bluuebunny/crossref_metadata_2025_split huggingface dataset:
Acartia arbruta (previously A. tonsa) in British Columbia: a bioindicator of climate-driven ecosystem variability in the northeast Pacific Ocean
Authors: Smith Julian A C , Galbraith Moira , Young Kelly , Perry R Ian , Sastri Akash , Nelson R John 
Published: June 2021

Abstract
Climate change is driving biogeographic shifts in marine zooplankton. In the northeast (NE) Pacific, the distribution of the estuarine copepod, Acartia tonsa ( Dana, 1849), is generally limited to California except during marine warming events where it is found as far north as British Columbia (BC). Documentation of such events relies on accurate species identification. Phylogenetic reconstruction of the genus Acartia using 768 mitochondrial cytochrome oxidase subunit I Deoxyribonucleic Acid (DNA) sequences collected worldwide demonstrates that NE Pacific A. tonsa is distinct from all conspecifics and congeners. Males of NE Pacific A. tonsa are larger with slight differences in the fifth pair of legs as compared to geographically isolated conspecifics. Accordingly, we propose NE Pacific A. tonsa be reclassified to Acartia arbruta. Analysis of mitochondrial 16S ribosomal RNA DNA sequences from 154 specimens of A. arbruta collected from California, Oregon and BC suggests that A. arbruta detected in BC is a mixture of southern populations. Southern populations are likely driven north during “warm” phases of the oceanographic processes indexed by the Pacific Decadal Oscillation, which is positively correlated with A. arbruta biomass anomalies on the continental shelf of Vancouver Island, BC. The presence of A. arbruta in BC waters is a useful bioindicator of marine warming events.
From hesitancy to confidence: Filipinos’ shifting attitude toward COVID-19 vaccination program
Authors: Macaraan Willard Enrique R 
Published: June 2021

Abstract
In earlier correspondence, the authors have explored the vaccine hesitancy among the Filipino public. But I argue that the current situation from the ground has already been seeing shifting attitude of many Filipinos toward the government’s vaccination program. There is a significant increase of confidence among the public in getting inoculated. This development is crucial in hastening the achievement of the so-called herd immunity.
Sustainable diet and cruciform ethics during COVID-19
Authors: Kahambing Jan Gresil S 
Published: June 2021

Abstract
Health inequalities in food challenge sustainable prospects during the pandemic. Basic sustainable diet practices may address this issue, but problems of nutrition arise due to unhealthy eating habits. An inductive approach through curbing one’s diet forms certain ethics, which takes into account one’s sacrifices for the collective. This article proposes that cruciform ethics can introduce a reimagination of sustainable diets during coronavirus disease 2019.
Living with COVID-19: mass gatherings and minimizing risk
Authors: Murakami M , Yasutaka T , Onishi M , Naito W , Shinohara N , Okuda T , Fujii K , Katayama K , Imoto S 
Published: June 2021

Abstract
During the COVID-19 pandemic, it has been important to both minimize the risk of infection and restore daily life. As a typical example, mass gathering events, such as sporting events, are gradually becoming more common, thanks to the measures taken to contain COVID-19. Some pilot studies have been launched at governments’ initiative to investigate the risk of infection without measures such as face masks and physical distancing at mass gathering events, but the ethics of these studies should be carefully considered. On the other hand, it is still beneficial to implement infection control measures at mass gathering events and, in parallel, to estimate the risk of infection with measures in place, especially under a lack of vaccination progress or the spread of mutant strains possibly resistant to vaccines. To help improve compliance with measures taken by spectators and organizers and to ensure their effectiveness, we have conducted quantitative evaluations of the implementation of such measures by monitoring CO2 concentrations, assessing the proportion of people wearing face masks and analysing human flow at the event. This approach allows us to share our observations with stakeholders and participants, enabling us to protect the culture of mass gathering events, minimize the risk of infection and restore a sense of well-being in daily life.
Oxidative stress-induced senescence mediates inflammatory and fibrotic phenotypes in fibroblasts from systemic sclerosis patients
Authors: Kizilay Mancini Ozge , Acevedo Mariana , Fazez Nesrine , Cuillerier Alexanne , Fernandez Ruiz Ana , Huynh David N , Burelle Yan , Ferbeyre Gerardo , Baron Murray , Servant Marc J 
Published: June 2021

Abstract

Objective
SSc is an autoimmune connective tissue disorder characterized by inflammation and fibrosis. Although constitutive activation of fibroblasts is proposed to be responsible for the fibrotic and inflammatory features of the disease, the underlying mechanism remains elusive, and effective therapeutic targets are still lacking. The aim of this study was to evaluate the role of oxidative stress-induced senescence and its contribution to the pro-fibrotic and pro-inflammatory phenotypes of fibroblasts from SSc patients.

Methods
Dermal fibroblasts were isolated from SSc (n = 13) and healthy (n = 10) donors. Fibroblasts’ intracellular and mitochondrial reactive oxygen species (ROS) were determined by flow cytometry. Mitochondrial function was measured by Seahorse XF24 analyser. Fibrotic and inflammatory gene expressions were assessed by qPCR and key pro-inflammatory components of the fibroblasts’ secretome (IL-6 and IL-8) were quantified by ELISA.

Results
Compared with healthy fibroblasts, SSc fibroblasts displayed higher levels of both intracellular and mitochondrial ROS. Oxidative stress in SSc fibroblasts induced the expression of fibrotic genes and activated the TGF-β-activated kinase 1 (TAK1)–IκB kinase β (IKKβ)–IFN regulatory factor 5 (IRF5) inflammatory signalling cascade. These cellular responses paralleled the presence of a DNA damage response, a senescence-associated secretory phenotype and a fibrotic response. Treatment of SSc fibroblasts with ROS scavengers reduced their pro-inflammatory secretome production and fibrotic gene expression.

Conclusions
Oxidative stress-induced cellular senescence in SSc fibroblasts underlies their pro-inflammatory and pro-fibrotic phenotypes. Targeting redox imbalance of SSc fibroblasts enhances their in vitro functions and could be of relevance for SSc therapy.
Characterization and Expression of Conserved Skeletal Proteins in Echinoderms
Authors: Flores Rachel Lauren , Livingston Brian Thomas 
Published: June 2021

Specification of the cell fate of skeleton‐forming cells in developing sea urchin embryos has been well characterized and the skeletal proteome of both adult and larval skeleton has been determined. Little is known, however, of the mechanism and proteins involved in the mineralization process. A number of spicule matrix proteins have been identified in sea urchins and are present in the organic matrix during spicule formation. However, loss of function studies have indicated they may not be required for mineralization. We have taken a comparative, evolutionary approach to try and elucidate what proteins may be required for the process of mineralization. Here we report the characterization of the skeletal proteome of the sea star Patiria miniata. Our hypothesis is that there are proteins utilized in skeleton formation that are conserved between all echinoderm groups, and possibly among all deuterostomes. First we have isolated skeletal proteins from P. miniata, and then used LC/MS/MS to obtain peptide sequences of those proteins. Characterization of skeletal proteins was accomplished utilizing the NCBI non‐redundant protein database. By comparing the proteins present in all mineralized tissues of the sea urchin with those found in other echinoderm groups we have identified a set of conserved proteins containing similar functional domains. The skeletal proteome from the two echinoderms, P. miniata and Strongylocentrotus purpuratus, groups also shared novel proteins with similar functional domains. We have analyzed the sequences of the proteins we identified as potentially important to determine the evolutionary relationship and to identify the sequences most highly conserved. Additionally, some of these proteins are also found in vertebrate bone. We have also shown that some skeletal proteins prevalent in one group are not found in other echinoderms. This suggests independent co‐option of proteins utilized in mineralization in some groups. The conserved proteins were then analyzed for temporal expression at eight different stages of the developing embryo of S. purpuratus. Some of these stages, such as mesenchyme blastula, were predicted to show higher level of expression for some of the conserved skeletal proteins. Utilizing gel electrophoresis and quantitative polymerase chain reaction (qPCR), we analyzed the temporal expression of conserved skeletal proteins and the relative expression of those proteins during the eight stages of the developing embryo. We found that expression of the conserved skeletal proteins varied, but all were present when skeleton formation occurred in the embryo.Support or Funding InformationNIH/NIGMS T34GM008074, NSF grant 09097979
Regulation of Notch signaling by O‐glucosylation: Notch‐modifying xylosyltransferase‐substrate complexes support an SNi‐like retaining mechanism
Authors: Haltiwanger Robert S , Yu Hongjun , Takeuchi Megumi , LeBarron Jamie , Kantharia Joshua , London Erwin , Bakker Hans , Li Huilin , Takeuchi Hideyuki 
Published: June 2021

A major question remaining in glycobiology is how a glycosyltransferase (GT) that retains the anomeric linkage of a sugar catalyzes the reaction. Xyloside α‐1,3‐xylosyltransferase (XXYLT1) is a retaining GT that regulates Notch receptor activation by adding xylose to the Notch extracellular domain. Here, using natural acceptor and donor substrates and active Mus musculus XXYLT1, we report a series of crystallographic snapshots along the reaction, including an unprecedented natural and competent Michaelis reaction complex for retaining enzymes. These structures strongly support the SNi‐like reaction as the retaining mechanism for XXYLT1. Unexpectedly, the epidermal growth factor–like repeat acceptor substrate undergoes a large conformational change upon binding to the active site, providing a structural basis for substrate specificity. Importantly, XXYLT1 is amplified in a number of squamous cell carcinomas and may be a target for therapeutics. Our improved understanding of this retaining enzyme will accelerate the design of retaining GT inhibitors that can modulate Notch activity in pathological situations in which Notch dysregulation is known to cause cancer or developmental disorders.Support or Funding InformationThe work is supported by NIH grants GM061126 (to R.S.H) and AG029979 (to H.L.), SBU‐BNL Seed Grant (to R.S.H. and H.L.), DFG grant BA4091/5‐1 (to H.B.) and NSF grant DMR 1404985 (to E.L.).
The Roll of COMMD1 in Membrane Protein Trafficking
Authors: Stewart Davis , Short Kristopher , Buglo Elena , Burkhead Jason 
Published: June 2021

Copper is essential for all life due to its role as a catalyst in redox reactions. However, it must be tightly regulated as excess copper can cause oxidative damage to the cell. One example of copper dyshomeostasis is the autosomal recessive condition is known as Wilson disease which can result in liver disease and neurological problems. To maintain copper homeostasis, cells rely on a system of chaperone proteins as well as three copper transporters; CRT1, ATP7A, and ATP7B. ATP7B is a large multidomain membrane‐spanning protein that exports copper from the cytosol and is highly expressed in liver, brain, and kidney cells. ATP7B has a dual role in maintaining copper homeostasis. In the liver, ATP7B functions in the trans‐Golgi network where it pumps copper into the lumen for biosynthesis of secreted cuproproteins. When cellular copper levels are elevated, ATP7B traffics in vesicles towards the apical membrane to move excess copper into bile for excretion from the body. This proves to be a complex decision for the cell as it must retain some ATP7B at the trans‐Golgi for continued biosynthesis of cuproproteins while simultaneously removing the excess. When copper levels are low, ATP7B returns to the Golgi, though it is likely that some is degraded. Although maintaining proper copper homeostasis is important, the mechanism that influences ATP7B distribution is poorly understood. Since being identified as mutated in Bedlington Terriers exhibiting canine copper toxicosis, the protein COMMD1 has been of particular interest as a regulator of cellular copper levels. COMMD1 exhibits both Phosphatidylinositol (PdtIns) effector and Ubiquitin ligase adaptor activity. COMMD1 interacts with a number of membrane proteins including ATP7B. Importantly, COMMD1 downregulation affects cellular copper levels. To investigate the relationship between COMMD1 and ATP7B we used quantitative immunofluorescence microscopy in HepG2 hepatoma cells to analyze the subcellular locations of ATP7B in response to misexpression of COMMD1. The overexpression of the COMMD1 T174M mutant, which was first identified in an atypical Wilson disease patient, significantly decreased the Golgi‐associated fraction of ATP7B and colocalization between ATP7B and lysosomes was also reduced during retrograde trafficking. The T174M mutation may affect PtdIns(4,5)P2 binding by COMMD1, thus we believe that PtdIns(4,5)P2 recruits and facilitates a functional interaction between COMMD1 and ATP7B.Support or Funding InformationNational Science Foundation (MCB‐1411890), NIH 8P20GM103395‐12 (JLB Sub‐Project)
Studies into the synthetic analogs of key intermediates, and ring precursors in the biosynthetic pathway of Coenzyme Q: Synthesis and metabolism
Authors: Nag Anish , He Cuiwen , Shepherd Jennifer N , Fernandez Lucia , Clarke Catherine F , Villalba Jose M 
Published: June 2021

Coenzyme Q (ubiquinone or Q) is a redox active lipid molecule, with a fully substituted benzoquinone ring and a polyisoprenoid tail, containing up to ten isoprene units. Q is an essential component of the mitochondrial respiratory electron transport chain. The exact biosynthetic pathway has still not been completely characterized. In this study, farnesylated analogs of several Q intermediates have been been chemically synthesized. The synthesis of 2‐farnesyl‐1,4‐hydroquinone serves as an analog of 3‐hexaprenyl‐4‐hydroxyphenol, which accumulates in yeast coq6 and coq9 mutants that over‐express the Coq8 polypeptide. In addition farnesylated analogs of 5‐demethoxy‐Q3 (DMQ3), 2‐demethyl‐5‐demethoxy‐Q3 (DDMQ3), and 2‐demethyl‐5‐demethoxy‐4‐amino‐Q3 (IDDMQ3H2) were chemically synthesized. The farnesylated analogs are added to yeast cell cultures to determine whether they serve as precursors and/or intermediates in the biosynthesis of Q3. Also, other selected farnesylated substrates such as 3‐farnesyl‐4‐hydroxybenzoic acid, 3‐farnesyl‐4,5‐dihroxybenzoic acid and others are being synthesized for studying Q metabolism. These substrates can also serve as ligands in protein binding assays and as substrates with isolated enzymes. In addition, a number of different compounds are being tested in assays with mammalian cells, to analyze their roles as ring precursors for Q biosynthesis. Thereby we hope to understand and further characterize the biosynthetic and metabolic pathways responsible for Q biosynthesis and function in different living systems.Support or Funding InformationThis research was funded by NSF MCB‐1330803
In Silico Phage‐Hunting in Sinorhizobium Genomes: Incorporating Original Research in Undergraduate Molecular Biology and Microbiology Courses
Authors: Martinez‐Vaz Betsy , Jensen Autumn , Vang Mandy 
Published: June 2021

The study of bacterial viruses (bacteriophages) is an excellent tool to teach basic principles of molecular biology and microbiology. The availability of numerous complete bacterial genome sequences in public databases provides a unique opportunity for in‐silico‐phage hunting. This approach consists of identifying and characterizing bacteriophages integrated in bacterial chromosomes using computational analyses. The objective of this project was to develop a set of investigative laboratory exercises to allow undergraduate students to participate in a study about the prevalence of bacteriophages in bacteria of the genus Sinorhizobium. These bacteria play a critical role in agriculture due their ability to form nitrogen‐fixing symbioses with alfalfa and related legumes. The role of bacteriophages in N2 fixation and on the physiology of rhizobia remains largely unexplored. The first part of the project consisted of searching Sinorhizobium genomes for the presence of bacteriophages using PHAST, a bioinformatics tool that identifies viral sequences integrated in bacterial chromosomes. Further bioinformatics analyzes were conducted to determine the numbers and types of proteins encoded by the viruses. The students then designed several procedures to activate and excise the predicted bacteriophages out of the Sinorhizobium genomes. Exposure to UV light and Mitomycin treatments led to the successful isolation and molecular characterization of three novel bacteriophages. This set of laboratory exercises was field tested in two undergraduate molecular biology and microbiology courses. The learning objectives of the project were assessed by comparing the scores of pre and post‐tests and by evaluating the bacteriophage characterization protocols designed by the students. Post‐tests were higher than pre‐test scores at or below p=0.005. Normalized learning gains showed improvement in the student's of bioinformatics analyzes skills, basic virology concepts and the structure and function of proteins encoded by bacteriophage genomes.Support or Funding InformationThis project was supported by a grant of the National Science Foundation.
Metabolic Changes Underlying Interactions Between Obesity and Non‐Alcoholic Fatty Liver Disease in South Asian Adults
Authors: Albracht‐Schulte Kembra , Kalupahana Nishan , Ramalingam Latha , Rosairo Shanthini , Wijetunge Sulochana , Kotakadeniya H.M.S.R.B. , Ratnayake R.M.C.J. , Moustaid‐Moussa Naima 
Published: June 2021

Non‐alcoholic fatty liver disease (NAFLD) is often referred to as the hepatic manifestation of the metabolic syndrome, which is characterized by at least three of the following: hypertension, hyperglycemia, abdominal obesity, elevated plasma triglycerides and reduced plasma high‐density lipoproteins. While hepatic steatosis has been well studied in animal models, the relationship between body weight, hepatic steatosis and insulin resistance is not well characterized in humans. Moreover, not all human subjects with obesity develop metabolic complications. In addition, it is unclear why South Asian adults develop insulin resistance and diabetes even at lower levels of adiposity and body mass index compared to their Western counterparts. To address this question, we used a convenient sample of Sri Lankan adult females (n = 30) who underwent routine abdominal surgery at the Teaching Hospital of Peradeniya. Anthropometric data, adipose tissue specimens and fasted serum samples were collected for analyses of glucose, lipid and inflammatory markers. Histological sections of adipose tissue were obtained from omental fat (OF) and anterior abdominal wall fat (AF), and adipocyte cross‐sectional area was measured using the ImageJ software. Further, the presence of hepatic steatosis was assessed using ultrasound scanning by a radiologist. Participants with higher grade of fatty liver had a significantly higher body mass index (BMI), fasting blood glucose and aspartate aminotransferase levels. Additionally, participants with higher grade of fatty liver also had significantly higher serum levels of non‐HDL cholesterol and the pro‐inflammatory adipokine, resistin. Interestingly, there were no significant differences in serum adiponectin levels between the groups. Individuals with fatty liver also had a higher mean adipocyte area in both OF and AF, indicating a higher degree of adipocyte hypertrophy associated with fatty liver. Currently, the measurements of additional biomarkers of inflammation and insulin resistance are underway. These findings indicate distinct metabolic differences between South Asian adults with varying degrees of fatty liver, and may help in establishing effective treatment strategies for obesity‐associated NAFLD.Support or Funding InformationFunded by an International Research/Development Seed grant from the Office of International Affairs and the Office of the Vice President for Research at Texas Tech university (TTU), and an International Research Seed Grant from The College of Human Sciences at TTU, and by the International Research Center, University of Peradeniya.
HomeStyles: Tracking Participant Progress in a Randomized Control Trial
Authors: Delaney Colleen , Martin‐Biggers Jennifer T , Koenings Mallory , Byrd‐Bredbenner Carol 
Published: June 2021

Tracking participant progress in large Randomized Control Trials (RCT) is essential to success, yet tracking procedures are seldom discussed in the research literature. This abstract describes the procedures used during recruitment and retention to track participants in the 18‐month HomeStyles RCT. Microsoft Excel was used to create recruitment‐tracking and retention‐tracking spreadsheets that organized participants by group (experimental, control), geographic location (NJ, AZ), delivery mode (online, home visitation), and language (English, Spanish). Recruitment‐spreadsheet data were used to plot recruited participants by group x location x mode x language to enable researchers to assess and target recruitment resources (e.g., staff time, recruitment flyer printing and distribution, recruitment activities) and project when recruitment goals would be reached. The retention‐tracking spreadsheet included participant stage of RCT participation (Survey 1, Instructional Guide [IG]1, IG2, IG3, IG4, Survey 2, IG5, IG6, IG7, IG8, Survey 3, IG9, Survey 4, IG10, Survey 5), and days elapsed since last communication with RCT team or website. Charting retention‐tracking spreadsheet data permitted researchers to visualize participant progress throughout the time course of the RCT; monitor the rate at which participants completed the RCT; and rapidly intervene when participants appeared to be experiencing barriers that may cause them to become inactive and drop out. The retention‐tracking spreadsheet was annotated to indicate when and how inactive participants were contacted. Staff training and twice weekly generation of recruitment and retention data summaries were essential to making timely, informed research management decisions. Recruitment and retention tracking procedures and algorithms from this RCT have the potential to improve RCT monitoring and management practices in a wide array of health promotion and nutrition communication research studies.Support or Funding InformationUSDA NIFA #2011‐68001‐30170