Expression of Sonic Hedgehog During Cell Proliferation in the Human Cerebellum

The regulation of cell proliferation in the external granular layer (EGL) of the developing cerebellum is important for its normal patterning. An important signal that regulates EGL cell proliferation is Sonic hedgehog (Shh). Shh is secreted by the Purkinje cells (PC) and has a mitogenic effect on the granule cell precursors of the EGL. Deregulation of Shh signaling has been associated with abnormal development, and been implicated in medulloblastomas, which are tumors that arise from the cerebellum. Given the importance of the Shh pathway in cerebellum development and disease, there has been no systematic study of its expression pattern during human cerebellum development. In this study, we describe the expression pattern of Shh, its receptor patched, smoothened, and its effectors that belong to the Gli family of transcription factors, during normal human cerebellum development from 10 weeks of gestational age, and in medulloblastomas that represents a case of abnormal cell proliferation in the cerebellum. This expression pattern is compared to equivalent stages in the normal development of cerebellum in mouse, as well as in tumors. Important differences between human and mouse that reflect differences in the normal developmental program between the 2 species are observed. First, in humans there appears to be a stage of Shh signaling within the EGL, when the PC are not yet the source of Shh. Second, unlike in the postnatal mouse cerebellum, expression of Shh in the PC in the postnatal human cerebellum is downregulated. Finally, medulloblastomas in the human but not in patched heterozygote mouse express Shh. These results highlight cross-species differences in the regulation of the Shh signaling pathway.

Comparative map between the domestic pig and dog

Cross-species chromosome painting with probes derived from flow-sorted dog and human chromosomes was used to construct a high-resolution comparative map for the pig. In total 98 conserved autosomal segments between pig and dog were detected by probes specific for the 38 autosomes and X Chromosome of the dog. Further integration of our results with the published human-dog and cat-dog comparative maps, and with data from comparative gene mapping, increases the resolution of the current pig-human comparative map. It allows for the conserved syntenies detected in the pig, human, and cat to be aligned against the putative ancestral karyotype of eutherian mammals and for the history of karyotype evolution of the pig lineage to be reconstructed. Fifteen fusions, 17 fissions, and 23 inversions are required to convert the ancestral mammalian karyotype into the extant karyotype of the pig.

The impact of chromosome sorting and painting on the comparative analysis of primate genomes

Chromosome sorting by flow cytometry is the main source of chromosome-specific DNA for the production of painting probes. These probes have been used for cross-species in situ hybridization in the construction of comparative maps, in the study of karyotype evolution and phylogenetics, in delineating territories in interphase nuclei, and in the analysis of chromosome breakpoints. We review here the contributions that this technology has made to the analysis of primate genomes. Copyright (C) 2005 S. Karger AG, Basel.

Karyotypic evolution of the family Sciuridae: inferences from the genome organizations of ground squirrels

Cross- species chromosome painting has made a great contribution to our understanding of the evolution of karyotypes and genome organizations of mammals. Several recent papers of comparative painting between tree and flying squirrels have shed some light

Complex mutation at a microsatellite locus in sturgeons: Acipenser sinensis, A-schrenckii, A-gueldenstaedtii and A-baerii

Cross-species amplifications of microsatellite locus Spl-106, which was originally screened from the genome of shovelnose sturgeon (Scaphirhynchus platorynchus) with a perfect TAGA repeat motif, were carried out in four other species of the genera Acipenser. A total of 34 polymerase chain reaction (PCR) products representing 16 different alleles of this locus was sequenced. Sequence analysis results showed that besides the number changes of repeat units, many mutational events, such as single-base substitutions and various insertion/deletion (indels) occurred not only at species level but also at individual level, even among the different alleles within the same individual. The repeat motifs varied from perfect (TAGA)n array to perfect compound (TAAA)m (GAAA)n and perfect or imperfect compound (TAAA)m (TAGA)n (TAAA)x arrays in different species and different individuals. The evolution dynamics of this locus in sturgeons was inferred in that it may evolve from a single perfect to different perfect or imperfect compounds.

Development of polymorphic EST markers in Penaeus monodon: applications in penaeid genetics

The objective of this study was to develop type I markers for genome mapping and other genetic studies of Penaeus monodon. Primers were designed based on expressed sequence tags (ESTs) from a P monodon cephalothorax cDNA library to amplify 100-300 bp products. 34 of the primer pairs successfully amplified PCR products from genomic DNA. Single-strand conformation polymorphism analysis showed that similar to 30% of the ESTs tested exhibit polymorphism in a test panel of P monodon individuals. Mendelian inheritance of the EST-derived markers has been established in two international reference mapping families of P monodon, and mapping of these markers is in progress. Some ESTs were successfully amplified from other Penaeus species (P. chinensis, P japonicus and P vannamei), indicating that the markers are applicable in cross-species comparison. Two populations of P. japonicus could be differentiated using one of the ESTS. In conclusion, the polymorphic EST markers developed in this study are applicable in genome mapping and population genetic studies of penaeid shrimp. (C) 2002 Elsevier Science B.V. All rights reserved.

贡嘎山植物小枝功能性状在不同生活型和不同海拔间的比较研究

植物功能生态学研究不仅提供了植物生理生态学与生态系统生态学的连接，还为植物种群生活史对策研究提供了材料。Westoby 等 (2002) 提出了利用植物功能性状变量的主导维度来确定和量化植物生活史的生态适应策略。在他们所提出四个主导维度中，叶大小－小枝大小是研究相对较少的一维；其内部各组分的关系、对环境的响应，以及与其它重要维度的关系，目前的理解非常有限。 本研究以贡嘎山不同海拔不同功能群物种为研究对象，采用种间比较和系统发生独立性比较等研究方法，系统研究了植物的功能特征及其相关性在不同生境及不同功能群间的差异，旨在分析不同功能群物种的叶大小－小枝大小的成本和收益。其研究结果将有助于我们理解植物生活史对策的进化，进而理解物种共存和维持物种多样性的机制。主要研究结果如下： 1. 叶大小－小枝大小关系 小枝茎横截面积与单叶面积和总叶面积均呈异速生长关系，即总叶面积和单叶面积的增加比茎横截面积的增加速度快。但是，总叶面积和叶片干重的增加却基本上与小枝茎干重的增加等速。系统发生独立性比较研究的结果与此相一致。表明，在某一给定的茎投入时，至少大叶大枝物种不比小叶小枝物种在支撑叶面积和叶片干重方面具有优势。同时，在某一给定的小枝茎投入时，常绿阔叶物种比落叶阔叶物种支撑更少的叶面积。在茎干重与总叶面积的关系中，落叶复叶物种比落叶单叶物种具有更高的y轴截距，表明复叶物种比单叶物种在展叶面积方面更有效。复叶物种与单叶物种相比，通常具有较大的叶大小和小枝大小。 2. 叶大小－叶数量关系 叶大小与数量间在不同的叶片习性、不同的叶片形态以及不同的生境类型的物种间均存在稳定的负的等速生长关系，且这种关系在系统发生独立性比较时依然成立。然而，在某一给定的出叶强度 (单位小枝的叶数量) 时，常绿阔叶物种比落叶物种具有更小的叶面积。而在给定体积基础上的出叶强度时，落叶复叶物种的叶面积显著大于落叶单叶物种，且复叶物种比单叶物种具有更大的叶大小和更小的出叶强度。但是，叶大小与数量间的关系在不同的海拔间并没有显著的差异。 3. 小枝大小－总叶面积关系 在不同的生活型或不同的生境下，小枝上总叶面积与茎干重和小枝干重均呈正的异速生长关系，且斜率显著小于1.0，表明小枝上总叶面积的增加都不能赶上小枝及茎大小的增加。这种“收益递减”表明随着小枝干重的增加，光截取的收益递减。此外，叶面积比 (总叶面积与小枝干重的比值) 与单叶干重呈显著负相关关系，系统发生独立性比较的结果与此相一致。根据以上结果，可以推测，大叶的物种在质量较好的生境中出现，而群落内部小枝茎的寿命较长的物种可以拥有较大的叶片。 4. 叶片色素浓度－LMA关系 随着海拔的升高，阔叶木本植物和草本植物的叶片色素浓度减少，叶绿素a/b和类胡萝卜素/叶绿素比值以及比叶重 (LMA) 增加。然而，在草本植物中的色素浓度、色素比值和LMA的变化比阔叶木本植物的更明显。同时，LMA与叶片色素浓度呈负相关关系，但是在落叶物种中的LMA对色素浓度的影响比常绿阔叶物种更强烈。总之，草本植物的叶片特征对海拔梯度的变化似乎比木本植物更敏感，LMA对叶片色素的保护作用在落叶物种中比在常绿阔叶物种显得更重要。这些结果表明不同生活型物种可能采取不同的保护机制来降低叶绿体器官的损伤和增加他们的碳获取能力。 Studies on plant functional ecology not only bridge plant eco-physiology and ecosystem functioning, but also enrich plant population biology. As pointed out by Westoby et al (2002), plant life history strategies can be identified and quantified by four leading dimensions of variations in plant functional traits, i.e., seed size/output, leaf mass per area and leaf life span, plant height, and leaf size-twig size. Compared to the other dimensions, the cost/benefit of the leaf size-twig size spectrum has scarcely been analyzed in relation to environmental gradients and life form types, and the adaptive significance of this spectrum is not fully understood. In the present study, the relationships between functional traits of plant twigs are determined for the species with different life forms along an altitudinal gradient of Gongga Mountain with both cross-species analysis and evolutionary divergence analysis. The primary objective of this study is to examine the cost/benefit of leaf size-twig size in plants. The study results are supposed to provide insights into the understanding of the mechanism of species coexistences. The results are shown in the following. 1. The relationship between leaf size and twig size Twig cross-sectional area allometrically scaled with both individual leaf area and total leaf area supported by the twigs. However, the increase in total lamina mass/area was generally proportional to the increase in stem mass. These correlations between trait variations were significant in both interspecies analysis and phylogenetically independent comparison (PIC) analysis, which indicated that thick-twigged/large-leaved species, at least, do not have an advantage in supporting leaf/lamina area and lamina mass for the same twig stem investment than thin-twigged/ small-leaved species. Meanwhile, the evergreen broad-leaved species supported a smaller leaf area for the same twig stem investment in terms of both cross-sectional area and stem mass than the deciduous species. The deciduous compound-leaved species have a higher y-intercept in the scaling relationship of twig stem mass versus total leaf area than the deciduous simple-leaved species, indicating that compound-leaved species were more efficient in displaying leaf area. The compound-leaved species were larger in both leaf size and twig size than their counterpart in the present study. 2. The relationship between leaf size and leaf number Significantly negative and isometric scaling relationships between leaf size and leafing intensity (leaf number per twig mass or volume) were found to be consistently conserved across species independent of leaf habit, leaf form and habitat type. The negative correlations between leaf size and leafing intensity were also observed across correlated evolutionary divergences. However, leaf area was smaller in the evergreen broad-leaved species at a given leafing intensity than in the deciduous species. The deciduous compound-leaved deciduous species were higher in leaf area than deciduous simple-laved species at a given volume-based leafing intensity. Moreover, the compound-leaved deciduous species were larger in leaf size but smaller in leafing intensity than their simple counterparts. No significant difference was found in the scaling relationships between altitudes. 3. The relationship between twig size and total leaf area Leaf area was found to scale positively and allometrically with both stem and twig mass (stem mass plus leaf mass) with slopes significantly smaller than 1.0, independent of life form and habitat type, indicating that the increase in total leaf area fails to keep pace with increasing twig size and stem size. This ‘diminishing returns’ suggests that the benefit of light intercept decreased with increasing twig mass. Moreover, the leaf area ratio (the ratio of total leaf area to stem or twig mass) correlated negatively with individual leaf mass. The results of PIC were consistent with the correlations. According to the results, it is speculated that large-leaved species may be favored when habitat is good and when stem longevity are long within community. 4. The relationship between leaf pigment concentrations and leaf mass per area With increasing altitude, the concentrations of pigments decreased, but the ratios of chlorophyll a/b and carotenoid/chlorophyll, and LMA increased, in both the broad-leaved woody species and herbaceous species groups. However, the changes in the pigment concentrations, ratios and LMA were more profound in the herbaceous species than in the woody species. In addition, pigment concentrations were negatively correlated with LMA in each life form type and in the pooled dataset. However, the LMA effect on leaf pigment concentrations was more profound in the deciduous species than in the evergreen braode-leaved species. In general, herbaceous species seemed more sensitive to the increasing altitude compared to woody species, and LMA seemed to be a more important mechanism for protecting leaf pigments in deciduous species than in evergreen broad-leaved species. These results suggested that the species with different life forms may employ different protective mechanisms to decrease the chloroplast apparatus damage and increase their carbon gain.

Isolation and characterization of microsatellite loci from mangrove red snapper Lutjanus argentimaculatus

Lutjanus argentimaculatus, also called mangrove red snapper, is a commercially important fish in East Asia. A proper understanding of population structure is primarily linked with the management of genetic resources in exploiting marine fisheries. Herein, seven microsatellite loci, which showed high polymorphism (observed heterozygosity per locus ranging from 0.3571 to 0.7857 and expected heterozygosity per locus ranging from 0.6236 to 0.8821), were isolated and characterized from L. argentimaculatus. Cross-species amplifications also indicate that primers designed for these loci may be useful for further studies about other closely phylogenetic species of the family Lutjanidae.

Hematopoietic gene promoters subjected to a group-combinatorial study of DNA samples: identification of a megakaryocytic selective DNA signature

Identification of common sub-sequences for a group of functionally related DNA sequences can shed light on the role of such elements in cell-specific gene expression. In the megakaryocytic lineage, no one single unique transcription factor was described as linage specific, raising the possibility that a cluster of gene promoter sequences presents a unique signature. Here, the megakaryocytic gene promoter group, which consists of both human and mouse 5' non-coding regions, served as a case study. A methodology for group-combinatorial search has been implemented as a customized software platform. It extracts the longest common sequences for a group of related DNA sequences and allows for single gaps of varying length, as well as double- and multiple-gap sequences. The results point to common DNA sequences in a group of genes that is selectively expressed in megakaryocytes, and which does not appear in a large group of control, random and specific sequences. This suggests a role for a combination of these sequences in cell-specific gene expression in the megakaryocytic lineage. The data also point to an intrinsic cross-species difference in the organization of 5' non-coding sequences within the mammalian genomes. This methodology may be used for the identification of regulatory sequences in other lineages.

Modeling the evolution of regulatory elements by simultaneous detection and alignment with phylogenetic pair HMMs.

The computational detection of regulatory elements in DNA is a difficult but important problem impacting our progress in understanding the complex nature of eukaryotic gene regulation. Attempts to utilize cross-species conservation for this task have been hampered both by evolutionary changes of functional sites and poor performance of general-purpose alignment programs when applied to non-coding sequence. We describe a new and flexible framework for modeling binding site evolution in multiple related genomes, based on phylogenetic pair hidden Markov models which explicitly model the gain and loss of binding sites along a phylogeny. We demonstrate the value of this framework for both the alignment of regulatory regions and the inference of precise binding-site locations within those regions. As the underlying formalism is a stochastic, generative model, it can also be used to simulate the evolution of regulatory elements. Our implementation is scalable in terms of numbers of species and sequence lengths and can produce alignments and binding-site predictions with accuracy rivaling or exceeding current systems that specialize in only alignment or only binding-site prediction. We demonstrate the validity and power of various model components on extensive simulations of realistic sequence data and apply a specific model to study Drosophila enhancers in as many as ten related genomes and in the presence of gain and loss of binding sites. Different models and modeling assumptions can be easily specified, thus providing an invaluable tool for the exploration of biological hypotheses that can drive improvements in our understanding of the mechanisms and evolution of gene regulation.

Quantitative structure-toxicity relationships for chlorophenols to bioluminescent lux-marked bacteria using atom-based semi-empirical molecular-orbital descriptors

Literature data on the toxicity of chlorophenols for three luminescent bacteria (Vibrio fischeri, and the lux-marked Pseudomonas fluorescens 10586s pUCD607 and Burkholderia spp. RASC c2 (Tn4431)) have been analyzed in relation to a set of computed molecular physico-chemical properties. The quantitative structure-toxicity relationships of the compounds in each species showed marked differences when based upon semi-empirical molecular-orbital molecular and atom based properties. For mono-, di- and tri-chlorophenols multiple linear regression analysis of V. fischeri toxicity showed a good correlation with the solvent accessible surface area and the charge on the oxygen atom. This correlation successfully predicted the toxicity of the heavily chlorinated phenols, suggesting in V. fischeri only one overall mechanism is present for all chlorophenols. Good correlations were also found for RASC c2 with molecular properties, such as the surface area and the nucleophilic super-delocalizability of the oxygen. In contrast the best QSTR for P. fluorescens contained the 2nd order connectivity index and ELUMO suggesting a different, more reactive mechanism. Cross-species correlations were examined, and between V. fischeri and RASC c2 the inclusion of the minimum value of the nucleophilic susceptibility on the ring carbons produced good results. Poorer correlations were found with P. fluorescens highlighting the relative similarity of V. fischeri and RASC c2, in contrast to that of P. fluorescens.

Use of SLAM and PVRL4 and Identification of Pro-HB-EGF as Cell Entry Receptors for Wild Type Phocine Distemper Virus

Signalling lymphocyte activation molecule (SLAM) has been identified as an immune cell receptor for the morbilliviruses, measles (MV), canine distemper (CDV), rinderpest and peste des petits ruminants (PPRV) viruses, while CD46 is a receptor for vaccine strains of MV. More recently poliovirus like receptor 4 (PVRL4), also known as nectin 4, has been identified as a receptor for MV, CDV and PPRV on the basolateral surface of polarised epithelial cells. PVRL4 is also up-regulated by MV in human brain endothelial cells. Utilisation of PVRL4 as a receptor by phocine distemper virus (PDV) remains to be demonstrated as well as confirmation of use of SLAM. We have observed that unlike wild type (wt) MV or wtCDV, wtPDV strains replicate in African green monkey kidney Vero cells without prior adaptation, suggesting the use of a further receptor. We therefore examined candidate molecules, glycosaminoglycans (GAG) and the tetraspan proteins, integrin β and the membrane bound form of heparin binding epithelial growth factor (proHB-EGF),for receptor usage by wtPDV in Vero cells. We show that wtPDV replicates in Chinese hamster ovary (CHO) cells expressing SLAM and PVRL4. Similar wtPDV titres are produced in Vero and VeroSLAM cells but more limited fusion occurs in the latter. Infection of Vero cells was not inhibited by anti-CD46 antibody. Removal/disruption of GAG decreased fusion but not the titre of virus. Treatment with anti-integrin β antibody increased rather than decreased infection of Vero cells by wtPDV. However, infection was inhibited by antibody to HB-EGF and the virus replicated in CHO-proHB-EGF cells, indicating use of this molecule as a receptor. Common use of SLAM and PVRL4 by morbilliviruses increases the possibility of cross-species infection. Lack of a requirement for wtPDV adaptation to Vero cells raises the possibility of usage of proHB-EGF as a receptor in vivo but requires further investigation.

The specificity of TRIM5 alpha-mediated restriction is influenced by its coiled-coil domain.

Retroviruses are both powerful evolutionary forces and dangerous threats to genome integrity. As such, they have imposed strong selective pressure on their hosts, notably triggering the emergence of restriction factors, such as TRIM5 alpha, that act as potent barriers to their cross-species transmission. TRIM5 alpha orthologues from different primates have distinct retroviral restriction patterns, largely dictated by the sequence of their C-terminal PRYSPRY domain, which binds the capsid protein of incoming virions. Here, by combining genetic and functional analyses of human and squirrel monkey TRIM5 alpha, we demonstrate that the coiled-coil domain of this protein, thus far essentially known for mediating oligomerization, also conditions the spectrum of antiretroviral activity. Furthermore, we identify three coiled-coil residues responsible for this effect, one of which has been under positive selection during primate evolution, notably in New World monkeys. These results indicate that the PRYSPRY and coiled-coil domains cooperate to determine the specificity of TRIM5 alpha-mediated capture of retroviral capsids, shedding new light on this complex event.

Generation and characterization of function-blocking anti-ectodysplasin A (EDA) monoclonal antibodies that induce ectodermal dysplasia.

Development of ectodermal appendages, such as hair, teeth, sweat glands, sebaceous glands, and mammary glands, requires the action of the TNF family ligand ectodysplasin A (EDA). Mutations of the X-linked EDA gene cause reduction or absence of many ectodermal appendages and have been identified as a cause of ectodermal dysplasia in humans, mice, dogs, and cattle. We have generated blocking antibodies, raised in Eda-deficient mice, against the conserved, receptor-binding domain of EDA. These antibodies recognize epitopes overlapping the receptor-binding site and prevent EDA from binding and activating EDAR at close to stoichiometric ratios in in vitro binding and activity assays. The antibodies block EDA1 and EDA2 of both mammalian and avian origin and, in vivo, suppress the ability of recombinant Fc-EDA1 to rescue ectodermal dysplasia in Eda-deficient Tabby mice. Moreover, administration of EDA blocking antibodies to pregnant wild type mice induced in developing wild type fetuses a marked and permanent ectodermal dysplasia. These function-blocking anti-EDA antibodies with wide cross-species reactivity will enable study of the developmental and postdevelopmental roles of EDA in a variety of organisms and open the route to therapeutic intervention in conditions in which EDA may be implicated.

The geometric structure of the brain fiber pathways.

The structure of the brain as a product of morphogenesis is difficult to reconcile with the observed complexity of cerebral connectivity. We therefore analyzed relationships of adjacency and crossing between cerebral fiber pathways in four nonhuman primate species and in humans by using diffusion magnetic resonance imaging. The cerebral fiber pathways formed a rectilinear three-dimensional grid continuous with the three principal axes of development. Cortico-cortical pathways formed parallel sheets of interwoven paths in the longitudinal and medio-lateral axes, in which major pathways were local condensations. Cross-species homology was strong and showed emergence of complex gyral connectivity by continuous elaboration of this grid structure. This architecture naturally supports functional spatio-temporal coherence, developmental path-finding, and incremental rewiring with correlated adaptation of structure and function in cerebral plasticity and evolution.