bluuebunny/crossref_metadata_2025 huggingface dataset:
Molecular‐scale structure of a high‐curvature membrane
Authors: Frost Adam , Moss Frank R. , Lincoff James , Tucker Maxwell , Mohammed Arshad , Grabe Michael
Published: May 2022

Cells utilize molecular machines to form and remodel their membrane‐defined compartments’ compositions, shapes, and connections. The regulated activity of these membrane remodeling machines drives processes like vesicular traffic and organelle homeostasis. Although molecular patterning within membranes is essential to cellular life, characterizing the composition and structure of realistic biological membranes on the molecular length scale remains a challenge, particularly during membrane shape transformations. Here, we employed an ESCRT‐III protein coating model system to investigate how membrane‐binding proteins bind to and alter the structural patterns within lipid bilayers. We observe leaflet‐level and localized lipid structures within a constricted and thinned membrane nanotube. To map the fine structure of these membranes, we compared simulated bilayer nanotubes with experimental cryo‐EM reconstructions of native membranes and membranes containing halogenated lipid analogs. Halogenated lipids scatter electrons more strongly, and analysis of their surplus scattering enabled us to estimate the concentrations of lipids within each leaflet and to estimate lipid shape and sorting changes induced by high curvature and lipid‐protein interactions. Specifically, we found that cholesterol enriched within the inner leaflet due to its spontaneous curvature, while acidic lipids enriched in the outer leaflet due to electrostatic interactions with the protein coat. The docosahexaenoyl (DHA) polyunsaturated chain‐containing lipid SDPC enriched strongly at membrane‐protein contact sites. Simulations and imaging of brominated SDPC showed how a pair of phenylalanine residues opens a hydrophobic defect in the outer leaflet and how DHA tails stabilize the defect and “snorkel” up to the membrane surface to interact with these side chains. This highly curved nanotube differs markedly from protein‐free, flat bilayers in leaflet thickness, lipid diffusion, and other structural asymmetries with implications for our understanding of membrane mechanics.
Structural basis for signaling by the HER3 pseudokinase receptor
Authors: Jura Natalia
Published: May 2022

The Human Epidermal Growth Factor Receptor 3 (HER3) is a pseudokinase receptor which contains a catalytically inactive kinase domain in its intracellular region. Despite lack of catalytic activity, HER3 is an essential signaling receptor serving as an allosteric activator of other HER receptors (EGFR and HER2), and a potent scaffold for recruitment an activation of PI3K. To form an active complex, HER3 and the orphan receptor HER2 assemble into a singly liganded, pro‐oncogenic heterocomplex upon binding to the HER3 ligand neuregulin‐1b (NRG1b). In the absence of structures of the HER2/HER3 heterodimer, the mechanism by which HER2 and HER3 interact upon ligand binding remains unknown. We isolated the near full‐length HER2/HER3 heterocomplex with their growth factor neuregulin (NRG) and obtained a 2.9Å cryo‐EM reconstruction of the extracellular domain module. We discovered an unexpected dynamics at the HER2/HER3 dimerization interface, which is exploited by oncogenic mutations and known therapeutics targeting HER2 – such as trastuzumab. The unique features of the NRG‐bound HER2/HER3 heterodimer underscore an allosteric connection between the ligand‐binding pocket and the dimerization interface, and explain why extracellular domains of unliganded HER2 do not homo‐associate via canonical active dimer interfaces.
Interorgan crosstalk and metabolism regulation in Drosophila
Authors: Perrimon Norbert
Published: May 2022

I will discuss our ongoing studies to identify and characterize communication pathways between major organs in Drosophila. Organ‐to‐organ communications are critical to living systems and play major roles in homeostasis. For example, the vertebrate CNS receives information regarding the status of peripheral metabolic processes via hormonal signaling and direct macromolecular sensing. In addition, skeletal muscles produce various myokines that influence metabolic homeostasis, lifespan, and the progression of age‐related diseases and aging in non‐muscle tissues. Using genetic screening, transcriptome analyses and proteomic approaches, we are identifying and characterizing secreted factors by which organs communicate their physiological state to others in both homeostasis and altered metabolism, as well as tumor models. These studies are providing fundamental insights into how biological processes observed in one tissue/organ (e.g., decreased cellular metabolism, mitochondrial dysfunction) influence the state of other tissues/organs.
A high dimensional map of phosphorylation‐dependent signaling in budding yeast
Authors: Villen Judit , Leutert Mario , Barente Anthony , Petsalaki Eirini , Fukuda Noelle , Beltrao Pedro
Published: May 2022

Development of mass spectrometry‐based phosphoproteomics has substantially expanded our understanding of cellular processes regulated by protein phosphorylation. However, most phosphoproteomic studies are low dimensional (<5 conditions) due to analytical limitations. Phosphoproteomic profiling at much higher dimensionality is required to obtain systematic insight into the architecture and function of phosphorylation‐dependent signaling networks.

Here we present a high‐dimensional quantitative phosphoproteomic perturbation atlas in Saccharomyces cerevisiae at large scale (>100 perturbations, ~600 samples). We applied a combination of novel methods for automated sample‐preparation, prioritization of functional phosphosites by machine learning and advanced data‐analysis to overcome current limitations in large‐scale phosphoproteomics. Integrating this massive quantitative resource gave us the unique opportunity to systematically elucidate signaling modules, profile kinase activities, and predict functional phosphorylation sites at the organismal scale.
Metabolic Adaptation to Oxidative Stress at the Host‐Microbe Interface
Authors: Hatzios Stavroula
Published: May 2022

Bacteria that chronically colonize the host must adapt to various forms of stress in the host environment. The molecular mechanisms bacteria use to sense and respond to these environmental signals are crucial for maintaining symbiotic associations with host cells. My laboratory uses chemical and biological tools to uncover new molecular mechanisms of bacterial adaptation to oxidative stress. In this talk, I will describe our recent discovery of a widely conserved transporter that enables microbial uptake of a diet‐derived antioxidant from the host.
Deconvoluting host‐gut microbiota co‐metabolism
Authors: Chang Pamela , Parasar Bibudha , Zhao Hao , Xiao Xieyue , Shi Qiaojuan , Brito Ilana
Published: May 2022

The metagenome of the gut microbiome encodes tremendous potential for the biosynthesis and transformation of small‐molecule metabolites through the activity of many enzymes expressed by the intestinal bacteria. The metabolic activity of this gut bioreactor provides numerous important functions for the host, including breaking down indigestible components of our diet, biosynthesizing essential vitamins and nutrients, and regulating the development of our immune system. Accordingly, elucidating the metabolic potential of the multitude of potential enzymatic reactions is critical for understanding how the activities of the gut microbiota contribute to human health and physiology. Therefore, there is a critical need for new technologies that can determine the enzymatic activities of the gut microbiome because these activities cannot be directly determined by existing metagenomic approaches used to profile microbial taxonomy by genetic content. Activity‐based probes, which are mechanism‐based covalent tags for enzyme active sites, represent a powerful chemical approach for directly identifying and profiling enzymatic activities. Here, we have developed activity‐based probes for a class of cysteine proteases known as bile salt hydrolases (BSHs), which are master regulators of gut microbial transformation of host‐derived, or primary, bile acids into a large and diverse group of secondary bile acids. These important metabolites regulate myriad host biological processes, including lipid metabolism, energy metabolism, and immune homeostasis. In addition, changes in bile acid levels are known to accompany different physiological states. However, the role of BSH activity in these processes remains poorly understood due to the lack of adequate tools to address its function. To address this critical gap in knowledge, we have applied our chemical approach to profile BSH activity in gut microbiomes using healthy and diseased samples.
Metabolic outliers in human disease
Authors: DeBerardinis Ralph
Published: May 2022

Many human diseases are caused by mutations that perturb metabolism at the cellular level and result in tissue dysfunction. Some metabolic perturbations result in disease by interrupting the canonical functions of the metabolic network: producing energy, generating precursors for macromolecular synthesis, maintaining redox balance, disposing of waste, etc. Others interfere with processes beyond the conventional metabolic network, interfering with signaling and gene expression networks. Understanding these pathological states of metabolic perturbation may help us develop rational approaches to normalize metabolism and restore health. We study two types of diseases characterized by metabolic dysfunction: inborn errors of metabolism and cancer. I will discuss ongoing work in these diseases that seeks to characterize abnormal metabolic states directly in human subjects, then uses experimental models to explore disease mechanisms and propose potential therapies. I will emphasize methods in metabolomics and stable isotope tracing that allow us observe metabolic phenotypes in intact systems relevant to physiology and disease, highlighting recent work on tumor metabolism in patients and genetically‐defined metabolic anomalies that interfere with mammalian developmental programs.
Chemical Tools for Understanding Phosphatidic Acid Signaling
Authors: Baskin Jeremy M.
Published: May 2022

Phosphatidic acid (PA) is an important phospholipid biosynthetic intermediate and a lipid second messenger. Both the metabolism of PA and the interactions of PA with its effector proteins can occur on numerous organelle membranes, raising important questions about how cells direct specificity into the outcomes of PA signaling. We have endeavored to ‘uncouple the pleiotropy’ of PA signaling through the development of two complementary types of chemical biology toolsets for, respectively, visualizing and manipulating PA metabolism and signaling. The first of these, IMPACT, harnesses bioorthogonal chemistry to generate fluorescent lipids whose localization and abundance report on the activity of phospholipase D (PLD) enzymes that generate ‘signaling pools’ of PA. The second tool, optoPLD, involves the use of light‐controlled, or optogenetic, PLD enzymes capable of generating pools of PA at precise organelle locations upon blue light illumination. We will describe the development of these tools, including newer, second‐generation IMPACT probes and optimized ‘superPLD’ enzymes with much better catalytic properties than our original optoPLD systems. Further, we will describe select applications of IMPACT and optoPLD. These include the use of IMPACT as a readout in genome‐wide CRISPR screening to discover new regulators of PLD signaling and the use of these tools to examine the spatiotemporal dynamics of important pathways that intersect with PLD activation, such as GPCR signaling and the Hippo pathway. Collectively, this work highlights the power of applying diverse chemical biology approaches to shed light on cellular lipid signaling pathways.
The biosynthesis of lipoic acid: A saga of death, destruction, and rebirth
Authors: Booker Squire
Published: May 2022

Lipoyl synthase (LipA) catalyzes the terminal step in the biosynthesis of the lipoyl cofactor, which is the attachment of sulfur atoms at C6 and C8 of an n‐octanoyl chain connected in an amide linkage to a specific lysine residue on a lipoyl carrying protein. The protein belongs to the radical S‐adenosylmethionine (SAM) superfamily of enzymes, which use a [4Fe–4S] cluster cofactor to catalyze a reductive cleavage of SAM to generate a 5’‐deoxyadenosyl 5’‐radical (5’‐dA•). The 5’‐dA• removes the C6 and C8 hydrogen atoms for subsequent sulfur attachment; however, the identity of the immediate sulfur source has been controversial. LipA contains a second [4Fe–4S] cluster, which has been proposed to provide the sulfur atoms during the reaction, limiting the enzyme just to one turnover due to destruction of a required cofactor. In this lecture, biochemical, spectroscopic, and structural evidence for this unique sacrificial role in catalysis will be provided. Moreover, evidence that the cluster can be reconstructed after each turnover will be presented.
Epigenetic marks identify asthma susceptibility in African Americans
Authors: Yang Ivana V.
Published: May 2022

Despite advances in therapeutics and a better understanding of environmental contributions, ethnic disparities are profound in asthma; asthma prevalence is >2 times higher in African compared to European Americans, and African American children are >3 times more likely to be hospitalized and die from asthma than whites. Epigenetic marks, including DNA methylation, are a key mechanistic component of gene‐environment interactions that affect gene expression, respiratory epithelial dysfunction, and immune cell skewing in asthma. Our group performed pioneering work to identify asthma associated‐DNA methylation changes that affect gene expression in African American inner city children. Our work identified 81 differentially methylated regions (DMRs) in peripheral blood mononuclear cells (PBMCs) associated with allergic asthma. DNA methylation changes in PBMCs are small (median 1.3%; range 0.02%‐3.1%) but consistent with the majority of DMRs hypomethylated in asthma, including important immune genes such as IL‐13, RUNX3, and TIGIT. In the nasal epithelia, we identified much larger (median 9.5%, range: 2.6‐29.5%) methylation changes, both in the form of single CpG methylation (differentially methylated positions[DMPs]) and regions (DMRs). 60% of genes that are differentially expressed in the asthmatic nasal epithelium have significant associations of DNA methylation and gene expression; these include asthma genes (ALOX15, CAPN14, POSTN), genes involved in inflammation and immunity, cell adhesion, extracellular matrix, obesity and autophagy, and epigenetic regulators, among others. Importantly, these results have been replicated in multiple cohorts, including a cohort of Puerto Rican children, another population that shares an unproportional disease burden. We are currently involved in projects that aim to integrate genetic ancestry, DNA methylation, and gene expression data to better understand genetic underpinnings of these DNA methylation changes. Our earlier work also showed that nasal epithelia capture disease activity seen in the lung airway epithelia but that there are many more significant associated DNA methylation changes in the nasal epithelia, suggesting an important role for the environment in influencing these epigenetic changes and the need to understand environmental exposures that are driving these changes. In summary, our findings that epigenetic marks in respiratory epithelia are associated with allergic asthma in inner‐city children provide new targets for understanding the biology of the disease, developing biomarkers of exposure or disease, and potentially identifying novel therapeutic approaches for this disease.
Ubiquitin and the Control of Translation During Oxidative Stress
Authors: Silva Gustavo M.
Published: May 2022

During exposure to environmental stresses, eukaryotic cells must reprogram gene expression at the transcriptional and translational levels in order to thrive under these new conditions. Dysregulation of gene expression under stress can lead to molecular damage, cellular death, and the progression of diseases. Therefore, regulation of gene expression is dynamic, requires multiple layers of control, and is critical for cellular adaptation and survival. However, many of these control mechanisms, particularly at the translational level, remain elusive. In response to oxidative stress, we observed in budding yeast a massive accumulation of K63 ubiquitin conjugates that supports cellular resistance to stress. By developing a sequential enrichment methodology, our proteomics analysis revealed that ribosomal proteins are the main targets of K63 ubiquitination under stress. Moreover, we determine that accumulation of K63 ubiquitinated ribosomes relies on the activity of two redox‐sensitive ubiquitin enzymes: the E2 conjugase Rad6 and the deubiquitinating enzyme Ubp2. Activity and cryo‐EM structural analysis revealed that K63 ubiquitin modifies fully assembled monosomes and polysomes and is required for pausing translation at the elongation step. We named this pathway Redox control of Translation by Ubiquitin (RTU), a novel mechanism that supports cellular resistance to stress by aiding the reprogramming of gene expression at the translational level.
Defining pseudoenzymes in glycosylation pathways
Authors: Kannan Natarajan
Published: May 2022

Glycosylation pathways regulate diverse cellular processes from protein quality control to host‐pathogen interactions and the enzymes that catalyze glycosidic linkages, glycosyltransferases (GTs), are a large super‐family of proteins that display extensive variation in primary sequence and three‐dimensional structure. A large fraction of GTs also display variations in key active site residues, but the functional and evolutionary implications of these variations are not well understood. In this talk, I will describe our ongoing efforts to map and classify GTs and pseudoGTs across the tree of life. A phylogenetic tree relating diverse GT‐A fold enzymes reveals that pseudoGTs evolved multiple independent times during evolution and variations in the catalytic base (xED‐Asp) correlate with the stereochemistry of glycosidic linkages in the acceptor substrate i.e., inverting vs retaining. Co‐evolutionary analysis reveals that active site variations in GTs are accommodated through compensatory interactions in distal functional sites associated with substrate recognition. Our studies support the “Red Queen” hypothesis in which the selective pressure to catalyze glycosidic linkages between diverse donor and acceptor substrates led to the emergence and expansion of pseudoGTs across the tree of life. Our findings have important implications for understanding other pseudoenzyme families such as pseudokinases.
Too much and never enough: Synthetic excess and metabolic inefficiency of aneuploidy in tumorigenesis
Authors: Watson Emma V.
Published: May 2022

Aneuploidy is a hallmark feature of cancer. Relative to normal diploid tissue, aneuploid tumors are often net copy number increased, in a range from hyper‐diploid to tetraploid. This results in widespread replication stress and proteotoxic stress that affects diverse cellular complexes. Utilizing multi‐omics approaches in novel models of cancer‐associated copy number alterations derived from diploid human mammary epithelial cells, we uncovered an aneuploidy stress response driven in part by Myc that transcriptionally upregulates biomass production capacity and stresses metabolic capacity. Basal and peak glycolytic and oxidative rates are increased in aneuploid cells compared to diploids, however free nucleotide pools and metabolic intermediates, particularly pyrimidines, are depleted. CRISPR screens revealed a universally increased dependence on de novo pyrimidine synthesis genes in aneuploid cells with diverse CNAs, suggesting a struggle to match pyrimidine synthesis capacity with need. The biosynthetic demand and inefficiency driven by aneuploidy may partially explain the switch to aerobic glycolysis in tumors and present vulnerabilities to be therapeutically exploited.
Flavivirus NS1: Structure and Function of an Enigmatic Virulence Factor
Authors: Smith Janet L.
Published: May 2022

Viruses employ a variety of molecular strategies to carve out an existence in their host and to thwart host defenses. Crystal structures of viral proteins and of the host proteins deployed as molecular weapons contribute enormously to our understanding of viral pathogenesis and our efforts to combat viral infection. Mosquito‐borne flaviviruses, including the dengue, Zika, yellow fever, Japanese encephalitis and West Nile viruses, cause serious human diseases in much of the world. A growing number of diverse functions has been discovered for the enigmatic virulence factor known as NS1: it is an essential cofactor in viral genome replication, a mediator of the host immune response, and a trigger of host vascular leakage. NS1 lacks precedent in the structure and sequence databases, so an accurate 3D structure was key to understanding the basis for its various functions. A high‐throughput survey of expression conditions in baculovirus‐infected insect cells was essential to identifying conditions for production of recombinant NS1 in its natural glycosylated, disulfide‐linked form. We solved a crystal structure of West Nile virus NS1 from the anomalous scattering of the native sulfur atoms using an 18‐crystal data set [1,2]. The structure revealed a previously unknown protein fold with a fundamentally dimeric architecture, and led to assigned functions for two of the three NS1 structural domains. Subsequent structures of NS1 from dengue virus and Zika viruses established the basis for its membrane association in cells and its lipid encapsidation when secreted [3]. Recently discovered functions of this remarkable virulence factor emerged in follow‐up studies that built upon the crystal structures. Prime among these is the discovery that the NS1 protein, in a mouse model of dengue disease and in absence of virus, can induce the vascular leak that is a hallmark of severe dengue disease [4,5]. Clues to the molecular mechanism of NS1‐induced endothelial dysfunction emerged from a study of the protection afforded by a monoclonal antibody and the structure of the Fab fragment bound to the NS1 epitope [6].

[1] Akey DL et al. & Smith JL (2014) Science 343, 881‐885.

[2] Akey DL et al. & Smith JL (2014) Acta Crystallogr D70, 2719‐2729.

[3] Brown WC et al. & Smith JL (2016) Nature Struct Molec Biol 23, 856‐867.

[4] Beatty PR et al. & Harris E (2015) Science Trans Med 7, 304ra141.

[5] Modhiran N et al. & Young PR (2015) Science Trans Med 7, 304ra142.

[6] Biering SB, Akey DL et al. Smith JL & Harris E (2021) Science 371, 194‐200.
Using Single Cell Omics to Understand Posterior Neural Crest Differentiation in Zebrafish
Authors: Uribe Rosa A. , Howard Aubrey A. G.
Published: May 2022

Neural crest cells (NCCs) are a migratory, multipotent, and transient stem cell population essential to vertebrate development. Born along the neural tube, NCCs are regionally specified along the anterior‐posterior axis to contribute to a vast number of cell lineages; such as craniofacial cartilage, pigment cells, and large aspects of the peripheral nervous system. In our recently published single‐cell RNA‐sequencing (scRNA‐seq) analysis of posterior NCC lineages in zebrafish embryos, we discovered a combinatorial expression code of transcripts that encode for posterior Hox transcription factors, which was especially specific to NCC‐derived neural lineages. While Hox expression combinations had been characterized within pre‐migratory and recently delaminated cranial NCCs in prior studies, such a high‐resolution signature had not been described within the context of posterior NCC lineages during their differentiation. Here, we report a lifetime atlas of NCC and NCC‐derived cells along the posterior zebrafish body, greatly expanding our prior analyses. To achieve this, several published and publicly‐available zebrafish scRNA‐seq studies characterizing NCC and NCC‐derived cells were computationally merged with our prior data sets and integrated, encompassing: 24 hours post fertilization (hpf), 48‐50 hpf, 68‐70 hpf, 5 days post fertilization (dpf), juvenile, and adult tissues—producing a cohesive distribution of cell identities. Within the lifetime atlas, various Hox gene transcript signatures were observed where numerous discrete cell lineages formed over time and unique Hox expression codes resolved within these incipient lineages. The generation of a multi‐stage comprehensive transcriptional atlas from multiple scRNA‐seq studies will serve as a valuable tool for the NCC and zebrafish communities. Additionally, this atlas of cell lineages demonstrates the complexity and robustness of combinatorial Hox expression codes in posterior NCC throughout development and suggests possible functional roles therein.
MicroRNAs promote neural crest multipotency
Authors: Parchem Ronald
Published: May 2022

Restriction of developmental potential occurs when pluripotent cells undergo gastrulation and germ layer specification. Although cranial neural crest cells are specified from the ectoderm, they are capable of generating both ectodermal and mesodermal lineages. How mammalian neural crest give rise to multiple lineages is not well understood. Here, we use single‐cell ATAC sequencing to characterize chromatin accessibility of cranial neural crest and identify a transient increase in accessibility during specification. This increase in chromatin accessibility coincides with co‐expression of both pluripotency and neural crest transcriptional programs. Analysis of the differentiation trajectory during neural crest specification using single‐cell mRNA sequencing revealed that pluripotent cells of the anterior epiblast resolve into two populations of premigratory cranial neural crest corresponding to ectoderm and mesoderm fates. Our data identify two populations of premigratory cranial neural crest cells that deploy distinct pluripotency programs and rely upon post‐transcriptional gene regulation to expand developmental potential and direct cell fate.
Musculoskeletal and Biomechanical Adaptations Post‐Amputation
Authors: Finco MG
Published: May 2022

Individuals with lower‐limb amputations tend to experience a wide variety of negative secondary health conditions associated with impaired functional mobility. Reduced musculoskeletal and biomechanical loading on the prosthetic limb compared to the intact limb has been associated with increased risks of experiencing falls and developing overuse injuries, which are prevalent in this population. Further understanding of musculoskeletal and biomechanical asymmetries in this population could help inform interventions to proactively improve musculoskeletal health, as well as reduce risks of experiencing falls and developing overuse injuries.

This presentation will discuss a range of our structural, physiological, and gait findings from the cellular level in cadavers to clinical rehabilitation in living individuals. Specifically, we will discuss: 1) structural adaptations of bone mineral density and histological examination of muscle fiber types, 2) physiological adaptations of hip and knee joint spaces as an indicator of osteoarthritis and cross‐sectional muscle area as an indicator of muscle atrophy, and 3) gait adaptations and the potential of wearable sensors to predict fall risk.

Overall, our findings suggest increased risks of osteopenia/porosis, muscle atrophy/sarcopenia, and osteoarthritis in this population. Specific musculoskeletal screenings, rehabilitation exercises, clinical outcome measures, and gait parameters may help clinicians proactively assess and reduce these risks to improve functional mobility in this population.
Maximizing Opportunities for Anatomy Learning: Use of Authentic OSPE as Part of Assessment in Anatomy
Authors: Inuwa Ibrahim M. , Srinivasan Dinesh Kumar , Taranikanti Varna
Published: May 2022

In the care of patients, a practicing physician performs a selected and integrated set of individually skillful acts that are pertinent to each patient encounter. These include, for example, engaging the patient in a professional relationship, taking a clinical history, performing a mental and physical examination, performing, or initiating clinical tests or procedures, and undertaking diagnostic and therapeutic interventions. From an analytic perspective, these component acts of medical care reflect the generic competencies which comprise the practitioner’s basic clinical method1.

Skill learning requires the demonstration of skill proficiency that must be observable. This observation is necessary to evaluate performance. Moreover, learners need repeated and deliberate practice followed by constructive feedback to continually refine and improve their performance of the skill. Therefore, the evaluation of skill proficiency requires the direct involvement of a trained observer, such as a supervising expert or an experienced patient2.

The utility or value of assessment items (question used in an examination) depends on; their validity, reliability, educational impact, cost, and acceptability3. For instance, a written examination item had good value and utility if it tests learning in the knowledge domain. In the same way, a written examination item has poor utility if used for testing psychomotor skills.

The so‐called OSPE (Objective Structured Practical Examination) has its origins in physiology4 where competence in performing physiological tests (e.g. Rinne’s test) are examined through observation by an examiner using a structured checklist (similar to Objective Structured Clinical Examination, OSCE). Within the context of medical education, an activity could be regarded as a clinical skill if it satisfies three conditions namely, the activity must be demonstrable, observable, and employs using knowledge, psychomotor and attitude components of learning (Fig 1).

Anatomy learning in medical education underpins the development of clinical reasoning, understanding of medical imaging, the basis of clinical procedures, and physical examination of patients. An authentic utilization of the concept of OSPE in anatomy education should be in the context of evaluating a true skill competence. This will include evaluating competence in physical examination and/or clinical procedural skill (Fig 2). In current undergraduate medical education, these skills and more are now part of a comprehensive and integrated clinical skills curriculum.

References

AAMC, (2005). Recommendations for Clinical Skills Curricula for Undergraduate Medical Education. Association of American Medical Colleges.

Duvivier et al. (2011) BMC Medical Education 11:101

Van der Vleuten CPM, (1996). Advances in Health Sciences Education 1 (1), 41‐67

Nayar U et al. (1986). Med Educ 20 (3):204‐9
Can Simulation be a Learning and Assessment Tool for Collaborative Learning in the Preclinical Years?
Authors: Srinivasan Dinesh Kumar , Taranikanti Varna , Inuwa Ibrahim M.
Published: May 2022

Collaborative learning cases (CLC) is a new model of teaching and learning in healthcare education based on patient problems. Basic medical sciences and clinical sciences are integrated in case‐based scenarios simulating with real‐life situations1. The most common problem in the medical curriculum is that medical students have poor understanding of clinical conditions due to the inability to apply basic concepts to clinical practice. This is largely due to some curricula having a didactic teaching pedagogy with a teacher‐centric and discipline‐specific format along with content overload. The imperative was to develop teaching‐learning formats based on collaborative learning, breaking away from the traditional didactic large group lecture sessions. This would promote self‐directed, student‐centred learning, which would lead to deeper learning, the acquisition of meaningful content and consequently, ideal educational outcomes2. Furthermore, these learning methods would promote and develop domain‐independent skills such as collaboration, respect, leadership, communication and research skills, professionalism/ ethical behaviours, and lifelong learning skills.

CLCs also serve as the capstone to align the lectures, tutorials, simulations, and practical sessions. Prior to a CLC session, students take the pre‐reading and pre‐quiz (Fig. 1), and the in‐class activities are facilitated by trained tutors (Fig. 2). During the CLC, a simulated patient (SP) and videos are shared in a sequential manner to facilitate discussion and strengthen student clinical reasoning skills. Evaluation of the CLCs are conducted through surveys involving students, tutors and SPs who observe the interaction between them and the students. These feedbacks are valuable and are frequently used as formative and summative assessment.

Thus, CLCs can help students to better understand the relevance of basic medical sciences by integrating it with clinical sciences, encourage deeper learning, promote collaboration and lifelong learning. In this symposium, we will discuss the rationale and process of developing CLCs as well as the strengths and limitations. Further, we will explore these ideas in more details and engage in a collegial discussion that will broaden our perspective on collaborative learning.

References

Thistlethwaite JE, Davies D, Ekeocha S, Kidd JM, MacDougall C, Matthews P, Clay D. The Effectiveness of Case‐Based Learning in Health Professional Education. A BEME Systematic Review: BEME Guide No. 23. Medical Teacher. 2012; 34(6),e421‐e444.

Samarasekera DD, Nayak D, Yeo SP, Gwee, MCE. Teaching for effective learning in higher education: Focusing on learning and moving from a “based learning” mind‐set. Asian Journal of the Scholarship of Teaching and Learning. 2014;4(2): 113‐123.
Tril dampens Nodal signaling through Pellino2‐ and Traf6‐mediated activation of Nedd4l
Authors: Christian Jan L. , Kim Hyung‐Seok , Green Yangsook S.
Published: May 2022

Toll‐like receptor 4 (Tlr) interactor with leucine‐rich repeats (Tril) functions as a Tlr co‐receptor to mediate innate immunity in adults. In Xenopus embryos, Tril triggers degradation of the Transforming Growth Factor ß (Tgfß) family inhibitor, Smad7. This enhances Bone morphogenetic protein (Bmp) signaling to enable ventral mesoderm to commit to a blood fate. Here we show that Tril simultaneously dampens Nodal signaling by catalytically activating the ubiquitin ligase Nedd4l. Nedd4l then targets Nodal receptors for degradation. How Tril signals are transduced in a non‐immune context is unknown. We identify the ubiquitin ligase Pellino2 as a protein that binds to the cytoplasmic tail of Tril, and subsequently forms a complex with Nedd4l and another E3 ligase, Traf6. Pellino2 and Traf6 are essential for catalytic activation of Nedd4l, both in Xenopus and in mammalian cells. Traf6 ubiquitinates Nedd4l, which is then recruited to membrane compartments where activation occurs. Collectively, our findings reveal that Tril initiates a non‐canonical Tlr‐like signaling cascade to activate Nedd4l, thereby coordinately regulating the Bmp and Nodal arms of the Tgfß superfamily during vertebrate development.
Genetics of Craniofacial Variation in the Domestic Pigeon
Authors: Shapiro Michael D. , Boer Elena F.
Published: May 2022

The domestic rock pigeon (Columba livia) comprises more than 350 breeds with spectacular variation in a variety of anatomical and behavioral traits. Diversity in the beak skeleton is particularly striking, and ranges from the short, blunt beak of the “owl” breeds to the elongated, curved beak of the Scandaroon. We used a combination of laboratory crosses and whole‐genome resequencing to map the genetic architecture of beak variation among pigeon breeds. We found that beak reduction mapped to a region of the Z chromosome that explains more than half of the variance in craniofacial morphology in a laboratory cross. Fine‐mapping across numerous breeds showed that this region includes ROR2, which encodes a receptor tyrosine kinase protein that plays key roles in skeletal development. Short‐beak pigeons have a missense mutation in ROR2 that is predicted to be deleterious. In contrast, the genetic architecture of beak elaboration was more complex, with several loci controlling smaller proportions of size and shape differences. Some of these loci control coordinated changes between different structures, while others explain variation in the size and shape of specific skull and jaw regions. In this and other studies of both wild and domestic avian species, major shifts in beak morphology can result from changes to a single gene and appear to be relatively simple, or they can be complex with detectable effects throughout the genome.
The Importance of Gender Inclusive Terminology in Anatomy Education
Authors: Haseen Ben
Published: May 2022

Current medical and health care programs lack formal and longitudinal integration of gender inclusive curricula, including consistent and up to date use of gender inclusive language. This roundtable presentation will focus on how moving towards more gender inclusive language when teaching pelvic anatomy will benefit the professor‐student relationship between anatomy educators and their students. Gender neutral language also creates a framework for future medical practitioners to obtain gender inclusive histories with their patients. Patients who are gender minorities are often subject to gender dysphoria during pelvic examinations due to a lack of gender inclusive language and clinical training among medical students in the traditional medical school curriculum. The current use of pelvic anatomy language can subject transgender and gender expansive students to feeling ostracized or like an invisible demographic in the classroom setting. We must teach students culturally sensitive language before students begin clinical practice to promote effective patient‐provider relationships, thereby optimizing outcomes for transgender and gender expansive patients (i.e “person who is pregnant” or “person with a prostate”). This session will address several questions relevant to developing a gender inclusive classroom environment. A lecture‐style presentation will be given followed by small group discussion to address the following questions:

How do you create a learning environment that is inclusive to all students?

How do you incorporate pre‐established curricula into your courses to gender inclusive cultural sensitivity and language?
Paligenosis: A conserved program differentiated cells use in regeneration and misuse in cancer
Authors: Mills Jason
Published: May 2022

This presentation will explore the re‐mergence of cell plasticity as a way to understand how tissues repair themselves after injury. Before the hegemony of stem cell theory during the later decades of the twentieth century, it was mostly understood that cells could be plastic in adapting to injury. For example, even by 1900, it had been proposed that differentiated cells must have a program in cases like experimental partial hepatectomy, for switching their metabolic program from focusing energy on performing physiological functions to focusing energy on cell division. Our lab is beginning to identify the molecular mechanisms that dictate just such a shared program, which has been termed paligenosis. Paligenosis involves three sequential stages, each of which can be blocked to stop the entire program: autodegradation (with massive upregulation of lysosomes and autophagy), induction of progenitor gene expression, and then cell cycle re‐entry. We discuss how there may be paligenosis‐dedicated genes that regulate the energy hub mTORC1 to allow proper paligenosis, and we discuss how aberrant paligenosis may lead to a chronic precancerous (metaplastic) state and increase risk for cancer.
Spinning the Matrix – Mechanisms of Basement Membrane Secretion and Assembly
Authors: Horne‐Badovinac Sally
Published: May 2022

Basement membranes (BMs) are sheet‐like extracellular matrices that line the basal surfaces of epithelial tissues and surround muscles, adipose tissue, and nerves. My lab studies how regulated changes to BM architecture contribute to tissue morphogenesis. In Drosophila, elongation of the initially spherical egg chamber coincides with the generation of a polarized network of fibrils in its surrounding BM. We found that BM fibrils are assembled from newly synthesized proteins in the pericellular spaces between the egg chamber’s epithelial cells and undergo oriented insertion into the planar BM network by directed epithelial migration. We further found that a Rab10‐dependent secretion pathway ensures that a subset of new BM proteins exit the cell through a basal region of the lateral membrane for fibril formation. Rab10 recruits kinesin motors to BM secretory vesicles and transports them to this location on a polarized microtubule array. Finally, by manipulating Rab10 function, we showed for the first time that BM fibrils play an instructive role in egg chamber elongation. This work identifies a novel intracellular trafficking pathway for BM proteins and highlights how regulated protein secretion can synergize with tissue movement to build a polarized BM architecture that controls tissue shape.
The Evolutionary History of Human Microbiota and Why it Matters for Human Health Today
Authors: Weyrich Laura S.
Published: May 2022

Understanding the evolutionary history of microbial communities within the human body (microbiota) will provide key insights into the origins of numerous modern‐day diseases. Ancient microbial DNA preserved in calcified dental plaque (calculus) now provides an opportunity to reconstruct past oral microbiota and examine how these microbes are linked with health and disease through time. We use High Throughput Sequencing to obtain ancient and modern microbial DNA from dental calculus on four continents over the past 48,000 years, reconstructing distinct oral microbiota evolutionary histories at each location. Highly resolved microbiota histories in Europe suggest that local environments, adoption of different diets, interbreeding with other hominids, and exposure to the Industrial Revolution are key drivers of microbiota shifts over time and likely underpin both oral and chronic disease origins. On other continents, oral microbial communities were distinct from those in Europe, highlighting the need to include diverse populations in evolutionary reconstructions. For example, South American oral microbiota was influenced by corn utilization and adaptation to specific environments (i.e., high altitude vs coastal) and contained distinct species linked with oral disease. As microbiota histories in each location are distinct, we theorize that they play distinct roles in the development of disease, both oral and systemic, across different populations, with profound implications for the Indigenous health gap. Together, these data provide the first glimpse of global human microbiota evolution in real‐time and provide the foundation to understand why certain bacterial communities are now linked to disease in a modern world.
Micronutrient Balance Related to Neural Tube Defects and Prevention
Authors: Niswander Lee , Li Huili , Kakebeen Anneke
Published: May 2022

Neural tube defects (NTDs) are a common congenital disorder resulting from failed neural tube formation, the precursor of the brain and spinal cord. The complex etiology of NTDs involve both genetic and environmental factors, thus investigating gene‐environment interactions is critical to understanding how NTDs occur or how NTDs may be prevented. For example, iron deficiency is among the most prevalent micronutrient deficiencies in pregnancy and there is evidence that iron deficiency can increase the risk of NTDs. Folic acid (FA) fortification in grain was implemented in the US in 1998 and now in many countries for the purpose of prevention of neural tube defects (NTDs). In 2017, the US Preventive Services Task Force further recommended the consumption of FA‐containing multivitamin/minerals (MVM) for women of childbearing age. Despite the great benefit of FA on NTD prevention, NTDs remain a serious risk.

Our studies focus on mouse models of NTDs and I will discuss two projects. First, the benefits of MVM supplementation are emphasized, but a comparison between MVM supplementation and FA alone on neural tube closure and organ development has not been evaluated, particularly in the context of genetic mutations that lead to NTDs. Using a set of NTD models we have compared MMV to FA supplementation. MVM supplementation shows better improvement than FA alone in the penetrance of spinal and cranial NTDs. We are also using human iPSCs to generate organoids that assume a shape similar to the human spinal neural tube, and display neural tube characteristics, for example apical constriction and interkinetic nuclear migration. Subjecting the organoids to various molecular perturbations, such as Rho‐kinase inhibitor‐induced defects in apical constriction, we have found that both MVM and FA largely prevents this molecular deficit. The goal is to use the mouse NTD model and organoid system to better understand how FA/MVM act to prevent NTDs.

Second, we are striving to move beyond the relatively non‐specific recommendations of FA/MVM supplementation to more personalized therapies that take into account the molecular underpinning of the NTD. For example, Iron homeostasis is not only controlled by the concentration of iron in diet, but by proteins responsible for its cellular uptake and metabolism. Sorting nexin 3 (Snx3) is known to regulate recycling of the transferrin receptor (TFRC), a mechanism necessary for cellular uptake of iron, and when Snx3 is knocked out in mice, embryos develop cranial NTDs. We hypothesize that in Snx3 mutants, mistrafficking of TFRC results in disrupted iron homeostasis which contributes to the failure of NT closure. Our current studies are evaluating whether intracellular iron levels are altered in Snx3 mutants and whether maternal diets supplemented with iron can prevent NTDs in the Snx3 background. The hope is that by taking into account the biological process that is disrupted, more tailored therapies can be envisioned to better prevent NTDs.
Role of Pharmacological Modulation of Tonic Inhibition in Hippocampal Sharp Wave Ripples Amplitude and Place Cell Firing Dynamics
Authors: Ratner Marcia , Downing Scott , Guo Ouyang , Odamah Kathryn A. , Stewart Tara , Kumaresan Vidhya , Xia Weiming , Farb David
Published: May 2022

Hippocampal hyperactivity is a hallmark of memory dysfunction associated with age related mild cognitive impairment (aMCI) and Alzheimer’s disease, leading to the hypothesis that hippocampal trisynaptic circuit hyperactivity impairs memory function. As a test of this hypothesis, we sought to pharmacologically recapitulate hyperactivity in young adults by attenuating tonic inhibition in the hippocampal trisynaptic circuit. We used chronically implanted arrays of 96 electrodes arranged as tetrodes and 32 channel silicon probes to record place cell activity within and across the CA1 subregion of young adult rats either foraging in familiar and novel environments or resting in a familiar environment (without foraging) while awake but immobile for ripple band recordings. We demonstrate that oral administration of the nootropic drug α5IA, a selective negative modulator of tonically active predominantly extrasynaptic α5 GABA receptors, enhances CA1 place cell firing rates but does not augment spatial information content or pattern separation expected a priori to reflect nootropic drug action. This conundrum is resolved by the finding that α5IA substantially increases the sharp wave ripple (SPW‐R) amplitude, which is known to correlate with improved remembering. We replicated to result in three strains of rats (Long Evans, Fisher 344, and Sprague Dawley) and found that the outcomes were not strain specific. These observations indicate that the nootropic actions of α5IA may result from enhancement of aspects of memory function influenced by CA1 SPW‐R amplitude such as consolidation of encoded information. We posit that modulation of ripple dynamics may be controlled via alterations in extrasynaptic tonic inhibition mediated in part by α5 GABA‐A receptors.