bluuebunny/crossref_metadata_2025_split huggingface dataset:
Disordered regions as regulators of phase transitions in multivalent proteins
Authors: Pappu Rohit V. 
Published: June 2021

This talk will present a synthesis of findings from theory, computation, and experiment highlighting the roles of intrinsically disordered regions as regulators and modulators of phase transitions for linear multivalent proteins. These phase transitions determine the organization, dynamics, and functions of membraneless organelles and other biomolecular condensates. The insights obtained are paving the way for designing condensates with bespoke sequence‐encoded phase behavior and material properties.Support or Funding InformationThis work is supported by the National Science Foundation, the National Institutes of Health, the Human Frontier Science Program, and the St. Jude Children's Research Hospital Research Collaborative.This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Promoting hypothesis‐driven thinking in the undergraduate biochemistry lab
Authors: Craig Paul A. 
Published: June 2021

We have developed a Course‐based Undergraduate Research Experience (CURE), which is built on a combination of traditional wet lab techniques (protein expression, chromatography, electrophoresis, protein and activity assays) and bioinformatics tools (sequence and structure alignment, visualization and molecular docking). Two major factors have led to this project ‐ the initiative of students and the influence of collaborators. Students in our research groups at the Rochester Institute of Technology and Dowling College developed the ProMOL plugin for PyMOL, which enabled us to perform active site alignments between two enzymes. They then enhanced ProMOL to include a library of one thousand enzyme active site templates, which they used to predict functions for unannotated protein structures in the Protein Data Bank. They added sequence and backbone alignments to our bioinformatics approach, then insisted on moving into the wet lab to validate the functions they had predicted. In this process, we saw our students make such remarkable strides as scientists that we decided to replicate this approach in an undergraduate biochemistry teaching lab. The project, which we call BASIL, for Biochemistry Authentic Scientific Inquiry Lab, now involves thirteen faculty members teaching the lab on eight campuses. We are now engaged in a longer term assessment and evaluation of student growth as scientists in this teaching lab setting.Support or Funding InformationThis work is supported by the National Science Foundation under Awards #1503811 and #1709170, the National Institute of General Medical Sciences under Award #78077, and the campuses represented in the BASIL project.This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Selective imaging of internalized proteopathic α‐synuclein seeds in primary neurons reveals mechanistic insight into transmission of synucleinopathies
Authors: Karpowicz Richard J. , Haney Conor M. , Mihaila Tiberiu S. , Sandler Raizel M. , Petersson E. James , Lee Virginia M.‐Y. 
Published: June 2021

Direct cell‐to‐cell transmission of proteopathic alpha‐synuclein (α‐syn) aggregates is thought to underlie the progression of neurodegenerative synucleinopathies. However, the specific intracellular processes governing this transmission remain unclear because currently‐available model systems are limited. For example, in cell culture models of α‐syn–seeded aggregation, it is difficult to discern intracellular from extracellular exogenously applied α‐syn seed species. Herein, we employed fluorescently labeled α‐syn preformed fibrils (pffs) in conjunction with the membrane‐impermeable fluorescence quencher trypan blue to selectively image internalized α‐syn seeds in cultured primary neurons and to quantitatively characterize the concentration dependence, time course, and inhibition of pff uptake. To study the long‐term fates of exogenous α‐syn pffs in neurons, we developed a pff species labeled at amino acid residue 114 with the environmentally insensitive fluorophore BODIPY or the pH‐sensitive dye pHrodo red. We found that pffs are rapidly trafficked along the endolysosomal pathway where most of the material remains for days. We also found that brief pharmacological perturbation of lysosomes shortly after the pff treatment causes aberrations in intracellular processing of pff seeds concomitant with an increased rate of inclusion formation via recruitment of endogenous α‐syn to a relatively small number of exogenous seeds. Our results validate a quantitative assay for pff uptake in primary neurons, implicate lysosomal processing as the major fate of internalized proteopathic seeds, and suggest lysosomal integrity as a significant rate‐determining step in the transmission of α‐syn pathology. Further, lysosomal processing of transmitted seeds may represent a new therapeutic target to combat the spread of synucleinopathies.Support or Funding InformationThis work was supported by funding from the National Institutes of Health (NS053488‐08 to VMYL and NIH NS081033 to EJP), the Ofer Nemirovsky Family Fund, as well as the University of Pennsylvania. Instruments supported by the National Science Foundation include: CD spectrometer (NSF DMR05‐20020) and MALDI MS (NSF MRI‐0820996). CMH is supported by an Age Related Neurodegenerative Disease Training Grant fellowship (NIH T32AG000255).This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Molecular Mechanisms of Enzyme Catalyzed Protein Unfolding and Translocation by Class 1 AAA+ Motors
Authors: Lucius Aaron L. 
Published: June 2021

AAA+ molecular motors involved in protein quality control are at the heart of many biological functions. Here I will discuss our efforts on two model AAA+ driven motors, prokaryotic ClpA and ClpB. ClpA is a hexameric ring motor that uses the energy from ATP binding/hydrolysis to processively translocate a polypeptide substrate through its axial channel for one of two purposes: protein remodeling or ATP dependent proteolysis. When catalyzing proteolysis, ClpA associates with the tetradecameric serine protease, ClpP, to form the ATP dependent protease ClpAP, which is architecturally identical to the 26 S proteasome in humans. ClpB, on the other hand, has the unique ability to disrupt protein aggregates in vivo and does not associate with any known protease. Due to the structural similarity between ClpA and ClpB it has long been proposed that ClpB processively translocates a polypeptide through the axial channel of its hexameric ring structure; as do ClpA and ClpX. However, for ClpB and related enzymes, this has been difficult to show because ClpB does not covalently modify the substrate on which it translocates. We have developed a transient state polypeptide translocation strategy that is sensitive to processive translocation catalyzed by ClpA in the absence of proteolytic degradation catalyzed by ClpP. Using this approach, we have shown that ClpA employs a different molecular mechanism when translocating polypeptide in the absence of the protease vs. when it is associated with the protease. Applying this approach to ClpB, we have shown that ClpB takes, at most, two translocation steps on the polypeptide substrate before rapid dissociation. These results reveal ClpB to be a non‐processive translocase that is not likely to fully translocate a polypeptide through its axial channel during protein disaggregation. These findings and the application of these approaches have broad impact on the examination of many AAA+ molecular motors that do not covalently modify the substrate on which they operate.Support or Funding InformationNSF MCB‐1412624This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Sex Differences in Sympathetic Control of Vascular Tone: Influences of Aging
Authors: Charkoudian Nisha 
Published: June 2021

Reproductive hormones have important non‐reproductive influences on cardiovascular structure and function. In women, these include important effects on the autonomic control of the circulation. Women under the age of 40 tend to have less tonic activity of sympathetic vasoconstrictor nerves in the periphery (usually measured as muscle sympathetic nerve activity), as well as smaller hearts and lower cardiac output compared to men of similar age and health status. Together, these result in a tendency for lower blood pressures in young women, including decreased risk for hypertension, and increased risk of hypotensive disorders such as orthostatic intolerance. Female reproductive hormones (particularly estrogen) appear to contribute to increased functional activity of vascular beta‐2 adrenergic receptors, which offset alpha‐adrenergic vasoconstriction and result in less vasoconstriction for a given amount of sympathetic neural activity (or local norepinephrine), also contributing to the lower blood pressure in young women compared to young men. At menopause, the influences of the hormones decreases, and sex differences are minimized or reversed: sympathetic nerve activity and blood pressure increase to levels similar to, or higher than, those seen in older men. The vasodilator influence of beta‐2 receptors decreases, and sympathetic nerve activity becomes more tightly linked to vasoconstriction and blood pressure. Sympathetic neural activity thus becomes a greater contributor to blood pressure with aging in both men and women, and is a factor in the increased risk of hypertension in older age in both sexes.Support or Funding InformationFunded by USAMRMC; author views not official US Army or DOD policyThis abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Dietary Adaptations of the Feeding Apparatus in Bats
Authors: Santana Sharlene 
Published: June 2021

Diet evolution is considered a major driver of morphological differences and species diversification in mammals, but quantitative tests of morphological adaptation and diversification are scarce. Bats are an ideal system to investigate dietary adaptations; they represent 20% of all mammals, encompass nearly the full spectrum of mammal diets, and have highly diverse cranial morphologies and feeding behaviors. Here, we present research aimed at identifying whether and how the bat feeding apparatus has diversified in conjunction with diet evolution. We combine modern laboratory and field approaches to quantify and map the evolution of skull shape, muscle morphology, and feeding performance across major bat lineages. These methods include: Computed Tomography (CT) scanning and Diffusible Iodine Contrast Enhanced CT scanning, three‐dimensional biomechanical modeling, in vivo bite force measurements, and statistical tests of evolutionary adaptive regimes. With these detailed anatomical and performance datasets, we have been able to identify potential drivers and mechanisms of morphological and functional diversification of the bat feeding apparatus. Analyses of selective regimes indicate that the current diversity of bat skull shapes is best explained by adaptive evolution for both dietary and sensory demands, with striking differences among bats that use different forms of echolocation, or none at all, and among diet specialists. Species that specialize on different diets differ in skull size and shape and in the morphology of their jaw muscles, including physiological cross‐sectional areas, origin and insertion areas, and fiber architecture. Importantly, our biomechanical models indicate that these morphological differences translate into differences in feeding performance metrics that are relevant to food processing, including maximum bite force and gape. For example, for their size, species with a foreshortened rostrum and large temporalis muscles are able to generate high bite forces at the expense of a wide gape, and this allows them to consume tough but relatively small food items. Altogether, these results illuminate the potential drivers and mechanisms of morphological and ecological diversification in bats, and possibly other mammals.Support or Funding InformationNational Science Foundation award 1557125This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Engineering Plant Signal Transduction for Water Smart Crops
Authors: Cutler Sean R. 
Published: June 2021

Plant hormones are a structurally diverse collection of small molecules that control plant growth, development, and environmental responses. Work over the past two decades has established that many plant hormones directly stabilize protein‐protein complexes and act analogously to chemical dimerization agents, which were first described for the immunosuppressants rapamycin, FK506, and cyclosporin. For example, abscisic acid (ABA), which regulates plant transpiration, stabilizes a complex between soluble ABA receptors and downstream phosphatases; the ABA‐induced complex inhibits phosphatase activity, which in turn derepresses downstream kinases and activates signaling. I will describe my lab's work in discovering this intriguing sensing module and our efforts to design both synthetic ABA receptor agonists and engineer receptors with altered ligand binding properties. An unusually large family of receptors encodes ABA receptors and, until recently, it was unclear if selective or pan‐agonists would be required to effectively control plant water use and drought tolerance. Our discovery and characterization of multiple selective agonists resolved this issue and defined the ABA receptor Pyrabactin Resistance 1 (PYR1) and its close relatives as key targets that can be leveraged to control transpiration. I will also describe a new fully orthogonal signaling module that is insulated from endogenous signaling components and controlled by a non‐native agrochemical. This engineered dimerization module provides a simple platform technology for programming crops with agrochemically controlled traits.Support or Funding InformationSupported by NSF (IOS1258175 and 1656890) and Syngenta Crop Protection AG.This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Beyond the Central Dogma: The tRNA epitranscriptome and an alternative genetic code tune translation during stress in eukaryotes, prokaryotes and viral infections
Authors: Dedon Peter 
Published: June 2021

The Central Dogma defines the “what” of biology: genes are transcribed into messenger RNAs that are translated into proteins. But it says nothing about the “when” or “how much” of gene expression. Application of new convergent and data‐driven technologies to the already‐known >150 chemical modifications of DNA, RNA and histone proteins is revealing information‐rich systems for scheduling gene expression ‐‐ the epigenome, the epitranscriptome and the epiproteome. Here we explore one of the newest of these ‐‐ a universal “system of systems” in which the transfer RNA epitranscriptome interacts with an alternative genetic code to fast‐track production of survival proteins during stress in eukaryotes, prokaryotes and viruses. The tRNA molecules themselves are further repurposed as small regulatory RNAs in a system that is only now emerging with the development of new analytical and data mining tools. We will explore examples of the epitranscriptome and small regulatory RNAs in model bacterial and viral pathogens, and in human cells. The components of these systems are now being recognized as drivers of many human diseases and are emerging as new tools for academic and industrial research and development.Support or Funding InformationThis work has been funded by the US National Institutes of Health, the US National Science Foundation, the National Research Foundation of Singapore through the Singapore‐MIT Alliance for Research and Technology, the United States‐Israel Binational Science Foundation, Agilent Technologies and NTUitive.This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Triacylglycerol synthesis, energy metabolism, and glucose homeostasis: A gut reaction?
Authors: Yen C.‐L. Eric , Nelson David , Yen Mei‐I , Amador‐Noguez Daniel , Veldkamp Kelsey 
Published: June 2021

The intestine plays a pivotal role in regulating systemic metabolism. It is the portal and sensor for incoming nutrients and the origin of neural and endocrine signals that determine responses to diet. Importantly, the intestine is the location where host, diet, and gut microbiota interact. We have discovered that acyl CoA:monoacylglycerol acyltransferase 2 (MGAT2) catalyzes triacylglycerol synthesis in enterocytes, mediates fat absorption in the intestine, and regulates whole body energy balance. Mice without a functional gene encoding the enzyme (Mogat2−/−) absorb a normal amount of dietary fat. However, they exhibit delayed fat absorption, altered gut hormone secretion, and increased energy expenditure. As a result, they are resistant to obesity and related metabolic disorders induced by a high‐fat diet. Using tissue‐specific gain‐ and loss‐of‐function models, we showed that intestinal MGAT2 enhances metabolic efficiency and promotes weight gain. When fed a fat‐free diet, Mogat2−/− mice still exhibit increased energy expenditure, suggesting the effects are not limited to calories from fat. Accordingly, MGAT2 deficiency protects the genetically hyperphagic Agouti mouse fed a regular chow from excessive weight gain, hepatic steatosis, and glucose intolerance. We also found that inactivation of MGAT2 in adult mice decreases weight gain and enhances glucose regulation, even in already obese mice. Surprisingly, Mogat2−/− mice are also protected from both chemical and genetic insults to the pancreatic beta‐cells. We hypothesize that loss of MGAT2 may act on beta‐cells through its effect on bile acid‐modifying gut microbiota. Some of these findings and approaches we are taking to test this hypothesis will be discussed in this presentation.Support or Funding InformationWe gratefully acknowledge our funding support from the U.S. National Institutes of Health (DK088210) and U.S. Department of Agriculture (WIS01442).This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
First detailed anatomical study of bonobos exposes bonobos as best model for human‐chimp ancestor and just‐so stories of human evolution, bipedalism and tool use
Authors: Diogo Rui 
Published: June 2021

Just‐so stories are prominent in human evolution literature because of our tendency to create simple progressionist narratives about our ‘special’ place in nature, despite the fact that these stories are almost exclusively based on hard tissue data. How can we be so certain about the evolution of human facial communication, bipedalism, tool use, or speech without detailed knowledge of the internal anatomy of, for instance, one of the two extant species more closely related to us, the bonobos? Here I show how many of these stories now become obsolete, after such a comprehensive knowledge on the anatomy of bonobos and other primates is finally put together. Specifically, each and every muscle that has been long accepted to be ‘uniquely human’ and to provide ‘crucial singular functional adaptations' for our bipedalism, tool use and/or vocal/facial communication, is actually present as a variant or even as normal phenotype in bonobos and/or other apes. Importantly, chimps and in particular bonobos also provide a remarkable case of evolutionary stasis: within >120 head‐neck (HN) and forelimb (FL) muscles, since the chimp‐human split c.8Mya there were only four minor changes in the chimp clade, and all were reversions to the ancestral condition. Outstandingly, since the common chimp‐bonobo split c.2 Mya not even a single change occurred in bonobos, i.e. regarding the HN‐FL musculature bonobos are the best living model for the common chimp‐bonobo LCA and the chimp‐human LCA. The extremely static Pan evolution becomes even clearer when hindlimb data are added: only two muscle absence/presence differences occur between common chimps‐bonobos, and none of these species has muscles not found in other primates. Puzzlingly, there is an evolutionary mosaicism between each of these species and humans. I discuss these data in the context of available genomic information and debates on whether the common chimp‐bonobo divergence is linked to heterochrony, and put these data together with that available for humans and other other primates in order to provide a more comprehensive, and less biased, understanding of primate and human anatomical evolution.Support or Funding InformationThis project has received funding from NSF grants 1516557 and 1440624, as well as an American Association of Anatomists Innovation grant to RDThis abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Structural and Biochemical Investigation of Plant‐Nematode Interactions
Authors: De Santiago Perez Alejandro , Holland Cynthia , Jez Joseph 
Published: June 2021

Chorismate, the branch point metabolite in aromatic amino acid biosynthesis, is synthesized by plants, bacteria, and fungi. In plants, the three aromatic amino acids, phenylalanine, tyrosine, and tryptophan produce several compounds such as plant growth hormone indole‐3‐acetic‐acid (IAA) and the defense compound salicylic acid (SA). Several plant parasitic nematodes, such as Meloidogyne javanica and Heterodera schachtii secrete chorismate mutase (MjCM and HsCM, respectively), an enzyme that converts chorismate to prephenate, during early stages of infection. The secretion of chorismate mutase competes with the plant for chorismate, reducing IAA and SA, and inhibiting the vascularization and formation of roots. A recently discovered Arabidopsis thaliana (thale cress) protein, GH3.7, is capable of conjugating chorismate to cysteine, and may play an important role during nematode infections. Here, we found that wild‐type and gh3.7 plants infected with the pathogenic bacterium Pseudomonas syringae pv. tomato do not show a significant difference in pathogenic susceptibility. Steady‐state kinetic assays determined that the turnover rate and catalytic efficiency of MjCM and HsCM is significantly reduced compared to the chorismate mutases in Arabidopsis thaliana. MjCM and HsCM structural models were generated through computation modeling and most closely resembled Mycobacterium tuberculosis chorismate mutase. The kinetic and structural characterization of nematode chorismate mutase will provide an insight into the molecular machinery used by plants to ward off parasitic infections.Support or Funding InformationThis work was funded by the National Science Foundation and supported by the Howard Hughes Medical Institute.This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.