bluuebunny/crossref_metadata_2025_split huggingface dataset:
Deletion of five senescence‐associated lncRNAs in Saccharomyces cerevisiae
Authors: Krauss Katarzyna , McMurdie Karen , Zappulla David 
Published: November 2023

Telomerase is a ribonucleoprotein composed of a long noncoding RNA (lncRNA), reverse transcriptase, and associated proteins. This enzyme is responsible for maintaining telomere length, and when it is inactive, as in most somatic cells, telomeres gradually shorten, leading to aging and aging‐related illnesses. In contrast, telomerase activity is high in approximately 90% of cancers, allowing for the cells to continuously divide. To better understand the cellular mechanisms surrounding senescence and determine the role that lncRNAs have in this process, RNA sequencing was performed on a strain of Saccharomyces cerevisiae that lacked functional telomerase both during and after senescence, resulting in the identification of 112 novel senescence‐associated lncRNAs. Five of these lncRNAs were further characterized because they were highly conserved among yeast species and appeared to be independently transcribed. Each lncRNA was knocked out in both a diploid and haploid yeast strain, creating ten novel strains. The budding yeast strains were tested at varying temperatures and in the presence of caffeine, which is known to cause telomere shortening, to search for phenotypic responses in these conditions. Future research in this area and in a wider variety of conditions could increase understanding of lncRNAs associated with aging and senescence.Support or Funding InformationFunding for this project was provided by the National Science Foundation REU site award DBI‐1262985
Non‐Coding RNA Regulations in Pseudomonas aeruginosa
Authors: Ammons Mary Cloud B 
Published: November 2023

Bacterial biofilms are the major bioburden contributing to pathogenesis in chronic wounds such as diabetic foot ulcers, pressure ulcers, and veins leg ulcers. Mechanisms of biofilm formation are still under intense investigation and targets of precision therapeutics. Virulence and quorum sensing genes are increasingly appreciated as transcriptionally directed by non‐coding RNAs. Typically associated with eukaryotic regulation, bacterial have recently been appreciated as utilizing ncRNAs for gene and post‐transcriptional regulation. Using a RNseq and bioinformatic approach, we demonstrate significant utilization of ncRNAs in the biofilm phenotype when compared to planktonic cultures in Pseudomonas aeruginosa PAO1 biofilms. Through this analysis and network analysis, we confirm recently identified ncRNA regulation of quorum sensing and virulence factors, was well as identify novel ncRNAs associated with biofilm formation. Specifically, we find ncRNA regulation associated with the metabolic phenotype of P. aeruginosa PAO1 biofilms and confirm the transcriptional regulation of this phenotype through 1H NMR metabolomics profiling.Support or Funding Information5K01GM103821‐041R03AR060995‐0116‐746Q‐MSU‐PG51‐00, a pilot and feasibility award of parent grant 5U54GM104944‐03
What pathological mutants tell us about synuclein aggregation pathways
Authors: Bhumkar Akshay , Gambin Yann , Leitao Andre , Bowden Quill , Giles Nichole , Francois Bill , Hunter Dominic , Boecking Till , Sierecki Emma 
Published: November 2023

Misfolding and pathological aggregation of proteins is a hallmark of many neurodegenerative diseases. α‐synuclein (α‐Syn) is one of the major components of the Lewy bodies associated with Parkinson's disease and other neurodegenerative disorders called synucleinopathies. Mutations in the SNCA gene were the first reported links between familial sporadic Parkinson's disease and perturbations at the molecular level.We compared the behavior of α‐synuclein and five pathological mutants (A30P, E46K, H50Q, G51D and A53T). To gain insights into the aggregagtion behavior of these proteins, we developed a method coupling single molecule detection and cell‐free expression to measure precisely the oligomerisation of proteins, without purification and denaturation steps, in completely undisturbed samples. In these conditions, α‐Syn oligomerisation and aggregation is a rapid process that occurred co‐translationally, at nM concentrations.Surprisingly, the pathogenic mutants segregated into two classes: one group forms large aggregates and fibrils while the other tends to form smaller oligomers and fewer fibrils. Strikingly, co‐expression experiments reveal that members from the different groups tend to not interact with each other, both at the fibril and monomer levels. Further biochemical analyses revealed differences of structure between the aggregates. Therefore, the different mutants could provide access to different species formed along the fibrillation path of α‐Syn.We then examined the effects of a variety of chaperones on the aggregation propensity of the different mutants. This uncovers the specificty of the different chaperones for specific species in the aggregation pathway and identifies new therapeutic targets in Parkinson's disease and multiple sceloris atrophy (MSA).
Dynamic Organellar Maps, a Tool to Study Proteome‐Wide Subcellular Localization Changes
Authors: Itzhak Daniel , Tyanova Stefka , Cox Jürgen , Mann Matthias , Borner Georg 
Published: November 2023

Most biological process involve changes in protein subcellular localization that are critical for cellular function. However, there is currently no method for monitoring such translocation events on a systems‐wide level. We have combined subcellular fractionation with mass‐spectrometry based proteomics in a robust workflow for the reliable determination of protein subcellular localization. Using this method, we have localized ~8,700 proteins in cultured cells to 14 different subcellular compartments, making it the largest repository of human protein subcellular localization of a single system. The method is robust enough to apply the maps comparatively, which we assessed using EGF signaling as a model system. We captured ligand‐induced movement of EGFR from the plasma membrane to the endosome, as well as accompanying known and novel translocation events, validating the method for use in dynamic studies. We then investigated localization changes induced during treatment with several small molecules, leading us to a rapid understanding of the molecular mechanism of these compounds. In conclusion, we have generated an extensive resource for protein subcellular localization, and developed a method for determining protein subcellular localization changes at the proteome‐wide level. This method adds a novel dimension to the systems biologist handbook. It provides a powerful tool in drug discovery, and will also grant unprecedented insights into processes such as cell signaling, trafficking, and cellular differentiation.Support or Funding InformationMax Planck Society
Targeted drug delivery system for ribonuclease A
Authors: Barceló‐Bovea Vanessa Celeste , Griebenow Kai , Cruz‐Montañez Alejandra 
Published: November 2023

Ribonuclease A is a very accessible protein that has been tested as a therapeutic for cancer in vitro and in vivo due to its ability to hinder protein production and induce cell death. However, the results in vivo were only positive when high amounts of enzyme were injected directly in the tumors. To overcome this limitation we are testing the use of a drug delivery system consisting of nanoparticles made out of the protein itself coated with poly(lactic‐co‐glycolic acid)‐poly(ethylene glycol)‐folate conjugates (PLGA‐PEG‐FA), in which the folate moiety confers selectivity towards cells overexpressing folic acid receptors on their membrane. Using a solvent displacement nanoprecipitation method we obtained nanoparticles constituted of ribonuclease A. Nanoparticles obtained under different conditions were analyzed by scanning electron microscope and dynamic light scattering, confirming spherical shape and an average size of 600 nm. The FA‐PEG‐PLGA copolymer to coat the nanoparticles was synthesized by conjugating the free alcohol group in PLGA with the carboxyl group in the folate‐conjugated‐PEG. The structure of the product was confirmed by 1H‐NMR. Experiments for coating optimization are in process and the efficacy of the system will be tested in HeLa cells as well as normal cells to confirm the selectivity. This drug delivery system does not have the limitation of a maximum loading capacity, and has been proven by us to efficiently deliver other proteins to cancer cells. Therefore, it is expected to selectively deliver higher amounts of ribonuclease A to cancer cells than previously reported systems.Support or Funding InformationSupported by the MSRC (Molecular Science Research Center)
Omics approaches for discovery of natural anti‐aging and anti‐cancer compounds and defining mechanisms of their action
Authors: Titorenko Vladimir , Leonov Anna , Arlia‐Ciommo Anthony , Medkour Younes , Svistkova Veronika 
Published: November 2023

Caloric restriction (CR) and dietary restriction (DR) extend lifespan across species and improve health by delaying the onset of age‐related diseases. All currently known anti‐aging chemical compounds (1) mimic lifespan‐extending and health‐improving effects of CR and DR without restricting caloric and nutrient intake; and (2) target signaling pathways that are under the stringent control of calorie and/or nutrient availability. It was believed therefore that all longevity pathways are “adaptable” by nature because they modulate longevity only in response to certain changes in the extracellular and intracellular nutrient and energy status of an organism. However, it is possible that that some longevity pathways could be “constitutive” or “housekeeping” because they control longevity irrespective of calorie and/or nutrient availability. We designed a high‐throughput chemical genetic screen for compounds that increase the lifespan of yeast under CR by modulating such housekeeping pathways. Our screen identified lithocholic acid (LCA) as one of them. Using proteomics, lipidomics, metabolomics and cell biological approaches, we found that LCA delays aging by: (1) remodeling lipid metabolism in the endoplasmic reticulum, lipid droplets and peroxisomes ‐ thereby preventing liponecrotic programmed cell death caused by the age‐related accumulation of fatty acids; (2) remodeling the repertoire of mitochondrial membrane lipids ‐ thereby reducing the number of mitochondria, increasing their size, expanding their cristae, elevating the abundance of respiratory supercomplexes in the inner mitochondrial membrane, and altering the age‐related dynamics of changes in mitochondrial respiration, membrane potential and reactive oxygen species; (3) attenuating age‐related mitochondrial fragmentation ‐ thereby suppressing mitochondria‐controlled apoptosis; and (4) promoting “mitohormesis” through the activation of several stress response‐related processes in mitochondria. Our findings also imply that, in addition to its robust anti‐aging effect, LCA exhibits a potent and selective anti‐tumor effect in cultured human neuroblastoma, glioma, breast cancer and prostate cancer cells by activating both the intrinsic and extrinsic pathways of apoptotic death.Support or Funding InformationSupported by NSERC of Canada.
Skin Preparations from Catfish (Arius bilineatus, Val.) Contain a Lipid Which Inhibits Cancer Cell Survival In Vitro
Authors: Al‐Hassan Jassim M. , Afzal Mohammad , Paul Bincy Maniyalil , Oommen Sosamma , Liu Yuan Fang , Pace‐Asciak Cecil 
Published: November 2023

The Catfish (Arius bilineatus, Val.) secretes a gelatinous substance composed of biochemically active lipids and proteins from its skin upon stress or injury. Preparations from the skin have previously been shown to affect blood clotting, accelerates healing of non‐healing diabetic foot ulcers and relief from neuropathic pain in man1. Chromatographic separation of the crude lipid preparation on silica gel column gave a fraction eluted with chloroform that apoptosed human cancer cell lines (K562 and DU‐145) in vitro, observed IC50 was between 5 – 10 ug/0.1ml/1e4 cells. Identification of the active substance(s) is currently under way.Support or Funding Information(Supported by a grant from Kuwait Foundation for the Advancement of Science No. KFAS 201320701A‐D, and Kuwait University Research Grant No. SL03/14).
Antiproliferative effect of curcumin and kaempferol on colon cancer cells
Authors: Kaverimanian Arjun , Khatwani Natasha , Ezekiel Uthayashanker 
Published: November 2023

Results of epidemiological studies show that people who consume diets rich in phytochemicals (such as individuals living in India) have lower rates of colorectal cancer. Occasional exposure of colonic cells to a single phytochemical may be insignificant in inhibiting growth of cancer cells, whereas regular and repeated exposure of colonic cells to phytochemicals alone or in combination with other phytochemicals may be efficacious in preventing colon cancer. Combinations of phytochemicals may provide additive or synergistic effects and could be a potent way to prevent or eliminate colon cancer initiation and/or progression. The focus of this project was to determine the effect of phytochemicals alone or in combination on cancer cell proliferation. Of interest were curcumin, a phytochemical in turmeric, and kaempferol, a phytochemical in many vegetables, fruits and beans, since they both have been reported to have anti‐cancer potential. Antiproliferative effects of curcumin and kaempferol were assessed using the DLD‐1 colon cancer cell line of epithelial origin. Initial findings indicated that both phytochemicals inhibited proliferation of DLD‐1 cells to varying extents. In particular, curcumin inhibited DLD‐1 proliferation at relatively low concentrations while kaempferol showed a significant antiproliferative effect only at high concentrations. When the concentration of curcumin was kept constant at 12.5 μM (IC50) and concentration of kaempferol was varied, a synergistic anti‐proliferative effect was observed. In fact, even the lowest concentrations of kaempferol combined with curcumin significantly inhibited colon cancer cell proliferation. Results of this study suggest that a combination of curcumin and kaempferol has significant inhibitory effects on proliferation of colon cancer cells.Support or Funding InformationFinancial support for AK, NK and TA was received from the DeNardo Education and Research Foundation.
ENGINEERED FGF‐1 DERIVATIVES LACKING CYSTEINE FOR TREATING CORNEAL ENDOTHELIAL DYSTROPHY
Authors: Eveleth David , Bradshaw Ralph , Blaber Michael 
Published: November 2023

Fibroblast growth factor‐1(FGF‐1) binds and stimulates all members of the FGF class of tyrosine kinase receptors, thus making it a potent agent in tissue regeneration, but its value as a therapeutic is greatly compromised by poor stability and a dependency on heparin as a co‐factor. As the mature form is not exported from cells via the endoplasmic reticulum/Golgi system, its three cysteine residues are all present in reduced form and the presence of these free cysteines limit the biological half‐life of the protein considerably. Substitution of these and other residues has yielded a variety of engineered FGF‐1 derivatives with greatly improved stability and pharmaceutical properties (1), We have tested two of these derivatives, in which the Cys residues have been eliminated, for their ability to stimulate proliferation of corneal endothelial cells as a potential treatment of corneal endothelial dystrophies, such as Fuch's Dystrophy, a condition that leads to the deterioration of the endothelial layer on the back side of the cornea and can only be presently treated effectively by corneal transplants. THX 1011 is a triply substituted derivative in which the Cys at 16, 83 and 117 have been substituted by Val and THX 1114 has the Cys at 16 and 117 changed to Ser and Val, respectively, with the Cys at 83 converted to an internal disulfide bond by mutating the Ala at 66 to Cys. As compared to native FGF‐1 both derivatives were more active stimulators of proliferation of primary cultures of corneal endothelial cells from rabbits or humans with THX 1114 being an order of magnitude more potent than THX 1011. TTHX1011 potently accelerated the regeneration of the corneal endothelium in vivo following cryogenic injury in the rabbit. These data suggest that eFGF‐1s may be a useful therapeutic for corneal endothelial dystrophies.Support or Funding InformationTrefoil Therapeutics LLC
L‐ to D‐ amino acid substitution impacts the cellular penetration activity and the intracellular behavior of the endosomolytic delivery agent dfTAT
Authors: Najjar Kristina , Erazo‐Oliveras Alfredo , Pellois Jean‐Philippe 
Published: November 2023

The plasma membrane acts as a selectively permeable membrane hindering the entrance of large hydrophilic molecules into the cytosolic space of cells. Cell‐penetrating peptides (CPPs) have since been used to internalize macromolecules by using the endocytic pathway as a route of cellular entry. However, only about 1% of endosomal content is released making endosomal entrapment a severe bottleneck in the field of macromolecular delivery. Achieving efficient cytosolic release of macromolecules from endosomes could increase the potential use of CPPs for therapeutic and cell biology applications. In our laboratory, we have generated a peptide L‐dfTAT, derived from the prototypical CPP TAT, which penetrates live cells by escaping from endosomes with a particularly high efficiency. L‐dfTAT can deliver proteins into live cells through a simple co‐incubation protocol and shows no negative impact on cell physiology. L‐dfTAT delivery is efficient however; this peptide is synthesized with L‐amino acids making it susceptible to protease degradation, which could diminish its true cell permeation activity. In this study, we establish the effect of circumventing this issue by substituting L‐ with D‐amino acids, which are protease resistant. We show, D‐dftat is protease resistant and enters cells through a two‐step process similar to L‐dfTAT. D‐dftat impacts endocytic uptake negatively, however endosomal escape is enhanced. Interestingly, D‐dftat severely impacts cellular proliferation rates and has a dramatic effect on the transcriptome when compared to L‐dfTAT. With this, understanding the molecular basis that are required for the endosomolytic activity of L‐dfTAT is of great significance and have not been identified yet. Therefore, this project also focuses on synthesizing, a focused library of peptide analogues based on the L‐dfTAT prototype to establish the structure activity relationships that will facilitate in identifying the molecular features that are required for this efficient endosomolytic and cell permeation activity. This project also lays a foundation for the future design of delivery agents with improved therapeutic significance.Support or Funding InformationThis article was supported by Award Number R01GM110137, R01GM087981 and R01GM087227
Defects in protein O‐mannosylation result in abnormal muscle contractions and aberrant neural sensory feedback in Drosophila
Authors: Panin Vlad , Baker Ryan , Nakamura Nausuke , Lyalin Dmitry 
Published: November 2023

Protein O‐mannosylation pathway is evolutionarily conserved in metazoan organisms. In a wide range of species, from Drosophila to humans, defects in protein O‐mannosylation was found to be associated with abnormal muscle and neural development, as well as postdevelopmental pathologies, including muscle degeneration. In humans, mutations in genes involved in the biosynthesis of O‐mannosyl glycans result in severe muscular dystrophies that are called dystroglycanopathies because of prominent defects in glycosylation and function of Dystroglycan, a cell membrane protein mediating interactions of cells with the extracellular matrix. While recent studies shed more light on important structural features of O‐mannosyl glycans and revealed numerous new targets of O‐mannosylation in mammals, the mechanisms that underlie functions of O‐mannosyl glycans in vivo remain poorly understood. In our study, we focused on elucidating these functions using Drosophila as a model system. Our experiments concentrated on analyses of phenotypes associated with defects in the protein O‐mannosyltransferase (POMT) genes, rotated abdomen (rt) and twisted (tw). We characterized temporal and cell‐specific requirements of POMT genes for normal neuromuscular physiology and proper body posture. Using a combination of genetic, immunofluorescent and live imaging approaches, we unveiled new phenotypes, including defects of embryonic body posture caused by uncoordinated muscle contractions. Our experiments indicated that POMT activity is simultaneously required in muscles and neurons, suggesting that POMT genes affect communication between these cells. We found that coordinated waves of muscle contractions induce rolling behavior, which also suggested an innate chirality of embryo ‐ shell interactions. Our data provided evidence that abnormal protein O‐mannosylation result in a defect of the sensory feedback that controls the pattern of muscle contractions. Our experiments also suggested that peripheral multidendritic neurons play an important role in the pathogenic mechanism of abnormal muscle contractions and the body rotation phenotype. Taken together, our results elucidated in vivo functions mediated by the POMT pathway in Drosophila, which could shed light on potential analogous mechanisms in mammals.Support or Funding InformationThis project was supported in part by NIH/NS075534
Lectin Nucleotide Phosphohydrolases may function as co‐receptors or modulators of several chitin‐based oligosaccharide signaling events in plants
Authors: Etzler Marilynn E. , Roberts Nicholas , Kalsi Gurpreet 
Published: November 2023

Chitin oligosaccharidic signals play important roles in plant defense and the initiation of symbiotic interactions of plants with microorganisms. Two of these symbioses which have great agricultural importance are the symbiosis of arbuscular mycorrhizal fungi with about 80% of land plants that leads to the facilitation of nutrient absorption and the host/strain specific nitrogen‐fixing symbiosis between rhizobial strains of bacteria and leguminous plants. Similarities in structures of the Myc factor and Nod factor signals that initiate these two respective symbioses as well as some common features of the early stages of these symbioses have suggested that the rhizobium‐legume symbiosis may have evolved from the more ancient mycorrhizal symbiosis by gene duplication and divergence. This possibility is supported by our recent transgenic studies in which inhibition of expression of a Nod factor‐binding protein in legume roots inhibited both of these symbioses. The above Nod factor‐binding protein represents a new category of lectins (LNPs) that have both Lectin and Nucleotide Phosphohydrolase activity. These LNPs are members of the apyrase family of enzymes which are found in a wide variety of organisms. Phylogenetic comparisons have shown that the above LNP, (LNP1), represents a unique subcategory of apyrases found in leguminous plants. LNP1 is a peripheral membrane protein localized on the surface of root hairs in the nodulation zone of the root.Using a combination of biochemical, molecular and cell biological techniques we identified a number of other apyrases in the tissues of the legume, Dolichos biflorus, several of which bind to the hog blood group A + H gastric mucin affinity resin used in the isolation of LNP1. We now report the comparison of these LNPs with respect to their structures, carbohydrate‐ and nucleotide‐binding activities and differential expression in the plant. Phylogenetic analysis shows that these other LNPs are not confined to leguminous plants. The data suggest that these LNPs may function as co‐receptors or modulators of other chitin‐related oligosaccharide signaling events found in plants.Support or Funding InformationThis research was supported by NIH Grant GM21882 and by Ceres, Inc.