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The biological motivation for Artificial Neural Net developments is briefly discussed, and the most popular paradigm, the feedforward supervised learning net with error back propagation training algorithm, is introduced. Possible approaches for utilization in structural optimization is illustrated through simple examples. Other currently ongoing developments for application in structural mechanics are also mentioned.
Topics covered include plant and animal gravity receptors and transduction; the role of gravity in growth and development of plants and animals; biological support structures and the role of calcium; mechanisms and responses of gravity sensitive systems; and mechanisms of plant responses to gravity.
A high resolution x ray microscope for imaging microscopic structures within biological specimens has an optical system including a highly polished primary and secondary mirror coated with identical multilayer coatings, the mirrors acting at normal incidence. The coatings have a high reflectivity in the narrow wave bandpass between 23.3 and 43.7 angstroms and have low reflectivity outside of this range. The primary mirror has a spherical concave surface and the secondary mirror has a spherical convex surface. The radii of the mirrors are concentric about a common center of curvature on the optical axis of the microscope extending from the object focal plane to the image focal plane. The primary mirror has an annular configuration with a central aperture and the secondary mirror is positioned between the primary mirror and the center of curvature for reflecting radiation through the aperture to a detector. An x ray filter is mounted at the stage end of the microscope, and film sensitive to x rays in the desired band width is mounted in a camera at the image plane of the optical system. The microscope is mounted within a vacuum chamber for minimizing the absorption of x rays in air from a source through the microscope.
The objectives are to demonstrate how we can make direct measurements of the mechanical properties of a special structure in biology, namely the lipid bilayer membrane, using a micromanipulation technique, and how these properties compare and contrast with 'more traditional' technological/engineering materials. Given that the investment in equipment and expertise to carry out these experiments is probably beyond the scope of most teaching labs, the described experiment is not intended as one that can actually be demonstrated in a student laboratory class. The intention behind presenting this work is to begin to raise awareness in the Material Science community about the material properties of biological material that form a new (to us) category of soft engineering materials that have dimensions on the nanoscale.
We present calculations of linear energy transfer (LET) spectra in low earth orbit from galactic cosmic rays and trapped protons using the HZETRN/BRYNTRN computer code. The emphasis of our calculations is on the analysis of the effects of secondary nuclei produced through target fragmentation in the spacecraft shield or detectors. Recent improvements in the HZETRN/BRYNTRN radiation transport computer code are described. Calculations show that at large values of LET (> 100 keV/micrometer) the LET spectra seen in free space and low earth orbit (LEO) are dominated by target fragments and not the primary nuclei. Although the evaluation of microdosimetric spectra is not considered here, calculations of LET spectra support that the large lineal energy (y) events are dominated by the target fragments. Finally, we discuss the situation for interplanetary exposures to galactic cosmic rays and show that current radiation transport codes predict that in the region of high LET values the LET spectra at significant shield depths (> 10 g/cm2 of Al) is greatly modified by target fragments. These results suggest that studies of track structure and biological response of space radiation should place emphasis on short tracks of medium charge fragments produced in the human body by high energy protons and neutrons.
Background: Catalytic RNAs, or ribozymes, possessing both a genotype and a phenotype, are ideal molecules for evolution experiments in vitro. A large, heterogeneous pool of RNAs can be subjected to multiple rounds of selection, amplification and mutation, leading to the development of variants that have some desired phenotype. Such experiments allow the investigator to correlate specific genetic changes with quantifiable alterations of the catalytic properties of the RNA. In addition, patterns of evolutionary change can be discerned through a detailed examination of the genotypic composition of the evolving RNA population. Results: Beginning with a pool of 10(13) variants of the Tetrahymena ribozyme, we carried out in vitro evolution experiments that led to the generation of ribozymes with the ability to cleave an RNA substrate in the presence of Ca2+ ions, an activity that does not exist for the wild-type molecule. Over the course of 12 generations, a seven-error variant emerged that has substantial Ca(2+)-dependent RNA-cleavage activity. Advantageous mutations increased in frequency in the population according to three distinct dynamics--logarithmic, linear and transient. Through a comparative analysis of 31 individual variants, we infer how certain mutations influence the catalytic properties of the ribozyme. Conclusions: In vitro evolution experiments make it possible to elucidate important aspects of both evolutionary biology and structural biochemistry on a reasonable short time scale.
BACKGROUND: The timescale of prokaryote evolution has been difficult to reconstruct because of a limited fossil record and complexities associated with molecular clocks and deep divergences. However, the relatively large number of genome sequences currently available has provided a better opportunity to control for potential biases such as horizontal gene transfer and rate differences among lineages. We assembled a data set of sequences from 32 proteins (approximately 7600 amino acids) common to 72 species and estimated phylogenetic relationships and divergence times with a local clock method. RESULTS: Our phylogenetic results support most of the currently recognized higher-level groupings of prokaryotes. Of particular interest is a well-supported group of three major lineages of eubacteria (Actinobacteria, Deinococcus, and Cyanobacteria) that we call Terrabacteria and associate with an early colonization of land. Divergence time estimates for the major groups of eubacteria are between 2.5-3.2 billion years ago (Ga) while those for archaebacteria are mostly between 3.1-4.1 Ga. The time estimates suggest a Hadean origin of life (prior to 4.1 Ga), an early origin of methanogenesis (3.8-4.1 Ga), an origin of anaerobic methanotrophy after 3.1 Ga, an origin of phototrophy prior to 3.2 Ga, an early colonization of land 2.8-3.1 Ga, and an origin of aerobic methanotrophy 2.5-2.8 Ga. CONCLUSIONS: Our early time estimates for methanogenesis support the consideration of methane, in addition to carbon dioxide, as a greenhouse gas responsible for the early warming of the Earths' surface. Our divergence times for the origin of anaerobic methanotrophy are compatible with highly depleted carbon isotopic values found in rocks dated 2.8-2.6 Ga. An early origin of phototrophy is consistent with the earliest bacterial mats and structures identified as stromatolites, but a 2.6 Ga origin of cyanobacteria suggests that those Archean structures, if biologically produced, were made by anoxygenic photosynthesizers. The resistance to desiccation of Terrabacteria and their elaboration of photoprotective compounds suggests that the common ancestor of this group inhabited land. If true, then oxygenic photosynthesis may owe its origin to terrestrial adaptations.
Since the dawn of human civilization, there has been a delicate balance between the use of resources as human frontiers expanded and the need to have a minimum influence on the ecosystem. The first 200 years of the industrial revolution essentially solved the problem of production. However, the massive production of goods also generated tremendous amounts of byproducts and wastes. In the new millennium, to sustain a healthy life in harmony with nature, it will be extremely important for us to develop various materials, products, and processes that minimize any harmful influence on the environment. Environment-conscious ceramics (ecoceramics) are a new class of materials that can be fabricated with renewable resources (wood) and wood waste material (wood sawdust). Wood is a "lignocellulosic" material formed by the photosynthetic reaction within the needles or leaves of trees. The photosynthesis process uses sunlight to take carbon dioxide from air and convert it into oxygen and organic materials. Wood has been known to be one of the best and most intricate engineering materials created by nature and known to mankind. In addition, natural woods of various types are available throughout the world. On the other hand, wood sawdusts are generated in abundant quantities by sawmills. Environment-conscious ceramic materials, fabricated via the pyrolysis and infiltration of natural wood-derived preforms, have tailorable properties with numerous potential applications. The experimental studies conducted to date on the development of materials based on biologically derived structures indicate that these materials behave like ceramic materials manufactured by conventional approaches. These structures have been shown to be quite useful in producing porous or dense materials having various microstructures and compositions.
Microdosimetry consists of studying energy deposition events in irradiated targets of volume typically of the order of a cell. The probability density 𝑓(𝑧,𝐷) of energy deposition𝑧(specific energy) in a target, exposed to an irradiation dose 𝐷,can be used to correlate inhomogeneous energy deposition events at the micro-scale(track structure)with biological responses(e.g., cell injury)[1]. Microdosimetry studies allow a better understanding of basic mechanisms of the biological response, such as the origin of the increased biological effectiveness of high Linear Energy Transfer (LET) ions, partly responsible of radiation-exposure induced cancer risks of astronauts [2].
Marine cyanobacteria are infected by phages whose genomes encode ferredoxin (Fd) electron carriers. These Fds are thought to redirect the energy harvested from light to phage-encoded oxidoreductases that enhance viral fitness, but it is unclear how the biophysical properties and partner specificities of phage Fds relate to those of photosynthetic organisms. Here, results of a bioinformatics analysis using a sequence similarity network revealed that phage Fds are most closely related to cyanobacterial Fds that transfer electrons from photosystems to oxidoreductases involved in nutrient assimilation. Structural analysis of myovirus P-SSM2 Fd (pssm2-Fd), which infects the cyanobacterium Prochlorococcus marinus, revealed high levels of similarity to cyanobacterial Fds (root mean square deviations of ≤0.5 Å). Additionally, pssm2-Fd exhibited a low midpoint reduction potential (–336 mV versus a standard hydrogen electrode), similar to other photosynthetic Fds, although it had lower thermostability (Tm = 28 °C) than did many other Fds. When expressed in an Escherichia coli strain deficient in sulfite assimilation, pssm2-Fd complemented bacterial growth when coexpressed with a P. marinus sulfite reductase, revealing that pssm2-Fd can transfer electrons to a host protein involved in nutrient assimilation. The high levels of structural similarity with cyanobacterial Fds and reactivity with a host sulfite reductase suggest that phage Fds evolved to transfer electrons to cyanobacterially encoded oxidoreductases.
Biological cell, protoplasm structure, and vital characteristics of living organisms
The present invention provides a digital topography imaging system for determining the crystalline structure of a biological macromolecule, wherein the system employs a charge coupled device (CCD) camera with antiblooming circuitry to directly convert x-ray signals to electrical signals without the use of phosphor and measures reflection profiles from the x-ray emitting source after x-rays are passed through a sample. Methods for using said system are also provided.
System for the 3D Construction of Biologically Derived Materials, Structures, and Parts NASA has developed a novel approach for macroscale biomaterial production by combining synthetic biology with 3D printing. Cells are biologically engineered to deposit desired materials, such as proteins or metals, derived from locally available resources. The bioengineered cells build different materials in a specified 3D pattern to produce novel microstructures with precise molecular composition, thickness, print pattern, and shape. Scaffolds and reagents can be used for further control over material product. This innovation provides modern design and fabrication techniques for custom-designed organic or organic-inorganic composite biomaterials produced from limited resources. Benefits Conserves resources. Few raw or bulk starting materials needed Enables custom design of diverse materials Fast, portable, macroscale, on-demand manufacturing High-fidelity microstructures Uses commercially available parts Applications Biomaterials, biotechnology Organic-inorganic composite materials On-demand manufacturing In situ resource utilization Space stations Military Infrastructure materials The Technology Once genes for a desired material type, delivery mode, control method and affinity have been chosen, assembling the genetic components and creating the cell lines can be done with well-established synthetic biology techniques. A 3D microdeposition system is used to make a 3D array of these cells in a precise, microstructure pattern and shape. The engineered cells are suspended in a printable 'ink'. The 3D microdeposition system deposits minute droplets of the cells onto a substrates surface in a designed print pattern. Additional printer passes thicken the material. The cell array is fed nutrients and reagents to activate the engineered genes within the cells to create and deposit the desired molecules. These molecules form the designed new material. If desired, the cells may be removed by flushing. The end product is thus a 3D composite microstructure comprising the novel material. This innovation provides a fast, controlled production of natural, synthetic, and novel biomaterials with minimum resource overhead and reduced pre- and post-processing requirements.
This report documents the scientific activities on board the Royal Research Ship (RRS) 'James Clark Ross' during the irst Atlantic Meridional Transect (AMT-1), 21 September to 24 October 1995. The ship sailed from Grimsby (England) for Montevideo (Uruguay) and then continued on to Stanley (Falkland Islands). The primary objective of the AMT program is to investigate basic biological processes in the open Atlantic Ocean over very broad spatial scales. For AMT-1, the meridional range covered was approximately 50 deg N to 50 deg S or nearly 8,000 nmi. The measurements to be taken during the AMT cruises are fundamental for the calibration, validation, and continuing understanding of remotely sensed observations of biological oceanography. They are also important for understanding plankton community structure over latitudinal scales and the role of the world ocean in global carbon cycles. During AMT-1 a variety of instruments were used to map the physical, chemical, and biological structure of the upper 200 m of the water column. Ocean color measurements were made using state-of-the-art sensors, whose calibration was traceable to the highest international standards. New advances in fluorometry were used to measure photosynthetic activity, which was then used to further interpret primary productivity. A unique set of samples and data were collected for the planktonic assemblages that vary throughout the range of the transect. These data will yield new interpretations on community composition and their role in carbon cycling. While the various provinces of the Atlantic Ocean were being crossed, the partial pressure of CO2 was related to biological productivity. This comparison revealed the areas of drawdown of atmospheric CO2 and how these areas relate to the surrounding biological productivity. These data, plus the measurements of light attenuation and phytoplankton optical properties, will be used as a primary input for basin-scale biological productivity models to help develop ecosystem dynamics models which will be important for improving the forecasting abilities of modelers. The AMT program is also attempting to meet the needs of international agencies in their implementation of Sensor Intercomparison and Merger for Biological and Interdisciplinary Ocean Studies (SIMBIOS), a program to develop a methodology and operational capability to combine data products from the various ocean color satellite missions.
Ionene polymers are polyammonium salts with positive nitrogens in the backbone, resulting from the polycondensation of diamines with dihalides or from the polycondensation of halo amines. The mechanism of formation of ionene polymers of different structures and their biological activity is reviewed. The antimicrobial and antifungal properties are compared with low molecular weight ammonium salts. Ionenes were found to combine with DNA by means of ionic bonds to yield similar complexes to those obtained with polyamines (spermine and spermidine). They also combine with nerve cell receptors and exercise a more powerful and longer duration ganglionic blocking action than their monomeric analogs. The antiheparin activity of ionenes and the thromboresistance of elastomeric ionene heparin coatings is described. The enhanced biological activity of ionenes as compared with low molecular weight compounds is attributed to a cooperative effect of a large number of positive charges on the polymeric chains.
Global land use and climate variability alter ecosystem conditions - including structure, function, and biological diversity - at a pace that requires unambiguous observations from satellite vantage points. Current global measurements are limited to general land cover, some disturbances, vegetation leaf area index, and canopy energy absorption. Flora is a pathfinding mission that provides new measurements of ecosystem structure, function, and diversity to understand the spatial and temporal dynamics of human and natural disturbances, and the biogeochemical and physiological responses of ecosystems to disturbance. The mission relies upon high-fidelity imaging spectroscopy to deliver full optical spectrum measurements (400-2500 nm) of the global land surface on a monthly time step at 45 meter spatial resolution for three years. The Flora measurement objectives are: (i) fractional cover of biological materials, (ii) canopy water content, (iii) vegetation pigments and light-use efficiency, (iv) plant functional types, (v) fire fuel load and fuel moisture content, and (vi) disturbance occurrence, type and intensity. These measurements are made using a multi-parameter, spectroscopic analysis approach afforded by observation of the full optical spectrum. Combining these measurements, along with additional observations from multispectral sensors, Flora will far advance global studies and models of ecosystem dynamics and change.
Biological redox reactions drive planetary biogeochemical cycles. Using a novel, structure-guided sequence analysis of proteins, we explored the patterns of evolution of enzymes responsible for these reactions. Our analysis reveals that the folds that bind transition metal–containing ligands have similar structural geometry and amino acid sequences across the full diversity of proteins. Similarity across folds reflects the availability of key transition metals over geological time and strongly suggests that transition metal–ligand binding had a small number of common peptide origins. We observe that structures central to our similarity network come primarily from oxidoreductases, suggesting that ancestral peptides may have also facilitated electron transfer reactions. Last, our results reveal that the earliest biologically functional peptides were likely available before the assembly of fully functional protein domains over 3.8 billion years ago. Thus, life is a special, very complex form of motion of matter, but this form did not always exist, and it is not separated from inorganic nature by an impassable abyss; rather, it arose from inorganic nature as a new property in the process of evolution of the world. We must study the history of this evolution if we want to solve the problem of the origin of life.
Molecular biology, genetics, molecular structure of DNA, and mutations