In silico analysis of lactic acid secretion metabolism through the top-down approach: Effect of grouping in enzyme kinetics

A top-down approach is known to be a useful and effective technique for the design and analysis of metabolic systems. In this study, we have constructed a grouped metabolic network forLactococcus lactis under aerobic conditions using grouped enzyme kinetics. To test the usefulness of grouping work, a non-grouped system and grouped systems were compared quantitatively with each other. Here, grouped systems were designed as two groups according to the extent of grouping. The overall simulated flux values in grouped and non-grouped models had pretty similar distribution trends, but the details on flux ratio at the pyruvate branch point showed a little difference. This result indicates that our grouping technique can be used as a good model for complicated metabolic networks, however, for detailed analysis of metabolic network, a more robust mechanism should be considered. In addition to the data for the pyruvate branch point analysis, some major flux control coefficients were obtained in this research.     

The value of enzyme histochemical techniques in classifying fibre types of human skeletal muscle

Summary Fibre-type classification of human skeletal muscle into type I and type II fibres is mostly based on their slight or strong staining with the myosin adenosine triphosphatase reaction. In order to evaluate the reliability of this screening technique a combined histochemical and biochemical study was performed on normal and diseased skeletal muscle of human subjects. In the present investigation activities of enzymes which play a role in the aerobic and anaerobic pathways and which can characterize fibre type, were examined in muscle specimens, with no apparent disease of the neuromuscular system. Special attention is given to the maximal activities of phosphofructokinase and fructose-1,6-diphosphatase, the rate limiting enzymes for the regulation of the glycolysis and glyconeogenesis, respectively. A most important feature of the biochemical findings is the constancy of the activity ratios of the examined enzymes. From these results and from the histochemical results it can be concluded that in apparently normal adult human skeletal muscle the ATP-ase technique for type I and type II typing is reliable. For fibres with an intermediate intensity of staining with the myosin ATPase technique of typing it is also necessary to apply other enzyme histochemical techniques.     

The value of enzyme histochemical techniques in classifying fibre types of human skeletal muscle. 1. Adult skeletal muscles with no apparent disease of the neuromuscular system.

Fibre-type classification of human skeletal muscle into type I and type II fibres is mostly based on their slight or strong staining with the myosin adenosine triphosphatase reaction. In order to evaluate the reliability of this screening technique a combined histochemical and biochemical study was performed on normal and diseased skeletal muscle of human subjects. In the present investigation activities of enzymes which play a role in the aerobic and anaerobic pathways and which can characterize fibre type, were examined in muscle specimens, with no apparent disease of the neuromuscular system. Special attention is given to the maximal activities of phosphofructokinase and fructose-1,6-diphosphatase, the rate limiting enzymes for the regulation of the glycolysis and glyconeogenesis, respectively. A most important feature of the biochemical findings is the constancy of the activity ratios of the examined enzymes. From these results and from the histochemical results it can be concluded that in apparently normal adult human skeletal muscle the ATP-ase technique for type I and type II typing is reliable. For fibres with an intermediate intensity of staining with the myosin ATPase technique of typing it is also necessary to apply other enzyme histochemical techniques.     

Microdensitometric analysis for study of skeletal growth and aging in the living subject

Microdensitometric analysis of a radiographic image of mineralized tissue offers information on the morphologic characteristics of the specimen examined. The use of microstructure (such as individual trabecula of bone) and macrostructure (such as Harris lines of arrest) as in vivo bone markers allows for assessment of gross skeletal changes in nondestructive fashion. This technique is also applicable to the study of the interrelationship of tooth and bone. In addition, microdensitometry offers precise information on the fine structure of bone as regards the trabecular elements. This technique is applicable in determining the size and quantity of trabeculae, their persistence over long periods of time, and the factors responsible for change or lack of change in trabeculae during growth and aging.     

Cytoskeleton of embryonic skeletal muscle cells

Cytoskeletal organization in embryonic skeletal muscle cells has been examined by transmission electron microscopy; the technique involves preparation using the platinum replication method of freezedried samples, with and without cryofracture. The cytoskeletons in developing muscle cells appear to play a role in preserving cell shape as well as in anchoring myofibrils to cell membrane.     

Developmentally regulated troponin C mRNAs of chicken skeletal muscle.

Fast and slow/cardiac troponin C (TnC) are the two different isoforms of TnC. Expression of these isoforms is developmentally regulated in vertebrate skeletal muscle. Therefore, in our studies, the pattern of their expression was analyzed by determining the steady-state levels of both TnC mRNAs. It was also examined if mRNAs for both isoforms of TnC were efficiently translated during chicken skeletal muscle development. We have used different methods to determine the steady-state levels of TnC mRNAs. First, probes specific for the fast and slow TnC mRNAs were developed using a 390 base pair (bp) and a 255 bp long fragment, of the full-length chicken fast and slow TnC cDNA clones, respectively. Our analyses using RNA-blot technique showed that fast TnC mRNA was the predominant isoform in embryonic chicken skeletal muscle. Following hatching, a significant amount of slow TnC mRNA began to accumulate in the skeletal (pectoralis) muscle. At 43 weeks posthatching, the slow TnC mRNA was nearly as abundant as the fast isoform. Furthermore, a majority of both slow and fast TnC mRNAs was found to be translationally active. A second method allowed a more reliable measure of the relative abundance of slow and fast TnC mRNAs in chicken skeletal muscle. We used a common highly conserved 18-nucleotide-long sequence towards the 5'-end of these mRNAs to perform primer extension analysis of both mRNAs in a single reaction. The result of these analyses confirmed the predominance of fast TnC mRNA in the embryonic skeletal muscle, while significant accumulation of slow TnC mRNA was observed in chicken breast (pectoralis) muscle following hatching. In addition to primer extension analysis, polymerase chain reaction was used to amplify the fast and slow TnC mRNAs from cardiac and skeletal muscle. Analysis of the amplified products demonstrated the presence of significant amounts of slow TnC mRNA in the adult skeletal muscle.     

The value of enzyme histochemical techniques in the classification of fibre types of human skeletal muscle

Summary Classification of human skeletal muscle into type I and type II fibres is frequently based on their weak or strong staining with the myosin adenosine triphosphatase reaction. In order to evaluate the reliability of this screening technique a combined histochemical and biochemical study was performed on normal and diseased skeletal muscle of human subjects. In the present investigation activities of enzymes which play a role in the aerobic and anaerobic pathways and which can characterize fibre type, were examined in human muscle specimens with disease of the neuromuscular system.Special attention is given to the maximal activities of phosphofructokinase and fructose-1,6-diphosphatase, the rate limiting enzymes for the regulation of the glycolysis and gluconeogenesis respectively. Moreover the activities of enzymes of the pentose phosphate pathway are determined.A most important feature of the biochemical findings is that the constancy of activity ratios of the examined enzymes, as is found apparently normal human skeletal muscle, was frequently not present in diseased human skeletal muscle. From these results and from the histochemical results it can be concluded that for fibre classification in diseased human skeletal muscle the histochemical demonstration of myosin ATPase activity exclusively is not sufficient, but that it is necessary to apply other enzyme histochemical techniques too.Moreover it was found that in diseased human skeletal muscles the activity of the NADPH regenerating enzymes glucose-6-phosphate dehydrogenase and 6-phosphogluconate dehydrogenase was strongly increased. A third observation was the relative decrease of the activity of the examined aerobic enzymes in affected muscle fibres of neurogenic muscle diseases.     

Relative brain size: A critique of a new measure

An analysis of a relative brain size measuring technique proposed by Radinsky ('67) shows it to be inapplicable on lower taxonomic levels of primates. The relationship among foramen magnum area, total skeletal weight (a suggested index of body size) and cranial capacity are analyzed by a partial correlation technique. Results indicate that foramen magnum size is significantly associated with total skeletal weight through its relationship to cranial capacity.     

The relationship of body segment length and vertical jump displacement in recreational athletes

The purpose of this study was to determine if segmental skeletal length contributes to vertical jump (VJ) displacement in recreational athletes. Skeletal length measurements of the trunk, femur, tibia, and foot were obtained by palpation of bony landmarks and a standard tape measure. A pilot study (n = 10) examined the intratester and intertester reliability for each skeletal measure. The pilot investigation revealed fair to excellent intratester and intertester reliability. Seventy-eight recreational athletes (55 men and 23 women) with a mean age of 21.9 +/- 2.9 years participated in the investigation. Multiple regression analysis with gender as a categorical indicator variable revealed a significant gender difference; therefore, men and women were analyzed separately. Regression analysis for men identified foot length (p < 0.033, R(2) = 0.08) as the only significant skeletal length predictor of VJ displacement. None of the skeletal length measures was predictive of VJ displacement in women. Based on the results of this investigation, intrinsic skeletal length is not a strong predictor of VJ displacement in young adult recreational athletes.     

Compressive axial mechanical properties of rat bone as functions of bone volume fraction,apparent density and micro-ct based mineral density

Mechanical testing has been regarded as the gold standard to investigate the effects of pathologies on the structure–function properties of the skeleton. With recent advances in computing power of personal computers, virtual alternatives to mechanical testing are gaining acceptance and use. We have previously introduced such a technique called structural rigidity analysis to assess mechanical strength of skeletal tissue with defects. The application of this technique is predicated upon the use of relationships defining the strength of bone as a function of its density for a given loading mode. We are to apply this technique in rat models to assess their compressive skeletal response subjected to a host of biological and pharmaceutical stimulations. Therefore, the aim of this study is to derive a relationship expressing axial compressive mechanical properties of rat cortical and cancellous bone as a function of equivalent bone mineral density, bone volume fraction or apparent density over a range of normal and pathologic bones.We used bones from normal, ovariectomized and partially nephrectomized animals. All specimens underwent micro-computed tomographic imaging to assess bone morphometric and densitometric indices and uniaxial compression to failure.We obtained univariate relationships describing 71–78% of the mechanical properties of rat cortical and cancellous bone based on equivalent mineral density, bone volume fraction or apparent density over a wide range of density and common skeletal pathologies. The relationships reported in this study can be used in the structural rigidity analysis introduced by the authors to provide a non-invasive method to assess the compressive strength of bones affected by pathology and/or treatment options.     

Temporal aspects of biological distance: serial correlation and trend in a prehistoric skeletal lineage

A number of previous studies have examined biological variability within individual human skeletal samples, using internal chronology as an explanatory source for variation. In this paper time series and matrix comparison methods are used to examine temporal serial correlation and trend of biological characteristics within a skeletal sample. These methods follow appropriately upon the assumption that the processes of genetic drift and migration lead to temporal autocorrelation of the mean genotype within individual genetic lineages. In the current analysis, using skeletal material from the Pete Klunk Mound Group, temporal serial correlation is demonstrated between samples from different mounds. This indicates that a previous provisional archaeological ordering of the mounds is probably correct. Absence of temporal trend for any of the nonmetric traits examined here suggests a lack of directional evolutionary forces operating on these traits.     

Community Structure Analysis of Gene Interaction Networks in Duchenne Muscular Dystrophy

Duchenne Muscular Dystrophy (DMD) is an important pathology associated with the human skeletal muscle and has been studied extensively. Gene expression measurements on skeletal muscle of patients afflicted with DMD provides the opportunity to understand the underlying mechanisms that lead to the pathology. Community structure analysis is a useful computational technique for understanding and modeling genetic interaction networks. In this paper, we leverage this technique in combination with gene expression measurements from normal and DMD patient skeletal muscle tissue to study the structure of genetic interactions in the context of DMD. We define a novel framework for transforming a raw dataset of gene expression measurements into an interaction network, and subsequently apply algorithms for community structure analysis for the extraction of topological communities. The emergent communities are analyzed from a biological standpoint in terms of their constituent biological pathways, and an interpretation that draws correlations between functional and structural organization of the genetic interactions is presented. We also compare these communities and associated functions in pathology against those in normal human skeletal muscle. In particular, differential enhancements are observed in the following pathways between pathological and normal cases: Metabolic, Focal adhesion, Regulation of actin cytoskeleton and Cell adhesion, and implication of these mechanisms are supported by prior work. Furthermore, our study also includes a gene-level analysis to identify genes that are involved in the coupling between the pathways of interest. We believe that our results serve to highlight important distinguishing features in the structural/functional organization of constituent biological pathways, as it relates to normal and DMD cases, and provide the mechanistic basis for further biological investigations into specific pathways differently regulated between normal and DMD patients. These findings have the potential to serve as fertile ground for therapeutic applications involving targeted drug development for DMD.     

A Multivariate Analysis of the Fristoe Burial Complex in Southwestern Missouri

Abstract

This paper presents the result of an analysis of 24 burial mounds and cairns in southwest Missouri. All of the sites belong to the Fristoe Burial Complex with an estimated age of A. D. 500 to A.D. 1000. Data selected for analysis consisted of 41 traits distributed in varying numbers among the sites. In order to observe relationships between sites, a Q-type factor analysis was used. An orthogonal rotation yielded five factors. Three factors are discussed. Factors 2 and 5 are not discussed because of the small number of sites explained by them. Factor 1 loads heavily on eight sites and Factors 3 and 4 each on seven sites. Seventeen of the 24 sites are explained by the three factors which are hypothesized to represent three distinct temporal groupings. Factor 1 is thought to depict a late grouping based on trade relationships between the Gulf Coast and the Ozark Highlands. Factor 4 appears to be a grouping of Late Woodland elements, and Factor 3 possibly represents a set of Mississippian and Late Woodland elements. Results of the analysis allow us to hypothesize three temporal groupings within the Fristoe Burial Complex. The results further indicate that factor analysis can be used as a technique to order archeological materials and generate hypotheses.     

Spatial variation in porosity and skeletal element characteristics in apical tips of the branching coral Acropora pulchra (Brook 1891)

Micro-CT scanning techniques were used to investigate fine-scale variation in porosity along branch tips of Acropora pulchra. Porosity variation is a result of progressive thickening of skeletal elements away from the apical tip of branches, rather than changes in the spacing of skeletal elements. A linear fit was found to describe the relationship between distance along the tip and both porosity and skeletal thickness. The slope of the line obtained may relate to branch extension rates and allow retrospective data to be obtained from Acropora specimens. Skeletal morphology examined by 2D and 3D imaging shows a progressive gradation in thickness occurring in the axial corallite wall and thickness changes at a site of incipient branch formation. The application of the micro-CT technique to museum and fossil specimens is illustrated.     

The skeletal taphonomy of Archaeopteryx: a quantitative approach

A new technique is described for taphonomic investigation of fossil vertebrates with a high degree of skeletal articulation and completeness, and applied to analysis of the taphonomy of Archaeopteryx. The known skeletal remains of Archaeopteryx can be assigned to two preservational types: (A) well-articulated and almost complete skeletons, and (B) less complete and more disarticulated skeletons, but with some well-articulated sub-units. Differences between these categories are most likely a function of time elapsed between death and burial, and these groups are interpreted as samples of a larger possible range of taphonomic variation. The specimens represent parts of a decay spectrum rather than a decay sequence, and there is no evidence for a regional drift pattern. Digital crossover in the hands of Archaeopteryx , previously considered an anatomical condition, is interpreted as a post-mortem artefact.     

Perceptual organization at attended and unattended locations

This study examined the effects of attention on forming perceptual units by proximity grouping and by uniform connectedness (UC). In Experiment 1 a row of three global letters defined by either proximity or UC was presented at the center of the visual field. Participants were asked to identify the letter in the middle of stimulus arrays while ignoring the flankers. The stimulus onset asynchrony (SOA) between stimulus arrays and masks varied between 180 and 500 ms. We found that responses to targets defined by proximity grouping were slower than to those defined by UC at median SOAs but there were no differences at short or long SOAs. Incongruent flankers slowed responses to targets and this flanker compatibility effect was larger for UC than for proximity-defined flankers. Experiment 2 examined the effects of spatial precueing on discrimination responses to proximity- and UC-defined targets. The advantage for targets defined by UC over targets defined by proximity grouping was greater at uncued relative to cued locations. The results suggest that the advantage for UC over proximity grouping in forming perceptual units is contingent on the stimuli not being fully attended, and that paying attention to the stimuli differentially benefits proximity grouping.     

Perceptual organization at attended and unattended locations

In order to perceive complex visual scenes, the human perceptual system has to organize discrete enti-ties in the visual field into chunks or perceptual units for higher-level processing. Perceptual organization is governed by Gestalt principles such as proximity, similarity, and continuity[1]. Thus spatially close ob-jects tend to be grouped together, as do elements that are similar to one another. Grouping based on the Ge-stalt laws (particularly proximity) is critical for the perception of…     

Anatomical, physiological, and epidemiological correlates of the aging process: a confirmation of multifactorial age determination in the Libben skeletal population

Paleodemographic analyses based on estimates of skeletal age at death consistently report high levels of young adult mortality with few individuals living in excess of 50 years. Critics assert these data indicate systematic underaging of adults and justifiably remark that criteria for estimating skeletal age at death may be unreliable, age determinations are too frequently based on one or two criteria alone, and adult paleodemographic age profiles often mimic the age distribution of the modern population from which an age indicator's standards were originally derived. This study reports a series of tests based on well-documented biological aging phenomena that can be used to investigate potential effects of systematic underaging in adults, assuming the skeletal population is of sufficient size to permit such tests. These include patterns of third decade sternal clavicular epiphyseal fusion, multiple age and sex criteria associated with cortical bone dynamics, and fractures known to occur throughout the entire adult ages range. These phenomena are examined here for the Libben site skeletal population where adult age at death was determined by the multifactorial summary age technique. None of the biological criteria reported here were used in the Libben summary age analysis and thus serve as an independent test of accuracy in age determination. In addition, the summary age method has recently been applied to a series of modern skeletons of known age (Todd samples 1 and 2). Age standards for criteria employed with Libben and Todd 1 were identical. Since Todd 1 displayed underaging in older adults, a second Libben age distribution adjusted for Todd 1 bias was generated for comparison. A third Libben adult survivorship profile based on a Coale and Demeny West level 3 mortality experience, considered by some to be a more realistic model for skeletal populations, was produced for comparison. For all criteria examined, original Libben summary ages provided superior concordance with known patterns of biological aging in human populations. While Libben ages adjusted for Todd 1 bias were slightly better in the third decade, both Todd 1 adjusted and Coale and Demeny West level 3 age distributions produced unrealistic patterns of biological aging for individuals greater than 35 years. Implications of these results are discussed.     

Measurement of the protein-synthetic activity in vivo of various tissues in rats by using [3H]Puromycin.

The validity of a new technique was examined for estimating the protein-synthetic activity of various tissues in vivo. The basic assumption underlying the method is that the number of peptide chains growing on each active ribosome would increase as the protein-synthetic activity of each tissue increases. The principle of the procedure, which was devised originally by Wool & Kurihara [(1967) Proc. Natl. Acad. Sci. U.S.A. 58, 2401-2407] to determine in vitro the number of functional ribosomes in skeletal muscle, is as follows. Puromycin is known to bind easily to the C-terminal end of the growing peptide on ribosomes and thus stop further chain elongation. Hence, if the number of puromycin molecules attached to the nascent peptide is determined by using radioactive puromycin as a tracer, one can estimate the number of growing peptides, i.e. the activity of tissue protein synthesis. By using this technique, it is shown that both starvation and the feeding of a protein-free diet caused marked decreases in the relative rate of formation of peptidyl-puromycin, i.e. activity of protein synthesis in liver, skeletal muscle, heart, spleen, testis, lung, kidney and intestine.     

Divergent selection for skeletal malformations in chickens alters polymorphism at microsatellite loci

The objective of this study was to determine microsatellite polymorphism in Rhode Island Red (RIR) and Sussex (SX) chickens, divergently selected over six generations for high (H) or low (L) incidence of skeletal defects in embryos (30.7% for H lines, 3.7% for L lines). The polymorphism analysis covered 15 microsatellite markers within four lines (a total of 60 individuals). Eight alleles were identified as specific to H lines and six alleles as specific to L lines. The selection for skeletal malformation appears to have affected the frequency of microsatellite alleles. The experimental material examined constitutes a valuable source for identification of real genes causing skeletal defects.