bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genesis of Antibiotic Resistance XVI: “Role of Lax Regulations on Pharmaceuticals and personal care products (PPCPs) in AR Pandemic” – Antibiotics, and Estradiol are detected in four surface water sites of Edwards Aquifer Authority (EAA), San Antonio, Texas
Authors: Kannan Subburaj , Carrizales Diana , Carrizales Tania , Hernandez Martin , Moody Martin 
Published: November 2023

EAA, Hydrologic Data Report, Report No:14‐02, December 2014 for 2013, for the calendar year 2013 was reviewed regarding the detection of PPCPs. In view of the public sentiments, information pertaining to detection of PPCPs, reported on page 58–59 of the report is presented verbatim: Water samples collected from four surface water sites and four springs were analyzed for PPCPs in 2013. PPCPs compounds were detected in all four surface sites, and none of the spring samples tested positive for PPCP compounds. These detections are in the nanogram per liter (ng/L) range. Detections are summarized by sample site below. Surface Water PPCPs: Blanco River at Wimberley: Trimethoprim—(antibiotic) detected at 5.45 J ng/L ; Cibolo Creek (near the Nature Center in Kendall County): 17a‐Estradiol—(synthetic estrogen hormone) detected at 1.57 J ng/L ; Trimethoprim—(antibiotic) detected at 10.6 ng/L; Triclocarban—(ingredient in antibacterial soaps) detected at 3.95 J ng/L; Sulfamethoxazole— (antibiotic) detected at 391 ng/L ; Triclosan—(ingredient in antibacterial soaps) detected at 9.41 J ng/L ; Frio River at Concan: Diltiazem—(blood pressure medication) detected at 0.997 J ng/L; San Geronimo Creek: 17a‐Estradiol—(synthetic estrogen hormone) detected at 1.27 J ng/L ; Taken together, presence of PPCP in EAA, pose a insurmountable and also a vital contributing factor for development of AR in the consumers. The prospect and scope of lax regulations (in Texas! / United States!) on PPCPs level in water quality analysis and its role in AR pandemic shall be discussed in EB2016. Acknowledgement: http://www.edwardsaquifer.org/scientific‐research‐and‐reports/hydrologic‐data‐reports & Technical Staff of Water Quality – EAA, San Antonio, Texas)Support or Funding InformationProfessional development funds provided by SWTJC to S.Kannan for 2014–2015
Inclusion of Chicken Broth AAC1 as a Dietary Supplement Modulates the Gut Microbiome: Results of Next‐Generation DNA Sequencing
Authors: Hawkins Jordan , Norton Rhy , Durham Paul 
Published: November 2023

ObjectiveThe focus of this study was to characterize shifts in the rodent gut microbiota that occur as a result from the oral administration of the commercial chicken broth formulation AAC1.BackgroundThere is emerging evidence of the importance of maintaining a healthy gut microbiome. Changes in the ratio of the phylum Bacteroidetes to the phylum Firmicutes are associated with various metabolic disorders, obesity, and aging. Diet plays a key role in helping to promote the growth of bacteria that function to modulate inflammation in the gut and other tissues including the nervous system. Although many cultures report the benefit of chicken broth, the effect on the gut microbiome is not well understood.MethodsYoung adult male Sprague‐Dawley rats received 0.5% solid (w/v) AAC1 dissolved in their drinking water for three weeks. Basal fecal samples were collected prior to the inclusion of chicken broth into the diet. An additional control group was included that only received tap water. Fecal samples were collected from each animal at day 0 (basal) and day 21 (end of feeding). Also on day 21, animals were euthanized and caecal samples were collected. Total DNA was extracted and amplified from the V3‐V4 region of the 16S rRNA gene with sample‐specific barcode sequences prior to 454‐pyrosequencing. Returned sequences were assigned taxonomic classification using the SILVA rRNA database. Microbial community analysis was performed using phylogenetic packages in R. Only returned sequences greater than 96% identical to a known, published sequence were included in this analysis.ResultsA phylogenetic analysis of this raw data produced a total of 106 operational taxonomic units. Importantly, AAC1 did not alter the Bacteroidetes: Firmicutes ratio in fecal samples after 21 days while promoting the growth of Proteobacteria. Inclusion of AAC1 in the diet resulted in an increase in several operational taxonomic units including Faecalibacterium, Parasutterella, Morganella, and Oscillospira. In the cecum samples, AAC1 selectively increased expression of Lactobacillus as well as Odoribacter, Gastranaerophilales, Faecalibacterium, Allabaculum, Coprococcus, and Oscillibacter while decreasing the levels of Intestimonas.ConclusionsResults from our study provide evidence that dietary inclusion of AAC1 chicken broth causes a shift in composition of the rodent gut microbiota to increase the percentage of bacteria reported to aid in overall digestive health, decrease inflammation, mitigate the disruptive effects of antibiotics, and reduce the number of sick leave days in adults. Thus, our findings support the notion that AAC1 might be useful as a therapeutic prebiotic.Support or Funding InformationInternational Dehydrated Food
Protein Dynamics Defines Allostery in the Conserved EPK Core
Authors: Ahuja Lalima G , Kornev Alexandr P , McClendon Christopher , Veglia Gianluigi , Taylor Susan 
Published: November 2023

The Eukaryotic Protein Kinases (EPKs) share a conserved hydrophobic core that conceptualizes our understanding of their regulation and catalysis. This EPK core was first described by 12 subdomains, which were later mapped to conserved elements of secondary structure in the EPK core when the first structure of PKA kinase became available. Much biochemistry, thermodynamics and biophysics has been subsequently done on many EPKs since then to explore similarities and differences in their allosteric control. The discovery of the Hydrophobic Spines in recent years has provided a novel tool for understanding both entropy driven allostery and catalysis. Both entropy driven allostery and catalysis are essentially dependent on internal protein dynamics that has been described by NMR as slow motions in the millisecond time frame. Although time and cost intensive, these NMR studies are essential and provide information for residue side chain and main chain dynamics. However, a number of sites in the EPK core evade labeling, and it becomes difficult to study them. To understand these protein dynamics further we have hence ventured into the in‐silico system of Molecular Dynamics simulations that are increasingly providing convincing information on par with NMR details. Our Graph theory methods applied to these simulations have allowed us to define dynamic clusters of residues whose correlated motions define the allosteric network of the EPK core in the PKA catalytic subunit. We call these clusters as ‘Communities’ and the cluster network is defined by a ‘Community Map’. Community maps of PKA at different steps of the catalytic cycle have allowed for dissection of internal protein dynamics that must work alongside catalysis. These community maps also allow for understanding allosteric mutations such as Y204A in PKA that are far from the active site but affect EPK function. Many such sites in EPKs, which remain unexplained, are found to be mutated in cancer genes. These Community maps hence allow for a novel, yet unexplored dynamics‐based criterion for understanding EPK modulation in molecular medicine.Support or Funding InformationNIH grant GM19301 and the Howard Hughes Medical Institute
PKA and Calcineurin Scaffolding on AKAP79: A Small Angle Xray/Neutron Scattering Profile
Authors: Hall James , Copps Jeffrey , Zhang Ping , Heck Albert , Heller William , Blumenthal Don , Taylor Susan 
Published: November 2023

cAMP‐dependent protein kinase (PKA) regulates many cell processes including development, differentiation, and memory. In its resting state, PKA is a tetrameric holoenzyme consisting of a regulatory (R) subunit dimer and two catalytic (C) subunits. Four isoforms of the R‐subunit exist (RIa, RIb, RIIa, and RIIb). Although each isoform varies in sequence and quaternary structure, all share a common domain organization. The strength, duration, and specificity of PKA activity within the cell are mostly dependent upon isoform specific subcellular localization. The D/D domain interface of the R‐subunits serves as a docking site for A Kinase Anchoring Proteins (AKAPs) that target PKA to specific cellular locations. In cardiac myocytes and neurons, PKA is localized to Cav1.2 L‐type calcium channels by AKAP79 and up‐regulates calcium influx by phosphorylating the channel's cytosolic C‐terminal tail. AKAP79 also binds the Ca2+/calmodulin‐dependent protein phosphatase type 2B (PP2B, or calcineurin) at a site very close to that of PKA binding. Given the close proximity of the calcineurin and PKA binding sites on AKAP79, calcineurin has been suggested to play roles in regulation of calcium channels, along with regulation of PKA activity itself. Using a variety of biochemical and biophysical techniques, we have isolated and characterized a stable complex of the C‐terminal tail of AKAP79, RIIb holoenzyme, and calcuneurin (“ARC” for short). We show a stoichiometry of 1:1:1 (AKAP79: RIIb2C2:CN) using native mass spectroscopy, and SAXS/SANS techniques confirm that this is a compact complex, suggesting a close interaction between PKA and calcineurin when bound to AKAP79. Furthermore, we have identified a functional interaction between RIIb and CN using peptide arrays. It involves the flexible linker regions of RIIb including both of LxVP and RRxSV motifs. Altogether, we suggest beyond its function of localizing PKA and CN in close spatial proximity to the Cav1.2 L‐type calcium channel, the ARC signalosome fosters extended protein‐protein interactions and regulations that provide tight spatiotemporal control.Support or Funding InformationSupport for this work was provided through NIH GM034921
An Optogenetic Toolkit for Spatial and Temporal Control of the cAMP Dependent Protein Kinase
Authors: OBanion Colin Padraic , Hughes Robert , Priestman Melanie , Lawrence David 
Published: November 2023

Cellular signaling is highly compartmentalized in both time and space as exemplified by the cyclic adenosine monophosphate (cAMP)/protein kinase A (PKA) pathway. PKA and associated signaling proteins are sequestered to specific subcellular compartments by A‐kinase anchoring proteins to generate distinct signaling microenvironments. These signaling nodes provide spatial specificity to PKA so that this otherwise ubiquitous signaling pathway is only activated in the right location and at the right time. Although many tools are available to manipulate cellular signaling on a global scale, it is difficult to control intracellular signaling with any degree of spatiotemporal resolution. Here, we present a set of optogenetic tools to control PKA signaling at the plasma membrane, cytoskeleton, and outer mitochondrial membrane. We used molecular engineering approaches in conjunction with biochemical and cell biology assays such as western blotting and fluorescent microscopy to show that activation of our optogenetic toolset in cells results in compartment specific PKA phosphorylation events upon stimulation with light, and that activity is localized to discrete locations within the cell using a PKA reporter system generated by our group.Support or Funding InformationThis work is supported by NINDS 1R21NS093617‐01
SIRT3 prevents bleomycin induced lung fibrosis in mice by blocking mitochondrial DNA damage and ROS synthesis
Authors: Bindu Samik 
Published: November 2023

Background and objectiveTissue fibrosis is one of the most critical mechanisms in the pathogenesis of wide range of diseases. Fibrosis is also hallmark of organ dysfunction associated with aging. The process of fibrosis begins with transformation of fibroblast into myofibroblast, a cell which deposits extracellular matrix proteins and contributes to scar formation. Recently a group of NAD‐dependent deacetylases, called sirtuins, have been identified which are capable of regulating variety of cellular processes including extending lifespan of the organism. One of them is SIRT3, which is considered guardian of mitochondria. SIRT3 activation has been shown to ameliorate many aging‐associated diseases including development of metabolic syndrome, heart failure, hearing loss and cancer. SIRT3 activation has been also linked to longevity of the man. This study was undertaken to examine the role of SIRT3 in protecting the lungs from development of fibrosis.Methods and ResultsOne of the most important contributors of tissue fibrosis is activation of transforming growth factor‐β (TGFβ1) signaling. To determine the role of SIRT3 in the induction of fibrosis, we treated human fetal lung fibroblasts (IMR‐90) with TGFβ1 (10ng/ml) for 48 hours. The results showed that there was a significant increase in the expression of fibrotic markers, including smooth muscle alpha‐actin (α‐SMA), type I collagen and fibronectin in TGFβ1 treated cells. TGFβ1 treatment also caused depletion of endogenous SIRT3 levels, which correlated with increased ROS production, DNA damage and subsequent reduction in levels of OGG1, a major DNA glycosylase which hydrolyzes oxidized‐guanine (8‐Oxo‐dG) and protects the DNA from oxidative damage. We also found increased expression of inflammosome markers such as caspase‐1, and IL‐1β in TGFβ1 treated IMR‐90 cells. These changes were blocked when cells were infected with adenovirus expressing wild‐type SIRT3, but not the mutant, thus suggesting the ability of SIRT3 to block transformation of lung fibroblasts to myofibroblasts. To determine the anti‐fibrotic effect of SIRT3 in vivo, we induced lung fibrosis in mice by intra‐tracheal instillation of bleomycin for three weeks. As compared to wild‐type controls, SIRT3‐KO mice showed exacerbated fibrosis after bleomycin treatment, as measured by increased expression of fibrotic marker collagen‐1 and inflammasome marker caspase 1 and subsequent decreased levels of OGG1. However, the transgenic mice having whole body SIRT3 over expression were protected from bleomycin‐induced lung fibrosis.ConclusionThese data demonstrate that loss of mitochondrial SIRT3 promotes transformation of lung fibroblasts to myofibroblasts and development of lung fibrosis. Therefore, SIRT3 activation may be considered a medical therapy for the management of lung fibrosis.Support or Funding InformationThis study was supported by the NIH‐RO1 grants HL117041 and HL111455.
Investigations of Functional Interactions Between Env7 and TOR Complex 1 in Saccharomyces cerevisae
Authors: Shaoulian Jonathan , Gharakhanian Editte 
Published: November 2023

In eukaryotic cells, deficiencies in proteins involved in lysosomal trafficking and function result in serious human disorders like Tay‐Sach's Disease or Alzheimer's. Our lab has identified ENV7, a novel gene involved in the late‐endosome‐to vacuole interface in Saccharomyces cerevisae. ENV7, (a homolog of human STK16) encodes Env7, a vacuolar membrane kinase that negatively regulates vacuolar fusion. Tor1 is another vacuolar membrane kinase, and has been identified as a vacuolar fragmentation factor. Activated Tor Complex 1 (TORC1) stimulates vacuolar fragmentation, as well as cell growth and proliferation. Tor1 and TORC1 are also evolutionarily conserved, and in mammals, hyperactivity of TORC1 plays a major role in cancers. Furthermore, inhibition of TORC1 is associated with the initiation of autophagy, which itself involves a number of fusion events at the vacuole. Because of this, we hypothesized that there is a functional interface between the vacuolar membrane kinases Env7 and Tor1 in TORC1. Here, using confocal microscopy techniques, we report that while the absence of TOR1 is not sufficient to affect the localization of exogenously expressed GFP‐Env7, when TORC1 is inhibited by rapamycin in the same cells, there is a significant mislocalization of the GFP‐Env7 fusion protein to the plasma membrane. Cells of the tor1Δ strain treated by rapamycin also display an enlarged vacuole morphology. Additionally, this enlarged vacuole morphology in tor1Δ seems to be associated with slightly increased levels of autophagy. Therefore, the results thus far suggest a functional interaction between Env7 and TORC1. We are currently investigating the localization of native levels of Env7‐GFP when TORC1 is inhibited by rapamycin. We are also further exploring the TORC1 and Env7 interface by studying additional deletion mutants of TORC1 components.Support or Funding InformationThis project is supported by funding from the NIH (grant SC1 GM112560‐01 to Editte Gharakhanian)
ER‐associated SNAREs are involved in atlastin‐mediated ER membrane fusion
Authors: Lee Miriam , Moon Yeojin , Kim Su Yoon , Jun Youngsoo 
Published: November 2023

The endoplasmic reticulum (ER) is a key player in the maintenance of cellular functions. Its functions are thought to be closely related with its unique structure, which forms a network of sheets and tubules that are maintained by homotypic ER membrane fusion. Although the exact mechanism and players of homotypic ER fusion is yet to be unveiled, the dynamin‐like GTPases of the atlastin family are thought to mediate homotypic ER membrane fusion. In this study, we developed a simple and quantitative in vitro assay using isolated yeast microsomes for measuring yeast atlastin Sey1p‐dependent ER fusion. Using this assay, we found that Sey1p‐mediated ER fusion requires ER SNAREs Sec22p and Sec20p. Consistently, ER fusion was significantly inhibited by Sec18p and Sec17p, which regulate SNARE‐mediated membrane fusion. The physical interaction of Sey1p with Sec22p and Ufe1p, another ER SNARE, further suggested the involvement of SNAREs in Sey1p‐dependent ER fusion. Furthermore, our estimation of the concentration of Sey1p on isolated microsomes, together with the lack of fusion between Sey1p proteoliposomes even with a 25‐fold excess of the physiological concentration of Sey1p, suggests that Sey1p requires additional factors to support ER fusion in vivo. Collectively, our data strongly suggest that SNARE‐mediated membrane fusion is involved in atlastin‐initiated homotypic ER fusion.Support or Funding InformationThis research was supported by grants from the Silver Health Bio Research Center at GIST and the BK21 plus program of Korea.
Purification and characterization of the Drosophila melanogaster (Dm) IKKβ/IKKγ complex
Authors: Rogers William Eric , Huxford Tom 
Published: November 2023

Inhibitor of KappaB Kinase (IKK) is a major regulation point in the activation of innate immunity. The kinase subunit of the complex has undergone extensive study including biophysical and structural characterization. The IKK complex that includes the regulatory subunit has been extremely difficult to study due to its inherent instability, and propensity to aggregate. Analysis of this type of complex in a Dm background has allowed for the purification of a stable single particle containing both the kinase and regulatory subunits. Here we present initial purification and characterization of the in vivo functional IKK complex from Drosophila melanogaster.Support or Funding InformationW.E.R is a recipient of an Arne N. Wick pre‐doctoral research fellowship from the California Metabolic Research Foundation.
Overcoming challenges in the diagnosis of Schistosoma mansoni infections using recombinant protein technology
Authors: Queiroz Rafaella F G , Silva‐Moraes Vanessa , Almeida Nathalie B F , Harn Donald A , Coelho Paulo Marcos Z 
Published: November 2023

Control constraints of Schistosomiasis include the lack of diagnostic methods with high sensitivity. We develop a prospective study in southeast Brazil to standardize new sensitive diagnostic methods for Schistosoma mansoni infection. Currently, we are investigating 6 endemic areas (>1000 individuals with chronic infection) and 84 travelers infected in a freshwater pool (with acute infection). Sera, urine, feces, saliva and spinal cord liquid samples were used for the standardization/validation of innovative methods, including acute, chronic, post‐treatment and myeloradiculopathy schistosomiasis patients. Comparisons are performed with eggs in feces, IgG titers, encephalomyelitis by NMR and clinical symptoms. With our new method using a selected recombinant protein called CCAr, we were able to detect the disease early as 10 days post‐infection and more than 95% of positive cases from chronic and low endemicity areas were obtained. Recombinant protein technology allowed a superior detection method when comparing it to the purified glycoprotein and/or its synthetic peptides. Now, monoclonal antibodies anti‐CCAr are been produced for improvement of the diagnosis by promoting direct diagnosis, together with implementation of large scale recombinant production. Data showed 100% of sensitivity of chronic patients and 98% of acute patients.Support or Funding InformationFapemig, CNPq, Capes, Fiocruz, Fiotec, PDTIS (Brazil). Fulbright, NIH, University of Georgia (USA).
Autophagy regulates the early secretory pathway through interaction between ULK1 and Sec23
Authors: ZHAO Shan , Gan Wenjia , Chan Hsaio Chang , YU Sidney 
Published: November 2023

Autophagy is an autodigestive process that maintains the intracellular homeostasis under starvation. Although it has been intensely studied, how it affects the early secretory pathway has not been well characterized. In this study, we found that autophagy changes the morphology of ER exit sites and causes delay in the export of transport cargo proteins from ER exit sites. The serine/threonine kinase ULK1 is a kinase regulating the activation of autophagy. We found that the morphological and functional changes of ER exit sites are mediated by the phosphorylation of Sec23 by ULK1. This event weakens the interaction between Sec23 and Sec31 but strengthens the binding of Sec23 to Sar1. These results uncover connection between the autophagic pathway and the exocytic pathway such that ULK1 decreases traffic of protein vesicles at the stage of ER exit and such regulation helps save energy for the cells when they are under starvation condition.Support or Funding InformationThis project was supported by Research Grant Council (RGC 14118914)