Identification of nitrifying bacteria contained in a commercial inoculant using molecular biology techniques

Nitrifying bacteria play an important role in aquatic and terrestrial environments through the nitrogen cycle. Nitrification, one of the processes of the nitrogen cycle, refers to the oxidation of ammonia to nitrate. This process requires two types of chemoautotrophic bacteria, ammonia-oxidizing bacteria (AOB), and nitrite-oxidizing bacteria (NOB). These bacteria are essential in maintaining an optimal environment for plants and aquatic organisms, such as fish. Current applications of nitrifiers include: inoculants for aquariums, biofertilizers, and nitrogen removal in wastewater treatment plants. This study wants to identify a consortium of nitrifers that can be used to produce sufficient nitrate for plants in a hydroponic system. Previous studies have shown that Fritz-zyme turbostart 700, a commercial freshwater inoculant has had success in a semi-hydroponic system, zeoponics. Our lab’s preliminary data has shown that Fritz-zyme contains more than the specific nitrifying bacteria. In order to create the optimal consortium, it would be mandatory that we know exactly what bacteria we are working with. Using 16s rDNA universal primers and PGEM-T easy vector cloning kit, this study will amplify the 16s rDNA present in different enrichment samples and clone it into the PGEM-T easy vector E. coli plasmid. The cloned plasmids are transformed into competent E. coli cells and sequenced to identify the bacteria present in each sample. This study will determine whether the current enrichment techniques being used are sufficient to eliminate the heterotrophic and sporeforming bacteria present in the original Fritz-zyme

3D Assessment of Nasopharyngeal and Craniofacial Phenotypes in Ts65Dn Down Syndrome Mice Treated with a Dyrk1a Inhibitor

Background: Down syndrome (DS) originates from having three copies of chromosome 21 (i.e. Trisomy 21). DS is associated with many detrimental phenotypes including intellectual disabilities, heart defects, abnormal craniofacial development, and obstructive sleep apnea, which develops from restricted nasopharyngeal airways and an underdeveloped mandible. Ts65Dn mice are trisomic for about half of the orthologs on human chromosome 21 and display many phenotypes associated with DS including craniofacial abnormalities. Dyrk1a is found in three copies in Ts65Dn mice and individuals with DS, and thought to be a root cause of the craniofacial phenotypes. Epigallocatechin 3-gallate (EGCG) is a green tea polyphenol and inhibitor of Dyrk1a activity. Purpose: We hypothesize that decreased Dyrk1a activity in Ts65Dn mice will ameliorate craniofacial dysmorphology. Methods: To test our hypothesis we compared Ts65Dn mice with two or three copies of Dyrk1a and compared Ts65Dn mice with and without prenatal EGCG treatment. EGCG treated mothers were fed 200mg/kg EGCG on gestational day 7. Six week old mice were sacrificed and their heads imaged using micro-computed tomography (μCT). From μCT images, we measured nasopharyngeal airway volume and anatomical landmarks (n = 54) from the facial skeleton, cranial vault, cranial base, and mandible. Mean nasopharyngeal airway volumes were graphically compared, and a landmark-based multivariate geometric morphometric approach known as Euclidean Distance Matrix Analysis (EDMA) was carried out to assess local differences in craniofacial morphology between trisomic mouse samples. Results: Our preliminary results indicate that EGCG treatment and reduced Dyrk1a copy number increases mean nasopharyngeal airway volume in Ts65Dn mice. Craniofacial morphometric differences were found among all samples. EGCG treatment increased portions of the mandible and decreased portions of the cranial vault and cranial base. Conclusion: Preliminary analyses suggest that both EGCG treatment and reduced Dyrk1a copy number affect craniofacial morphology.Three Dimensional Imaging of the Craniofacial Complex Center (3D ICCC)--IUPUI Signature Center Initiative

Beyond Nanopore Sequencing in Space: Identifying the Unknown

Astronaut Kate Rubins sequenced DNA on the International Space Station (ISS) for the first time in August 2016 (Figure 1A). A 2D sequencing library containing an equal mixture of lambda bacteriophage, Escherichia coli, and Mus musculus was prepared on the ground with a SQK_MAP006 kit and sent to the ISS frozen and loaded into R7.3 flow cells. After a total of 9 on-orbit sequencing runs over 6 months, it was determined that there was no decrease in sequencing performance on-orbit compared to ground controls (1). A total of ~280,000 and ~130,000 reads generated on-orbit and on the ground, respectively, identified 90% of reads that were attributed to 30% lambda bacteriophage, 30% Escherichia coli, and 30% M. musculus (Figure 1B). Extensive bioinformatics analysis determined comparable 2D and 1D read accuracies between flight and ground runs (Figure 1C), and data collected from the ISS were able to construct directed assemblies of E.coli and lambda genomes at 100% and M. musculus mitochondrial genome at 96.7%. These findings validate sequencing as a viable option for potential on-orbit applications such as environmental microbial monitoring and disease diagnosis. Current microbial monitoring of the ISS applies culture-based techniques that provide colony forming unit (CFU) data for air, water, and surface samples. The identity of the cultured microorganisms in unknown until sample return and ground-based analysis, a process that can take up to 60 days. For sequencing to benefit ISS applications, spaceflight-compatible sample preparation techniques are required. Subsequent to the testing of the MinION on-orbit, a sample-to-sequence method was developed using miniPCR and basic pipetting, which was only recently proven to be effective in microgravity. The work presented here details the in- flight sample preparation process and the first application of DNA sequencing on the ISS to identify unknown ISS-derived microorganisms

Fall Faculty Conference: The Future of the University

This was the first fall of President Robert Eckley\u27s time in office. The first part of the recording is an open Q&A session, followed by division-based reports. There are frequent references to a recent North Central reaccreditation visit in this meeting. In a memo distributed a day later President Eckley notes that the North Central visit and the recent changes in the general education requirements indicate the importance of a re-assessment of our departmental-divisional-university structural relationships. His proposal formed a structure with three colleges: Liberal Arts, Fine Arts and Applied Arts. Speakers include President Robert Eckley; Robert Harrington, Business & Economics; Justus Pearson, Humanities; Wayne Wantland, Natural Sciences; Emily Dale, Social Sciences; John Ficca, Art & Drama; Richard Hishman, Music; and Mary Shanks, Nursing

Astro2020 Project White Paper: The Cosmic Accelerometer

We propose an experiment, the Cosmic Accelerometer, designed to yield velocity precision of $\leq 1$ cm/s with measurement stability over years to decades. The first-phase Cosmic Accelerometer, which is at the scale of the Astro2020 Small programs, will be ideal for precision radial velocity measurements of terrestrial exoplanets in the Habitable Zone of Sun-like stars. At the same time, this experiment will serve as the technical pathfinder and facility core for a second-phase larger facility at the Medium scale, which can provide a significant detection of cosmological redshift drift on a 6-year timescale. This larger facility will naturally provide further detection/study of Earth twin planet systems as part of its external calibration process. This experiment is fundamentally enabled by a novel low-cost telescope technology called PolyOculus, which harnesses recent advances in commercial off the shelf equipment (telescopes, CCD cameras, and control computers) combined with a novel optical architecture to produce telescope collecting areas equivalent to standard telescopes with large mirror diameters. Combining a PolyOculus array with an actively-stabilized high-precision radial velocity spectrograph provides a unique facility with novel calibration features to achieve the performance requirements for the Cosmic Accelerometer

Achievable rates for the Gaussian quantum channel

We study the properties of quantum stabilizer codes that embed a finite-dimensional protected code space in an infinite-dimensional Hilbert space. The stabilizer group of such a code is associated with a symplectically integral lattice in the phase space of 2N canonical variables. From the existence of symplectically integral lattices with suitable properties, we infer a lower bound on the quantum capacity of the Gaussian quantum channel that matches the one-shot coherent information optimized over Gaussian input states.Comment: 12 pages, 4 eps figures, REVTe

Gaussian bosonic synergy: quantum communication via realistic channels of zero quantum capacity

As with classical information, error-correcting codes enable reliable transmission of quantum information through noisy or lossy channels. In contrast to the classical theory, imperfect quantum channels exhibit a strong kind of synergy: there exist pairs of discrete memoryless quantum channels, each of zero quantum capacity, which acquire positive quantum capacity when used together. Here we show that this "superactivation" phenomenon also occurs in the more realistic setting of optical channels with attenuation and Gaussian noise. This paves the way for its experimental realization and application in real-world communications systems.Comment: 5 pages, 4 figures, one appendi