The inheritance of the leopard complex of spotting patterns in horses

The leopard complex of white spotting patterns in horses consists of the leopard, few-spot leopard, blanket, blanket with spots, varnish roan (or marble), snowflake, frosted, speckled, and mottled patterns. Horses with any of these patterns can produce the other patterns when mated to nonpatterned horses. Twenty-two horses of the Welsh Pony, Noriker, Appaloosa, and Pony of the Americas breeds produced 270 foals in a distribution consistent with a single dominant allele being responsible for the patterns. The symbol for this dominant allele, Lp, is retained from previous work on the leopard pattern. Heterozygotes are less extensively marked than are homozygotes, but the two classes overlap. The differences in the patterns are related to varying degrees of expression of this allele.     

A pattern formation mechanism to control spatial organization in the embryo of Drosophila melanogaster

It is known that cells are already committed to a particular segment at the cellular blastoderm stage during embryogenesis of Drosophila melanogaster. Recently, several segmentation genes have been observed to be expressed in a sequence of banded spatial patterns in the syncytial blastoderm, prior to the formation of the cellular blastoderm. It is demonstrated in this paper that a two component reaction-diffusion (RD) system with net production functions which are antisymmetric with respect to the uniform steady-state values, is capable of producing a sequence of seven spatial patterns in the syncytial blastoderm. The sequence of patterns obtained exhibit a strong preference for banded or striped patterns. The first pattern is a simple anteroposterior gradient while the second is a gradient in the dorsoventral direction. The next five patterns are a sequence of banded patterns which exhibit frequency doubling, i.e. the number of bands in each pattern tend to be double the number in the previous pattern. The predicted pattern sequence is comparable to that observed in the expression of some segmentation genes. It is suggested that a pattern formation mechanism based on such an RD system may exist in the embryo where it produces a sequence of prepatterns to regulate the expression of various segmentation genes leading ultimately to a segmented embryo. There is sufficient spatial information in the sequence of banded prepatterns for the segments to be unique.     

Identification and Characterization of a Bidirectional Promoter from the Intergenic Region between the Human DDX13 and RD Genes

The human DDX13 gene encodes a putative RNA helicase of the DExH-box family. In an earlier report we showed that the human DDX13 and RD genes were arranged head-to-head in the class III MHC complex and their ATG start codons were separated by 745 base pairs. We have now analyzed the common 745 bp intergenic region in detail and characterized their promoters. Northern blot analysis revealed that DDX13 and RD exhibit distinct patterns of steady-state expression among multiple human tissues. The promoter regions for DDX13 and RD genes were identified by deletion analysis from 740 bp to 176 bp of the intergenic region fused to a chloramphenicol acetyltransferase (CAT) reporter gene using transient transfection assays. Results indicated that a promoter sequence as small as 176 bp is sufficient for basal expression of both genes in HeLa and HepG2 cells. Functional analysis using a bidirectional reporter system demonstrates that the sequence 262 bp proximal to the DDX13 gene is sufficient for concurrent expression in both directions. However, the common 740 bp intergenic region showed promoter activity in DDX13 only, suggesting the presence of a negatively acting region for the RD gene within the region -267 to -744. It appears that RD expression is controlled by a complex system of positively and negatively acting elements present on distant portions of both genes.     

四川邛崃山脉雪豹与赤狐时空生态位关系

食肉动物是生态系统中关键的功能类群,探究顶级捕食者和次级捕食者的种间作用和共存机制有助于我们深入理解生态系统变化和物种种群动态变化的驱动机制,是目前全球大型兽类种群衰退背景下的重要议题。在动物物种生态位的诸多维度中,空间与时间生态位是其中最为关键的两个维度,了解同域分布物种之间在时、空生态位上的相互关系是探究物种共存机制的基础。本研究以邛崃山脉中部的卧龙国家级自然保护区为研究区域,使用红外相机技术与粪便DNA技术在区内的高山生境开展野外调查,收集雪豹（Panthera uncia,分布点数量n=198）与赤狐（Vulpes vulpes,n=68）的分布数据,分别使用MaxEnt物种分布模型和日活动模式分析来探究区内雪豹和赤狐在时、空生态位上的相互作用关系。结果显示,在空间上,研究区域内雪豹和赤狐的潜在适宜分布区重叠面积404.08 km²,主要集中在保护区西北部的高海拔区域,分别占二者适宜栖息地总面积的77.74%和80.79%,重叠程度较高;在垂直分布上,区内雪豹分布的平均海拔较赤狐稍高,赤狐的海拔分布范围较雪豹稍广,但两物种在垂直方向上的重叠程度也较高,均在海拔4 300 m左右出现分布高峰。在时间生态位上,雪豹（独立探测数n=351）与赤狐（n=155）的日活动模式均为双峰型,雪豹偏向晨昏性而赤狐更偏向夜行性,整体上二者日活动节律重叠度较高（Δ=0.68）;在有雪豹活动的位点上以及两周内曾有雪豹活动的情况下,赤狐会加强夜间活动,降低其日活动节律与雪豹之间的重叠程度,但其日活动模式未有显著改变。本研究的结果初步揭示了雪豹与赤狐的时空生态位关系,将为深入理解高山生态系统中顶级捕食者与次级捕食者的共存机制提供实例与基础信息,同时也将为保护区针对这些食肉动物种群的精细化管理提供支持。     

Genes@Work: an efficient algorithm for pattern discovery and multivariate feature selection in gene expression data

MOTIVATION: Despite the growing literature devoted to finding differentially expressed genes in assays probing different tissues types, little attention has been paid to the combinatorial nature of feature selection inherent to large, high-dimensional gene expression datasets. New flexible data analysis approaches capable of searching relevant subgroups of genes and experiments are needed to understand multivariate associations of gene expression patterns with observed phenotypes. RESULTS: We present in detail a deterministic algorithm to discover patterns of multivariate gene associations in gene expression data. The patterns discovered are differential with respect to a control dataset. The algorithm is exhaustive and efficient, reporting all existent patterns that fit a given input parameter set while avoiding enumeration of the entire pattern space. The value of the pattern discovery approach is demonstrated by finding a set of genes that differentiate between two types of lymphoma. Moreover, these genes are found to behave consistently in an independent dataset produced in a different laboratory using different arrays, thus validating the genes selected using our algorithm. We show that the genes deemed significant in terms of their multivariate statistics will be missed using other methods. AVAILABILITY: Our set of pattern discovery algorithms including a user interface is distributed as a package called Genes@Work. This package is freely available to non-commercial users and can be downloaded from our website (http://www.research.ibm.com/FunGen).     

Changing clothes easily: connexin41.8 regulates skin pattern variation

The skin patterns of animals are very important for their survival, yet the mechanisms involved in skin pattern formation remain unresolved. Turing's reaction-diffusion model presents a well-known mathematical explanation of how animal skin patterns are formed, and this model can predict various animal patterns that are observed in nature. In this study, we used transgenic zebrafish to generate various artificial skin patterns including a narrow stripe with a wide interstripe, a narrow stripe with a narrow interstripe, a labyrinth, and a 'leopard' pattern (or donut-like ring pattern). In this process, connexin41.8 (or its mutant form) was ectopically expressed using the mitfa promoter. Specifically, the leopard pattern was generated as predicted by Turing's model. Our results demonstrate that the pigment cells in animal skin have the potential and plasticity to establish various patterns and that the reaction-diffusion principle can predict skin patterns of animals.     

甘肃祁连山脉雪豹及其同域分布大型食肉动物时间生态位关系

<正>群落内多物种如何共存是群落生态学和生物多样性研究的核心内容之一。经典物种共存理论强调物种之间的生态位分化,侧重于物种对环境的需求,Hutchinson (1957)提出超体积生态位概念,认为物种适合度是由多个因素共同决定,即物种只有在满足其生态位需求的多维空间,     

Formation of the adult pigment pattern in zebrafish requires leopard and obelix dependent cell interactions

Colour patterns are a prominent feature of many animals and are of high evolutionary relevance. In zebrafish, the adult pigment pattern comprises alternating stripes of two pigment cell types, melanophores and xanthophores. How the stripes are defined and a straight boundary is formed remains elusive. We find that mutants lacking one pigment cell type lack a striped pattern. Instead, cells of one type form characteristic patterns by homotypic interactions. Using mosaic analysis, we show that juxtaposition of melanophores and xanthophores suffices to restore stripe formation locally. Based on this, we have analysed the pigment pattern of two adult specific mutants: leopard and obelix. We demonstrate that obelix is required in melanophores to promote their aggregation and controls boundary integrity. By contrast, leopard regulates homotypic interaction within both melanophores and xanthophores, and interaction between the two, thus controlling boundary shape. These findings support a view in which cell-cell interactions among pigment cells are the major driving force for adult pigment pattern formation.     

Labyrinthine versus straight-striped patterns generated by two-dimensional Turing systems

Striped patterns are often observed on fish skin. Such patterns have been accounted for by reaction-diffusion (RD) Turing-type models, in which two substances can spontaneously form a spatially heterogeneous pattern in a homogeneous field. Among the striped patterns generated by Turing-type models, some are "straight-striped patterns," with many stripes running in parallel, while others are "labyrinthine patterns," in which the stripes often change direction, merge with each other, and frequently branch out. RD models differ in terms of their tendency to generate either labyrinthine or straight-striped patterns. Here, we studied the conditions under which either a labyrinthine or straight-striped pattern would emerge. First, we defined an index for stripe clearness, Sh. Straight-striped patterns (large Sh) are formed if only a narrow range of spatial periods corresponds to an unstable mode. Labyrinthine patterns (small Sh) are formed when a wide range of spatial periods is unstable. More specifically, labyrinthine patterns are formed when the maximum spatial period of unstable modes is more than twice that of the minimum spatial period of unstable modes; otherwise, straight-striped patterns are formed. We then examined RD models with nonlinear reaction terms, including both activator-inhibitor and substrate-depletion models, and we demonstrated that the same conclusions hold with respect to the conditions required for labyrinthine versus straight-striped patterns.     

The Role of Early Learning in Determining Shoaling Preferences Based on Visual Cues in the Zebrafish, Danio rerio

Social preferences for specific colour patterns learned in early development, termed imprinting, may influence social and mating decisions. Imprinting has been demonstrated in both birds and fish and has been proposed to play a role in speciation. We raised wild‐type zebrafish, Danio rerio, either with individuals of the same colour pattern, an alternative colour pattern (leopard), or a closely related, unpatterned species, D. albolineatus. We also cross‐reared individual ‘leopard’D. rerio and D. albolineatus with wild‐type D. rerio. We tested the prediction that Danio would prefer to shoal with fish of the colour pattern with which they had been raised, irrespective of their own appearance. Rearing condition affected shoaling preferences between D. rerio and D. albolineatus, with individuals of both colour patterns preferring to associate with shoals of the colour pattern with which they had been raised. The more subtle distinction between the wild‐type and ‘leopard’D. rerio colour patterns did not elicit a shoaling preference. Thus, zebrafish exhibit shoaling preferences based on visual cues, the effect being stronger when patterns are more distinct. There is a strong learned component to these preferences, although the extent to which they may influence mating decisions is unclear.     

The interplay between phenotypic and ontogenetic plasticities can be assessed using reaction-diffusion models

Every morphological, behavioral, or even developmental character expression of living beings is coded in its genotype and is expressed in its phenotype. Nevertheless, the interplay between phenotypic and ontogenetic plasticities, that is, the capability to manifest trait variations, is a current field of research that needs morphometric, numerical, or even mathematical modeling investigations. In the present work, we are searching for a phenotypic index able to identify the underlying correlation among phenotypic, ontogenetic, and geographic distribution of the evolutionary development of species of the same genus. By studying the case of Pseudoplatystoma fishes, we use their skin patterns as an auxiliary trait that can be reproduced by means of a reaction diffusion (RD) model. From this model, we infer the phenotypic index in terms of one of the parameters appearing in the mathematical equations. To achieve this objective, we perform extensive numerical simulations and analysis of the model equations and link the parameter variations with different environmental and physicochemical conditions in which the individuals develop, and which may be regulated by the ontogenetic plasticity of the species. Our numerical study indicates that the patterns predicted by a set of reaction diffusion equations are not uniquely determined by the value of the parameters of the equation, but also depend on how the process is initiated and on the spatial distribution of values of these parameters. These factors are therefore significant, since they show that an individual’s growth dynamics and apparent secondary transport processes, like advection, can be determinant for the alignment of motifs in a skin pattern. Our results allow us to discern the correlation between phenotypic, ontogenetic, and geographic distribution of the different species of Pseudoplatystoma fishes, thus indicating that RD models represent a useful taxonomic tool able to quantify evolutionary indexes.     

Molecular cloning of P450 aromatase from the leopard gecko and its expression in the ovary

In this study, we identified the cDNA of P450 aromatase in the leopard gecko, a lizard with temperature-dependent sex determination. The cDNA encodes a putative protein of 505 amino acids. The deduced amino acid sequence of leopard gecko aromatase cDNA showed 80% identity with that of turtles, 70% with humans and 77% with chickens. This is the first report of the identification of P450 aromatase cDNA in squamata species. It has been reported that this gene is expressed in different layers of cells in the ovary of mammalian species and avian species. Thus, we also investigated cells expressing the mRNA of this gene in the ovary of the leopard gecko by RT-PCR and in situ hybridization. The mRNA expression of leopard gecko P450 aromatase was localized in both the thecal and granulosa cell layers in the ovary. The expression in thecal and granulosa cell layers was examined in the largest follicle, second largest follicle and third largest follicle by RT-PCR. A higher level of mRNA expression was observed in the granulosa cell layer of the second largest follicle than in other cell layers. This result may reflect the characteristics of follicles in species with automonochronic ovulation.     

基于分子宏条形码分析四川卧龙国家级自然保护区雪豹的食性

作为中亚和青藏高原山地生态系统中的顶级捕食者, 雪豹(Panthera uncia)对于维持食物网结构和生态系统稳定性有重要作用。了解雪豹的食性组成和变化对于理解其生态系统功能和物种间相互作用有重要意义。以往的雪豹食性分析多基于对其粪便中食物残渣的形态学鉴定, 但准确度受人员经验和主观因素影响较大。邛崃山脉位于雪豹分布区东南缘, 该区域的雪豹种群规模小且相对孤立, 研究匮乏。本研究基于非损伤性取样, 在邛崃山脉的卧龙国家级保护区采集疑似雪豹粪便样品38份, 首先提取粪便DNA, 并扩增线粒体DNA 16S rRNA基因片段进行分子物种鉴定, 确定其中22份为雪豹粪便样品。随后, 利用脊椎动物通用引物和雪豹特异性阻抑引物扩增粪便DNA中的食物成分, 并进行高通量测序, 分析雪豹食性构成。食性分析结果显示岩羊(Pseudois nayaur)是卧龙地区雪豹最主要的食物, 在67%的样品中均有检出。家牦牛(Bos grunniens)在33%的样品中出现, 也在雪豹食性中占较高比例。此外, 鼠兔(Ochotona spp.)和鸟类也在少量样品中发现。可见, 野生猎物是卧龙地区雪豹的主要食物资源; 与大世界大多数其他地区的雪豹食性相同, 野生大型有蹄类是雪豹最重要的食物。然而家畜(牦牛)在卧龙雪豹食谱中有相当高的占比, 显示该区域内可能存在较为严重的由雪豹捕食散养家畜引起的人兽冲突问题。