bluuebunny/crossref_metadata_2025_split huggingface dataset:
Altered CD4+ T cell subset balance in lymphoid organs of mouse model of colorectal cancer (397.2)
Authors: Tanner Scott , Hill Stephanie , Martin Colin , Lorenz Robin 
Published: June 2021

The adenomatous polyposis coli (APC) gene is a known tumor suppressor gene, and mutations resulting in APC inactivation leads to the formation of multiple intestinal neoplasms (Min) within mutant mice (APCMin/+). Thus, the APCMin/+ mouse is used as a model of human colorectal cancer (CRC). The intestinal compartment is especially susceptible to tumor formation due the high turnover rate of epithelial cells. Also, the presence of the intestinal microbiota makes the intestines a very immunologically active site. Reports show that tumor associated CD4+ T cell derived IL‐17 promotes intestinal tumor development in APCMin/+ mice. To further investigate the role of the APCMin/+ mutation on CD4+ T cell function, we performed flow cytometric, histochemical, and immunofluorescent studies on both wild type (APC+/+) and APCMin/+ mice. We identified increased levels of IFN‐+ CD4+ and IL‐17A+ CD4+ cells, and decreased levels of IFN‐+IL‐17+ double positive CD4+ cells in the mesenteric lymph nodes and Peyer’s patches of APCMin/+mice. Culture of naïve CD4+ T cells from the spleens of APCMin/+mice lead to increased regulatory T cell development and lower IL‐17A expression. These results suggest an altered T cell balance in APCMin/+ mice. This intrinsic imbalance in CD4+ T cell subsets may disrupt the intestinal immune environment, inhibiting intestinal tumor destruction in the APCMin/+mouse.Grant Funding Source: UAB Comprehensive Cancer Center
Quality of MCQ‐based exams: why functioning distractors matter (533.4)
Authors: Ali Syed Haris 
Published: June 2021

BACKGROUND: Item difficulties on Free‐response (FR) and MCQ versions of an exam were compared over four study cohorts in this experimental study. The purpose was to investigate factors underlying differential performance on these two versions and the resultant threat to validity of obtained scores.METHODS: The two versions (FR and MCQ) of a Neurohistology practice exam comprising 23 items were randomly distributed among Year 1 medical students in four study cohorts. An index of expected MCQ difficulty was calculated via expected inflation in each item’s ease due to provision of options, and was then compared with the actually observed MCQ difficulty. No significant difference between expected and observed MCQ difficulty indices was hypothesized.RESULTS: A significant difference between FR and observed MCQ difficulty indices (p < 0.05), and not between FR and expected MCQ difficulty indices, was found in all cohorts. Moreover, a consistently low mean number of functioning distractors (0.95, 0.95, 0.86, 0.87), and a significant correlation (p < 0.01) between number of functioning distractors and MCQ difficulty were also noted.CONCLUSION: Low number of functioning distractors threatens the validity of scores obtained on MCQ‐based exams. To assess true knowledge, careful evaluation of plausibility of every provided MCQ option or a mix of MCQs and alternate assessment tools is recommended.
Moderately high fructose (6%) ingestion reduces the vascular reactivity to vasoconstrictors and vasodilators in rats (546.1)
Authors: Fonseca da Silva Rita de Cássia , de Souza Priscila , Marques Maria Consuelo , da Silva Santos José Eduardo 
Published: June 2021

It has been shown that very high amounts of fructose in the diet may induce vascular dysfunction in rats. We hypothesized that significantly small amounts of fructose ingested in early life stages is enough to impair the vascular function. Wistar rats were fed with a moderately high (6%) fructose diet (6% F group) for six weeks from weaning (control group received regular chow). Endothelium‐intact (E+) aortic rings and perfused mesenteric arteries from 6% F rats presented reduced responses to phenylephrine (PE, 1 μM: 0.59 ± 0.05 g against 1.26 ± 0.22 g in control), and vasopressin (30 nM: 0.26 ± 0.07 g against 0.61 ± 0.11 g in control). PE‐induced constriction was reestablished in endothelium‐denuded (E‐) rings and after incubation with L‐NAME (100 μM) or ODQ (10 μM). However, PE‐contracted aortic rings (E+) displayed reduced relaxation (~ 60%) induced by acetylcholine (ACh, 1 μM), but not by sodium nitroprusside. E‐ aortic rings from 6% F group maintained in Ca2+‐free solution presented enhanced contractile responses to caffeine (100 mM), but not to PE. This study shows that the ingestion of moderately high fructose in early life stages is enough to impair the vascular reactivity of rats.Grant Funding Source: Supported by Coordenação de Aperfeiçoamento de Pessoal de Nível Superior, CAPES, Brazil; Conselho Na
Coupling between alternative polyadenylation and alternative splicing is limited to terminal introns (560.2)
Authors: Movassat Maliheh , Crabb Tara , Busch Anke , Shi Yongsheng , Hertel Klemens 
Published: June 2021

Alternative polyadenylation (APA) has been implicated as an important regulator of gene expression. In some cases APA is known to couple with alternative splicing to influence last intron removal, however it is unknown whether APA events influence alternative splicing decisions at upstream exons. A genome‐wide approach was used to examine the correlation between APA and upstream alternative splicing. CstF64 knockdown in HeLa cells coupled with Pas‐Seq was used to trigger and identify APA events. APA genes were then evaluated for changes in alternative splicing using RNA‐seq analyses of the same knockdown samples. Although a significant number of alternative splicing events were identified, no general correlation between APA and upstream alternative splicing events were observed. These results suggest that the coupling and diversification achieved between APA and alternative splicing in general is fixed to defining the last exon. iClip‐Seq experiments identified CstF64 binding to be predominantly in intronic regions. Interestingly, the genome‐wide binding analysis also showed that CstF64 density is elevated upstream of skipped exons indicating a potential role for CstF64 in alternative splicing. We conclude that while the influence of APA on alternative splicing is generally limited to terminal introns, CstF64 binding to nascent pre‐mRNA may contribute to the modulation of splicing patterns.Grant Funding Source: NIH
Somatic spliceosomal factor mutations in bone marrow neoplasms ő downstream effects and mechanistic insights (560.3)
Authors: Padgett Richard , Dietrich Rosemary , Singh Jarnail , Przychodzen Bartlomiej , Makishima Hideki , Maciejewski Jaroslaw 
Published: June 2021

Somatic mutations of spliceosomal proteins such as U2AF1, SF3B1, SRSF2 and PRPF8 have been identified in myeloid malignancies. These mutations are usually single heterozygous missense mutations at highly recurrent sites. While all of these mutations affect proteins in the common splicing pathway, their downstream consequences may be diverse and involve distinct oncogenic pathways. To identify affected genes and gain mechanistic insight into the effects of these mutations, we have analyzed the tumor transcriptomes of multiple AML patients with and without spliceosomal factor mutations. For U2AF1, we analyzed 6 tumors with U2AF1 mutations and 14 tumors that had no known splicing factor mutations. Focusing on cases of alternative exon inclusion, we identified 35 exons in 35 genes whose inclusion was altered using stringent statistical cutoffs. Of these, 8 exons were more included while 27 were more excluded in the U2AF1 mutant tumors. We examined the splice site signals flanking the alternative exons and noted a highly unusual sequence pattern adjacent to the 3’ AG dinucleotide, which is the recognition site of U2AF1. The sequence at this position showed a mutually exclusive pattern upon comparing the excluded to the included exons and this pattern also differed from the consensus 3’ splice site sequence. Biochemical analysis of the RNA binding specificities of purified mutant and wild type U2AF1/U2AF2 heterodimers showed alterations that correlated with the splicing alterations observed in vivo. Engineered cell lines expressing the mutant U2AF1 protein recapitulated the splicing alterations observed in vivo. These results suggest that the mutations in U2AF1 lead to altered splice site recognition and aberrant splicing of a subset of genes that contribute to the neoplastic state. Similar analyses of the splicing effects of mutations in other spliceosomal factors showed that there is little overlap in the most affected genes.Grant Funding Source: Supported by NIH grant HL118281
Use of genetic markers to determine change in population structure of deer ticks in Wisconsin (570.2)
Authors: Much Cody , Caporale Diane , Swiatnicki Mathew 
Published: June 2021

During the early 2000’s, tick infection rates in the endemic Northwest and nonendemic Central areas of WI were 36% and 4%, respectively, for Borrelia burgdorferi, the Lyme disease pathogen. In 2004, Borrelia populations and deer ticks populations were both found distinct among Northwest WI, Central WI, and Northeast WI, with very little gene flow among them. However, in 2013, Borrelia abundance has increased with 44% infection rate in Central WI. Possible cause for increased prevalence may be due to increased tick abundance and increased gene flow from high to low endemic regions in the state. The use of 16S mtDNA sequences was used to assess the current population structure of deer ticks in Northern Wisconsin. In 2013, tick 16S haplotypes were identified from Northwest WI, Central WI, and Northeast WI and the distribution of haplotypes among the study sites were determined. Several unique haplotypes found only in Northwest WI from 1999 are now found in Central WI. Phi statistical estimates may reveal ticks as being one population between the Northeast and Central WI, due to an increase in gene flow. This may be the possible cause of increased incidences of tick‐borne disease in Wisconsin. The study may also be informative for medical professionals in Wisconsin.Grant Funding Source: Supported by UWSP College of Letters and Science
IUGR disrupts the PPARγ‐Setd8‐H4K20me1 loop in male rat adipose tissue (577.5)
Authors: Riddle E , Zou C.J. , Trevenzoli I , Joss‐Moore L 
Published: June 2021

Intrauterine growth restriction (IUGR) programs adipose dysfunction. Appropriate adipose function is, in part, maintained by the peroxisome proliferator activated receptor gamma (PPARγ)‐Setd8‐H4K20me1 (histone 4, lysine 20, methylation) positive feedback loop. This loop relies on PPARγ’s direct transcriptional control of Setd8, as well as Setd8’s placement of H4K20me1 on PPARγ. We previously showed that IUGR causes adipose dysfunction and increases total PPARγ mRNA levels in male rat adipose tissue. However, the effect of IUGR on the PPARγ‐Setd8‐H4K20me1 loop in male rat adipose tissue is unknown.We hypothesize that IUGR disrupts the PPARγ‐Setd8‐H4K20me1 loop in male rat adipose tissue.IUGR was induced by bilateral uterine artery ligation in rat dams at E19 of gestation. Subcutaneous adipose tissue of male IUGR and control rats was assessed at postnatal day 21 (n=4 per group). PPARγ1, PPARγ2, and Setd8 mRNA levels were measured using real‐time PCR. Chromatin immunoprecipitation was used to quantify H4K20me1 at Promoter 1 (P1), P2 and the 3’UTR of the PPARγ gene.Results are IUGR as % of Control ± SEM, *p<0.05. IUGR increased PPARγ1 (227 ± 40*), PPARγ2 (195 ± 29*), and Setd8 (171 ± 28*) mRNA levels in male rat adipose tissue. IUGR decreased H4K20me1 at P1 of the PPARγ gene (44 ± 6*), with no significant changes at P2 or the 3’UTR.The PPARγ‐Setd8‐H4K20me1 loop plays an important role in adipose function and is disrupted by IUGR. Increased PPARγ and Setd8 mRNA in conjunction with decreased H4K20Me1 at PPARγ P1, suggests dysregulation of H4K20me1 placement or H4K20 demethylation. Our ongoing studies examine regulation of H4K20me1 placement on PPARγ as well as the function of the H4K20 demethylase, PHF8.Grant Funding Source: Supported by NIH grant DK084036(LJM)
Design and synthesis of albuterol‐derivatives as selective β2‐adrenoceptor agonists with potential biased signaling (588.2)
Authors: Lopez‐Cabrera Yessica , Trujillo‐Ferrara Jose , Cuevas‐Hernandez Roberto , Correa‐Basurto Jose , Soriano‐Ursua Marvin 
Published: June 2021

The development of new drugs based on the selectivity for recognition and coupling on receptors is increasing. Recent studies of β‐adrenoceptors and their associated ligands allow us to explore properties about interactions and receptor activation, which modulated the response produced in a organism. Those responses are related with the preference of the G‐protein‐dependent pathway or the β‐arrestin pathway.In present work, we designed albuterol derivatives and we studied them through a computational study analyzing interactions on β2 adrenoceptor using in silico tools. Furthermore, we carried out the synthesis of some of these compounds. From our in silico results, we suggest that chemical structure of albuterol derivatives influence in both orthosteric and allosteric binding sites on the receptor, in such manner which could be involved in their potencial biased signaling. Also, we suggest the potential of in silico details for suggesting biased signaling on β2 adrenoceptor. Finally, regarding the synthesis of these compounds, we identified the specific values for temperature and pH variables favoring yield and purity.Grant Funding Source: Supported by CONACyT (CB168116), COFAA, and SIP‐IPN, México.
The effect of hypoxia on lipid raft organization and host‐pathogen interactions of intestinal epithelial cells (599.2)
Authors: Zeitouni Nathalie , Branitzki‐Heinemann Katja , von Koeckritz‐Blickwede Maren , Naim Hassan 
Published: June 2021

Oxygen stress, or hypoxia, occurs in tissues during an infection, mostly due to overconsumption of oxygen by pathogens and recruited immune cells. The aim of this study is to analyze the effect of hypoxia on host‐pathogen interactions and cellular responses of the intestinal epithelium upon infection. Therefore, Caco‐2 cells were grown under normoxia or hypoxia and were infected with Yersinia enterocolitica, a Gram‐negative bacterium that can cause severe gastrointestinal infections. Results show that invasion of Caco‐2 by Y. enterocolitica was significantly reduced in hypoxia‐treated cells while adherence remained unchanged. Since intestinal epithelial cells have been shown to regulate host‐pathogen interactions by means of detergent‐resistant membrane domains called lipid rafts, we further investigated the effect of hypoxia on lipid rafts. Interestingly, separation of lipid rafts isolated from Caco‐2 cells grown under hypoxia demonstrated that flotillin, a lipid rafts protein marker, exhibits a diffuse pattern in the rafts as well as non‐rafts fractions. By contrast, cells grown under normoxia revealed a clear flotillin distribution in the floating lipid rafts fractions. These results indicate that hypoxia leads to alterations of the intestinal epithelial cell membrane and suggests a protective effect of these membrane changes on host cells by hindering invasion of Y. enterocolitica.Grant Funding Source: Supported by DAAD and the German Research Council (DFG, grant number KO355214).
Functional motif analysis for glycosyltransferases in apicomplexan genomes (608.5)
Authors: Datta Arun , Sinai Anthony , Kissinger Jessica 
Published: June 2021

Parasitic protozoa of the Phylum Apicomplexa include the genus Plasmodium (causative agents of malaria) and Toxoplasma gondii which causes toxoplasmosis. Little is known about glycosylation pathways and their contributions to pathogenesis. Increased glycosylation is known to be a feature of the chronic infection with Toxoplasma defined by the formation of the tissue cyst. Lectin reactivity and biochemical identification indicate that Toxoplasma tissue cysts contain diverse glycan modifications that are hypothesized to originate from both the parasite and the host. In order to establish the potential extent of host derived glycan modifications we have undertaken a comprehensive survey of the encoded potential in the toxoplasma genome (www.toxodb.org) by conducting a rigorous bioinformatics survey for predicted glycosyltransferases (GT). In addition to the identification of a truncated pathway for the synthesis of N‐linked glycans predicting simple (ConA positive) but not complex (LCA positive) labeling we find a complete absence of any of the machinery to permit modification with sialic acid. The presence in tissue cysts of both complex N‐linked glycans and sialic acid (SNA, MALII, Limax agglutinin and anti Sia‐Tn antigen) implicates host cell involvement. In order to understand the full extent of the novel form of parasitism, the hijacking of host glycan modifying enzymes, we are now investigating whether the Toxoplasma genome encodes other classes of glycosyltransferases. We hypothesize that the absence of a specific GT encoded in the parasite genome coupled with its phenotypic detection implicates thievery from the host cell. The current interrogation is being extended to other parasitic protozoa for which the genomes are now available (www.eupathdb.org). Such a broad survey across Apicomplexa and other parasitic Phyla may reveal insights into the evolution of the glycosylation machinery in these early branching eukaryotes and provide insights into infection and immunity.Grant Funding Source: NIHR21 AI099509 (to APS)
Increased retention from a summer‐bridge program focused on academics, community, and leadership (618.34)
Authors: Lo Stanley , Flores Luke , Drane Denise , Swarat Su , Beitel Greg , Light Gregory 
Published: June 2021

Under‐represented minority students leave science, technology, engineering, and mathematics (STEM) majors at high rates. As an intervention, pre‐college summer‐bridge programs have been successful. However, evaluations of existing programs focus on degree attainment and lack information on student experience while in college. Traditional summer‐bridge programs also emphasize ethnic backgrounds and academic under‐preparedness. We report a new summer‐bridge program that aims to address gaps in the literature described above.The new summer‐bridge program is different from traditional programs in significant ways. First, the definition of under‐representation is expanded to include socioeconomic need, first‐generation college student, and multilingualism. Second, the selection criteria focus on demonstrated commitments to promoting diversity and inclusion instead of ethnic backgrounds to avoid activation of stereotype threat. Third, courses are offered at different levels to challenge students regardless of academic preparation. Finally, the program is designed to engage participants in activities that focus on community building, leadership development, and authentic practices in biological research.A quasi‐experimental design with a historical comparison group (n=708) is used to study the effectiveness of this program. To date, three cohorts of participants (n=58) have completed the program. Pre‐ and post‐surveys reveal significant increases in reported help‐seeking, propensity for critical thinking, and knowledge of research process. In focus groups and interviews, participants reported that the program helped them connect with faculty, establish social networks, and become part of the university community. Critically, compared to a historical cohort, participants have higher grades (2.53±0.62 vs. 1.94±0.92, p<0.01) and retention rates (73% vs. 30%, p<0.01) in General Chemistry, the gateway course to many STEM disciplines including biology.Grant Funding Source: Howard Hughes Medical Institute
Prevalence and risk factors for malnutrition in children with congenital heart disease, Ho Chi Minh City, Viet Nam (620.12)
Authors: Tin Hoang , Nhan Le , Hoa Nguyen , Giang Do Thi , Ziegler Thomas , Lenders Carine 
Published: June 2021

Objective: To determine the prevalence and risk factors for malnutrition in children with congenital heart disease (CHD) attending a cardiology clinic in Vietnam.Methods: Cross‐sectional survey of all children with CHD aged <5 years old at Children’s Hospital #1 (March‐August 2012). Data included weight (W), height (H), age (A), gender, cardiac diagnosis, severity of CHD, corrective surgery status, birth order, preterm delivery, low‐birth‐weight (LBW), breastfeeding initiation and cessation, age at weaning, parent education and income stability. Patients with genetic syndromes, dysmorphic features, or neurologic disabilities were excluded (n=9). Nutrition status was classified using WHO standards.Results: Participants were 410 children; 153 had previous corrective surgery. The rate of stunting (H/A 蠄‐2SD) was 153/410 (37.4%) and that of wasting (W/H 蠄‐2SD) was 136/410 (33.3%). These rates did not differ according to surgery status (P>0.05). Risk factors for stunting included preterm delivery, LBW, mother’s income stability, and father’s education, (P<0.05). Risk factors for wasting included age 6‐12 mo, LBW, breastfeeding cessation at <6 mo and weaning at <6 mo (p<0.05).Conclusion: Malnutrition rates are high in this cohort of Vietnamese children with CHD. Modifiable factors (breastfeeding and age at weaning) play a role. Prospective studies on nutritional status in this CHD patient population are needed to inform intervention studies.Grant Funding Source: Support from the Abbott Fund
Adjustment of RNA‐Seq data for the effect of highly abundant transcripts: a case study in milk production (622.4)
Authors: Beck Kristen , Turco Gina , Bradnam Keith , Rijnkels Monique , Nommsen‐Rivers Laurie , Korf Ian , Lemay Danielle 
Published: June 2021

During lactation, profound changes occur in the mammary gland and thousands of genes undergo differential regulation. RNA‐seq data analysis reveals a tiny minority of milk genes account for the vast majority of total gene expression. This striking imbalance in transcript abundances poses a significant problem for data analysis, e.g. low abundance genes may be incorrectly identified as downregulated. To tackle this problem, we developed a ‘Dilution Adjustment Model’ which more accurately classifies changes in levels of low abundance transcripts between transcriptomes at two developmental stages (baseline and mature lactation). Applying this model to human and bovine milk data led us to reclassify 2,155 human (971 bovine) genes as ‘upregulated’ instead of ‘not differentially expressed’ and 2,524 human (1,732 bovine) as ‘unregulated’ instead of ‘downregulated’. Changes in gene classification were supported by analysis of Gene Ontology and TFBS enrichment profiles. Investigation of ChIP‐Seq data showed genes reclassified as ‘upregulated’ exhibit signs of active transcription and reclassified ‘unregulated’ genes match marks of others in this set. This work leads to a better understanding of transcription mechanisms in milk production. Application of this model to other biological systems is relevant where transcripts from a minority of genes dominate transcriptome composition.Grant Funding Source: K.B was supported by Grant Number T32‐GM008799 from NIGMS‐NIH