bluuebunny/crossref_metadata_2025_split huggingface dataset:
Antidepressant Effect of Methanol Root Bark Extract of Acacia seyal: Involvement of Monominergic, Nitric Oxide and Opiodergic Pathways
Authors: Magaji Mohammed Garba , Gambo Amanda Yelmis , Shehu Aishatu Garba , Danjuma Nuhu Mohammed 
Published: April 2020

BackgroundDepression is a common mental disorder which affects more than 300 million people and is a leading cause of disability worldwide (
WHO, 2017). Available antidepressants are only effective in 50% of patients (
Simon, 2002). The treatment resistance has been linked to the multiple pathways involved in the pathology of depression. Acacia seyal root is used traditionally for the management of depression (
Shehu, 2017). However, there is no report of the scientific validation of this ethnomedicinal claim.ObjectiveTo determine the antidepressant activity of the methanol root bark extract of A. seyal (AS) and its possible mechanism(s) of antidepressant action.Materials and MethodsEthical Approval for the use of laboratory animals was sought and obtained from Ahmadu Bello University Committee on Animal Use and Care (ABUCAUC/2018/094). Antidepressant activity of AS was evaluated using tail suspension test (TST) at a dose of 250, 500 and 1000 mg/kg. For the mechanistic studies, mice were pretreated with Sulpiride (50 mg/kg), Prazosin (1 mg/kg), Yohimbine (1 mg/kg), Metergoline (1 mg/kg), Cyproheptadine (3 mg/kg), L‐Arginine (50 mg/kg), L‐NNA (50 mg/kg), atropine (1 mg/kg) and naloxone (2 mg/kg) 15 minutes prior to AS (500 mg/kg) administration, then assessed using TST one hour later.ResultsThe extract (at the doses of 250–1000 mg/kg) significantly (p<0.05) decreased the duration of immobility in the TST. Sulpiride (D2 receptor antagonist), Prazosin and Yohimbine (α1 and α2 receptor antagonists respectively), Metergoline, Cyproheptadine (5‐HT1 and 5‐HT2 receptor antagonist respectively), L‐Arginine and L‐NNA (substrate and inhibitor of nitric oxide synthase enzyme respectively) and naloxone (opioid receptor antagonist) significantly (p<0.05) reversed the antidepressant effect of ASConclusionThe methanol root bark extract of Acacia seyal possesses antidepressant activity possibly mediated via the dopaminergic, serotonergic, adrenergic, nitric oxide and opioidergic pathways.Effect of Methanol Root Bark Extract of Acacia seyal on Duration Immobility of Mice in Tail Suspension TestAnimals were acutely treated with AS (250, 500 or 1000 mg kg, po), distilled water (10 ml/kg, po), or Fluoxetine (20 mg/kg, po). Each column represents the mean ± SEM of 8 animals. Data was analyzed using one‐way ANOVA followed by Bonferroni post hoc test, *p≤0.05, **p≤0.001, ***p≤0.0001 significantly different from distilled water treated group.AS=Acacia seyal, DW= 10 ml/kg of Distilled water, FTX= FluoxetineFigure 1AcknowledgementThe technical assistance of staff of the Department of Pharmacology and Therapeutics, Ahmadu Bello University, Zaria‐Nigeria is acknowledged
Staphylococcus aureus Evasion Proteins EapH1 and EapH2: Residue‐Level Investigation of an Alternative Binding Motif for Human Neutrophil Elastase
Authors: Herdendorf Timothy , Geisbrecht Brian 
Published: April 2020

The Staphylococcus aureus
Extracellular
Adherence
Protein (Eap) and its homologs, EapH1 and EapH2, are a family of secreted proteins that potently inhibit the neutrophil serine proteases Neutrophil Elastase (hNE), Cathepsin G, and Proteinase 3. Similarly to EapH1, inhibition of hNE by EapH2 is characterized by a rapid association rate (2.9×105 M−1s−1) coupled with a very slow dissociation rate (5.9×10−4 s−1), yielding an apparent inhibition constant of 2.11 nM. Due to this slow off‐rate, inhibition of hNE by EapH2 is time‐dependent. A phenylalanine in EapH2 replaces the leucine in EapH1 that sits over the hNE catalytic serine and creates a potential steric clash. Indeed, the EapH1 L59F mutant is severely decreased in its ability to inhibit hNE (~9,500‐fold). When compared to the EapH1:hNE co‐crystal structure, a model of the EapH2:hNE complex predicts an alternative binding motif comprised of EapH2 residues 120 – 127. These putative interfacing residues were individually mutated and kinetically interrogated. The EapH2 N127A mutant resulted in the largest decrease in hNE inhibition (~200‐fold) and loss of the time‐dependent characteristic. Surprisingly, the time‐dependent characteristic was still abolished in the EapH2 T125A mutant, even though it was less perturbed in hNE inhibition (~25‐fold). T125 forms an intra‐molecular hydrogen bond to the carbonyl oxygen of N127 in the EapH2 crystal structure. Given these observations, we conclude (i) that EapH2 has an altogether distinct hNE binding motif than EapH1, (ii) that N127 is the main functional determinant in EapH2, and (iii) that T125 serves an ancillary role aiding in the optimal orientation of N127.Support or Funding InformationFunding was provided by a grant from the National Institute of General Medical Sciences (R01‐GM121511) to B.V.G.Comparison of EapH1 and EapH2 binding motifs.(A) EapH2 (magenta) binding to hNE, based on the energy minimized model. (B) EapH2 residues involved in the interface with hNE. (C) EapH1(green) binding to hNE (PDB:4nzl). (D) EapH1 residues involved in the interface with hNE.Figure 1
Threshold Concepts in Medical Physiology
Authors: Derias Nardin , Loftus Stephen , Kamel-ElSayed Suzan 
Published: April 2020

INTRODUCTIONThreshold concepts are those ideas that learners often find difficult, but must understand in order to master the discipline. In order for a concept to be defined as a threshold concept, it must meet at least three out of five characteristics: transformative, irreversible, integrative, bounded, and troublesome. In the realm of threshold concepts research, there has been very little conducted in regards to medical school curriculum specifically. Medical physiology has often been a challenging core topic for medical students. The goal of this study is to better understand what students considered to be threshold concepts in physiology so medical school curricula can better address the needs of students and ensure that they have a strong foundation.METHODSVolunteers from a medical school were recruited and three focus groups were conducted during the preclinical years. Each focus group consisted of 7–8 students. The focus groups began with a brief introduction of what threshold concepts are followed by the presentation of a brief clinical case. The students were given a case that integrated knowledge that had been taught in organ system courses prior to the focus groups. Students were asked to come up with a differential diagnosis and suggestions for underlying pathophysiology. After this, they were allowed to ask questions to gather a history and explain the underlying physiological concepts that led them to their differential diagnoses. A fourth focus group was conducted in the early weeks of the clinical years and after USMLE Step 1 examination. Following all focus groups, the audio was transcribed and thematic analysis was conducted.RESULTSBased on the four focus groups conducted, several potential candidate threshold concepts emerged including secondary messenger pathways, Starling forces, preload and afterload, and cell membrane potentials.CONCLUSIONThis study identified a set of candidate threshold concepts in medical physiology from the students’ perspective. Further characterization of these candidate threshold concepts can be used as a foundation for designing an effective and powerful physiology curriculum.Figure 1
How Well Does the Biochemistry Authentic Scientific Inquiry Lab (BASIL) Promote Expert Understanding of Michaelis‐Menten Kinetics by Undergraduate Students?
Authors: Roberts Rebecca , Palaez Nancy , Anderson Trevor 
Published: April 2020

BASIL is a course‐based undergraduate research experience (CURE) that focuses on enzyme function prediction. The Protein Data Bank (PDB) contains the structures of over 4000 proteins of unknown function and BASIL provides a basis to assign functions by combining in silico and in vitro analyses. The final BASIL module focuses on a kinetic analysis of the purified protein. In this study we investigate if the BASIL CURE promotes the development of student understanding of Michaelis‐Menten kinetics. Through content analysis of the written BASIL modules and inductive analysis of instructor interview transcripts, we have determined an “expert answer” that has been categorized into three overarching themes: the function of an enzyme is to convert a substrate to a product; the conversion of substrate to product can be tested with experimental assays; and data from assays can be visualized with a graph to characterize the kinetics of enzyme function. These ideal answer subthemes then were aligned with the course‐based undergraduate research abilities (CURAs) identified by Irby et al. (2018). We analyzed student research posters and coded semi‐structured interviews with students who have participated in BASIL at Ursinus College in order to compare them with the “expert answer”. Results suggest that students appear to understand the function of an enzyme and can interpret findings from an activity assay, yet they are lacking in a full understanding of the required data manipulation or underlying meaning of a graphical analysis of kinetics data. In the longer term, this research is aimed at informing improvements in the teaching, learning, and assessment of this area of the BASIL CURE. In particular, the findings will focus on addressing the various identified student difficulties so that the BASIL CURE can come closer to achieving its main goal of developing students as research scientists.Support or Funding InformationThis work was supported by the National Science Foundation under grants #1503811 & 1709805 for the Biochemistry Authentic Scientific Inquiry Lab (BASIL) CURE and #1346567 for the Advancing Competencies in Experimentation ‐ Biology (ACE‐Bio) Network. Any opinions, findings, and conclusions or recommendations expressed in this workshop are those of the authors and do not necessarily reflect the views of the National Science Foundation.Biochemistry Authentic Scientific Inquiry LabFigure 1
Energetic dependencies dictate folding mechanism in a complex protein
Authors: Kaiser Christian , Chen Xiuqi , Liu Kaixian 
Published: April 2020

Large proteins composed of multiple domains are abundant in all proteomes, but their folding and structural dynamics remain poorly understood. Multi‐domain proteins are thought to fold sequentially as they emerge from the ribosome, which minimizes interdomain misfolding. Once folded, domains interact with each other through the formation of extensive interfaces that are important for protein stability and function. In elongation factor G (EF‐G), a highly conserved protein composed of five domains, the two N‐terminal domains form a stably structured unit co‐translationally. Using single‐molecule optical tweezers, we have defined the steps leading to fully folded EF‐G. We find that the central domain III of EF‐G is highly dynamic and does not fold upon emerging from the ribosome. Surprisingly, a large interface with the N‐terminal domains does not contribute to the stability of domain III. Instead, it requires interactions with its folded C‐terminal neighbors to be stably structured. Because of the directionality of protein synthesis, this energetic dependency of domain III on its C‐terminal neighbors disrupts co‐translational folding and imposes a post‐translational mechanism on the folding of the C‐terminal part of EF‐G. As a consequence, unfolded domains accumulate during synthesis, leading to the extensive population of misfolded species that interfere with productive folding. Domain III flexibility enables large‐scale conformational transitions that are part of the EF‐G functional cycle during ribosome translocation. Our results suggest that energetic tuning of domain stabilities, which is likely crucial for EF‐G function, complicates the folding of this large multi‐domain protein. EF‐G thus provides an example of how distinct biological ends – robust folding and functionally important flexibility – come into conflict during protein biogenesis.Support or Funding InformationThis work was supported by a grant from the National Institutes of Health (5R01GM121567)Coupled synthesis and folding of the multi‐domain protein EF‐G. Domain III (green) is highly dynamic in the absence of fully folded domains IV (blue) and V (purple). As a consequence, co‐translational folding is interrupted. Accumulation of unfolded polypeptide results in the formation of misfolded species, sidetracking the molecule into non‐productive states and slowing down folding.Figure 1
HIV Tat Protein Induces the TGF‐β Signaling Pathway and Suppresses the CFTR Biogenesis and Activity by microRNA‐Regulated Gene‐Silencing Mechanism
Authors: Dutta Rajib Kumar , Chinnapaiyan Srinivasan , Unwalla Hoshang 
Published: April 2020

The advent of combination antiretroviral therapy (cART) has led to a dramatic decline in morbidity and mortality from HIV/AIDS. HIV infected subjects are still six times more likely to contract pneumonia compared to non‐infected age matched controls. Mortality, following an episode of bacterial pneumonia was also four times higher in HIV infected subjects compared to non‐infected controls. Thus, pneumonia can also contribute to HIV progression. Understanding the pathophysiological mechanisms that lead to microbial colonization of the airways in HIV infected patients is therefore important to public health. HIV Tat and CS can suppress CFTR function, which is a critical determinant of ASL depth and this can lead to depressed MCC and consequent microbial colonization. Our study showed that HIV‐infected cells in the airway namely alveolar macrophages, other immune cells or bronchial epithelial cells can serve as reservoirs and a source of HIV proteins like Tat which upregulates TGF‐beta mRNA in primary human bronchial epithelial cells with a corresponding decrease in CFTR mRNA. Chromatin immunoprecipitation with RNA Polymerase II demonstrated that transcription from the CFTR promoter is unaffected and blocking the miRNA processing pathway with Aurin Tricarboxylic acid (ATA) restore CFTR inhibition caused by TGF‐ beta. Our data showed that HIV infection suppress CFTR mRNA and function and blocking TGF‐beta signaling rescues this. Together this posits a strong role for (TGF‐beta induced) miRNA in Tat mediated CFTR gene silencing.Support or Funding InformationFlight Attendant Medical Research Institute (FAMRI)HypothesisFigure 1HIV Tat suppresses CFTR via common TGF‐beta signalingFigure 2
Difficulties Learning Bones and Muscles? Study at Home with 3D‐Printed Bones
Authors: Cevallos Manuel , Butler Jessica , Stabile Diana 
Published: April 2020

Some schools of Medicine are giving 3D‐skull models to students. Those models can be taken home to improve the association, memorization, and integration of structures and function in the learning process. On the other hand, studies conducted on Healthcare students reported that the most common learning styles are kinesthetic and visual.The problemThe course BIO 201 Laboratory (Anatomy and Physiology I) offers multiple topics to support lectures in a span of 15–16 weeks but with typically only one 2–3 hour session per week. In the chapters of Bones, Muscles, and Joints, the time in the lab in which the student is exposed to those materials is about three to five Labs in the semester. At that time, the student must memorize multiple structures and relate them with their function (physiological movements). Students are studying with the help of 3D models (skeleton and isolated bones) in the Lab, and 2D‐images (book or computer). In some institutions, BIO 201 labs can have digital support with 2D‐images projected to a 3D‐image, a significant advance. However, the learning style plays an essential role in healthcare students.The SurveyA voluntary survey was conducted in the BIO 201 class in Fall 2019. Of 118 students in the class, 74 students answered the survey. The primordial Learning style was 66.2% visual followed by a 25% kinesthetic. Moreover, from all the groups, 76.4% reported having difficulties in learning Bones, muscles, and joints. Interestingly, from the students having difficulties in the learning, 70.9% answered having problems to transform 2D‐images into 3D structures (visualize and identify structures in bones and 3D models). Let us remember, in most institutions, 3D models only are accessible in Lab time, and schedules on labs are not always ideal for students for extra‐reviews. In our survey, 70.5% students are studying at home with 2D‐image (book and or computer) and 19.7% from videos. Then, how can we bring bones, joints, and muscles to students with those difficulties?The feasible solutionReal 3D‐bones are expensive and bulky. The alternative is to use a 3D printer as a tool to prepare a set of bones for students. The quality these days is fantastic; bones can show features and students can mark them to identify origin and insertion of muscles. A 3D‐printed bones set can be reused and easily repaired in case of loss. 97.3% of students are willing to use them at home, and 98.6% of the group consider it an excellent tool for helping them to learn.ConclusionWe believe that 3D‐printed bone support in the BIO 201 course can help students with difficulties in the transformation from 2D‐images to 3D‐structures. It is an easy access tool and accepted by students, cheap, reusable and replaceable in case of loss. Students can easily identify a structure in the 3D models.Studying Bones, Joints and Muscles with 3D‐Printed Models at Home.Figure 1
The Filament Forming Mechanism of SgrAI Endonuclease‐Structural and Kinetic Analysis
Authors: Horton Nancy C. 
Published: April 2020

Filament formation by enzymes has recently emerged as a new paradigm of enzyme regulation
1.Wide‐spread reversible self‐assembly of enzymes in cells has also been shown to occur in all branches of life and diverse metabolic and biological pathways. We use the model system, SgrAI, to investigate the filament forming enzyme mechanism.Filaments formed by SgrAI have been structurally characterized using cryo‐electron microscopy
2 and the full reaction pathway including all rate constants has been determined using single turnover enzyme reactions, FRET, and global kinetic modeling
3–
4.The structural studies uncover the mechanism of activation of enzyme activity in SgrAI by filament formation, as well as the origin of the unusual expansion of substrate specificity in SgrAI within the filament. A conformational change in the SgrAI dimer, stabilized by protein‐protein and protein‐DNA contacts in the filament, leads directly to a shift in the active site, hypothesized to lead to stronger binding of a second catalytic Mg2+ ion. DNA structure and energetics is hypothesized to control substrate specificity and filament formation by SgrAI such that the secondary class of DNA sequences are cleaved by SgrAI only upon joining a filament formed by SgrAI bound to a primary class of DNA sequences. The full kinetic model showed a slow second order step in filament formation which is shown to control enzyme activity such that only invading phage DNA is cleaved, leaving the host genome untouched. This model also shows that the filament forming mechanism is superior in fast activation of enzyme activity upon initial recognition of primary DNA sequences.Using the SgrAI endonuclease as a model system to study filament forming enzymes, we have discovered that the enzyme is activated by stabilization of an activated conformation by contacts made within the filament. Control of the equilibrium between a low activity, non‐filamentous state and the high activity, filamentous state by DNA structural energetics gives rise to the unusual apparent expansion of DNA sequence specificity of SgrAI by filament formation. Simulations using the full kinetic pathway reveal an advantage in the filament mechanism over other non‐filamentous mechanisms in the speed of activation in response to invading phage DNA, giving strong evolutionary advantage to this filament forming mechanism.Support or Funding InformationThis work was supported by the National Science Foundation under Grant No. MCB‐1410355.
Lepidium meyenii L. and Isolated Macamides Reduces Lipopolysaccharide‐Induced Inflammatory Response in THP‐1 Cells
Authors: Gonzales-Urday Ana Lucia , Martínez-Málaga Jimena Alexandra , Rondón-Ortiz Alejandro Nico , Böhlke Mark , Chocano-Coralla Edward Joel , Pino-Figueroa Alejandro 
Published: April 2020

Inflammation is a vital component of the immune system response to injury and infection, and it is linked to autoinflammatory and autoimmune disorders. Toll‐like receptor 4 (TLR4) has been identified as a receptor for lipopolysaccharide (LPS), a bacterial endotoxin which can induce systemic inflammation and sepsis. The LPS/TLR4 pathway triggers downstream signaling cascades, producing proinflammatory cytokines and chemokines. Therefore, the search for novel compounds that can reduce inflammation at this level is of great interest. The plant Lepidium meyenii L., known as maca, has attracted attention in the past several years due to its traditional uses in folk medicine, which include treating anemia and gastritis, preventing cancer, high blood pressure and depression, as well as enhancing fertility and sexual performance. Macamides are secondary metabolites isolated from maca which cause pharmacological inhibition of fatty acid amide hydrolase (FAAH), and this inhibition has been found to lead to anxiolytic, anti‐inflammatory and analgesic effects. However, the anti‐inflammatory mechanisms by which these natural compounds act remain to be elucidated. The purpose of this study was to evaluate the anti‐inflammatory effects of the n‐pentane extract of Lepidium meyenii L. (PELM), N‐(benzyl) linolenamide (compound 1) and N‐(3‐methoxybenzyl) linolenamide (compound 2) utilizing THP‐1 cells. To assess these effects, THP‐1 cells were treated with either 10 μg/mL PELM, 10 μM Cmpd 1, 10 μM Cmpd 2 or 0.5 % DMSO (vehicle); then, inflammation was induced for 24 h with 30 ng/mL LPS. Media supernatants were used to evaluate protein levels of cytokines in a human protein array. From 36 cytokines, maca and macamides reduced IL‐1β and IL‐6 protein levels following a 24 h stimulation with LPS. In order to confirm these results, ELISA was utilized to determine IL‐1β and IL‐6 cytokine levels in LPS‐stimulated THP‐1 cells. After a 24 h treatment with either 10 μg/mL PELM, 10 μM Cmpd 1 or 10 μM Cmpd 2, these treatments reduced protein levels of both cytokines IL‐1β and IL‐6. The transcriptional levels of these cytokines were also monitored by RT‐qPCR; treatment with 10 μM Cmpd 1 and 10 μM Cmpd 2 significantly decreased mRNA levels of IL‐1β. But, interestingly with a 10 μg/mL treatment of PELM the reduction of IL‐1β mRNA levels was not significant. Furthermore, IL‐6 mRNA levels were significantly reduced by the n‐pentane extract and isolated macamides. Taken together, these results demonstrated that Lepidium meyenii L. and isolated macamides reduced LPS‐induced inflammatory response by decreasing pro‐inflammatory cytokine production in THP‐1 cells.Effect of PELM, Cmpd 1 and Cmpd 2 on IL‐1β production in THP‐1 cells.Figure 1Effect of PELM, Cmpd 1 and Cmpd 2 on IL‐1β mRNA levels in THP‐1 cells.Figure 2