bluuebunny/crossref_metadata_2025_split huggingface dataset:
Decoding molecular plasticity of the dark proteome
Authors: Lemke Edward A. 
Published: May 2022

The mechanisms by which intrinsically disordered proteins (IDPs) engage in rapid and highly selective binding is a subject of considerable interest and represents a central paradigm to nuclear pore complex (NPC) function. Nuclear transport receptors (NTRs) can move through the central channel of the NPC which is filled with hundreds of phenylalanine‐glycine‐rich nucleoporins (FG‐Nups) reaching millimolar concentrations with elusive conformational plasticity. Since site‐specific labeling of proteins with small but highly photostable fluorescent dyes inside cells remains the major bottleneck for directly studying protein dynamics in the cellular interior, we have now developed a semi‐synthetic strategy based on novel artificial amino acids that are easily and site‐specifically introduced into any protein by the natural machinery of the living cell via a newly developed thin‐film synthetic organelle that equips the living cell with up to three genetic codes. This allowed us to develop an experimental approach combining site‐specific fluorescent labeling of IDPs in non‐fixed cells with fluorescent lifetime imaging microscopy (FLIM) to directly decipher the plasticity of FG‐Nups via FRET. Our study enabled a conformational look on the condensated IDPs in the sub‐resolution (roughly (50 nm)3 small cavity) cavity of the NPC. By measuring the end‐to‐end distances of different segments of the labeled FG‐Nups using FLIM‐FRET, we can extract the scaling exponent, which directly describes the conformations of FG‐Nups at their functional status as well as the solvent quality in the cellular and even inner NPC environment.Reinkemeier CD, Lemke EA. Dual film‐like organelles enable spatial separation of orthogonal eukaryotic translation. Cell. 2021 Sep 16;184(19):4886‐4903.e21Celetti G, Paci G, Caria J, VanDelinder V, Bachand G, Lemke EA. The liquid state of FG‐nucleoporins mimics permeability barrier properties of nuclear pore complexes. J Cell Bio. (2020) Jan 6;219(1).Reinkemeier CD, Estrada Girona G, Lemke EA, 2019 Designer membraneless organelles enable codon reassignment of selected mRNAs in eukaryotes. Science, Mar 29;363(6434)Nikić I, Estrada Girona G, Kang JH, Paci G, rei S, Koehler C, Shymanska NV, Ventura Santos C, Spitz D, Lemke EA, Debugging Eukaryotic Genetic Code Expansion for Site‐Specific Click‐PAINT Super‐Resolution Microscopy. Angew Chem Int Ed Engl. (2016) Dec 23;55(52):16172‐16176
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.
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.
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.ReferencesThistlethwaite 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.
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?
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.
SARM1 NAD Hydrolase Deficiency Normalizes Fibrosis and Ameliorates Cardiac Dysfunction in Diabetic Hearts
Authors: Lee Chi Fung , Nizami Hina , Gu Haiwei , Light Christine 
Published: May 2022

Decline in cellular NAD levels emerges as a hallmark of diseases such as diabetes and heart failure. Strategies to activate NAD synthesis pathways and replenish NAD levels have shown promises to treat heart disease. However, how NAD consumption mechanisms lead to NAD depletion and disease pathogeneses are less understood. SARM1 is an intracellular NAD hydrolase, and its role in heart disease has never been investigated. We therefore hypothesized that SARM1 deficiency may protect hearts against diabetic cardiomyopathy. Male C57BL/6 wild‐type (WT) and SARM1‐KO mice were challenged with 16‐week diabetic stress initiated by streptozotocin injections (STZ). Longitudinal cardiac function was measured by echocardiography after 8 or 16 weeks of diabetes, and tissue and plasma samples were harvested for biochemical and molecular analyses. Chronic diabetic stress lowered cardiac NAD levels and led to progressive decline in systolic function of WT mice. Diabetic SARM1‐KO mice showed improved systolic function and increased cardiac NAD levels, compared to diabetic WT mice. Progressive decline in diastolic function induced by chronic diabetes was also improved by SARM1 deficiency. Heart weights and hyperglycemia were similar in diabetic WT or diabetic SARM1‐KO mice. Metabolomic analyses of plasma showed significant changes in 58 out of ~300 aqueous metabolites assessed when comparing non‐diabetic WT to diabetic WT plasma, including increased levels of glucose and branched‐chain amino acids. However, the 58 metabolites showed no changes in levels when comparing diabetic WT to diabetic SARM1‐KO plasma. Similarly, we found that 26 out of 85 lipid species showed significant changes when comparing non‐diabetic WT to diabetic WT plasma, and only one of these 26 lipid metabolites showed a significant change between diabetic WT and diabetic SARM1‐KO plasma. The data suggest that cardioprotection in SARM1‐KO mice was likely due to the reversal of cardiac pathogenic mechanisms but not improved systemic metabolic state.To determine how SARM1 deficiency affects cardiac NAD metabolism, expression of genes in NAD metabolic pathways were assessed. Levels of Bst1 and Cd38 did not change in SARM1‐KO hearts, suggesting that SARM1 deficiency did not induce compensatory changes in expression of the other NAD hydrolases. SARM1‐KO hearts showed lower expressions in some of the NAD consuming genes (e.g. Sirtuins) and NAD synthesis genes (e.g. Nmnats). Cardiac dysfunction marker, Nppb expression, was induced in diabetic WT hearts, and was reversed by SARM1 deficiency. Cardiac fibrosis and pro‐fibrotic genes (e.g. ctgf) were induced in diabetic WT hearts and were suppressed by SARM1 deficiency. Using the total SARM1 KO mice, our data support that SARM1 deficiency normalizes decline in NAD levels and pro‐fibrotic pathways to ameliorate diabetic cardiomyopathy. Further experiments are warranted to dissect the cell‐type specific roles of SARM1 in diabetic hearts.