Postgenomic futures: translations across the machine-nature border in systems biology

Abstract

This article discusses the production of new “postgenomic” knowledges that aim to be more ecological and “wholistic” than the reductionist genetics of the last forty years. It examines systems biology and, briefly, developmental systems theory, which are two approaches that attempt to model complexities in biology. System biological metaphors and languages have been in part taken from engineering models of automobiles, airplanes and robots and then applied to complex living systems. Systems biology is only the most recent example and perhaps an excellent case in which to study this movement back and forth across the machine-living organism border in Euro-American biology to track how what we know to be nature and machine is constituted. This article argues for a careful analysis of this historical production specifically around the question of what is lost in translation at these border crossings and their potential consequences.     

MRI-based assessment of hip joint translations

To better understand movement limitations and, to some extent, the pathogenesis of osteoarthritis, it is important to quantitatively measure femoroacetabular translations to assess if any joint subluxation occurs. In this paper, we aim at measuring hip joint displacements from magnetic resonance images (MRI) based on a surface registration technique. Because this measurement is related to the location of the hip joint center (HJC), we investigate and compare different HJC estimation approaches based on patient-specific 3D bone models. We estimate the HJC based on a simulated circumduction while minimizing inter-articular distance changes. Measurements of femoroacetabular translations during low amplitude abductions ($80$ samples) and extreme flexions ($60$ samples) in female professional dancers, which is a population potentially exposed to femoroactebaluar impingements, do not show any significant subluxation.     

Biological control impacts and the Cartesian mirage

正As humans spread over the globe,they carried with themselves plants and animals that they considered useful at their new residences. Sometimes they did this because they depended on them. Typically,domesticated plants are not the most common or widespread today where they were domesticated—they have been spread over vast areas,and also outside their original area of distribution (Piperno,2017).     

Neuropharmacology and behavior in planarians: translations to mammals

Planarians are the simplest animals to exhibit a body plan common to all vertebrates and many invertebrates, characterized by bilateral rather than radial symmetry, dorsal and ventral surfaces, and a rostrocaudal axis with a head and a tail, including specialized sense organs and an aggregate of nerve cells in the head. Neurons in planarian more closely resemble those of vertebrates than those of advanced invertebrates, exhibiting typical vertebrate features of multipolar shape, dendritic spines with synaptic boutons, a single axon, expression of vertebrate-like neural proteins, and relatively low spontaneously generated electrical activity. Here we report the most relevant contribution to the knowledge of the neuropharmacology of planarians, with particular reference to the behavioral consequences of the exposure to drugs acting on neural transmission. Neurochemical and histochemical data indicate the presence of several neurotransmitter-receptor systems in planarians. Moreover, a variety of experimental studies characterized specific behavioral patterns of these animals following the exposure to drugs acting on neural transmission. There is also evidence of the interactions between discrete neurotransmitter-receptor systems in modulating behavior in planarians. Finally, the model has proved efficacy for investigating the neurotoxicology of the dopamine neurons, and for the initial screening of the neuroprotective potential of drugs. In conclusion, these findings indicate that interactions between discrete neurotransmitter-receptor systems occur very early along phylogeny, although they may have evolved from very fundamental behaviors, such as motor activity in planarian, to more complex and integrated functions in vertebrates.     

Quantifying translations in the radiohumeral joint: application of a floating axis analysis

The purpose of this study was to apply the Floating Axis analysis technique to the elbow joint, and to verify its ability to quantify clinically relevant radiohumeral translation in vitro using an electromagnetic tracking device. Of particular interest was the ability to quantify changes in anterior-posterior radial head translation, which is associated with the clinical condition of posterolateral rotatory instability of the elbow. Following the method proposed by Grood and Suntay to determine motions in the knee, an elbow coordinate system with axes representing the flexion-extension axis of the humerus, the long axis of the radius, and their mutual perpendicular, was developed. The algorithm was tested using a mechanical articulator that modeled the Floating Axis approach. Translation errors using this articulator were 0.1+/-0.1mm. The algorithm was applied to kinematic data collected from 12 cadaveric elbows that underwent a pivot shift test prior and subsequent to transection of the lateral collateral ligament. Anterior-posterior radiohumeral translation increased significantly in these elbows following the ligament sectioning (p<0.0001), with the average magnitude of posterior translation increasing from 0.9 to 19.8mm at 90 degrees of flexion. This approach will provide valuable information related to alterations in elbow motion pathways, especially for studies aimed at quantifying changes in joint stability.     

Morphometric analysis of Cartesian coordinates of the human skull

A method for locating the three dimensional coordinates of cranial landmarks with respect to the Frankfort, midsagittal, and coronal planes is presented. Sliding calipers were used to obtain the distances from left and right porion and apex to each landmark, except for a few points where spreading calipers are required. In the present example, 35 landmarks (for a total of 105 measurements) were located for each of 35 Peruvian precolumbian skulls. These distances were entered into a program (SKULL) which calculates the Cartesian coordinates of each landmark. The XYZ coordinates of each landmark contain all the information necessary for calculation of the distances between any two landmarks, and these distances may also be obtained as output from program SKULL, if desired (595 distances if all 35 landmarks are used). Reliability of the location of coordinates was determined by comparing computed distances among selected landmarks from program SKULL with traditional anthropometric measurements. Satisfactory agreements were found. Direct multivariate analysis of the coordinates of the landmarks produced insights not available in traditional multivariate analysis of conventional anthropometric measurements.     

Uneasy translations: vernacularizing demography for post-Soviet statecraft

The article explores a series of professional development seminars for state bureaucrats in the context of the moral panic over Russia's ‘demographic crisis’. It follows the vernacularization of social knowledge for state bureaucrats – a central practice that marks these pedagogical engagements. The article explores this practice's potentialities and limitations for effectively communicating social knowledge to administrative audiences. It grounds itself in the theoretical discussions of expertise and demonstrates how vernacularizing social knowledge for post-Soviet statecraft shapes the social and political meanings of Russia's demographic crisis, investing state policies and discourses with authority.     

Accessibility percolation on Cartesian power graphs

Journal of Mathematical Biology -     

Analysis of the hominoid os coxae by Cartesian coordinates.

This study is based upon 48 3-dimensional coordinates taken on 4 fossil hominid and 127 extant hominoid coxal bones. The follis include Sts 14, SK 3155, MLD 7, and MLD 25. The comparative sample consists of 42 Homo sapiens, 27 Pan troglodytes, 29 Gorilla gorilla and 29 Pongo pygmaeus. The coordinates improve the metrical representation of the bone beyond what can be done with linear measurements because the shape complexity of the os coxae is so great. The coordinates are rotated and translated so that all bones are in a standard position. The coordinates are then standardized for each specimen by dividing all coordinates by the pooled standard deviation of X, Y, and Z coordinates. These data are treated to standard statistical analyses including analysis of variance, Penrose size and shape statistics, principal coordinates and components, and canonical variates analysis. The data are then further altered by using some specimen as a standard and rotating each specimen until the total squared distance between its coordinates and those of the standard are minimized. The same statistics are applied to these "best fit" data. The results show a high degree of agreement between the methods. The hominid os coxae are dundamentally different from the other hominoids and the fossil hominids share the basic hominid configuration but with some unique differences.     

Non-contact measuring of small translations and rotations in all degrees of displacement]

The investigation of biomechanical problems often makes it necessary to measure displacements and rotations in space. An easy-to-handle optical measuring system has been developed that permits non-contact simultaneous determination of small translations and rotations in all degrees of freedom. Three two-dimensional light-sensitive sensors (PSD [position sensing detector] elements) were arranged spatially to form a measuring sensor. After processing in a computer, the signals definitively determine relative shift and rotation. Thus it is possible, for example, to measure the relative movement between two adjacent spinal vertebrae under different loads.     

Calculation of rigid-body conformational changes using restraint-driven Cartesian transformations

We present an approach for calculating conformational changes in membrane proteins using limited distance information. The method, named restraint-driven Cartesian transformations, involves 1) the use of relative distance changes; 2) the systematic sampling of rigid body movements in Cartesian space; 3) a penalty evaluation; and 4) model refinement using energy minimization. As a test case, we have analyzed the structural basis of activation gating in the Streptomyces lividans potassium channel (KcsA). A total of 10 pairs of distance restraints derived from site-directed spin labeling and electron paramagnetic resonance (SDSL-EPR) spectra were used to calculate the open conformation of the second transmembrane domains of KcsA (TM2). The SDSL-EPR based structure reveals a gating mechanism consistent with a scissoring-type motion of the TM2 segments that includes a pivot point near middle of the helix. The present approach considerably reduces the amount of time and effort required to establish the overall nature of conformational changes in membrane proteins. It is expected that this approach can be implemented into restrained molecular dynamics protocol to calculate the structure and conformational changes in a variety of membrane protein systems.