The Use of Microarrays in the Detection of the Gene Expression of Ribulose- 1,5- Bisphosphate Carboxylase/Oxygenase (RubisCO) in the Marine Environment
Bibliographic record
Abstract
The Calvin-Benson-Bassham (CBB) pathway is the primary pathway for the entry of inorganic carbon in the biosphere. Autotrophic organisms use this cycle to ultimately convert CO2 into carbohydrates using a key enzyme known as ribulose-1,5-bisphosphate carboxylase/oxygenase (RubisCO). The gene that encodes for the large subunit of RubisCO is rbcL and detection of its expression can be used to determine the autotrophic organisms present in the environment. Recently, microarrays have been used to study functional gene expression from environmental samples such as those obtained from sediments and soil. The purpose of this thesis is to combine microarray technology and rbcL expression analysis to investigate phytoplankton populations in the Mississippi River Plume (MRP). Initially, a macroarray was constructed to determine its capabilities of quantifying gene expression in MRP. PCR amplicons were spotted onto a nylon membrane and labeled transcript RNA was hybridized to each array. Due to the large amount of cross hybridization that was observed, a microarray was used. Microarray analysis revealed large amounts of Synechococcus, pelagophyte and prymnesiophyte expression in the surface waters. Furthermore, there was no chlorophte or Prochlorococcus expression observed in the surface waters. Subsurface microarray data showed high levels of pelagophytes and other Form ID organisms. A significant chlorophyte signal was also observed in the subsurface. This study provides a third level of specificity at which phylogenetic diversity has been sampled in the MRP. Although a limited number of samples were analyzed by microarrays, this technology shows promise and this study was viewed as a pilot for their application. The rbcL probes designed were based upon published sequences from 2003 and we now have a much greater understanding of the diversity of rbcL-containing phytoplanktonic phylotypes. Future studies should employ this knowledge for judicious probe selection.
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How this classification was reachedexpand
Full frame distilled prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. Learned from the 10,348 direct Codex labels and 10,348 direct Gemma labels. Candidate is the union of thresholded teacher heads; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels or direct frontier model labels.
Codex and Gemma teacher scores by category
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.001 | 0.000 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.000 |
| Bibliometrics | 0.000 | 0.000 |
| Science and technology studies | 0.000 | 0.000 |
| Scholarly communication | 0.000 | 0.000 |
| Open science | 0.000 | 0.000 |
| Research integrity | 0.000 | 0.000 |
| Insufficient payload (model declined to judge) | 0.000 | 0.000 |
Machine scores (provisional)
The two teacher heads of the student model, read on this work. A score orders the frame for review; it never asserts a category, and the validation status ships verbatim with every row.
Baseline scores from an immature model (maturity gate not passed, 7 training rounds). Scores rank; they never assert a category.
score_only:v0-immature-baseline · verbatim from the scoring run: score_only means the number may rank works, and no category label ships from itClassification
machine, unvalidatedMachine predicted; a candidate call from one teacher head, not a consensus.
How this classification was reached, model by model and score by score, is at the end of the page under "How this classification was reached".