Anabaena planktonica

Anabaena planktonica is a harmful, bloom-forming freshwater cyanobacterium.

 Anabaena planktonica

 

 

 

 

Pseudo-nitzschiamarine rbcS qRT-PCR assay

 Pseudo-nitzschiamarine, a genus of diatom, includes species that produce domoic acid, a neurotoxin
responsible for illness and mortality in both humans and marine wildlife. 

Pseudo-nitzschia has been identified as one of the main genera to increase in cell numbers during iron fertilization experiments in high nitrate low chl (HNLC) regions of the Southern Ocean, the subarctic Pacific, and the east equatorial Pacific (de Baar et al. 2005). 

https://en.wikipedia.org/wiki/Pseudo-nitzschia#/media/File:Pseudonitzschia2.jpg

 

Although no additional human cases have been confirmed, bioaccumulation of domoic acid has resulted in illness and mortalities of many birds and marine mammals, especially along the Pacific coast of North America (Gulland, 2006; Scholin et al., 2000; Sierra-Beltra´n et al., 1997; Work et al., 1993). 

Domoic acid

https://caseagrant.ucsd.edu/project/frequently-asked-questions-domoic-acid-in-california-crabs

 

The threat posed by human consumption of contaminated shellfish has led to periodic closures of commercial and recreational harvesting areas, resulting in significant economic
losses around the world (Gallacher et al., 2001; Trainer, 2002; Tweddle et al., 2010).  

The genus Pseudo-nitzschia is composed of at least 30 species and is common to diatom assemblages in all ocean basins, both in coastal and offshore waters.  Morphological species complexes and/or cryptic species are increasingly described for the genus (Hasle 1995, Manhart et al. 1995, Villac and Fryxell 1998, Lundholm et al. 2002, 2003, 2006, Orsini et al. 2004, Hasle and Lundholm 2005).

Molecular methods provide early detection of blooms Pseudo-nitzschiamarine and predict toxin accumulation.

Delaney et al. (2011) developed a quantitative reverse transcription PCR (qRT-PCR) assay for the detection of ribulose-1,5-biphosphate carboxylase/oxygenase small subunit (rbcS) gene. 

The rbcS qRT-PCR assay is useful for the detection and enumeration of low concentrations of P. multiseries in the environment.

Nucleic acids

The nucleic acids, the vital constituents of living beings, are long-chain polymers composed of nucleotides. Nucleic acids were named based partly on their chemical properties and partly on the observation that they represent a major constituent of the cell nucleus. The fact that they form the chemical basis for the transmission of genetic traits was not realized until 1941. Among other important roles, nucleotides can serve as sources of energy in the form of ATP, physiological signaling mediators, secondary messengers, and allosteric enzyme effectors.

Effects of eutrophication of ecosystems

Anthropogenic activities are increasing. Activities include urban, agricultural, and industrial land development. The activity has resulted in the eutrophication of numerous fresh-water ecosystems worldwide. The excess of nutrients, such as phosphorus and nitrogen increase the growth rate of phytoplankton resulting in the formation of dense populations (i.e., algae blooms). 

Algae blooms, cyanobacterial blooms, have been shown to pose environmental and social
problems (Vargas-Montero and Freer 2004; Haande et al. 2007; Stone and Bress 2007; Zhang et al. 2007). 

Blooms reduce water quality and the recreational value of aquatic ecosystems (Rahman at al. 2005; Smith and Lester 2006).

 Cyanobacterial species produce potent toxins, which pose serious health risks to both human and animals (Codd et al. 2005).

qPCR

 

Quantitative real-time PCR technologies (what is Taqman qPCR):

 

https://www.ncbi.nlm.nih.gov/probe/docs/techqpcr/

Quantitative real-time PCR (qrt-PCR) is a good option to generate ‘real-time’ data regarding the presence of harmful algal species. The major goal of a qrt-PCR project is to design and test a qrt-PCR assay that will accurately identify and estimate marine algal species. 

Quantification is performed during the exponential phase of the PCR, where amplification efficiency is maximum. In real-time PCR, amplicon formation is monitored after each cycle by measuring a fluorescence signal.

An amplicon is a piece of DNA or RNA that is the source and/or product of natural or artificial amplification or replication events. It can be formed using various methods including polymerase chain reactions (PCR) or natural gene duplication.

In qrt-PCR, the increase in fluorescence observed during the reaction will be proportional to the starting quantity of the target molecule. Fluorescence can be generated by using fluorescent probes such as TaqMan®. Since there is a correlation between the cycle number at which the amplicon is initially detected (threshold cycle, Ct) and the starting amount of target molecules, it is possible to calculate the amount of target sequence in an unknown sample by using a standard reference curve generated using DNA extracted from a known number of cultured cells. 

Postdoctoral Molecular Researcher position at Northwest Indian College

 

As a Postdoc and Molecular Researcher at Northwest Indian College on the Lummi main campus at the Salish Sea Research Center (SSRC), I will monitor harmful agal bloom species (Alexandrium catenella, Azadinium poporum, and Pseudo-nitzschia multiseries) in the Bellingham and Lummi Bays (Washington State) using molecular techniques. 

Protocols for monitoring harmful algal bloom species will used in inform the local Lummi Nation. This project will provide food and data sovereignty for the Lummi Nation and Lummi Natural Resources deparment about annual harmful algal blooms. 

Gooseberry Point along the Bellingham Bay

 

Career update for years 2008-2020

Background:

LSAMP-Bridge to the Doctorate cohort VI.

As I have not updated this blog since I was a Master's student at the University of New Mexico (Image above taken in 2008) working with Professor Laura Crossey on the biogeochemistry of the Tierra Amarilla Anticline in northern New Mexico, I thought it was a good idea to catch up on my background. As a biogeochemist, I have used and become an expert in a variety of different imaging and spectroscopy tools. 

(from left to right) Brandi Cron, Professor Brandy Toner, Robert Atticus Kamermans and Aubrey Dunshee taking a photo break with Robert Atticus Kameramans at BL 12.3.2 at the Advanced Light Source.

As a Ph.D. candidate at the University of Minnesota (image above taken in 2017), I gained expertise characterizing abiotic and biotic mineral precipitates in deep-sea hydrothermal vents, using Scanning Transmission X-ray Microscopy, X-ray Absorption Near Edge Structure (XANES) and X-ray diffraction.

Pennsylvania State University geosciences professor Julie Cosmidis and postdoctoral fellow Brandi Kamermans prepare to change out samples on the SM beamline. Photo is from the Canadian Light Source.

Most recently, I have been using Scanning Transmission X-ray Microscopy, Raman, and Scanning Electron Microscopy at the Pennsylvania State University Material Characterization Laboratory to characterize both elemental sulfur and organics produced by Sulfuricurvum kujiense, in an effort to distinguish chemical versus microbial induced mineral production.