Chuan-Yih, Yu » Bioinformatics

Worlds within worlds: evolution of the vertebrate gut microbiota

paulyu — Tue, 13 Apr 2010 23:11:50 +0000

Worlds within worlds: evolution of the vertebrate gut microbiota

Ruth E. Ley, et al., Nature Reviews Microbiology

A human gut is an extreme environment for the microorganisms. The authors try to find out whether the different habitat affects the microorganism or not by using published 16S rRNA data. They compare humans with other mammals, metazoan, and other free-living microbial communities. Before the modern age, human’s diet is heavily related to the environment. They only consume the food from the seed or fruit. When the times files, the tools and technologies help people to have their favorable food without controlling by the environment. Therefore, the differences of microorganisms comminutes within humans, which live in distinct geographic location, are getting smaller. They compare the difference of facial microorganisms comminutes inter human and human with other mammals. The result supports the previous assumption.

They took 99,801 16S rRNA from 464 samples and 181 studies. The samples contain 202 samples in mammalian, 34 samples from large sequencing efforts if free-living communities, other human body habitats, the guts of non-mammal vertebrates and from the guts or whole body of diverse metazoan. They apply principal component analysis on the final sets.

The first principal component can separate vertebrate gut-associated communities from free-living communities. Almost entire nonvetebrate gut communities clustered with free-living communities. They conclude that mammals have a strong host phylogenetic effect on the structure of microbiota of arthropods. The third principal component can separate saline and non-saline free-living environmental communities.

The Firmicutes and Bacteroidetes are the most common and ubiquitous in vertebrate gut samples including human. The other types of sample also contain high abundance of Firmicutes and Bacteroidetes but other phyla tend to have highly represented in non-gut samples. The phylum-specific analysis indicate the gut samples of carnivores tend to cluster closer to free-living communities.

Finally, the authors say the globalization and frequented movement increase the microbial transmission. This phenomenon rapidly lost the biodiversity. Plants and animals are becoming extinct and microbial communities as well. It is very important to maintain those microorganisms, because recent research said that terrestrial microbial community composition change might be resulting in global change.

This is really an exhausted work to analysis such as large amount data. It is, however, important to do such large-scale study. I believe all the living species are connected together. We cannot live alone without other species. Save the earth, save yourself.

Paper Link

New MultiNGlycan website

paulyu — Fri, 05 Feb 2010 03:04:30 +0000

Here is the new MultiNGlycan website. Previous one is ugly and I don’t like it.
Now it looks pretty and have lightbox to display the photo

http://mendel.informatics.indiana.edu/~chuyu/MultiNGlycan/

58th ASMS Conference 2010 Abstract

paulyu — Mon, 01 Feb 2010 17:18:26 +0000

I world like to publish a poster in 2010. I wrote a abstract on my capstone project.

After my Prof. Tang revise my abstract, it seem more clear than I wrote before.

I want to improve my English writing, any idea?

Original Abstract

Revised Abstract

Carbohydrate microarrays for the recognition of cross-reactive molecular markers of microbes and host cells

paulyu — Tue, 01 Dec 2009 17:29:09 +0000

This paper try to use microarray technique applied to carbohydrate analysis. Firstly, they need to know if the glycoconjugates can be immobilized on the microarray surface. Secondly, if it can be immobilized, will it have the same properties or not. Thirdly, is the sensitivity can be use in the clinical sample. Finally, is this microarray can be another tool for carbohydrate-mediated molecular recognition discovery.

They use dextrans and anti-dextran antibodies as model system. The dextrans have different linkage types such as solelyα(1,6)-linked, multiple glycosidic linkages including α(1,6)-linked,α(1,2)-linked andα(1,3)-linked, and β(2,1)-linked. According previous study these different structures can be identify by different antibodies. They use different molecular weight dextrans and find out large dextran molecular were better than smaller ones. They use N279, B1299s, LD7 three different structure antigens to the preserve properties. The results show the dextrans molecules immobilized on a nitrocellulose-coated glass slide have preserve properties. For sensitivity testing, they detected 12 distinct IgM antibodies (12/48) and 35 distinct IgG antibodies (35/48). These different binding show glycan microarrays have high sensitivity to detected specific antibodies.

The glycan microarrays can do glycan profiling also quantify the expression level. With high-throughput modern technology, we can decipher more biology information in the near future. Now we can not synthesize any glycan structure we want, and it will become a problem. As long as we can synthesize specific glycoconjugates, we can solve more questions by having more clues.

Carbohydrate microarrays for the recognition of cross-reactive molecular markers of microbes and host cells

Glycan microarray of Globo H and related structures for quantitative analysis of breast cancer

paulyu — Tue, 01 Dec 2009 14:45:08 +0000

This paper talks about how to use Globo H antigen as a breast cancer biomarker. Globo H which is a hexasaccharide and belongs to antigenic carbohydrates is highly expressed on some cancers cell surface. Breast cancer patients have highly expression antibodies against the Globo H epitope. They used Mbr1 and VK9 antibodies which can specific recognize Globo H epitope. Use these two findings they can specific differentiate health and cancer sample. They use glycan microarray to assay the finding.

Firstly, they test the specificities of antibodies. They use two different class of antibodies IgG and IgM( Mbr1 and VK9), and one stage-specific antibody (anti SSEA-3) which is the pentasaccharide precursor of Globo H¹. The results show Mbr1 and VK9 can bind to those antigens (GH, Bb4) with fucose, and anti SSEA-3 only bind with Gb5; therefore the binding is very specific. The antibodies might bind in multivalent manner, so they need to determinate dissociation constants. They use different concentration of antibodies to build the binding curve. The binding specificity of Mbr1 and VK9 for sugar epitopes is Globo H > Bb4. The binding affinity of antibodies for Globo H is Mbr1 > VK9, but for Bb4 is opposite order. Secondly, they use Cy3-labeled secondary antibodies to quantify the reaction. The VK9 and Mbr1 antibodies bind with GH and Bb4 were relative high intensity, others GH analogs were weak. According the result, the level of IgG and IgM against Globo H were significantly higher in breast cancer than normal. Finally, they compare the glycan microarray with traditional method, ELISA. They found glycan microarray is more sensitive than ELISA. Based on above evidences, they claim glycan microarray can be a sensitive rapid device for breast cancer

I read another paper which also published by the same group. It mentions about the only 61% of breast cancer cell express Globo H and 20% of breast cancer stem cell express Globo H; but there are 77.5% of breast cancer cell express SSEA-3 and 62.5% of breast cancer stem cell express SSEA-3¹. I think kill the cancer stem cell is more important than mature cancer cell. The cancer cell will replicate as long as the stem cell were present in the host cell. If we can kill the stem cell, it will stop produce new cancer cell. Our Immune system will kill the rest cancer cell.

1.Chang WW, et al. (2008) Expression of Globo H and SSEA3 in breast cancer stem cells and the involvement of fucosyl transferase 1 & 2 in Globo H synthesis. Proc Natl Acad Sci USA 105:11667–11672

Glycan microarray of Globo H and related structures for quantitative analysis of breast cancer

Complexities and algorithms for glycan structure sequencing using tandem mass spectrometry

paulyu — Tue, 24 Nov 2009 19:45:29 +0000

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

de novo, ab initio

paulyu — Tue, 24 Nov 2009 05:22:42 +0000

de novo is a Latin expression meaning “from the beginning,” “afresh,” “anew,” “beginning again.”

ab initio means “from the beginning”

In bioinformatics, de novo is a form of sequencing, as in “de novo peptide sequencing.” De novo may also be a term used to define methods for making predictions about biological features using only a computational model without extrinsic comparison to existing data. In this context, it may be sometimes interchangeable with the Latin term ab initio.

Did not find the difference of this term.