Pascal Lapierre and J. Peter Gogarten, Trends in Genetics

Evolution of Symbiotic Bacteria in the Distal Human Intestine

Jian Xu, et al., PLOS Biology

Estimating the size of the bacterial pan-genome

Evolution of Symbiotic Bacteria in the Distal Human Intestine.

Estimating the [...]]]> Estimating the size of the bacterial pan-genome

Pascal Lapierre and J. Peter Gogarten, Trends in Genetics

Evolution of Symbiotic Bacteria in the Distal Human Intestine

Jian Xu, et al., PLOS Biology

Estimating the size of the bacterial pan-genome

Evolution of Symbiotic Bacteria in the Distal Human Intestine.

Estimating the size of the bacterial pan-genome

Pan-genome includes two groups of gene: the core genome and dispensable genome. The core genome contains genes present in all strains, and the dispensable genome contains genes present in two or more strains. This paper use pan-genome concept and try to predict the size of bacterial pan-genome using 293 sequenced genomes. They extend pan-genome categories from two categories to three categories: extended core, character genes and accessory genes. The extend category is highly conserved because it is the result of highly selective pressure. They present around 8% in the 99% of sample genomes. The character genes category is the largest part of bacterial genome, and around 64% genes in the pan-genome are in this category. These genes are the essential genes for colonization and survival, but there are only 7900 protein family was found in this category which is a small number. Although it only has small number of protein family, these genes have flexibility to form a new function. This characteristic made these diverse genes become substrate specificity. The final category, accessory genes, presents around 28% of the bacterial pan-genome. This category contains more than 139,000 gene families in 293 genomes. There are lots of genes are ORFans and most of their functions are remain unknown. This uncertain function genes might be converge to other categories if we can do some process to make it become to proteins. The authors conclude different of view for each category. The extend core gene mainly transfer vertically from the ancestor to offspring, and only allow a slice change on the sequence level. The character genes are transferred between organisms. The accessory genes might be the genes which have function in the past. Those genes become pseudogenes. They also conclude that protein evolution not only can derive from exist protein selection or rearrangements but also has new protein involve in the evolution.

It is so surprised that the differences of gene between different strains and also scientist claim there are infinite genomes¹. Every time you sequence a genome you will found another set of genes according their prediction 33 new genes will be added after add another genome. I think the idea form author is quite brilliant, divide into three different categories: core, character, accessory. We can use only character to differentiate different strains.

1. Hervé Tettelin, et al., Genome analysis of multiple pathogenic isolates of Streptococcus agalactiae: Implications for the microbial “pan-genome”, PNAS 2005

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Evolution of Symbiotic Bacteria in the Distal Human Intestine

The human gut has tons of microbes, and the authors want to know how the evolution processes happen. Does this evolution affect by host or by other microorganisms? They use two commonly bacteria inside the human gut, Bacteroides vulgates and Bacteroides distasonis which have highly divergent 16S rRNA. They compare these two bacteria with other two gut Bacteroidetes, Bacteroides thetaiotaomicron and Bacteroides fragilis, and two non-gut Bacteroidetes, Porphyromonas gingivalis which found in human oral and Cytophaga hutchinsonii which found in soil. They first assemble two gut genomes to get complete genome, total coverage are 12.6X and 13.2X respectively. The gene is predicted by the BLASTN and tRNASCAN then use GLIMMER, ORPHEUS, CRITICA and WUBLAST to predict the protein coding region. After prediction, they use ClustalW to align the sequence and NAST to construct phylogenetic tree. They mainly focus on LGT, laterally transferred genes; these genes are laterally acquired after speciation which might involve the difference of niche. They can identify two types of genes by their method. One is the LTG genes, and the other is genes which are lost in others species except one. They choose LTG as their target set although this LGT may cause by other species gene lost; they make an assumption this also could be an indicator of species-specific selection. They found an average of 5.5% of the genes belong LTG which are transfer from outside the gut Bacteroidetes in each genomes. They also found in CPS loci, Capsular Polysaccharide Biosynthesis, have enriched glycosyltransferases and genes for LTG. This phenomenon is not present in non-gut Bacteroidetes P. gingivalis. The CPS loci are most polymorphic sites in the gut Bacteroidetes. Moreover the conjugative transposons (CTns) are found to be related to duplication of CPS loci within a genome. Each copy contains a CTn followed by a complete CPS locus. After that they provide a case study of SusC/SusD paralogs to verify their assumptions. The different host will result in a homogenized microbiome and intermicrobial dynamic result in completely differentiated genomes; these are both happen in the human gut. The LTG play an important role for gut Bacteroidetes to adapted within human gut, but the how and when the LTG affect the Bacteroidetes still unclear.

Determination of Glycan Structure from Tandem Mass Spectra

Identification and quantification of N-linked glycoproteins using hydrazide chemistry, stable isotope labeling and [...]]]> Complexities and algorithms for glycan structure sequencing using tandem mass spectrometry

Determination of Glycan Structure from Tandem Mass Spectra

Identification and quantification of N-linked glycoproteins using hydrazide chemistry, stable isotope labeling and mass spectrometry

Determination of Glycan structure use MS

After presentation, Prof. Memo give me some advise. I will modify and upload it.

Title: Determination of N-Glycan structure use MS/MS

isomeric molecules isoform

De novo De novo

biology biological

Why my problem is NP-Hard?

Because the glycan structures is diverse, the number of candidate glycan structures is huge.