Analyzing and Designing an Arduino Controlled System to Study the Effect of Changing Water Levels on Water Flow Through Sediments

The hyporheic zone is the region of sediment under a stream where water from the stream flows before returning to the stream itself. Many studies focus on steady water flow through this region, however, in natural systems, water levels and water flow rates change due to storms, tides, dams, or melting snow. To investigate flow under unsteady conditions, we built a system that allows us to control the water level and thus the flow rates. We used a pressure sensor that is connected to an Arduino board to measure the water level. The Arduino board uses the measured pressure value to control a water pump. When the water level is lower than desired, the pump will turn on and when it is higher than desired, it will turn off. This allowed us to hold the water level constant or tell it to oscillate. We then evaluated our system by comparing our desired water level functions to those measured with our pressure sensor, those measured by a pressure transducer connected to a separate Arduino, and those we extracted from videos of our system.Faculty Sponsor: Susa H. Stonedah

Analyzing and Designing an Arduino Controlled System to Study the Effect of Changing Water Levels on Water Flow Through Sediments

The hyporheic zone is the region of sediment under a stream where water from the stream flows before returning to the stream itself. Many studies focus on steady water flow through this region, however, in natural systems, water levels and water flow rates change due to storms, tides, dams, or melting snow. To investigate flow under unsteady conditions, we built a system that allows us to control the water level and thus the flow rates. We used a pressure sensor that is connected to an Arduino board to measure the water level. The Arduino board uses the measured pressure value to control a water pump. When the water level is lower than desired, the pump will turn on and when it is higher than desired, it will turn off. This allowed us to hold the water level constant or tell it to oscillate. We then evaluated our system by comparing our desired water level functions to those measured with our pressure sensor, those measured by a pressure transducer connected to a separate Arduino, and those we extracted from videos of our system

Ringed, Bearded, and Ribbon Seal Vocalizations North of Barrow, Alaska: Seasonal Presence and Relationship with Sea Ice

The acoustic repertoires of ringed, bearded, and ribbon seals are described, along with their seasonal occurrence and relationship to sea ice concentration. Acoustic recordings were made between September and June over three years (2006 – 09) along the continental slope break in the Chukchi Sea, 120 km north-northwest of Barrow, Alaska. Vocalizations of ringed and bearded seals occurred in winter and during periods of 80% – 100% ice cover but were mostly absent during open water periods. The presence of ringed and bearded seal calls throughout winter and spring suggests that some portion of their population is overwintering. Analysis of the repertoire of ringed and bearded seal calls shows seasonal variation. Ringed seal calls are primarily barks in winter and yelps in spring, while bearded seal moans increase during spring. Ribbon seal calls were detected only in the fall of 2008 during the open water period. The repertoire of known ribbon seal vocalizations was expanded to include three additional calls, and two stereotyped call sequences were common. Retrospective analyses of ringed seal recordings from 1982 and ribbon seal recordings from 1967 showed a high degree of stability in call repertoire across large spatial and temporal scales.Le répertoire acoustique des phoques annelés, des phoques barbus et des phoques à bandes sont décrits, de même que leur présence saisonnière et leur rapport avec la concentration de glace de mer. Des enregistrements acoustiques ont été effectués entre septembre et juin sur une période de trois ans (2006 – 2009), le long de la rupture de la pente continentale, dans la mer des Tchouktches, à 120 km au nord-nord-ouest de Barrow, en Alaska. Les vocalisations de phoques annelés et de phoques barbus étaient présentes pendant l’hiver et pendant les périodes où la concentration de glace était de 80 % à 100 %, mais elles se faisaient rares pendant les périodes d’eau libre. La présence des cris de phoques annelés et de phoques barbus tout au long de l’hiver et du printemps suggère qu’une partie de leur population hiverne. L’analyse du répertoire de cris de phoques annelés et de phoques barbus indique une variation saisonnière. L’hiver, le cri du phoque annelé prend principalement la forme d’aboiements, tandis que le printemps, il prend la forme de glapissements. Les gémissements du phoque barbu s’intensifient au printemps. Le cri des phoques à bandes n’a été capté qu’à l’automne 2008, pendant la période des eaux libres. Le répertoire des vocalisations connues du phoque à bandes a été élargi pour inclure trois autres cris, bien que deux séquences de cris stéréotypées étaient courantes. L’analyse rétrospective des enregistrements de cris de phoques annelés de 1982 et de phoques à bandes de 1967 a laissé entrevoir une grande stabilité du point de vue du répertoire des cris, et ce, sur de vastes échelles spatiales et temporelles

Optofluidic Particle Manipulation: Optical Trapping in a Thin-Membrane Microchannel

We demonstrate an optofluidic device which utilizes the optical scattering and gradient forces for particle trapping in microchannels featuring 300 nm thick membranes. On-chip waveguides are used to direct light into microfluidic trapping channels. Radiation pressure is used to push particles into a protrusion cavity, isolating the particles from liquid flow. Two different designs are presented: the first exclusively uses the optical scattering force for particle manipulation, and the second uses both scattering and gradient forces. Trapping performance is modeled for both cases. The first design, referred to as the orthogonal force design, is shown to have a 80% capture efficiency under typical operating conditions. The second design, referred to as the gradient force design, is shown to have 98% efficiency under the same conditions

Steric-Induced Layer Flection in Templated Vanadium Tellurites

A series of organically templated vanadium tellurites has been prepared under mild hydrothermal conditions. Single crystals were grown from mixtures of NaVO₃, Na₂TeO₃, and either 1,4-diaminobutane, 1,6-diaminohexane, or <i>N</i>,<i>N</i>,<i>N</i>′,<i>N</i>′-tetramethylethylenediamine in H₂O. Each compound contains similar [V₂Te₂O₁₀]_<i>n</i>^2<i>n</i>– layers. The layer metrics of [1,4-diaminobutaneH₂]­[V₂Te₂O₁₀], [1,6-diaminohexaneH₂]­[V₂Te₂O₁₀], [<i>N</i>,<i>N</i>,<i>N</i>′,<i>N</i>′-tetramethylethylenediamineH₂]­[V₂Te₂O₁₀], and [piperazineH₂]­[V₂Te₂O₁₀] reflect the steric bulk of the respective amines. Topotactic conversions between compounds through amine exchange are possible in reactions in which an increase in the strength of the amine–[V₂Te₂O₁₀]_<i>n</i>^2<i>n</i>– hydrogen-bonding network is observed

Sequence Assembly of <i>Yarrowia lipolytica</i> Strain W29/CLIB89 Shows Transposable Element Diversity

<div><p><i>Yarrowia lipolytica</i>, an oleaginous yeast, is capable of accumulating significant cellular mass in lipid making it an important source of biosustainable hydrocarbon-based chemicals. In spite of a similar number of protein-coding genes to that in other Hemiascomycetes, the <i>Y</i>. <i>lipolytica</i> genome is almost double that of model yeasts. Despite its economic importance and several distinct strains in common use, an independent genome assembly exists for only one strain. We report here a <i>de novo</i> annotated assembly of the chromosomal genome of an industrially-relevant strain, W29/CLIB89, determined by hybrid next-generation sequencing. For the first time, each <i>Y</i>. <i>lipolytica</i> chromosome is represented by a single contig. The telomeric rDNA repeats were localized by Irys long-range genome mapping and one complete copy of the rDNA sequence is reported. Two large structural variants and retroelement differences with reference strain CLIB122 including a full-length, novel Ty3/Gypsy long terminal repeat (LTR) retrotransposon and multiple LTR-like sequences are described. Strikingly, several of these are adjacent to RNA polymerase III-transcribed genes, which are almost double in number in <i>Y</i>. <i>lipolytica</i> compared to other Hemiascomycetes. In addition to previously-reported dimeric RNA polymerase III-transcribed genes, tRNA pseudogenes were identified. Multiple full-length and truncated LINE elements are also present. Therefore, although identified transposons do not constitute a significant fraction of the <i>Y</i>. <i>lipolytica</i> genome, they could have played an active role in its evolution. Differences between the sequence of this strain and of the existing reference strain underscore the utility of an additional independent genome assembly for this economically important organism.</p></div

Steric-Induced Layer Flection in Templated Vanadium Tellurites

A series of organically templated vanadium tellurites has been prepared under mild hydrothermal conditions. Single crystals were grown from mixtures of NaVO₃, Na₂TeO₃, and either 1,4-diaminobutane, 1,6-diaminohexane, or <i>N</i>,<i>N</i>,<i>N</i>′,<i>N</i>′-tetramethylethylenediamine in H₂O. Each compound contains similar [V₂Te₂O₁₀]_<i>n</i>^2<i>n</i>– layers. The layer metrics of [1,4-diaminobutaneH₂]­[V₂Te₂O₁₀], [1,6-diaminohexaneH₂]­[V₂Te₂O₁₀], [<i>N</i>,<i>N</i>,<i>N</i>′,<i>N</i>′-tetramethylethylenediamineH₂]­[V₂Te₂O₁₀], and [piperazineH₂]­[V₂Te₂O₁₀] reflect the steric bulk of the respective amines. Topotactic conversions between compounds through amine exchange are possible in reactions in which an increase in the strength of the amine–[V₂Te₂O₁₀]_<i>n</i>^2<i>n</i>– hydrogen-bonding network is observed

Families of transposable elements in CLIB89 and CLIB122.

<p>Families of transposable elements in CLIB89 and CLIB122.</p

CIRCOS overview of YALI1 gene features.

<p><b>(A)</b> Chromosomal genes. Outer ring, chromosomes. First mapping track [RNA polymerase II (POL2)-transcribed genes]: LINE retroelements (outward light grey posts), overlapping genes on both strands (inward blue posts), POL2 less than 1 kb (blue rings), POL2 between 1 kb and 5 kb (light green rings), POL2 between 5 kb and 10 kb (green rings), and POL2 > 10 kb (red rings). The next inner track (POL3 and POL2 ncRNA genes), tRNA (green), rRNA (orange), and ncRNA genes (dark yellow). <b>(B)</b> Mitochondrial genes. Transcripts from exons (longer spanning light blue wedges); transcripts from introns (narrower and taller overlapping wedges); CDS (gray); tDNA (purple); and rDNA (yellow). Outer track shows variants comparison with the CLIB122 assembly (<a href="http://www.ncbi.nlm.nih.gov/nuccore/NC_002659.1" target="_blank">http://www.ncbi.nlm.nih.gov/nuccore/NC_002659.1</a>): mismatches (black posts); insertions (green) and deletions (red) relative to the CLIB122 assembly.</p

CLIB89 YALI1 sequence read statistics.

<p>CLIB89 YALI1 sequence read statistics.</p