Quantifying nitrogen fixation by heterotrophic bacteria in sinking marine particles.

Nitrogen ([Formula: see text]) fixation by heterotrophic bacteria associated with sinking particles contributes to marine N cycling, but a mechanistic understanding of its regulation and significance are not available. Here we develop a mathematical model for unicellular heterotrophic bacteria growing on sinking marine particles. These bacteria can fix [Formula: see text] under suitable environmental conditions. We find that the interactive effects of polysaccharide and polypeptide concentrations, sinking speed of particles, and surrounding [Formula: see text] and [Formula: see text] concentrations determine the [Formula: see text] fixation rate inside particles. [Formula: see text] fixation inside sinking particles is mainly fueled by [Formula: see text] respiration rather than [Formula: see text] respiration. Our model suggests that anaerobic processes, including heterotrophic [Formula: see text] fixation, can take place in anoxic microenvironments inside sinking particles even in fully oxygenated marine waters. The modelled [Formula: see text] fixation rates are similar to bulk rates measured in the aphotic ocean, and our study consequently suggests that particle-associated heterotrophic [Formula: see text] fixation contributes significantly to oceanic [Formula: see text] fixation.

The cost of toxin production in phytoplankton: the case of PST producing dinoflagellates.

Many species of phytoplankton produce toxins that may provide protection from grazing. In that case one would expect toxin production to be costly; else all species would evolve toxicity. However, experiments have consistently failed to show any costs. Here, we show that costs of toxin production are environment dependent but can be high. We develop a fitness optimization model to estimate rate, costs, and benefits of toxin production, using PST (paralytic shellfish toxin) producing dinoflagellates as an example. Costs include energy and material (nitrogen) costs estimated from well-established biochemistry of PSTs, and benefits are estimated from relationship between toxin content and grazing mortality. The model reproduces all known features of PST production: inducibility in the presence of grazer cues, low toxicity of nitrogen-starved cells, but high toxicity of P-limited and light-limited cells. The model predicts negligible reduction in cell division rate in nitrogen replete cells, consistent with observations, but >20% reduction when nitrogen is limiting and abundance of grazers high. Such situation is characteristic of coastal and oceanic waters during summer when blooms of toxic algae typically develop. The investment in defense is warranted, since the net growth rate is always higher in defended than in undefended cells.

Trophic Strategies of Unicellular Plankton.

Unicellular plankton employ trophic strategies ranging from pure photoautotrophs over mixotrophy to obligate heterotrophs (phagotrophs), with cell sizes from 10-8 to 1 µg C. A full understanding of how trophic strategy and cell size depend on resource environment and predation is lacking. To this end, we develop and calibrate a trait-based model for unicellular planktonic organisms characterized by four traits: cell size and investments in phototrophy, nutrient uptake, and phagotrophy. We use the model to predict how optimal trophic strategies depend on cell size under various environmental conditions, including seasonal succession. We identify two mixotrophic strategies: generalist mixotrophs investing in all three investment traits and obligate mixotrophs investing only in phototrophy and phagotrophy. We formulate two conjectures: (1) most cells are limited by organic carbon; however, small unicellulars are colimited by organic carbon and nutrients, and only large photoautotrophs and smaller mixotrophs are nutrient limited; (2) trophic strategy is bottom-up selected by the environment, while optimal size is top-down selected by predation. The focus on cell size and trophic strategies facilitates general insights into the strategies of a broad class of organisms in the size range from micrometers to millimeters that dominate the primary and secondary production of the world's oceans.

Modeling succession of key resource-harvesting traits of mixotrophic plankton.

Unicellular eukaryotes make up the base of the ocean food web and exist as a continuum in trophic strategy from pure heterotrophy (phagotrophic zooplankton) to pure photoautotrophy ('phytoplankton'), with a dominance of mixotrophic organisms combining both strategies. Here we formulate a trait-based model for mixotrophy with three key resource-harvesting traits: photosynthesis, phagotrophy and inorganic nutrient uptake, which predicts the trophic strategy of species throughout the seasonal cycle. Assuming that simple carbohydrates from photosynthesis fuel respiration, and feeding primarily provides building blocks for growth, the model reproduces the observed light-dependent ingestion rates and species-specific growth rates with and without prey from the laboratory. The combination of traits yielding the highest growth rate suggests high investments in photosynthesis, and inorganic nutrient uptake in the spring and increased phagotrophy during the summer, reflecting general seasonal succession patterns of temperate waters. Our trait-based model presents a simple and general approach for the inclusion of mixotrophy, succession and evolution in ecosystem models.

Spatial dynamics of a nutrient-phytoplankton system with toxic effect on phytoplankton.

The production of toxins by some species of phytoplankton is known to have several economic, ecological, and human health impacts. However, the role of toxins on the spatial distribution of phytoplankton is not well understood. In the present study, the spatial dynamics of a nutrient-phytoplankton system with toxic effect on phytoplankton is investigated. We analyze the linear stability of the system and obtain the condition for Turing instability. In the presence of toxic effect, we find that the distribution of nutrient and phytoplankton becomes inhomogeneous in space and results in different patterns, like stripes, spots, and the mixture of them depending on the toxicity level. We also observe that the distribution of nutrient and phytoplankton shows spatiotemporal oscillation for certain toxicity level.

Determination of HER2/neu status: a pilot study comparing HER2/neu dual in situ hybridization DNA probe cocktail assay performed on cell blocks to immunohistochemisty and fluorescence in situ hybridization performed on histologic specimens.

CONTEXT: Validation of new methodologies for determining human epidermal growth factor receptor 2 gene (HER2/neu) amplification status is crucial for advancing the standard of care and determining treatment for patients with primary and/or metastatic breast carcinoma. OBJECTIVE: To compare results of HER2/neu gene amplification status by 2-color chromogenic in situ hybridization (ISH) on cell block material to HER2/neu status by immunohistochemistry (IHC) and/or fluorescence in situ hybridization (FISH) in the corresponding resection specimen or previous biopsy specimen. DESIGN: Formalin, thrombin, and Cellient cell blocks were prepared from cytologic samples obtained from resection specimens from 27 patients with invasive breast carcinoma. In situ hybridization was performed on cell block sections from 18 of the collected cases, on both the Ventana BenchMark ULTRA and the Ventana BenchMark XT, and the HER2/neu gene amplification status was determined. This was then compared to the HER2/neu status by IHC and/or FISH in the resection specimen or previous biopsy specimen. RESULTS: Comparison of HER2/neu status by ISH on the quantifiable cell block sections showed 100% correlation with the HER2/neu status determined by IHC or FISH in the corresponding histologic specimens. The results from thrombin and formalin cell blocks were statistically superior to the results from Cellient cell blocks on both Ventana instruments. CONCLUSIONS: While further validation and study are needed, preliminary results show that the HER2/neu gene amplification status of breast carcinomas can reliably be determined on thrombin and formalin cell block material by using ISH. More consistent staining and better signal integrity was obtained with the Ventana BenchMark ULTRA than the BenchMark XT.

Digital slide imaging in cervicovaginal cytology: a pilot study.

CONTEXT: Digital whole slide imaging is the anticipated future of anatomic pathology, where sign-out of glass slides will be replaced by scanned images. Whole slide imaging has been successfully used in surgical pathology, but its usefulness and clinical application have been limited in cytology for several reasons, including lack of availability of z-axis depth focusing and large file size. Recently, several systems have become available in the United States for whole slide imaging with z-axis technology. OBJECTIVE: To determine the accuracy and efficiency of whole slide imaging, as compared with traditional glass slides, for use in cervicovaginal diagnostic cytology. DESIGN: Eleven cervicovaginal cytology cases (ThinPrep and SurePath) scanned at ×20, ×40, and ×40 z-stack magnifications using the BioImagene iScan Coreo Au 3.0 scanner were evaluated by 4 cytotechnologists and 3 pathologists in a blinded study. Different magnification scans were recorded as separate cases and presented in a randomized sequence. Corresponding glass slides were also reviewed. For each case, the diagnoses and total time to reach each diagnosis were recorded. RESULTS: Diagnostic accuracy was higher and average time per case was lower with glass slides as compared with all digital images. Among the digital images, the ×40 or ×40 z-stack had the highest diagnostic accuracy and lowest interpretation time. CONCLUSIONS: Whole slide imaging is a viable option for the purposes of teaching and consultations, and as a means of archiving cases. However, considering the large file size and total time to reach diagnosis on digital images, whole slide imaging is not yet ready for daily cervicovaginal diagnostic cytology screening use.

Comparison of breast carcinoma prognostic/predictive biomarkers on cell blocks obtained by various methods: Cellient, formalin and thrombin.

OBJECTIVE: To compare results of immunohistochemical (IHC) assays for estrogen receptor (ER), progesterone receptor (PR) and human epidermal growth factor receptor 2 (HER2) performed on thrombin, formalin and Cellient cell blocks to those performed on tissue. STUDY DESIGN: Formalin, thrombin and Cellient cell blocks were prepared from cytologic samples obtained from resection specimens of 31 patients with invasive breast carcinoma. ER, PR, HER2 and MIB-1 (Ki-67) IHC stains were performed on all three types of cell blocks and compared to the same stains performed on the patient's paraffin-embedded biopsy or resection. Cell and tissue blocks with equivocal staining for HER2 were submitted for fluorescence in situ hybridization (FISH). RESULTS: Adequate Cellient blocks were obtained for all 31 cases. Comparison of results of ER IHC assays on all three types of cell blocks showed 100% correlation with tissue. Both Cellient and thrombin blocks showed 100% correlation with tissue for HER2 IHC and FISH results. The only statistically significant difference between cell block methods was found in PR staining, where false-negative results occurred with Cellient and thrombin blocks. CONCLUSION: Breast biomarker IHC assays performed on Cellient blocks are reliable and correlate with tissue block results, particularly for ER and HER2, the most clinically important markers.

A liquid concept--do classic preparations of body cavity fluid perform differently than ThinPrep cases? Observations from the College of American Pathologists Interlaboratory Comparison Program in Nongynecologic Cytology.

CONTEXT: Newer liquid-based preparations differ morphologically from classic preparations (smears, filters, and cytocentrifuged preparations). Is adenocarcinoma more readily detected in liquid-based preparations? We reviewed responses from 16,750 fluid challenges of adenocarcinoma distributed in 2005 in the College of American Pathologists Interlaboratory Comparison Program in Nongynecologic Cytology (CAP NGC). OBJECTIVE: To compare the performance of body cavity fluid liquid-based preparations with adenocarcinoma to that in classic preparations in the CAP NGC. DESIGN: Responses for ThinPrep challenges were compared with classic preparations for exact match diagnoses of adenocarcinoma from pelvic washes, pleural fluid, pericardial fluid, and peritoneal fluids in the 2005 CAP NGC. RESULTS: A total of 13,690 pathologists, 8345 cytotechnologists, and 5958 laboratories submitted responses to fluid challenges in 2005. Adenocarcinoma comprised 16,750 of the fluid challenges; 88% were classic preparations, and 12% were ThinPrep challenges. The exact match to the reference diagnosis of adenocarcinoma was seen in 77% of conventional preparations and 81% of ThinPrep challenges when a general category of "positive for malignancy" was assigned. When "suspicious for malignancy," an exact match diagnosis of adenocarcinoma was made in 5% and 4% of classic and ThinPrep challenges, respectively. CONCLUSIONS: ThinPrep challenges performed slightly better overall, but only pelvic washings and peritoneal fluids demonstrated statistically significant improved performance with ThinPrep challenges. Use of liquid-based preparation is widespread for nongynecologic preparations and performs as well, and sometimes better than, classic preparations in an interlaboratory comparison program.

Recurring plankton bloom dynamics modeled via toxin-producing phytoplankton.

A simple nutrient-phytoplankton model is proposed and analyzed in the presence of toxic chemicals released by toxin-producing phytoplankton (TPP) to understand the dynamics of seasonally recurring bloom phenomena. We observe that the presence of toxic chemicals helps to explain the bloom phenomenon. We have further studied our proposed system by varying the toxin liberation rate. Our model displays a wide range of dynamical behaviours, from simple cyclical blooms to irregular chaotic blooms. We also observe skipping phenomenon. The effect of toxic chemicals released by TPP cannot, thus, be ignored in 'bottom-up' models.

Large B-cell lymphomas: fine-needle aspiration plays an important role in initial diagnosis of cases which are falsely negative by flow cytometry.

Large B-cell lymphomas (LBCLs) have significant false-negative results when immunophenotyped by flow cytometry (FC). To clarify the role fine-needle aspiration (FNA) in reducing this false-negative rate, 28 cases ultimately diagnosed as LBCL that had FNA as part of the workup and a negative FC were identified. We examined their clinical and cytologic features, in comparison with cases of LBCL with FNAs that were positive by FC. In 24/28 FC-negative cases (86%) a cytologic diagnosis of suspicious or positive for malignancy was rendered. We conclude that cytologic analysis is more sensitive than FC in the diagnosis of malignancy in FNA of LBCL, particularly in aspirates with low cellularity and/or low viability. Examination of cytospin preparations of the actual material analyzed by FC may provide an indication that an FC result is falsely negative. It is important to recognize the potential of false-negativity by FC of LBCLs when interpreting FNAs with features suggesting lymphoma.