Science and Family pt. 2

In a few days my mom, dad, my son, and I will be moving to Everson, WA. I started a new postdoc at the Salish Sea Research Center. Our belongings are now on a truck and on their way to Washington State.

One year ago my husband moved to State College to start medical residency. Previous to this he was separated from my son and me. This is because three years ago I started my first postdoc at Penn State University. Now, we are separating again. Hopefully, for the last time in our lifetime.

In the meantime, my mom and dad continue to travel with me on this academic journey. They are raising my son while I pursue science as a career. My mom is a teacher and she is homeschooling my son this year. He will hopefully start Kindergarten next fall. We are moving into a cabin on 5 acres. We are all very excited to start this next phase. We are also very sad to leave my husband and our house in State College, PA.

My son, my mom, my dad in Coburn, PA ( January 2019).

Science and Family pt. 1

My husband and I attended the 2011 Geological Society of America meeting in Minneapolis, MN. This is us posing in front my poster.

 

My husband, my son, and I posing in front of beamline 12.3.2 at the Advanced Light Source in 2016.

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.