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Análise metagenómica de um reactor Nitritation - Anammox: membros da comunidade e processos
No full textDissertação de mestrado em BioinformaticsNitrogen is a fundamental element for all organisms. It is nevertheless predominantly
found in the atmosphere, in the form of unreactive nitrogen. In the last century, a manmade
method for nitrogen fixation improved the crops yield, fuelling a populational growth.
The exponential increase of anthropogenic nitrogen in soils and water bodies has, however,
affected the environment and deregulated the natural biogeochemical nitrogen cycle. Currently,
the costs of repairing the damage caused by the reactive nitrogen load from human
activities have overcome the profits of the agricultural improvement, derived from the application
of fertilizers. Wastewater treatment plants remove the excessive amounts of nutrients
such as carbon, nitrogen and phosphorus from wastewater to prevent environmental
impacts derived from excessive nitrogen in the biosphere, like eutrophication.
The current conventional wastewater treatment applied is nitrification coupled with denitrification.
However, the requirement for an external carbon source and aeration render
this process costly. Furthermore, one of the intermediates of denitrification is nitrous oxide,
a greenhouse gas with an effect three hundred times worse than carbon dioxide and with
a lifespan of one hundred and twenty years in the ozone layer.
The Partial Nitrification/Anammox (PNA) process combines aerobic ammonium oxidation
with anaerobic ammonium oxidation while suppressing the activity of nitrite oxidizing
bacteria. This efficient process of nitrogen removal from wastewater reduces the aeration
cost and the need for external carbon with zero nitrous oxide emissions.
Unknown microbial interactions may, on the other hand, impair this process, resulting in
suboptimal performance such as, excessive nitrate and nitrous oxide emissions. To better
understand the microbial community and its interactions and to find the causes of the treatments
instability, metabolic analysis and genomic annotation was performed, using two
complementary binning methods. The biological samples used in this study were retrieved
from a high-rate PNA sequencing batch reactor, fed with carbon-free ammonium-rich synthetic
wastewater.
Fifty-seven draft genomes making up about eighty percent of the total community metagenome
were recovered. In addition to the three genomes each from Nitrosomonas and Candidatus
Brocadia, several genomes belonged to Proteobacteria, Chloroflexi, Planctomycetes, Bacteroidetes, Armatimonadetes, Ignavibacteriae, Acidobacteria, Chlorobi, Verrucomicrobia, Actinobacteria
and Gemmatimonadetes phyla.
In this study, the heterotrophic organisms encoding partial denitrification could be divided
into niches accordingly to their role in this pathway, describing their interactions as
a community. The complexity of the community was also ascertained with the discovery of
putative heterotrophic hydroxylamine oxidizing bacteria and putative heterotrophic nitrite
oxidizing bacteria.
Overall, high quality genomes that constitute a high fraction of the metagenome were
recovered, allowing for a precise description of the PNA reactors community and the flow
of nitrogen oxides. A complex community with high redundancy was uncovered basing
the main interactions on the partitioning of the nitrogen oxides respiratory pathway.O azoto é um elemento essencial para todos os organismos. No entanto, este é predominantemente
encontrado na atmosfera, sob a forma de azoto não-reativo. No século passado,
um método artificial para a fixação de azoto melhorou o rendimento das culturas, alimentando
um crescimento populacional. O aumento exponencial do azoto antropogénico nos
solos e massas de água afetou o meio ambiente e desregulou o ciclo natural de azoto.
Atualmente, os custos de reparação dos danos causados pela inserção excessiva de azoto
reativo, fruto das atividades humanas, superam os lucros da melhoria na produção agrícola,
derivada da aplicação de fertilizantes. As centrais de tratamento de águas residuais eliminam
quantidades excessivas de nutrientes, como o carbono, azoto e fosforo das águas
residuais, para prevenir impactos ambientais derivados do excesso de azoto na biosfera,
como a eutrofização.
O tratamento convencional de águas residuais aplicado é a nitrificação juntamente com
a desnitrificação. No entanto, a necessidade de uma fonte externa de carbono e de aeração
tornam esse processo bastante caro. Além disso, um dos intermediários da desnitrificação
é protóxido de azoto, ou óxido nitroso, um gás de efeito de estufa com um efeito trezentas
vezes pior que o dióxido de carbono, e uma vida útil na camada de ozono de cento e vinte
anos.
O processo de Nitrificação parcial /Anammox (PNA) comina a oxidação aeróbica de
amónia com a oxidação anaeróbica de amónia enquanto a atividade de bactéria que oxidam
nitrito é suprimida. Este eficiente processo de remoção de azoto de águas residuais reduz
o custo de aeração, não requer uma fonte de carbono e gera zero emissões de protóxido de
azoto.
As interações microbianas desconhecidas podem, por outro lado, prejudicar este processo,
resultando num desempenho inferior, como produção excessiva de nitrato e emissão
de protóxido de azoto. Para entender melhor a comunidade microbiana, as suas interações
e as causas da instabilidade do tratamento, foi realizada uma análise metagenómica seguida
de anotação genómica, utilizando dois métodos complementares de binning. As amostras
biológicas utilizadas como dados neste estudo foram obtidas de um reator de PNA de alta
performance, alimentado com águas residuais sintéticas ricas em amónio sem adição de carbono.
Foram recuperados cinquenta e sete genomas que compõem cerca de oitenta por cento do
metagenoma. Além dos três genomas de cada de Nitrosomonas e Candidatus Brocadia, vários
genomas pertenciam aos filos de Proteobacteria, Chloroflexi, Planctomycetes, Bacteroidetes, Armatimonadetes,
Ignavibacteriae, Acidobacteria, Chlorobi, Verrucomicrobia, Actinobacteria e Gemmatimonadetes.
Neste estudo, os organismos heterotróficos que codificam a desnitrificação parcial podem
ser divididos em grupos de acordo com o seu papel nesta via metabólica, descrevendo as
suas interações na comunidade. A complexidade da comunidade também foi verificada
com a descoberta das bactérias heterotróficas putativas que oxidam hidroxilamina e as
bactérias heterotróficas putativas que oxidam nitrito.
Em geral, foram recuperados genomas de alta qualidade que constituem uma grande
fração do metagenoma, permitindo uma descrição precisa da comunidade do reator e o
fluxo de óxidos de azoto. Uma comunidade complexa com enorme redundância e com as
suas principais interações baseadas na partição da via respiratória de óxidos de azoto
Going Beyond Counting First Authors in Author Co-citation Analysis
Full text linkThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
Variations on the Author
Full text link“Variations on the Author” discusses two of Eduardo Coutinho’s recent films (Um Dia na Vida, from 2010, and Últimas Conversas, posthumously released in 2015) and their contribution to the general question of documentary authorship. The director’s filmography is characterized by a consistent yet self-effacing form of authorial self-inscription: Coutinho often features as an interviewer that rather than express opinions propels discourses; an interviewer that is good at listening. This mode of self-inscription characterizes him as an author who is not expressive but who is nonetheless markedly present on the screen. In Um Dia na Vida, however, Coutinho is completely absent form the image, while Últimas Conversas, on the contrary, includes a confessional prologue that moves the director from the margins to the center of his films. This article examines the ways in which these works stand out in the filmography of a director who offers new insights into the notion of cinematic authorship
Appropriate Similarity Measures for Author Cocitation Analysis
Full text linkWe provide a number of new insights into the methodological discussion about author cocitation analysis. We first argue that the use of the Pearson correlation for measuring the similarity between authors’ cocitation profiles is not very satisfactory. We then discuss what kind of similarity measures may be used as an alternative to the Pearson correlation. We consider three similarity measures in particular. One is the well-known cosine. The other two similarity measures have not been used before in the bibliometric literature. Finally, we show by means of an example that our findings have a high practical relevance.information science;Pearson correlation;cosine;similarity measure;author cocitation analysis
Dispelling the Myths Behind First-author Citation Counts
Full text linkWe conducted a full-scale evaluative citation analysis study of scholars in the XML research field to explore just how different from each other author rankings resulting from different citation counting methods actually are, and to demonstrate the capability of emerging data and tools on the Web in supporting more realistic citation counting methods. Our results contest some common arguments for the continued
use of first-author citation counts in the evaluation of scholars, such as high correlations between author rankings by first-author citation counts and other citation
counting methods, and high costs of using more realistic citation counting methods that are not well-supported by the ISI databases. It is argued that increasingly available digital full text research papers make it possible for citation analysis studies to go beyond what the ISI databases have directly supported and to employ more
sophisticated methods
koamabayili/VECTRON-author-checklist: VECTRON author checklist
No full textWe have done our best to complete the author checklist relating to the use of animals in the hut study. Note that the objective for the hut study was to evaluate the IRS treatment applications for residual efficacy against Anopheles mosquitoes, including the local An. coluzzii mosquito population. Cows were only used to attract mosquitoes into the huts and no tests were carried out directly on the cows. The author checklist is intended for use with studies where experiments are carried out on animals, which is why we have had such difficulty in completing this for the hut study, as many of the questions do not relate to how the cows were used
Udvidelser til ASM Process Modeller til at bestemme lattergas emission fra renseanlæg
Full text linkLattergas (N2O) er en betydningsfuld drivhusgas idet opvarmningspotentialet for et N2O molekyle er omkring 300 gange større end for CO2. Lattergas dannes under fjernelsen af kvælstof i biologiske rensningsanlæg. Vi har udviklet den første matematiske model der beskriver lattergas produktion og forbrug via nitrifikation og denitrifikation i aktiv slam. Den pseudo-mekanistiske model er baseret på eksperimentelle data fra fire forskellige reaktor studier med blandede nitrificerende og denitrificerende bakteriekulturer. Modellens resultater viste at lattergas produktionen via det første trin i nitrifikationsprocessen - ammonium oxidation - er mere betydningsfuld end lattergas produktionen fra de dentrificerende bakterier, hvilket var i overensstemmelse med de eksperimentelle observationer. N2O produktion kan tegne sig for 0,1% til 25% af den forbrugte N i forskellige Nitrifikation / Denitrifikation konfigurationer Vi kan således konkludere at modellen på tilfredsstillende vis simulerer lattergas dynamikken ved biologisk kvælstoffjernelse (nitrikation-denitrifikation). Modellen kan bruges som et redskab i optimering af målsætning for kvaliteten af vand og luft i spildevandsrensningsanlæg og til at forbedre IPCC´s beregninger for lattergas frigivelse fra spildevandsrenseanlæ
Author-wise bibliometric analysis based on entropy.
No full textAuthor-wise bibliometric analysis based on entropy.</p
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