The control of leaf development

The formation of a leaf is a basic aspect of plant development. This review provides an overview of our present understanding of the process from initiation to the final form of the leaf. Molecular genetic and cell biology approaches have yielded significant advances in this area, adding not only to our knowledge of leaf development but also to fundamental principles in plant biology. These principles will be highlighted, as well as areas where our understanding is still incomplete, in particular the problem of coordinating the multifaceted steps involved in the generation of the leaf structure.     

From genes to networks: in systematic points of view

We present a report of the BIOCOMP'10 - The 2010 International Conference on Bioinformatics & Computational Biology and other related work in the area of systems biology.     

Homeobox genes in the genetic control of eye development

Vertebrate eye formation is a complex process which involves early specification of the prospective eye territory, induction events, patterning along the polarity axes and regional specification, to bring about the proper morphogenetic movements, cell proliferation, cell differentiation and neural connections allowing visual function. The molecular machinery underlying such complex developmental events is presently under an intense research scrutiny and many associated genetic factors have been isolated and characterized. These studies produced striking knowledge in the field, especially with respect to uncovering the role of key genes and their possible evolutionary conservation. Presently, a major task is to define the complex interactions connecting the multiplicity of molecular players that regulate eye development. We recently identified two homeobox genes, Xrx1 and Xvax2, and studied their function by using the Xenopus embryo as a developmental model system. Xrx1 and Xvax2 control key aspects of eye development. In particular, Xrx1 appears to play a role in the early specification of anterior neural regions fated to give rise to retina and forebrain structures, and in promoting cell proliferation within these territories. On the other hand, Xvax2 is involved in regulating the eye proximo-distal and/or dorsoventral polarity, and the morphogenetic movements taking place during formation of the optic stalk and cup. Here we review the experimental results addressing the roles of Xrx1 and Xvax2 and their vertebrate orthologues, and discuss their relationship with other molecules also playing a related function in eye development.     

From genes to ecosystems: a genetic basis to ecosystem services

Ecosystems provide services, many of which are regulated through species interactions. Emerging research in the fields of community and ecosystem genetics indicate that genetic variation in one species can influence species interactions and affect subsequent patterns of energy flow and nutrient cycles. Because there can be a genetic basis to community- and ecosystem-level processes, evolutionary processes that alter standing genetic variation can have extended consequences that matter to patterns of biodiversity and ecosystem function that exist on the landscape. Here we explore some emerging areas of research in the field of community and ecosystem genetics and discuss the general importance of this approach to evolutionary ecology.     

Identification and genetic mapping of four novel genes that regulate leaf development in Arabidopsis

Molecular and genetic characterizations of mutants have led to a better understanding of many developmental processes in the model system Arabidopsis thaliana.However,the leaf development that is specific to plants has been little studies.With the aim of contributing to the genetic dissection of leaf development,we have performed a large-scare screening for mutants with abnormal leaves.Among a great number of leaf mutants we have generated by T-DNA and transposon tagging and ethylmethae sulfonate (EMS) mutagenesis,four independent mutant lines have been identified and studied genetically.Phenotypes of these mutant lines represent the defects of four novel muclear genes designated LL1(LOTUS LEAF 1),LL2(LOTUS LEAF2),URO(UPRIGHT ROSETTE),and EIL(ENVIRONMENT CONDITION INDUCED LESION).The phenotypic analysis indicates that these genes play important roles during leaf development.For the further genetic analysis of these genes and the map-based cloning of LL1 and LL2,we have mapped these genes to chromosome regions with an efficient and rapid mapping method.     

From single genes to gene networks: high-throughput-high-content screening for neurological disease

Neuronal development, function, and the subsequent degeneration of the brain are still an enigma in both the normal and pathologic states, and there is an urgent need to find better targets for developing therapeutic intervention. Current techniques to deconstruct the architecture of brain and disease-related pathways are best suited for following up on single genes but would take an impractical amount of time for the leads from the current wave of genetic and genomic data. New technical developments have made combined high-throughput-high-content (HT-HC) cellular screens possible, which have the potential to contextualize the information, gathered from a combination of genetic and genomic approaches, into networks and functional biology and can be utilized for the identification of therapeutic targets. Herein we discuss the potential impact of HT-HC cellular screens on medical neuroscience.     

Shaping up: the genetic control of leaf shape

Leaf initiation at the shoot apical meristem involves a balance between cell proliferation and commitment to make primordia. Several genes, such as CLAVATA1, CLAVATA3, WUSCHEL, KNOTTED1, and PHANTASTICA, play key roles in these processes. When expressed in the leaf primordium, however, these 'meristem' genes can profoundly affect leaf shape and size, possibly by regulating hormone gradients and transport. The KNOTTED1-like genes are involved in regulating changes in hormonal levels. Recent studies have elaborated on the role that hormones, such as auxin, play in releasing biophysical constraints on leaf initiation and growth. Final leaf form is elaborated by a coordination of these hormonally regulated processes, cell division and cellular differentiation.     

Growing genetic regulatory networks from seed genes

MOTIVATION: A number of models have been proposed for genetic regulatory networks. In principle, a network may contain any number of genes, so long as data are available to make inferences about their relationships. Nevertheless, there are two important reasons why the size of a constructed network should be limited. Computationally and mathematically, it is more feasible to model and simulate a network with a small number of genes. In addition, it is more likely that a small set of genes maintains a specific core regulatory mechanism. RESULTS: Subnetworks are constructed in the context of a directed graph by beginning with a seed consisting of one or more genes believed to participate in a viable subnetwork. Functionalities and regulatory relationships among seed genes may be partially known or they may simply be of interest. Given the seed, we iteratively adjoin new genes in a manner that enhances subnetwork autonomy. The algorithm is applied using both the coefficient of determination and the Boolean-function influence among genes, and it is illustrated using a glioma gene-expression dataset. AVAILABILITY: Software for the seed-growing algorithm will be available at the website for Probabilistic Boolean Networks: http://www2.mdanderson.org/app/ilya/PBN/PBN.htm     

From weeds to crops: genetic analysis of root development in cereals

Root development of Arabidopsis, Zea mays (maize) and Oryza sativa (rice) differs in both overall architecture and the anatomy of individual roots. In maize and rice, the post-embryonic shoot-borne root system becomes the major backbone of the root stock; in Arabidopsis, the embryonic root system formed by a simple primary root and its lateral roots remains dominant. Recently, several specific root mutants and root-specific genes have been identified and characterized in maize and rice. Interestingly, some of these mutants indicate that the formation of primary-, seminal-, crown- and lateral roots is regulated by alternative root-type-specific pathways. Further analyses of these unique pathways will contribute to the understanding of the complex molecular networks involved in cereal root formation.     

The genetic basis of alcoholism: multiple phenotypes,many genes,complex networks

Alcoholism is a significant public health problem. A picture of the genetic architecture underlying alcohol-related phenotypes is emerging from genome-wide association studies and work on genetically tractable model organisms.     

A Markovian approach to the control of genetic regulatory networks

This paper presents an approach for controlling gene networks based on a Markov chain model, where the state of a gene network is represented as a probability distribution, while state transitions are considered to be probabilistic. An algorithm is proposed to determine a sequence of control actions that drives (without state feedback) the state of a given network to within a desired state set with a prescribed minimum or maximum probability. A heuristic is proposed and shown to improve the efficiency of the algorithm for a class of genetic networks.     

The leaf index: heteroblasty, natural variation, and the genetic control of polar processes of leaf expansion

The morphology of the leaves of angiosperms exhibits remarkable diversity. One of the factors showing the greatest variability is the leaf index, namely, the ratio of leaf length to leaf width. In some cases, different varieties of a single species or closely related species can be distinguished by differences in leaf index. To some extent, the leaf index reflects the morphological adaptation of leaves to a particular environment. Moreover, physiological conditions or environmental factors can change the leaf index of an individual plant. No good tools have been available for studies of the mechanisms that underlie such biodiversity. However, we have recently obtained some, albeit fragmentary, information about molecular mechanisms of leaf morphogenesis as a result of studies of leaves of the model plant, Arabidopsis thaliana (L.) Heynh. For example, the ANGUSTIFOLIA gene, a homolog of animal CtBP genes, controls leaf width. ANGUSTIFOLIA appears to regulate the polar elongation of leaf cells via control of the arrangement of cortical microtubules. By contrast, the ROTUNDIFOLIA3 gene controls leaf length via the biosynthesis of steroid(s). We provide here an overview of the biodiversity exhibited by the leaf index of angiosperms. In particular, we consider information obtained from studies of mutants and transgenic strains of A. thaliana, from the so-called Evo/devo perspective.     

The molecular and genetic control of ovule development

A genetic approach has resulted in an extensive framework for the methodical analysis of ovule development. The most recent progress was accomplished in the areas of primordium formation and integument morphogenesis. Furthermore, systematic screens have identified a number of gametophytic mutations disrupting several distinct steps of embryo sac ontogenesis.