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Thakor, N.

Publications and source records attributed to Thakor, N..

6 recordsLinked to original sources

Scalable high-density tactile arenas for measuring ground-contact forces in freely moving animals

Understanding how animals physically interact with their environment is fundamental to studying movement, sensorimotor control, and neurological function. Yet most behavioral measurement systems primarily capture movement and posture, while direct measurements of contact forces often require specialized instrumentation or involve trade-offs among spatial coverage, resolution, and acquisition speed. Here, we introduce a scalable tactile sensing platform that transforms the surface beneath freely moving animals into a high-resolution contact-imaging instrument. By combining modular sensor arrays with adaptive compressive tactile sampling, the platform provides 16,384 tactile sensing elements at 2-mm pitch across a 512 x 128-mm runway, with nominal 1 kHz acquisition. Rather than exhaustively scanning the entire array, the system concentrates measurements around active contacts, enabling high-speed sensing across an extended behavioral surface. Synchronized overhead video and a camera-assisted analysis pipeline enable paw-resolved measurements of contact loading, stance dynamics, footprint morphology, interlimb weight redistribution, and center-of-pressure trajectories. In a longitudinal rat model of sciatic nerve injury, the platform detected reduced loading of the injured hindlimb and increased loading of the contralateral limb, including changes that conventional gait timing measures underestimated. The modular architecture, together with openly available hardware designs, software and data, provides an accessible framework for studying the mechanical interactions underlying freely moving behavior, with potential applications across neuroscience, injury, and motor recovery research.

bioengineering↗

Nanopore Direct RNA Sequencing Enables Reproducible, Site-Resolved Pseudouridine Quantification in Human Ribosomal RNA

Pseudouridine is the most abundant post-transcriptional modification in human ribosomal RNA, with over 110 annotated sites and variable stoichiometry across biological contexts. Existing quantification methods are low-throughput or constrained to predefined panels. We benchmarked nanopore direct RNA sequencing using the Dorado v5.1 model against mass spectrometry-validated sites in human liver tissue, induced pluripotent stem cells, and HeLa cells. Nanopore sequencing detected 95 of 117 validated sites and accurately quantified stoichiometry at 85% of sites with high reproducibility. Low GC-content environments were the primary source of failure. These results establish nanopore sequencing as a scalable tool for epitranscriptomic pseudouridine profiling.

biochemistry↗

Eukaryotic Initiation Factor 5B (eIF5B)-Driven Translational Control Impacts Oral Squamous Cell Carcinoma Pathophysiology

The non-canonical translation of specific mRNAs has been implicated in oncogenesis and cancer progression. We previously identified eukaryotic Initiation Factor 5B (eIF5B) as a key factor in Internal Ribosome Entry Site (IRES)-mediated translation of a subset of mRNAs encoding anti-apoptotic proteins. Here, we demonstrate that EIF5B is predominantly expressed in cancer cells compared to other cell types in the Oral Squamous Cell Carcinoma (OSCC) microenvironment. Higher EIF5B mRNA and protein expression are associated with poor patient outcomes. We show that eIF5B depletion in OSCC cells blunted pro-growth, pro-inflammatory, and pro-angiogenic signaling pathways and significantly increased TNF-related apoptosis-inducing ligand (TRAIL)-induced cell death. This is achieved through decreased translation of mRNAs encoding critical factors associated with OSCC pathophysiology. Importantly, the level of interaction of eIF5B with tRNAiMet was significantly higher in OSCC cells compared to non-cancerous fibroblasts. This suggests that OSCC cells (but not non-cancerous fibroblasts) rely heavily on eIF5B for translation initiation. In an in vivo flank xenograft model using nude mice, eIF5B knockdown in UMSCC-29 cells led to a significant reduction in tumor volume compared to control tumors. Also, the immunohistochemical analysis of the xenografted tumor sections demonstrated decreased staining intensity of critical factors associated with OSCC pathophysiology in eIF5B-depleted tumors relative to controls. Collectively, our data demonstrate that OSCC cells are uniquely dependent on eIF5B-tRNA interactions to sustain translation of pro-survival mRNAs. Targeting eIF5B disrupts these oncogenic programs, sensitizing OSCC cells to apoptosis and suppressing pro-angiogenic and pro-growth signaling.

cancer biology↗

Eukaryotic initiation factor 3F (eIF3F) regulates the IRES-mediated translation of Bcl-xL via its interaction with programmed cell death 4 (PDCD4) protein

Programmed cell death 4 (PDCD4) protein is a well-characterized tumor suppressor protein. PDCD4 inhibits mRNA translation by inhibiting the activity of an RNA helicase, eukaryotic initiation factor 4A (eIF4A). We have previously reported that PDCD4 interacts with the internal ribosome entry site (IRES) element that is found within the 5 untranslated region (UTR) of mRNA encoding B-cell lymphoma extra-large (Bcl-xL) protein. PDCD4s interaction with the Bcl-xL IRES element inhibits the IRES-mediated translation initiation on Bcl-xL mRNA. However, S6 kinase (S6K)-mediated phosphorylation of PDCD4 activates its degradation by proteasomal degradation pathway and derepress IRES-mediated translation initiation of Bcl-xL mRNA. Interestingly, eIF3F (one of the 13 subunits of eIF3) was reported to recruit S6K to phosphorylate eIF3. Therefore, we were intrigued by the possibility of co-regulation of PDCD4 and eIF3F by S6K and the regulation of IRES-mediated translation initiation by PDCD4-eIF3F. To this end, using co-immunoprecipitation (co-IP), we demonstrated that PDCD4 interacts with several subunits of eIF3. Reciprocal co-IP, endogenous IP, and in vitro pull-down assays demonstrated that eIF3F directly interacts with PDCD4 in an RNA-independent manner. In order to functionally characterize the PDCD4-eIF3F complex, we depleted PDCD4 from the glioblastoma (GBM) cells, which resulted in decreased levels of eIF3F. Also, depletion of eIF3F from GBM cells reduced the levels of PDCD4 protein. However, this was not observed in non-cancer cells. Overexpression of PDCD4 resulted in enhanced levels of eIF3F, and vice versa. We further confirmed that the interaction of eIF3F and PDCD4 proteins prevents each others proteasomal degradation. By performing RNA-IP, we showed that PDCD4 and eIF3F interact with Bcl-xL RNA independently. Moreover, our IRES-bi-cistronic reporter assay and polysome profiling experiments demonstrated that eIF3F regulates IRES-mediated translation of Bcl-xL mRNA, likely via its interaction with PDCD4. SignificanceThis study uncovers the fundamental mechanism of the internal ribosome entry site (IRES)- mediated translation regulation of B-cell lymphoma extra-large (Bcl-xL) mRNA by programmed cell death 4 (PDCD4) protein, and the eukaryotic initiation factor 3F (eIF3F). Our results show that PDCD4 and eIF3F interact with each other directly and they also interact with Bcl-xL mRNA independently. We show that PDCD4 works via eIF3F to regulate Bcl-xL levels. We also show that the PDCD4-eIF3F-dependent mechanism of Bcl-xL mRNA translation is implicated in glioblastoma (GBM) cells, including the primary brain tumor stem cells (BTSCs), and would likely affect the GBM pathophysiology.

molecular biology↗

Myomatrix arrays for high-definition muscle recording

Neurons coordinate their activity to produce an astonishing variety of motor behaviors. Our present understanding of motor control has grown rapidly thanks to new methods for recording and analyzing populations of many individual neurons over time. In contrast, current methods for recording the nervous systems actual motor output - the activation of muscle fibers by motor neurons - typically cannot detect the individual electrical events produced by muscle fibers during natural behaviors and scale poorly across species and muscle groups. Here we present a novel class of electrode devices ("Myomatrix arrays") that record muscle activity at unprecedented resolution across muscles and behaviors. High-density, flexible electrode arrays allow for stable recordings from the muscle fibers activated by a single motor neuron, called a "motor unit", during natural behaviors in many species, including mice, rats, primates, songbirds, frogs, and insects. This technology therefore allows the nervous systems motor output to be monitored in unprecedented detail during complex behaviors across species and muscle morphologies. We anticipate that this technology will allow rapid advances in understanding the neural control of behavior and in identifying pathologies of the motor system.

neuroscience↗

Toward Minimally Invasive Therapeutic Ultrasound: Ultrasound-guided Ablation in Neuro-oncology

IntroductionTo improve patient outcomes (eg, reducing blood loss and infection), practitioners have gravitated toward noninvasive and minimally invasive surgeries (MIS), which demand specialized toolkits. Focused ultrasound, for example, facilitates thermal ablation from a distance, thereby reducing injury to surrounding tissue. Focused ultrasound can often be performed noninvasively; however, it is more difficult to carry out in neuro-oncological tumors, as ultrasound is dramatically attenuated while propagating through the skull. This shortcoming has prompted exploration of MIS options for intracranial placement of focused ultrasound probes, such as within the BrainPath (NICO Corporation, Indianapolis, IN). Herein, we present the design, development, and in vitro testing of an image-guided, focused ultrasound prototype designed for use in MIS procedures. This probe can ablate neuro-oncological lesions despite its small size. Materials & MethodsPreliminary prototypes were iteratively designed, built, and tested. The final prototype consisted of three 8-mm-diameter therapeutic elements guided by an imaging probe. Probe functionality was validated on a series of tissue-mimicking phantoms. ResultsLesions were created in tissue-mimicking phantoms with average dimensions of 2.5x1.2x6.5mm and 3.4x3.25x9.36mm after 10- and 30-second sonification, respectively. 30s sonification with 118W power at 50% duty cycle generated a peak temperature of 68{degrees}C. Each ablation was visualized in real time by the built-in imaging probe. ConclusionWe developed and validated an ultrasound-guided focused ultrasound probe for use in MIS procedures. The dimensional constraints of the prototype were designed to reflect those of BrainPath trocars, which are MIS tools used to create atraumatic access to deep-seated brain pathologies. HIGHLIGHTSO_LIAn ultrasound-guided, focused ultrasound prototype was developed and validated C_LIO_LIThe therapeutic transducer (1.5MHz) consisted of three 8-mm circular elements C_LIO_LIElements were placed on a 9x32mm curved rectangular aperture: 45mm radius curvature C_LIO_LIFunctionality was examined on tissue-mimicking phantoms C_LIO_LI2.5x1.2x6.5mm and 3.4x3.25x9.36mm lesions were seen for 10 and 30s sonification C_LI

bioengineering↗