ABSTRACT
The analysis of curated genomic, metagenomic and proteomic data is of paramount importance in the fields of biology, medicine, education, and bioinformatics. Although this type of data is usually hosted in raw format on free international repositories, the full access requires lots of computing power and large storage disk space for the domestic user. The purpose of the study is to offer a comprehensive set of microbial genomic and proteomic reference databases in an accessible and easy-to-use form to the scientific community and demonstrate its advantages and usefulness. Also, we present a case study on the applicability of the sketched data, for the determination of overall genomic coherence between two members of the Brucellacea family, which suggests they belong to the same genomospecies that remain as discrete ecotypes. A representative set of genomes, proteomes (from type material), and metagenomes were directly collected from the NCBI Assembly database and Genome Taxonomy Database (GTDB), associated with the major groups of Bacteria, Archaea, Virus, and Fungi. Sketched databases were subsequently created and stored on handy reduced representations by using the MinHash algorithm implemented in Mash software. The obtained dataset contains more than 133 GB of space disk reduced to 883.25 MB and represents 125,110 genomics/proteomic records from eight informative contexts, which have been prefiltered to make them accessible, usable, and user-friendly with limited computational resources. Potential uses of these sketched databases are discussed, including but not limited to microbial species delimitation, estimation of genomic distances and genomic novelties, paired comparisons between proteomes, genomes, and metagenomes; phylogenetic neighbor's exploration and selection, among others.
A análise de dados genômicos, metagenômicos e proteômicos com curadoria é de suma importância nos campos da biologia, medicina, educação e bioinformática. Embora esse tipo de dados geralmente seja hospedado em formato bruto em repositórios internacionais gratuitos, o acesso total requer muita capacidade de computação e grande espaço em disco de armazenamento para o usuário doméstico. Os objetivos do estudo são oferecer um conjunto abrangente de bancos de dados de referência genômica e proteômica microbiana de forma acessível e fácil de usar para a comunidade científica e demonstrar suas vantagens e utilidade. Além disso, apresentamos um estudo de caso sobre a aplicabilidade dos dados esboçados para a determinação da coerência genômica geral entre dois membros da família Brucellacea, o que sugere que eles pertencem às mesmas genomoespécies que permanecem como ecótipos discretos. Um conjunto representativo de genomas, proteomas (de material tipo) e metagenomas foi coletado diretamente do banco de dados NCBI Assembly e do banco de dados de taxonomia do genoma (GTDB), associada aos principais grupos de bactérias, Archaea, vírus e fungos. Bancos de dados esboçados foram subsequentemente criados e armazenados em representações reduzidas práticas usando o algoritmo MinHash implementado no software Mash. O conjunto de dados obtido contém mais de 133 GB de espaço em disco reduzido para 883,25 MB e representa 125,110 registros genômicos/proteômicos de oito contextos informativos, que foram pré-filtrados para torná-los acessíveis, utilizáveis ââe amigáveis ââcom recursos computacionais limitados. Os usos potenciais desses bancos de dados esboçados são discutidos, incluindo, mas não se limitando, a delimitação de espécies microbianas, estimativa de distâncias genômicas e novidades genômicas, comparações emparelhadas entre proteomas, genomas e metagenomas, exploração e seleção filogenética de vizinhos, entre outros.
Subject(s)
Classification , Genome , Genes, MicrobialABSTRACT
Liver disease poses a substantial burden in Latin America. This burden is primarily attributed to a high level of alcohol consumption and the increasing prevalence of risk factors associated with metabolic dysfunction-associated steatotic liver disease (MASLD), such as sedentary lifestyles, easy access to ultra-processed foods, obesity, and type 2 diabetes mellitus. These epidemiological trends are cause for concern, especially considering that there are significant challenges in addressing them, due to disparities in access to liver disease screening and care. In this article, we aim to provide an overview of the current situation regarding liver disease in Latin America. We also discuss recent multinational proposals designed to address the growing MASLD burden via its integration into existing non-communicable diseases policies, at both local and global levels. Additionally, we emphasize the urgent need to establish effective public health policies that target both MASLD risk factors and excessive alcohol consumption. Furthermore, we discuss the development of liver transplantation programs, areas for improvement in medical education and research capabilities, and how the fostering of extensive collaboration among all stakeholders is crucial for addressing liver disease in the region.
ABSTRACT
BACKGROUND: In recent years, the desire to adopt a healthy diet has drawn attention to legume seeds and food products derived from them. Mash bean is an important legume crop used in Pakistan however a systematic mapping of the chemical composition of mash bean seeds is lacking. Therefore seeds of four mash bean (Vigna mungo (L.) Hepper, family Leguminoseae) cultivars (NARC-Mash-1, NARC-Mash-2, NARC-Mash-3, NARC-Mash-97) commonly consumed in Pakistan have been analyzed for their chemical composition, antioxidant potential and biological activities like inhibition of formation of advanced glycation end products (AGE) activity and tyrosinase inhibition activity. RESULTS: The investigated cultivars varied in terms of biochemical composition to various extents. Mineral composition indicated potassium and zinc in highest and lowest amounts respectively, in all cultivars. The amino acid profile in protein of these cultivars suggested cysteine is present in lowest quantity in all cultivars while fatty acid distribution pattern indicated unsaturated fatty acids as major fatty acids in all cultivars. All cultivars were found to be rich source of tocopherols and sterols. Fourier transform infrared spectroscopy (FTIR) fingerprints of seed flour and extracts indicated major functional groups such as polysaccharides, lipids, amides, amines and amino acids. Results indicated that all investigated cultivars possessed appreciable antioxidant potential. CONCLUSIONS: All cultivars are rich source of protein and possess sufficient content of dietary fiber, a balanced amino acid profile, low saturated fatty acids and antioxidant capacity that rationalizes many traditional uses of seeds of this crop besides its nutritional importance. The collected data will be useful for academic and corporate researchers, nutritionists and clinical dieticians as well as consumers. If proper attention is paid, it may become an important export commodity and may fetch considerable foreign exchange for Pakistan.
Subject(s)
Seeds/chemistry , Crops, Agricultural/chemistry , Fabaceae/chemistry , Pakistan , Phenols/analysis , Riboflavin/analysis , Seeds/metabolism , Sterols/analysis , Tannins/analysis , Thiamine/analysis , Trace Elements/analysis , Flavonoids/analysis , Plant Extracts/chemistry , Free Radical Scavengers , Monophenol Monooxygenase/antagonists & inhibitors , Glycation End Products, Advanced/metabolism , Crops, Agricultural/metabolism , Reducing Agents/metabolism , Cysteine/analysis , Tocopherols/analysis , Fabaceae/metabolism , Niacin/analysis , Antioxidants/metabolism , Nutritive ValueABSTRACT
The objective was to verify the occurrence of antibodies to Leptospira and to evaluate the spatial dispersion of free living mash deer (Blastocerus dichotomus) reactors, in the basin of Paraná River, states of São Paulo and Mato Grosso do Sul. Through the microscopic agglutination test, we examined 217 serum samples (77 males and 140 females) of mash deer caught in six locations in the Paraná river basin between the states of São Paulo and Mato Grosso do Sul. From this total, 130 (59.91%) samples reacted to 12 different serovars of pathogenic Leptospira, and 87 (40.09%) did not react. The more prevalent serovars found were Autumnalis (20.28% of the samples examined), Castellonis (13,36%) and Hardjo (11,98%). The serologic titers obtained in the reactive samples ranged from 100 to 800. Regarding the gender, 52 (67.5%) of the males and 78 (55.7%) of the females were reactors. There was no statistically significant difference between genders (P>0.05). The comparison between the frequency of reactors among adult and among young animals revealed a significant difference (P<0.01); 65.1% of the adult and 34.9% of the young animals were reactors. A significant difference was also observed among the local where animals were captured. The spatial dispersion, obtained by satellite images and georeferenced information of each mash deer captured, showed the distribution of mash deer reactors on the area studied.
Objetivou-se verificar a ocorrência de anticorpos contra Leptospira e avaliar espacialmente a dispersão de cervos-do-pantanal (Blastocerus dichotomus) de vida livre, que fossem reagentes, na bacia do Rio Paraná, estados de São Paulo e Mato Grosso do Sul. Foram examinadas, por meio do teste de soroaglutinação microscópica (SAM), 217 amostras de soro sanguíneo (77 machos e 140 fêmeas) de cervos-do-pantanal capturados em seis localidades na bacia do rio Paraná, entre os estados de São Paulo e Mato Grosso do Sul. Desse total, 130 (59,91%) amostras foram reagentes contra 12 diferentes sorovariedades de leptospiras patogênicas e 87 (40,09%) foram não reagentes. As sorovariedades mais encontradas foram: Autumnalis (20,28% dos animais examinados), Castellonis (13,36%) e Hardjo (11,98%). Os títulos sorológicos obtidos nas amostras reagentes variaram de 100 a 800. Com relação ao sexo, 52 (67,5%) machos e 78 (55,7%) fêmeas foram reagentes, não sendo observada diferença estatisticamente significativa (P>0,05). A comparação entre os animais jovens e adultos sororreagentes revelou que houve diferença significativa (P 0,01) com relação à idade; 65,1% dos adultos e 34,9% dos jovens foram reagentes. Quanto ao local de captura, observou-se que as frequências de reagentes diferiram significativamente. A dispersão espacial, obtida por imagens de satélite aliadas às informações do geoposicionamento de cada cervo-do-pantanal capturado, mostrou distribuição de cervos-do-pantanal reagentes na área estudada.
Subject(s)
Animals , Antibodies , Deer/immunology , Leptospira , Serotyping/veterinary , Animal Distribution , Serologic Tests/veterinaryABSTRACT
The objective was to verify the occurrence of antibodies to Leptospira and to evaluate the spatial dispersion of free living mash deer (Blastocerus dichotomus) reactors, in the basin of Paraná River, states of São Paulo and Mato Grosso do Sul. Through the microscopic agglutination test, we examined 217 serum samples (77 males and 140 females) of mash deer caught in six locations in the Paraná river basin between the states of São Paulo and Mato Grosso do Sul. From this total, 130 (59.91%) samples reacted to 12 different serovars of pathogenic Leptospira, and 87 (40.09%) did not react. The more prevalent serovars found were Autumnalis (20.28% of the samples examined), Castellonis (13,36%) and Hardjo (11,98%). The serologic titers obtained in the reactive samples ranged from 100 to 800. Regarding the gender, 52 (67.5%) of the males and 78 (55.7%) of the females were reactors. There was no statistically significant difference between genders (P>0.05). The comparison between the frequency of reactors among adult and among young animals revealed a significant difference (P<0.01); 65.1% of the adult and 34.9% of the young animals were reactors. A significant difference was also observed among the local where animals were captured. The spatial dispersion, obtained by satellite images and georeferenced information of each mash deer captured, showed the distribution of mash deer reactors on the area studied.(AU)
Objetivou-se verificar a ocorrência de anticorpos contra Leptospira e avaliar espacialmente a dispersão de cervos-do-pantanal (Blastocerus dichotomus) de vida livre, que fossem reagentes, na bacia do Rio Paraná, estados de São Paulo e Mato Grosso do Sul. Foram examinadas, por meio do teste de soroaglutinação microscópica (SAM), 217 amostras de soro sanguíneo (77 machos e 140 fêmeas) de cervos-do-pantanal capturados em seis localidades na bacia do rio Paraná, entre os estados de São Paulo e Mato Grosso do Sul. Desse total, 130 (59,91%) amostras foram reagentes contra 12 diferentes sorovariedades de leptospiras patogênicas e 87 (40,09%) foram não reagentes. As sorovariedades mais encontradas foram: Autumnalis (20,28% dos animais examinados), Castellonis (13,36%) e Hardjo (11,98%). Os títulos sorológicos obtidos nas amostras reagentes variaram de 100 a 800. Com relação ao sexo, 52 (67,5%) machos e 78 (55,7%) fêmeas foram reagentes, não sendo observada diferença estatisticamente significativa (P>0,05). A comparação entre os animais jovens e adultos sororreagentes revelou que houve diferença significativa (P 0,01) com relação à idade; 65,1% dos adultos e 34,9% dos jovens foram reagentes. Quanto ao local de captura, observou-se que as frequências de reagentes diferiram significativamente. A dispersão espacial, obtida por imagens de satélite aliadas às informações do geoposicionamento de cada cervo-do-pantanal capturado, mostrou distribuição de cervos-do-pantanal reagentes na área estudada.(AU)