Writing in Biology - Section 1

HOX genes are a group of highly conserved genes in organisms that dictates their body plans. To determine whether HOX genes are a reliable indicator of phylogeny, we look to determine the reliability of the phylogenetic trees made using the HOXC gene and comparing it to the existing phylogenetic tree. The analysis would highlight differences in HOXC gene expression, which is gathered using MEGA software. The conclusion to this study will allow for the determination of phylogeny in a new species using the sequence of the HOXC gene.

It is clear that this process is very complex and multi-staged; non-coding RNAs are involved in it. To a complete understanding of all these processes in different animals, science is still very far away. When the basic mechanisms of gene regulation during early ontogenesis are deciphered, biologists will be able to address fundamental questions. A modified phylogenetic tree allows us to map where organisms may have originated based on HOX similarities. A heat graph showing HOX gene interactions will let us see the expression of unique HOX genes. By doing this analysis, we can know more about HOXC genes and how they manifest in the animal kingdom. Such techniques with animals can lead to answering important questions on the evolution of various animals.

The overall objective of our proposal was to identify subjects that contain a highly conserved gene that can be characterized by the amount of expression. One specific aim the proposal had was to identify highly conserved genes that are present in the Animalia kingdom. In the development of animals, there is a period of embryonic similarity, where both the appearance of the embryos and the expression of their genes are conserved. The existence of this period is associated with the appearance in the evolution of stable building plans. In HOXC genes, the genes themselves are located in a specific order on chromosomes. Therefore, a consistent pattern of activation of HOXC genes is necessary in order for the body to form correctly. However, the mechanism and regulation of the HOXC genes themselves remain unclear.

In this project, we will be making nine different phylogenetic trees based on the nine HOXC genes. Each phylogenetic tree will retrieve a human HOXC reference sequence from the NCBI gene database and then search again on the NCBI gene database for the rest of the HOXC genes that are available for all species that lie in the Animalia kingdom. Of the available sequences, we will use MEGA software to align the sequence. The sequence is then saved. Using MEGA’s software, a phylogenetic tree will be created. The tree is then exported as a NEXUS file and uploaded into the iTOL website to create a phylogenetic tree that may be manipulated. The phylogenetic tree will then be evaluated for their reliability by obtaining the tree’s bootstrap value from MEGA.

    HOX genes, specifically HOXC genes and their homeodomains, are vital to the development of vertebrates. The HOXC genes function in cell differentiation, proliferation, and epithelial tissue development, with associations to lymphoma and club foot in humans (Gene Cards, 2019). Some studies have also indicated that the genes may be important in vertebrae (Carrasco, 1994) and other bone development such as craniofacial morphogenesis (Hirata, 2016). Mutations in these genes can often result in a homeotic mutation, where certain body parts end up growing where it is not usually grown, or a severe malformation of certain limbs and organs (Alvarado, 2016).

HOX genes specify the regions in an anterior-posterior axis of an animal. Because the organization of the body depends on these genes, a mutation in them often results in misformation of limbs and other body parts. Because HOX genes are highly conserved across species, making it useful in determining the phylogeny of species. However, the determination of the HOXC gene as an indicator of phylogeny across all vertebrae species is something that has not been examined as of now.

Another specific aim the proposal has is to isolate and characterize the expression of highly conserved genes identified in Specific Aim 1 from the Animalia kingdom. The expansion of our subject of interest from chicken, zebrafish, Xenopus, and newt to the Animalia kingdom will allow for the comparison of the HOX gene in all vertebrate and invertebrate animals, which is different from species to species. Characterization methods of our data include a phylogenetic tree and a heat graph of gene expression. A modified phylogenetic tree allows us to map where organisms may have originated based on HOX similarities. The phylogenetic tree will take into account the Animalia kingdom.

The statement motivated our group to propose that the HOX genes express little variation in vertebrae, and test the statement by knowing how consistent this data would be if we were to expand our subject of interest to a whole kingdom, rather than specific subjects used for their evidence (chicken, zebrafish, Xenopus, and newt). We will now look into HOX genes to see how similar or different expression of the HOX gene is throughout the Animalia kingdom.

The objective of our proposal is to create a phylogenetic tree examining the possibility of using the HOXC gene as an indicator of the phylogeny. One specific aim of the proposal is to identify highly conserved genes that are present in vertebrates. In preliminary work, we found that one example of a highly conserved gene is the BOP1 gene present in ribosomal DNA. Further research done on HOX genes has noted that the duplication of HOX clusters is shared by all vertebrae (Ruddle et al. 1994).

The objective of our proposal is to create a phylogenetic tree examining the possibility of using the HOXC gene as an indicator of the phylogeny. One specific aim of the proposal is to identify highly conserved genes that are present in vertebrates. In preliminary work, we found that one example of a highly conserved gene is the BOP1 gene present in ribosomal DNA. Further research done on HOX genes has noted that the duplication of HOX clusters is shared by all vertebrae (Ruddle et al. 1994). The statement motivated our group to propose that the HOX genes express little variation in vertebrae, and test the statement by knowing how consistent this data would be if we were to expand our subject of interest to a whole kingdom, rather than specific subjects used for their evidence (chicken, zebrafish, Xenopus, and newt). We will now look into HOX genes to see how similar or different expression of the HOX gene is throughout the Animalia kingdom.