HDelgadi Week 11

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Contents

10 Term Definitions

  1. Obligate-Capable of functioning or surviving only in a particular condition or by assuming a particular behavior
  2. Paralogs-genes or gene products that are homologous (descended from a common ancestor) and that result from a gene duplication. Paralogous genes typically occur in a single species but are also visible when species are compared. For example, human hemoglobin alpha is paralogus to human hemoglobin beta. human hemoglobin alpha is also paralogous to horse hemoglobin beta, but is orthologous to horse hemoglobin alpha
  3. Entner-Doudoroff pathway-a degradative pathway for carbohydrates in certain microorganisms (for example, Pseudomonas sp.) that lack hexokinase, phosphofructokinase, and glyceraldehyde-3-phosphate dehydrogenase
  4. Exogenous-originating outside or caused by factors outside the organism
  5. Halophilic-pertaining to or characterized by an affinity for salt; requiring a high concentration of salt for optimal growth
  6. Auxotroph-A mutated microorganism having nutritional requirements that differ from those of unmutated microorganisms from the same strain
  7. Diaminopimelate-C7H14O4N2 A compound that serves as a component of cell wall mucopeptide in some bacteria and as a source of lysine in all bacteria. Abbreviated DAP
  8. Symporter-A symporter is an integral membrane protein that is involved in movement of two or more different molecules or ions across a phospholipid membrane such as the plasma membrane in the same direction, and is, therefore, a type of cotransporter. Typically, the ion(s) will move down the electrochemical gradient, allowing the other molecule(s) to move against the concentration gradient. The movement of the ion(s) across the membrane is facilitated diffusion, and is coupled with the active transport of the molecule(s). Although two or more types of molecule are transported, there may be several molecules transported of each type
  9. Porins-porins are beta barrel proteins that cross a cellular membrane and act as a pore through which molecules can diffuse.[1] Unlike other membrane transport proteins, porins are large enough to allow passive diffusion, i.e., they act as channels that are specific to different types of molecules. They are present in the outer membrane of Gram-negative bacteria and some Gram-positive bacteria of the group Mycolata (mycolic acid-containing actinomycetes), the mitochondria, and the chloroplast
  10. Sporulation-in biology, a spore is a unit of asexual reproduction that may be adapted for dispersal and for survival, often for extended periods of time, in unfavorable conditions. By contrast, gametes are units of sexual reproduction. Spores form part of the life cycles of many plants, algae, fungi and protozoa.[1] In bacteria, spores are not part of a sexual cycle but are resistant structures used for survival under unfavourable conditions

MOD

The Model Organism Database is for the strain Chlamydia trachomatis A/HAR-13 which is the strain we are looking at through our microarray paper. Hence, the database is not based on the strain Chlamydia trachomatis D/UW-3/Cx that is talked about in the genome paper.

  1. What types of data can be found in the database (sequence, structures, annotations, etc.); is it a primary or “meta” database; is it curated electronically, manually [in-house], or manually [community])?
    • Protein-coding, non-coding genes, splice variants, cDNA, protein sequences, non-coding RNAs, Gene families based on HAMAP and PANTHER classification. This database is a meta database and curated electronically.
  2. What individual or organization maintains the database?
    • The European Bioinformatics Institute which is part of the European Molecular Biology Laboratory.
  3. What is their funding source(s)?
    • European Molecular Biology Laboratory
  4. Is there a license agreement or any restrictions on access to the database?
    • There are no restrictions to access the database.
  5. How often is the database updated?
    • The database is updated every few months.
  6. Are there links to other databases?
    • Yes there are links to other databases like UniProt.
  7. Can the information be downloaded?
    • Yes the information can be downloaded.
  8. In what file formats?
    • The information can be downloaded through FASTA.
  9. Evaluate the “user-friendliness” of the database.
    • The database does provide tutorials and provides a lot of information to acclimate to the database. This help is provided through the link 'Help & Documentation' at the top of the database page next to Downloads.
  10. Is the Web site well-organized?
    • The website is well organized with headings, descriptions, and subheadings.
  11. Does it have a help section or tutorial?
    • Yes it does have a help section which includes tutorials under the section 'Help & Documentation'.
  12. Run a sample query. Do the results make sense?
    • I ran the sample CT119 and it took me to a 'Your search for 'CT119' returned no results', but gave me the choice to click on "wildcards, e.g. 'CT119*'" and upon clicking on this it took me to the original ID that I had initially typed in.
  13. What is the format (regular expression) of the main type of gene ID for this species? (for example, for Vibrio cholerae it was VC#### or VC_####).
    • The format of the main type of gene ID for this species is CTA_####.

Outline for “Genome Sequence of an Obligate Intracellular Pathogen of Humans: Chlamydia trachomatis”

  1. Importance of Chlamydia trachomatis
    • Bacterial pathogen leads to human diseases such as ocular infection leads to trachoma (primary cause of preventable blindness)
    • Chlamydial genital tract infections are the most common according to the U.S. state health departments and the U.S. Centers for Disease Control and Prevention
    • Genital tract infection can lead to pelvic inflammatory disease, ectopic pregnancy, chronic pelvic pain, epididymitis, infant pneumonia
    • May increase risk of HIV infection
  2. Infectious Development
    • After infecting Eukaryotic cells, chlamydia grow within an intracellular vacuole also known as an inclusion
    • Elementary body (EB)-inactive infectious developmental form
    • Once in target host cell it becomes an active infectious developmental form Reticulate Body (RB)
    • 20 hours after Chlamydia has infected the cell and after binary fission divisions—RB becomes EB and these EBs are infectious so they continue to infect host cells
  3. Transcription and Translation
    • Large size of elongation factor GreA (CT636)
    • Aminoacyl-transfer RNA (tRNA)synthetase genes
    • Operon encoding three subunits of glutamyl-tRNA amidotransferase
    • Translational machinery:two identical ribosomal RNA operons, complete set of ribosomal proteins, genes for a typical bacterial complement of translation factors, and RNA modification enzymes
  4. Sigma Factors and their Significance
    • Sigma 28 and 54 possibly play a role in developmental stage processes
    • System consisting of RbsW-like single-domain histidine kinase, two RsbV orthologs, and RsbU-like protein phosphate may initiate Chlamydia developmental cycle
  5. Chlamydia outer membrane
    • Lipopolysaccharide (Major Outer Membrane Protein) (MOMP)
    • Cysteine-rich proteins
    • Both Disulfide crossed-link throughout the EB form of Chlamydia
    • Membrane can withstand osmotic stress
  6. Figure 1
    • Plasma Membrane Protein (PMP) and proteases’ relationship with virulence and organization of the two clusters of PMP genes. The coding strand direction is outlined through the arrows. The predicted molecular mass and pI for each PMP is also shown. Motifs containing predicted catalytic residues are shown in part C of Figure 1.
  7. Table 1
    • Genes found to be virulent determinant for gram-negative species and plant pathogens are horizontally transferred. These genes are orthologous to type III secretion systems which is probable in being crucial for host cell invasion and manipulation in host cell regulatory pathways.
  8. Figure 2
    • HKD Superfamily may be crucial in understanding Chlamydia modification of host cell phospholipids
  9. Figure 3
    • Chlamydia enoyl-acyl carrier protein reductase is an example of horizontal transfer
  10. Genome Sequencing Methods
    • Chlamydia trachomatis D/UW-3/Cx EBs were isolated
    • EBs pelleted and in HBSS containing 2% Triton X-100 to make proteins soluble
    • Incubated for 30 minutes with 5 μg/ml DNase and RNase to remove extracellular DNA
    • Purification using discontinuous gradients consisting of 30%, 40%, 45%, and 50% Renografin
    • DNA isolated to an average of 1.6 kbp
  11. Genome Annotation Methods
    • PEPDATA and FRAMES program
    • Gapped BLASTP program was used for the
    • The entire nucleotide sequence was looked at through BLASTN to identify RNAse P RNA, tRNAs and rRNAs


HDelgadi (talk) 01:30, 12 November 2013 (PST) Class Journal Week 1

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HDelgadi Week 11

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Hilda Delgadillo

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