Experimental and theoretical studies of Notch signaling-mediated spatial pattern

Notch signaling acts in many diverse developmental spatial patterning processes. To better understand why this particular pathway is employed where it is and how downstream feedbacks interact with the signaling system to drive patterning, we have pursued three aims: (i) to quantitatively measure the Notch system's signal input/output (I/O) relationship in cell culture, (ii) to use the quantitative I/O relationship to computationally predict patterning outcomes of downstream feedbacks, and (iii) to reconstitute a Notch-mediated lateral induction feedback (in which Notch signaling upregulates the expression of Delta) in cell culture. The quantitative Notch I/O relationship revealed that in addition to the trans-activation between Notch and Delta on neighboring cells there is also a strong, mutual cis-inactivation between Notch and Delta on the same cell. This feature tends to amplify small differences between cells. Incorporating our improved understanding of the signaling system into simulations of different types of downstream feedbacks and boundary conditions lent us several insights into their function. The Notch system converts a shallow gradient of Delta expression into a sharp band of Notch signaling without any sort of feedback at all, in a system motivated by the Drosophila wing vein. It also improves the robustness of lateral inhibition patterning, where signal downregulates ligand expression, by removing the requirement for explicit cooperativity in the feedback and permitting an exceptionally simple mechanism for the pattern. When coupled to a downstream lateral induction feedback, the Notch system supports the propagation of a signaling front across a tissue to convert a large area from one state to another with only a local source of initial stimulation. It is also capable of converting a slowly-varying gradient in parameters into a sharp delineation between high- and low-ligand populations of cells, a pattern reminiscent of smooth muscle specification around artery walls. Finally, by implementing a version of the lateral induction feedback architecture modified with the addition of an autoregulatory positive feedback loop, we were able to generate cells that produce enough cis ligand when stimulated by trans ligand to themselves transmit signal to neighboring cells, which is the hallmark of lateral induction.

Developmentally regulated transcription factors in Drosophila melanogaster

During early stages of Drosophila development the heat shock response cannot be induced. It is reasoned that the adverse effects on cell cycle and cell growth brought about by Hsp70 induction must outweigh the beneficial aspects of Hsp70 induction in the early embryo. Although the Drosophila heat shock transcription factor (dHSF) is abundant in the early embryo, it does not enter the nucleus in response to heat shock. In older embryos and in cultured cells the factor is localized within the nucleus in an apparent trimeric structure that binds DNA with high affinity. The domain responsible for nuclear localization upon stress resides between residues 390 and 420 of the dHSF. Using that domain as bait in a yeast two-hybrid system we now report the identification and cloning of a nuclear transport protein Drosophila karyopherin-α3(dKap- α3). Biochemical methods demonstrate that the dKap-α3 protein binds specifically to the dHSF's nuclear localization sequence (NLS). Furthermore, the dKap-α3 protein does not associate with NLSs that contain point mutations which are not transported in vivo. Nuclear docking studies also demonstrate specific nuclear targeting of the NLS substrate by dKap-α3.Consistant with previous studies demonstrating that early Drosophila embryos are refractory to heat shock as a result of dHSF nuclear exclusion, we demonstrate that the early embryo is deficient in dKap-α3 protein through cycle 12. From cycle 13 onward the transport factor is present and the dHSF is localized within the nucleus thus allowing the embryo to respond to heat shock.

The pair-rule gene fushi tarazu (ftz) is a well-studied zygotic segmentation gene that is necessary for the development of the even-numbered parasegments in Drosophila melanogastor. During early embryogenesis, ftz is expressed in a characteristic pattern of seven stripes, one in each of the even-numbered parasegments. With a view to understand how ftz is transcriptionally regulated, cDNAs that encode transcription factors that bind to the zebra element of the ftz promoter have been cloned. Chapter Ill reports the cloning and characterization of the eDNA encoding zeb-1 (zebra element binding protein), a novel steroid receptor-like molecule that specifically binds to a key regulatory element of the ftz promoter. In transient transfection assays employing Drosophila tissue culture cells, it has been shown that zeb-1 as well as a truncated zeb-1 polypeptide (zeb480) that lacks the putative ligand binding domain function as sequencespecific trans-activators of the ftz gene.

The Oct factors are members of the POU family of transcription factors that are shown to play important roles during development in mammals. Chapter IV reports the eDNA cloning and expression of a Drosophila Oct transcription factor. Whole mount in-situ hybridization experiments revealed that the spatial expression patterns of this gene during embryonic development have not yet been observed for any other gene. In early embryogenesis, its transcripts are transiently expressed as a wide uniform band from 20-40% of the egg length, very similar to that of gap genes. This pattern progressively resolves into a series of narrower stripes followed by expression in fourteen stripes. Subsequently, transcripts from this gene are expressed in the central nervous system and the brain. When expressed in the yeast Saccharomyces cerevisiae, this Drosophila factor functions as a strong, octamer-dependent activator of transcription. The data strongly suggest possible functions for the Oct factor in pattern formation in Drosophila that might transcend the boundaries of genetically defined segmentation genes.

Social saliency : visual psychophysics and single-neuron recordings in humans

My thesis studies how people pay attention to other people and the environment. How does the brain figure out what is important and what are the neural mechanisms underlying attention? What is special about salient social cues compared to salient non-social cues? In Chapter I, I review social cues that attract attention, with an emphasis on the neurobiology of these social cues. I also review neurological and psychiatric links: the relationship between saliency, the amygdala and autism. The first empirical chapter then begins by noting that people constantly move in the environment. In Chapter II, I study the spatial cues that attract attention during locomotion using a cued speeded discrimination task. I found that when the motion was expansive, attention was attracted towards the singular point of the optic flow (the focus of expansion, FOE) in a sustained fashion. The more ecologically valid the motion features became (e.g., temporal expansion of each object, spatial depth structure implied by distribution of the size of the objects), the stronger the attentional effects. However, compared to inanimate objects and cues, people preferentially attend to animals and faces, a process in which the amygdala is thought to play an important role. To directly compare social cues and non-social cues in the same experiment and investigate the neural structures processing social cues, in Chapter III, I employ a change detection task and test four rare patients with bilateral amygdala lesions. All four amygdala patients showed a normal pattern of reliably faster and more accurate detection of animate stimuli, suggesting that advantageous processing of social cues can be preserved even without the amygdala, a key structure of the “social brain”. People not only attend to faces, but also pay attention to others’ facial emotions and analyze faces in great detail. Humans have a dedicated system for processing faces and the amygdala has long been associated with a key role in recognizing facial emotions. In Chapter IV, I study the neural mechanisms of emotion perception and find that single neurons in the human amygdala are selective for subjective judgment of others’ emotions. Lastly, people typically pay special attention to faces and people, but people with autism spectrum disorders (ASD) might not. To further study social attention and explore possible deficits of social attention in autism, in Chapter V, I employ a visual search task and show that people with ASD have reduced attention, especially social attention, to target-congruent objects in the search array. This deficit cannot be explained by low-level visual properties of the stimuli and is independent of the amygdala, but it is dependent on task demands. Overall, through visual psychophysics with concurrent eye-tracking, my thesis found and analyzed socially salient cues and compared social vs. non-social cues and healthy vs. clinical populations. Neural mechanisms underlying social saliency were elucidated through electrophysiology and lesion studies. I finally propose further research questions based on the findings in my thesis and introduce my follow-up studies and preliminary results beyond the scope of this thesis in the very last section, Future Directions.

The Madden-Julian Oscillation : observation, modeling, and theory

The Madden-Julian Oscillation (MJO) is a pattern of intense rainfall and associated planetary-scale circulations in the tropical atmosphere, with a recurrence interval of 30-90 days. Although the MJO was first discovered 40 years ago, it is still a challenge to simulate the MJO in general circulation models (GCMs), and even with simple models it is difficult to agree on the basic mechanisms. This deficiency is mainly due to our poor understanding of moist convection—deep cumulus clouds and thunderstorms, which occur at scales that are smaller than the resolution elements of the GCMs. Moist convection is the most important mechanism for transporting energy from the ocean to the atmosphere. Success in simulating the MJO will improve our understanding of moist convection and thereby improve weather and climate forecasting.

We address this fundamental subject by analyzing observational datasets, constructing a hierarchy of numerical models, and developing theories. Parameters of the models are taken from observation, and the simulated MJO fits the data without further adjustments. The major findings include: 1) the MJO may be an ensemble of convection events linked together by small-scale high-frequency inertia-gravity waves; 2) the eastward propagation of the MJO is determined by the difference between the eastward and westward phase speeds of the waves; 3) the planetary scale of the MJO is the length over which temperature anomalies can be effectively smoothed by gravity waves; 4) the strength of the MJO increases with the typical strength of convection, which increases in a warming climate; 5) the horizontal scale of the MJO increases with the spatial frequency of convection; and 6) triggered convection, where potential energy accumulates until a threshold is reached, is important in simulating the MJO. Our findings challenge previous paradigms, which consider the MJO as a large-scale mode, and point to ways for improving the climate models.

Steady surface wave pattern in a shear flow

The subject under investigation concerns the steady surface wave patterns created by small concentrated disturbances acting on a non-uniform flow of a heavy fluid. The initial value problem of a point disturbance in a primary flow having an arbitrary velocity distribution (U(y), 0, 0) in a direction parallel to the undisturbed free surface is formulated. A geometric optics method and the classical integral transformation method are employed as two different methods of solution for this problem. Whenever necessary, the special case of linear shear (i.e. U(y) = 1+ϵy)) is chosen for the purpose of facilitating the final integration of the solution.

The asymptotic form of the solution obtained by the method of integral transforms agrees with the leading terms of the solution obtained by geometric optics when the latter is expanded in powers of small ϵ r.

The overall effect of the shear is to confine the wave field on the downstream side of the disturbance to a region which is smaller than the wave region in the case of uniform flows. If U(y) vanishes, and changes sign at a critical plane y = y_cr (e.g. ϵy_cr = -1 for the case of linear shear), then the boundary of this asymmetric wave field approaches this critical vertical plane. On this boundary the wave crests are all perpendicular to the x-axis, indicating that waves are reflected at this boundary.

Inside the wave field, as in the case of a point disturbance in a uniform primary flow, there exist two wave systems. The loci of constant phases (such as the crests or troughs) of these wave systems are not symmetric with respect to the x-axis. The geometric optics method and the integral transform method yield the same result of these loci for the special case of U(y) = U_o(1 + ϵy) and for large Kr (ϵr ˂˂ 1 ˂˂ Kr).

An expression for the variation of the amplitude of the waves in the wave field is obtained by the integral transform method. This is in the form of an expansion in small ϵr. The zeroth order is identical to the expression for the uniform stream case and is thus not applicable near the boundary of the wave region because it becomes infinite in that neighborhood. Throughout this investigation the viscous terms in the equations of motion are neglected, a reasonable assumption which can be justified when the wavelengths of the resulting waves are sufficiently large.