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Full-Text Articles in Life Sciences
Survey Of Microbial Populations Within Lake Michigan Nearshore Waters At Two Chicago Public Beaches, Kema Malki, Katherine Bruder, Catherine Putonti
Survey Of Microbial Populations Within Lake Michigan Nearshore Waters At Two Chicago Public Beaches, Kema Malki, Katherine Bruder, Catherine Putonti
Catherine Putonti
Lake Michigan is a critical resource for the residents of Chicago, providing drinking water to its 9+ million area residents. Along Chicago׳s 26 miles of public beaches the populous urban environment and this freshwater environment meet. While city-led monitoring initiatives investigate pathogenic bacteria in these nearshore waters, very little is known about other microbial species present. We collected surface water samples from two Chicago public beaches – Montrose Beach and 57th Street Beach – every ten days from June 5 through August 4, 2013 as well as once in early Fall (October 4, 2013). Sixteen bacterial communities in total were …
Survey Of Viral Populations Within Lake Michigan Nearshore Waters At Four Chicago Area Beaches, Emily Sible, Alexandria Cooper, Kema Malki, Katherine Bruder, Siobhan C. Watkins, Yuriy Fofanov, Catherine Putonti
Survey Of Viral Populations Within Lake Michigan Nearshore Waters At Four Chicago Area Beaches, Emily Sible, Alexandria Cooper, Kema Malki, Katherine Bruder, Siobhan C. Watkins, Yuriy Fofanov, Catherine Putonti
Catherine Putonti
In comparison to the oceans, freshwater environments represent a more diverse community of microorganisms, exhibiting comparatively high levels of variability both temporally and spatially Maranger and Bird, Microb. Ecol. 31 (1996) 141–151. This level of variability is likely to extend to the world of viruses as well, in particular bacteria-infecting viruses (bacteriophages). Phages are known to influence bacterial diversity, and therefore key processes, in environmental niches across the globe Clokie et al., Bacteriophage 1 (2011) 31–45; Jacquet et al., Adv. Ocean Limn. 1 (2010) 97–141; Wilhelm and Suttle, Bioscience 49 (1999) 781–788; Bratback et al., Microb. Ecol. 28 (1994) 209–221. …
18s Rdna Dataset Profiling Microeukaryotic Populations Within Chicago Area Nearshore Waters, Daniel Searle, Emily Sible, Alexandria Cooper, Catherine Putonti
18s Rdna Dataset Profiling Microeukaryotic Populations Within Chicago Area Nearshore Waters, Daniel Searle, Emily Sible, Alexandria Cooper, Catherine Putonti
Catherine Putonti
Despite their critical role in the aquatic food web and nutrient cycling, microeukaryotes within freshwater environments are under-studied. Herein we present the first high-throughput molecular survey of microeukaryotes within Lake Michigan. Every two weeks from May 13 to August 5, 2014, we collected surface water samples from the nearshore waters of four Chicago area beaches: Gillson Park, Montrose Beach, 57th Street Beach, and Calumet Beach. Four biological replicates were collected for each sampling date and location, resulting in 112 samples. Eighty-nine of these samples were surveyed through targeted sequencing of the V7 and V8 regions of the 18S rDNA gene. …
Assessment Of Microbial Populations Within Chicago Area Nearshore Waters And Interfaces With River Systems, Emily Sible, Alexandria Cooper, Kema Malki, Katherine Bruder, Thomas Hatzopoulos, Siobhan C. Watkins, Catherine Putonti
Assessment Of Microbial Populations Within Chicago Area Nearshore Waters And Interfaces With River Systems, Emily Sible, Alexandria Cooper, Kema Malki, Katherine Bruder, Thomas Hatzopoulos, Siobhan C. Watkins, Catherine Putonti
Catherine Putonti
The Chicago area locks separate and control water flow between the freshwaters of Lake Michigan and the network of Illinois waterways. Under extreme storm conditions, however, the locks are opened and storm waters, untreated waste, and runoff are released directly into the lake. These combined sewer overflow (CSO) events introduce microbes, viruses, and nutrients such as nitrogen and phosphorous into nearshore waters which likely affect the native species. We collected surface water samples from four Chicago area beaches – Gillson Park, Montrose Beach, 57th Street Beach, and Calumet Beach – every two weeks from May 13 through August 5, 2014. …
The Use Of Informativity In The Development Of Robust Viromics-Based Examinations, Siobhan C. Watkins, Catherine Putonti
The Use Of Informativity In The Development Of Robust Viromics-Based Examinations, Siobhan C. Watkins, Catherine Putonti
Bioinformatics Faculty Publications
Metagenomics-based studies have provided insight into many of the complex microbial communities responsible for maintaining life on this planet. Sequencing efforts often uncover novel genetic content; this is most evident for phage communities, in which upwards of 90% of all sequences exhibit no similarity to any sequence in current data repositories. For the small fraction that can be identified, the top BLAST hit is generally posited as being representative of a viral taxon present in the sample of origin. Homology-based classification, however, can be misleading as sequence repositories capture but a small fraction of phage diversity. Furthermore, lateral gene transfer …
K-Mer Analysis Pipeline For Classification Of Dna Sequences From Metagenomic Samples, Russell Kaehler
K-Mer Analysis Pipeline For Classification Of Dna Sequences From Metagenomic Samples, Russell Kaehler
Graduate Student Theses, Dissertations, & Professional Papers
Biological sequence datasets are increasing at a prodigious rate. The volume of data in these datasets surpasses what is observed in many other fields of science. New developments wherein metagenomic DNA from complex bacterial communities is recovered and sequenced are producing a new kind of data known as metagenomic data, which is comprised of DNA fragments from many genomes. Developing a utility to analyze such metagenomic data and predict the sample class from which it originated has many possible implications for ecological and medical applications. Within this document is a description of a series of analytical techniques used to process …