School of Chemical Engineering School at State University of Campinas/ Brazil, supervised by Prof. Lucia H. Innocentini-Mei, blends of poly (e-caprolactone)/modified starch, soy protein isolate (SPI) and sorbitol were prepared by extrusion in single-screw extruder and hot pressing machine. The samples obtained were subjected to characterization and study of biodegradation in different soils, with the support of the Laboratory of Soil Microbiology (ESALQ/USP), under the supervision of Professor Elke J. B. N. Cardoso. The characterization of the material has focused on thermal, mechanical and morphological properties, and also on the biodegradation capacity in soils of different textures, and with or without the addition of N-fertilizer. It was observed that the incorporation of modified starch and soy protein isolate were responsible for the reduction of thermal and mechanical properties of materials but, for many applications, these properties are not necessaries. With respect to soy protein isolate (SPI), it reduced the carbon / nitrogen (C/N) of the blend as expected, an attribute which was decisive in the process of biodegradation of the studied formulations in different soils. Mineralization of the formulations was higher in sandy soil, with the higher conversion of carbon to carbon dioxide (CO2) compared to the clay soil, which did not show high rates of conversion but was more efficient in the formation of microbial biomass.
Doutorado
Ciencia e Tecnologia de Materiais
Doutor em Engenharia Química
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