bluuebunny/crossref_metadata_2025_split huggingface dataset:
Interrogating the role of eIF3 on the ribosome and across the transcriptome
Authors: Aitken Colin Echeverría , Yoo Kyungyoon , Stanciu Andrei , Luo Juncheng 
Published: April 2020

Translation initiation is the rate‐limiting and most‐regulated phase of translation. Misregulation of translation initiation has been implicated in myriad maladies, including cancer and neurodegenerative disease. In eukaryotes, initiation is a complex pathway requiring the participation of at least twelve initiation factors (eIFs). Eukaryotic translation initiation factor 3 (eIF3) is the largest and most complex of these factors and appears to participate in events throughout the pathway.In particular, eIF3 is a pivotal player in the recruitment of mRNA to the translation pre‐initiation complex (PIC). Biochemical and genetic studies have identified interactions of eIF3 with the PIC near the mRNA entry and exit channels of the ribosome; structural studies have revealed that eIF3 binds the solvent face of the small (40S) ribosomal subunit, projecting arms into both mRNA channels and ultimately encircling the PIC.These two arms appear to play distinct roles during translation initiation. The exit channel arm has been shown to interact with mRNA sequences 5′ of the AUG and to stabilize mRNA binding at the exit channel of the PIC. While mutations throughout eIF3 disrupt its interaction with the PIC and diminish its ability to accelerate recruitment of a native yeast mRNA, mutations in the entry channel have the most pronounced effects.eIF3 also appears to collaborate with Rps3/uS3 in stabilizing mRNA within the mRNA entry channel. Rps3/uS3 residues previously implicated in the helicase activity of the elongating ribosome stabilize mRNA binding within the ribosomal entry channel and enhance the effects of eIF3 on mRNA binding in both channels. The eIF3i and eIF3g components of the entry‐channel arm also appear to contribute to the PIC‐dependent enhancement of eIF4A ATPase activity. Recent work suggests that eIF4A may function to remodel the mRNA entry channel and thereby promote mRNA recruitment or scanning.Our current work is focused on dissecting the interactions between eIF3, the PIC, and other initiation factors in both the mRNA entry and exit channels, as well as on the inter‐subunit face of the PIC, using both in‐vitro and next‐generation sequencing approaches. In particular, we are exploring the transcriptome‐wide translational effects of depleting or disrupting the eIF3 complex, using ribosome profiling. We observe dramatic decreases in global translation for both eIF3 variants, as well as specific mRNAs whose translation is hypersensitive to each. In both cases, these mRNAs possess longer and more structured 5′ UTRs, consistent with the role of eIF3 in mRNA recruitment and scanning. In parallel, we are investigating the effects of mutations to the 40S protein Rps2 on the PIC:mRNA interaction, as well as how mutations to Rps2 and Rps3 affect the sensitivity of this interaction to mutations within the eIF3 complex.
Morphometric Characterization of Extracellular Vesicles in Adults with Obesity
Authors: Alvarado Herminia Mendivil , Munguia Bibiana Chavez , Millan Elizabeth Carvajal , Hernandez Manuel Hernandez , Teros Veronica Lopez , Moreno Bertha Pacheco , Duran Lucila Rascon , Garcia Humberto Astiazaran 
Published: April 2020

Extracellular vesicles (EVs) are an extracellular communication system. Recently, they have more studied for their function as intercelular communication vehicles and their participation in physiological processes and specific health conditions. However, little is know about the influence of excess weight on their morphometric characteristics. The aim was to characterize populations of extracellular vesicles in adults with obesity and normal weight. Study design was cross‐sectional and subjects were assigned to: group A (n=10) which included participants with obesity (Body Mass Index (BMI)>30 kg/m2), and group B (n=10) included subjects with normal weight (BMI 18 – <25 kg/m2). Subjects were free of co‐morbidities. Weight, height, electrical bioimpedance, and serum lipids were evaluated. EVs were isolated from blood plasma using Invitrogen total exosome isolation reagent. Isolation was later corroborated by detecting the expression of the marker ALIX, an EV‐associated protein by Western blot (WB), and the particle size was assessed using Zetasizer Nano ZS. The isolated EVs were also analyzed by transmission electron microscopy (TEM). We identified two sizes of EVs, that were later classified as exosomes and microvesicles. The characterization of EVs was confirmed with the expression of ALIX and the images of TEM. In subjects from group A, EVs size (65.9 ± 16.1nm) was larger than in those subjects without obesity (42.3 ± 10.7nm), but this was not statistically significant. Body weight and tryglycerides concentration were positively associated (p<0.05) with EVs’ size. The variability in the size of EVs between groups could reflect different composition or maturation level of EVs. The size of EVs is related with state of obesity, also its content could reflect higher risk of developing comorbidities associated with excess weight and nutritional status.Support or Funding InformationThe project was funded by CIAD and MAH received a scholarship from CONACYT.
A Morphometric Analysis of Early Eocene Euprimate Calcanei from Gujarat, India
Authors: Llera Catherine J. , Rose Kenneth D. , Sylvester Adam D. 
Published: April 2020

Postcrania dating back to the early Eocene from the Cambay Shale Formation of Gujarat, India, provide a unique window for understanding early primate behavior. Previous metric analyses of postcrania assigned to Asiadapinae indicate that these primates were generalized arboreal quadrupeds. Examination of long bone cross‐sectional properties, however, complicates the initial behavioral interpretations because it shows that these fossils overlap with primates of differing locomotor behaviors. The purpose of this study is to re‐examine calcaneal morphology of the Indian material in order to refine the locomotor reconstructions of these fossils.Surface models of fossil calcanei (n=6) were generated from micro‐computed tomography scans while those (n=73) representing 23 extant primate species were downloaded from MorphoSource. A weighted spherical harmonics analysis was carried out on the total sample. This morphological analysis represents genus‐zero surfaces using a common set of spherical harmonic functions. The harmonic coefficients associated with each calcaneus serve as shape descriptors that can be summarized via principal components (PC) analysis. Bivariate plots and models representing plus and minus two standard deviations of each PC were created to visualize morphological differences.The first three PCs explain 52.4%, 9.7%, and 9.3% of the morphological variation in the sample respectively (71.4% combined). The first PC differentiates primates with elongated calcanei that are more likely to engage in vertical clinging and leaping, from more quadrupedal primates. The second PC distinguishes calcanei of slow climbers from primates that engage in other forms of locomotion (e.g., leaping and quadrupedalism). Extant primate morphology seems to follow a continuum in which relative anteroposterior calcaneal elongation negatively correlates with slow climber calcaneal morphology. As expected, the calcaneal morphology of Marcgodinotius indicus aligns with that of extant lemuriforms, and most closely resembles that of a generalized arboreal quadruped with some leaping ability. There are two fossils tentatively attributed to Asiadapis cambayensis included in the analysis. One groups with other generalized arboreal quadrupeds, while the other falls outside the range of calcaneal variation observed in extant primates. The outlier does not follow the general pattern of calcaneal morphology observed in extant primates; instead it is characterized by some aspects of slow climber morphology, but with a relative anteroposterior calcaneal elongation. These results may reflect the generalized morphology of this fossil, and consequently the behavior of this primitive euprimate.Support or Funding InformationSupported by NSF DGE‐1746891, National Geographic Society, Leakey Foundation
Translational Study Tracking Dynamic Changes in Cardiac Pattern Variability and Systemic Inflammation in Critically Ill Patients
Authors: Tackett Shiloh , Guo Fei , Clifford Caitlyn , Campanaro Cara , Nethery David , Horton Kofe-Kermit , Fletcher David , Kaffashi Farhad , Hsieh Yee-Hsee , Bonfield Tracey , Loparo Kenneth , Dick Thomas , Jacono Frank 
Published: April 2020

Sepsis is a dynamic complex condition with high patient mortality and health‐care system cost for which the understanding of underlying pathophysiology is still evolving. We hypothesize that pattern variability of centrally controlled physiological rhythms, like cardiac and respiratory rhythms, decreases with an increase in systemic inflammation, such as sepsis. In our lab, we have previously demonstrated in an animal sepsis model that respiratory pattern predictability will increase with disease onset and progression. We describe a complementary IRB approved clinical study, in which physiological waveform data were recorded continuously from consented adult patients (n=43 to date) admitted to the medical intensive care unit (MICU). Serum was collected at intervals determined clinically and subsequently quantified using Luminex assays. The electrocardiogram data was analyzed for heart rate variability (HRV) indices, including Coefficient of Variation, Poincare Plots and Power Spectral Density (high frequency power (HFP)) for the hour preceding and succeeding each serum sampling. Of the 15 patients analyzed, we identified 18 intervals between successive blood draws with a significant change in IL‐6 serum concentration, defined as a 20% relative change accompanied by >20 pg/mL absolute change. In each of the 6 time intervals where IL‐6 was significantly increased there was an associated decrease in HRV and/or HFP. In 12 time intervals IL‐6 decreased; 7 of these were associated with an increase in HRV and/or HFP. Previous studies and our own studies on humans and rats conclude that decreases in the variability, or increases in the predictability, of physiological rhythms correlate to diseased state. Our working hypothesis is that neural inflammation in the brainstem alters central regulation of cardio‐respiratory rhythms and their coupling. As sepsis has had consistent and widespread negative impact on patients, the heath‐care system, and healthcare economy, it is imperative to identify and describe biometrics that serve as early warnings to clinicians.Support or Funding InformationNIH U01 EB021960‐01A1 and VA Research Service Merit Award I01BX004197‐01A1
Oxycodone‐induced Gene adaptations in the brain reward center in a murine Model of Neuropathic pain
Authors: Pryce Kerri D. , Kronman Hope , Ramakrishnan Aarthi , Torres-Berrio Angelica , Polizu Claire D. , Pena Catherine , Shen Li D. , Nestler Eric , Zachariou Venetia 
Published: April 2020

The long‐term use of opioids for the treatment of chronic pain can lead to physical dependence and transition to addiction. Recent studies from our group revealed that chronic neuropathic pain promotes several adaptations in the brain reward regions (Descalzi et al., Sci. Signaling, 2017). Here, we are using Next Generation RNA sequencing and upstream pathway analysis to gain insight on gene expression adaptations triggered by persistent exposure to oxycodone in the presence and in the absence of pain. To this extent, we employed the spared nerve injury model (SNI) of neuropathic pain in adult C57Bl/6 mice and assessed peripheral neuropathy symptoms for 9 weeks. We then applied an oxycodone misuse paradigm, where mice were treated daily with oxycodone for two weeks, and gene expression was monitored three weeks after oxycodone withdrawal. Mice were also assessed for emotional and pain‐related behaviors during the three‐week drug withdrawal period. Oxycodone treatment‐induced thermal hyperalgesia regardless of pain states, while withdrawal produced significant mechanical allodynia and deficits in social interaction. Using RNA Sequencing, we monitored changes in gene expression in the medial prefrontal cortex, the nucleus accumbens, and the ventral tegmental area. Although oxycodone treatment promotes mostly unique transcriptome profiles across brain regions, we observed similar downstream effectors and transcription factors to be affected in pain states when compared with non‐pain states. Furthermore, our findings suggest that chronic pain states exacerbate the behavioral and transcriptomic signatures of oxycodone withdrawal. Overall this work will provide new insights on the influence of long term pain in oxycodone‐induced plasticity in the brain reward center.Support or Funding Information5T32DA007135‐34, NIDA, R01 NS086444, R56 NS111351 NINDS, and P01 DA008227, NIDA
A cellular model of human mesothelium to study the physiology of water transport during peritoneal dialysis and the biocompatibility of innovative glucose‐sparing solutions.
Authors: Procino Giuseppe , Piccapane Francesca , Arduini Arduino , Corciulo Roberto , Carmosino Monica , Gerbino Andrea , Caroppo Rosa , Svelto Maria 
Published: April 2020

The three pore model postulates that the endothelium of peritoneal capillaries is the major limiting barrier regulating water transport across peritoneal membrane during peritoneal dialysis (PD).We hypothesize that the mesothelium may represent an additional selective barrier to water diffusion in PD.We characterized an immortalized cell line of human mesothelium (HMC) to study the functional role of the water channel AQP1 expressed in vivo by mesothelial cells and also to test the biocompatibility of glucose‐sparing PD solutions containing xylitol and carnitine as the main osmotic agents.Transepithelial water transport was measured by TEA+‐sensitive microelectrodes. The biocompatibility of conventional versus innovative PD solutions was evaluated by MTT‐test, measurement of transepithelial electrical resistance (TEER) and production of pro‐inflammatory cytokines.HMCs showed polarized expression of Na+/K+‐ATPase and tight junctions markers but no endogenous expression of AQP1.HMC showed a low TEER compared to renal cells not expressing AQP1. However, the transepithelial water transport was comparable between the two cell types.Experiments in HMCs transfected with AQP1 cDNA, suggest that the water permeability of HMC is strictly dependent of the presence of AQP1.Biocompatibility assays indicate that conventional dialysis solutions with high glucose significantly reduce both cell viability and TEER, and increase pro‐inflammatory cytokines production.Interestingly, innovative PD solutions minimize these effects. These results suggest that the mesothelium may represent an additional selective barrier regulating water transport in PD. Importantly, we also demonstrated that the formulation of glucose‐sparing PD solutions containing xylitol and carnitine better preserve mesothelial cells viability and may represent a useful means to prolong the dialysis life of patients undergoing peritoneal dialysis.Support or Funding InformationApulian Region NATURe project Code: XUANRO4
Bringing 23andMe Into the Human Genetics Classroom
Authors: Smith Emmett M. 
Published: April 2020

Research has shown that using a direct‐to‐consumer (DTC) genetic test in a genetics course enhances student performance (Adams 2016, Linderman 2018, Weber 2015, Weitzel 2016). I incorporated the 23andMe Health+Ancestry kit into my upper‐class undergraduate BIOL351 Human Genetics and Genomics course at Earlham College in 2018. Students opted in and were given informational forms, consent documentation and a list of local genetic counselors (approved by the college IRB, Parker and Grubs 2014). Students were never required to share their personal results in the classroom. Throughout the semester, I identified 23andMe tests that aligned with the disorders we studied. Students were asked to complete a scaffolded assignment about DTC genetic testing companies, beginning with an understanding of 23andMe’s privacy policy, extending to analysis of 11 DTC genetic testing companies’ validity (ranging from
Ancestry.com to Vinome), culminating in the creation and presentation of infographics to the general public in collaboration with our local Joseph Moore Museum. Students responded favorably in course evaluations. Of the 7 evaluations submitted (9 total students), 4 relayed that 23andMe was the most positive part of the course, stating “Seeing my own results … helped broaden my understanding of the subject;” “the 23andMe opportunity was very positive;” “23andMe … helped me to relate more to the material.” Here I present materials and projects that will help you incorporate DTC genetic testing into your own genetics course.Support or Funding InformationEmmett M SmithEarlham College, Richmond IN
Smithem3@earlham.edu
Endocannabinoid hydrolases are differentially distributed in human blood fractions and differentially influenced by thrombin
Authors: Alexander Stephen , O’Sullivan Saoirse , Anajirih Nuha 
Published: April 2020

Plasma levels of the endocannabinoids anandamide and 2‐arachidonoylglycerol have been reported in a number of studies using both humans and laboratory animals, with typically much higher levels of 2‐arachidonoylglycerol than anandamide. In this investigation, we sought to characterize activities of the two primary endocannabinoid hydrolases, fatty acid amide hydrolase (FAAH) and monoacylglycerol lipase (MAGL) responsible for anandamide and 2‐arachidonoylglycerol hydrolysis, respectively, in different fractions from human blood.Following approval from the School of Life Sciences Ethics Committee, University of Nottingham, overnight fasting blood samples were taken in the morning from otherwise healthy volunteers. Blood fractions were isolated, including platelet‐rich plasma, packed erythrocytes (RBC), washed platelets, plasma and serum. Thrombin was employed to trigger clot formation, particularly with RBC and platelet‐rich plasma. Following the generation of a clot, the supernatant layer from a low speed centrifugation, equivalent to serum, was harvested and assayed for endocannabinoid hydrolase activity. The activities of FAAH and MAGL were quantified using both radiometric and ABPP assays.Of the blood fractions examined, MAGL activity was highest in platelets (92 % of the MAGL activity in whole blood), while FAAH activity was highest in RBC. Intriguingly, expressing the FAAH activity of various fractions relative to whole blood summated to 854 %, with RBC constituting 824 % of the whole blood activity. There were no differences between male and female volunteers in the levels and pattern of enzyme activities in the different blood fractions. Assessing enzyme activities from individual donors in these fractions on three visits separated by two week intervals showed no significant differences. The level of FAAH and MAGL activities was relatively stable in washed platelet and RBC samples after being stored in liquid nitrogen, while more than 50 % of their activities were lost after 3 days of storage at −80 °C.Interestingly, FAAH activity was low but detectable, while MAGL was essentially undetectable in serum. Thrombin addition to a washed platelet or RBC fraction caused clot formation within 5 min. FAAH activity in the supernatant fraction following thrombin exposure was much higher from RBC relative to platelets, in accordance with the activities in those fractions. In contrast, the activity of MAGL was significantly reduced in RBC and platelet fractions induced by thrombin compared to nonactivated erythrocytes and platelets, with negligible activities present in the releasate.In summary, we have identified a differential distribution of endocannabinoid hydrolases across different fractions of human blood, and identified the potential for FAAH, but not MAGL, release from RBC and platelets during thrombus formation.Support or Funding InformationFunded by the Saudi Cultural Bureau
Systemic blockade of adenylyl cyclase type 1 (AC1) prevents the recall of extinction memory
Authors: Gonzalez Alexandra , Brust Tarsis , Santini Edwin 
Published: April 2020

Previous transgenic studies have shown that the expression of adenylyl cyclases is necessary for memory consolidation. Studies using genetically modified mice have shown that the expression of the type 1 adenylyl cyclase (AC1) is required for hippocampal‐dependent long‐term memories, including the acquisition of contextual fear conditioning. However, to our knowledge, no pharmacological study has been done to examine the role of AC1 in auditory fear conditioning and extinction. To test the effects of pharmacological inhibition of AC1 during fear extinction, rats were fear conditioned and divided into the control (n=12) and experimental groups (n=12) on day 1. Groups were matched based on equivalent levels of conditioned freezing (p > 0.05). On day 2, rats were injected with vehicle control or the selective AC1 inhibitor, ST034307, prior to extinction training. On day 3, both groups were tested for recall of extinction memory. During extinction training, ST034307‐injected rats showed similar rates of extinction within a session compared to vehicle controls (p > 0.05). However, 24‐hrs later at test, ST034307‐injected rats showed significantly higher levels of conditioned freezing compared to vehicle‐injected rats (p < 0.01). Together these data suggest that AC1 plays a critical role in memory consolation and long‐term recall of fear extinction memory. Based on clinical data, it has been proposed that patients suffering from anxiety disorders, such as post‐traumatic disorder (PTSD) might be deficient in extinction‐related mechanisms. A better understating the role of AC1 might lead to the identification of novel targets for drug pharmacotherapy aimed for the treatment of PTSD.Support or Funding InformationPalm Beach Atlantic University Quality Initiative (QI) Grant to ES; Intergra Connect Faculty Research Grant at Palm Beach Atlantic University to ES; New Investigator Award, American Association of Colleges of Pharmacy to TB