bluuebunny/crossref_metadata_2025_split huggingface dataset:
Fractional‐nucleotide translocation in sequence‐dependent pausing by RNA polymerase: Single‐molecule picometer‐resolution nanopore tweezers (SPRNT)
Authors: Ebright Richard , Nova Ian , Yang Shuya H. , Mazumder Abhishek , Laszlo Andrew , Derrington Ian , Gundlach Jens 
Published: June 2021

Single‐molecule picometer‐resolution nanopore tweezers (SPRNT) enables monitoring of translocation of a nucleic‐acid motor protein on a nucleic‐acid track with sequence registration, sub‐nucleotide spatial resolution, sub‐millisecond temporal resolution, and the ability to apply assisting and opposing forces.We have demonstrated the ability of SPRNT to monitor translocation of RNA polymerase (RNAP) relative to the DNA template strand, the DNA non‐template strand, and the RNA product strand in transcription, and we have applied SPRNT to analyze RNAP translocation in transcription elongation and sequence‐dependent transcriptional pausing.The results show that sequence‐dependent transcriptional pausing involves a “half‐translocated” state in which RNAP translocates relative to the DNA template strand by 0.5 nucleotides. The “half‐translocated” state is unable to bind the next NTP substrate, presumably because RNAP translocation by 0.5 nt does not align the next template‐strand nucleotide with the RNAP active‐center NTP addition site. The half‐translocated state interconverts rapidly (~0.1–1 s) with the “pre‐translocated” state and converts slowly (~1 s) to the NTP‐binding‐competent “post‐translocated state.” In the presence of saturating NTPs, conversion to the post‐translocated state is followed by pause escape. In the presence of limiting NTPs, conversion to the post‐translocated state is followed by return to interconverting half‐translocated and pre‐translocated states and continued pausing.This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Dynamics and Spatial Genomics of the Nascent Transcriptome by Intron seqFISH
Authors: Cai Long , Shah Sheel , Tekei Yodai , Zhao Wen , Lubeck Eric , Yun Jina , Eng Chee‐Haut Linus , Koulena Noushin , Cronin Christopher , Karp Christopher , Liaw Eric J. , Amin Mina J. 
Published: June 2021

Visualization of the transcriptome and the nuclear organization in situ in individual cell is the holy grail of single cell analysis. Here, we demonstrate a multiplexed single molecule in situ method, intron seqFISH, that allows imaging of 10,421 genes at their nascent transcription active sites in single cells, followed by mRNA and lncRNA seqFISH and immunofluorescence. This nascent transcriptome profiling method can identify different cell types and states with mouse embryonic stem cells and fibroblasts. The nascent sites of RNA synthesis tend to be localized on the surfaces of chromosome territories and their organization in individual cells is highly variable. Surprisingly, the global nascent transcription oscillated asynchronously in individual cells with a period of 2 hours in mouse embryonic stem cells as well as in fibroblasts. Together, spatial genomics of the nascent transcriptome by intron seqFISH reveals nuclear organizational principles and fast dynamics in single cells that are otherwise obscured.This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Retinol Binding Protein 4 (RBP4) in Adipocytes and Obesity
Authors: Shmarakov Igor , Lee Seung‐Ah , Blaner William S. 
Published: June 2021

We have earlier reported the generation and study of transgenic mice that express human RBP4 (hRBP4) in both white and brown adipocytes (Lee et al. Hepatology 2016, 64:1534–1546). Our published studies of these mice (adi‐hRBP4 mice) established that white adipocyte expression RBP4 induces inflammation in white adipose tissue (WAT) that is responsible for the hepatic steatosis phenotype seen in chow fed adi‐hRBP4 mice. When maintained on a high fat diet, adi‐hRBP4 mice gain significantly more body weight than matched control mice. We have investigated the basis for this weight gain phenotype and found that this involves marked RBP4‐induced changes in brown adipose tissue (BAT) physiology. H&E stained BAT obtained from adi‐hRBP4 mice shows the presence of large unilocular lipids in brown adipocytes. Biochemical measures establish that there is elevated triglyceride accumulation in BAT of adi‐hRBP4 mice that is accompanied by increased expression in BAT of genes involved in triglyceride synthesis. In addition, BAT from adi‐hRBP4 mice shows diminished expression levels for genes involved in BAT identity and function. Most importantly, uncoupling protein‐1 (UCP1) mRNA and protein levels are markedly reduced. This is accompanied by significantly diminished BAT levels of all‐trans‐retinoic acid. In vitro studies involving the use of mouse embryonic fibroblasts (MEFs) obtained from adi‐hRBP4 and matched control mice as well as brown and white stromal vascular cells induced to differentiate to adipocytes, confirmed that RBP4 expression in brown adipocytes alters gene expression patterns in the differentiated adipocytes. Collectively, our data suggest that elevated RBP4 expression in BAT effects all‐trans‐retinoic acid‐mediated processes giving rise to a whitening of BAT and diminished BAT actions. We propose that this underlies the weight gain phenotype we have observed.Support or Funding InformationSupported by NIH grants R01 DK068437 and R01 DK101251This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Downregulations of Aldolase C Are Correlated with IDH1 Wild‐type Overexpressions and Predict Significant Poor Prognosis in Glioblastoma Patients
Authors: Tsai Hsing Fang , Chang Yu Chan , Tsai Wen Chiuan , Hsiao Michael 
Published: June 2021

BackgroundAldolases family is the one of the main enzymes involved in the process of glycolysis. The expression of aldolases family is tissue‐specific, and Aldolase C (ALDOC) is found expressed mainly in the normal brain especially in the adult brain and is also found important in the brain development of infant. ALDOC catalyzes the reversible conversion of fructose‐1,6‐bisphosphate to glyceraldehydes‐3‐phosphate (G3P), or glyceraldehyde, and dihydroxyacetone phosphate (DHAP) by aldol cleavage to exert it function in brain hippocampus and purkinje cells. However, the role of ALDOC in glioblastoma remains unclear.DesignIn this study, we data‐mined the in silico databases to evaluate the RNA expression of aldolase family members in glioblastoma (GBM) patient cohorts to determine its prognostic values. We further performed Immunohistochemical staining (IHC) analysis to evaluate protein expression levels of ALDOC in GBM patients. The correlation of ALDOC and GBM patient survival were examined.ResultsOur results from TCGA database analyses showed higher expression of ALDOC RNA expression levels in the normal brain tissue compared to GBM (P=0.0004). Expression levels of ALDOC were found significantly downregulated in high grade GBM compared to low grade glioma. In addition, the expression level of ALDOC is associated with molecular subtypes (proneural, neural, classical and mesenchymal) and recurrent status in several GBM datasets. The expression level of other Aldolase family members ALDOA and ALDOB have no significant prognostic impacts in the GBM cohorts. We further examined the correlations of wild‐type IDH1, one of the most significant poor prognostic markers in GBM, with ALDOC in GBM patient cohorts. Interestingly, our results showed there was a strong negative correlation between IDH1 and ALDOC expression in RNA levels at TCGA cohorts as well as in protein expression levels in our GBM patient cohorts. Combination of low ALDOC and high IDH1 wilt‐type expressions predicts a stronger poor significance in GBM patient compared to ALDOC or wild‐type IDH alone. Moreover, we found there is also a strong IDH1 mutant expression with increase ALDOC expression levels that predicts a significant good prognosis in GBM patient cohorts. The plausible ALDOC and IDH1 regulatory mechanism was further elucidated.ConclusionThese results indicate ALDOC downregulation correlates with IDH1 wild‐type overexpression and predicts stronger poor prognosis in glioblastoma patients. ALDOC may play critical roles in inhibiting IDH1 functions to inhibit the progression of glioblastoma.This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Brain Cancer: Failure of Resolution of Inflammation?
Authors: Hallisey Victoria , Barksdale Chantal A , Chang Jaimie , Sulciner Megan L , Bielenberg Diane R. , Schmidt Brigitta A , Keiran Nicholas , Haung Sui , Serhan Charles N , Keiran Mark W , Panigrahy Dipak 
Published: June 2021

Medulloblastoma therapy, including radiation and chemotherapy, induces cell death resulting in tumor cell debris assumed to be inert or inhibitory to tumor growth. However, tumor cell death (debris) produced by cytotoxic therapy can accelerate tumor progression through the inflammatory response, suggesting that every attempt to kill tumor cells is a double‐edged sword. Inflammation is regulated by endogenous specialized pro‐resolving lipid mediators (SPMs), such as resolvins and protectins, which are present in the brain and CSF. These lipid autacoids stimulate the clearance of cellular debris by macrophages, resulting in reduced localized pro‐inflammatory cytokines. A loss of SPMs is associated with several neurodegenerative diseases but has not been studied in brain cancer. We hypothesize that reduced levels of SPMs correlate with brain cancer progression and that control of tumor cell debris‐mediated inflammation through resolvins and protectins represents a novel approach to brain cancer treatment. Here, we show that SPM receptors are expressed by human brain tumors including glioblastoma and medulloblastoma. Medulloblastoma tumor cell debris generated by front‐line chemotherapy or targeted therapy stimulates primary tumor growth when co‐injected with a subthreshold (non‐tumorigenic) inoculum of tumor cells by triggering the release of pro‐inflammatory cytokines. Stimulation of the resolution of inflammation via protectins and resolvins suppressed orthotopic medulloblastoma. Protectins and resolvins down‐regulated proinflammatory cytokine release in debris‐activated microglia and stimulate the clearance of tumor debris by inducing macrophage phagocytosis of apoptotic tumor cells. Histological analysis of SPM‐treated medulloblastoma and glioblastoma tumors revealed suppressed Ki‐67‐stained tumor cell proliferation. Thus, brain tumor progression results from a loss of resolution of tumor debris‐associated inflammation. Enhancing endogenous clearance of tumor cell debris via protectins and resolvins is a novel biological target to complement current cytotoxic brain cancer therapy and addresses the intrinsic limitation of current cancer therapy involving cell death. Our studies provide a new strategy for the prevention and treatment of therapy‐induced resistance in medulloblastoma and other brain cancers.Support or Funding InformationThis work was supported by the National Cancer Institute grant RO1 01CA170549‐02 (D.P.); ROCA148633‐01A4 (D.P.); and the Credit Unions Kids at Heart Team (D.P.)This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Investigating Novel Roles for Hedgehog Co‐Receptors During Craniofacial Development
Authors: Echevarria‐Andino Martha Luz , Allen Benjamin 
Published: June 2021

Hedgehog (HH) signaling is essential for correct patterning of vertebrate embryos, including during craniofacial development. HH ligands signal through the canonical receptor Patched1 (PTCH1), and three co‐receptors–growth arrest specific 1 (GAS1), cell adhesion molecule‐related/down‐regulated by oncogenes (CDON), and brother of CDON (BOC). Together, these co‐receptors are required during embryogenesis to mediate proper HH signaling. However, recent genetic studies suggest tissue‐specific, antagonistic roles for these proteins. For example, Gas1 restricts the HH pathway during mouse tooth development, while Boc antagonizes HH signaling during zebrafish jaw formation. Here I explored possible antagonistic roles for GAS1, CDON and BOC in HH‐dependent mammalian craniofacial development. Genetic deletion of these co‐receptors results in variable holoprosencephaly (HPE) phenotypes (failure to divide the forebrain into two cerebral hemispheres). Gas1 mutant mice display a spectrum of HPE phenotypes, and significant patterning defects in the neural tube and limb. In contrast, genetic deletion of Boc does not perturb patterning in any of these tissues. Strikingly, the combined deletion of Boc and Gas1 results in more severe neural tube and limb patterning defects than those observed in Gas1 single mutants. However, the Gas1 craniofacial phenotype is partially ameliorated in Gas1;Boc double mutant embryos as determined by the levels of NKX2.1, Gli1, Ptch1 and internasal distance quantitation. Micro‐computed tomography and skeletal analyses reveal that the rescue of the craniofacial defects in Gas1;Boc double mutants is restricted to the nasal bone and nasal capsule; other craniofacial bones are more severely affected, similar to what is observed in the neural tube and the limb. This effect does not appear to be due to differential GAS1 and BOC function in the forebrain neuroepithelium as overexpression of these co‐receptors in the developing chicken forebrain both promote HH signaling. Instead, I hypothesize that these co‐receptors have distinct, tissue‐specific functions in the craniofacial mesenchyme or the surface ectoderm. To further explore an antagonistic role for BOC during craniofacial development, I am currently deleting Boc in a sensitized HH genetic background through breeding with Ptch1 and Shh heterozygous mutant animals. These findings suggest that GAS1 and BOC do not function simply as redundant HH co‐receptors, but instead display distinct, tissue‐specific functions, particularly during craniofacial development.Support or Funding InformationNational Sciences Foundation Graduate Research Fellowship Program (DGE 1256260), Rackham Pre‐Candidate Graduate Student Research Grant, Bradley Merill Patten Fellowship and Organogenesis Training Grant (NIH T32HD007505)This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
The intersection of chimpanzee science, ethics and policy: The rapid reformation of a research landscape
Authors: Ross Steve 
Published: June 2021

Chimpanzees, along with bonobos, are the closest living relatives of human beings. As such, this species shares myriad genetic, physiological, anatomical, behavioral and cognitive traits with our own species and has served as a research proxy for humankind for over a hundred years. While much of the history of chimpanzee research is focused use as biomedical subjects, the past two decades of policy reform have radically reshaped when and how we utilize chimpanzees in research settings. In this talk, I will examine these historical trends and characterize the unprecedented way in which the research community has shaped and been shaped by these changes. Focusing on the growth of non‐traditional research venues such as zoos and sanctuaries, I will illustrate new opportunities for the study of chimpanzee biology, behavior and cognition while highlighting the inherent challenges that arise from a rapid restructuring of research paradigms.This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Genetic or Pharmacological Induction of the Hypoxia Response Enhances Functional Regeneration Following Peripheral Nerve Injury
Authors: Smaila Brittney D , Erskine Erin L , Holland Seth D , Hunter Diana V , Babaeijandaghi Farshad , Rossi Fabio M , Ramer Matt S 
Published: June 2021

Peripheral nerve injuries (PNIs) occur in 1–3% of patients with traumatic injuries. While peripheral axons have the ability to regenerate at ~1mm/day, the distance over which they must do so means lengthy recovery times, which are associated with regenerative failure due to a decline in supporting cells' ability to maintain axon growth. Successful axonal regeneration depends heavily upon the neuronal response to injury, as well as that of myeloid cells recruited to the damaged nerve. In injured neurons, transcriptomic changes occur which mirror those observed in hypoxia. Hypoxia inducible factors (HIFs) effect these transcriptomic changes; these are governed in turn by prolyl hydroxylase domain (PHD) proteins. Under normoxic conditions, PHDs act as master regulators of the hypoxia response, targeting HIFs for proteasomal degradation. We hypothesize that deleting any or all of the PHDs (PHD1, 2, and 3), or inhibiting PHDs pharmacologically, will induce the hypoxia response and enhance axonal regeneration and functional recovery following PNI. We used global PHD1 knockout, global PHD3 knockout, and heterozygous PHD2 transgenic mice, as well as non‐transgenic mice treated with DMOG, a pan‐PHD inhibitor. We used a sciatic nerve crush model of injury and assessed functional recovery at various time points post‐injury using toe pinch and grasping tests, and electromyography. Using immunohistochemistry we characterized macrophage and axon densities in the nerves after injury. We also assessed DMOG‐induced changes in macrophage phenotype using FACS, RT‐PCR and immunohistochemistry. We found that deletion of PHD1 or PHD3, or inhibition of all three PHDs resulted in earlier functional recovery after injury, increased macrophage infiltration in the injured nerve, an M2‐skewed macrophage phenotype, and enhanced axonal regrowth. In addition, deletion of any of the PHDs, or their inhibition by DMOG, resulted in improved electromyographical responses of the nerve one month post injury. Our findings suggest that functional recovery after peripheral nerve injury can be aided by hypoxia‐independent induction of the hypoxia response.Support or Funding InformationWings for Life; ICORD Blusson Integrated Cures PartnershipThis abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Prosecting Human Cadaveric Donors in Stages to Mimic Dissection
Authors: Curran Shannon 
Published: June 2021

Gross anatomy lab contact hours are decreasing for many health professions students, yet the quantity and importance of the anatomical information they are required to learn remains the same. In an attempt to maintain the benefits of cadaver‐based study, many programs are using prosections as an alternative to dissection when student lab time is limited. Although prosection‐based instruction is a valuable and time‐efficient method for students, students can struggle to understand important anatomical relationships that are typically mastered during dissection. Creating prosections that mimic the progressive stages of dissection, presented in a sequential and structured manner, can maximize learning while mitigating the challenges of prosection use. Whole human cadaveric donors were prosected to demonstrate either superficial or deep structures for first year Physician Assistant students. Superficial preparations demonstrated superficial relationships. Generally, these donors had no muscles reflected, no organs removed, and limited amounts of fat and fascia removed. Deep preparations demonstrated intermediate and deep relationships for the different systems and regions of the body. Generally, these donors had muscles reflected and fat and fascia removed to show all neurovasculature. To maximize donor use and student learning opportunities, different organs and muscles were removed and different regions were hemisected on the deep preparations to provide several deep views and relationships. By prosecting in this way, the layers and steps of dissection from superficial to deep were represented and anatomical relationships that are frequently lost while preparing prosections were maintained. Students were able to appreciate anatomical relationships and variability from human cadaveric donors in a way similar to dissection while accounting for reduced gross anatomy lab instruction time.This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Meniscofemoral Ligaments: Under Emphasized in Anatomy Literature Despite Being Evolutionarily Preserved and Surgically Repaired
Authors: Stevens Kelsey , Immonen Jessica , Gilmer Les , Albin Alexa 
Published: June 2021

Purpose and BackgroundAnatomical literature, including medical hallmarks such as Gray's Anatomy, variably discuss the location and prevalence of the anterior and posterior meniscofemoral ligaments (aMFL, pMFL). These ligaments can be seen in an intracapsular knee joint dissection emerging from the posterior horn of the lateral meniscus and flanking the posterior cruciate ligament (PCL) anteriorly and posteriorly. Anatomical teaching resources including some of the most widely used textbooks and atlases for students of allied health professions typical make no mention of the aMFL and variably label the pMFL in medical images.Methods66 cadaveric knee joints were dissected using a novel approach that improves preservation of the aMFL and pMFL. Prevalence of the meniscofemoral ligaments were recorded individually and together. Current and popular medical resources were reviewed for the presence of information on the meniscofemoral ligaments.ResultsIt was determined that 100% of cadaveric knee joints possess at least one of the meniscofemoral ligaments hence, these structures have been evolutionarily preserved to carry out a significant function. One of the most convincing hypotheses on the function of the aMFL and pMFL claims they serve to guide the movements of the lateral meniscus during joint flexion and extension. Other hypotheses state these ligaments may function to oppose the popliteus' pull on the lateral meniscus to prevent tears, structurally reinforce the PCL or provide proprioceptive feedback. Large structures that currently do not possess concrete functional descriptions should not be left out of the anatomical literature as this promotes confusion and decreases the potential for future practitioner innovation.ConclusionsNew aMFL and pMFL prevalence data and the hypothesized biomechanical functions of the ligaments should be receiving more attention in the medical research and teaching literature. Select orthopedic surgeons perform surgical repairs of the meniscofemoral ligaments and their associated structures. The posterior horn of the lateral meniscus may also be surgically excised after tear although it is the origin of the meniscofemoral ligaments. A more thorough surgical attempt to repair posterior horn tears prior to meniscectomy should become the gold standard of practice as the fields of surgery and orthopedics advance and make final conclusions on the role of the meniscofemoral ligaments. Currently anatomical literature should more consistently address and discuss the anatomy of these ligaments.Support or Funding InformationInternal Grant from Rocky Mountain University of Health ProfessionsThis abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.