Carnegie-Mellon University

NIH Research Projects · FY 2025 · 2016-05

This Multi-PI project combines the efforts of two research groups with different areas of expertise to address the long-term goal of developing bioengineered corneal stroma and endothelial tissues to provide therapy for individuals with corneal blindness. These tissues will be bioengineered from adult stem cells, which can be obtained from the individuals to be treated as autologous or from allogeneic cell storage since the stem cells are immunosuppressive. Over the past 5 years we have demonstrated that organization of these cells into tissues can be guided by scaffolds constructed of native extracellular matrix proteins, fabricated using a biomimetic, surface-induced assembly process. The Du Lab at the University of Pittsburgh will obtain stem cells from limbal stroma of donated human corneas. Their extensive work with these corneal stromal stem cells (CSSC) shows that they differentiate to stromal keratocytes and to corneal endothelial cells, tissues responsible for most corneal opacity. We have demonstrated that CSSC can be obtained from biopsy samples, presenting the opportunity to generate patient-specific, autologous bioengineered tissues. The Feinberg Lab at Carnegie Melon University has developed novel approach of assembling native extracellular matrix proteins to produce tissue-like scaffolding with defined 3-D architecture. Aim 1 will build on our previous work, which has showed that we can engineer spatial and biochemical cues provided by the scaffolding to generate stroma-like tissue from CSSCs that can be stacked to form multilamellar 3-D tissue similar to that of the corneal stroma. Bioengineered stroma produced in the proposed experiments will be subjected to biomechanical loading to simulate cornea development and further improve mechanical and optical properties. Function of the bioengineered stroma in lamellar keratoplasty will be evaluated in an in vivo rabbit model. Aim 2 will build on our work differentiating CSSC into endothelial cells and growing these on engineered basement membrane protein scaffolds to form polygonal monolayers that express genes typical of corneal endothelium. Previously, we demonstrated the ability to create the equivalent of Descemet's membrane to bioengineer an entire sheet of endothelium suitable for lamellar keratoplasty, but we also developed an alternative approach to engineer small patches of endothelium and deliver these via simple injection. Bioengineered endothelium produced in the proposed studies will use our newly developed “shrink-wrapping” technology to create microscale patches of corneal endothelium that can be injected into the anterior chamber for injury-free engraftment. Functionality of the constructs will be demonstrated in rabbit models in vivo, focused on boosting cell-density to improve pump function as an alternative to lamellar keratoplasty for endothelial disease. This project will build on the innovative experimental approaches we developed during the first 5 years of this project. Importantly, tissues developed and validated in vivo during this proposed study hold the potential of being advanced into clinically relevant studies to provide a novel therapeutic approach to the age-old problem of corneal blindness.

NIH Research Projects · FY 2026 · 2015-04

SUMMARY The ability to identify common objects in our environment (forks, pens, mugs) and grasp and manipulate them according to their function in support of behavioral goals is a tacit skill woven into everyday activities. Those abilities are supported by an integrated network of occipital and temporal lobe regions (supporting visual object processing and conceptual knowledge) and parietal and frontal areas (supporting active maintenance of object representations and object-directed actions). This object-processing network can be reliably mapped at the single participant and the group level using functional MRI when participants view images of manipulable objects. The key theoretical gap addressed by this research program concerns how neural representations of objects and actions in one region of the object processing network causally depend on processing in other regions within the network. This program tackles this issue via a new analytic approach, `Voxel-based Lesion Representational Similarity Analyses (VL-RSA). VL-RSA tests how lesions in one part of the brain affect fMRI-measured neural representational spaces in anatomically distant areas. VL-RSA capitalizes on the complementary strengths of neuropsychology (causal inference) and fMRI (high-sensitivity to information decoding). Hypothesis testing across Aims compare representational similarity spaces for a common set of objects and actions in functionally defined ROIs distal to the location of a brain tumor—before and after resective surgery. This approach offers a powerful model to derive causal inferences about processing dependencies across a network of brain regions. Aim 1 studies patients with brain tumors (and surgeries) that spare occipito-temporal cortex (OTC). Aim 1 tests the predictions that lesions to parietal regions of the object processing network will reduce neural responses and within-category multi-voxel pattern similarity specifically for objects (and not for faces, animals, places), and specifically in object-preferring subregions of OTC (as opposed to face/animal preferring regions). Aim 2 studies patients with brain tumors that spare parietal cortex. Aim 2 tests the predictions that occipito- temporal lesions will disrupt representational similarity spaces for object-associated manipulation (praxis) in the supramarginal gyrus, while frontal motor lesions will disrupt grasp representations in aIPS. Clinically oriented Aim 3 tests if representational spaces for objects and actions shift to the right hemisphere regions homologous to the site of the tumor, and the surgery to remove the tumor, and how such reorganization relates behavioral ability. Extensional analyses evaluate the roles of monocular vs binocular cues to depth and `tangibility' of the visual stimuli, and the relation between structural integrity of white matter pathways and core functional outcomes. Fulfilment of the Aims of this program will advance understanding of how brain lesions affect processing distal to the injury with causal evidence. A deeper understanding of how brain lesions affect network function is important for understanding variability across patients in recovery after brain injury.

NIH Research Projects · FY 2025 · 2014-08

Project Summary The endoplasmic reticulum (ER) is a dynamic membrane bound organelle whose polygonal branched network morphology is required for optimal protein targeting and secretion, lipid droplet formation and autophagy, among others. The branched structure of the ER is sustained through recurring membrane tubule extension events followed by homotypic tubule fusion events. The fusion events are catalyzed by the dynamin related ER membrane anchored GTPase atlastin (ATL). Absence of ATL activity in cells causes loss of ER network structure, while purified Drosophila ATL protein reconstituted into synthetic vesicles is sufficient to drive vesicle fusion. Vertebrates encode three distinct ATL paralogs. ATL2/3 are expressed broadly across diverse tissues while ATL1 is predominantly neuronal. In humans, mutations in ATL1 and ATL3 cause Hereditary Spastic Paraplegia (HSP) and Hereditary Sensory Neuropathy (HSN), respectively. Given the vital role of the ATL proteins in ER network homeostasis and their link to human disease, it is important to understand the respective roles of the paralogs and their regulation. However, while the study of Drosophila ATL has enabled a detailed understanding of the core ATL fusion mechanism, information regarding the human ATL1/2/3 paralogs, has been scant. This has been, in large part, due to a failure to reconstitute membrane fusion by any human paralog in vitro. In a recent breakthrough, our lab successfully reconstituted the fusion activity of all three human ATL paralogs. In the process, we discovered extensive autoinhibitory regulation of ATL1/2 by their variable C-terminal extensions. For ATL2, our preliminary results suggest that the inhibitory C-terminus forms a membrane inserted amphipathic helix that holds ATL2 in an orientation incompatible with fusion. For ATL1, C-terminal autoinhibition is less potent. However, our preliminary results also show that ATL1 both regulates, and is regulated by another HSP protein REEP1. ATL1 promotes membrane tubulation by REEP1, while REEP1 suppresses ATL1 fusion. In addition, a third HSP protein M1-spastin, a microtubule regulator, was reported to activate ATL1 fusion. These findings lead to a hypothesis that the three HSP proteins regulate each other, possibly to coordinate on another's ER structuring function. This proposal seeks to both unravel the autoinhibitory mechanisms controlling ATL1/2 fusion activity in diverse cell types (aim 1), and to test our hypothesis that ATL1, REEP1 and M1-spastin participate in a tripartite network to maintain ER homeostasis in neurons (aim 2).

NIH Research Projects · FY 2026 · 2007-05

This project seeks to enhance the value of the AphasiaBank database and tools for the study of spoken language and communication as used by people with aphasia. We will do this through the introduction of innovative methods for automatic speech recognition, discourse analysis, gesture analysis, corpus analysis, and a new system called collaborative commentary. We will apply these new methods to the analysis of the current database, as well as many new corpora. We will configure these new methods for widespread use by both researchers and clinicians.

NIH Research Projects · FY 2024 · 2007-05

Summary The Child Language Data Exchange System (CHILDES) Project seeks to broaden and deepen our scientific understanding of language development by providing new ways of analyzing real world face-to-face interactions. The computational tools that had been developed in the previous phases of the project constitute the primary methodological basis for new empirical research on the development of spontaneous use of a first language. This work has resulted in over 10,000 published articles examining all aspects of language development, including word learning, sound learning, grammatical development, and communicative development. All of the programs and data sets are provided over the web without charge to researchers. The database that has been collected using these tools is now the largest database on natural spoken language interactions available anywhere. However, we can achieve still greater efficiency and analytic precision by building even more powerful computational tools. The next phase of this project will develop new techniques to support analytic methods in the study of language development. These methods include rapid computer-assisted transcription of interactions, diarization of daylong audio recordings made in the home, automatic analysis of morphological and syntactic structures, a simple user interface for searches, web-based support for collaborative commentary between research groups, construction of standard comparison group norms, and methods for moving data between different programs for alternative analyses. In addition, we will promote the use of the database and programs by constructing web-based tutorials, by improving the current user interface, and by conducting workshops and presentations at conferences.

NIH Research Projects · FY 2026 · 2006-08

This project integrates five NIH-supported components of TalkBank by linking phonological codes from PhonBank, fluency codes from FluencyBank and lexical and grammatical codes from CHILDES, AphasiaBank, and DementiaBank. This integrated database will give us an improved way of studying profiles in various language disorders and types of development.

NIH Research Projects · FY 2024 · 2001-09

SUMMARY Much mental health research uses neurophysiological measurements to describe the way neural activity within and across brain regions is related to behavioral function and dysfunction. One kind of signal, known as a spike train, comes from an individual neuron. Another, the local field potential (LFP), is based on activity from large numbers of neurons within specified parts of the brain. For both kinds of data, scientifically rigorous statistical analysis must accommodate unstable fluctuations, associated with movement or thought, known in statistics as non-stationarity. The continuing research program of this grant is to develop methods for analyzing non-stationary neural data. The number of neural signals that can be recorded simultaneously has been increasing rapidly. Because neural network dysfunction is widely considered to be associated with psychopathology, improvements in recording technologies offer exciting opportunities, but they also create big statistical challenges due to greatly increased complexity. To provide the most useful information for designing novel therapies it is important to characterize the interactions among different parts of the brain, and the timing of these interactions relative to behavior. The research in this grant aims to develop methods for analyzing the ways that a network of brain areas may change with particular variables, including those that help characterize behavior. This involves the transmission of neural information at multiple timescales: slower timescales can provide insight into states of the brain, such as the extent to which a subject is paying attention to a task; fast timescales include oscillations and neural synchrony, which could provide an essential mechanism of neural network information flow and may be a marker that distinguishes normal from diseased states. New methods investigated in this research program can accommodate both faster and slower timescales, and they can also accommodate relationships arising from the spatial configuration of electrodes that record neural signals. Because a neural spike train is a set of times at which a neuron fired, it is common to consider it to be a point process, which is the statistical model set up to handle sequences of event times. The research supported by this grant concerns development and investigation of statistical techniques involving both multi-dimensional continuous time series (for LFPs) and multi-dimensional point processes (for spike trains).

NIH Research Projects · FY 2025 · 1980-08

PROJECT SUMMARY/ABSTRACT Ribosomes are complex ribonucleoprotein particles that catalyze protein synthesis in almost all cells in nature. The long-term goal of this project is to understand how the 80 proteins and four rRNAs comprising eukaryotic ribosomes are assembled in vivo. We use the yeast Saccharomyces cerevisiae to facilitate molecular genetic approaches, and cultured Hela cells to enable us to visualize the nucleolus, the cellular compartment where ribosomes are made. Production of ribosomes is tightly linked to cell growth and proliferation. Consequently, dysregulation of ribosome biogenesis and nucleolar integrity is linked to many diseases such as cancer, neurodegenerative diseases, or developmental disorders. Because pathways of ribosome biogenesis are very conserved, our studies in yeast will help understand mechanisms of regulation and dysregulation of ribosome production in humans. Ribosome biogenesis requires a dynamic series of remodeling steps in which protein and RNA interactions are established and reconfigured. These steps are made more efficient and more accurate by the activities of more than 200 assembly factors present in nascent yeast ribosomes, which are required for their assembly, and conserved across eukaryotes. To enable in-depth studies of mechanisms driving ribosome assembly, we focus on one interval: just prior to, during, and immediately after exit of large ribosomal subunit precursors from the nucleolus into the nucleoplasm. During this stage, several domains of ribosomal RNA are rearranged, numerous assembly factors complete their functions and exit from pre-ribosomes, and new assembly factors enter the particles. We want to learn how these dynamic remodeling steps are powered forward by energy-consuming assembly factors present at this stage. We are also investigating interconnections between ribosome assembly and the nucleolus, the prominent biomolecular condensate thought to be formed through multivalent interactions between pre-ribosomes and other nucleolar components. However, it is not clear exactly how ribosome assembly creates a nucleolus, nor how material properties of the nucleolus enable efficient ribosome assembly. We propose experiments to address the following questions: (1) How do the RNA helicases/ATPases Drs1, Has1, Dbp10, and Spb4 power maturation of pre-60S subunits during mid to late nucleolar stages of assembly? (2) How does the structure and composition of pre- ribosomes enable them to be retained in the nucleolus? (3) How does ribosome assembly contribute to the morphology and fluidity of the nucleolus?