Pathway analysis, engineering, and physiological considerations for redirecting central metabolism

The rate and yield of producing a metabolite is ultimately limited by the ability to channel metabolic fluxes from central metabolism to the desired biosynthesis pathway. Redirection of central metabolism thus is essential to high-efficiency production of biochemicals. This task begins with pathway analysis, which considers only the stoichiometry of the reaction networks but not the regulatory mechanisms. An approach extended from convex analysis is used to determine the basic reaction modes, which allows the determination of optimal and suboptimal flux distributions, yield, and the dispensable sets of reactions. Genes responsible for reactions in the same dispensable set can be deleted simultaneously. This analysis serves as an initial guideline for pathway engineering. Using this analysis, we successfully constructed an Escherichia coli strain that can channel the metabolic flow from carbohydrate to the aromatic pathway with theoretical yield. This analysis also predicts a novel cycle involving phosphoenolpyruvate (PEP) carboxykinase (Pck) and the glyoxylate shunt, which can substitute the tricarboxylic acid cycle with only slightly less efficiency. However, the full cycle could not be confirmed in vivo, possibly because of the regulatory mechanism not considered in the pathway analysis.In addition to the kinetic regulation, we have obtained evidence suggesting that central metabolites are involved in specific regulons in E. coli. Overexpression of PEP-forming enzymes (phosphoenolpyruvate synthase [Pps] and Pck) stimulates the glucose consumption rate, represses the heat shock response, and negatively regulates the Ntr regulon. These results suggest that some glycolytic intermediates may serve as a signal in the regulation of the phosphotransferase system, heat shock response, and nitrogen regulation. However, the role of central metabolites in these regulations has not been determined conclusively. (c) 1996 John Wiley & Sons, Inc.     

Lateralisation in birds of prey: adaptive and phylogenetic considerations

Lateralisation, the different use of one or other side or appendix of the body, is basically determined by brain asymmetry which, in turn, is likely to be due to adaptive reasons. Several studies have been carried out on birds in general. However, birds of prey in particular, although they are very good candidates, have not been investigated from the sensory lateralisation point of view. In fact, many species scan for prey while perched and capture terrestrial prey with the feet, having at the same time the obvious necessity to keep their balance. This paper, therefore, investigates the existence of some sort of lateralisation in several species of both Falconiformes and Strigiformes temporarily in captivity. Attention is given to: (a) the direction of body rotation when perceiving a sound stimulus from behind the body and (b) the use of the feet when grasping a terrestrial prey. Lateralisation was found to be clearly present in both types of tests, although with some difference in its expression. In fact, almost every species tested rotated its body anti-clockwise, i.e. to the left, both in the first test and in repeated tests, with no noticeable difference between Falconiformes and Strigiformes. Also prey grasping showed a preferential use of one foot. Falconiformes preferred clearly to grasp the prey with one foot only in both the first test and in subsequent ones. Strigiformes, on the other hand, preferred using both feet, although a not insignificant proportion of individuals used one foot. Only the little owl seemed to have the tendency to prefer to use the right foot only, in a similar manner to Falconiformes. In fact, this bird is the most "diurnal" owl species among those tested, suggesting that lateralisation in footedness might be affected by adaptive constraints more than by phylogenetic similarities. Lateralisation, therefore, seems to be very widespread among birds of prey. Preferential use of the right foot also appears to be a general habit, and this is probably connected to the use of left hemisphere when manipulating food items.     

Anatomy of the trunk mesoderm in tunicates: homology considerations and phylogenetic interpretation

The tadpole stage of tunicates has played a pivotal role in understanding chordate evolution. While the organization of the mesoderm has been given high importance in comparative anatomical studies of Bilateria, this morphological character remains largely unexplored in tunicate tadpoles. For larvae of the phlebobranch ascidian Ciona intestinalis, the presence of two mesodermal pockets had been claimed, raising the possibility that paired coelomes are present in the larval ascidian. Using computer assisted 3D-reconstructions based on complete series of 1 μm-sections analyzed by light microscopy complemented by TEM-investigation of selected regions a comparative anatomical study of tadpole stages from four major tunicate clades, Aplousobranchiata, Phlebobranchiata, Stolidobranchiata, and Appendicularia is presented. In the aplousobranch Clavelina lepadiformis numerous mesodermal cells are found throughout the entire trunk plus the unpaired ventral rudiment of the pericardium. In the phlebobranch Ascidia interrupta, massive mesodermal components occur in the posterior trunk, whereas more anteriorly situated mesoderm consists of loose streaks of cells or isolated cells. This is also the case in the stolidobranch ascidians Herdmania momus and Styela plicata. In the stolidobranch Molgula occidentalis and the appendicularian Oikopleura dioica the anterior trunk is entirely devoid of mesodermal cells. TEM-investigation revealed that all mesodermal structures in the trunk of tunicate tadpoles were mesenchymal with the exception of a ventral portion of the mesoderm in C. lepadiformis, which probably corresponds to the developing pericardium, and the differentiated pericardium of the juvenile O. dioica. Thus no evidence for paired coelomic cavities in Tunicata was found. Outgroup comparison suggests that the reduction of paired coelomic cavities is an apomorphic trait of Tunicata. Within Tunicata a stepwise evolutionary reduction of the anterior larval mesenchyme is documented.     

The dipteran sperm tail: ultrastructural characteristics and phylogenetic considerations

The sperm tail from representatives of several families of Diptera has been examined by high resolution electron microscopy and a computer analysis that improved the visualization of recorded patterns. A considerable variability in sperm tail structure is found within Diptera, and is actually greater than that of any other insect order. The 'generalized insect sperm axoneme'. which is characterized as a 9+9+2 axoneme and by the accessory microtubules having 16 protofilaments, was found only in some dipterans; these are members of Mycetophilidae. From this fact we conclude that Mycetophilidae is likely to be the most primitive extant dipteran group. Another mycetophilid, Boletina , was seen to have accessory tubules with 15 protofilaments as have members of families Dixidae, Chironomidae, Culicidae, and Bibionidae. The last two families have spermatozoa of a type designated as 9+9+'1' there is a central rod rather than two microtubules. We regard this 9+9+'1'pattern with 15 protofilaments to represent a synapomorphic feature. Representatives of the neatoceran families Tipulidae and Trichoceridae have accessory tubules with 13 protofilaments as do examined members of several brachyceran families. Brachycera is hence likely to be derived from the vicinity of the tipulid family. The intertubular material is small in Mycetophilidae and most nematoceran groups, whereas in Tipulidae and Brachycera it is enlarged; here it bridges the space between the accessory tubules and contains various inclusions.     

The evolution of the terrestrial vertebrates: environmental and physiological considerations

Physiological evidence has long been used to suggest that the gnathostomous vertebrates (those possessing jaws) were primitively fresh water. The same was also the case for the Osteichthyes (bony fish) and the Tetrapoda (Amphibia, Reptilia, Aves, Mammalia). However, the geological evidence favours a marine origin for the vertebrates as a whole, and, for the gnathostomes and the osteichthyans in particular. Some of the earliest amphibian remains may be associated with tidally influenced sediments. Furthermore, during the early part of the Devonian, fresh water chemistry may well have been different from that of today, lessening the divide between marine and non-marine environments. Urea formation via the ornithine cycle, and urea retention in the body fluids, are useful adaptations for terrestrial life. They prevent excessive water loss associated with the elimination of nitrogenous waste. These abilities may have been primitive for the gnathostomes, and were developed in the marine environment to reduce osmotic dehydration. In the aqueous medium, gaseous exchange is effected by the gills. These organs are, on the whole, useless in air. For vertebrates, air-breathing is effected by an inflatable sac, with moist linings, and an internal location. Some form of air-breathing sac was primitive for the osteichthyans, and may have been primitive for the gnathostomes. Again, this adaptation for terrestrial life developed in response to conditions experienced in the marine, aquatic environment. A new model of tetrapod evolution is proposed in the light of the basic marine origin and character of the ancestors of the tetrapods.     

Image analysis of the leaf vascular network: physiological considerations

The study of leaf vascular systems is important in order to understand the fluid dynamics of water movement in leaves. Recent studies have shown how these systems can be involved in the performance of photosynthesis, which is linked to the density of the vascular network per unit of leaf area. The aim of the present study was to highlight the correlation between a leaf vein density (V_D) and net photosynthetic rate (P_N), which was undertaken using a digital camera, a stereoscopic microscope, and a light source. The proposed hypothesis was tested, for the first time, on the leaves of two cultivars of Vitis vinifera (L.). A significant difference was found between the V_D of mature leaves of the two cultivars. V_D was also significantly correlated with the maximum leaf P_N. These findings support the hypothesis that the vascular system of grape leaves can be correlated with leaf photosynthesis performance.     

Ecological consequences of the phylogenetic and physiological diversities of acetogens

Acetogens reduce CO₂ to acetate via the acetyl-CoA pathway and have been classically thought of as obligately anaerobic bacteria. Nearly 100 acetogenic species from 20 different genera have been isolated to date. These isolates are able to use very diverse electron donors and acceptors, and it is thus very likely that the in situ activities of acetogens are very diverse and not restricted to acetogenesis. Since acetogens constitute a very phylogenetically diverse bacteriological group, it should be anticipated that they can inhabit, and have impact on, diverse habitats. Indeed, they have been isolated from a broad range of habitats, including oxic soils and other habitats not generally regarded as suitable for acetogens. Although the ecological impact of acetogens is determined by the in situ manifestation of their physiological potentials, assessing their in situ activities is difficult due to their physiological and phylogenetic diversities. This mini-review will highlight a few of the physiological and ecological realities of acetogens, and will focus on: (i) metabolic diversities and regulation, (ii) phylogenetic diversity and molecular ecology, and (iii) the capacity of acetogens to cope with oxic conditions under both laboratory and in situ conditions. This revised version was published online in August 2006 with corrections to the Cover Date.     

Measurement of plasma adenosine concentration: methodological and physiological considerations

This study tested the hypothesis that measurements of plasma adenosine concentration made on samples of blood obtained in dipyridamole and EHNA (i.e., "stopping solution") may be falsely elevated as a result of ongoing in vitro production and accumulation of adenosine during sample processing. Studies were performed with samples of anticoagulated blood obtained from anesthesized domestic swine. Adenosine concentration of ultra filtrated plasma was determined by high-pressure liquid chromatography (HPLC). The following parameters were evaluated: (i) rate of clearance of [3H]adenosine added to plasma, (ii) endogenous adenosine concentration of matched blood samples obtained in "stopping solution" alone, "stopping solution" plus EDTA, and perchloric acid (PCA), (iii) plasma and erythrocyte endogenous adenosine concentration in nonhemolyzed samples, and (iv) plasma adenosine concentration of samples hemolyzed in the presence of "stopping solution" alone or "stopping solution" plus EDTA. We observed that (i) greater than or equal to 95% of [3H]adenosine added to plasma is removed from it by formed elements of the blood in less than 20 s, (ii) plasma adenosine concentration of samples obtained in "stopping solution" alone is generally 10-fold greater than that of matched samples obtained in "stopping solution" plus EDTA, (iii) deliberate mechanical hemolysis of blood samples obtained in "stopping solution" alone resulted in substantial augmentation of plasma adenosine levels in comparison with matched nonhemolyzed specimens--addition of EDTA to "stopping solution" prevented this, and (iv) adenosine content of blood samples obtained in PCA agreed closely with the sum of plasma and erythrocyte adenosine content of samples obtained in "stopping solution" plus EDTA. The data obtained demonstrate that (i) plasma adenosine concentrations are falsely elevated in samples of blood obtained in "stopping solution" alone, and (ii) addition of EDTA to "stopping solution" blocks in vitro production and accumulation of adenosine. Finally, rapid removal of adenosine from plasma by formed elements of blood may make it difficult to employ measurements of plasma adenosine concentration to assess physiological processes even in the absence of in vitro production of the nucleoside.     

Ultrastructural diversity in the egg chorion of Hawaiian Drosophila and Scaptomyza: ecological and phylogenetic considerations

Formation of the egg shell (chorion) inDrosophila and Scaptomyza (Diptera : Drosophilidae) is a complex developmental process involving coordinated synthesis and secretion of multiple proteins by the monolayer of follicle cells surrounding the egg. Using scanning electron microscopy, the ultrastructure of the chorion in 37 endemic Hawaiian drosophilids, representing the genera Drosophila and Scaptomyza, were analyzed and compared with 7 representative species of continental Drosophila. The detailed structure of the chorion was described for 8 chorionic regions: the respiratory filaments, follicle imprints, operculum, micropyle, dorsal ridge, ventral rim, posterior pole, and the chorion cross-section. The morphology of each region is similar among related species, but strikingly different among groups. The main functions of the chorion are to protect the developing embryo from the vicissitudes of the environment and to provide channels for gas exchange during embryogenesis. Adaptation to the diverse ovipositional substrates used by Drosophila in general, and the Hawaiian species in particular, has resulted in extraordinary diversity in the various chorionic structures. The respiratory filaments differ in number and have evolved to different lengths and degrees of porosity. Furthermore, other regions also involved in respiratory exchange (the operculum, follicle imprints, the pole region, and the dorsal ridge) have diverged in parallel to the ecological divergence. The thickness and complexity of the outer endochorion are dramatically different in various groups, providing varying degrees of mechanical strength to the eggshell, which promotes embryonic survival in the diverse microenvironments. These varied chorionic structures have been found to provide useful morphological characters for phylogenetic analyses of the drosophilids.     

Iridoid patterns in Galium L. and some phylogenetic considerations

From 19 species of Galium, members of 6 European sections of the genus, 24 compounds were isolated, namely 16 iridoid glucosides, 2 secoiridoid glucosides and 6 triterpene saponins (the later found only in G. rivale (Sibth. & Sm. Griseb.) The iridoid content was analyzed by thin layer chromatography - densitometry. An effort was made to clarify interspecies relationships, based on the obtained results and previous data. Generally, a nearly uniform iridoid pattern in the studied species was observed. Nevertheless, some distinctions gave reason the following chemical characters to be treated as taxonomic markers: iridoids, secogalioside (characteristic of G. mollugo group), iridoids V1 and V2 (G. humifusum Bieb. and G. verum L.), 6-acetylscandoside (G. incurvum group and G. verum) and the triterpene saponins, rivalioside A and rivalioside C (characteristic of G. rivale). The studied species regarding to the iridoids could be attributed to three lines of evolutionary differentiation. One line is leading to the differentiation of G. rivale. It contains specific triterpenoids as well as iridoid acids, which show parallel development of both glyceraldehyde 3-phosphate/pyruvate and mevalonate biosynthetic routes in this species. A second line includes G. mollugo and G. incurvum species groups and the species G. humifusum and G. verum. Variety of iridoid esters, hydroxy and carboxy derivatives of iridoids and secoiridoids characterised this line. Third line comprises the remaining studied species, members of different sections and species groups. They posses a nearly identical iridoid pattern, which suggests a convergent evolution regarding to the iridoids.     

Plasma levels of human neurotensin: methodological and physiological considerations

The ingestion of a meal high in fat content is known to increase circulating levels of neurotensin (NT) in humans. However, the magnitude of the postprandial rise of NT in the general circulation and its physiological significance have been subject of much debate. The present study examines circulating levels of NT in male volunteers prior to and following each of their three daily meals (ca. 31 g fat/meal). The response observed are also compared to that elicited by the direct instillation of intralipid (ca. 44 g fat) into the duodenum. NT levels were determined by radioimmunoassay of acid/acetone extracted plasma fractionated by high pressure liquid chromatography. Meals caused a significant but modest increase in NT levels, with the largest increment (ca. 4 fmol/ml) occurring after breakfast. In contrast, NT levels increased ca. 20 fmol/ml with intraduodenal instillation of lipid. The meal-stimulated increases in circulating NT measured here are 4- to 5-fold less than those reported by others, the difference most likely reflecting the lesser amount of lipid ingested. Previous studies provided subjects with single meals containing in excess of 120 g of fat; the 30 g of fat ingested by our subjects, ca. 33% of total caloric intake, is near that recommended by the U.S. Senate, Select Committee on Nutritional and Human Needs. These data show that diets with a reasonable fat content have only a modest effect on circulating levels of NT.     

Geometric morphometric analyses of hominid proximal femora: Taxonomic and phylogenetic considerations

The proximal femur has long been used to distinguish fossil hominin taxa. Specifically, the genus Homo is said to be characterized by larger femoral heads, shorter femoral necks, and more lateral flare of the greater trochanter than are members of the genera Australopithecus or Paranthropus. Here, a digitizing arm was used to collect landmark data on recent human (n=82), chimpanzee (n=16), and gorilla (n=20) femora and casts of six fossil hominin femora in order to test whether one can discriminate extant and fossil hominid (sensu lato) femora into different taxa using three-dimensional (3D) geometric morphometric analyses. Twenty proximal femoral landmarks were chosen to best quantify the shape differences between hominin genera. These data were first subjected to Procrustes analysis. The resultant fitted coordinate values were then subjected to PCA. PC scores were used to compute a dissimilarity matrix that was subjected to cluster analyses. Results indicate that one can easily distinguish Homo, Pan, and Gorilla from each other based on proximal femur shape, and one can distinguish Pliocene and Early Pleistocene hominin femora from those of recent Homo. It is more difficult to distinguish Early Pleistocene Homo proximal femora from those of Australopithecus or Paranthropus, but cluster analyses appear to separate the fossil hominins into four groups: an early australopith cluster that is an outlier from other fossil hominins; and two clusters that are sister taxa to each other: a late australopith/Paranthropus group and an early Homo group.     

Estimates of nuclear DNA content in bryophyte sperm cells: phylogenetic considerations

Nuclear DNA contents of developing sperm were estimated for 17 species of bryophytes by cytophotometry in squash preparations of antheridia after Feulgen staining. Genome sizes are in the lower end of the range for land plants. Two homwort C-values have the lowest recorded for bryophytes at 0.17 and 0.26 pg DNA per nucleus. In liverworts, C-values range from 0.49 pg in Blasia pusilla to 4.05 pg in Pellia epiphylla, while moss genome sizes are less variable, ranging from 0.38 pg in Takakia ceratophylla to 0.92 pg in Atrichum oerstedianum. DNA content is not correlated with chromosome number in these bryophytes, but sperm cell size and cellular complexity are directly related to C-value. Structural variations in the locomotory apparatus are viewed as evolutionary modifications associated with changes in genomic complexity, with a generalized increase in complexity of the motile assemblage accompanying increases in DNA content. Nuclear DNA values are not as variable in bryophytes as they are in pteridophytes and seed plants. We suggest that in plants producing biflagellated gametes, lower DNA contents afford a selective advantage. Comparisons with plants that produce multiflagellated or pollen-dispersed sperm indicate operation of a nucleotypic effect in archegoniates with biflagellated sperm. This effect may be on sperm cell functioning, which in turn influences reproductive success.     

Chromosomal analysis in Cathartidae: distribution of heterochromatic blocks and rDNA, and phylogenetic considerations

Three species of Cathartidae (Sarcoramphus papa, Cathartes aura and Cathartes burrovianus) were cytogenetically characterized by G- and C-banding. 18S–28S rDNA was used as a probe to map major ribosomal clusters. These species showed very similar karyotypes, with 2n = 80, 10 pairs of macrochromosomes, a submetacentric Z and a metacentric W chromosome. However, differences were found in the amount and distribution of heterochromatic blocks: S. papa showed heterochromatin only in the pericentromeric region and in chromosome W, while both species of Cathartes had heterochromatic blocks also in the long arm of two acrocentric pairs. Ribosomal clusters were found in a small pair in all three species. Karyotype analysis in Cathartidae revealed that this family has retained similarities to the putative avian ancestral karyotype, and placed Cathartidae in a more basal position in relation to Accipitridae and Falconidae. However, the cytogenetic data still cannot clarify the phylogenetic relationship between this family and other groups, such as Ciconiidae, considered its sister-group according to nucleic acid hybridization studies. J. C. Pieczarka and C. Y. Nagamachi—Researcher from CNPq, Brazil.