The Influence of Course Format, Student Characteristics, and Perceived Teacher Communication and Behavior on Instructional Outcomes Before and During the COVID-19 Pandemic

Two studies examined instructional format (intact vs. hybrid and remote vs. online), classroom climate, student characteristics (engagement and communication apprehension), perceived teacher communication and behavior (teacher competence, clarity, caring), and their influence on instructional outcomes, including cognitive learning, communication satisfaction, and intent to persist in college pre-pandemic and during the pandemic. The findings highlight the important role teacher characteristics (caring, clarity, competence) played in instructional outcomes. This study also revealed that high levels of engagement signals students’ willingness to participate in the learning process. Students are a driving force in their own cognitive learning, communication satisfaction, and intent to persist in college. No statistically significant differences were found in instructional outcomes across various instructional formats

Lipocalin 2 protects from lung tumorigenesis associated with gut microbiota alterations

https://openworks.mdanderson.org/sumexp22/1112/thumbnail.jp

Comparative transcriptomics of an arctic foundation species, tussock cottongrass (Eriophorum vaginatum), during an extreme heat event

© The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Mohl, J. E., Fetcher, N., Stunz, E., Tang, J., & Moody, M. L. Comparative transcriptomics of an arctic foundation species, tussock cottongrass (Eriophorum vaginatum), during an extreme heat event. Scientific Reports, 10(1), (2020): 8990, doi:10.1038/s41598-020-65693-8.Tussock cottongrass (Eriophorum vaginatum) is a foundation species for much of the arctic moist acidic tundra, which is currently experiencing extreme effects of climate change. The Arctic is facing higher summer temperatures and extreme weather events are becoming more common. We used Illumina RNA-Seq to analyse cDNA libraries for differential expression of genes from leaves of ecologically well-characterized ecotypes of tussock cottongrass found along a latitudinal gradient in the Alaskan Arctic and transplanted into a common garden. Plant sampling was performed on a typical summer day and during an extreme heat event. We obtained a de novo assembly that contained 423,353 unigenes. There were 363 unigenes up-regulated and 1,117 down-regulated among all ecotypes examined during the extreme heat event. Of these, 26 HSP unigenes had >log2-fold up-regulation. Several TFs associated with heat stress in previous studies were identified that had >log2-fold up- or down-regulation during the extreme heat event (e.g., DREB, NAC). There was consistent variation in DEGs among ecotypes, but not specifically related to whether plants originated from taiga or tundra ecosystems. As the climate changes it is essential to determine ecotypic diversity at the genomic level, especially for widespread species that impact ecosystem function.We thank Thomas Parker for providing crucial logistical support at Toolik Field station and Darrel Dech, Stephen Turner, and Mayra Melendez for assistance in field sampling. Funding for this research was provided through the National Science Foundation (NSF/PLR 1418010 to NF, NSF/PLR 1417645 to MLM, NSF/PLR 1417763 to JT) and JEM received funding in part from NIH Grant #5G12RR007592 from the National Center for Research Resources (NCRR)/NIH to UTEP’s Border Biomedical Research Center. Significant logistic support came from Toolik Field Station and the Arctic LTER (NSF/PLR 1637459)

Eating As Treatment (EAT): A Stepped-Wedge, Randomized Controlled Trial of a Health Behavior Change Intervention Provided by Dietitians to Improve Nutrition in Patients With Head and Neck Cancer Undergoing Radiation Therapy (TROG 12.03)

Purpose: Malnutrition in head and neck cancer (HNC) treatment is common and associated with poorer morbidity and mortality outcomes. This trial aimed to improve nutritional status during radiation therapy (RT) using a novel method of training dietitians to deliver psychological techniques to improve nutritional behaviors in patients with HNC. Methods and Materials: This trial used a stepped-wedge, randomized controlled design to assess the efficacy of the Eating As Treatment (EAT) program. Based on motivational interviewing and cognitive behavioral therapy, EAT was designed to be delivered by oncology dietitians and integrated into their clinical practice. During control steps, dietitians provided treatment as usual, before being trained in EAT and moving into the intervention phase. The training was principles based and sought to improve behavior-change skills rather than provide specific scripts. Patients recruited to the trial (151 controls, 156 intervention) were assessed at 4 time points (the first and the final weeks of RT, and 4 and 12 weeks afterward). The primary outcome was nutritional status at the end of RT as measured by the Patient-Generated Subjective Global Assessment. Results: Patients who received the EAT intervention had significantly better scores on the primary outcome of nutritional status at the critical end-of-treatment time point (β = −1.53 [−2.93 to −.13], P =.03). Intervention patients were also significantly more likely than control patients to be assessed as well-nourished at each time point, lose a smaller percentage of weight, have fewer treatment interruptions, present lower depression scores, and report a higher quality of life. Although results were not statistically significant, patients who received the intervention had fewer and shorter unplanned hospital admissions. Conclusions: This trial is the first of its kind to demonstrate the effectiveness of a psychological intervention to improve nutrition in patients with HNC who are receiving RT. The intervention provides a means to ameliorate malnutrition and the important related outcomes and consequently should be incorporated into standard care for patients receiving RT for HNC

Landscape genomics provides evidence of ecotypic adaptation and a barrier to gene flow at treeline for the arctic foundation species Eriophorum vaginatum0

© The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Stunz, E., Fetcher, N., Lavretsky, P., Mohl, J., Tang, J., & Moody, M. Landscape genomics provides evidence of ecotypic adaptation and a barrier to gene flow at treeline for the arctic foundation species Eriophorum vaginatum. Frontiers in Plant Science, 13, (2022): 860439, https://doi.org/10.3389/fpls.2022.860439.Global climate change has resulted in geographic range shifts of flora and fauna at a global scale. Extreme environments, like the Arctic, are seeing some of the most pronounced changes. This region covers 14% of the Earth’s land area, and while many arctic species are widespread, understanding ecotypic variation at the genomic level will be important for elucidating how range shifts will affect ecological processes. Tussock cottongrass (Eriophorum vaginatum L.) is a foundation species of the moist acidic tundra, whose potential decline due to competition from shrubs may affect ecosystem stability in the Arctic. We used double-digest Restriction Site-Associated DNA sequencing to identify genomic variation in 273 individuals of E. vaginatum from 17 sites along a latitudinal gradient in north central Alaska. These sites have been part of 30 + years of ecological research and are inclusive of a region that was part of the Beringian refugium. The data analyses included genomic population structure, demographic models, and genotype by environment association. Genome-wide SNP investigation revealed environmentally associated variation and population structure across the sampled range of E. vaginatum, including a genetic break between populations north and south of treeline. This structure is likely the result of subrefugial isolation, contemporary isolation by resistance, and adaptation. Forty-five candidate loci were identified with genotype-environment association (GEA) analyses, with most identified genes related to abiotic stress. Our results support a hypothesis of limited gene flow based on spatial and environmental factors for E. vaginatum, which in combination with life history traits could limit range expansion of southern ecotypes northward as the tundra warms. This has implications for lower competitive attributes of northern plants of this foundation species likely resulting in changes in ecosystem productivity.This research was made possible by funding provided by NSF/PLR-1417645 to MM. The Botanical Society of America Graduate Student Research Award and the Dodson Research Grant from the Graduate School of the University of Texas at El Paso provided assistance to ES. The grant 5U54MD007592 from the National Institute on Minority Health and Health Disparities (NIMHD), a component of the National Institutes of Health (NIH) provided bioinformatics resources and support of JM

Epstein-Barr virus-specific methylation of human genes in gastric cancer cells

<p>Abstract</p> <p>Background</p> <p>Epstein-Barr Virus (EBV) is found in 10% of all gastric adenocarcinomas but its role in tumor development and maintenance remains unclear. The objective of this study was to examine EBV-mediated dysregulation of cellular factors implicated in gastric carcinogenesis.</p> <p>Methods</p> <p>Gene expression patterns were examined in EBV-negative and EBV-positive AGS gastric epithelial cells using a low density microarray, reverse transcription PCR, histochemical stains, and methylation-specific DNA sequencing. Expression of PTGS2 (COX2) was measured in AGS cells and in primary gastric adenocarcinoma tissues.</p> <p>Results</p> <p>In array studies, nearly half of the 96 human genes tested, representing 15 different cancer-related signal transduction pathways, were dysregulated after EBV infection. Reverse transcription PCR confirmed significant impact on factors having diverse functions such as cell cycle regulation (<it>IGFBP3</it>, <it>CDKN2A, CCND1, HSP70, ID2, ID4)</it>, DNA repair <it>(BRCA1, TFF1</it>), cell adhesion (<it>ICAM1</it>), inflammation (<it>COX2</it>), and angiogenesis (<it>HIF1A</it>). Demethylation using 5-aza-2'-deoxycytidine reversed the EBV-mediated dysregulation for all 11 genes listed here. For some promoter sequences, CpG island methylation and demethylation occurred in an EBV-specific pattern as shown by bisulfite DNA sequencing. Immunohistochemistry was less sensitive than was western blot for detecting downregulation of COX2 upon EBV infection. Virus-related dysregulation of COX2 levels <it>in vitro </it>was not recapitulated <it>in vivo </it>among naturally infected gastric cancer tissues.</p> <p>Conclusions</p> <p>EBV alters human gene expression in ways that could contribute to the unique pathobiology of virus-associated cancer. Furthermore, the frequency and reversability of methylation-related transcriptional alterations suggest that demethylating agents have therapeutic potential for managing EBV-related carcinoma.</p

The Stability of Retrospective Pre-injury Symptom Ratings Following Pediatric Concussion.

Objective: To determine the stability of children\u27s retrospective ratings of pre-injury levels of symptoms over time following concussion. Methods: Children and adolescents (n = 3,063) between the ages of 5–17 diagnosed with a concussion by their treating pediatric emergency department (PED) physician within 48 h of injury completed the Post-Concussion Symptom Inventory (PCSI) at the PED and at 1, 2, 4, 8, and 12-weeks post-injury. At each time point, participants retrospectively recalled their pre-injury levels of post-injury symptoms. The PCSI has three age-appropriate versions for children aged 5–7 (PCSI-SR5), 8–12 (PCSI-SR8), and 13–18 (PCSI-SR13). Total scale, subscales (physical, cognitive, emotional, and sleep), and individual items from the PCSI were analyzed for stability using Gini\u27s mean difference (GMD). Results: The mean GMD for total score was 0.31 (95% CI = 0.28, 0.34) for the PCSI-SR5, 0.19 (95% CI = 0.18, 0.20) for the PCSI-SR8, and 0.17 (95% CI = 0.16, 0.18) for the PCSI-SR13. Subscales ranged from mean GMD 0.18 (physical) to 0.31 (emotional) for the PCSI-SR8 and 0.16 (physical) to 0.31 (fatigue) for the PCSI-SR13. At the item-level, mean GMD ranged from 0.13 to 0.60 on the PCSI-SR5, 0.08 to 0.59 on the PCSI-SR8, and 0.11 to 0.41 on the PCSI-SR13. Conclusions: Children and adolescents recall their retrospective pre-injury symptom ratings with good-to-perfect stability over the first 3-months following their concussion. Although some individual items underperformed, variability was reduced as items were combined at the subscale and full-scale level. There is limited benefit gained from collecting multiple pre-injury symptom queries

Characterization of inositol lipid metabolism in gut-associated Bacteroidetes

Inositol lipids are ubiquitous in eukaryotes and have finely tuned roles in cellular signalling and membrane homoeostasis. In Bacteria, however, inositol lipid production is relatively rare. Recently, the prominent human gut bacterium Bacteroides thetaiotaomicron (BT) was reported to produce inositol lipids and sphingolipids, but the pathways remain ambiguous and their prevalence unclear. Here, using genomic and biochemical approaches, we investigated the gene cluster for inositol lipid synthesis in BT using a previously undescribed strain with inducible control of sphingolipid synthesis. We characterized the biosynthetic pathway from myo-inositol-phosphate (MIP) synthesis to phosphoinositol dihydroceramide, determined the crystal structure of the recombinant BT MIP synthase enzyme and identified the phosphatase responsible for the conversion of bacterially-derived phosphatidylinositol phosphate (PIP-DAG) to phosphatidylinositol (PI-DAG). In vitro, loss of inositol lipid production altered BT capsule expression and antimicrobial peptide resistance. In vivo, loss of inositol lipids decreased bacterial fitness in a gnotobiotic mouse model. We identified a second putative, previously undescribed pathway for bacterial PI-DAG synthesis without a PIP-DAG intermediate, common in Prevotella. Our results indicate that inositol sphingolipid production is widespread in host-associated Bacteroidetes and has implications for symbiosis

Study protocol of a phase 2, dual-centre, randomised, controlled trial evaluating the effectiveness of probiotic and egg oral immunotherapy at inducing desensitisation or sustained unresponsiveness (remission) in participants with egg allergy compared with placebo (probiotic egg allergen oral immunotherapy for treatment of egg allergy: PEAT study)

Introduction Egg allergy is the most common food allergy in children but recent studies have shown persistence or delayed resolution into adolescence. As there is currently no effective long-term treatment, definitive treatments that improve quality of life and prevent fatalities for food allergies are required. We have previously shown that a novel treatment comprising a combination of the probiotic Lactobacillus rhamnosus CGMCC 1.3724 with peanut oral immunotherapy (OIT) is highly effective at inducing sustained unresponsiveness, with benefit persisting to 4 years after treatment cessation in the majority of initial treatment responders. In this study, we plan to extend the probiotic food OIT platform to another allergen, namely egg. We describe the protocol for a phase 2, dual-centre, randomised, controlled trial evaluating the effectiveness of probiotic and egg OIT at inducing desensitisation or sustained unresponsiveness (remission) in participants with egg allergy compared with placebo. Methods and analysis 80 participants aged 5-30 years of age with current egg allergy confirmed by double-blind placebo-controlled food challenge at study screening will be recruited from Australia and Singapore. There are two intervention arms - probiotic and egg OIT (active) or placebo. Interventions are administered once daily for 18 months. The primary outcome is the proportion of participants who attain 8-week sustained unresponsiveness in the active group versus placebo group. Ethics and dissemination This study has been approved by the Human Research Ethics Committees at the Royal Children's Hospital (HREC 2019.082) and the National Healthcare Group Domain Specific Review Board (2019/00029). Results will be published in peer-reviewed journals and disseminated via presentations at international conferences. Trial registration number ACTRN12619000480189

Comparative genomics of Toll-like receptor signalling in five species

<p>Abstract</p> <p>Background</p> <p>Over the last decade, several studies have identified quantitative trait loci (QTL) affecting variation of immune related traits in mammals. Recent studies in humans and mice suggest that part of this variation may be caused by polymorphisms in genes involved in Toll-like receptor (TLR) signalling. In this project, we used a comparative approach to investigate the importance of TLR-related genes in comparison with other immunologically relevant genes for resistance traits in five species by associating their genomic location with previously published immune-related QTL regions.</p> <p>Results</p> <p>We report the genomic localisation of <it>TLR1-10 </it>and ten associated signalling molecules in sheep and pig using <it>in-silico </it>and/or radiation hybrid (RH) mapping techniques and compare their positions with their annotated homologues in the human, cattle and mouse whole genome sequences. We also report medium-density RH maps for porcine chromosomes 8 and 13. A comparative analysis of the positions of previously published relevant QTLs allowed the identification of homologous regions that are associated with similar health traits in several species and which contain TLR related and other immunologically relevant genes. Additional evidence was gathered by examining relevant gene expression and association studies.</p> <p>Conclusion</p> <p>This comparative genomic approach identified eight genes as potentially causative genes for variations of health related traits. These include susceptibility to clinical mastitis in dairy cattle, general disease resistance in sheep, cattle, humans and mice, and tolerance to protozoan infection in cattle and mice. Four TLR-related genes (<it>TLR1</it>, <it>6</it>, <it>MyD88</it>, <it>IRF3</it>) appear to be the most likely candidate genes underlying QTL regions which control the resistance to the same or similar pathogens in several species. Further studies are required to investigate the potential role of polymorphisms within these genes.</p