The Relationship between Gene Network Structure and Expression Variation among Individuals and Species

Variation among individuals is a prerequisite of evolution by natural selection. As such, identifying the origins of variation is a fundamental goal of biology. We investigated the link between gene interactions and variation in gene expression among individuals and species using the mammalian limb as a model system. We first built interaction networks for key genes regulating early (outgrowth; E9.5–11) and late (expansion and elongation; E11-13) limb development in mouse. This resulted in an Early (ESN) and Late (LSN) Stage Network. Computational perturbations of these networks suggest that the ESN is more robust. We then quantified levels of the same key genes among mouse individuals and found that they vary less at earlier limb stages and that variation in gene expression is heritable. Finally, we quantified variation in gene expression levels among four mammals with divergent limbs (bat, opossum, mouse and pig) and found that levels vary less among species at earlier limb stages. We also found that variation in gene expression levels among individuals and species are correlated for earlier and later limb development. In conclusion, results are consistent with the robustness of the ESN buffering among-individual variation in gene expression levels early in mammalian limb development, and constraining the evolution of early limb development among mammalian species.     

qPCR array检测分析 C57BL/6小鼠胚胎后肢发育基因表达谱

目的:胚胎生育过程中因肢体发育异常造成的出生缺陷比率不低,其相关基因表达模式尚不明确。本实验通过建立实时定量PCR芯片(Real-time quantitative polymerasechain reaction array,qPCR array)检测方案,研究C57BL/6品系小鼠后肢发育相关基因的表达谱。方法:以同源异形盒基因家族(Hox)、Wnt5a、配对同源结构域基因(Pitx1)、成纤维生长因子(Fgf8)、音猬因子(Shh)等小鼠肢体发育相关的重要基因制作基因检测表达谱,以C57BL/6品系怀孕雌鼠为材料,取胚胎肢芽发育的四个关键时期(E10.5,E11.5,E12.5,E13.5)的胎鼠后肢,利用qPCR array方案检测表达谱中基因的相对表达水平差异。结果:通过已建立的qPCR array检测了C57BL/6品系小鼠胚胎后肢发育时期Hox家族、Wnt5a、Pitx1、Fgf8、Shh等基因的表达差异。以E10.5为对照,检测出在后肢发育时期基因呈三种表达模式,即Hoxb6、Hoxb8、Hoxc8、Hoxc9、Hoxc10、Hoxd9和Shh基因的表达水平呈上调;Hoxa11、Hoxa13、Hoxc12、Hoxc13、Hoxd13等基因表达出现下调;Hoxc9、Hoxc10、Hoxc11、Hoxd9、Hoxd12、Fgf8和Pitx1等基因的相对表达量呈先上调后下调的曲线表达模式,且有少部分基因在小鼠后肢发育时期表达水平无明显变化。结论:Hox家族、Wnt5a、Pitx1、Fgf8、Shh等基因在小鼠后肢发育时期表达,并且表达模式存在明显差异。     

Integration and dissociation of limb elements in flying vertebrates: a comparison of pterosaurs, birds and bats

Flapping flight has evolved independently in three vertebrate clades: pterosaurs, birds and bats. Each clade has a unique flight mechanism involving different elements of the forelimb. Here, patterns of limb integration are examined using partial correlation analysis within species and matrix correlation analysis across species to test whether the evolution of flapping flight has involved developmental dissociation of the serial homologues in the fore- and hind limb in each clade. Our sample included seven species of birds, six species of bats, and three species of pterosaurs for which sufficient sample sizes were available. Our results showed that, in contrast to results previously reported for quadrupedal mammals, none of the three clades demonstrated significant integration between serial homologues in the fore- and hind limb. Unexpectedly, there were few consistent patterns of within-forelimb correlations across each clade, suggesting that wing integration is not strongly constrained by functional relationships. However, there was significant integration within the hind limbs of pterosaurs and birds, but not bats, possibly reflecting the differing functions of hind limbs (e.g. upright support vs. suspension) in these clades.     

Comparative analysis of the kinematics of hind limb movements in rats during different kinds of locomotion

A comparative analysis of phases of the locomotor cycle and the dynamics of changes in hind limb joint angles during swimming and stepping movements (on a treadmill), involving the fore- and hind limbs to different degrees, were undertaken in rats. Differences in the sequence and degree of changes in joint angles during locomotion of the types investigated were participation of the forelimbs in locomotion was found to be accompanied by more marked forward carrying of the hind limb. Dependence of the swing phase on duration of the cycle was observed and differences were found in the period of protraction of the limb (F period) during swimming and stepping. The role of central spinal processes and influences of peripheral afferents in the formation of different types of locomotion is discussed.A. A. Bogomolets Institute of Physiology, Academy of Sciences of the Ukrainian SSR, Kiev. Translated from Neirofiziologiya, Vol. 17, No. 2, pp. 189–198, March–April, 1985.     

TGFalpha reactivates imprinted Igf2 in the parthenogenetic mice embryos and placenta

Imprinted genes play important roles in the mammalian development. In the parthenogenetic embryos (PE) there is only expression of maternally expressed genes. Therefore, PEs are appropriate experimental models to study genomic imprinting controlling mechanisms. The maternally expressed H19 and paternally expressed Igf2 are reciprocally imprinted genes in normal embryos. Here we studied effect of transforming growth factor alpha (TGFalpha) treatment in vitro (10 ng/ml at the morula stage) on the expression of Igf2/H19 locus in mice PE (9.5-days of gestation, 25 somites) and their placentas (PP). Using RT-PCR we showed that TGFalpha reactivated maternally imprinted Igf2 gene in parthenogenetic embryos and placentas. In spite of similar Tgfalpha expression in the pre-implantation stages, its expression in the 9.5-day parthenogenetic embryos is significantly less than in normal embryos (NE). In our experiments it was shown that reactivation of Igf2 gene occurred independently of H19 gene. In vitro TGFalpha treatment of mouse PE reactivated paternally expressed Igf2 gene in the PE and PP. In the PE and PP both Igf2 and H19 were expressed. It seems that TGFalpha can play an important role as modulator of the Igf2/H19 locus.     

Selection,Morphological Integration,and Strepsirrhine Locomotor Adaptations

Clades with taxa that have multiple locomotor adaptations represent a direct way to test the relationship between adaptation and integration. If integration is influenced by functional requirements, integration should be most apparent where selection is strongest and less evident where selection has been relaxed. If integration is primarily regulated by genetic constraints, integration should be present irrespective of selection pressures. Here we use patterns of integration in the strepsirrhine fore- and hind limbs as a test case. Strepsirrhine locomotion is relatively well-studied, and there are multiple clades that share different locomotor modes. We found that quadrupeds have greater limb integration than vertical leapers. These results suggest that variation can be expressed if selection for integration is relaxed. However, an unexpected pattern was revealed, in which there appears to be some broader regulatory mechanism controlling overall limb integration. Our tests identified a strong correlation between integration of the forelimb and integration of the hind limb. This broader mechanism may be evidence of the primitive genetic control of limb integration.     

The recombinant limb as a model for the study of limb patterning, and its application to muscle development

The recombinant limb is a model system that has proved fruitful for analyzing epithelial-mesenchymal interactions and understanding the functional properties of the components of the limb bud. Here we present an overview of some of the insights obtained through the use of this technique. Among these are the understanding that fore or hind limb identity is inherent to the limb bud mesoderm, that the apical ectodermal ridge (AER) is a permissive signaling center and that the limb bud ectoderm plays a central role in the control of dorsoventral polarity. Recombinant limb studies have also allowed the identification of the affected tissue component in several limb mutants. More recently this model has been applied to the study of regulation of gene expressions related to patterning. In this report we use recombinant limbs to analyze pattering of the Pax3 expressing limb muscle cell lineage in the early stages of limb development. In recombinant limbs made without the zone of polarizing activity (ZPA), myoblasts appear intermingled with other mesodermal cells at the beginning of the recombinant limb development. Rapidly thereafter, the muscle precursors segregate and organize around the central forming chondrogenic core of the recombinant. Although this segregation is reminiscent of that occurring during normal development, the myoblasts in the recombinant fail to proliferate appropriately and also fail to migrate distally. Consequently, the muscle pattern in the recombinant limb is defective indicating that normal patterning cues are absent. However, recombinant limbs polarized with a ZPA exhibited a larger mass of muscle cells and a more normal morphogenesis, supporting a role for this signaling center in limb muscle development. Finally, we have ruled out host somite contributions to recombinant limbs by grafting chick recombinant limbs to quail hosts. This initial report demonstrates the value of the recombinant limb model system for dissecting the environmental cues required for normal muscle limb patterning. Received: 31 August 1998 / Accepted: 29 September 1998     

Postnatal allometry of the skeleton in Tupaia glis (Scandentia: Tupaiidae) and Galea musteloides (Rodentia: Caviidae)--a test of the three-segment limb hypothesis

During the evolution of therian mammals, the two-segmented, sprawled tetrapod limbs were transformed into three-segmented limbs in parasagittal zig-zag configuration (three-segment limb hypothesis). As a consequence, the functional correspondence of limb segments has changed (now: scapula to thigh, upper arm to shank, fore arm plus hand to foot). Therefore, the scapula was taken into account in the current study of the postnatal growth of the postcranial skeleton in two small mammalian species (Tupaia glis, Galea musteloides). Comparisons were made between the functionally equivalent elements and not in the traditional way between serially homologous segments. This study presents a test of the three-segment limb hypothesis which predicts a greater ontogenetic congruence in the functionally equivalent elements in fore and hind limbs than in the serially homologous elements. A growth sequence, with decreasing regression coefficients from proximal to distal, was observed in both species under study. This proximo-distal growth sequence is assumed to be ancestral in the ontogeny of eutherian mammals. Different reproductive modes have evolved within eutherian mammals. To test the influence of different life histories on ontogenetic scaling during postnatal growth, one species with altricial juveniles (Tupaia glis) assumed to be the ancestral mode of development for eutherians and one species with derived, precocial young (Galea musteloides) were selected. The growth series covered postnatal development from the first successive steps with a lifted belly to the adult locomotory pattern; thus, functionally equivalent developmental stages were compared. The higher number of allometrically positive or isometrically growing segments in the altricial mammalian species was interpreted as a remnant of the fast growth period in the nest without great locomotor demands, and the clearly negative allometry in nearly all segments in the precocial young was interpreted as a response to the demand on early locomotor activity. Different life histories seem to have a strong influence on postnatal ontogenetic scaling; the effects of the developmental differences are still observable when comparing adults of the two species.     

Foot structure and phylogeny in the Viverridae (Carnivora)

The structure of feet is widely used as a diagnostic feature in mammalian taxonomy. The relationship between the lengths of the metacarpals and foot pads are described with regard to plantigrade and digitigrade feet in the Viverridae. Although species in the Herpestinae, Paradoxurinae and Galidiinae vary considerably in size (from 450 g to 10 kg), the increase in length of the metapodial is isometric. Feet in which the metacarpals are less than 15 % of total limb length are plantigrade (Paradoxurinae and Cryptoproctinae) while those larger than 15% are digitigrade (Herpestinae and Galidiinae). The Viverrinae are composed of two natural groups, one in which the species have plantigrade forefeet and digitigrade hind feet and one in which both fore- and hind feet are digitigrade. The Hemigalinae does not appear to be a natural grouping, because the banded palm civet has plantigrade fore- and hind feet while other members of the subfamily have digitigrade feet; it may be better to reclassify the subfamily into three (Hemigalinae, Fossinae and Euplerinae).     

Cell death and abnormalities in limb morphogenesis ofPleurodeles waltlii Michah. (urodela,amphibia) after nitrogen mustard treatment

Summary The effects of nitrogen mustard (methylbis-chlorethylamine) on limb organogenesis were studied inPleurodeles waltlii at different stages of fore and hind limb development.The effects of four different doses of nitrogen mustard (1.25; 2.5; 5 and 10 g/ml) on the limb bud mesoderm and epidermis were studied histologically. This analysis was carried out on cylindrical unchondrified hind limb buds treated at stage 45.The effects of these doses on all stages of fore and hind limb development were investigated. This included the effect on the establishment of the proximo-distal sequence (segment chondrification) and the antero-posterior sequence (pre-postaxial zeugopod, basipod chondrification and progressive pre-postaxial organization of fingers and toes.Correlations were established between the mesodermal necrosis observed in hind limb buds treated at stage 45 and the skeletal abnormalities occurring in fore and hind limbs after treatment at all stages of their development.Thus, it appears that the effects of nitrogen mustard on organogenesis demonstrates the existence of a state in the differentiation of the mesoderm that is not revealed by morphological studies.     

Effects of phosphoramide mustard and acrolein, cytotoxic metabolites of cyclophosphamide, on mouse limb development in vitro

Phosphoramide mustard and acrolein are toxic and reactive metabolites of the widely used anticancer drug and known teratogen cyclophosphamide. To study the mechanism(s) involved and to determine which of the active metabolites of cyclophosphamide is responsible for the production of limb malformations, the effects of exposure of cultured limb buds to phosphoramide mustard and acrolein were investigated. Fore- and hindlimbs were excised from ICR mice on day 12 of gestation and cultured in roller bottles for 6 days. Limbs were exposed to either phosphoramide mustard or acrolein (10 or 50 micrograms/ml) for the first 20 hours of the culture period. Exposure to phosphoramide mustard produced limb reduction malformations in both the fore- and hindlimbs; total limb bone area was greatly reduced, while the relative contribution of the paw to this area in forelimbs was increased. There was a fourfold reduction in both DNA and RNA; protein content was reduced only by one-half. Alkaline phosphatase activity was significantly decreased in fore- and hindlimbs exposed to phosphoramide mustard, whereas creatine phosphokinase activity was only reduced in hindlimbs in the limbs exposed to the higher concentration of phosphoramide mustard. Exposure to acrolein also produced malformed limbs with a mangled appearance; however, total limb bone area and the relative contribution of the long bones versus paw structures were not altered. Acrolein exposure had little effect on growth parameters such as DNA (decreased only in hindlimbs exposed to 50 micrograms/ml), RNA (increased in hindlimbs exposed to 50 micrograms/ml), or protein content. Alkaline phosphatase and creatine phosphokinase activities were not altered in acrolein-exposed fore- or hindlimbs. Thus, phosphoramide mustard and acrolein have dramatically different effects on developing limbs in vitro; this observation may indicate that they have different targets and/or mechanisms of action as teratogens in the limb. The effects of phosphoramide mustard are very similar to those of "activated" cyclophosphamide (4-hydroperoxycyclophosphamide).     

Hip extensor EMG and forelimb/hind limb weight support asymmetry in primate quadrupeds

Higher weight support on the hind limb than forelimb is among the distinctive characteristics of primate quadrupeds. Although often assumed to be due to a more posteriorly positioned whole body center of mass, there are little data to support such a difference. Reynolds (1985. Am J Phys Anthropol 67:335-349) notes that the distribution of forces on the limbs can also be influenced by average limb posture, but suggests that this effect is too small to account for the asymmetry in weight support observed in primates. Instead, he proposes that high hind limb forces are brought about by an active process of shifting weight off the forelimbs and onto the hind limbs through use of hind limb retractors. In this study, we use video records of walking animals to explore the degree to which average limb posture in primates and other quadrupedal mammals deviates from vertical, and use electromyography to test Reynolds' model of hind limb retractor activity and posterior weight shift. The limb posture results indicate that primate forelimbs oscillate about a vertical or slightly retracted axis, and though the hind limbs are slightly protracted, the magnitude of deviation from vertical is too small to have a major effect on weight support distribution. The electromyographic results reveal higher levels of hip extensor activity in antipronograde primates that bear a higher proportion of weight on their hind limbs. This lends support to Reynolds' suggestion that some primates use muscles to actively shift weight onto hind limbs to relieve stresses on forelimbs less well structured for weight support.     

Increased SCE levels in Mediterranean Italian buffaloes affected by limb malformation (transversal hemimelia)

In recent years some buffalo farms in Campania have reported the birth of calves with limb malformation, especially with transversal hemimelia. We investigated 20 Mediterranean Italian buffaloes (8 males and 12 females) from one day to six months of age, of which 10 were affected by transversal hemimelia (group 1) and 10 were healthy controls (group 2). The following clinical and radiological patterns were observed in the malformed animals: hind limbs amputated, the right amputated off the second tarsus bones and the left amputated off the proximal epiphysis metatarsus, and the right thoracic limb hypoplasic (1 female); left hind limb amputated off the proximal epiphysis metatarsus (2 females and 1 male); left hind limb amputated off the third tarsus bones (1 female); left hind limb amputated off the tibia (1 female and 1 male); left hind limb amputated off the distal epiphysis metatarsus (1 female); left hind limb amputated off the first phalanx (1 male); right hind limb amputated off the proximal epiphysis metatarsus (1 male). In their malformed limbs all the animals presented more or less developed outlines of claws. The mean rate of SCE/cell in animals with transversal hemimelia was 8.80 +/- 3.19, that of the controls 6.61 +/- 2.73. The difference was statistically significant (P < 0.001).     

Limb development in chick embryos: cyclic AMP-dependent protein kinase activity, cyclic AMP, and prostaglandin concentrations during cytodifferentiation and morphogenesis

The effects of prostaglandin E2 (PGE2) on cyclic AMP (cAMP) concentrations of chick limb bud cells obtained from limbs at various stages of development were investigated. In addition, endogenous concentrations of PGE2 were examined in whole limbs from comparable stages. Prior to either chondrogenesis or myogenesis (stages 20-23), cells were more responsive to PGE2, in terms of cAMP levels, than those of differentiated phenotypes, obtained at stages 25-28. This greater responsiveness to PGE2 of undifferentiated cells was correlated with endogenous concentrations of PGE2 which were significantly higher in undifferentiated limbs than in limbs containing differentiated cartilage and muscle. Cyclic AMP-dependent protein kinase (PKA) activity was detectable in cell homogenates at each stage examined and did not appear to change in cAMP dependency at any stage. The majority (80-85%) of total enzyme activity was localized in soluble fractions of cell homogenates while the residual activity was localized to membrane-enriched, particulate fractions. The results demonstrate that both responsiveness of limb mesenchyme to PGE2 and endogenous concentrations of PGE2 are maximal prior to cytodifferentiation of limb tissues. The presence of cAMP-dependent protein kinase in these undifferentiated cells supports a regulatory role for both PGE2 and a cAMP-protein phosphorylation system in the differentiation of limb tissues.     

Follistatin-like 1, a secreted muscle protein, promotes endothelial cell function and revascularization in ischemic tissue through a nitric-oxide synthase-dependent mechanism

Myogenic Akt signaling coordinates blood vessel recruitment with normal tissue growth. Here, we investigated the role of Follistatin-like 1 (Fstl1) in the regulation of endothelial cell function and blood vessel growth in muscle. Transgenic Akt1 overexpression in skeletal muscle led to myofiber growth that was coupled to an increase in muscle capillary density. Myogenic Akt signaling or ischemic hind limb surgery led to the induction of Fstl1 in muscle and increased circulating levels of Fstl1. Intramuscular administration of an adenoviral vector expressing Fstl1 (Ad-Fstl1) accelerated flow recovery and increased capillary density in the ischemic hind limbs of wild-type mice, and this was associated with an increase in endothelial nitric oxide synthase (eNOS) phosphorylation at residue Ser-1179. In cultured endothelial cells, Ad-Fstl1 stimulated migration and differentiation into network structures and inhibited apoptosis under conditions of serum deprivation. These cell responses were associated with the activating phosphorylation of Akt and eNOS. Conversely, transduction with dominant-negative Akt or LY294002 blocked Fstl1-stimulated eNOS phosphorylation and inhibited Fstl1-stimulated cellular responses. Treatment with the eNOS inhibitor N(G)-nitro-L-arginine methyl ester also reduced endothelial cell migration and differentiation induced by Ad-Fstl1. The stimulatory effect of Ad-Fstl1 on ischemic limb reperfusion was abolished in mice lacking eNOS. These data indicate that Fstl1 is a secreted muscle protein or myokine that can function to promote endothelial cell function and stimulates revascularization in response to ischemic insult through its ability to activate Akt-eNOS signaling.