bluuebunny/crossref_metadata_2025 huggingface dataset:
Dinitrogen fixation rates in the Bay of Bengal during summer monsoon
Authors: Saxena Himanshu , Sahoo Deepika , Khan Mohammad Atif , Kumar Sanjeev , Sudheer A K , Singh Arvind
Published: April 2020

Biological dinitrogen (N2) fixation exerts an important control on oceanic primary production by providing bioavailable form of nitrogen (such as ammonium) to photosynthetic microorganisms. N2 fixation is dominant in nutrient poor and warm surface waters. The Bay of Bengal is one such region where no measurements of phototrophic N2 fixation rates exist. The surface water of the Bay of Bengal is generally nitrate-poor and warm due to prevailing stratification and thus, could favour N2 fixation. We commenced the first N2 fixation study in the photic zone of the Bay of Bengal using 15N2 gas tracer incubation experiment during summer monsoon 2018. We collected seawater samples from four depths (covering the mixed layer depth of up to 75 m) at eight stations. N2 fixation rates varied from 4 to 75 μmol N m−2 d−1. The contribution of N2 fixation to primary production was negligible (<1%). However, the upper bound of observed N2 fixation rates is higher than the rates measured in other oceanic regimes, such as the Eastern Tropical South Pacific, the Tropical Northwest Atlantic, and the Equatorial and Southern Indian Ocean.
Shear-induced crystallisation in binary colloidal suspensions investigated using confocal microscopy
Authors: Maßhoff P , Elsner I , Escobedo-Sánchez M A , Segovia-Gutiérrez J P , Pamvouxoglou A , Egelhaaf S U
Published: April 2020

Hard sphere colloids crystallise at large volume fractions. However, crystallisation is suppressed in the presence of large polydispersities. We investigate the effect of polydispersity on shear-induced crystallisation using binary suspensions of hard spheres. Depending on the size ratio, the samples fully crystallise, partially crystallise or remain amorphous. Using confocal microscopy, the structural changes are characterised on a single particle level. This allows us to determine the local bond order parameter, the number of nearest neighbours, the Voronoi volume, the local volume fraction and other quantities. Upon the application of shear, only minor changes of these quantities are detected in regions that remain amorphous whereas noticeable changes are observed in regions where shear-induced crystallisation occurs. These changes mainly reduce the effects of the different particle sizes on the particle arrangement. This allows substitutionally disordered crystals to form. However, with increasing size disparity the volume fraction in substitutionally disordered crystals decreases while the volume fraction in amorphous regions slightly increases. Beyond a size ratio of 1.18, the volume fraction of the crystals is smaller than the volume fraction of the amorphous regions. At the same size ratio shear-induced crystallisation ceases. The terminal size ratio of 1.18 is close to the value given by the empirical Hume-Rothery rule for metallic alloys and the corresponding polydispersity (about 0.1) is consistent with the polydispersity beyond which crystallisation is found to be suppressed.
Debunking Eurocentrism in Organizational Communication Theory: Marginality and Liquidities in Postcolonial Contexts
Authors: Cruz Joëlle M , Sodeke Chigozirim Utah
Published: April 2020

This article centers marginal organizational actors—the disenfranchised of the Global South—to remedy their theoretical erasure and disrupt the Anglo-American grand narrative of organizational communication. This task is urgent amidst discussions of decolonization and whiteness in the discipline. We reengage Western theory on liquidity, hereby conceptualized as shape-shifting and adaptive organizing, moving like a liquid at the margins. We draw on fieldworks in Nigeria and Liberia to unearth three properties of liquidity in postcolonial contexts: motion, solvency, and permeability. Motion refers to movement, solvency refers to the ability to dissolve into one's surroundings, and permeability refers to organizing that infiltrates life and vice versa. This article bears three theoretical contributions. First, it provides a blueprint to dislodge Eurocentric biases (Anglo-American) in organizational communication theory. Second, it models what decolonizing theory may look like. Finally, it provides more complex, nuanced, and inclusive theoretical accounts of liquidities in global landscapes.
Prediction of Nephrotoxicity Associated With Cisplatin-Based Chemotherapy in Testicular Cancer Patients
Authors: Garcia Sara L , Lauritsen Jakob , Zhang Zeyu , Bandak Mikkel , Dalgaard Marlene D , Nielsen Rikke L , Daugaard Gedske , Gupta Ramneek
Published: April 2020

Background

Cisplatin-based chemotherapy may induce nephrotoxicity. This study presents a random forest predictive model that identifies testicular cancer patients at risk of nephrotoxicity before treatment.

Methods

Clinical data and DNA from saliva samples were collected for 433 patients. These were genotyped on Illumina HumanOmniExpressExome-8 v1.2 (964 193 markers). Clinical and genomics-based random forest models generated a risk score for each individual to develop nephrotoxicity defined as a 20% drop in isotopic glomerular filtration rate during chemotherapy. The area under the receiver operating characteristic curve was the primary measure to evaluate models. Sensitivity, specificity, and positive and negative predictive values were used to discuss model clinical utility.

Results

Of 433 patients assessed in this study, 26.8% developed nephrotoxicity after bleomycin-etoposide-cisplatin treatment. Genomic markers found to be associated with nephrotoxicity were located at NAT1, NAT2, and the intergenic region of CNTN6 and CNTN4. These, in addition to previously associated markers located at ERCC1, ERCC2, and SLC22A2, were found to improve predictions in a clinical feature–trained random forest model. Using only clinical data for training the model, an area under the receiver operating characteristic curve of 0.635 (95% confidence interval [CI] = 0.629 to 0.640) was obtained. Retraining the classifier by adding genomics markers increased performance to 0.731 (95% CI = 0.726 to 0.736) and 0.692 (95% CI = 0.688 to 0.696) on the holdout set.

Conclusions

A clinical and genomics-based machine learning algorithm improved the ability to identify patients at risk of nephrotoxicity compared with using clinical variables alone. Novel genetics associations with cisplatin-induced nephrotoxicity were found for NAT1, NAT2, CNTN6, and CNTN4 that require replication in larger studies before application to clinical practice.
SMARCB1 Gene Mutation Predisposes to Earlier Development of Glioblastoma: A Case Report of Familial GBM
Authors: Mukherjee Sanjib , Stroberg Edana , Wang Fengfei , Morales Linden , Shan Yuan , Rao Arundhati , Huang Jason H , Wu Erxi , Fonkem Ekokobe
Published: April 2020

Glioblastoma (GBM) is the most aggressive adult brain tumor. While GBM typically occurs sporadically, familial GBM can be associated with certain hereditary disorders and isolated familial GBMs in the absence of syndrome are rare. Relevant hereditary factors have remained elusive in these cases. Understanding specific genetic abnormality may potentially lead to better treatment strategies in these patients. Here, we analyzed GBM tissue from our patient and 2 afflicted family members, with next generation sequencing to better understand the genetic alterations associated with this disease development. DNA was extracted and sequenced and the data were then analyzed. Results revealed 2 common mutations in afflicted family members; PDGFRA and HRAS. In addition, both siblings showed a mutation of the SMARCB1 gene. The sister of our patient exhibited a homozygous mutation, while our patient had heterozygous mutation of this gene in the tumor tissue. This result suggests that mutation of SMARCB1, either alone or in the presence of PDGFRA and HRAS mutations, is associated with earlier onset GBM.
CHIELD: the causal hypotheses in evolutionary linguistics database
Authors: Roberts Seán G , Killin Anton , Deb Angarika , Sheard Catherine , Greenhill Simon J , Sinnemäki Kaius , Segovia-Martín José , Nölle Jonas , Berdicevskis Aleksandrs , Humphreys-Balkwill Archie , Little Hannah , Opie Christopher , Jacques Guillaume , Bromham Lindell , Tinits Peeter , Ross Robert M , Lee Sean , Gasser Emily , Calladine Jasmine , Spike Matthew , Mann Stephen Francis , Shcherbakova Olena , Singer Ruth , Zhang Shuya , Benítez-Burraco Antonio , Kliesch Christian , Thomas-Colquhoun Ewan , Skirgård Hedvig , Tamariz Monica , Passmore Sam , Pellard Thomas , Jordan Fiona
Published: April 2020

Language is one of the most complex of human traits. There are many hypotheses about how it originated, what factors shaped its diversity, and what ongoing processes drive how it changes. We present the Causal Hypotheses in Evolutionary Linguistics Database (CHIELD, https://chield.excd.org/), a tool for expressing, exploring, and evaluating hypotheses. It allows researchers to integrate multiple theories into a coherent narrative, helping to design future research. We present design goals, a formal specification, and an implementation for this database. Source code is freely available for other fields to take advantage of this tool. Some initial results are presented, including identifying conflicts in theories about gossip and ritual, comparing hypotheses relating population size and morphological complexity, and an author relation network.
Legal framework for the interstate cooperation on development and transport of fossil natural resources of the Caspian Sea†
Authors: Janusz-Pawletta Barbara
Published: April 2020

This article focuses on the regulations of the Convention on the legal status of the Caspian Sea (hereinafter as Caspian Sea Convention), which was adopted in 2018. It regulates the development and access to Caspian fossil fuel resources and protects its environment, which are important factors for the sustainable development of the region. The main finding of this article is that the Caspian Sea Convention, having established the maritime zones, has, for the first time ever, recognized the territorial sovereignty of the individual riparian states in the Caspian Sea and defined its territorial scope. After presenting to the riparian states’ their rights and obligations within the newly defined maritime zones, the article analyses the new legal framework for the development and use of the natural resources of the Caspian Sea. It also elaborates on the new legal regime for the transportation of resources by means of vessels and submarine pipelines.
Real-Time Overlapping of Indocyanine Green—Video Angiography With White Light Imaging for Vascular Neurosurgery: Technique, Implementation, and Clinical Experience
Authors: Athanasopoulos Dimitrios , Heimann Axel , Nakamura Makoto , Kakaletri Irini , Kempski Oliver , Charalampaki Patra
Published: April 2020

BACKGROUND

Fluorescent-guided techniques in vascular neurosurgery can be demonstrated via black and white indocyanine green videoangiography (ICG-VA). Multispectral imaging (MFL) is a new method, which overlaps fluorescence with the white light and provides a fluorescent white light augmented reality image to the surgeon.

OBJECTIVE

To investigate (a) whether MFL can enhance the visualization of the blood-flow with simultaneous visualization of the anatomic structures and (b) if MFL can ergonomically improve the microvascular surgical treatment compared to ICG-VA.

METHODS

A digital imaging of the blood flow after intravenous injection of ICG on 7 pigs was performed in real time under white light, standard fluorescence, and MFL. The blood flow was interrupted with a surgical clip, demonstrating the blockage of the blood flow. We prospectively included 30 patients with vascular deformities. The vasculature was visualized on the microscope's monitor and through the microscope's eyepiece.

RESULTS

In the animal experiment, the visualization of the anatomy and the blood flow under MFL produced high resolution images. The occlusion of blood vessels demonstrated sufficiently the blockage of tissue perfusion and its reperfusion after clip removal. During all 30 surgical cases, the MFL technique and the direct delivery of the pseudo-colored image through the eyepiece allowed for enhanced anatomic and dynamic data.

CONCLUSION

MFL was shown to be superior to the classic ICG-VA, delivering enhanced data and notably improving the workflow due to the simultaneous and precise white light visualization of the blood flow and the surrounding anatomic structures.
ADHD Symptoms and Financial Distress
Authors: Liao Chi
Published: April 2020

We examine the effect of attention-deficit/hyperactivity disorder (ADHD) on individual-level financial distress. ADHD is the most common mental disorder among children and is characterized by behaviors such as inattention, hyperactivity, and impulsiveness that interfere with school and home life. In a representative panel, we find that individuals with more severe ADHD symptoms during childhood have more difficulty paying bills and are more likely to be delinquent on bill payments in adulthood. Further, those with more severe symptoms are less likely to have precautionary savings and more likely to have to delay buying necessities. These effects exist across the full range of ADHD symptom scores and are not driven by the most severe cases of ADHD; this is consistent with recent evidence that ADHD symptoms occur on a continuum. Preliminary evidence suggests that medication for behavioral issues may mitigate the effect of ADHD symptoms on financial distress.
First insights into the phylogeny of tok-tokkie beetles (Tenebrionidae: Molurina, Phanerotomeina) and examination of the status of thePsammodes vialisspecies-group
Authors: Kamiński Marcin J , Gearner Olivia M , Kanda Kojun , Swichtenberg Kali , Purchart Luboš , Smith Aaron D
Published: April 2020

The first molecular phylogeny of the tribe Sepidiini is inferred from analyses of DNA sequence data from the following five loci (CAD, wg, COI, COII, 28S rRNA). Bayesian and maximum likelihood analyses were performed on a dataset containing 41 taxa, of which a majority represent Molurina (27) and Phanerotomeina (6). The resulting topologies were used to discuss phylogenetic placement and diagnostic characters of all of the genera representing Molurina. Within the subtribe, the results revealed paraphyly of the genus Psammodes. The P. vialis species-group, currently classified within Psammodes, was recovered as sister to all other Molurina genera. Based on this topology and morphological investigations, a new genus named Toktokkus gen. nov. is established. Within Phanerotomeina, Ocnodes is paraphyletic with regard to Tarsocnodes. In order to restore the monophyly of Ocnodes, the subgenus Chiliarchum stat. nov. is elevated to generic level. Finally, as the homology of female terminalia structures has never been fully assessed for Sepidiini, a comparative study of ovipositor morphology was conducted. As a result, this paper presents the first fully annotated ovipositors for tok-tokkie beetles.
Beta‐caryophyllene, a Volatile Phytocannabinoid, Attenuates Cocaine Self‐administration and Relapse in Rats
Authors: Galaj Ewa , Bi Guo-Hua , Gardner Eliot , Xi Zheng-Xiong
Published: April 2020

Cocaine abuse continues to be a serious health problem worldwide. Despite intense research, there is still no FDA‐approved medication to treat cocaine use disorder. The recent search for effective therapeutics has been focused on the endocannabinoid system because of its critical role in the neurobiology of drug addiction. In the last decade, there has been a growing interest in beta‐caryophyllene (BCP), a volatile phytocannabinoid present in high proportions in cannabis and large number of spice and food plants including black pepper, thyme and cloves. This dietary additive that has a CB2 receptor (CB2R) agonist profile, has shown to produce promising therapeutic effects for multiple neuropsychiatric disorders. Surprisingly, the therapeutic potential of BCP in the treatment of drug abuse and addiction has not been explored. Here, using gold standard animal models of drug abuse, we systematically evaluated the potential utility of BCP against cocaine‐related behaviors in rodents and its mechanisms of action. In a series of experiments we found that BCP attenuated cocaine‐enhanced electrical brain‐stimulation reward and optogenetic intracranial self‐stimulation driven by activation of dopamine (DA) neurons in DAT‐cre mice, both outcomes indicating reduced reward. Intriguingly, when administered systemically or orally, BCP attenuated cocaine self‐administration in rats, suggesting an ability to reduce drug abuse. BCP also reduced drug‐primed reinstatement of cocaine seeking and cocaine conditioned place preference, indicative of its preventative effects against relapse. When BCP was substituted for cocaine, rats ceased responding, suggesting BCP has low liability abuse. In regards to the receptor mechanisms, our pharmacological approach (along with our transgenic approach utilizing with CB1, CB2, GPR55 knockout mice) indicates that BCP produces attenuating effects on cocaine self‐administration that are mediated by non‐cannabinoid receptors. We are now exploring the involvement of peroxisome proliferator‐activated receptor (PPAR) and transient receptor potential vanilloid 1 cation channels (TRPV1) in BCP action against cocaine. Our findings suggest that BCP shows exceptional promise as a therapeutic candidate in the treatment of cocaine use disorder. Importantly, given its good oral bioavailability and the advantage of being an already FDA‐approved non‐toxic dietary additive, BCP is a valuable candidate for drug repurposing programs in translational medicine.
Identification of MicroRNAs as Biomarkers in Colorectal Cancer Diagnostics: An In silico approach
Authors: Fadaka Adewale Oluwaseun , Pretorius Ashley , Klein Ashwil
Published: April 2020

Colorectal cancer (CRC) is the most common malignancy in the gastrointestinal tract, the third most commonly diagnosed cancer, and a leading cause of cancer‐related deaths worldwide. The involvement of microRNAs in cancers plays a significant role in their pathogenesis. Specific expressions of these non‐coding RNAs also serve as biomarkers for early CRC diagnosis but their laboratory/molecular identification is challenging and expensive. Current diagnostic methods are invasive, more expensive, and lack specificity and sensitivity. Therefore the need for a less invasive, more sensitive and specific biomarkers for early detection of CRC. The present study aimed to identify potential microRNAs and their target genes for CRC diagnosis using in silico approach. Sequence similarity search was employed to obtain the candidate microRNA from two different datasets and target prediction tools were employed to determine their target genes. The involvement of these microRNAs was carried out through the intersection analysis between the candidate microRNAs target gene list and experimentally validated CRC expressed genes. This was further strengthened by determining their enrichment in DAVID. Gene ontology, pathway analysis, and protein network interactions were further evaluated using UniProt, and KEGG, and STRING respectively and visualized by Cytoscape. The cBioPortal was used to prioritize the candidate microRNAs target genes. Prognostic and expression analysis were finally performed on both the candidate microRNAs and the prioritized targets using PROGmiRV2, and PrognoScan, and SurvExpress, and FIREBROWSE respectively. This study, therefore, identified five candidate microRNAs, two hub genes (CTNNB1 and EGFR) and seven statistically significant target genes (p< 0.05) associated with CRC. The molecular validation study of these microRNAs and their targets are pivotal to ascertain the biological fitness of these finding.
Exposure to 4,4′‐Methylene Diphenyl Diisocyanate Upregulates Chemokines CCL2, CCL3, CCL5, and IL‐8 Transcription Through Activation of Calcineurin/NFAT Signaling in Macrophages
Authors: Lin Chen-Chung , Law Brandon F , Hettick Justin M
Published: April 2020

Exposure to the most widely used monomericdiisocyanate, 4,4′‐methylene diphenyl diisocyanate (MDI), in the occupational setting may lead to the development of occupational asthma (OA). Currently, the underlying molecular mechanism(s) by which MDI induces OA remain an active area of research. Airway macrophage dysfunctions such as decreased phagocytosis and efferocytosis as well as increased production of reactive oxygen species (ROS), nitric oxide(NO) and immune mediators, etc., play important roles in asthma pathogenesis. Previously, we demonstrated that the downregulation of microRNA (miR)‐206‐3p and miR‐381‐3p mediated activation of the Calcineurin/nuclear factors of activated T‐cells (NFATs) signaling pathway which induced endogenous inducible nitric oxide synthase (iNOS) transcription in macrophages and bronchoalveolarlavage cells (BALCs) after acute MDI exposure. However, whether MDI may affect expression of other asthma‐associated immune mediators in macrophages/BALCs and the underlying molecular mechanisms driving these effects are currently unknown. We hypothesize that MDI exposure induces several asthma‐associated mediators through Calcineurin/NFAT signaling activation in macrophages. We determined the expression of macrophage‐secreted, asthma‐associated mediators including cytokines (IL1‐β, TNF‐α, and IL‐6); chemokines (CCL2, CCL3, CCL5, CCL11, and IL‐8), and growth factors (GM‐CSF and TGF‐β) from both MDI‐exposed murine BALCs and MDI‐glutathione(GSH) conjugate‐treated differentiated THP‐1 macrophages using RT‐qPCR. Both in vivo murine MDI aerosol and in vitro MDI‐GSH exposures result in the upregulation of endogenous IL1‐β, TNF‐α, IL‐6, CCL2, CCL3, CCL5, and TGF‐β. Treatment of THP‐1 macrophages with 1 μM Tacrolimus (FK506), a specific Calcineurin/NFAT signaling inhibitor, blocked the induction of CCL2, CCL3, CCL5, and IL‐8 expression by MDI‐GSH conjugates but not IL1‐β, TNF‐α, IL‐6, and TGF‐β. These results indicate that Calcineurin/NFAT signaling activation plays an important role for CCL2, CCL3, CCL5, and IL‐8 transcriptional upregulation following MDI exposure in macrophage. These results suggest MDI exposure may result in recrutement of many different cell types such as eosinophils, T‐cells, monocytes, macrophages, etc., into the airway by induction of chemokines transcription via Calcineurin/NFAT signaling activation in the macrophages/BALCs.

Support or Funding Information

This work was supported by intramural funds from the National Institute for Occupational Safety and Health, Centers for Disease Control and Prevention.
Intricacies of students attending medicine programs and their salivary microbiomes
Authors: Prasad Samiksha , Wrench Algevis
Published: April 2020

The human microbiome is defined as microbes, their collective genetic material and ecosystems established within and on the human body. These microbes and their genomes play a role in human physiology and homeostasis as well as may potentially be associated with disease onset and progression. As a result, understanding the human microbiome is essential for maintaining overall health and wellbeing. Researchers have found that the human microbiome can be affected by different environmental factors. Yet, the complexities of how these factors affect the diversity of the salivary microbiome are not well understood. Thus, for this pilot study, we aim to gain improved insight into the role of environmental factors on the salivary microbiome of students from Nova Southeastern University (NSU) medicine programs, which include Dr. Kiran C. Patel College of Allopathic Medicine (NSU MD) and Dr. Kiran C. Patel College of Osteopathic Medicine (KPCOM). Specifically, we plan to evaluate the role of perceived stress, diet, and lifestyle tied to an advanced and intense curriculum among 100 medical students. We will obtain saliva samples from these students, which will be categorized by program and further subcategorized by the year of their program and other demographic parameters. Extracted bacterial DNA will be subjected to sequencing analysis and results will be compared based on perceived stress level, diet and lifestyle variables. Finally, bioinformatics analysis (co‐occurrence, network analysis and function predictions) and statistical significance will be performed. Previous research efforts have yet to evaluate the combined effects of perceived stress, diet and lifestyle factors on the salivary microbiome in a student population. Medical school students provide a unique population to study, as they undergo an intense and overwhelming curriculum. The results from this study will serve as preliminary data to expand the project to a larger population in the community, with the potential to benefit the overall public health.

Support or Funding Information

HPD Research Grant, Nova Southeastern University
H‐current blocker (ZD 7288) reduces firing patterns on putative dopaminergic neurons of the Ventral Tegmental Area
Authors: Bosque-Cordero Karl Yomar , Vazquez-Torres Rafael , Calo-Guadalupe Cristhian , Consuegra-Garcia Daisy , Fois Giulia , Georges Francois , Jimenez-Rivera Carlos A.
Published: April 2020

The hyperpolarization‐activated cation current (H‐current) is a major determinant of neuronal intrinsic excitability in various cells including dopaminergic neurons of the Ventral Tegmental Area (VTA DA). In contrast to other cellular conductances, the H‐current activates through hyperpolarizing voltage steps to potentials negative to −55mV and depolarizes the membrane potential. We explored through in vivo anesthetized single unit extracellular electrophysiology the contribution of the H‐current on VTA DA neurons spontaneous firing patterns in naïve rats. A key feature of evaluating spontaneous excitability is the detection of bursting activity. Bursting is defined as trains of two or more spikes occurring within a short interval and followed by a prolonged period of inactivity (Grace et al., 1984). It has been well documented that burst formation increases the reliability of information transfer. Additionally, bursts and spikes can develop a parallel code, in which they can promote various stimulus features in the same spike train. To elucidate the contribution of H‐current on VTA DA neurons spontaneous firing patterns we perfused H‐current blocker (ZD 7288) through a double barrel pipette and evaluated its effect. H‐current blockade significantly reduced firing rate, bursting frequency and percent of spikes in burst in VTA DA neurons. Neuroadaptations in this network are hypothesized to trigger various neurobiological diseases including drug addiction. Reduction of spontaneous firing patterns through H‐current blockade could serve as a possible modulator of conditions related to VTA DA hyperexcitability.

Support or Funding Information

National Institute of General Medical Sciences (2SC1GM084854) National Center for Research Resources (5R25GM061838‐15, 2G12‐RR003051) National Institute on Minority Health and Health Disparities (8G12‐MD007600) NSF Partnerships in International Research and Education (PIRE) program Neural Mechanisms of Reward & Decision (OISE‐1545803) Research initiative for Scientific Enhancement RISE (5R25GM061151‐18)
Do folding elements trade‐off with function in the human mitochondrial metabolite transporter?
Authors: Mahalakshmi Radhakrishnan
Published: April 2020

In humans, transmembrane β‐barrels are found exclusively in the outer mitochondrial membrane (OMM). They comprise metabolite transporters, translocases, and chaperones, which together control cellular homeostasis. The metabolite transporters — known as voltage‐dependent anion channels (VDACs) – are the most abundant OMM barrels. They are 19‐stranded β‐barrel structures that also form important pharmacological targets due to their roles in metabolite flux, steroidogenesis, gametogenesis, and ROS regulation. Despite long‐standing efforts, molecular factors that regulate VDAC function and folding at the atomistic level are not known. Here, we map the folding nucleus and the assembly pathway of human VDAC isoform 2 in phosphocholine vesicles. We carry out a comprehensive measurement of hVDAC2 folding kinetics, and equilibrium thermodynamic contribution, of each of the 270 non‐Ala residues of the 294‐residue barrel. Interestingly, we obtain a two‐state thermodynamic equilibrium that is attained through two detectable on‐pathway early folding intermediates, which are assembled in milliseconds – seconds. These intermediates undergo slow conformational restructuring to form the folded VDAC2 barrel. We find that specific charged residues that form a part of these early intermediates also positively regulate the gating characteristics of VDAC2. This observation is unprecedented, as directed evolution of protein sequences in favor of function usually place a stability burden on its structure that additionally impedes protein assembly. Our findings provide molecular insight on the assembly pathway of human VDAC2, and directly link these folding elements with VDAC2 function as the metabolite transporter of human mitochondria.

Support or Funding Information

This work was supported by the Wellcome Trust/DBT India Alliance Fellowship [grant number IA/I/14/1/501305] awarded to RM.
Early Findings from the NIH BEST Cross‐Site Evaluation
Authors: Lenzi Rebecca N , Korn Stephen , Wallace Madeleine , Labosky Patricia A , Desmond Nancỳ A
Published: April 2020

In 2013 and 2014, the NIH Common Fund issued its Broadening Experiences in Scientific Training (BEST) awards to 17 research sites. The BEST awards focused on enabling institutions to develop innovative programs to increase biomedical trainee exposure to a range of research‐related career options through activities like coursework, workshops, and active learning experiences.

The NIH outlined three goals of all BEST awardees: 1) trainee confidence and knowledge to make career decisions, 2) influence of this added activity on time in training, and 3) ability of the institutions to sustain activities deemed beneficial. Three methods were used to collect data: 1) a Data Form completed by BEST awardee institutions, including detailed tracking of all activities and participation 2) multiple surveys of graduate students and postdoctoral researchers at BEST institutions, and 3) yearly teleconferences with BEST site coordinators to gather contextual information.

Through all years, the activity offered most often across BEST institutions was single‐day workshops. These workshops had high trainee attendance (ex: 1749 graduate students and 821 postdoctoral scientists in Year 3 attended 377 single day workshops across the 17 sites). Interestingly, entrance survey data also suggest many trainees are familiar with broad career options (64% and 57.8% of graduate student and postdoctoral scientist survey respondents reporting familiarity with “all” or “most” of the 20 myIDP career paths). Questions were also posed to assess confidence levels related to career awareness and preparation. Over 80% percent of all graduate students and postdoctoral scientists reported being moderately, highly, or completely confident across all five questions. While many BEST graduate students and postdoctoral scientists are still in training, for those that have completed training, participation in BEST activities did not increase time in training.

Overall, our data suggest trainees are generally aware of current career options beyond traditional academic research‐intensive positions. BEST awardee institutions also made great strides in collecting data on career development activities and tracking participation for thousands of trainees.
Structural and Functional Characterization of the Integrase HK022
Authors: Kennedy Madison Arza , Stoddard Barry
Published: April 2020

There is great demand for sophisticated molecular tools for precise genome editing and engineering. The current state of the art for this purpose is to use site‐specific nucleases to generate targeted double‐stranded breaks (DSBs) that are repaired by the cell. Though effective, nucleases often display off‐target cleavage and generate heterogeneous repair products via operations such as non‐homologous end joining. In contrast, tyrosine site‐specific recombinases (SSRs), like Cre and FLP which function biologically to drive integration of phage/viral genomes, generate precise repair outcomes. These outcomes include genetic insertions, deletions or inversions and are performed with considerably lower off‐target activity. HK022 is a relatively under‐studied tyrosine SSR with considerable sequence similarity to the well‐studied lambda phage integrase. In contrast to that enzyme, HK022 displays a recognition profile that is appropriate for targeting disease‐causing mutations, is highly site‐specific, and does not require auxiliary proteins for its function. Additionally, HK022 has the potential to recognize and recombine non‐identical DNA sites which provides the ability to selectively promote recombination in one direction, instead of an equilibrium between non‐recombined and recombined forms. The flexibility and small size of the DNA recognition site, combined with its ability to utilize large DNA cassette inserts make HK022 a promising candidate for optimization for genome engineering. Three forms of HK022 (optimized for synaptic, post‐strand exchange, and Holliday junction structures with DNA) have successfully been expressed and purified for co‐crystallization with unique DNA of interest. Given the success with the lambda integrase, we suspect that HK022 will be equally amenable to crystallization. Solving the structure of HK022 in its many forms provides the ability to compare its recognition pattern to lambda integrase to further understand the diversity of this enzyme class. In addition to generating the first crystal structure of HK022, we wish to enhance the overall stability and activity of the enzyme and optimize it for therapeutic and biotechnological purposes.

Support or Funding Information

National Science Foundation Graduate Research Fellowship Program (NSF GRFP) DGE‐1762114. National Institute of Health (NIH) R01 GM105691.
Purification of Eukaryotic Initiation Factor 2B complex from a predominantly diploid organism, C. albicans by FLAG‐epitope tagging of the two alleles of GCDI
Authors: Egbe Nkechi Eucharia , Onuh Kingsley
Published: April 2020

To study protein interaction and expression in cells, the cells are usually tagged to enable location of proteins within cells and for isolation and purification of the protein complexes of interest. Epitope tags are useful for affinity purification and immunochemistry. This strategy has been successfully utilized in Saccharomyces cerevisiae and many other model organisms. The human pathogenic yeast, C. albicans, however is predominantly diploid, and autonomous plasmid systems developed for routine use are unstable in this organism, therefore, tagging just a single copy of a gene, as is done in other organisms with stable haploid state, will not permit maximal protein expression of the tagged allele, as the organism will also be expressing the untagged allele of the gene of interest. In an attempt to circumvent some of these potential bottlenecks, we designed a tagging strategy with four FLAG epitopes making use of a mini URA3 blaster (URA3‐dpl200) cassette. This strategy enabled the epitope tagging of the two alleles of GCD1, which code for a subunit of the eukaryotic initiation factor 2B (eIF2B). The eIF2B is a heteropentameric guanine nucleotide exchange factor that functions during translation initiation. The tagged protein complex was purified by a single affinity chromatography step and yielded the expected sized bands on SDS PAGE gel. The sub‐complex of the protein subunits were enriched in the purified sample detected by mass spectrometry. Therefore, these data shows that tagging of the two GCD1 alleles with 4xFLAG epitope has successfully allowed the eIF2B to be purified.

Support or Funding Information

Tertiary Education Trust Fund, Nigeria
Pre‐Clinical Evaluation of Drug Induced Proteolysis of MLL‐Fusions in Acute Leukemia
Authors: Looi-Somoye Remi , Cantilena Sandra , de Boer Jasper
Published: April 2020

The mixed‐lineage leukemia (MLL) gene is often susceptible to chromosomal rearrangements in pediatric leukemias. The resulting chimeric proteins are a product of reciprocal translocations between the gene and various fusion partners. In MLL‐rearranged leukemia, these fusion proteins drive leukemogenesis by interfering with transcriptional elongation to deregulate target gene expression. MLL fusion proteins, indicative of a more aggressive disease, are responsible for a large proportion of acute infant leukaemias. Therapeutic methods to target oncogenic fusion proteins, such as PML‐RARA, have proven pharmacologically achievable and highly successful. For this purpose, our lab has established a drug screening program using in cellulo bio‐luminescence with the objective of repositioning drugs that cause MLL‐fusion protein degradation. Compounds that produced a 30% reduction in MLL fusion protein expression via two different screening methods, luminescence and western blotting, were considered positive hits. In this present study I validate and characterize one of these positive hits. Upon treatment of MLL‐rearranged cell lines, the compound was capable of ablating MLL fusion protein expression resulting in the down regulation of target gene HOXA10. Furthermore, treatment caused loss of leukaemic stem cell activity via induction of cell death and inhibition of self‐renewal capacity. To further analyze the mechanism of this compound, RNA‐sequencing and Gene Set Enrichment Analysis will be performed to identify gene sets associated with the disease treated phenotype. Overall this study identifies a potential repurposed therapeutic for the treatment of MLL‐rearranged leukaemias.

Support or Funding Information

This work was supported by the UCL Child Health Research Studentship.
Neurotoxic Effect of Paracetamol on Female Rats: Role of Antioxidant Treatment and Prevention
Authors: Al-Qirim Tareq , Jasim Suhair , Shawaqfeh Bara’a
Published: April 2020

Paracetamol (Acetaminophen) is the most common nonprescription analgesic and antipyretic drug used. It can be found in different pharmaceutical dosage forms such as syrup, capsule, suppositories and intravenous (I.V) infusion solution. The intake frequency and the dose of paracetamol usually varied during pregnancy with a tendency toward higher doses in the last trimester. The effect of Paracetamol overdose was extensively studied on hepatocyte and nephrocyte of laboratory animals. The aim of this study is to focus on the effect of paracetamol overdose on Neurotoxicity (within Hippocampus, Cerebellum, and Olfactory Bulbs) of Paracetamol in the last trimester of pregnant rats. And this will be done through studying oxidative stress markers, the biochemical and antioxidant tests that indicate the presence of Hepatotoxicity and Nephrotoxicity, along with the protective effect of Vitamin E as antioxidant in pre‐ and post‐single toxic dose administration. Twenty female pregnant Wistar rats (average weight 200 gm ± 10) at gestational day 18 (GD18) were used. The pregnant rats were divided into four groups; the first (control) group received a 0.5 ml p.o of corn oil. The second group (paracetamol) group received a 3000 mg/kg p.o paracetamol dissolved in corn oil. The third (E + paracetamol) group received a 3000 mg/kg paracetamol one hour after 300 mg/kg p.o vitamin E. The fourth (paracetamol + E) group received a 3000 mg/kg paracetamol one hour before 300 mg/kg p.o vitamin E dissolved in corn oil. Twenty‐four hours After Paracetamol administration the rats were anesthetized and the brain, the liver, the kidney, and the blood were collected. Various biochemical tests were performed to show the effect of paracetamol overdose on liver including Alanine aminotransferase (ALT), Aspartate aminotransferase (AST). Additionally, the effect of paracetamol on Blood urea nitrogen (BUN) and Creatinine levels were determined to detect nephrotoxicity, and the results showed significant elevation within the paracetamol treated group and levels were restored to the normal levels with vitamin E treated groups. Uric acid (UA) and superoxide dismutase (SOD) were used to detect the oxidative stress within the Liver, the Kidney, the Hippocampus, the Cerebellum, and the Olfactory Bulbs.

Support or Funding Information

This research is supported form Al‐Zaytoonah University of Jordan
Decoding Inflammatory Signals from the Extracellular Matrix for the Development of New Immunotherapies
Authors: Midwood Kim S.
Published: April 2020

An immune response to pathogen invasion is triggered upon detection of pathogenic molecules by innate immune sensors, whilst non‐infectious threat is signalled by endogenous inflammatory stimuli. Although insights into pathogen pattern recognition have revealed a great deal about the molecular basis of host defence against infection, it is not well understood how endogenous molecules activate immunity. Previous work revealed how extracellular matrix molecules specifically induced during tissue damage and cellular stress, or associated with tumorigenesis, create a pro‐inflammatory niche that enables resident stromal cells and infiltrating immune cells to survive and thrive, and within which matrix molecules directly activate site‐specific inflammatory programmes. Our new data detail how matrix molecules are recognized as inflammatory triggers, the distinct immune signalling pathways they activate, and the importance of identifying pathologically relevant forms of matrix constituents to understanding their contribution to inflammation. Current work focuses on translating these discoveries into novel diagnostic tools, and developing new drugs that target the microenvironment to enable selective amelioration of aberrant ‘sterile’ inflammation in autoimmune and fibrotic diseases, and to re‐educate immunity against tumors.
A Genetic Approach to Display and Dissect the Cancer‐Associated O‐Glycoepitome
Authors: Clausen Henrik , Nason Rebecca , Mandel Ulla , Narimatsu Yoshiki
Published: April 2020

A hallmark of cancer is aberrant protein O‐glycosylation with expression of truncated immature O‐glycans including the classical Tn, STn, and T pancarcinoma antigens. The truncation of O‐glycans not only present epitopes recognized by the natural low affinity antibodies to the TTn glycan haptens, which are the basis for the polyagglutination phenomena, but also expose composite aberrant O‐glycopeptide epitopes that are not normally expressed and can elicit high affinity IgG antibodies. Several examples of monoclonal antibodies with high selectivity for truncated O‐glycopeptide epitopes, which in effect selectively target the cancer form of O‐glycoproteins, have been produced in the past. Studies demonstrate that such epitopes serve as highly cancer‐specific targets potentially amenable for potent T‐cell engaging strategies, however, the current insight into the abundance and distribution of aberrant O‐glycopeptide epitopes and the optimal glycoforms for these remain limited. To systematically explore antibody epitopes available in the cancer‐associated O‐glycoproteome, we have developed a cell‐based platform for display and production of human O‐glycoproteins with homogeneous truncated glycoforms. This platform includes CHO and HEK293 cells stably engineered with homogeneous glycosylation capacities for the Tn, STn, and T glycoforms, and a panel of reporter expression constructs containing segments of human mucins and mucin‐like domains from O‐glycoproteins for display of these with different O‐glycans. An overview of these efforts will be presented.

Support or Funding Information

Danish National Research Foundation (DNRF107) and the Lundbeck Foundation
Role of Ascorbic Acid in Skeletal Muscle Regeneration
Authors: Yatsu Tomofumi , Takino Yuka , Ishigami Akihito
Published: April 2020

Total amount of L‐ascorbic acid (AsA) in human skeletal muscle is approximately 40%. As satellite cells, muscle specific stem cells, are responsible for providing new myoblast cells during the muscle regeneration process. Myoblast cells construct myofibers in the regenerative process including proliferation and differentiation. AsA is known to prevent scurvy helping dioxygenases for the prolines hydroxylation in collagen. It has been reported that AsA accelerated Ten‐Eleven Translocation (Tet) methylcytosine dioxygenase‐mediated generation of 5‐hydroxymethylcytosine (5hmc) from 5‐methylcytosine. We have previously reported that AsA deficiency causes skeletal muscle atrophy and deterioration in physical performance in senescence marker protein 30 knockout (SMP30‐KO) mice. In this study, we showed that AsA deficiency causes a delay of skeletal muscle regeneration in SMP30‐KO mouse which is unable to biosynthesis of AsA. Moreover, AsA administration after skeletal muscle injury recovered it regeneration. In vitro experiment, AsA treated C2C12 mouse myoblast cells showed higher cell proliferation rate, mRNA expression levels of myogenic differentiation markers such as myogenin and myomaker, and fusion index compared to untreated cells. Finally, we examine the 5hmc levels in AsA‐treated and untreated C2C12 cells. The 5hmc levels was higher in AsA‐treated cells than untreated cells. These results suggest that AsA induced skeletal muscle regeneration by enhancing the myoblast proliferation, differentiation, and DNA demethylation.

Support or Funding Information

Grant‐in‐Aid for Early‐Career Scientists. Funding Agency: Japan Society for the Promotion of Science. Project number: 19K19822
Piezo1 activation gains traction
Authors: Pathak Medha
Published: April 2020

A major unanswered question in biology is how mechanical forces are generated, detected and transduced by cells to impact biochemical and genetic programs. Our work is aimed at uncovering the mechanical principles at play in cells and tissues using novel molecular, imaging and bioengineering tools. Here we present insights gleaned from non‐invasive approaches to measure and manipulate mechanical signals in native cellular conditions. We find that the mechanically‐activated ion channel Piezo1 transduces cell‐generated traction forces to regulate lineage choice of neural stem cells. We show that actomyosin‐based cellular traction forces generate spatially‐restricted Piezo1 Ca2+ flickers in the absence of externally‐applied mechanical forces. Although Piezo1 channels diffuse readily in the plasma membrane and are widely distributed across the cell, their Ca2+ flicker activity is enriched in regions proximal to force‐producing adhesions. The mechanical force that activates Piezo1 arises from Myosin II phosphorylation by Myosin Light Chain Kinase. We propose that Piezo1 Ca2+ flickers allow spatial segregation of mechanotransduction events, and that mobility allows channel molecules to efficiently respond to local mechanical stimuli.

Support or Funding Information

NIH grants R01 NS109810 and DP2 AT010376