Identification of genes downstream of the Shh signalling in the developing chick wing and syn-expressed with <i>Hoxd13</i> using microarray and 3D computational analysis

Sonic hedgehog (Shh) signalling by the polarizing region at the posterior margin of the chick wing bud is pivotal in patterning the digits but apart from a few key downstream genes, such as Hoxd13, which is expressed in the posterior region of the wing that gives rise to the digits, the genes that mediate the response to Shh signalling are not known. To find genes that are co-expressed with Hoxd13 in the posterior of chick wing buds and regulated in the same way, we used microarrays to compare gene expression between anterior and posterior thirds of wing buds from normal chick embryos and from polydactylous talpid mutant chick embryos, which have defective Shh signalling due to lack of primary cilia. We identified 1070 differentially expressed gene transcripts, which were then clustered. Two clusters contained genes predominantly expressed in posterior thirds of normal wing buds; in one cluster, genes including Hoxd13, were expressed at high levels in anterior and posterior thirds in talpid wing buds, in the other cluster, genes including Ptc1, were expressed at low levels in anterior and posterior thirds in talpid wing buds. Expression patterns of genes in these two clusters were validated in normal and talpid mutant wing buds by in situ hybridisation and demonstrated to be responsive to application of Shh. Expression of several genes in the Hoxd13 cluster was also shown to be responsive to manipulation of protein kinase A (PKA) activity, thus demonstrating regulation by Gli repression. Genes in the Hoxd13 cluster were then sub-clustered by computational comparison of 3D expression patterns in normal wing buds to produce syn-expression groups. Hoxd13 and Sall1 are syn-expressed in the posterior region of early chick wing buds together with 6 novel genes which are likely to be functionally related and represent secondary targets of Shh signalling. Other groups of syn-expressed genes were also identified, including a group of genes involved in vascularisation

Point-of-care testing for disasters: needs assessment, strategic planning, and future design.

Objective evidence-based national surveys serve as a first step in identifying suitable point-of-care device designs, effective test clusters, and environmental operating conditions. Preliminary survey results show the need for point-of-care testing (POCT) devices using test clusters that specifically detect pathogens found in disaster scenarios. Hurricane Katrina, the tsunami in southeast Asia, and the current influenza pandemic (H1N1, "swine flu") vividly illustrate lack of national and global preparedness. Gap analysis of current POCT devices versus survey results reveals how POCT needs can be fulfilled. Future thinking will help avoid the worst consequences of disasters on the horizon, such as extensively drug-resistant tuberculosis and pandemic influenzas. A global effort must be made to improve POC technologies to rapidly diagnose and treat patients to improve triaging, on-site decision making, and, ultimately, economic and medical outcomes

Sterol 14α-demethylase mutation leads to amphotericin B resistance in Leishmania mexicana

Amphotericin B has emerged as the therapy of choice for use against the leishmaniases. Administration of the drug in its liposomal formulation as a single injection is being promoted in a campaign to bring the leishmaniases under control. Understanding the risks and mechanisms of resistance is therefore of great importance. Here we select amphotericin B-resistant Leishmania mexicana parasites with relative ease. Metabolomic analysis demonstrated that ergosterol, the sterol known to bind the drug, is prevalent in wild-type cells, but diminished in the resistant line, where alternative sterols become prevalent. This indicates that the resistance phenotype is related to loss of drug binding. Comparing sequences of the parasites’ genomes revealed a plethora of single nucleotide polymorphisms that distinguish wild-type and resistant cells, but only one of these was found to be homozygous and associated with a gene encoding an enzyme in the sterol biosynthetic pathway, sterol 14α-demethylase (CYP51). The mutation, N176I, is found outside of the enzyme’s active site, consistent with the fact that the resistant line continues to produce the enzyme’s product. Expression of wild-type sterol 14α-demethylase in the resistant cells caused reversion to drug sensitivity and a restoration of ergosterol synthesis, showing that the mutation is indeed responsible for resistance. The amphotericin B resistant parasites become hypersensitive to pentamidine and also agents that induce oxidative stress. This work reveals the power of combining polyomics approaches, to discover the mechanism underlying drug resistance as well as offering novel insights into the selection of resistance to amphotericin B itself

Discovery of four recessive developmental disorders using probabilistic genotype and phenotype matching among 4,125 families.

Discovery of most autosomal recessive disease-associated genes has involved analysis of large, often consanguineous multiplex families or small cohorts of unrelated individuals with a well-defined clinical condition. Discovery of new dominant causes of rare, genetically heterogeneous developmental disorders has been revolutionized by exome analysis of large cohorts of phenotypically diverse parent-offspring trios. Here we analyzed 4,125 families with diverse, rare and genetically heterogeneous developmental disorders and identified four new autosomal recessive disorders. These four disorders were identified by integrating Mendelian filtering (selecting probands with rare, biallelic and putatively damaging variants in the same gene) with statistical assessments of (i) the likelihood of sampling the observed genotypes from the general population and (ii) the phenotypic similarity of patients with recessive variants in the same candidate gene. This new paradigm promises to catalyze the discovery of novel recessive disorders, especially those with less consistent or nonspecific clinical presentations and those caused predominantly by compound heterozygous genotypes

From the Philippines to Iraq Investigating Counterinsurgency Operations, Atrocity, and Race

This thesis asks two central questions: (1.) Is there a link between atrocities committed during American counterinsurgency campaigns and race? (2.) Is there continuity between the counterinsurgency techniques deployed in the Philippines and in Iraq in this respect? In an effort to answer these questions I propose to briefly outline the chapters which are to follow. In Chapter 1 I propose to tackle the question of race using the following questions as broad guides to my investigation: what is it? how do we understand it? how will it be operationalized? In other words, this first chapter serves both as a literature review and an outline of the theoretical framework to be adopted in the later sections of this thesis. It outlines the current state of the concept ‘race’ in the literature of various fields of politics with an eye to finding space for a critical approach. In the end, I settle on the elegant framework set forth by Roxanne Lynn Doty. In Chapter 2, carrying forward Doty’s operationalized concept of race, I undertake an analysis of the discourse and practice surrounding American Counterinsurgency Policy during the invasion of the Philippines from 1899-1903. First; I investigate the role that racialized discourse played in the domestic and international contexts surrounding the invasion of the Philippines. Second; I delve into the empirical historical record to attempt to sketch out how racism was deployed on the ground in the counterinsurgency in the Philippines and what relationship the acts of atrocity committed there had with racial discourse. Following the findings of Chapter 2 I attempt to investigate the extent to which these mechanisms existed in the counterinsurgency in Iraq in Chapter 3. The investigation of Iraq is structured similarly to that of the Philippines but, due to the absolute abundance of information on Iraq, it is broken into three sections. The first section examines the role of race in the 2 domestic politics of the United States before, during, and after September 11, 2001. The second section sketches out an emerging international logic concerning military intervention and development. The final section sketches out the empirical reality of how race was used in atrocity in Iraq

First report of Ixodes kopsteini Oudemans (Acari: Ixodida: Ixodidae) from the Kingdom of Cambodia, with a summary of known hosts of this tick in continental southeastern Asia

Volume: 106Start Page: 472End Page: 47