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Fractals in biology and medicine

Our purpose is to describe some recent progress in applying fractal concepts to systems of relevance to biology and medicine. We review several biological systems characterized by fractal geometry, with a particular focus on the long-range power-law correlations found recently in DNA sequences containing noncoding material. Furthermore, we discuss the finding that the exponent alpha quantifying these long-range correlations ("fractal complexity") is smaller for coding than for noncoding sequences. We also discuss the application of fractal scaling analysis to the dynamics of heartbeat regulation, and report the recent finding that the normal heart is characterized by long-range "anticorrelations" which are absent in the diseased heart.

Review

Assessment of wetland productive capacity from a remote-sensing-based model - A NASA/NMFS joint research project

NASA and the U.S. National Marine Fisheries Service have undertaken the development of Landsat Thematic Mapper (TM) technology for the evaluation of the usefulness of wetlands to estuarine fish and shellfish production. Toward this end, a remote sensing-based Productive Capacity model has been developed which characterizes the biological and hydrographic features of a Gulf Coast Marsh to predict detrital export. Regression analyses of TM simulator data for wetland plant production estimation are noted to more accurately estimate the percent of total vegetative cover than biomass, indicating that a nonlinear relationship may be involved.

Butera, M. K.

Aircraft laser derived chlorophyll distribution across the Iceland-Faeroe front

The ocean surface color (water-leaving radiances) and thermal structure across the Iceland-Faeroe Front under both clear and cloudy conditions were measured from a NASA research aircraft on 25 May 1989. The measurements were made along four north-south lines that were 125 km in length and spaced 35 km apart. The color measurements were made with a 14 channel, non-polarized Multispectral Airborne Radiometer System (MARS) while the thermal data were collected by a thermal radiometer and aircraft bathythermographs. The satellite imagery (NOAA AVHRR) sequence show the development of meanders through the frontal region. These aircraft ocean color and thermal data characterize the biological distribution and are closely coupled to the physical processes occurring in the frontal systems. The ratio of several channels of the ocean color data are used to determine the surface chlorophyll. The retrieved data correlate well with laser-induced chlorophyll fluorescence obtained at the same time and historical chlorophyll data. The observed chlorophyll patchiness appearing across the Iceland-Faeroe Front is believed to be directly and indirectly related to primary and secondary circulation processes in ocean frontal systems. High chlorophyll concentrations were observed on the north side of the front and are inferred to be the result from the advection of Icelandic Coastal Water into the region. The sharp chlorophyll decline at and south of the thermal frontal boundary is clearly related to the subsurface thermal structure.

Arnone, Robert A.

New Chemical, Bio-Optical and Physical Observations of Upper Ocean Response to the Passage of a Mesoscale Eddy Off Bermuda

A mesoscale eddy advected across the Bermuda Testbed Mooring site over a 30-day period centered on July 14, 1995. Temperature and current measurements along with biogeochemical measurements were used to characterize the biological response of the upper ocean associated with the introduction of nitrate into the euphotic layer due to the doming of isotherms associated with the eddy. Complementary shipboard data showed an anomalous water mass, which extended from a depth of approximately 50 to 1000 m, manifesting as a cold surface expression and warm anomaly at depth. Although mesoscale eddies are frequently observed in the Sargasso Sea, the present observations are particularly unique because of the high-temporal-resolution measurements of the new instrumentation deployed on the mooring. Analyzers that measure nitrate plus nitrite were placed at depths of 80 and 200 m and bio-optical sensors were located at depths of 20, 35, 45, 71, and 86 m. Peak nitrate values of nearly 3.0 micro-M at 80 m and chlorophyll a values of 1.4 mg/cubic m at 71 m were observed, a well as a 25- to 30-meter shoaling of the 1% light level depth. A Doppler shift from the inertial period (22.8 hours) to 25.2 hours was observed in several time series records due to the movement of the eddy across the mooring. Inertial pumping brought cold, nutrient-rich waters farther into the euphotic zone than would occur solely by isothermal lifting. Silicic acid was depleted to undetectable levels owing to the growth of diatoms within the eddy. The chlorophyll a values associated with the eddy appear to be the largest recorded during the eight years of the ongoing US JGOFS Bermuda Atlantic Time Series Study program.

McNeil, J. D.

New Chemical, Bio-Optical and Physical Observations of Upper Ocean Response to the Passage of a Mesoscale Eddy off Bermuda

A mesoscale eddy advected across the Bermuda Testbed Mooring site over a 30-day period centered on July 14, 1995. Temperature and current measurements along with biogeochemical measurements were used to characterize the biological response of the upper ocean associated with the introduction of nitrate into the euphoric layer due to the doming of isotherms associated with the eddy. Complementary shipboard data showed an anomalous water mass, which extended from a depth of approximately 50 to 1000 m, manifesting as a cold surface expression and warm anomaly at depth. Although mesoscale eddies are frequently observed in the Sargasso Sea, the present observations are particularly unique because of the high-temporal-resolution measurements of the new instrumentation deployed on the mooring. Analyzers that measure nitrate plus nitrite were placed at depths of 80 and 200 m and bio-optical sensors were located at depths of 20, 35, 45, 71, and 86 m. Peak nitrate values of nearly 3.0 microns at 80 m and chlorophyll alpha values of 1.4 mg/cu m at 71 m were observed, as well as a 25- to 30-meter shoaling of the 1% light level depth. A Doppler shift from the inertial period (22.8 hours) to 25.2 hours was observed in several time series records due to the movement of the eddy across the mooring. Inertial pumping brought cold, nutrient-rich waters farther into the euphotic zone than would occur solely by isothermal lifting. Silicic acid was depleted to undetectable levels owing to the growth of diatoms within the eddy. The chlorophyll alpha values associated with the eddy appear to be the largest recorded during the 8 years of the ongoing U.S. JGOFS Bermuda Atlantic Time Series Study (BATS) program.

McNeil, J. D.

Short Time Scale Evolution of Microbiolites in Rapidly Receding Altiplanic Lakes: Learning How to Recognize Changing Signatures of Life

As part of the exploration of high altitude lakes as analogs to Martian paleolakes environment, we are investigating a remarkably large and diverse field of lacustrine stromatolites located at 4,365m in the Bolivian Altiplano (22 deg 47 00 min S and 67 deg 47.00 min W).The field is composed of both early Holocene fossil structures located on paleoshorelines and present-day active cyanobacterial communities on the shore and at the bottom of the current Laguna Blanca and Verde. Its physical environment, broad diversity of morphologies, and their associated spatial heterogeneity, origin, and scale offer a unique opportunity to explore microbiolites in conditions reminiscent of early Earth and Mars. At this altitude and latitude, UV radiation levels are enhanced (40% higher than sea level) and harmful to microorganisms living in shallow waters which provide only minimal protection from UV. Similar conditions prevailed on early Earth when the ozone layer had yet to be formed in the atmosphere. Compared to those studied at sea levels, these stromatolites could yield new insights about the earliest terrestrial forms of life. Moreover, the combination of physical and geological environment of this site is exceptionally analogous to conditions believed to be prevalent on Mars at the end of the Noachian (3.5 Ga ago), allowing to test the potential for forming stromatolites in martian paleolakes and learn how to identify their fossil record remotely. Our overarching goal is to generate new astrobiological information on high-altitude stromatolites as clues to early biospheres with implications for Earth and Mars. Our two central objectives are: (1) characterize the biological, geological, and mineralogical features and significance of this field, and to identify geo-signatures such as morphology, geology, chronostratigraphy, mineralogy and biosignatures, and (2) to facilitate remote-sensing and ground robotic detection capabilities for future astrobiological missions to Mars.

Cabrol, N. A.

Nanoscale Bio-engineering Solutions for Space Exploration: The Nanopore Sequencer

Characterization of biological systems at the molecular level and extraction of essential information for nano-engineering design to guide the nano-fabrication of solid-state sensors and molecular identification devices is a computational challenge. The alpha hemolysin protein ion channel is used as a model system for structural analysis of nucleic acids like DNA. Applied voltage draws a DNA strand and surrounding ionic solution through the biological nanopore. The subunits in the DNA strand block ion flow by differing amounts. Atomistic scale simulations are employed using NASA supercomputers to study DNA translocation, with the aim to enhance single DNA subunit identification. Compared to protein channels, solid-state nanopores offer a better temporal control of the translocation of DNA and the possibility to easily tune its chemistry to increase the signal resolution. Potential applications for NASA missions, besides real-time genome sequencing include astronaut health, life detection and decoding of various genomes.

Stolc, Viktor

Nanoscale Bioengineering Solutions for Space Exploration the Nanopore Sequencer

Characterization of biological systems at the molecular level and extraction of essential information for nano-engineering design to guide the nano-fabrication of solid-state sensors and molecular identification devices is a computational challenge. The alpha hemolysin protein ion channel is used as a model system for structural analysis of nucleic acids like DNA. Applied voltage draws a DNA strand and surrounding ionic solution through the biological nanopore. The subunits in the DNA strand block ion flow by differing amounts. Atomistic scale simulations are employed using NASA supercomputers to study DNA translocation. with the aim to enhance single DNA subunit identification. Compared to protein channels, solid-state nanopores offer a better temporal control of the translocation of DNA and the possibility to easily tune its chemistry to increase the signal resolution. Potential applications for NASA missions, besides real-time genome sequencing include astronaut health, life detection and decoding of various genomes. http://phenomrph.arc.nasa.gov/index.php

Ioana, Cozmuta

LIFT Tenant Is Off and Running

Lewis Incubator for Technology (LIFT) tenant, Analiza Inc., graduated from the incubator July 2000. Analiza develops technology and products for the early diagnosis of diseases, quality control of bio-pharmaceutical therapeutics, and other applications involving protein analyses. Technology links with NASA from existing and planned work are in areas of microfluidics and laser light scattering. Since their entry in LIFT in May, 1997, Analiza has: Received a $750,000 grant from the National Institutes of Health. Collaborated with a Nobel Prize winner on drug design. Collaborated with Bristol-Myers Squibb on the characterization of biological therapeutics. Added a Ph.D. senior scientist and several technicians. Received significant interest from major pharmaceutical companies about collaborating and acquiring Analiza technology.

Steele, Gynelle C.

New Species of Fire Discovered: Fingering Flamelets Form a Dynamic Population

Poets and artists have long used fire as a metaphor for life. At the NASA Glenn Research Center, recent experiments in a subcritical Rayleigh number flow channel demonstrated that this analogy holds up surprisingly well when tools developed to characterize a biological population are applied to a class of fire that occurs in near-extinction, weakly convective environments (such as microgravity) or in vertically confined spaces (such as our apparatus). Under these conditions, the flame breaks into numerous 'flamelets" that form a Turing-type reaction-diffusion fingering pattern as they spread across the fuel. It is standard practice on U.S. spacecraft for the astronaut crew to turn off the ventilation to help extinguish a fire, both to eliminate the fresh oxygen supply and to reduce the distribution of the smoke. When crew members think that the fire is fully extinguished, they reactivate the ventilation system to clear the smoke. However, some flamelets can survive, and our experiments have demonstrated that flamelets quickly grow into a large fire when ventilation increases.

Olson, Sandra L.

Comparison of the Microbial Diversity and Abundance Between the Freshwater Land-Locked Lakes of Schirmacher Oasis and the Perennially Ice-Covered Lake Untersee in East Antarctica

Extreme conditions such as low temperature, dryness, and constant UV-radiation in terrestrial Antarctica are limiting factors of the survival of microbial populations. The objective of this study was to investigate the microbial diversity and enumeration between the open water lakes of Schirmacher Oasis and the permanently ice-covered Lake Untersee. The lakes in Schirmacher Oasis possessed abundant and diverse group of microorganisms compared to the Lake Untersee. Furthermore, the microbial diversity between two lakes in Schirmacher Oasis (Lake L27C and L47) was compared by culture-based molecular approach. It was determined that L27Chad a richer microbial diversity representing 5 different phyla and 7 different genera. In contrast L47 consisted of 4 different phyla and 6 different genera. The difference in microbial community could be due to the wide range of pH between L27C (pH 9.1) and L47 (pH 5.7). Most of the microbes isolated from these lakes consisted of adaptive biological pigmentation. Characterization of the microbial community found in the freshwater lakes of East Antarctica is important because it gives a further glimpse into the adaptation and survival strategies found in extreme conditions.

Huang, Jonathan

Characterization of the corrosion resistance of biologically active solutions: The effects of anodizing and welding

An understanding of fabrication processes, metallurgy, electrochemistry, and microbiology is crucial to the resolution of microbiologically influenced corrosion (MIC) problems. The object of this effort was to use AC impedance spectroscopy to characterize the corrosion resistance of Type II anodized aluminum alloy 2219-T87 in sterile and biologically active media and to examine the corrosion resistance of 316L, alloy 2219-T87, and titanium alloy 6-4 in the welded and unwelded conditions. The latter materials were immersed in sterile and biologically active media and corrosion currents were measured using the polarization resistance (DC) technique.

Walsh, Daniel W.

Next-Generation Fluids-Related Biology Research Utilizing the Zero Gravity Research Facility at NASA Glenn Research Center

In order to gain insight into how cells sense gravity, NASA has developed a platform to investigate the transient (short-term) response of biological cells to a sudden exposure to microgravity. Utilizing NASA's Zero Gravity Research Facility offers unique capabilities and opportunity to investigate this phenomena. A review of current literature indicates that it remains unclear how biological cells sense and respond to gravitational forces. It is believed that a combination of bio-structural and fluid transport mechanisms are at play. This Technical Memorandum outlines a pathway to address this fundamental biological challenge. A series of low-cost systematic drop tower experiments were conducted to observe the biomechanical behavior of cell membranes (such as vestibular hair, endothelial, and bone cells) that are known to exhibit sensitivity to gravity. These experiments demonstrated a useful, low cost experiment concept that can potentially be employed by researchers interested in observing, identifying and characterizing changes in biological cell morphology.

Fluids for Biology

Overview of Mars Science Laboratory (MSL) Environmental Program

This viewgraph presentation is an overview of the Mars Science Laboratory (MSL) program. The engineering objectives of the program are to create a Mobile Science Laboratory capable of one Mars Year surface operational lifetime (670 Martian sols = 687 Earth days). It will be able to land and operation over wide range of latitudes, altitudes and seasons It must have controlled propulsive landing and demonstrate improved landing precision via guided entry The general science objectives are to perform science that will focus on Mars habitability, perform next generation analytical laboratory science investigations, perform remote sensing/contact investigations and carry a suite of environmental monitoring instruments. Specific scientific objectives of the MSL are: (1) Characterization of geological features, contributing to deciphering geological history and the processes that have modified rocks and regolith, including the role of water. (2) Determination of the mineralogy and chemical composition (including an inventory of elements such as C, H, N, O, P, S, etc. known to be building blocks for life) of surface and near-surface materials. (3) Determination of energy sources that could be used to sustain biological processes. (4) Characterization of organic compounds and potential biomarkers in representative regolith, rocks, and ices. (5) Determination the stable isotopic and noble gas composition of the present-day bulk atmosphere. (6) Identification potential bio-signatures (chemical, textural, isotopic) in rocks and regolith. (7) Characterization of the broad spectrum of surface radiation, including galactic cosmic radiation, solar proton events, and secondary neutrons. (8) Characterization of the local environment, including basic meteorology, the state and cycling of water and C02, and the near-surface distribution of hydrogen. Several views of the planned MSL and the rover are shown. The MSL environmental program is to: (1) Ensure the flight hardware design is capable of surviving all the environments throughout its mission life time, including ground, transportation, launch, cruise, entry decent and landing (EDL) and surface operation environments. (2) Verify environmental testing and analysis have adequately validated the flight hardware's ability to withstand all natural, self-induced, and mission-activity-induced environments. The planned tests to ascertain the capability of the MSL to perform as desired are reviewed.

spacecraft

Evaluation of Performance of Five Parallel Biological Water Proce

The objective of the work entitled Molecular Characterization of Eubacteria in a Biological Water Processor was to gain an understanding of the microbial diversity and species stability of the consortia that inhabit an anoxic bioreactor and to correlate those factors with functional performance, mechanical reliability, and stability. The evaluation was divided into four studies. During Study 1, replicate biological water processor (BWP) systems were operated to evaluate variability in the microbial diversity over time as a function of the initial consortia used for inoculation of the BWP reactors. Study 2 was designed to investigate the impact of an inoculum source on BWP performance. Study 3 was a modification of Study 2 where the impact of inoculum on BWP performance from inoculation until steady state operations was monitored. In Study 4, the reactors were divided into three different operational periods, based on the operational periods of the integrated water recovery test at the Johnson Space Center (JSC) in 2001.

Vega, Leticia M.

Detection of Objects Hidden in Highly Scattering Media Using Time-Gated Imaging Methods

Non-intrusive and non-invasive optical imaging techniques has generated great interest among researchers for their potential applications to biological study, device characterization, surface defect detection, and jet fuel dynamics. Non-linear optical parametric amplification gate (NLOPG) has been used to detect back-scattered images of objects hidden in diluted Intralipid solutions. To directly detect objects hidden in highly scattering media, the diffusive component of light needs to be sorted out from early arrived ballistic and snake photons. In an optical imaging system, images are collected in transmission or back-scattered geometry. The early arrival photons in the transmission approach, always carry the direct information of the hidden object embedded in the turbid medium. In the back-scattered approach, the result is not so forth coming. In the presence of a scattering host, the first arrival photons in back-scattered approach will be directly photons from the host material. In the presentation, NLOPG was applied to acquire time resolved back-scattered images under the phase matching condition. A time-gated amplified signal was obtained through this NLOPG process. The system's gain was approximately 100 times. The time-gate was achieved through phase matching condition where only coherent photons retain their phase. As a result, the diffusive photons, which were the primary contributor to the background, were removed. With a large dynamic range and high resolution, time-gated early light imaging has the potential for improving rocket/aircraft design by determining jets shape and particle sizes. Refinements to these techniques may enable drop size measurements in the highly scattering, optically dense region of multi-element rocket injectors. These types of measurements should greatly enhance the design of stable, and higher performing rocket engines.

Galland, Pierre A.

Rapid Biochemical Analysis on the International Space Station (ISS): Preparing for Human Exploration of the Moon and Mars

The Lab-on-a-Chip Application Development - Portable Test System, known as LOCAD-PTS, was launched to the International Space Station (ISS) aboard Space Shuttle Discovery (STS-116) on December 9th,2006. Since that time, it has remained onboard ISS and has been operated by the crew on 10 separate occasions LOCAD-PTS is a handheld device for rapid biochemical analysis; it consists of a spectrophotometer, a series of interchangeable cartridges, a pipette and several clean/sterilized swabbing kits to obtain samples from ISS surfaces. Sampling, quantitative analysis and data retrieval is performed onboard, therefore reducing the need to return samples to Earth. Less than 20 minutes are required from sampling to data, significantly faster than existing culture-based methods on ISS, which require 3-5 days. Different cartridges are available for the detection of different target molecules (simply by changing the formulation within each cartridge), thereby maximizing the benefit and applications addressed by a single instrument. Initial tests on ISS have focused on the detection of the bact.erial macromolecule endotoxin, a component of bacterial cell walls. LOCAD-PTS detects endotoxin with a cartridge that contains a formulation known as Limulus Amebocyte Lysate (LAL) assay. LAL is derived from blood of the horseshoe crab, Limulus polyphemus, and detects enodotoxin with an enzyme cascade that triggers generation Of a yellow colored dye, p-nitroanaline. The more p-nitroanaline product, the more endotoxin is in the original sample. To enable quantitative analysis, the absorbance of this color is measured by LOCAD-PTS through a 395 nm filter and compared with an internal calibration curve, to provide a reading on the LED display that ranges from 0.05 Endotoxin Units (EU)/ml to 5 EU/ml. Several surface sites were analyzed within ISS between March 2007 and February 2008, including multiple locations in the US Laboratory Destiny, Node 1 Unity, AMock, and Service Module Zvezda. The goals of this initial study were to i) test the cleanliness of reagents/supplies on orbit, ii) test the crew's ability to collect and process a sample in microgravity without contamination, iii) demonstrate nominal function of the LOCAD-PTS, and iv) provide a general survey of endotoxin within the ISS. The surface sites varied greatly in terms of their frequency-of-use and material texture/composition; from relatively smooth aluminum, to fabric, to the room temperature vulcanizing (RTV) rubber of a Extravehicular Mobility Unit (EMU) spacesuit. Results showed that: i) the swabbing kits and reagents remained clean on orbit, ii) the crew could collect and process a sample without contamination, and iii) the LOCAD-PTS functioned nominally in > 99% of the 55 tests completed. We will present detailed results of the survey of endotoxin on ISS surfaces. These results and technology are important in the near-term - by providing an extra tool in the toolbox for ISS microbial monitoring. They are also important in the longer term as valuable preparation for human exploration of the Moon and Mars. One of the proposed science goals for the human exploration of Mars will be to detect and characterize any indigenous biological molecules that may exist on the Martian surface. To achieve that goal, the crew must have the technology available onboard to differentiate indigenous biology from any terrestrial biological material brought to Mars by the spacecraft and crew (termed 'forward contamination'). The LAL assay is already one of the official methods used by NASA's planetary protection program to certify cleanliness of interplanetary robotic spacecraft prior to launch; and therefore endotoxin is a good marker of forward contamination (as well as other microbial molecules detectable with LOCAD-PTS e.g. box-1, 3-glucan and lipoteichoic acid). Furthermore, the distribution and abundance of these molecules on the ISS provides a good indicator of what to expect on the Crew Exploratioehicle Orion, the lunar lander Antares, and future crewed spacecraft destined for Mars. In addition, technology such as LOCAD-PTS has been proposed to help evaluate forward contamination during lunar surface operations by the crew, as preparation for the human exploration of Mars.

Maule, J.