{"id":300,"date":"2018-12-18T10:58:28","date_gmt":"2018-12-18T15:58:28","guid":{"rendered":"http:\/\/www.montclair.edu\/csam\/?page_id=300"},"modified":"2018-12-18T10:58:28","modified_gmt":"2018-12-18T15:58:28","slug":"equipment","status":"publish","type":"page","link":"https:\/\/www.montclair.edu\/csam\/research\/equipment\/","title":{"rendered":"Equipment in CSAM"},"content":{"rendered":"
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Biology<\/h2>\n
Applied Biosystems Model 3130 Genetic Analyzer (DNA Sequencer)<\/div>
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\n

The Biology Department has a DNA Sequencing Core Facility, servicing several CSAM Departments<\/p>\n

This state-of-the-art instrument is used worldwide for genetic sequencing and fragment analysis (AFLP, SNP, and microsatellite analysis)<\/p>\n

Common applications include:<\/p>\n

    \n
  • DNA fingerprinting in crime labs<\/li>\n
  • identification of genetic diseases in hospitals<\/li>\n
  • identification of horses for thoroughbred breeding and racing<\/li>\n<\/ul>\n

    This facility has been used to support both work of individual laboratories as well as sequencing projects in undergraduate teaching laboratories<\/p>\n

    Examples of recent projects:<\/p>\n

      \n
    • human mitochondrial D-loop analysis<\/li>\n
    • identification of fungal pathogens in amphibians<\/li>\n
    • bacterial metagenomic analysis in soil and water samples using the 16S locus<\/li>\n
    • genetic barcoding of jellyfish from Barnegat Bay<\/li>\n<\/ul>\n<\/div>
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      \"Applied<\/figure>\n<\/div><\/div>\n<\/div><\/div>\n
      Nikon Eclipse Ti inverted microscope (modified)<\/div>
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      \n

      This inverted microscope is set-up to measure bioelectrical currents and study the activity of specialized membrane proteins, called ion channels, using a technique known as patch clamping.<\/p>\n

      Usage:<\/p>\n

        \n
      1. Glass pipettes are fabricated with tips only a few micrometers in diameter to be directed towards the cell using a micromanipulator until it makes contact with the cell membrane.<\/li>\n
      2. The cell membrane forms a tight seal with the pipette glass and can be ruptured by applying suction opening the electrical environment inside the cell to an electrode housed higher in the pipette.<\/li>\n
      3. An ionic solution fills the pipette allowing the control of the ionic environment both inside and outside the cell.<\/li>\n
      4. To maintain mechanical stability, the microscope is housed on an air-suspended vibration isolation table.<\/li>\n<\/ol>\n

        Since the currents are often on the order of one billionth of an ampere, the set-up is protected from outside electrical noise by a housing of conductive material, known as a Faraday cage.<\/p>\n

        This technique can be combined with fluorescence microscopy techniques, such as calcium imaging, in order to tease out the activity of different ion channels.<\/p>\n<\/div>

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        \"Nikon<\/figure>\n<\/div><\/div>\n<\/div><\/div>\n
        PhaseContrast Inverted Microscope<\/div>
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        \n

        Used for tissue culture work<\/p>\n

        Enables one to see living growing cells<\/p>\n

        Currently, the equipment is being used to study the effects of the dust from the World Trade Center 9-11 attack on human lung cells<\/p>\n<\/div>

        \n
        \"PhaseContrast<\/figure>\n<\/div><\/div>\n<\/div><\/div>\n
        StepOne Plus from Applied Biosystems, a real-time PCR<\/div>
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        \n
          \n
        • For quantification of DNA (or RNA)<\/li>\n
        • PCR (Polymerase Chain Reaction)<\/li>\n
        • Provides a very accurate determination of DNA copy number in samples<\/li>\n
        • Great when looking at relative abundance\/diversity of species or gene expression<\/li>\n
        • Used frequently for both research and teaching laboratories<\/li>\n
        • Capable of performing both SYBR-Green and Taqman-based assays<\/li>\n
        • Has four channels permitting multiplexing of samples<\/li>\n
        • Examples of recent projects:\n
            \n
          • microbial source tracking of nonpoint source pollution in New Jersey rivers<\/li>\n
          • temporal and spatial distribution of sea nettle (Chrysaora quinquecirrha) DNA in Barnegat Bay<\/li>\n
          • detection of fungal pathogens in amphibian populations<\/li>\n<\/ul>\n<\/li>\n
          • Department taught a laboratory methods class (BIOL598) on quantitative PCR where students were able to quantify microbial contamination of food and environmental samples<\/li>\n<\/ul>\n<\/div>
            \n
            \"StepOne<\/figure>\n<\/div><\/div>\n<\/div><\/div>\n<\/div><\/div>
            \n

            Computer Science<\/h2>\n
            SOC 700 – Hyperspectral Camera<\/div>
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            \n

            Used in the Computational Sensing Laboratory managed by Dr. Stefan Robila.<\/p>\n

            Hyperspectral imagery (HSI) collects data as hundreds of images (spectral images or spectral bands), with each image corresponding to narrow contiguous wavelength intervals.<\/p>\n

            Hyperspectral sensors cover wavelengths from the visible range (0.4\u03bcm-0.7\u03bcm) to the middle infrared range (2.4\u03bcm).<\/p>\n

            The ability to distinguish minute differences between materials\u2019 spectral properties lead to HSI based solutions in agriculture, mining, environmental sciences, food production, etc.<\/p>\n

            Introduced only a few decades ago, it is clear that HSI is now a well-established tool that has been used here for a variety of projects including face detection and recognition, real-time collection and processing of data, as well as spectral unmixing.<\/p>\n

            Students at all levels (graduate, undergraduate and high school) with interests in computing, biology and environmental sciences have the opportunity to design and implement experiments using the camera.<\/p>\n<\/div>

            \n
            \"SOC<\/figure>\n<\/div><\/div>\n<\/div><\/div>\n
            High Performance Computing (HPC) Systems<\/div>
            \n
            \n

            Refers to computational environments comprised of tens to hundreds of thousands of computing units, all working together and delivering extraordinarily large computational power.<\/p>\n

            Montclair State hosts several HPC environments including two as part of the Computational Sensing Laboratory led by Dr. Stefan Robila, professor of Computer Science.<\/p>\n

            The first HPC system is a computer cluster formed of a master node and (64) compute nodes. Each node consists of two, quad-core 2.4GHz processors, 16GB of RAM and 50GB of storage. \u00a0In total, the cluster provides (520) 64-bit, 2.4GHz cores, 1.008TB of RAM and 3.7TB of storage. Programming on the cluster can be done in multiple languages and development environments including MPI and OpenMP.<\/p>\n

            The second HPC system is formed of a Microway computer equipped with a Graphics Processing Unit (GPU). The GPU, part of the NVIDIA Tesla series has 2,496 computing cores and a total of 5GB on chip memory.<\/p>\n

            Both systems were extensively used in projects by faculty and students in the departments of Computer Science, Biology, Linguistics and Mathematics.<\/p>\n<\/div>

            \n
            \"High<\/figure>\n<\/div><\/div>\n<\/div><\/div>\n<\/div><\/div>
            \n

            Earth and Environmental Studies<\/h2>\n
            GSSI Ground Penetrating Radar SIR-3000<\/div>
            \n
            \n

            Allows for the investigation of the shallow subsurface.<\/p>\n

            Antenna emits electromagnetic waves into the ground and records wave reflections.<\/p>\n

            Lower frequency antennas (e.g., 100 MHz) can penetrate tens of meters into the ground.<\/p>\n

            Higher frequency antennas (e.g., 900 MHz) can only penetrate tens of centimeters into the ground and detect much smaller objects and finer features.<\/p>\n

            We have: 100 MHz and 270 MHz, which are most useful for geologic and environmental applications, such as mapping sediment layers, imaging shallow faults and sometimes detecting groundwater.<\/p>\n<\/div>

            \n
            \"GSSI<\/figure>\n<\/div><\/div>\n<\/div><\/div>\n
            Geometrics OhmMapper<\/div>
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            \n

            Used for resistivity profiling.<\/p>\n

            Electrical current is put into the ground via capacitors and the voltage drop between the transmitter and receiver is measured to determine the resistivity of the ground using Ohm\u2019s Law: voltage = current * resistance.<\/p>\n

            Increasing the spacing between the transmitter and receiver increases the depth of penetration of the electrical current and thus increases the depth of measurement.<\/p>\n

            Our configuration includes two receivers and one transmitter so that we can collect data at two depths with each pass.<\/p>\n

            Resistivity profiling is commonly used to map groundwater because the presence of water in soil or rock pores greatly reduces its resistivity.<\/p>\n<\/div>

            \n
            \"students<\/figure>\n<\/div><\/div>\n<\/div><\/div>\n
            Geometrics Geode Seismometer<\/div>
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            \n

            Using a sledgehammer and an aluminum plate as our source, we can send seismic waves into the subsurface to investigate shallow features like faults, sediment layers and depth to bedrock.<\/p>\n

            Our seismic system consists of 48 geophones to detect the seismic waves, two 24-channel Geometrics Geode seismometers to record and digitize the geode signals, and a rugged field laptop to control the system and process the data.<\/p>\n

            In seismic refraction surveying, the geophones are laid out in a line and the sledgehammer is used at several shot points along that line. In most places, the waves will be refracted – or bent – where they reach an interface between materials with different wave speed, for example, between soil and bedrock, similar to how light is refracted at the interface between air and water.<\/p>\n

            Arrival times of the first waves to reach the geophones are used to determine the depth of such interfaces below our survey line<\/p>\n<\/div>

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            \"Geometrics<\/figure>\n<\/div><\/div>\n<\/div><\/div>\n
            Topcon Total Station<\/div>
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            \n

            Surveying instrument that allows for site surveys and in-field measurements of river channels, hillslopes, and other topographic features<\/p>\n

            Has been used by our students to measure lake bathymetry, river channel dimensions and erosion on hillslopes<\/p>\n

            The precision is \u00b11mm<\/p>\n

            Great tool for measuring the Earth’s surface to high levels of precision<\/p>\n<\/div>

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            \"Topcon<\/figure>\n<\/div><\/div>\n<\/div><\/div>\n
            Geometrics G-858 Cesium Vapor Magnetometer<\/div>
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            \n

            Measures small variations in the magnetic field as it is carried over the ground<\/p>\n

            Materials with high magnetic susceptibility (e.g., ore bodies, buried metal objects) will produce a positive magnetic anomaly that the magnetometer can detect<\/p>\n

            Parallel survey lines over an area allow us to create maps of the magnetic anomalies<\/p>\n<\/div>

            \n
            \"Geometrics<\/figure>\n<\/div><\/div>\n<\/div><\/div>\n<\/div><\/div>\n","protected":false},"excerpt":{"rendered":"","protected":false},"author":34,"featured_media":1212,"parent":282,"menu_order":5,"comment_status":"closed","ping_status":"closed","template":"","meta":{"inline_featured_image":false,"footnotes":""},"class_list":["post-300","page","type-page","status-publish","has-post-thumbnail","hentry"],"_links":{"self":[{"href":"https:\/\/www.montclair.edu\/csam\/wp-json\/wp\/v2\/pages\/300","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/www.montclair.edu\/csam\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/www.montclair.edu\/csam\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/www.montclair.edu\/csam\/wp-json\/wp\/v2\/users\/34"}],"replies":[{"embeddable":true,"href":"https:\/\/www.montclair.edu\/csam\/wp-json\/wp\/v2\/comments?post=300"}],"version-history":[{"count":0,"href":"https:\/\/www.montclair.edu\/csam\/wp-json\/wp\/v2\/pages\/300\/revisions"}],"up":[{"embeddable":true,"href":"https:\/\/www.montclair.edu\/csam\/wp-json\/wp\/v2\/pages\/282"}],"wp:featuredmedia":[{"embeddable":true,"href":"https:\/\/www.montclair.edu\/csam\/wp-json\/wp\/v2\/media\/1212"}],"wp:attachment":[{"href":"https:\/\/www.montclair.edu\/csam\/wp-json\/wp\/v2\/media?parent=300"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}