bluuebunny/crossref_metadata_2025_split huggingface dataset:
A genetic screen for proteins involved in Non‐Stop mRNA decay in C. elegans
Authors: Diamandi Michelle , Brennan Catherine , Youngman Elaine M. 
Published: May 2022

Non‐stop mRNAs, which lack a stop codon due to mutation or errors in mRNA transcription or processing, serve as templates for production of aberrant and potentially toxic protein products. Ultimately, translation of non‐stop mRNAs leads to a failure in normal translation termination and ribosome collisions, which in eukaryotes initiates ubiquitin‐dependent degradation of the protein product and Non‐Stop Decay (NSD) of the problematic mRNA. Ribosome collisions in yeast are linked to activation of cellular stress responses and failure to resolve stalled ribosomes leads to neurodegeneration in mice, highlighting the biological importance of mRNA quality control.In the nematode Caenorhabditis elegans, loss of the core NSD components pelo‐1 and skih‐2 leads to temperature‐sensitive sterility, as does the loss of endogenous siRNAs that are triggered by NSD at some loci. To further probe the link between NSD and the biology of germ cells, we have used an RNAi approach to screen for temperature‐sensitive reduction in brood size for the C. elegans orthologs of several proteins known to be part of the NSD machinery in other organisms. Preliminary results have identified 2 NSD‐associated genes with conditionally reduced brood sizes. We will present progress on examining the requirement of these genes for Non‐Stop decay in C. elegans, as well as investigation of their specific contributions to the biology of the germ line.
Unfolding RFX1 Mediated Regulation of Cancer Stem Cells
Authors: Raveendran Pooja S. , Issaac Joby , Kunnummal Midhunaraj , Das Ani V. 
Published: May 2022

Regulatory factor X1(RFX1) is a unique transcription factor that can act both as an activator and repressor in a context‐dependent manner. In most of the cases, it has been shown to exert an inhibitory action on its targets. It belongs to the evolutionarily conserved RFX (Regulatory Factor binding to the X‐box) family of transcription factors consisting of eight homologs (RFX1‐8) in humans. RFX1 is seen down‐regulated in many cancers and is speculated to have a critical role in regulating stem cell properties. Cancer stem cells are major hurdles in cancer therapy as they are capable of repopulating a tumor after treatment. We aim to understand the regulation of cancer stemness by RFX1 in human teratocarcinomal (NTERA‐2) cancer stem like cells.We have chosen NTERA2 cl.D1 (NT2) embryonic carcinoma cells since they are the malignant counterparts of embryonic stem cells and are pluripotent in nature, making them an ideal candidate to be used as a cancer stem cell model. The cells were differentiated using DISC (Days in suspension culture) method to obtain differentiated populations (NT2D). Using real time analysis, the expression of RFX1 was evaluated in proliferating (NT2P) and differentiating (NT2D) cell populations. A significant increase in RFX1 expression was observed in NT2D cells compared to NT2P cells. For further validation, the same was done in stem cell population enriched using Abcg2 promoter where the stem (GFP+ve) and non‐stem (GFP‐ve) cell populations were sorted out by FACS. Further RFX1 expression was perturbed in NTERA cells, and the assessment of cardinal properties of CSCs, such as clonogenicity/self‐renewal properties, proliferation potential, and migration/invasive properties in vitro,revealed that RFX1 plays a significant role in cancer stemness. Therefore, understanding the regulation of cancer stemness by RFX1 will allow us to formulate better diagnostic and therapeutic approaches to address chemoresistant cancers.
Testing a multi‐factorial model of the role of Rhipicephalus sanguineus in the spread of Rocky Mountain Spotted Fever in the Arizona region
Authors: Allwardt Kayla , Roe Nicolette , Logue Mary G. , Mutterperl Jeffery , Oliva Alec , Schaefer Charles P. , Hernandez Jose , Kreisler Rachael , Lee Jung Keun , Quinlan Michael , VandenBrooks John 
Published: May 2022

Rocky Mountain Spotted Fever (RMSF) is the deadliest tick‐borne disease in the United States. RMSF is spread from a canine host to humans through incidental contact with a tick vector. Historically, transmission of R. rickettsii, the causative agent, has been associated with the American dog tick (Dermacentor variabilis) and the Rocky Mountain wood tick (Dermacentor andersoni). However, in 2003, an outbreak of RMSF in Arizona was associated with a novel vector, the brown dog tick (Rhipicephalus sanguineus). Since then, the vectoring capacity of the brown dog tick has spread across the American Southwest and into parts of Mexico. Currently, the brown dog tick is not known to vector the bacteria outside of this area despite brown dog ticks being present in every state in the U.S. If this vectoring capacity continues to expand, many parts of the country will be at risk due to the brown dog tick’s ubiquitous nature. This is especially alarming as failure to treat RMSF in humans within the first five days of infection can lead to mortality rates as high as 80%. Therefore, this research was aimed at determining the factors that are currently limiting the vectoring capacity of the brown dog tick to Arizona and the surrounding region in order to prevent further spread of RMSF.The results of our research show that the current spread of RMSF in the Arizona region is due to a combination of four factors: (1) the presence of a distinct population of brown dog ticks, (2) variation in the genetic strain of the causative agent R. rickettsii, (3) distribution of canine seroprevalence across the region, and (4) geographic and climatic factors. In support of this, we have identified three genetically distinct clades of brown dog tick across the region that vary in the R. rickettsii infection rate. In sequencing intergenic regions of the R. rickettsii isolated from these tick populations, we have identified variation in the rickettsial strain across the region. Using immunofluorescence assays, we determined that canine seroprevalence rates are rising and seropositive dogs were found in regions that have previously not reported any human cases including regions as far north as Petaluma, CA. Even more concerning, 14 of 16 counties surveyed were at medium to high risk for human outbreak. These data were then analyzed at a county level and the relative role of each of the factors varied by geographic location. Together, this multi‐factorial model is a first step towards understanding the epidemiology of RMSF in the Arizona region and provides insights into ways to improve human and canine health by stopping future spread of RMSF.
Incidence and clinical implications of anatomical variations of the pancreas. A systematic review
Authors: Martínez Daniela V. , Valenzuela Juan J. , Cariseo Carolina V. , Orellana Mathias V. , Iwanaga Joe , Gold Marjorie , Santana Andrés 
Published: May 2022

IntroductionThe pancreas is retroperitoneal gland located the posterior wall of the abdomen, and plays a central role in digestion and absorption, as well as in the use and storage of energy substrates. Due to its location, as an external organ deep in the retroperitoneum, its irregular surface, its smoothness, its close and varied relationships to adjacent structures, and its vague boundaries, its surgical intervention presents a challenge to the surgeon, hence knowing its anatomical variations is important information previous to consider.MethodsA systematized search of scientific articles and human anatomy books, written in Spanish or English, published between 1970 and 2020, was carried out in the following databases; MEDLINE, SCIELO, WOS, CINHAL, SCOPUS and GOOGLE SCHOLAR, to describe the characteristics of the anatomical region of the pancreas and clinical complications.ResultsAfter applying the eligibility criteria 32 studies were included in this review, of which 2 described an annular pancreas, 3 described an ansa pancreatica, 3 mentioned a bifid pancreas, 5 mentioned a circumportal pancreas, 12 mentioned a pancreas divisum, 5 described ductal variations such as the course of the pancreatic duct or anomalies of the ductal system, 2 mentioned variations of the pancreaticobiliary Union and 2 described vascular variations of nearby vessels.ConclusionsWe found that the annular pancreas, PD, ansa pancreatica and bifid pancreas are variations that play a predisposing role in developing pancreatitis, the annular pancreas could also give operative complications in a pancreatic head resection surgery and postoperative complications such as pancreatic fistula, and biliary duct system variations appear to be predisposing factors to gallbladder stones formation. Hence, incorporating the study of its anatomical variations in the training of health professionals is very important for the process of diagnosis, monitoring and treatment of pancreatic diseases.
Host lipids required for Membrane protein matrix formation in new severe acute respiratory syndrome‐related coronavirus (SARS‐CoV‐2), ribonucleocapsid packaging and viral assembly
Authors: Amiar Souad , Stahelin Robert V. 
Published: May 2022

The current model of SARS‐CoV‐2 assembly proposes a multistage process: (i) the viral RNA coated with the nucleoprotein (N) forms the ribonucleoprotein (RNP), (ii) traffics to the endoplasmic reticulum‐Golgi apparatus intermediate compartment (ERGIC)‐derived vesicles to (iii) interact with the membrane (M) assembled along with spike (S) and envelope (E) proteins. Coronaviruses’ M has been described as required for new virus particle assembly. To date, biochemical and structural information on M are unavailable and key host factors required for M lattice formation, trafficking and interaction with the RNP are poorly characterized. The objective of this research project is to progress our understanding of SARS‐CoV‐2 assembly. Our central hypothesis is that M through its interaction with host lipids coordinates viral protein interactions and RNP packaging as key processes for SARS‐CoV‐2 assembly and spread. The role of lipids as molecules regulating the viral life cycle is poorly investigated.Our current data demonstrates a clear binding of cell expressed M to a Golgi resident sphingolipid. Furthermore, mutations at the sphingolipid binding motif resulted in deficient pull down of M protein by sphingolipid coated beads. In cells, the M sphingolipid‐binding mutant failed to retain S protein at viral assembly membranes resulting in a reduced entry capacity of newly formed virus‐like particles. Our current study is providing a first insight on the direct role of host lipids during SARS‐CoV‐2 assembly, orchestrated by the M protein.
Exercise increases the expression of glucose transport and lipid metabolism genes at optimum level time point 6 hours post exercise in rat skeletal muscle
Authors: Fagbohun Oladapo F. , Joseph Jitcy C. 
Published: May 2022

AimType 2 diabetes constitutes more than 90% of all diabetic cases and is characterized by persistent increase in glucose level in the blood (hyperglycemia) as well as lipid and protein metabolic disorders that may induce insulin resistance. Increased lipid levels induce type 2 diabetes by interfering with the insulin‐signaling pathway responsible for glucose transport. Individuals who suffer from type 2 diabetes are usually characterized in part by down‐regulation of glucose transport genes such as glut4 and down‐regulation of mitochondrial lipid oxidizing genes such as carnitine palmitoyltransferase‐1 (Cpt‐1). Nuclear respiratory factor (NRF)‐1 is a mitochondrial transcriptional factor which is shown to be involved in glucose transport and is set as a potential therapeutic modality in the treatment and management of type 2 diabetes. In this study, we sought to access NRF‐1 and its target genes expression during exercise which is crucial in glucose transport and lipid oxidation.MethodFive to six weeks old male Wistar rats were exercised to identify the time point for an optimum increase in the levels of NRF‐1 and its target genes. Gastrocnemius muscles were harvested after 0, 2, 4, 6, 8, 10, 12, and 15 h post‐exercise and non‐exercise rats (control). Primers were used to amplify the region of following genes; Nrf‐1, glut 4, carnitine palmitoyl transferase (Cpt‐1 & Cpt‐2), peroxisome proliferator‐activated receptor gamma co‐activator 1 (Pgc‐1), mef2a, and acetyl‐CoA carboxylase‐1 (Acc‐1). Relative mRNA expression was normalized to the Actin reference gene.ResultsFrom the result of this study, cpt‐1, Nrf‐1, mef2a, glut4, cpt2, and Pgc‐1 showed 2.5, 8, 1.2, 4.1, 4.6, 3.5‐folds increases respectively after 8h post‐exercise compared with control whereas Acc‐1 showed a 3.1‐fold decrease in gene expression ratio after 6 h post‐exercise compared with control. Nrf‐1 binding to cpt‐1 and mef2a increased with 3 and 3.5‐folds respectively 6h post‐exercise compared with control.ConclusionConclusively, nrf‐1 was increased by exercise and also, it's binding to target genes which has huge implications in ameliorating type 2 diabetes and insulin resistance.
Implication of New identified Nicotine regulated genes in diabetic cardiomyopathy
Authors: Wang Yajing , Zhao Jing , Zhao Jianli , Xie Yaoli , Liu Caihong , Lau Wayne Bond , Lopez Bernard , Christopher Theodore , Ma Xinliang 
Published: May 2022

ObjectivesThere is a paradox of nicotine and diabetes in patients with cardiomyopathy. Although great progress has been made in understanding the pathogenesis, it is urgent to clarify the in‐depth mechanism and identify new therapeutic targets for preventing diabetic cardiomyopathy (DCM) in smoker.MethodsHuman gene expression profiles in DCM (GSE4745 and GSE99203) corrected by SVA algorithm were analyzed and then “limma” packet gene screening was performed. By constructing the related co‐expression WGCNA network of DCM, combined with the analysis of Metascape pathway, the correlation of module and genes with DCM was determined. Furthermore, the Drug bank and STRING databases were used to screen nicotine targets and expand the gene network. The hub gene was identified by crossing the targets with DCM, which was obtained by WGCNA analysis. r‐packet “clusterprofiler” was used for GO analysis and KEGG pathway analysis. Then, the network of hub genes affecting DCM and the interaction diagram of core target related pathways that influence DCM is constructed by using the Cytoscape software. The relationship between hub genes was analyzed by using “corrplot”, “vioplot” packages and cibersort algorithm, and the potential mechanism of hub genes affecting DCM progress was further explored. To explore the relationship between the targets in the process of DCM, ROC curve of diagnostic efficacy was drawn with “pROC” package. Finally, a miRNA‐mRNA regulatory network including hub genes was further constructed by Targetscan. The regulatory network of transcription factors of hub genes was constructed from TRRUST database.Results3 gene modules were detected by WGCNA analysis, blue (202), grey (31) and turquoise (397), among which turquoise module had the highest correlation with DCM (cor =0.87, P = (3e −10)). The genes rich in monocarboxylic acid and sulfur compound metabolic processes in response to extracellular stimulus were identified. The top 13 nicotine‐related are targeted. The intersection of 113 target genes and turquoise module gene were screened out. There are the two hub genes involved Iron (III) ion response and retinoic acid biosynthetic process, involving Tryptophan Metabolism and Ovarian steroidogenesis pathways. The AUC values of the two hub genes are Cyp1a1(AUC: 0.769 (0.580 ‐ 0.958)) and Chrnb4(AUC: 0.707 (0.511 ‐ 0.902)) and both genes are strongly correlated with immune cell response. A total of 40 miRNA‐mRNA pairs, including 35 miRNAs and 2 mRNAs, were predicted by Targetscan. Three Cyp1a1 transcription factors were predicted by TRRUST database.ConclusionWe demonstrated that two genes, Chrnb4 and Ccyp1a11, are the potential genes involved in nicotine modulating DCM, and these two genes may regulate DCM’s immune response through miRNA‐mRNA mode. It provides new potential targets for preventing DCM in smoking population.
Enhanced Cerebral Blood Flow and Hemodynamic Status with an Alternative Left Ventricle Chest Compression Position during Cardiopulmonary Resuscitation in Swine
Authors: Marshall Rory A. , Morton Jude S. , Luchkanych Adam M. S. , El Karsh Yehia , El Karsh Zeyad , Morse Cameron , Turnbull Katie Y. , Schaefer Nici N. , Tomczak Corey R. , Grunau Brian E. , Olver T. D. 
Published: May 2022

IntroductionThe standard chest compression (SCC) position for cardiopulmonary resuscitation (CPR) is the centre of the chest and typically central to the aortic root. An alternative left ventricle chest compression (LVCC) position may facilitate superior global blood flow. We tested the hypothesis that, consistent with improved ETCO2 (indicative of cardiac output) and blood pressure (BP), LVCC would promote greater cerebral blood flow (CBF) than SCC.MethodsFemale pigs (N=32; 35±2kg) were rotated systematically to receive either SCC (n=14) or LVCC (n=18). Transthoracic echocardiography was used to identify and externally mark: (1) the SCC position, the midline at the level of the aortic route, or (2) the LVCC position, the midpoint of the left ventricle. After 2 minutes of untreated asphyxiated cardiac arrest (CA), swine were treated with three 2‐minute cycles of mechanical chest compressions (LUCAS III). ETCO2 (in‐line sampling), BP (arterial catheter line), and CBF velocity (CBFv, transcranial Doppler, primary outcome) were measured during the pre‐CA, untreated‐CA, and CPR‐treated phases. Between‐group outcomes were compared using a mixed model ANOVA with significant differences considered at P<0.05 and data are presented as mean±standard deviation.ResultsPre‐ and untreated‐CA ETCO2, BP and CBFv were similar between the SCC and LVCC groups (P>0.100). During CPR, ETCO2 (36±6 mmHg versus 24±10 mmHg; P<0.001), Mean Arterial Pressure (MAP; 49±9 mmHg versus 37±9 mmHg; P=0.002), and Mean CBFv (11±5 cm/s versus 5±2 cm/s; P<0.001) were significantly higher in the LVCC, versus SCC, group.ConclusionIn comparison to SCC,LVCC resulted in higher ETCO2, MAP, and Mean CBFv values throughout CPR in a swine model of CA.New and NoteworthyWe provide novel evidence that compared with mechanical compressions performed over the centre of the chest, compressions performed over the left ventricle promote greater CBF during BLS CPR. Clinical validation of these results may improve survival rates and attenuate neurological deficits following CA.
Examining the Interaction Between Cas9 and Ku, and its Implications for Gene Editing
Authors: Hayes Catherine M. , Bharti Aditya , Hanakahi Les A. 
Published: May 2022

Gene editing via CRISPR/Cas9 is an innovative new tool that allows scientists and clinicians to alter DNA. This can be done by inserting new DNA or by knocking out the function of preexisting DNA. Both processes begin with Cas9, an enzyme that acts as molecular scissors to introduce a DNA double‐strand break (DSB) at a specific location. The way this DSB is repaired determines whether new DNA is inserted or preexisting DNA is knocked out.Insertion of the new DNA sequence relies on a DNA‐repair process called homologous recombination. Knocking out the function of a gene is achieved through the DNA‐repair process non‐homologous end joining (NHEJ). Unfortunately, the majority of Cas9‐induced DSBs are repaired by NHEJ, thereby posing a barrier to inserting new genes. So why is NHEJ so prominent at Cas9‐induced DSBs?We have evidence that Cas9 interacts with the NHEJ initiating factor Ku. We, and others, used lysates from Cas9‐expressing human cells and found that Cas9 co‐immunoprecipitated with Ku. These observations may reflect either a direct Ku‐Cas9 protein‐protein interaction, or an indirect interaction mediated by other human cellular proteins, DNA, or both.I hypothesize that Cas9 and Ku have a direct physical interaction. To test my hypothesis, I carried out affinity‐capture assays using purified recombinant proteins. I found that Cas9 captured Ku, indicating that the interaction is not dependent on other human cellular proteins. This interaction also occurred when Ku‐DNA interactions are disrupted by adding ethidium bromide or benzonase. This indicates that the interaction is not due to the DNA‐binding capabilities of Ku.These experiments indicate that Ku and Cas9 have a direct protein‐protein interaction. Because Ku initiates NHEJ, our results suggest the possibility that the Cas9‐Ku interaction may recruit NHEJ factors to Cas9‐induced DSBs and provides a plausible explanation of the bias towards NHEJ repair of Cas9‐induced DSBs.
The Utility of Anatomical Diagrams Shared on Social Media
Authors: Motzko Micaela , Dennis Jennifer F. 
Published: May 2022

Introduction/ObjectiveMedical schools have made an increasing effort to provide students with online anatomical resources. Yet, studies report that most students who encounter a question during their anatomy study will consult the internet or social media to find supplemental resources before using course materials. A quick internet search by a novel anatomist may lead to inaccurate information and overwhelming results. We created sets of accurate and unique anatomical diagrams and shared these via a social media account to assess their perceived utility and accessibility to students learning anatomy.Materials/MethodsAnatomical diagrams were created and shared on a public Instagram account, Anatomy Adventures, during the 2020‐21 academic year. The systems‐oriented graphics covered musculoskeletal, nervous, gastrointestinal, and reproductive systems, including the osteology, myology, and neurovasculature of each system. An IRB‐approved survey (10.6% response rate) was distributed from March‐April 2021, assessing: 1) the demographics of the surveyed population, 2) how the diagrams were utilized, and 3) how they could be improved. A free‐form space was included for optional feedback. Responses were tabulated and converted to frequencies and percentages; descriptive codes were applied to the data according to published methods to summarize verbatim responses. Chi square test assessed differences among the responses when applicable. Alpha<5%.ResultsOf the 111 survey responses, 95% participants fell within the 18‐30 age range, with 78% identifying as female. The majority of participants were medical students (69%), but the sample also included undergraduate/graduate students (16%), as well as fully employed participants (14%). Geographically, most participants were located in the North and Central (69%) or other (27%) regions of the United States (US), with 4% located outside of the US. As for utility, 54% of participants reported using the diagrams to study for medical school coursework or board examinations, and 42% of responses indicated non‐medical use of the diagrams, such as leisure viewing or reviewing for their occupation. Free‐form responses (n=65) were coded into categories characterizing the utility of the diagrams: 1) color‐coding (12.3%), 2) simplicity (43%), and 3) style (24.6%) (P=0.0025).SignificanceWe demonstrate that supplemental resources shared via social media have the potential to be widely used by students, specifically by those 18‐30 years. The inherent flexibility of social media is how consumers preferred to utilize information. Qualitative data indicated presentation style largely impacts how resources are utilized by students, as an overwhelming majority report gaining unique information from this resource.ConclusionSocial media platforms can be used by educators to disseminate accurate supplemental materials to students. Anatomy educators should consider utilizing social media to fill gaps in anatomy education to provide accurate and accessible resources.