bluuebunny/crossref_metadata_2025_split huggingface dataset:
Acid‐Base Compensation During Incremental Ascent to High Altitude
Authors: Zouboules Shaelynn M. , Nysten Heidi , Brutsaert Tom , Nysten Cassandra , O'Halloran Ken D. , Steinback Craig D. , Sherpa Mingma , Day Trevor A. 
Published: June 2021

Ascent to high altitude, and the associated hypoxic ventilatory response, imposes an acid‐base challenge, namely chronic hypocapnia and respiratory alkalosis. The kidneys act to compensate for this respiratory alkalosis via bicarbonate (HCO3−) excretion in urine to induce a compensatory metabolic acidosis. Although the importance of renal responsiveness through acid‐base modifications is well‐defined, the time course and extent of plasticity in this response during incremental ascent to altitude is unclear. Thus, we developed a practical index of renal reactivity (RR), indexing the relative change in arterial HCO3− concentration ([HCO3−]a; i.e., response) against the relative change in arterial partial pressure of CO2 (PaCO2; i.e., stimulus) during incremental ascent to high altitude (RR=Δ[HCO3−]a/ΔPaCO2). We sought to assess (1) if RR increased over time and with incremental ascent to high altitude and (2) if RR was correlated with relative changes in arterial pH (ΔpHa) throughout ascent. During ascent to 5160 m over 10 days in the Nepal Himalaya, arterial blood was drawn from the radial artery for measurement of acid‐base variables (Abbott i‐STAT portable blood gas/electrolyte analyzer; CG4+ and CHEM8+ cartridges) in lowlanders at 1045/1400 m (baseline) and at four different altitudes following one‐night sleep: 3440 m (n=18), 3820 m (n=17), 4370 m (n=15) and 5160 m (n=13). At 3820 m (day five of altitude exposure) and higher, RR significantly increased and plateaued in comparison to 3440 m (day three of altitude exposure; P<0.04), suggesting plasticity in renal acid‐base compensation. At all four altitudes, we observed a strong correlation (range: r=−0.71 to −0.98; P<0.001) between RR and relative ΔpHa from baseline, suggesting that the RR index accurately quantified acid‐base responsiveness via renal mechanisms throughout ascent. In conclusion, renal acid‐base compensation mechanisms demonstrate plasticity and a unique time course during incremental ascent to high altitude, which was detected using a novel RR index. The extent of plasticity and plateau in renal responsiveness may predict severity of altitude illness or acclimatization at higher or more prolonged stays at altitude.Support or Funding InformationThis work was supported by (a) Alberta Government Student Temporary Employment Program, (b) Alberta Innovates Health Solutions Summer Studentship, and (c) Natural Sciences and Engineering Research Council of Canada Discovery grant.This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Superior Cervical Ganglionectomy Affects the Cardiorespiratory Network of the In Situ Arterially Perfused Brainstem Preparation
Authors: Kola Gjinovefa , Coffee Gregory A. , Getsy Paulina M. , Dick Thomas E. , Hsieh Yee‐Hsee , Dutschmann Mathias , Lewis Stephen J. 
Published: June 2021

Recently we found that the superior cervical ganglia projects to the nucleus tractus solitarii. Here, we report the effect of superior cervical ganglionectomy (SCGx) on cardiorespiratory activity in the in situ, arterially perfused brainstem preparation. For these studies, we used male Sprague‐Dawley rat pups (P25). Five days after either bilateral removal of superior cervical ganglia (n=14) or sham surgery (n=14), we recorded efferent activities of the phrenic nerve, cervical vagus nerve, and thoracic sympathetic chain and monitored heart rate and perfusion pressure. Baseline cardio‐respiratory patterns were recorded for 10 min to assess differences in patterning between the SCGx and sham groups. Then, we evoked the peripheral chemoreceptor reflex by injecting (intra‐arterially) sodium cyanide (100 μL of a 0.03% solution) and the baroreceptor reflex by increasing perfusion pressure (increasing the speed of the roller pump to its maximum). Baseline respiratory frequency was similar in the SCGx and sham group. However, the SCGx group had a greater but delayed response to chemoreceptor stimulation. Similarly, the SCGx group had a greater response to baroreceptor stimulation. Baseline heart rates (HR) were similar in both groups. For the SCGx group, HR decreased less than sham group during chemoreceptor stimulation; but, decreased more than the sham group during baroreceptor stimulation. Finally, the SCGx group required a greater perfusion pressure (PP) than the sham group during baseline; and had smaller increase in PP during chemoreceptor stimulation. These data indicate that superior cervical ganglia modulate vasomotor tone at rest and buffer cardio‐respiratory responses to chemoreceptor and baroreceptor reflexes.Support or Funding InformationNIH‐SPARC 1OT2OD023860‐02SJLewisThis abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Nutrient Regulation of Signaling and Transcription
Authors: Hart Gerald W. 
Published: June 2021

O‐GlcNAc cycles on and off thousands of nucleocytoplasmic proteins and has extensive crosstalk with protein phosphorylation. O‐GlcNAc cycles on nearly all proteins involved in transcription, where it regulates gene expression in response to nutrients. O‐GlcNAc also regulates the cycling of the TATA‐binding (TBP) protein on and off DNA during the transcription cycle.Targeted, inducible, deletion of the O‐GlcNAc Transferase (OGT) in aCAMKII positive (excitatory) neurons of adult mice results in a morbidly obese mouse with a satiety defect. Thus, O‐GlcNAcylation not only serves as a nutrient sensor in all cells, but also is directly involved in appetite regulation. O‐GlcNAcylation also plays an important role in the trafficking of the AMPA receptors in neurons and in the development of functional synaptic spines. Recent studies have shown that more than one‐half of all human protein kinases are modified by O‐GlcNAc and all kinases that have been tested are indeed regulated in some way by the sugar. Abnormal O‐GlcNAcylation of CAMKII contributes directly to diabetic cardiomyopathy and to arrhythmias associated with diabetes. Prolonged elevation of O‐GlcNAc, as occurs in diabetes, contributes directly to diabetic complications and is a major mechanism of glucose toxicity. Drugs that elevate O‐GlcNAcylation in the brain, which, in‐turn, prevents hyperphosphorylation, appear to be of benefit for the treatment of Alzheimer's disease in animal models. To date, all cancers have elevated O‐GlcNAc cycling, which may play a key role in the regulation of metabolism in cancer cells.Support or Funding InformationSupported by NIH P01HL107153, R01GM116891, R01DK61671, and N01‐HV‐00240. Dr. Hart receives a share of royalty received by the university on sales of the CTD 110.6 antibody, which are managed by JHU.This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Genome‐wide analysis of single nucleotide variants on phosphorylation motifs
Authors: Yoshizaki Hisayoshi , Ling Yiwei , Kohno Miyuki , Okuda Shujiro 
Published: June 2021

In order to conveniently characterize enormous phosphorylation sites, we attempted to summarize them as phosphorylation motifs, extracting the motif structure from the features of the surrounding amino acid sequence of the phosphorylation sites. Approximately 100,000 known phosphorylation sites registered in PhosphoSitePlus (http://www.phosphosite.org) were clustered with the features of amino acids and were organized into about 200 phosphorylation motifs based on the distribution of amino acids in each cluster. The determined motifs were analyzed by signal transduction pathway analysis, GeneOntrogy analysis and comparative evolutionary analysis to determine gene function, signal pathway and physiological importance parameters (Yoshizaki H et al. BMC genomics 2014). In addition, a database was created in which the phosphorylation motifs, motif structures for approximately one million of serine, threonine and tyrosine residues on the human genome, and kinase‐substrate information for kinase prediction were stored (Yoshizaki H Gigascience 2015). Using these data, we investigated associations between cancer‐specific mutations and phosphorylation motifs. Of more than 16 million cancer specific mutations registered in the International Cancer Genome Consortium (ICGC) (https://icgc.org/), about 100,000 mutations were found on the phosphorylation motif sequences with amino acid substitutions. Distributions with these mutations and cancer tissues for these mutations and the evolutionary conservation of each phosphorylation motif were investigated. As a result, it was revealed that the frequency of cancer specific mutagenesis on the phosphorylation motif has a positive correlation with the evolutionary conservation of the motif. In addition, this correlation was not confirmed by healthy subject SNP data. This means that in cancer tissues, mutations tend to accumulate in physiologically important phosphorylation motifs, mutations on the phosphorylation motif in the cancer tissue are not random mutations due to genomic instability, suggesting spontaneously selective mutations. Furthermore, in cancer specific mutations, the position and frequency of mutations in the motif were biased due to the type of phosphorylation motif, and biases in the motif sequence change by amino acid substitution were also observed. Our results suggest that mutations on the phosphorylation motif affect not only the destruction of the motif structure but also the signal disruption due to the appearance of a new motif by amino acid substitution. This study combining tissue specific gene mutation information with our own phosphorylation motif data is expected to lead to predict the effect on canceration by gene mutation, to functionally unknown phosphorylation sites.This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Epigenome‐Wide Association Study of Incident Cardiovascular Disease
Authors: Westerman Kenneth , Ordovas Jose 
Published: June 2021

DNA methylation is an ideal biomarker for many applications, because it has both the stability for prognostic use and the plasticity to be altered by environmental variables including diet. Investigations of relationships between DNA methylation and cardiovascular disease (CVD) have been performed, but these cross‐sectional analyses are susceptible to reverse causation, making causal inference difficult. Thus, we hypothesized that analysis of methylation in large‐scale cohorts with follow‐up for CVD development could provide potential risk biomarkers as well as mechanistic insights into disease risk. We performed an epigenome‐wide association study for incident CVD in individuals from the Framingham Heart Study Offspring Cohort and Women's Health Initiative studies. Methylation data were previously collected from whole blood samples using the Illumina Infinium HumanMethylation450k platform. Cox regression methods were used to identify relationships between relative methylation levels and incident CVD both at specific CpG sites and using a region‐based approach. We identified 10 single CpG sites and 4 regions demonstrating suggestive associations with incident CVD. Mendelian randomization approaches provided preliminary evidence of a causal relationship between methylation within the APOB gene and CVD. Investigations of cell‐type specific relationships using available epigenomic annotations highlighted the importance of monocytes in mediating the risk captured by methylation data in blood. Finally, relationships between these CpG sites and known traditional cardiovascular risk factors were examined to understand how they might interact to increase CVD risk. Based on these results, DNA methylation may provide a useful complement to existing cardiovascular risk prediction methods, and provides insights into genomic processes that may mediate the effects of genetics and environmental factors on disease risk.This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Proteomic profiling of exosomes leads to the identification of novel biomarkers for prostate cancer progression
Authors: Shin Kyeong Jin , Seo Young‐kyo , Yoo Youngbum 
Published: June 2021

Exosomes are vesicles which have garnered interest due to their diagnostic and therapeutic potential. Isolation of cancer‐derived exosomes is a prerequisite for their better understanding. We have investigated a new biomarker for prostate cancer progression via quantitative proteomics. Exosomes from androgen‐independent PC‐3 and the androgen‐dependent LNCaP prostate cancer cells were isolated by ultracentrifugation. After tryptic digestion, proteomic analyses utilized a nanoLC coupled with an LTQ‐Orbitrap operated in tandem MS (MS/MS) mode. Accurate Mass and Time (AMT) tag approach was employed for peptide identification and quantitation. Proteomic characterization showed that 105 proteins from PC‐3 exosomes were 10‐fold higher than those from LNCap. Validation by Western blotting and qRT‐PCR confirmed a higher abundance of PFKL, NRP1 and MCAM(CD146) in PC‐3 cell exosomes, too, indicating that aggressive prostate cancer exhibit higher levels of adhesion or cohesion proteins. We also show that MCAM (CD146) was strongly associated to PC‐3 mobility in vitro. These data provided that MCAM should be useful as a new candidate biomarker for prostate cancer progression.Support or Funding InformationThis work was supported by Basic Science Research Program through the National Research Foundation of Korea (NRF) (OGM4391711)This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
The HUS‐box is required for allosteric regulation of the Sec7 Arf‐GEF
Authors: Halaby Steve , Fromme Chris 
Published: June 2021

The Golgi complex is the central membrane and protein sorting station of eukaryotic cells. Activation of Arf GTPases is essential for vesicle formation via recruitment of cargo adaptors and coat proteins necessary for Golgi trafficking. Arf activation is spatially and temporally regulated by distinct guanine nucleotide exchange factors (GEFs) at different Golgi compartments. The yeast Arf‐GEF Sec7 is a conserved and essential activator of Arf1 at the trans‐Golgi network. Sec7 contains a highly conserved regulatory region, the HUS‐box, with an unknown mechanistic role. In this study we explore how the HUS‐box, which is N‐terminal to the catalytic domain, acts together with C‐terminal regulatory domains in the allosteric activation of Sec7. We show that mutation of the HUS‐box disturbs positive feedback and allosteric activation of Sec7 by the GTPase Ypt31, the yeast Rab11 homolog. Taken together, our data lead to a model in which the inter‐ and intramolecular interactions of the HUS‐box and C‐terminus are necessary for the allosteric activation of Sec7.Support or Funding InformationThis work was supported by NIH/NIGMS award R01GM09861 to J.C.F. and NIH/NIGMS training grant T32GM007273 to S.L.H.This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Structure and function of N‐glycans in cobra venom glycoproteins: Site specific glycosylation for structural stability and terminal sialic acid for target selection
Authors: Chien Kun Yi , Wu Wen Guey , Bui Ba Han , Lin Chien Chu 
Published: June 2021

Snake venoms consist of glycoproteins such as phosphodiesterase (PDE), 5′‐nucleotidase (5NT), L‐amino acid oxidase (LAAO) and snake venom metalloprotease (SVMP) with different degree of glycosylations, but their structures and functions remain largely unknown. We purify these four enzymes from Taiwan cobra (N. atra) venoms and determine their respective glycosylation patterns at peptide level using mass spectrometry. Although the detected N‐glycan structures are diverse with mainly complex and high mannose type, they are found to be site specific. For instance, cobra PDE consists of 7 N‐glycans with 4 high mannose and 3 complex types without detectable sialic acid. In contrast, K‐like SVMP consists of 2 complex type N‐glycans with different degree of sialylations. Additional 3D structural and enzymatic characterizations indicate that the high mannose N‐glycan in PDE maintain the PDE 3D structures while the terminal sialic acid of the complex type glycan in SVMP play a role in target selection of fibrinogen. We conclude that the N‐glycans of snake venom glycoproteins play both structural and functional roles and likely involve in the action mechanism of venom toxicity.Support or Funding InformationMOST, TaiwanThis abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Identification of CRISPR‐Cas9 Mutants in Arabidopsis Glutaredoxin Genes AtGRXS11, AtGRXS6, and AtGRXS3/4/5/7/8 Gene Cluster
Authors: Fernandez Francisco , Sanchez Kassandra , Escobar Matthew 
Published: June 2021

Glutaredoxins are small redox enzymes that use glutathione as a substrate to reduce disulfide bonds in target proteins. Plants have a far greater number of glutaredoxins than other organisms, mostly due to a unique clade of class III glutaredoxins that is exclusively found in higher plants. Previous studies in our lab demonstrated that a small group of class III glutaredoxin genes are strongly upregulated by nitrate in Arabidopsis thaliana, and that RNA silencing of some of these glutaredoxins leads to increased primary root growth. Thus, glutaredoxins appear to link nutrient sensing with plant growth and root system architecture. To further explore this hypothesis, we are using CRISPR‐Cas9 technology to perform targeted mutagenesis of the AtGRXS11, AtGRXS6, and AtGRXS3/4/5/7/8 glutaredoxin genes in A. thaliana. CRISPR vectors have been assembled and utilized for Agrobacterium‐mediated plant transformation. Transgenic plant lines were initially screened by restriction enzyme‐mediated cleavage of glutaredoxin sequences amplified from genomic DNA, demonstrating the loss of restriction sites near presumptive Cas9 cut sites. The presence of small insertion‐deletion mutations in the AtGRXS11 and AtGRXS6 genes was then verified by Sanger sequencing. The AtGRXS3/4/5/7/8 genes are located in a ~10 kb tandem array on A. thaliana chromosome 4, and we have attempted to delete this entire region using two CRISPR guide RNAs that target the flanks of this gene cluster. PCR screening has identified transgenic lines which appear to contain the targeted large‐scale deletion. Because the nitrate‐regulated glutaredoxins appear to be important regulators of primary root growth, this work could have significant broader implications related to important agricultural traits such as root depth (drought tolerance) and nitrogen use efficiency.Support or Funding InformationThis research was supported by NSF RUI‐IOS grant 1651584. We would like to thank the MARC U*STAR Program (NIH GM‐08807) for funding the student researchers Francisco Fernandez, Kassandra SanchezThis abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Reenergized Adoptive Cell Transfer Immunotherapy
Authors: Kaiser Carl , Klestinski Keith , Cui Weiguo , Chang Mika , Cowan Nelson , Smith Sean , Strom Daniel , Strom James 
Published: June 2021

Immunotherapy, in treating solid tumors, has seen increased efficacy due to the development of novel strategies of implementation. One innovative strategy, in development by Dr. Weiguo Cui and his colleagues, combines adoptive cell transfer (ACT) with pathogen‐based vaccine techniques in what is called Reenergized ACT (ReACT). Tumor specific CD8 T‐Cells that already have a tumor specific T‐Cell Receptor (TCR), are genetically modified outside the body to express a second TCR that will recognize a bacterial antigen. These newly created, dual specific T cells, when introduced to mice in combination with intratumoral injection of bacterial vaccine, show a significant decrease in tumor volume than their mono‐specific T‐Cell counterparts. The Marquette High SMART (Students Modeling a Research Topic) Team used 3D printing technology, in partnership with the Milwaukee School of Engineering Center for Biomolecular Modeling, to model the TCR complex in order to study its structure and function to better understand ReACT. TCR is a heterodimeric protein consisting of highly variable alpha and beta chains. Both chains are composed of a variable region and a constant region, both of which form antiparallel beta sheets. The variable region binds to the MHC complex whereas the constant region is near the cell membrane of the T‐cell. The constant domains of the TCR consists of cysteine residues that form disulfide bonds, which form a link between the two chains. Further research into immunotherapy, TCR structure and function, and the implementation of Reenergized ACT has major promise in increasing the efficacy of treating disease in human beings now and in the future to come.Support or Funding InformationWeiguo Cui, MD, PhD at the Blood Research Institute, BloodCenter of Wisconsin & Medical College of WisconsinDiane Muzenmaier at the Milwaukee School of Engineering Center for Biomolecular ModelingThis abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
The Mechanism of RAS nucleotide exchange in the Mitogen Activating Pathway
Authors: Shannon Dan , Hall Ben , Peters Kyle , Glass Jake , Gutzwiller Leah , Buehler Sam , Shirley Connor , Lima Nick , Nassar Nicholas 
Published: June 2021

RAS is a protein that is integral to the mitogen activating pathway (MAP) that controls cell growth and division. Mutations in RAS deregulate the pathway, which can result in cancer. When bound to the substrate GTP, RAS is activated; when bound to the substrate GDP, RAS is deactivated. The substrate bound to RAS catalyzes conformation changes in two switch regions, which coordinate the interaction RAS has with its substrate. To switch between GTP and GDP, RAS requires assistance from other proteins. GEFs activate RAS by exchanging GDP for GTP; GAPs deactivate RAS by assisting in GTP hydrolysis. The Moeller SMART Team in conjunction with MSOE Center for Biomolecular Modeling used 3‐D modeling and printing technology to pinpoint amino acids that play a crucial role in RAS GTP to GDP exchange. Our mentor, Dr. Nicolas Nassar, created RAS mutations and observed the effect they had on RAS. In these mutations, the two switch regions are restructured, which affects the MAP activity. This alters Mg2+ ion coordination and guanine nucleotide stabilization. These mutations also prevent the coordination of the catalytic water molecule responsible for the hydrolysis of GTP. In mutated RAS, GEFs are not able to exchange GDP for GTP. These mutants transform RAS to stay active longer compared to wt‐RAS. By learning about RAS GTP and GDP exchange, Dr. Nassar hopes to dock a small molecule into the binding site of cancerous RAS thus inhibiting the mitogen activating pathway.This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.