"Anteroposterior Patterning: How the Hox Genes Help Us Tell Our Heads from Our ***es"

The fundamental problem of developmental biology is how a single cell- a fertilized egg- is able to produce an entire organism in all its complexity. One essential aspect of this process is spatial patterning-in essence, instructing cells as to their location in developing body so that they can exhibit characteristics appropriate to their functions. he Hox genes, first discovered in mutant fruit fly "hopeful monsters" with extra pairs of wings or legs growing out of their heads, confer spatial information along the anteroposterior axis in animals from worms to humans. Prof Marin's research focuses on the roles of specific Hox genes in sculpting the developing entral nervous system of the fruit fly and how the same gene can direct a neuron to die, survive, or send its axon in search of different connections, depending on cellular context.

The Role of Antennapedia in Anteroposterior Patterning of the Drosophila Melanogaster Ventral Nervous System

A major unresolved question in developmental neurobiology is how the nervous system is adapted to the specific needs of the organism at different life stages. In the holometabolous insect Drosophila melanogaster, the larval ventral nervous system (VNS) is comprised of similar repeating segments, as opposed to the adult VNS, which varies greatly from segment to segment both in number and types of neurons. The adult-specific neurons of each segment are generated by 25 distinct types of neuronal progenitor cells called neuroblasts (NBs) that appear in a stereotyped array (Truman et al., 2004). Each NB divides repeatedly to produce a distinct set of daughter cells termed a lineage, which is bilaterally symmetric but present to varying degrees in each segment. These daughter cells can be distinguished by their position within the nervous system as well as by their axonal projections. Each of the 25 NBs produces neurons; if both daughter cells are present in a lineage then both sibling populations survived, whereas if only one projection is seen cell death occurred, leaving a hemilineage (half lineage). In some lineages, the same sibling type survives in all segments in which the lineage appears, but in others, the surviving sibling type varies across segments, resulting in a different morphology for the same lineage in different segments. How are these differences in survival and morphology controlled? The Hox genes provide positional information for developing structures along the anterior-posterior (AP) axis of animals. They encode transcription factors, thereby controlling the activity of genes down stream. In the postembryonic VNS, each NB lineage features its own characteristic expression pattern of Hox genes Antp and Ubx, which can vary from segment-to-segment, and can thereby cause variation in the number of neural cells and axonal projections that survive. This study defines the wild-type expression pattern of Antp and elucidates the role of Antp in gain of function studies. These studies are possible due to the MARCM (Mosaic Analysis with a Repressible Cell Marker) method, which allows the genetically manipulated cells to be specifically labeled in an otherwise normal, unlabeled organism. The results indicate that Antp is expressed in a segment-, lineage-, and hemilineage-specific manner. Antp is sufficient for both anterior and posterior transformations of particular lineages, including promotion of cell death and/or survival as well as axon guidance.

Leaf Asymmetry as a Developmental Constraint Imposed by Auxin-Dependent Phyllotactic Patterning

In a majority of species, leaf development is thought to proceed in a bilaterally symmetric fashion without systematic asymmetries. This is despite the left and right sides of an initiating primordium occupying niches that differ in their distance from sinks and sources of auxin. Here, we revisit an existing model of auxin transport sufficient to recreate spiral phyllotactic patterns and find previously overlooked asymmetries between auxin distribution and the centers of leaf primordia. We show that it is the direction of the phyllotactic spiral that determines the side of the leaf these asymmetries fall on. We empirically confirm the presence of an asymmetric auxin response using a DR5 reporter and observe morphological asymmetries in young leaf primordia. Notably, these morphological asymmetries persist in mature leaves, and we observe left-right asymmetries in the superficially bilaterally symmetric leaves of tomato (Solanum lycopersicum) and Arabidopsis thaliana that are consistent with modeled predictions. We further demonstrate that auxin application to a single side of a leaf primordium is sufficient to recapitulate the asymmetries we observe. Our results provide a framework to study a previously overlooked developmental axis and provide insights into the developmental constraints imposed upon leaf morphology by auxin-dependent phyllotactic patterning.

Photolithography based patterning of bacteriorhodopsin films

The patterning of photoactive purple membrane (PM) films onto electronic substrates to create a biologically based light detection device was investigated. This research is part of a larger collaborative effort to develop a miniaturized toxin detection platform. This platform will utilize PM films containing the photoactive protein bacteriorhodopsin to convert light energy to electrical energy. Following an effort to pattern PM films using focused ion beam machining, the photolithography based bacteriorhodopsin patterning technique (PBBPT) was developed. This technique utilizes conventional photolithography techniques to pattern oriented PM films onto flat substrates. After the basic patterning process was developed, studies were conducted that confirmed the photoelectric functionality of the PM films after patterning. Several process variables were studied and optimized in order to increase the pattern quality of the PM films. Optical microscopy, scanning electron microscopy, and interferometric microscopy were used to evaluate the PM films produced by the patterning technique. Patterned PM films with lateral dimensions of 15 μm have been demonstrated using this technique. Unlike other patterning techniques, the PBBPT uses standard photolithographic processes that make its integration with conventional semiconductor fabrication feasible. The final effort of this research involved integrating PM films patterned using the PBBPT with PMOS transistors. An indirect integration of PM films with PMOS transistors was successfully demonstrated. This indirect integration used the voltage produced by a patterned PM film under light exposure to modulate the gate of a PMOS transistor, activating the transistor. Following this success, a study investigating how this PM based light detection system responded to variations in light intensity supplied to the PM film. This work provides a successful proof of concept for a portion of the toxin detection platform currently under development.

Banks and the Racial Patterning of Homicide: A Study of Chicago Neighborhoods

While bank investment is a driving force behind neighborhood viability, few studies have directly examined the effects of bank loan practices on neighborhood crime rates. This paper proposes that residential bank loan policies help explain the higher rates of homicide in minority neighborhoods in Chicago compared to white neighborhoods. It finds that black and Latino neighborhoods would experience fewer homicides if more financial capital were infused into these neighborhoods. These findings suggest that neighborhoods are shaped profoundly by the decisions of external economic actors.

Appraisal-driven somatovisceral response patterning: effects of intrinsic pleasantness and goal conduciveness.

Several componential emotion theories suggest that appraisal outcomes trigger characteristic somatovisceral changes that facilitate information processing and prepare the organism for adaptive behavior. The current study tested predictions derived from Scherer's Component Process Model. Participants viewed unpleasant and pleasant pictures (intrinsic pleasantness appraisal) and were asked to concurrently perform either an arm extension or an arm flexion, leading to an increase or a decrease in picture size. Increasing pleasant stimuli and decreasing unpleasant stimuli were considered goal conducive; decreasing pleasant stimuli and increasing unpleasant stimuli were considered goal obstructive (goal conduciveness appraisal). Both appraisals were marked by several somatovisceral changes (facial electromyogram, heart rate (HR)). As predicted, the changes induced by the two appraisals showed similar patterns. Furthermore, HR results, compared with data of earlier studies, suggest that the adaptive consequences of both appraisals may be mediated by stimulus proximity.

Vascular Patterning: More Than Just Auxin?

The plant hormone auxin has long been known to play a pivotal role in vascular patterning and differentiation. But auxin is not the whole story: recent genetic analyses have identified additional factors required for vascular patterning, one of them involving sterols.

Requirement of GCN5 histone acetyltransferase in mouse neural tube closure and skeletal patterning

Histone acetylation plays an essential role in many DNA-related processes such as transcriptional regulation via modulation of chromatin structure. Many histone acetytransferases have been discovered and studied in the past few years, but the roles of different histone acetyltransferases (HAT) during mammalian development are not well defined at present. Gcn5 histone acetyltransferase is highly expressed until E16.5 during development. Previous studies in our lab using a constitutive null allele demonstrated that Gcn5 knock out mice are embryonic lethal, precluding the study of Gcn5 functions at later developmental stages. The creation of a conditional Gcn5 null allele, Gcn5flox allele, bypasses the early lethality. Mice homozygous for this allele are viable and appear healthy. In contrast, mice homozygous for a Gcn5 Δex3-18 allele created by Cre-loxP mediated deletion display a phenotype identical to our original Gcn5 null mice. Strikingly, a Gcn5flox(neo) allele, which contain a neomycin cassette in the second intron of Gcn5 is only partially functional and gives rise to a hypomorphic phenotype. Initiation of cranial neural tube closure at forebrain/midbrain boundary fails, resulting in an exencephaly in some Gcn5flox(neo)/flox(neo) embryos. These defects were found at an even greater penetrance in Gcn5flox(neo)/Δ embryos and become completely penetrant in the 129Sv genetic background, suggesting that Gcn5 controls mouse neural tube closure in a dose dependent manner. Furthermore, both Gcn5flox(neo)/flox(neo) and Gcn5 flox(neo)/Δ embryos exhibit anterior homeotic transformations in lower thoracic and lumbar vertebrae. These defects are accompanied by decreased expression levels and a shift in anterior expression boundary of Hoxc8 and Hoxc9. This study provides the first evidence that Gcn5 regulates Hox gene expression and is required for normal axial skeletal patterning in mice. ^

The use of arc-erosion as a patterning technique for transparent conductive materials

Within the framework of cost-effective patterning processes a novel technique that saves photolithographic processing steps, easily scalable to wide area production, is proposed. It consists of a tip-probe, which is biased with respect to a conductive substrate and slides on it, keeping contact with the material. The sliding tip leaves an insulating path (which currently is as narrow as 30 μm) across the material, which enables the drawing of tracks and pads electrically insulated from the surroundings. This ablation method, called arc-erosion, requires an experimental set up that had to be customized for this purpose and is described. Upon instrumental monitoring, a brief proposal of the physics below this process is also presented. As a result an optimal control of the patterning process has been acquired. The system has been used on different substrates, including indium tin oxide either on glass or on polyethylene terephtalate, as well as alloys like Au/Cr, and Al. The influence of conditions such as tip speed and applied voltage is discussed

Solution-processed organic devices developed by a novel cost-effective patterning technique based on electrical erosion

Application of arc erosion to the patterning of metallic contacts in organic devices is presented. A home-made systems and details of the working principles are described. Advantages and drawbacks of this novel technology are discussed.

E-beam nano-patterning for the ordered growth of GaN/InGaN nanorods

E-beam lithography was used to pattern a titanium mask on a GaN substrate with ordered arrays of nanoholes. This patterned mask served as a template for the subsequent ordered growth of GaN/InGaN nanorods by plasma-assisted molecular beam epitaxy. The mask patterning process was optimized for several holes configurations. The smallest holes were 30 nm in diameter with a pitch (center-to-center distance) of 100 nm only. High quality masks of several geometries were obtained that could be used to grow ordered GaN/InGaN nanorods with full selectivity (growth localized inside the nanoholes only) over areas of hundreds of microns. Although some parasitic InGaN growth occurred between the nanorods during the In incorporation, transmission electron microscopy and photoluminescence measurements demonstrated that these ordered nanorods exhibit high crystal quality and reproducible optical properties.