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Biology Posters

It takes FASTA DNA sequence as input, and write GFF3 as output. It uses the new NHMMER tool that comes with HMMER 3.1 for HMM searching in RNA:DNA style. NHMMER binaries for 64-bit Linux and Mac OS X are included and will be auto-detected. Multithreading is supported and one can expect roughly linear speed-ups with more CPUs.

Title

Authors

  1. Install the Docker in your operating system. If you want to use PhySpeTree on other platforms, above all need to install docker on the appropriate platform. For Windows OS, you can install Docker for Windows. For Mac OS, you can install Docker for Mac. Pull the PhySpeTree image.
  2. Microsoft Windows, Unix and Mac OS X operating systems, Microsoft Office (Adobe Illustrator, Photoshop, Excel, Word, PowerPoint), specialist data-analysis (Sigma Plot, KaleidaGraph), NMR-analysis software (XWIN-NMR, nmrPipe, Sparky, nmrView), crystallography-analysis software, graphics programs (MOLMOL, PyMOL) Activity.

Document Type

Poster

Publication Date

Mac

2016

Abstract

Natural gas (methane) is emerging as a viable power source for many industrial, commercial, and domestic applications. Bio-methane provides a promising replacement for mined natural gas. Methanogenic bacteria produce this bio-methane. These anaerobic bacteria pertain to the Domain Archaea, and are found in extreme environments where few other bacteria survive. They are employed by Up-Flow Anaerobic Sludge Blanket (UASB) reactors in the digestion of wastes to a marketable product (methane). The genome of methanogenic bacteria can be amplified using polymerase chain reaction (PCR), a synthetic DNA replication system. This system employs specific sequences of DNA called primers. The primers employed in this study focused on 16S rRNA amplification providing a fingerprint of the organism’s identity. Previous design of these primers was unsuccessful and resulted in non-specific binding.

Recommended Citation

Walters, Andrew; Doloman, Anna; and Miller, Charles, 'Development of Archaeal and Algalytic Bacteria Detection Systems' (2016). Biology Posters. Paper 27.
https://digitalcommons.usu.edu/biology_posters/27

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My book, Evolution Since Coding, updates the story of genesis, told from an evolutionary point of view. The book is accessible to a broad audience. I stress code breaking in interpretation of ~4 billion year old protein and RNA motifs. The ancient codes are so dumb, even scientists could break them, but, perhaps, the stark simplicity of the codes has not been widely acknowledged. Because the earth is only ~4.6 billion years old, ~4 billion year old motifs and codes now can be collected as antiquities, and I show how to do this. Motifs and codes are best visualized and appreciated by learning molecular graphics software, which is about as complicated as an online computer game.

The core story of genesis requires explanation of RNA synthesis and protein synthesis. The story of RNA synthesis is a story of RNA polymerases, promoters and general transcription factors. The story of protein synthesis is a story of the evolution of transfer RNA, the ribosome and the genetic code.

The story of evolution of cellular life is the story of the RNA-protein world progressing to LUCA (the last universal cellular common ancestor) and DNA genomes. LUCA diverges to archaea and bacteria. Archaea and bacteria then fuse to form eukaryotes. The complexity of eukaryotes is explained from their tortured path of evolution.

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Models are advanced to explain each transition.

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I present a surprisingly simple and conceptual story of the evolution of life on earth since coding.