bluuebunny/crossref_metadata_2025_split huggingface dataset:
Telomerase holoenzymes
Authors: Collins Kathleen 
Published: May 2022

Telomerase is unusual genome replication machinery. The eukaryotic reverse transcriptase ribonucleoprotein (RNP) supplements telomeric simple‐sequence repeat tracts at chromosome ends by new repeat synthesis. Using each chromosome 3’ end as primer and an internal region of the integral telomerase RNA subunit as template, telomerase reiteratively reverse transcribes its short template into tandem single‐stranded telomeric repeats. Lagging‐strand DNA replication machinery and processing enzymes then create the functional telomere structure of duplex repeats with a 3’ overhang that can be single‐stranded, form alternative DNA structures such as G‐quadruplex, or invade the duplex region to form a displacment loop (D‐loop) of telomeric repeats termed the t‐loop.Two and a half decades of research in the Collins lab led the way to a resolution for several puzzles that were facing the telomere and telomerase field since soon after telomerase discovery by Carol Greider and Elizabeth Blackburn. How do telomerase reverse transcriptase protein (TERT) and telomerase RNA co‐fold in a hierarchical, complex process of cellular telomerase RNP biogenesis, and how does this drastically limit the amount of telomerase made by even the most strongly telomerase‐positive human cancer and stem cells? How can a precisely defined region within telomerase RNA be used as template? How does the template‐product duplex unpair and reform in a different template register to enable processive repeat synthesis? How is telomerase brought to telomeres and how does each telomere control telomerase activity according to its individual length to generate telomere length homeostasis?Human telomerase RNA (hTR) relies on proteins shared with H/ACA‐family small nucleolar RNAs for its processing, stability, and assembly with TERT. Inherited and spontaneous mutations in these H/ACA proteins cause disease syndromes by reducing telomerase function, as do subsequently identified mutations in hTR and TERT. Understanding of how these mutations compromise telomerase function has emerged from new high‐resolution structures of telomerase holoenzymes from the ciliate Tetrahymena thermophila and human cells, the two model systems of Collins lab research, and from understanding control of telomerase function at telomeres.
Methodological Approaches and Considerations for Generating Evidence that Informs the Science of Learning
Authors: Anderson Sarah J. 
Published: May 2022

Educational neuroscience is field with the goal of applying what we know about the brain to improve education through improvements to teaching, learning, assessment, and curricular design. Applying neuroimaging and biometric methodology can help inform this field by understanding the mechanisms underlying a learner’s behaviours and cognitive processing. Advantages of these approaches include the ability to measure more acute or subtle changes that are not always indexed by overt behavioral changes. However, generating evidence that appropriately informs our understanding of the science of learning can be complex. Some of the challenges associated with traditional neuroscientific research protocols in educational research is that they have low ecological validity; neuroscientific tasks are typically short, decontextualized, and isolated while educational research tasks are lengthy, context relevant, and incorporate the complexity of the typical learning environment.I will highlight approaches we have used on our lab to overcome methodological challenges to generate evidence that informs the science of learning. Discussion will focus on four key areas. First, meaningful study design will be addressed using an example of a novice‐expert design examining visual expertise. Second, the importance of appropriately combining multiple data sources (electroencephalography and eye‐tracking) will be discussed and a tool to support data collection will be shared. Third, a data analysis strategy that addresses the problems with time variability during cognitive tasks will be explored. Finally, one of the greatest challenges is to translate findings in a way that informs educational practice. In this case, an example of an evidence‐informed application of research generated through a cycle of basic and applied research will be followed to illustrate the cycle between research and practice in educational neuroscience. Together, this series will inform practical considerations and promote a shared discussion amongst our community for the advancement of educational neurosciences in anatomy education.
Without their Consent: Handling Legacy Collections and Anatomy Teaching Specimens Acquired without Informed Consent
Authors: Geller Pamela L. 
Published: May 2022

Legacy collections have proven invaluable for teaching students about anatomy and standard methods. It is safe to presume, however, that ancient and historic decedents never consented to their inclusion in collections or use as pedagogical tools. A utilitarian position—that the use of these human remains serves a higher scientific purpose—becomes even harder to justify when educators acknowledge the historic necropolitical projects and suffering that underpinned the formation of legacy collections. How then to proceed scholastically with such affective and politically charged human remains?As a complex case study, I consider the Samuel G. Morton Crania Collection. To instruct the medical students who populated his anatomy classes, the Philadelphia physician amassed over 900 crania from 1830 to 1851. After Morton’s death, the Academy of Natural Sciences purchased the collection, where it was all but forgotten. Almost a century later, in 1966, it came under the stewardship of the Penn Museum, its pedagogical purpose resurrected. While Stephen Jay Gould drew attention to the scientific racism of Morton’s research, it was not until the passage of the Native American Graves Protection and Repatriation Act of 1990 that ethical deliberations began in earnest. Here I continue these trains of thought with a discussion of the Afro‐Cuban crania in the Morton Collection.Morton acquired these decedents from his Cuban colleague Dr. José Rodriguez Cisneros in 1840. The latter designated them “negros bozales,” an indicator of their enslaved status and African origins; additional information about tribe and country was not provided. In summer 2020, in the wake of the murder of George Floyd and the racial justice protests his death catalyzed, these skulls erupted into the public consciousness. There were calls to “Return Them All.” I regard this response as well intentioned but also reactionary and unnuanced. To determine if sustained use is viable where consent is inadequate, for this case and more generally, I bring to the fore two concepts: the agentive corpse and ontological insecurity. Both concepts require educators and researchers to culturally contextualize human remains, as well as attend to the dynamic meanings attached to them—by past communities and their living descendants. With this knowledge in hand, I make some tentative recommendations about the fate of these controversial and highly sensitive human remains.
Sexual Dimorphism in Response to Vitamins B3, B9 and B12, Used in Combination, in a Mice Model of Heart Failure Induced by Pressure Overload
Authors: David Chloé , Deschêches Sonia , Bouchard Bertrand , Robillard Isabelle , Shi Yan Fen , Higgins Marie‐Eve , Tardif Jean‐Claude , Ruiz Matthieu 
Published: May 2022

IntroductionHeart failure (HF) is still a major cause of mortality worldwide. HF pathogenesis involves disturbances in cardiac energy metabolism. Studies have shown that preventive treatment with a diet supplemented with vitamins B3 or B9/B12 in experimental models of HF, exhibits beneficial effects on cardiac and mitochondrial functions and improves survival. Therefore, the overall objective of our pilot study is to evaluate the curative benefit of a synthetic diet enriched with vitamins B3 (nicotinamide riboside), B9 and B12 (BVit) in a mouse model of HF based on the hypothesis that this enriched diet is beneficial for cardiac function via an improvement of cardiac metabolism.MethodPressure overload was induced by transverse aortic constriction (TAC) in 8‐week‐old male and female C57Bl6/N mice. Four weeks post‐TAC and according to their cardiac function evaluated by echocardiography, mice were randomised to a BVit‐enriched diet or not and compared to SHAM animals. The criteria of selection for randomisation were as follows: 10% decrease in ejection fraction (EF), 30% increase in left ventricular (LV) mass and an average pressure gradient of 60mmHg. Mice survival was evaluated and cardiac function was assessed by echocardiography every 4 weeks. Blood samples were taken at 8 weeks of treatment in fasted mice (5 hours) for non‐targeted lipidomics mass spectrometry‐based analysis.ResultsOur pilot study show that survival is not improved in males while mortality is reduced in females from 12 weeks of treatment. In males, the reduced EF in the TAC group is not improved by BVit treatment and myocardial hypertrophy, as illustrated by the left ventricular mass (+20% in TAC), is exacerbated with BVit treatment. In contrast, in females, both EF and cardiac hypertrophy were improved (+20% and ‐13% respectively) after 12 weeks of BVit treatment. To better understand the sexual dimorphism in the response of BVit, non‐targeted lipidomics was used on plasma from mice following 8 weeks of treatment. In TAC‐females, compared to their SHAM controls, a decrease in triglycerides (TG) and an increase in choline phospholipids were observed while the lipid profile was normalized with BVit treatment. In TAC‐males vs SHAM, however, TGs were significantly increased and the treatment with BVit exacerbated the lipidomic profile both in terms of TGs and additional lipid species (identification in progress).ConclusionOur pilot study suggests a sexual dimorphism in the response to BVit treatment in experimental HF. Indeed, the benefit of BVit treatment is only shown in females with a delay in the mortality rate associated with improved cardiac function and normalisation of lipid disturbances. To explore and understand the mechanisms underlying this sexual dimorphism, the lipid profile hypothesis appears as a relevant avenue to explore in the future.
Targeting GCN2 Regulation of Amino Acid Homeostasis in Prostate Cancer
Authors: Cordova Ricardo , Misra Jagannath , Amin Parth H. , Damayanti Nur P. , Carlson Kenneth R. , Klunk Angela J. , Mirek Emily T. , Miller Marcus J. , Anthony Tracy G. , Pili Roberto , Wek Ronald C. , Staschke Kirk A. 
Published: May 2022

The Integrated Stress Response (ISR) plays a critical role in the adaptation and survival of tumor cells to exogenous and endogenous stresses. The ISR features four protein kinases (PERK, GCN2, PKR, and HRI), each activated by different stresses, that phosphorylate the eukaryotic translation initiation factor eIF2, resulting in repression of global protein synthesis. Paradoxically, eIF2 phosphorylation also enhances translation of select gene transcripts, including the transcription factor ATF4, which is central for ISR‐directed gene transcription. Therefore, the ISR directs translational and transcriptional control that is critical for cancer stress adaptation. Moreover, eIF2 phosphorylation and ATF4 have recently been suggested to play a role in prostate cancer (PCa) growth and survival; however, the specific function of ISR kinases, their mode of activation, and the mechanisms by which the ISR facilitate PCa progression are unknown.We discovered that GCN2 is activated in a range of PCa cell lines, contributing to enhanced eIF2 phosphorylation and ATF4 expression. Genetic or pharmacological inhibition of GCN2 reduces growth in androgen‐sensitive and castration‐resistant PCa cell lines in culture and cell line‐derived and patient‐derived xenograft mouse models in vivo. Induction of GCN2 is accompanied by limitations of select amino acids and accumulation of cognate tRNAs that are reported to be activators of GCN2.A transcriptome analysis of PCa cells treated with a specific GCN2 small molecular inhibitor indicates that GCN2 is critical for expression of SLCgenes involved in metabolite transport. We found that GCN2 inhibition decreases intracellular amino acid levels accounting for reduced growth in PCa cells. Using CRISPR‐based phenotypic screens and genome‐wide gene expression analyses of wild‐type and GCN2‐depleted PCa cells, we confirmed the importance of the transporter genes in PCa fitness. One transporter, SLC3A2 (4F2), is induced by GCN2 and is essential for PCa proliferation. SLC3A2 engages with many nutrient transporters, allowing for their localization to the plasma membrane. Importantly, expression of SLC3A2 reduced GCN2 activation and rescued decreased amino acid levels and growth inhibition due to loss of GCN2.Our results indicate that select amino acid limitations activate GCN2 in PCa, resulting in the upregulation of key amino acid transporters, including 4F2 (SLC3A2), which provide for nutrient import to facilitate protein synthesis and metabolism required for PCa progression. We conclude that GCN2 and the ISR are promising therapeutic targets for both androgen‐sensitive and castration‐resistant prostate cancer.
Adaptation of Native GELFrEE for HDL Particle Size Subtype Separation and Differential Apolipoprotein Proteoform Quantification
Authors: DiStefano Nicholas , Lloyd‐Jones Cameron , Seckler Henrique , Compton Philip , Sniderman Allan , Kelleher Neil , Wilkins John 
Published: May 2022

High‐density lipoproteins (HDL) are central to cholesterol transport, and higher concentration of HDL‐bound cholesterol (HDL‐C) is associated with lower coronary artery disease (CAD) risk. Recent reports refute a causal link between these variables, suggesting better understanding of HDL variation is necessary. HDL particles differ in size and size subtypes differ in proteome, lipidome, and functional characteristics. Apolipoprotein A‐I (ApoA‐I), a major determinant of HDL structure and biochemistry, is made up of 15 distinct proteoforms. ApoA‐I proteoforms correlate with HDL efflux, a measure of cholesterol transport efficiency, but it is unknown if ApoA‐I proteoforms vary with HDL particle size. Herein, we adapt a native separation methodology to inquire on the relationship between HDL size subtypes, their function, and apolipoprotein proteoform profiles.Pooled serum (20μl) from 30 individuals with high, medium and low HDL‐C levels, were loaded to CN‐GELFrEE, a native electrophoretic technique, to separate HDL particles by size. Mid‐resolution and high‐resolution modes were employed. Immunoassays were done to characterize ApoA‐I content and average particle size of the electrophoretic fractions. Proteoform quantification was performed on ApoA‐I‐containing fractions by top‐down LC‐MS. SIM scans were devised for higher sensitivity in ApoA‐I proteoform detection. Custom software matched, scored and quantified proteoform‐specific spectra, and calculated association to particle size.In both resolution modes, average fraction sizes were roughly linearly correlated to fraction collection time, and size‐range overlap between fractions was small. In mid‐resolution mode 3‐4 fractions contained ApoA‐I, while high‐resolution mode yielded 36 distinct HDL size fractions. Fractions roughly spanned the range between 5 to 11nm, similar to previously reported ranges for HDL particles.Proteoform quantification revealed significant variation of proteoform profiles in different size‐ranges of HDL. Fatty‐acylated ApoA‐I, a species previously correlated to higher cholesterol efflux, had higher relative abundance (~1.5x to 2x) in the pre‐beta‐1 (5‐7.1nm) and alpha‐3 (9‐11nm) size ranges of HDL, while glycated and oxidized proteoforms were significantly more abundant (~3x to 4x) in the medium size ranges (alpha‐4, alpha‐3 and alpha‐2). Interestingly, the truncated proteoform of ApoA‐I had no significant differences in abundance between different particle sizes.Our experimental data suggest that the profile of ApoA‐I proteoforms in HDL particles is size‐dependent and thus ApoA‐I proteoforms may be important markers or mediators of HDL size regulation. Notably, the differences in PTM prevalence from medium sizes to large and pre‐beta subtypes may be markers of the pathway of HDL maturation and/or different functions of each subtype.
Biological Evaluation of 3‐Aryl‐4‐indolylfuranones as potential anti‐cancer agents
Authors: Mowery Patricia , Dexter Molly S. , Hermann Andrew , Hurysz Brianna , Manning Maegan , McNulty Matthew , Pierce Kelsey 
Published: May 2022

The American Cancer Society estimates that this year there will be approximately 1.9 million new cases of cancer and nearly 610,000 cancer‐related deaths. The need for new and innovative anticancer drugs is increasingly crucial. One attractive anti‐cancer target is tubulin, which is involved in many cellular functions including cell shape, mitosis, migration, and movement of organelles. While anti‐tubulin drugs have been used to treat cancer for ~70 years, they tend to be complex molecules (derived from natural products), plus suffer from multi‐drug resistance, low solubility, toxicity issues, and/or the lack of multi‐cancer efficacy. These limitations highlight the continued need for the discovery and development of new and novel drugs to enter the pipeline, especially with the significant increase in understanding of tubulin and the mode of action of inhibitors.Using an interdisciplinary approach with undergraduate researchers, we previously developed a furanone‐containing small molecule, PY‐407‐C. The compound demonstrated strong (sub‐micromolar) anti‐proliferative activity in U937 cancer cells. It was submitted for NCI‐60 (National Cancer Institute) screening, which showed nanomolar activity against a variety of cell lines with tubulin as the potential target. We confirmed that it inhibited tubulin polymerization in vitro. We now report on a suite of compounds that are regioisomers of PY‐407‐C and with various moiety modifications. This work has identified new compounds with strong cytotoxicity and important structure‐function information. Overall, these studies provide basic research on small molecule inhibitors of cancer.
Investigating Mitochondrial Dysfunction in Barth Syndrome
Authors: Sniezek Olivia L. , Anzmann Arianna , Senoo Nanami , Butschek Grant , Claypool Steven , Vernon Hilary 
Published: May 2022

Barth syndrome (BTHS) is a rare, X‐linked disorder of mitochondrial phospholipid metabolism caused by variants in the gene TAFAZZIN.TAFAZZIN is a transacylase involved in the remodeling of cardiolipin (CL), a dimeric phospholipid localized to the inner mitochondrial membrane. Lack of TAFAZZIN‐based remodeling results in irregular cardiolipin content, characterized by increased unremodeled CL, increased monoloysocardiolipin (the CL remodeling intermediate), and a decrease in remodeled CL, which is enriched in polyunsaturated fatty acyl chains that are tissue‐specific in composition. BTHS is clinically characterized by cardiomyopathy, neutropenia, and myopathy, with a high morbidity and mortality. There are no approved disease‐specific therapies.To investigate the cellular pathology and to identify new areas of potential therapeutic intervention, we developed two CRISPR‐edited cell lines: TAFAZZIN‐knockout (KO) HEK293 cells and iPSCs with which to perform broad‐based discovery experiments and to study tissue‐specific disease effects, respectively. A combined multi‐omics approach including proteomics, lipidomics, and metabolomics in TAZ‐KO HEK293 cells revealed diverse mitochondrial abnormalities, including defects in complex I of the respiratory chain, abnormal PDK2 expression, and dysregulation of proteins involved in mitochondrial quality control including PARL and PGAM5. Importantly, we discovered that molecules that bind to cardiolipin (SS‐31) or inhibit nascent cardiolipin deacylation (bromoenol lactone), partially remediate these mitochondrial defects.We next explored cell‐type specific dysfunction in iPSC‐derived TAZ‐KO and wild‐type cardiomyocytes and neurons via lipidomics, RNA‐seq, and functional studies. We identified disturbances in cellular lipid content including an expected increase in the monolysocardiolipin content and a reduction that exhibited cell‐type specificity. RNAseq identified dysregulation in pathways regulated by PARL and PGAM5 including Wnt signaling, apoptosis, and autophagy in the undifferentiated state, with differentiated cell types highlighting pathways such as glucose metabolism and response to cellular stimuli. Oxygen consumption studies show impaired maximal respiratory capacity in TAZ‐KO cardiomyocytes and neurons. Ongoing investigations aim to address cell type specific mitochondrial dysfunction by characterizing PARL abundance, PGAM5 cleavage, and mitochondrial morphology in TAZ‐KO iPSC derived cell types. Additionally, we are currently targeting cardiolipin metabolism in differentiated TAZ‐deficient cells with the goal of remediating cellular lipids, mitochondrial gene expression, and oxygen consumption abnormalities.
Sex‐related differences in how hyperactive platelets exacerbate the cytokine storm in the peritoneal cavity during intra‐abdominal sepsis
Authors: Albayati Samara , Dorsam Glenn , Liverani Elisabetta 
Published: May 2022

Intra‐abdominal sepsis, a complex clinical syndrome resulting from a serious infection, is a major healthcare problem associated with high morbidity and mortality. Inflammatory cytokine levels in the peritoneal cavity (PC) are much higher than in blood, and the enhanced release of these mediators is a key participant to the deleterious effects of sepsis. Platelets are well‐known for their role in modulating proinflammatory cytokine secretion. We have previously shown that in vivo blockade of P2Y12 signaling, an important regulator for platelet secretion, resulted in lower inflammatory cytokines in the blood. We hypothesize that proinflammatory cytokine levels in the peritoneal cavity will be elevated in a murine model of sepsis. To this end, male and female mice underwent a cecal ligation and puncture (CLP) procedure to induce sepsis and were treated with ticagrelor to block P2Y12 signaling. Peritoneal cavity cells and fluid (PCF) were collected 24 hrs post‐surgery to measure changes in proinflammatory cytokine levels and immune cell interactions. Our data show that during CLP‐induced sepsis, PCF exhibited very low platelet counts and platelet‐immune cell aggregates compared to sham‐treated mice irrespective of sex (*p £ 0.05, n=4). Surprisingly, despite low platelet numbers, soluble p‐selectin and PF‐4 levels were elevated, indicative of platelet secretion. Moreover, P2Y12 antagonist treatment significantly decreased platelet markers and immune cell aggregates in PCF from male but not female mice (*p £ 0.05, n=5). In conclusion, intercellular communication mediated through systemic platelet activation influences the peritoneal cavity during intra‐abdominal sepsis, even in the absence of platelets locally in a sex‐related manner.Moreover, P2Y12 antagonist treatment significantly decreased platelet markers and immune cell aggregates in PCF from male but not female mice. In conclusion, intercellular communication mediated through systemic platelet activation influences the peritoneal cavity during intra‐abdominal sepsis, even in the absence of platelets locally in a sex‐related manner.