PUBLISHED PAPER 1
“Evolution: Revisiting the Root of the Eukaryote Tree”
Roger, Andrew J. Simpson, Alastair G.B. 2009. “Evolution: Revisiting the Root of the Eukaryote Tree” Accessed April 11, 2013.
Eukaryotes are organisms which have cell types containing specialized organelles in their cytoplasm. They also contain a membrane-bound nucleus which encloses their DNA or genetic material. This published paper goes into the evolution of the eukaryotes.
The 1980s-1990s saw the prevailing view that eukaryotes were influenced by ribosomal RNA genes. Recently, however, a ‘six-super groups’ hypothesis and the unikont-bikont root hypothesis had emerged to classify the deep eukaryote phylogeny, however, there was some controversy.
A recent paper had reported the classification of the enigmatic protist Breviata anathema which lives in oxygen poor conditions, lacks classical mitochondria and its flagellar apparatus has at least one additional non-flagellated basal body. It was originally classed in one of the “six-super groups” as an Archamoebea (a group of mitochondrion-lacking amoebozoans). However, it was found that this group of eukaryotes contained mitochondrial marker proteins and mitochondrion-derived organelles which proved the hypothesis of this group originating before the endosymbiotic era of mitochondria to be false. Thus it was found that no eukaryotic linkages persisted from a pre-mitochondrial phase of evolution. Analysis indicate that Breviatais closely related to Amoebozoa which is the super-group the Archamoebae also belong to. This relationship demonstrates that Breviata too descends from a mitochondrion-containing ancestor.
It is also suggested that Breviata be placed inside Amoebozoa as the sister group of Archamoebae, as they might share a common anaerobic ancestor. Cavalier-Smith had argued that ancestral eukaryotes had simple kinetid containing a basal body which anchored one flagellum. He suggested that unikonts retained ancestral organization and the bikonts came from an ancestor that had a posterior and anterior flagella.
However, recent studies showed that the bikonts characteristic occurs during cell division in the daughter cells. The problem of unikonts actually having more than one flagellum or basal body incorporated a problem with the hypothesis. These results were also based on a very narrowinf sampling of the available eukaryotes.
From this published paper, it was deduced that there are several important taxa whose phylogenetic affinities to the major super-groups have not really been delved into and as such there a lot unknown about them and how certain aspects of the eukaryote tree should be classified.
PUBLISHED PAPER 2
“pH affecting organelles of liver cells.”
Diwu, Zhenjun, Chii-Shiarng Chen, Cailan Zhang, Dieter H Klaubert and Richard P Haugland. 1999. “A novel acidotropic pH indicator and its potential application in labeling acidic organelles of live cells”. Accessed April 11,2013.
From the published paper it was understood that ‘ratio imaging’ is significantly limited due to the lack of appropriate fluorescent probes (mainly for acidic organelles). Fluorescent dyes are not appropriate for staining these acidic organelles (such as lysosomes) due to their fluorescence being decreased under neutral or acidic conditions thus limiting the labelling of the organelle. A compound 2-(4-pyridyl)-5-((4-(2-dimethylaminoethyl-aminocarbamoyl) methoxy)phenyl)oxazole (PDMPO) was prepared to combat this problem as it emits intense yellow fluorescence at low pH and gives an intense blue at higher pH.
Thus, with this new compound, it was possible to label the acidic lysosomes of liver cells. The two varying fluorescence colours given at low and high pH made the detection of pH fluctuation possible.
From this paper, it was deduced that the lysosomes of liver cells are extremely acidic and as such a compound had to be developed specifically to study these acidic organelles.