bluuebunny/crossref_metadata_2025_split huggingface dataset:
Learning the Legs When You Have None
Authors: Buckley Miracle 
Published: May 2022

Living life in a wheelchair was never part of the plan, but life comes the way it comes. The speaker has endured a spinal surgery combined with a lower extremity amputation, proceeded through public schools, learning to play piano without the use of pedals, learning to drive, ultimately deciding a future in the medical field was the way to go. One of the biggest decisions that would face her would be deciding to not want a wheelchair to define her life. Which is why she always chose things that were considered for “able‐bodied” people. Throughout her education, there have always been classes that have been a bit of a struggle. However, one of the hardest was Gross Anatomy.This session will focus on the speaker’s lived experience as a bilateral lower extremity amputee navigating life and the health professional curriculum. For most people anatomy class is a little easier because they have all their limbs and can demonstrate on their own. But for her, not having those major parts, it was a bit of a struggle until her anatomy professor helped relate the lower extremity to the upper extremity. She can ambulate on her hands when not using her power wheelchair, so this technique helped to make that topic stick. This speaker will help demonstrate how anatomy educators can facilitate success for students with disabilities through an individualized approach.
Making the Human Face: Elucidating the Role of Enhancers in Hominid Craniofacial Evolution
Authors: Mohammed Jaaved , Hansen Karissa , Claes Peter , Weinberg Seth , Selleri Licia , Swigut Tomek , Wysocka Joanna 
Published: May 2022

There is increasing evidence that morphological differences among individuals of the same species and between species are driven by changes in gene expression mediated by non‐coding mutations that are enriched at enhancer elements. The identification and comparative evaluation of these cis‐regulatory variants specific to human facial morphology have been facilitated by several recent advances. Among these are access to high‐quality genome sequences, especially from archaic hominins such as the Neanderthals, by expanded catalogs of SNPs implicated in normal range human facial variation from Genome‐wide Association Studies (GWAS), and by the curation of active human and chimp Cranial Neural Crest Cell (CNCC) enhancers that are important for facial development. To identify functional variants that mediate change in enhancer activity in recent human evolution and normal range variation and to nominate their target genes we employed two methods: (1) STARR‐seq, an enhancer reporter assay that permits accurate, comparative analysis of regulatory activity across enhancer homologs and their constituent cis‐mutations, and (2) H3K27ac HiChIP, a method to characterize the three‐dimensional interactome between enhancers and their target genes.We performed STARR‐seq and HiChIP experiments in the in vitro derived CNCCs, and early proliferative cranial chondrocytes. Comparisons of enhancer activity among the orthologs present in homo‐ or hominin species uncovered several classes of enhancers with species‐ or clade‐ restricted activity. Furthermore, for enhancers associated with facial shape GWAS signals, we identified genetic variants associated with changes in regulatory activity. By incorporating HiChIP labeled target genes, we found that biased intra‐species and GWAS enhancer homologs target important developmental transcription factors and signaling molecules. Our experiments have begun to provide insights into how evolutionarily important and functionally relevant enhancer cis‐variants can modulate gene regulatory programs at the individual‐ or species‐centric level with an outcome on facial phenotypes.
Mechanistic Insights into Deregulated TGF‐β Family Signalling in Human Disease
Authors: Hill Caroline S. , Gori Ilaria , Kjaer Svend , George Roger , Ramachandran Anassuya , Mehic Merima , Tolar Pavel , Hyvonen Marko , Jones Chris 
Published: May 2022

Deregulation of TGF‐β family signalling underlies some serious human diseases, including cancer, the Marfan syndromes, and other connective tissue disorders. Recent work in my lab has focused on working out how mutations in key components of TGF‐β family signalling pathways cause these diseases.Shprintzen‐Goldberg syndrome (SGS) is a Marfan‐related syndrome caused by heterozygous point mutations in the co‐repressor SKI, which is a negative regulator of TGF‐β signalling that is rapidly degraded upon TGF‐β or Activin stimulation. The molecular consequences of these mutations, however, have not been well understood. Using a combination of structural biology, genome editing and biochemistry we have shown that SGS mutations in SKI abolish its binding to phosphorylated SMAD2 and SMAD3, which are the downstream signal transducers of the TGF‐β and Activin signalling pathways. This results in stabilization of SKI and consequently attenuation of TGF‐β responses, in both knockin cells expressing an SGS mutation, and in fibroblasts from SGS patients. Thus, we conclude that SGS is associated with an attenuation of TGF‐β‐induced transcriptional responses, which has important implications for other Marfan‐related syndromes.Fibrodysplasia ossificans progressiva (FOP) and diffuse intrinsic pontine glioma (DIPG) are debilitating diseases that share causal mutations in ACVR1, a TGF‐β family type I receptor. ACVR1R206H is a frequent mutation found in patients with these diseases. The relevant ligand required to activate this mutant receptor is thought to be Activin A. To obtain insights into the underlying molecular mechanism we have used a combination of biochemistry, optogenetics and live imaging in both knockin cells and in cells from DIPG patients. Our results demonstrate that in contrast to wild type TGF‐β family receptors, ACVR1R206H activation does not require any upstream kinases. Instead we show that it is predominantly activated via Activin A‐dependent receptor clustering, which induces its auto‐activation, leading to downstream SMAD1/5 phosphorylation. The relevance of this for the pathogenesis of FOP and DIPG will be discussed.
Disparities in Cancer Incidence and Outcomes
Authors: Adebamowo Clement , Adebamowo Sally 
Published: May 2022

Considerable progress has been made in reducing the incidence, morbidity, and mortality of several cancers across the United States in recent decades. Nevertheless, the progress has been uneven with many areas of persistent disparities based on racial/ethnic, rural/urban, and geographical factors. In many cases, these determinants of disparities intersect to increase the overall burden of cancer on affected populations. The intersectionality of these determinants ‐ race, class, and gender – interact and overlap with genomic factors. Thus dedicated resources and funding are required to dissect the roles of these factors and the genomic inheritance.In this panel, speakers will discuss recent research findings, novel methods, and emerging technologies – polygenic genomic methods, epigenomics, gene‐environment interaction research, artificial intelligence, etc. ‐ that would enable appropriate interventions to reduce disparities in cancer incidence and outcomes. Clinical and research ethics, community engagement and community participatory and co‐produced research that is responsive to the highest priorities of populations most affected by health disparities would also be discussed as ways to earn and secure community participation in research production, dissemination and implementation of research findings.
Housing Temperature Alters Energy Expenditure and Adipose Tissue Bioenergetics in Mice
Authors: Sadler Daniel , Treas Lillie , Porter Craig 
Published: May 2022

BackgroundSub‐thermoneutral housing temperatures increase facultative thermogenesis in mice, a process which has been attributed in part to uncoupling protein 1 (UCP1). Typical vivarium temperatures (i.e., ~22‐26°C) likely represent mild cold stress for mice, yet the metabolic impact of modest changes in housing temperature in mice remains unclear. Here, we determined the impact of transitioning mice from 24°C to 30°C on total energy expenditure (TEE) and adipose tissue bioenergetics.MethodsMale and female C57BL/6J mice were studied for 6‐weeks. All mice were housed at 24°C (room temperature, RT) for two weeks, and then either remained at RT (n=16 per group, 8M/8F) or were transitioned to 30°C (thermoneutrality, TN) (n=16 per group, 8M/8F) for 4 weeks. Mice were housed in metabolic cages to determine TEE and its components via respiratory gas exchange. Interscapular brown adipose tissue (iBAT) and inguinal white adipose tissue (iWAT) were harvested at the end of the 6‐week study to assess mitochondrial respiratory function by high resolution respirometry.ResultsCompared to RT, total daily energy expenditure (TEE) was 25% and 16% lower in males and females at TN (M: TN, 8.4±0.6 vs. RT, 11.1±1.0 kcal/day; F: TN, 8.1±0.6 vs. RT, 9.6±1.6 kcal/day; P<0.05), which was partly due to a 36% and 40% decrease in basal metabolic rate (BEE) at TN (M: TN, 3.6±0.2 vs. RT, 5.6±0.8 kcal/day; F: TN, 3.2±0.2 vs. RT, 5.4±0.9 kcal/day; P<0.01). Wheel running distance completed by males was 50% lower at TN versus RT (P<0.05), and female mice ran 101% further than males at TN (P<0.05). iBAT depot mass was 73% and 76% greater at TN versus RT (P<0.01) in males and females, respectively, whereas iWAT mass was similar between conditions. At RT, total iBAT depot UCP1 protein content was 2‐fold greater than that at TN (P<0.01). Further, iBAT depot UCP1 protein content was respectively 20‐ and 40‐fold greater than the iWAT depot at TN and RT (P<0.01). However, iBAT UCP1‐dependent respiration per depot was unaltered by housing temperature, whereas iWAT UCP1‐dependent respiration per depot was 70% and 62% lower in males and females, respectively, at TN versus RT (P<0.01). Still, the absolute thermogenic capacity of UCP1 in the iBAT depot was 45‐ and 16‐fold greater than the iWAT depot at TN and RT, respectively.ConclusionA modest change in housing temperature markedly alters BEE and thus TEE in mice. Cooler housing temperature (even those within the National Research Council’s guide for housing laboratory rodents) results in marked hypermetabolism and recruitment of UCP1 in both iWAT and iBAT. Despite UCP1 recruitment in iWAT, iBAT is the principal site of UCP1‐dependent thermogenesis in mice housed at 24°C. These data may have important implications regarding the optimization of preclinical models of human disease.
An Enterprise in 3‐D Printed Smilodon fatalis Mandible Reconstruction: Experimentation Where No Fossil or Cast Has Gone Before
Authors: Haji‐Sheikh Misty , Naples Virginia L. , Haji‐Sheikh Michael 
Published: May 2022

Introduction and objectiveSmilodon fatalis went extinct approximately 10,000 years ago. During the fossilization process, changes occurred, including shrinkage, deformation, and misalignment. With no modern analog, studying how S. fatalis killed its prey, used its canines, and what bite force may have been exerted requires an accurate skull. 3‐D printing is a new way to manipulate, explore, and study fossils, in this case, the mandible of S. fatalis.Materials and methodsOur work uses modern techniques, specifically a 3‐D scanner, a 3‐D printer, and thermal plastic polyester, to accurately rebuild the mandible. These tools allowed the mandible to be manipulated from the original cast size, and width to the more correct alignment by widening the mandible so that the markers we took matched all along the maxilla.ResultsThe mandible casts we studied had narrowed over time and the upper teeth and the lower teeth did not occlude. Our novel 3‐D approach eliminates taphonomic problems including deformations that are often encountered when studying S. fatalis. This experiment created a mandible in which homologous points on the maxilla and mandible aligned correctly, and permitted the carnassial teeth to occlude properly.ConclusionsOur method allows repeatable experimental manipulation. The 3‐D printed mandible we modified became wide enough to be occluded more accurately with the glenoid fossa. The important aspects include differences between the cast mandible and the 3‐D printed one, specifically the size difference; the alignment of the incisor teeth, and the alignment of the carnassial teeth.Significance/importanceThese manipulations would not be possible with real fossils due to the rarity, texture, and fragile nature of the fossil. This is also not possible with a cast as the cast is usually a preformed plasticized unit. With this 3‐D method, researchers can make multiple copies for a variety of experiments. Until now there was no way to manipulate a fossil for better placement or alignment. Our method increases the opportunity for anatomical and functional details that can be obtained by no other means. Researchers can now use this method in studying the fossils they have on hand and the result will be a better understanding of extinct animals. These 3‐D methods are a new set of tools that can revolutionize the study of not only Smilodon but also of all other fossils.
Troubleshooting Real‐time PCR Data Online and on Ground to Develop Critical Inquiry and Problem Solving Skills
Authors: Bistulfi Gaia 
Published: May 2022

One of the most important skills for molecular biology students upon entering the workforce is their ability to problem solve. From answering research questions to diagnosing and troubleshooting, learning to interpret data and draw pertinent conclusions is essential for scientists.In the last decade, we devised a series of laboratory experiences during which students extract RNA from their own cells, retro‐transcribe it, design expression specific primers for a house‐keeping transcript using tools freely available online, perform polymerase chain reaction (PCR), amplicon purification and quantification, serial dilutions of the amplicon to prepare real‐time‐PCR standards, run real‐time PCR experiments, and finally analyze their data. To maximize student engagement and discussion during the labs, each module is weaved though with a gaming experience awarding students points for answering questions by themselves or as part of a team.During the pandemic, the curriculum was adapted to run online as a simulation.The gamification approach significantly increased student participation, both online and on ground, and it also increased camaraderie on ground. The discussion‐focused report made a significant difference in student understanding; 85% of the students, as compared to 40% with a regular lab report, where able to draw pertinent conclusions from their dataset pinpointing errors to one or more of the following: standard preparation, addition of standards to the plate, inconsistent pipetting, or contamination.The robust laboratory modules described here have been improved for the past decade and can be adapted to study any gene of interest.
Identification of a Novel Candidate to Promote Hepatic Maturation in HepG2 Cells In Vitro
Authors: De Vos Kristof , Annaert Pieter 
Published: May 2022

Drug‐induced cholestasis (DIC) is characterized by impaired bile flow caused by exogenous compounds and remains a major culprit of attrition of drug candidates, as illustrated by liver toxicity representing 40% of all clinical trial terminations. Strategies for earlier (preclinical) detection of DIC‐inducing drug candidates has thus been an area of extensive research. Nevertheless, the currently available in vitro models for DIC suffer from major knowledge gaps in terms of underlying mechanisms. The crux is the inability to fully mature hepatic phenotypes. Previous studies show a different transcriptome, proteome and epigenetic profile between iPSC‐derived hepatocyte‐like cells (HLCs) and primary human hepatocytes (PHHs), with low levels of hepatic transcription factors (TFs) and biotransformation CYP450 enzymes in HLCs.A recent mechanistic study revealed that maintenance of mature phenotypes of PHHs and their (glucose) metabolism in vitro, at least partially, depends on blocking epithelial‐mesenchymal transition (EMT) and subsequently identified TGF‐β, Wnt, BMP, Notch, and cAMP signaling as master regulators of this process. However, 5 different chemical compounds, each corresponding to a specific pathway, had to be administered into the culture medium for sufficient EMT inhibition. Building further on the previous knowledge that AKT/mTORC1 signaling is a strong inducer of gluconeogenesis and CYP450 activity, we hypothesized that an upstream pathway and/or common protein(s) could simultaneously activate AKT/mTORC1 and inhibit EMT. Not only would it lead to more mature hepatic phenotypes (and thus better models) in vitro, but it would also broaden the mechanistic understanding underlying hepatic maturation.Preliminary data suggests that this goal may be accomplished. After targeted inhibition with a small molecule in HepG2 cells, expression patterns were consistent with (i) an upregulation of AKT/mTORC1 as well as estrogen biosynthesis (indicative for strong CYP450 activation), and (ii) a shift in cell metabolism from glucose fueling to β‐oxidation and amino acid consumption with induction of gluconeogenesis (indicative for strong EMT inhibition). Furthermore, the epithelial marker CDH1 (encoding for E‐cadherin) was sharply increased and AKT/cAMP signaling together with typical hepatic TFs that serve as maturation biosensor (HNF4A, FOXO1 and FOXO3) were predicted to be significantly activated. Consistent with this expression data, mitochondrial functionality was confirmed to be improved by quantifying urea production and measuring mitochondrial membrane potentials.Taken together, gathered preliminary data points towards a novel link between (loss of) the identified target, inhibition of EMT and the enhancement of hepatic maturation TFs as well as CYP450 expression and activation. Generation of knock‐out cells and elaborate bile acid profiling is on‐going and will be applied in further mechanistic studies of DIC.
Teaching Biomolecular Visualization Literacy: Guidelines for Developing Assessments, Images and Rubrics Aligned with the BioMolViz Framework
Authors: Acevedo Roderico , Mertz Pam , Burch Charmita , Austin Shane , Nemmara Venkatesh , Mitton‐Fry Rachel , Hall Bonnie , Fox Kristin , Franzen Margaret A. , Beckham Josh , Procko Kristen 
Published: May 2022

Experts in the life sciences glean critical information from biomolecular visualizations. When teaching, we assume our students grasp the concepts in these depictions of biomolecules in the same way that experts do. However, biomolecular visualization (BMV) skills must be intentionally taught and assessed to gauge student understanding. To identify misperceptions and assess comprehension, BioMolViz developed a framework outlining the required skills for biomolecular visualization literacy. Over the past four years, BioMolViz conducted numerous workshops to engage the broader community in creating assessments aligned with the BMV framework, with the goal of developing a repository of validated assessments that can be used by the broader community. Workshops were shifted to an online format during the COVID‐19 pandemic, and a new working group emerged, the BioMolViz Fellows. This subset of workshop participants continued writing and revising assessments remotely, augmenting the group’s peer review and validation process. Our workshops and the ongoing work of the Fellows generated over 200 assessments at various stages in our validation process, with 80 that underwent at least two rounds of revision, and 27 assessments are pending review by an external expert panel. Here, the Fellows present guidelines for generating excellent images using popular visualization software, such as PyMOL, Chimera, and iCn3d. We also provide tips and tricks for designing or reframing questions and rubrics to help instructors maximize student understanding of important biomolecular concepts. Fellows crafted these guidelines using the BMV framework coupled with the lessons learned through workshops.If you are interested in joining our growing community of professionals dedicated to improving BMV instruction, then we’d be delighted to connect with you.
Selective targeting of the inactive state of hematopoietic cell kinase (Hck) with a stable curcumin derivative
Authors: Chakraborty Manas P. , Bhattacharyya Sudipta , Roy Souryadip , Bhattacharya Indira , Das Rahul , Mukherjee Arindam 
Published: May 2022

Hck, a Src family nonreceptor tyrosine kinase (SFK), has recently been established as an attractive pharmacological target to improve pulmonary function in COVID‐19 patients (Treon et al., Blood, 2020). Hck inhibitors are also well known for their regulatory role in various malignancies and autoimmune diseases (Ashleigh et al., Oncotarget,2015). Previous report shows that binding of curcumin to active conformation of DYRK2 at sub nanomolar range makes it an excellent DYRK‐2 inhibitor(Banerjee et al., PNAS,2018), but curcumin's fate is tainted by its instability in the cellular environment and its nonspecific binding nature(Kathryn et al., J. Med. Chem.,2017). Besides, the planar symmetry makes curcumin less druggable toward asymmetric binding pockets such as kinases (Knight et al., Chem. Biol. 2005). small molecules targeting the inactive states of a kinase are desirable to reduce promiscuity (Hanson et al., Chembiol., 2019). Here, we show that functionalization of the 4‐arylidene position of the fluorescent curcumin scaffold with an aryl nitrogen mustard provides a stable Hck inhibitor which binds specifically to the inactive conformation of Hck, similar to type‐II kinase inhibitors that are less promiscuous.Moreover, the lead compound showed no inhibitory effect on two other kinases (DYRK2 and Abl) which can be explained by difference in p‐loop dynamics between Abl and src family kinases. We demonstrate that the cytotoxicity may be mediated via inhibition of the SFK signalling pathway in triple‐negative breast cancer and murine macrophage cells. Our data suggest that curcumin is a modifiable fluorescent scaffold to develop selective kinase inhibitors by remodelling its target affinity and cellular stability.