Sea Urchin Body Plan Development and Evolution: An Integrative Transcriptomic Approach

My dissertation work integrates comparative transcriptomics and functional analyses to investigate gene expression changes underlying two significant aspects of sea urchin evolution and development: the dramatic developmental changes associated with an ecologically significant shift in life history strategy and the development of the unusual radial body plan of adult sea urchins.

In Chapter 2, I investigate evolutionary changes in gene expression underlying the switch from feeding (planktotrophic) to nonfeeding (lecithotrophic) development in sea urchins. In order to identify these changes, I used Illumina RNA-seq to measure expression dynamics across 7 developmental stages in three sea urchin species: the lecithotroph Heliocidaris erythrogramma, the closely related planktotroph Heliocidaris tuberculata, and an outgroup planktotroph Lytechinus variegatus. My analyses draw on a well-characterized developmental gene regulatory network (GRN) in sea urchins to understand how the ancestral planktotrophic developmental program was altered during the evolution of lecithotrophic development. My results suggest that changes in gene expression profiles occurred more frequently across the transcriptome during the evolution of lecithotrophy than during the persistence of planktotrophy. These changes were even more pronounced within the GRN than across the transcriptome as a whole, and occurred in each network territory (skeletogenic, endomesoderm and ectoderm). I found evidence for both conservation and divergence of regulatory interactions in the network, as well as significant changes in the expression of genes with known roles in larval skeletogenesis, which is dramatically altered in lecithotrophs. I further explored network dynamics between species using coexpression analyses, which allowed me to identify novel players likely involved in sea urchin neurogenesis and endoderm patterning.

In Chapter 3, I investigate developmental changes in gene expression underlying radial body plan development and metamorphosis in H. erythrogramma. Using Illumina RNA-seq, I measured gene expression profiles across larval, metamorphic, and post-metamorphic life cycle phases. My results present a high-resolution view of gene expression dynamics during the complex transition from pre- to post-metamorphic development and suggest that distinct sets of regulatory and effector proteins are used during different life history phases.

Collectively, my investigations provide an important foundation for future, empirical studies to investigate the functional role of gene expression change in the evolution of developmental differences between species and also for the generation of the unusual radial body plan of sea urchins.

The effects of curcumin (diferuloylmethane) on body composition of patients with advanced pancreatic cancer.

BACKGROUND: Curcumin is a natural product that is often explored by patients with cancer. Weight loss due to fat and muscle depletion is a hallmark of pancreatic cancer and is associated with worse outcomes. Studies of curcumin's effects on muscularity show conflicting results in animal models. METHODS AND RESULTS: Retrospective matched 1:2 case-control study to evaluate the effects of curcumin on body composition (determined by computerized tomography) of 66 patients with advanced pancreatic cancer (22 treated,44 controls). Average age (SEM) was 63(1.8) years, 30/66(45%) women, median number of prior therapies was 2, median (IQR) time from advanced pancreatic cancer diagnosis to baseline image was 7(2-13.5) months (p>0.2, all variables). All patients lost weight (3.3% and 1.3%, treated vs. control, p=0.13). Treated patients lost more muscle (median [IQR] percent change -4.8[-9.1,-0.1] vs. -0.05%[-4.2, 2.6] in controls,p<0.001) and fat (median [IQR] percent change -6.8%[-15,-0.6] vs. -4.0%[-7.6, 1.3] in controls,p=0.04). Subcutaneous fat was more affected in the treated patients. Sarcopenic patients treated with curcumin(n=15) had survival of 169(115-223) days vs. 299(229-369) sarcopenic controls(p=0.024). No survival difference was found amongst non-sarcopenic patients. CONCLUSIONS: Patients with advanced pancreatic cancer treated with curcumin showed significantly greater loss of subcutaneous fat and muscle than matched untreated controls.

The body language: The spontaneous influence of congruent bodily arousal on the awareness of emotional words

Nowadays, the idea of a reciprocal influence of physiological and psychological processes seems to be widely accepted. For instance, current theories of embodied emotion suggest that knowledge about an emotion concept involves simulations of bodily experienced emotional states relevant to the concept. In line with this framework, the present study investigated whether actual levels of physiological arousal interact with the processing of emotional words. Participants performed 2 blocks of an attentional blink task, once after a cycling session (increased arousal) and once after a relaxation session (reduced arousal). Concretely, participants were instructed to detect and report 2 target words (T1 and T2) presented among a series of nonword distractors. T1 and T2 were either neutral, high arousal, or low arousal words. Results revealed that increased physiological arousal led to improved reports of high arousal T2 words, whereas reduced physiological arousal led to improved reports of low arousal T2 words. Neutral T2 remained unaffected by the arousing conditions. These findings emphasize that actual levels of physiological arousal modulate the cognitive access to arousal (in-)congruent emotional concepts and suggest a direct grounding of emotion knowledge in our bodily systems of arousal.

Molecular dynamics simulation of fractures using an N-body potential

Molecular dynamics has been employed to model the fracture of a twodimensional triangular atomic lattice. The N-body Sutton-Chen potential developed for fcc metals and its extended version (Rafii-Tabar and Sutton) for fcc random binary alloys were used for the interatomic interactions. It is shown that at low temperatures cleavage fractures can occur in both an elemental metal and an alloy. At elevated temperatures the nucleation of dislocations is shown to cause a brittle-to-ductile transition. For the brittle crack propagation in the elemental metal, crack propagation speeds have been computed for different stress rates, and a crack instability found to exist as the speed reaches a critical value of about 32% of the Rayleigh wave speed. For the random alloy, we find that the dislocation movement can be affected by the distorted lattice.

Molecular dynamics simulation of fractures using an N-body potential

Molecular dynamics has been employed to model the fracture of a two dimensional triangular atomic lattice. The N-body Sutton-Chen potential developed for fcc metals and its extended version (Rafii-Tabar and Sutton) for fcc random binary alloys were used for the interatomic interactions. It is shown that at low temperatures cleavage fractures can occur in both an elemental metal and an alloy. At elevated temperatures the nucleation of dislocations is shown to cause a brittle-to-ductile transition. For the brittle crack propagation in the elemental metal, crack propagation speeds have been computed for different stress rates, and a crack instability found to exist as the speed reaches a critical value of about 32% of the Rayleigh wave speed. For the random alloy, we find that the dislocation movement can be affected by the distorted lattice.

Numerical experiments of some Krylov subspace methods for black oil model

This paper discusses preconditioned Krylov subspace methods for solving large scale linear systems that originate from oil reservoir numerical simulations. Two types of preconditioners, one being based on an incomplete LU decomposition and the other being based on iterative algorithms, are used together in a combination strategy in order to achieve an adaptive and efficient preconditioner. Numerical tests show that different Krylov subspace methods combining with appropriate preconditioners are able to achieve optimal performance.

The use of evacuation modelling techniques in the design of very large transport aircraft and blended wing body aircraft

Very Large Transport Aircraft (VLTA) pose considerable challenges to designers, operators and certification authorities. Questions concerning seating arrangement, nature and design of recreational space, the number, design and location of internal staircases, the number of cabin crew required and the nature of the cabin crew emergency procedures are just some of the issues that need to be addressed. Other more radical concepts such as blended wing body (BWB) design, involving one or two decks with possibly four or more aisles offer even greater challenges. Can the largest exits currently available cope with passenger flow arising from four or five aisles? Do we need to consider new concepts in exit design? Should the main aisles be made wider to accommodate more passengers? In this paper we demonstrate how computer based evacuation models can be used to investigate these issues through examination of staircase evacuation procedures for VLTA and aisle/exit configuration for BWB cabin layouts.

Property in body parts and products of the human body

An intriguing question, which until recently had not been directly explored by the courts, is the extent to which English law recognises body parts and products of the human body as property capable of ownership. Although the common law currently recognises no general property in a dead body (and only limited possessory rights in respect of it), this apparent “no-property rule” provides no justification, it is submitted, for denying proprietary status to parts or products of a living human body. The recent decision of the Court of Appeal in Yearworth v. North Bristol NHS Trust ([2009] EWCA Civ 37) lends strong support to the view that genetic material (as the product of a living human body) is capable of ownership, at least in the context of a claim in the tort of negligence and bailment. This article examines the various issues by reference to both English and Commonwealth authority.

Cooperative communications in ultra-wideband wireless body area networks: Channel modeling and system diversity analysis

In this paper, we explore the application of cooperative communications in ultra-wideband (UWB) wireless body area networks (BANs), where a group of on-body devices may collaborate together to communicate with other groups of on-body equipment. Firstly, time-domain UWB channel measurements are presented to characterize the body-centric multipath channel and to facilitate the diversity analysis in a cooperative BAN (CoBAN). We focus on the system deployment scenario when the human subject is in the sitting posture. Important channel parameters such as the pathloss, power variation, power delay profile (PDP), and effective received power (ERP) crosscorrelation are investigated and statistically analyzed. Provided with the model preliminaries, a detailed analysis on the diversity level in a CoBAN is provided. Specifically, an intuitive measure is proposed to quantify the diversity gains in a single-hop cooperative network, which is defined as the number of independent multipaths that can be averaged over to detect symbols. As this measure provides the largest number of redundant copies of transmitted information through the body-centric channel, it can be used as a benchmark to access the performance bound of various diversity-based cooperative schemes in futuristic body sensor systems.