Analyzing Neuronal Dendritic Trees With Convolutional Neural Networks,
2019
Yale University
Analyzing Neuronal Dendritic Trees With Convolutional Neural Networks, Olivier Trottier, Jonathon Howard
Yale Day of Data
In the biological sciences, image analysis software are used to detect, segment or classify a variety of features encountered in living matter. However, the algorithms that accomplish these tasks are often designed for a specific dataset, making them hardly portable to accomplish the same tasks on images of different biological structures. Recently, convolutional neural networks have been used to perform complex image analysis on a multitude of datasets. While applications of these networks abound in the technology industry and computer science, use cases are not as common in the academic sciences. Motivated by the generalizability of neural networks, we aim …
A Three State Model Can Explain The Dynamics Of Class Iv Drosophila Dendritic Tips,
2019
Yale University
A Three State Model Can Explain The Dynamics Of Class Iv Drosophila Dendritic Tips, Sabyasachi Sutradhar
Yale Day of Data
No abstract provided.
Deletion Of Mgr2p Affects The Gating Behavior Of The Tim23 Complex,
2019
CUNY Bernard M Baruch College
Deletion Of Mgr2p Affects The Gating Behavior Of The Tim23 Complex, Oygul Mirzalieva, Shinhye Jeon, Kevin Damri, Ruth Hartke, Layla Drwesh, Keren Demishtein-Zohary, Abdussalam Azem, Cory D. Dunn, Pablo M. Peixoto
Publications and Research
The TIM23 complex is a hub for translocation of preproteins into or across the mitochondrial inner membrane. This dual sorting mechanism is currently being investigated, and in yeast appears to be regulated by a recently discovered subunit, the Mgr2 protein. Deletion of Mgr2p has been found to delay protein translocation into the matrix and accumulation in the inner membrane. This result and other findings suggested that Mgr2p controls the lateral release of inner membrane proteins harboring a stop-transfer signal that follows an N-terminal amino acid signal. However, the mechanism of lateral release is unknown. Here, we used patch clamp electrophysiology …
Development Of Ultrafast Broadband Electronic Sum Frequency Generation For Charge Dynamics At Surfaces And Interfaces,
2019
Utah State University
Development Of Ultrafast Broadband Electronic Sum Frequency Generation For Charge Dynamics At Surfaces And Interfaces, Gang-Hua Deng, Yuqin Qian, Yi Rao
Chemistry and Biochemistry Faculty Publications
Understandings of population and relaxation of charges at surfaces and interfaces are essential to improve charge collection efficiency for energy conversion, catalysis, and photosynthesis. Existing time-resolved surface and interface tools are limited to either under ultrahigh vacuum or in a narrow wavelength region with the loss of spectral information. There lacks an efficient time-resolved surface/interface-specific electronic spectroscopy under ambient conditions for the ultra fast surface/interface dynamics. Here we developed a novel technique for surface/interface-specific broadband electronic sum frequency generation (ESFG). The broadband ESFG was based on a stable two-stage BiB3O6 crystal-based optical parametric amplifier, which generates a …
Co-Cultures Of Oophila Amblystomatis Between Ambystoma Maculatum And Ambystoma Gracile Hosts Show Host-Symbiont Fidelity,
2019
Gettysburg College
Co-Cultures Of Oophila Amblystomatis Between Ambystoma Maculatum And Ambystoma Gracile Hosts Show Host-Symbiont Fidelity, Ryan R. Kerney, Jasper S. Leavitt, Elizabeth M. Hill, Huanjia Zhang, Eunsoo Kim, John Burns
Biology Faculty Publications
A unique symbiosis occurs between embryos of the spotted salamander (Ambystoma maculatum) and a green alga (Oophila amblystomatis). Unlike most vertebrate host-symbiont relationships, which are ectosymbiotic, A. maculatum exhibits both an ecto- and an endo-symbiosis, where some of the green algal cells living inside egg capsules enter embryonic tissues as well as individual salamander cells. Past research has consistently categorized this symbiosis as a mutualism, making this the first example of a “beneficial” microbe entering vertebrate cells. Another closely related species of salamander, Ambystoma gracile, also harbors beneficial Oophila algae in its egg capsules. However, our …
Antisense Oligonucleotides Targeting Angiotensinogen: Insights From Animal Studies,
2019
University of Kentucky
Antisense Oligonucleotides Targeting Angiotensinogen: Insights From Animal Studies, Chia-Hua Wu, Ya Wang, Murong Ma, Adam E. Mullick, Rosanne M. Crooke, Mark J. Graham, Alan Daugherty, Hong S. Lu
Saha Cardiovascular Research Center Faculty Publications
Angiotensinogen (AGT) is the unique substrate of all angiotensin peptides. We review the recent preclinical research of AGT antisense oligonucleotides (ASOs), a rapidly evolving therapeutic approach. The scope of the research findings not only opens doors for potentially new therapeutics of hypertension and many other diseases, but also provides insights into understanding critical physiological and pathophysiological roles mediated by AGT.
Fabrication Of Miniaturized Paper-Based Microfluidic Devices (Micropads),
2019
California Polytechnic State University, San Luis Obispo
Fabrication Of Miniaturized Paper-Based Microfluidic Devices (Micropads), E. Brandon Strong, Spencer A. Schultz, Andres Martinez, Nathaniel W. Martinez
Chemistry and Biochemistry
Microfluidic paper-based analytical devices (microPADs) are emerging as cost-effective and portable platforms for point-of-care assays. A fundamental limitation of microPAD fabrication is the imprecise nature of most methods for patterning paper. The present work demonstrates that paper patterned via wax printing can be miniaturized by treating it with periodate to produce higher-resolution, high-fidelity microPADs. The optimal miniaturization parameters were determined by immersing microPADs in various concentrations of aqueous sodium periodate (NaIO4) for varying lengths of time. This treatment miniaturized microPADs by up to 80% in surface area, depending on the concentration of periodate and length of the reaction …
Differential Binding Of Tetrel-Bonding Bipodal Receptors To Monatomic And Polyatomic Anions,
2019
Utah State University
Differential Binding Of Tetrel-Bonding Bipodal Receptors To Monatomic And Polyatomic Anions, Steve Scheiner
Chemistry and Biochemistry Faculty Publications
Previous work has demonstrated that a bidentate receptor containing a pair of Sn atoms can engage in very strong interactions with halide ions via tetrel bonds. The question that is addressed here concerns the possibility that a receptor of this type might be designed that would preferentially bind a polyatomic over a monatomic anion since the former might better span the distance between the two Sn atoms. The binding of Cl− was thus compared to that of HCOO−, HSO4−, and H2PO4− with a wide variety of bidentate receptors. A pair …
Radiation Dose Estimation By Completely Automated Interpretation Of The Dicentric Chromosome Assay,
2019
The University of Western Ontario
Radiation Dose Estimation By Completely Automated Interpretation Of The Dicentric Chromosome Assay, Peter Rogan, Yanxin Li, Ben Shirley, Ruth Wilkins, Farrah Norton, Joan Knoll
Biochemistry Publications
Accuracy of the automated dicentric chromosome (DC) assay relies on metaphase image selection. This study validates a software framework to find the best image selection models that mitigate inter-sample variability. Evaluation methods to determine model quality include the Poisson goodness-of-fit of DC distributions for each sample, residuals after calibration curve fitting and leave-one-out dose estimation errors. The process iteratively searches a pool of selection model candidates by modifying statistical and filter cut-offs to rank the best candidates according to their respective evaluation scores. Evaluation scores minimize the sum of squared errors relative to the actual radiation dose of the calibration …
Touro College
A Bird's-Eye View Of The Multiple Biochemical Mechanisms That Propel Pathology Of Alzheimer's Disease: Recent Advances And Mechanistic Perspectives On How To Halt The Disease Progression Targeting Multiple Pathways., Caleb Vegh, Kyle Stokes, Dennis Ma, Darcy Wear, Jerome Cohen, Sidhartha D. Ray, Siyaram Pandey
Touro College of Pharmacy (New York) Publications and Research
Neurons consume the highest amount of oxygen, depend on oxidative metabolism for energy, and survive for the lifetime of an individual. Therefore, neurons are vulnerable to death caused by oxidative-stress, accumulation of damaged and dysfunctional proteins and organelles. There is an exponential increase in the number of patients diagnosed with neurodegenerative diseases such as Alzheimer’s (AD) as the number of elderly increases exponentially. Development of AD pathology is a complex phenomenon characterized by neuronal death, accumulation of extracellular amyloid-β plaques and neurofibrillary tangles, and most importantly loss of memory and cognition. These pathologies are most likely caused by mechanisms including …
Regulation Of Respiration And Apoptosis By Cytochrome C Threonine 58 Phosphorylation,
2019
Center for Molecular Medicine and Genetics, Wayne State University School of Medicine
Regulation Of Respiration And Apoptosis By Cytochrome C Threonine 58 Phosphorylation, Junmei Wan, Hasini A. Kalpage, Asmita Vaishnav, Jenney Liu, Icksoo Lee, Gargi Mahapatra, Alice A. Turner, Matthew P. Zurek, Qinqin Ji, Carlos T. Moraes, Maurice-Andre Recanati, Lawrence I. Grossman, Arthur R. Salomon, Brian Fp Edwards, Maik HüTtemann
Biochemistry and Molecular Biology Faculty Publications
Cytochrome c (cytc) is a multifunctional protein, acting as an electron carrier in the electron transport chain (ETC), where it shuttles electrons from bc1 complex to cytochrome c oxidase (COX), and as a trigger of type II apoptosis when released from the mitochondria. We previously showed that cytc is regulated in a highly tissue-specific manner: Cytc isolated from heart, liver, and kidney is phosphorylated on Y97, Y48, and T28, respectively. Here, we have analyzed the effect of a new Cytc phosphorylation site, threonine 58, which we mapped in rat kidney Cytc by mass spectrometry. We generated and overexpressed wild-type, phosphomimetic …
Ultrastructural Analysis Of The Digestive Gland Secretory And Absorptive Processes In Nepenthes Glandulifera,
2019
Connecticut College
Ultrastructural Analysis Of The Digestive Gland Secretory And Absorptive Processes In Nepenthes Glandulifera, Shannon Manuel
Biochemistry, Cellular and Molecular Biology Honors Papers
Nepenthes glandulifera is a carnivorous pitcher plant native to tropical environments, of which the majority live on the islands in the Malay Archipelago where sunlight and water are abundant. The pitcher trap style contains a modified pitfall trap that attracts insects and other small invertebrates through various attractive mechanisms. These plants also contain digestive glands that secrete digestive fluid to break down prey into nutrients for the plant. The digestive fluid, with remarkably unique properties, has been analyzed in relation to multiple areas of study including the development of an enzyme-supplementation strategy for the treatment of celiac disease and the …
Insights Into The Ribosomal, Extra-Ribosomal And Developmental Role Of Rp L13a In Mammalian Model,
2019
Cleveland State University
Insights Into The Ribosomal, Extra-Ribosomal And Developmental Role Of Rp L13a In Mammalian Model, Ravinder Kour
ETD Archive
Ribosomal protein L13a plays an extra-ribosomal function in translational silencing of GAIT (IFN-gamma-activated inhibitor of translation) element bearing mRNAs encoding inflammatory proteins but the underlying molecular mechanism of translational silencing and ribosomal incorporation of L13a remains poorly understood. Also, our laboratory showed that L13a acts as a physiological defense against uncontrolled inflammation in macrophage-specific knockout (KO) mice. However, the consequence of a total knockout of L13a in mammals remains unexplored. Therefore, our current study is focused on (i) identifying the amino acid residue(s) of L13a essential for incorporation and translational silencing of target mRNAs and (ii) studying the consequences of …
Identifying C-Mannosylatedproteins In Raw264.7 Cells Via In Vitro Hsc70 Co-Immunoprecipitation Strategies,
2019
Marshall University
Identifying C-Mannosylatedproteins In Raw264.7 Cells Via In Vitro Hsc70 Co-Immunoprecipitation Strategies, Nicholas Ryan Kegley
Theses, Dissertations and Capstones
C-mannosylation is a specific type of glycosylation in which α-mannose is covalently bound to the C2 atom of a tryptophan via a carbon-carbon bond. Presently, it is known to occur on proteins that contain the W-x-x-W-x-x-W/C motif found within the Thrombospondin Type-1 Repeat (TSR), with ‘x’ denoting any amino acid. C-mannosylation has been implicated in a number of cellular functions, including protein secretion and type I cytokine receptor function. Previous research has shown that exogenous C-mannosylated peptides derived from TSR-containing proteins upregulate the production of the pro-inflammatory cytokine Tumor Necrosis Factor alpha (TNF-α) in RAW264.7 macrophage cells. This upregulation is …
Characterizing The Effects Of Environmental Stressors On The Photosynthetic Capacity Of Chlorella Vulgaris,
2019
Marshall University
Characterizing The Effects Of Environmental Stressors On The Photosynthetic Capacity Of Chlorella Vulgaris, Amanda Louise Smythers
Theses, Dissertations and Capstones
Chlorella vulgaris is a unicellular green algae grown throughout the world. Due to its multiple trophic modes as well as its ability to maintain high rates of growth under adverse conditions, it has been of global interest for use in ecological contamination studies, biofuel feedstock optimization, and studies of photosynthetic electron transfer. Using a wide-range of methods for physiological and photosynthetic characterization, the studies within seek to further extend the usefulness of C. vulgaris in a variety of environmentally important studies. Once the protocols were optimized specifically for this alga, they could be applied in both ecologically relevant and biodiesel …
Isolation And Identification Of Hsc70 Conjugates In Raw264.7 Murine Macrophage-Like Cells,
2019
Marshall University
Isolation And Identification Of Hsc70 Conjugates In Raw264.7 Murine Macrophage-Like Cells, Michael Arland Parsons
Theses, Dissertations and Capstones
IL12R- β2 is a Type I cytokine receptor and contains the WXXW (WSNWS) sequence that often predicates the post-translational addition of mannose to a tryptophan residue via a carbon-carbon bond. This study will stimulate expression of IL12R- β2 in RAW 264.7 Macrophage-Like Cells by shutting down the extracellular signal kinase (ERK) pathway and introducing inflammatory agents lipopolysaccharide and CpG DNA in order to collect a concentrated sample of IL12R- β2. These samples will be analyzed for the presence of C-mannosyltryptophan residue
Method Development For Structural Assessment Of Nanolipoprotein Particles With And Without Cross-Linked Lipids,
2019
University of Oregon
Method Development For Structural Assessment Of Nanolipoprotein Particles With And Without Cross-Linked Lipids, Emma J. Mullen, Wei He, Sean Gilmore, Matthias Frank, Matthew Coleman, Megan Shelby
STAR Program Research Presentations
Membrane proteins make up approximately 30% of the cellular proteome and account for over 60% of pharmaceutical targets.1 Determining the structures of this class of proteins is critical to our understanding of disease states and will advance rational drug design. But membrane proteins have limited solubility, rarely form large crystals that diffract well, and often misfold outside of a bilayer, hindering crystallographic studies.1 Nanolipoprotein particles (NLPs) have arisen as a platform to readily solubilize membrane proteins while mimicking a native lipid environment. NLPs consist of a discoidal phospholipid bilayer encircled by an apolipoprotein belt. In an effort to optimize and …
Development Of Multifunctional Overhauser-Enhanced Magnetic Rresonance Imaging For Concurrent In Vivo Mapping Of Tumor Interstitial Oxygenation, Acidosis And Inorganic Phosphate Concentration,
2019
West Virginia University School of Medicine
Development Of Multifunctional Overhauser-Enhanced Magnetic Rresonance Imaging For Concurrent In Vivo Mapping Of Tumor Interstitial Oxygenation, Acidosis And Inorganic Phosphate Concentration, Artem A. Gorodetskii, Timothy D. Eubank, Benoit Driesschaert, Martin Poncelet, Emily Ellis, Valery V. Khramtsov, Andrey A. Bobko
Faculty & Staff Scholarship
Tumor oxygenation (pO2), acidosis (pH) and interstitial inorganic phosphate concentration (Pi) are important parameters of the malignant behavior of cancer. A noninvasive procedure that enables visualization of these parameters may provide unique information about mechanisms of tumor pathophysiology and provide clues to new treatment targets. In this research, we present a multiparametric imaging method allowing for concurrent mapping of pH, spin probe concentration, pO2, and Pi using a single contrast agent and Overhauser-enhanced magnetic resonance imaging technique. The developed approach was applied to concurrent multifunctional imaging in phantom samples and in vivo in a mouse model of …
Erk3 Negatively Regulates The Il-6/Stat3 Signaling Via Socs3,
2019
Wright State University
Erk3 Negatively Regulates The Il-6/Stat3 Signaling Via Socs3, Astha Shakya
Browse all Theses and Dissertations
Mitogen activated protein kinases (MAPKs) are Ser/Thr kinases that relay the extracellular signal into intracellular responses and regulate several biological responses. They are classified into conventional MAPKs and atypical MAPKs. Extracellular signal regulated kinase 3 (ERK3) is an atypical MAPK that has a single phospho-acceptor site (Ser 189) in its activation motif instead of the canonical Thr-Xaa-Tyr (TXY) motif of conventional MAPK like ERK1/2. ERK3 comprises of a unique C terminal tail and a central C34 domain that further distinguishes it from ERK1/2. Moreover, compared to ERK1/2, much less is known about the upstream activators and the downstream targets of …
Uncovering The Signaling Landscape Controlling Breast Cancer Cell Migration Identifies Novel Metastasis Driver Genes,
2019
Leiden University
Uncovering The Signaling Landscape Controlling Breast Cancer Cell Migration Identifies Novel Metastasis Driver Genes, Esmee Koedoot, Michiel Fokkelman, Vasiliki-Maria Rogkoti, Marcel Smid, Iris Van De Sandt, Hans De Bont, Chantal Pont, Janna E. Klip, Steven Wink, Mieke A. Timmermans, Erik A. C. Wiemer, Peter Stoilov, John A. Foekens, Sylvia E. Le Dévédec, John W. M. Martens, Bob Van De Water
Faculty & Staff Scholarship
Ttriple-negative breast cancer (TNBC) is an aggressive and highly metastatic breast cancer subtype. Enhanced TNBC cell motility is a prerequisite of TNBC cell dissemination. Here, we apply an imaging-based RNAi phenotypic cell migration screen using two highly motile TNBC cell lines (Hs578T and MDA-MB-231) to provide a repository of signaling determinants that functionally drive TNBC cell motility. We have screened ~4,200 target genes individually and discovered 133 and 113 migratory modulators of Hs578T and MDA-MB-231, respectively, which are linked to signaling networks predictive for breast cancer progression. The splicing factors PRPF4B and BUD31 and the transcription factor BPTF are essential …
