bluuebunny/crossref_metadata_2025 huggingface dataset:
Characterization and stability of dietary patterns in the year following head and neck cancer diagnosis
Authors: Arthur Anna E , Peterson K E , Hebert J R , Chepeha D B , Duffy S A , Bellile E L , Taylor J MG , Wolf G T , Rozek L S
Published: June 2021

Head and neck cancer (HNC) is characterized by malnutrition that may persist post‐treatment and lead to dietary changes due to a desire to improve health and decrease morbidity. No longitudinal studies have examined such changes. We characterized dietary pattern change in the year after HNC diagnosis in 128 newly diagnosed HNC patients enrolled in UM Head and Neck SPORE and determined correlations with patient and tumor characteristics. Principal components analysis of 42 FFQ‐derived food groups defined 3 patterns: Whole foods; High meat/saturated fat; Convenience foods. Scores for each pattern were categorized into 4 groups that defined a score trajectory from baseline to 1‐year: Low‐Low; Low‐High; High‐High; High‐Low. Chi‐squared tests and ANOVA were used to examine associations of changes in the 3 pattern scores with demographic, clinical and behavioral variables. Most participants’ pattern scores remained stable across time points (73, 72, and 57% for Whole foods, High meat, and Convenience foods, respectively). Whole foods pattern trajectory differed significantly by education (P = 0.04); High meat trajectory differed significantly by BMI and smoking (P = 0.02 and 0.01, respectively); and Convenience foods trajectory differed significantly by BMI, education and sex (P = 0.02, 0.02, and 0.05, respectively). Future studies should examine how dietary pattern changes are associated with HNC prognosis.
Kupffer cells potentiate the risk for liver sinusoidal endothelial cell injury in sepsis through programmed cell death receptor‐1 ligation
Authors: Hutchins Noelle Ariane , Wang Fei , Chung Chun‐Shiang , Ayala Alfred
Published: June 2021

Endothelial cell (EC) dysfunction contributes to multiple organ injury—the cause of fatality seen in critically ill patients. Studies suggest that liver sinusoidal ECs (LSECs) maintain immune tolerance by directly ligating programmed‐death receptor‐1 (PD‐1) on leukocytes by their cell surface expression of PD‐ligand‐1 (PD‐L1). Reports indicate that LSECs express PD‐L1, but its role in the septic liver remains unknown. Thus, we hypothesized that increased PD‐1+leukocyte & PD‐L1+LSEC interactions in sepsis, would lead to greater EC injury. We initially noted that increased EC permeability from septic livers induced by cecal ligation and puncture (CLP) in wild‐type (WT) mice decreased in CLP PD‐L1−/− mice. Isolated LSECs (CD146+CD45− cells) had an increase of PD‐L1 in CLP WT mice. We also found that LSECs from CLP PD‐L1−/− mice exhibit less apoptosis compared to CLP WT mice. Septic LSECs had lower expression of angiogenic marker VEGF‐R2, less proliferation, & a 2x‐fold decrease in number vs. Shams; all of which were rescued in CLP PD‐L1−/− mice. Finally, there was a rise in PD‐1+ Kupffer cells (KCs), which are needed for septic LSEC PD‐L1 expression. These data suggests that increased interactions between PD‐1+ KCs & PD‐L1+ LSECs results in injury during sepsis, yet suppresses tolerance, angiogenesis & proliferation—essential for normal EC function. Supported by: NIH—F31DK083873 (N.H.) & NIH—R01GM053209 (A.A.)
Absence of beta‐catenin in liver attenuates bile duct injury
Authors: Nejak‐Bowen Kari Nichole , Thompson Michael D , Monga Satdarshan P
Published: June 2021

While the pathology of biliary fibrosis is well described, the signaling pathways involved in the proliferation and activity of the cholangiocyte compartment during cholestatic liver injury are incompletely understood. β‐Catenin, the chief downstream effector of the Wnt signaling pathway, has been shown to play an important role during bile duct development but its role in adult bile duct homeostasis remains undetermined. Hepatocyte and cholangiocyte‐specific β‐catenin knockout (KO) when fed a diet containing 0.1% 3,5‐diethoxycarbonyl‐1,4‐dihydrocollidine (DDC) for 1–2 weeks showed decreased atypical ductular reaction as compared to wildtype littermates (WT). KO and WT were next subjected to bile duct ligation (BDL), which led to an increase in bilirubin in both WT and KO mice after 14 days. However, levels of aspartate aminotransferase (AST), alanine aminotransferase (ALT), alkaline phosphatase, and gamma glutamyl transpeptidase (GGTP) were significantly lower in KO when compared to WT. This was associated with a dramatic decrease in ductular reaction and fibrosis in β‐catenin KO livers. Further analysis yielded a notable decrease in total hepatic bile acids (BA) in the KO, which was associated with an increased FXR/SHP2 activation. This led to reduced BA synthesis and increased excretion. Thus, loss of β‐ catenin limits cholestatic injury in multiple models by modulating BA biosynthesis. These findings support an important role of Wnt/β‐catenin signaling in bile duct homeostasis and repair. This study was funded by NIH grant 1R01DK62277 to SPM.
“Getting a piece of the clinical research pie” – Why translational research should matter to you
Authors: Wisco Jonathan J. , Stark M. Elena , Lambert H. Wayne
Published: June 2021

The National Institutes of Health (NIH) estimates that it takes an average of 17 years for only 14 percent of scientific discoveries to become standard treatment in the community. In developing the Roadmap for Medical Research (2004), the NIH identified three themes of challenges to biomedical researchers: 1) New Pathways to Discovery, 2) Research Teams of the Future, 3) Re‐engineering the Clinical Research Enterprise. As a foundational science, anatomy is well positioned as a discipline to address all three themes of challenges. We discuss success strategies for establishing interdisciplinary collaborations with clinicians that specifically address areas of research directly related to the “new” anatomical sciences, including biological pathways and networks, structural biology, molecular libraries, nanotechnology, bioinformatics and computational biology, and biomedical imaging. We also highlight funding mechanism pathways and public‐private partnerships available to researchers to foster high‐risk/ high‐reward research, enable the development of transformative tools and methodologies, fill fundamental knowledge gaps, and change academic culture to foster collaboration.
Defending the Genome: Regulatory RNA in Humans and Bacteria
Authors: Doudna Jennifer
Published: June 2021

In eukaryotic cells, small RNA molecules regulate the expression of many genes. The enzyme Dicer plays a central role in producing these RNAs and ensuring that they assemble with other proteins into effector complexes. Recent findings show that Dicer and its partner RNA binding proteins can alter miRNA processing to change the set of mRNAs targeted for silencing. Although Dicer homologs do not occur in prokaryotic cells, bacteria possess distinct sets of enzymes that produce short RNA molecules to block the propagation of viral and plasmid sequences. In bacteria, these regulatory RNAs are produced from clustered regularly interspaced short palindromic repeats (CRISPRs). I will discuss our recent work to uncover the molecular basis for small RNA production and targeting. Molecular structures of the CRISPR machinery for targeting nucleic acids will be presented, revealing how the RNA is used to identify foreign sequences for destruction. Based on these structures and related biochemical studies, we find interesting similarities in target recognition mechanisms between RNAi‐type and CRISPR‐type systems.
ERK1/2‐RSK Regulation of Cell Fate in Human Mammary Ductal Development
Authors: Lannigan Deborah , Brenin David , Macara Ian , Pasic Lejla
Published: June 2021

Understanding the initiation and progression of breast cancer requires knowledge of the normal development of the mammary ductal network. We have developed a platform based on primary human breast tissue grown in a highly‐defined, 3D mammary explant system, which faithfully recapitulates the normal morphogenesis of human mammary ducts. This system allows for the study of signaling cues that regulate normal development. Strikingly, although different HER1 ligands all permit ductal development, they generate different distinct patterns of cell fate. The intensity of signaling through the ERK1/2‐RSK signaling pathways alters cell fate decisions by progenitor populations within the duct. EGF causes an expansion of basal cells whereas amphiregulin enables normal lineage specification. In EGF conditions inhibition of RSK restores normal ductal development. These findings are relevant to triple negative breast cancer (TNBC) in which increased RSK signaling is observed, and thus RSK may play a role in the inappropriate expansion of the basal population that occurs in some types of TNBC. Identifying the cell‐autonomous and extrinsic cues that regulate ductal development will aid in identifying novel drug targets for breast cancer.
Integration of 3′UTR regulatory signals in the worm germline
Authors: Ryder Sean P , Farley Brian M , Kaymak Ebru
Published: June 2021

Translational regulation of maternal mRNAs drives embryogenesis prior to zygotic transcription. Maternal mRNAs are transcribed during oogenesis and translationally silenced until fertilization. It is not clear how specific mRNAs are selected for translational regulation. C. elegans Notch receptor GLP‐1 serves as a model for studying this process. At least ten RNA‐binding proteins are required to restrict GLP‐1 expression via its 3′UTR. These proteins bind RNA with limited specificity, recognizing short partially degenerate sequence motifs. We have detected a cluster of eight highly conserved motifs within a 100 nucleotide element required for spatial patterning of GLP‐1 expresison. We are dissecting the contribution of each protein and each motif to binding and repression. Our results suggest that competition for binding to key regulatory sequences, driven by the context of overlapping binding motifs, is critical for appropriate expression patterning in the embryo. We have identified similar clusters in ~60 additional maternal transcripts, suggesting antagonism between multiple factors may be a general mechanism to coordinate regulation of mRNAs encoding critical cell fate determinants in the embryo.
Effects of high‐dose cholecalciferol on serum markers of inflammation and immunity in patients with early chronic kidney disease
Authors: Alvarez Jessica A , Zughaier Susu M , Law Jennie , Hao Li , Wasse Haimanot , Ziegler Thomas R , Tangpricha Vin
Published: June 2021

Objective

Few have investigated the anti‐inflammatory and immune‐regulating effects of vitamin D in patients with early chronic kidney disease (CKD). We aimed to determine if high‐dose cholecalciferol supplementation for 1 yr in subjects with early CKD reduced serum monocyte chemoattractant protein‐1 (MCP‐1) and other markers of inflammation and immunity.

Methods

In a double‐blind, randomized, placebo‐controlled trial, 46 subjects with stage 2–3 CKD were given oral cholecalciferol (50 000 IU weekly for 12 wks then 50 000 IU every other wk) or placebo for 1 yr. Serum MCP‐1, tumor necrosis factor‐α, interleukin‐6, and cathelicidin were measured. An in vitro experiment was performed to investigate the effect of 1,25‐dihydroxyvitamin D3 (1,25(OH)2D3) treatment on MCP‐1 secretion in THP‐1 monocytes activated with lipopolysaccharide and Pseudomonas aeruginosa.

Results

By 12 wks, serum MCP‐1 decreased in the cholecalciferol group (Figure). Other markers of inflammation and immunity did not change. Percent change in 25‐hydroxyvitamin D by 12 wks was associated with % change in MCP‐1 (r = −0.43, P = 0.005). In vitro, activated monocytes treated with1,25(OH)2D3 had less MCP‐1 secretion compared to control cells (P < 0.05).

Conclusions

These clinical and in vitro studies support a role for vitamin D in the regulation of immune‐mediated processes in patients with early CKD, specifically in the reduction of MCP‐1.

Grant Funding Source: NIH, Atlanta Research and Education Foundation
Ethnogenetic layering to link and predict African American breast cancer patient outcomes with specific African origins
Authors: Jackson Fatimah L.C.
Published: June 2021

Cancer is a dramatic case of multilevel selection that is highly influenced by an individual's genetic and epigenetic background. The high frequency of aggressive, early onset and highly fatal breast cancer among African American women suggests that there may be a contributing ancestral component. Using ethnogenetic layering (EL) we have integrated social/cultural/abiotic/biotic environmental data with that of genetic/epigenetic and clinical data to identify subgroups of African Americans at risk for particular kinds of breast cancer. We have also used this technique to identify the relevant West and West Central African microethnic groups that may be the sources of relevant polymorphisms contributing to breast cancer etiologies in specific US regions.
Use of GWAS to predict targets associated with cancer in African Americans
Authors: Kittles Rick
Published: June 2021

Understanding genetic and environment interactions that may influence cancer is the cornerstone of a personalized medicine approach built on diagnostics, risk assessment/risk modification, pharmacogenetics and biology. Although genetic and personalized medicine can influence clinical decision making, currently most genetic information is based on populations of European ancestry. Additional human genome research must include diverse populations in order to assess the impact DNA sequence variation and environmental influences have on human disease risk. Within this talk, I present a brief overview of human genome variation and discuss how we leverage genetic variation for mapping genes for disease. Examples of genome‐wide associations and admixture mapping studies are explored and linked to several cancer disparities and health outcomes among communities of color. We must be poised to take take advantage of genetic studies in diverse populations in order to move closer to a more inclusive personalized medicine goal.
Teaching and testing didactic material in integrated histology courses using virtual imaging
Authors: Heidger Paul M. , Swailes Nathan T.
Published: June 2021

We have employed virtual slides (VS) as the principal mode of our histology laboratory teaching and testing programs for over a decade. Most recently, we have integrated virtual images from the Iowa Virtual Slide Box of Histology (VSB) within our lecture presentations and examinations, as well. Medical and Dental Histology are delivered within integrated Histology‐Physiology and Histology‐Anatomy courses, respectively. Lecturers frequently incorporate VS within their lectures as dynamic correlates of structure and function. Students then engage directly in flexible, online laboratory study using the VSB. The use of VS in all aspects of a student's studies is ultimately reflected in computer‐delivered examinations. In both courses, lecture examinations consist of securely banked multiple choice questions designed to test mastery of integrated structure‐function concepts, many of which are linked to digitized images from the VSB. Continuous exposure to and use of the VSB, culminating in the use of digital images in examinations, promotes student engagement with Histology and encourages effective integration with other subjects. This also allows lecturers to generate more creative interdisciplinary questions that better serve integrated learning. Acceptance of such image‐linked testing by students has been high, and correlative learning of laboratory and lecture material encouraged.
Science communication activities within the taught curriculum: “Science and Society” final year research projects
Authors: Lewis David Ian
Published: June 2021

Many Life Sciences Departments are finding it difficult to provide wet, laboratory‐based final year projects for all their students. In addition, less than 20% of their graduates go into careers in scientific research. Our aim was to develop non laboratory‐based, alternative projects where students create and deliver science activities for local school children, evaluating and reporting on this exercise as their final year research project.

Students design a teaching session, suitable for either elementary or high school students. They are free to choose the format of their sessions but it has to be interactive, support and enhance the National Curriculum. Topics selected included: “Spinal cord injuries”, “Creating super humans, the ethics of performance enhancement” and “Don't Bug me!”. Pupil and teacher feedback forms the results section of their dissertations which were written up in the same format as standard laboratory‐based research projects.

These projects are an excellent means of engaging young people with science, a valuable tool in developing partnerships with local schools, promoting departments or faculties and encouraging school pupils to consider careers in science. For students delivering these sessions, they encourage them to be enterprising, innovative, enable the development of key employability skills and the opportunity to gain valuable experience.
Dissecting the genetic influence of the orofacial complex
Authors: Sherwood Richard James , Duren Dana L , Subedi Janardan , Williams‐Blangero Sarah
Published: June 2021

Disorders of the orofacial complex are among the most common congenital defects. Studies of these disorders have been confounded by a high level of genetic heterogeneity with single gene defects producing a variety of dysmorphisms or, conversely, by a variety of gene defects independently producing a similar phenotype. The identification of normal phenotypic variation, and their genetic basis, is critical to understanding the epidemiology of craniofacial anomalies.

To identify the genetic architecture influencing normal orofacial variation, we examined 15 quantitative traits describing the form of the upper and lower arcades taken from whole mouth dental casts of 447 healthy participants in the Jiri Dental Study from eastern Nepal. A variance components‐based linkage analysis method (SOLAR) was used to obtain estimates of heritability and multipoint LOD scores. All traits are significantly heritable with between 18% and 55% of the variation attributable to genetic factors. A measure of palate length (urmh) has an unambiguous significant linkage to chromosome 17 with a LOD score of 3.11. Interesting signals above 2 were found for seven other traits. Supported by DE018497, NIDCR.
Loss of Galectin‐9 from head and neck squamous cell carcinoma is a potent indicator of malignant transformation.
Authors: Steffl Martin , Fik Zdenek , Valach Jaroslav , Smetana Karel , Chovanec Martin , Kodet Ondrej , Gabius Hans Joachim , Plzak Jan
Published: June 2021

Galectins are potent effectors of many cell actions. However there are galectines, which are fully studied, in particular Gal‐1, Gal‐3 and Gal‐7 were acknowledged in connection to squamous cell cancer In the context of these observation we focused on the tandem‐repeat‐type galectin‐9, specifically its presence in normal squamous epithelium of the head and neck, cancer resecates and their marginal zones., Normally galectin‐9 was present in cells of the basal layer of the epithelium. If observing Galectin‐9‐negative tissues, aberrant expression of keratins 14 and 19 was found. Furthermore some of the marginal zones of tumors showed mosaic‐like expression of Galectin‐9 and aberrant expression of keratins as well. All studied specimens of squamous cell carcinoma were negative for galectin‐9. We have found no significant reactivity of tissues for biotinylated Galectin‐9 or its N‐terminal domain, however treatement with Neuraminidase generated reactivity to the N‐domain.

Summary we can say, that Galectin‐9 seems to be a marker of normal epithelium and its absence in squamous carcinomas could carry an information about radicality of cancer resection during surgery.

Grant Funding Source: N/A
Involvement of Disabled‐2 in early myogenesis
Authors: Chan Wood Yee , Shang Na , Mok Samuel C. , Zhao Hui
Published: June 2021

Dab2, one of the two mammalian homologues of the Drosophila Disabled gene product, is a tumor suppressor in ovarian cancerous cells and an adaptor protein involved in various signaling pathways, endocytosis, cell adhesion, apoptosis and differentiation. In this study, we showed that Dab2 was also involved in early myogenesis using Xenopus laevis embryos and mammalian C2C12 myoblasts as in vivo and in vitro models of myogenesis, respectively. We first cloned the XDab2 long and short isoforms and mapped their phylogenetic relationships with other vertebrate Dab2. In Xenopus embryos, XDab2 was expressed in somites and co‐localized with muscle marker genes XMyoD, XPax3, XMef2c and XMyoS. Morpholino‐mediated knockdown of XDab2 expression reduced expression of these muscle marker genes. In C2C12 myoblasts, Dab2 expression was induced during myotube formation, and up‐regulation of Dab2 expression by transfection with Dab2 expression plasmids resulted in enhanced myotube formation while knockdown of Dab2 expression by miRNAs reduced myotube formation. Lentivirus‐mediated Dab2 knockdown with shRNAs also reduced myotube formation, and re‐expression of Dab2 in Dab2‐deficient C2C12 myoblasts by transfection partially restored myotube formation. In conclusion, Dab2 was involved in early myogenesis as a positive regulator.

This work was supported by the one‐line budget of School of Biomedical Sciences CUHK.
Two distinct stem cells in the human small and large intestine
Authors: Chandler Julie M , Lagasse Eric
Published: June 2021

The epithelial layer of the small and large intestine is generated via self‐renewal and differentiation of tissue‐specific stem cells. Failure of intestinal stem cells (ISCs) to respond properly to proliferation and differentiation signals can lead to the formation of cancer, almost exclusively found in the large intestine. Due to the differences found between the small and large intestine, we hypothesize that there are distinct resident stem cells in the small versus large intestine leading to the increased frequency of human colon cancer.

Primary human fetal small and large intestinal cells were isolated and expanded in vitro in a unique culture system that enriches for cells having stem cell markers, as shown by flow cytometry. A three‐dimensional in vitro differentiation assay allows for the formation of organoids with architecture and cellular hierarchy similar to that found in vivo. Immunostaining and real‐time PCR indicate that both small and large intestinal stem cells maintain multipotentiality, while responding quite differently to the same exogenous proliferation and differentiation cues.

Normal large ISCs may be more susceptible to transformation, leading to colon cancer in humans. Identifying differences between normal small and large ISCs may reveal differential pathway regulation leading to the disparity in cancer frequency.
Histological validation of Alzheimer's disease and cerebrovascular disease imaging biomarkers
Authors: Barzee Brigham , Hansen Megan , Salin Ashley , Stone Megan , Bridgewater James , Kavafyan Talar , Steed Kevin , Stark Elena , Dong Hongwei , Toga Arthur W. , Vinters Harry V. , Wisco Jonathan J.
Published: June 2021

The purpose of this study is to analyze spatial co‐localizations between amyloid beta (Aβ), tau, and iron in postmortem brains of Alzheimer's disease (AD) and cerebrovascular disease (CVD) patients. Iron is readily visible in T2* magnetic resonance images (MRI), and has been shown to be spatially correlated with Aβ plaques in AD. Neurofibrillary tangles of tau protein are also associated with AD, and Aβ plaques are also found in the walls of the vessels in CVD. If iron co‐localizes with Aβ, then the location of the iron—parenchyma vs. sulci—as seen in MRI could reveal if the disease is possibly AD or CVD, respectively. Hence, MRI could be used in the future as a tool for earlier diagnosis of either disease. We have imaged stains of iron, Aβ, and tau in hippocampus sections of 8 different brains, and we are using Adobe Photoshop and OlyVia (image analysis software) to create digital images of iron's co‐localization with Aβ and tau. While CVD samples have yet to show a clear correlation, preliminary results indicate that iron does indeed co‐localize with both Aβ and tau aggregations in AD samples.

Grant Funding Source: NIH/NIA 1 R21 AG037843‐02, NIH/NCRR P41 RR013642‐12S1, Translational Research Fund (UCLA), and the McGinty Family Foundation
Evidence of functional interactions between the α‐subunit of Pol III and Pol IV (DinB) in Escherichia coli
Authors: Benson Ryan William , Rands Thomas J , Godoy Veronica G
Published: June 2021

Polymerase switching and protein‐protein interactions between DNA polymerases are still poorly understood processes. Pol IV (DinB) in E. coli has been shown to play a role separate from their translesion synthesis (TLS) or polymerase activities. DinB can affect replication checkpoints, although this has only been observed during DinB overexpression. By using different dnaE alleles that encode variants of the Pol IIIα‐subunit of the replicative polymerase, we have been able to study the in vivo interaction between this protein and DinB variants. Synthetic sickness or lethality is observed with combinations of different alleles of dnaE and dinB. Phenotypic variation and the subsequent reversion to wild type allow identification of various mutations in dinB that suppress growth defects. Our investigation allows greater understanding of the mechanisms regulating the TLS activity and alternative roles that these specialized DNA polymerases play in cells experiencing DNA damage or environmental stress, such as replication checkpoints.
Barley yellow dwarf virus (BYDV) utilizes a novel strategy for translation initiation.
Authors: Sharma Sohani Das , Goss Dixie J
Published: June 2021

Most commonly, gene expression in uncapped RNA viruses is regulated by either an internal ribosomal entry site (IRES) or cap independent translation element (CITE), which are located mostly in the 5′ untranslated region (UTR) of viral mRNA. BYDV, which lacks both a cap and poly(A) tail, has a CITE (called BTE) present in its 3′UTR that is essential for efficient translation initiation at the 5′ proximal AUG. The mechanism of BYDV translation initiation is not understood.

Using fluorescence anisotropy and gel mobility shift assays we demonstrated that the 40S ribosome has moderate binding affinity to the 3′ UTR (Kd~600nM) and has extremely low affinity for any other parts of mRNA. The binding affinity to 3′UTR increases nearly six fold (Kd~100nM) in the presence of the eIF4F‐4B‐4A‐ATP helicase complex. In order to identify the structural elements that interact with initiation factors or ribosomes, the secondary structure of both 3′ and 5′ UTR was probed using SHAPE technique. These results identified a very stable secondary structure for both 5′and 3′ UTRs. Primer extension inhibition (toe‐printing) was used to identify the initial 43S ribosome binding site. These results suggest a novel mechanism for 43S ribosome binding to the 3′BTE followed by subsequent transfer to the 5′end.
Analysis of the Replication Proteins and Satellites of the Turnip Crinkle Virus
Authors: Zinskie Jessica Anne , Myers Kenneth , Assiri Mohammed , Baumstark Tilman , Bruist Michael
Published: June 2021

The Turnip Crinkle Virus (TCV) is a single‐stranded, positivesense RNA plant virus that serves as a model organism for related human and animal RNA viruses, such as the West Nile, SARS‐CoV and Hepatitis C viruses. All positive‐sense RNA viruses replicate through asymmetrical replication; understanding the detailed biochemistry of this process should lead to potential drug targets for intervening in RNA viral infections.

TCV provides an attractive model because satellite RNAs can accompany TCV infection. These satellite RNAs are minimal replicons that contain all cis‐acting RNA sequences required for replication. The goal of this research is to develop a model of replication of TCV satellites in the non‐host Saccharomyces cerevisiae, baker's yeast. Yeast provides numerous biochemical and genetic techniques not available in turnips.

The key RNA replication proteins are p28 and p88. Their genes have been cloned into yeast shuttle vectors for expression in yeast and E. coli. The membrane binding protein, p28, has been visualized at its target membrane in yeast using fluorescence microscopy. Two natural satellites and a chimera of these two have also been cloned. The satellite constructs are bounded by self‐cleaving ribozymes that should generate active ends in vivo and in vitro for the replication system. An in vitro system for RNA recognition and eventually full replication will be established.
Biofilm Derived Legionella pneumophila Evades the Innate Immune Response in Macrophages
Authors: Khweek Arwa Abu , Amer Amal
Published: June 2021

Legionella pneumophila, a causative agent of Legionnaire's disease, replicates in human alveolar macrophages and establish infection in humans. There is no human to human transmission and the main source of infection is L. pneumophila biofilms established in air conditioners and water fountains. Biofilm structure provides protection for the organism from disinfectants and antibacterial agents. L. pneumophila infection in humans is characterized by subtle initial immune response giving time for the organism to establish infection before the patient succumbs to pneumonia. Planktonic L. pneumophila elicits a strong immune response in murine but not in human macrophages. The objective of this study is to elucidate the interface between biofilm‐derived L. pneumophila and macrophages. Using confocal laser scanning microscopy (CLSM) and Western blotting, we demonstrate that in contrast to planktonic bacteria, biofilm‐derived L. pneumophila differentially manipulate the innate immune response and the killing mechanisms employed by murine macrophages, thus establishing successful infection. This study advances our understanding to the innate immune response to biofilm‐derived L. pneumophila and closely reproduces the natural mode of infection in human. Studies is Dr. Amal Amer's laboratory are supported by grant R01HL094586
Exploring the substrate profile of CFTR Inhibitory Factor
Authors: Hvorecny Kelli L , Bahl Christopher D , Morisseau Christophe H , Bomberger Jennifer M , Stanton Bruce A , Hammock Bruce D , Madden Dean R
Published: June 2021

Chronic obstructive pulmonary disease (COPD), the third leading cause of death in the US, results in poor mucociliary clearance and increased lung colonization by opportunistic pathogens, such as Pseudomonas aeruginosa (PA). Previous work has shown that the ion channel CFTR, which regulates the fluid balance at the air‐liquid interface of the lungs, is downregulated in the presence of PA, through the secretion of an epoxide hydrolase virulence factor, CFTR Inhibitory Factor (Cif). Further, the Cif protein alone elicits a decrease in apical CFTR. Studies on other epoxide hydrolases, like the human soluble epoxide hydrolase, demonstrate that these enzymes act as regulators of signaling pathways. Cif's hydrolysis activity, therefore, may function in Cif's ability to alter CFTR regulation. In order to develop a better understanding of Cif's method of action in vivo, we have delineated a hydrolysis profile for xenobiotic substrates of Cif. Our enzymatic assays indicate that Cif has clear substrate preferences in terms of enantiomeric and substituent specificity and processivity. Using X‐ray crystallography, we are also able to describe how Cif accommodates various substrates. We hypothesize that these preferences contribute to Cif's ability to disrupt normal CFTR regulation.

Funding from the NIH and the CFF.
Screening for obesity genotypes from a set of established T2D associated SNPs in a Saudi population
Authors: Al‐Daghri Nasser , Albagha Omar , Alkharfy Khalid , Alokail Majed , Al‐Attas Omar , Krishnaswamy Soundararajan
Published: June 2021

Objective

To explore for any positive association between 36 type 2 diabetes (T2D) associated single nucleotide polymorphisms (SNP) and BMI in a population of Saudi subjects.

Methods

Study consisted of 72 obese and 78 control Saudi subjects. DNA samples from obese and controls subjects were genotyped for 36 T2D linked SNPs using the KASPar method. The mean BMIs corresponding to each of the individual genotypes were compared.

Results

Four of the 36 T2D related SNPs, rs10923931, rs6795735, rs11642841 and rs4430796, located in or near NOTCH2, ADAMTS9, FTO and HNF1B genes, respectively, were found to be associated with BMI even after adjusting the data for age. The allelic variants rs6795735‐C and rs4430796‐A showed significant association with BMI in both males and females even after adjusting the data for age. However, rs10923931‐T allele was associated to age adjusted BMI data only in females. Some of the 36 SNP variants were found to be significantly associated with obesity related disease markers like systolic and diastolic blood pressure, cholesterol, triglyceride and fasting blood glucose levels but not with BMI.

Conclusion

We identified positive association between allelic variants of 4 of the 36 T2D related SNPs and BMI in a Saudi population and the significance of which persisted even after adjusting the data for sex and age.
Phosphorescent nanoparticle based probes for imaging and measurement of cellular oxygen
Authors: Kondrashina Alina , Dmitriev Ruslan , Borisov Sergey , Klimant Ingo , Zhdanov Alexander , Papkovsky Dmitri
Published: June 2021

Cell and tissue oxygenation in vivo is maintained within narrow physiological range and its significant deviations from the norm can lead to pathological states. Real‐time monitoring of this parameter and oxygen consumption rate (OCR) in respiring samples provides valuable tool for cell metabolic assessment. We describe two new phosphorescent probes for the analysis of intracellular and extracellular O2 (icO2, ecO2) compatible with multiple detection platforms (ratiometric‐intensity and phosphorescence lifetime based) which are based on the combination of an oxygen‐sensitive PtTFPP dye and PFO antennae dye embedded in cationic or anionic polymer nanoparticles. The icO2 probe MM2 delivered in mammalian cells by passive means was applied in high‐resolution imaging experiments and monitoring of oxygenation within monolayer of adherent fibroblast cells and 3D neuronal spheroids by μs‐FLIM (PLIM), confocal microscopy and microplate reader analysis. The ecO2 probe MM2X was evaluated in OCR measurements in 96‐well microplates and perfusion microchambers. These probes can be used in drug toxicity, cell energy budget and cell physiology studies where high‐resolution 3D O2 imaging and high‐throughput analysis are required. Supported by the Research Executive Agency (REA) of the EU PITN‐GA‐2010–264772 (ITN CHEBANA) and SFI 07/IN.1/B1804 grant.
Identification of novel invertebrate TKR gene sequence in intertidal ribbon worms
Authors: Lee Thomas Chelsie , Stevens Rainee , Okazaki Robert , Chung Brian
Published: June 2021

The invertebrate ribbon worm, Paranemertes peregrina, serves as a unique model in that it thrives in an environment exposed to drastic fluctuations in salinity during tidal interchange. Its ability to sustain homeostatic integrity is not well understood. With an aim to clarify this phenomenon, total RNA was isolated, and reverse transcription with polymerase chain reaction allowed us to serendipitously clone and elucidate a 488 base pair region of a gene coding for a Tachykinin Receptor (TKR), a subtype of G‐protein coupled receptor (GPCR). This region shows 79% homology to the mouse TKR‐2 mRNA sequence, and 44% homology to human Neuromedin‐K receptor's amino acid sequence. Specifically, we have isolated a portion containing a cytosolic carboxy‐terminus that has classically been associated with palmitoylation or otherwise hydrophibicity‐enhancing interactions. This process facilitates the docking of cytosolic subunits to the membrane in the assembly of GPCRs, acting as a regulatory component. In vertebrate models, much of these proteins are conserved. Given that only a few of these genes have been reported for invertebrates, this suggests a critical need for investigation of the evolution of TKRs as they relate to stress response. Additionally, this receptor poses questions about its potential role in pain, with the prospect of revealing insight about the long‐elusive pain perception in invertebrates.
Electrode implantation trauma (EIT) initiates fibrosis by over‐expression of TGF‐β1 and activation of the Wnt/β‐catenin pathway in an in vitro model of cochlear implantation
Authors: Infante Esperanza Bas , Gupta Chhavi , Goldstein Bradley , Van De Water Thomas R.
Published: June 2021

Background

The insertion of a cochlear implant (CI) electrode array can be associated with an inflammatory response that induces loss of auditory hair cells and growth of fibrotic tissue around the electrode array. From previous work we know that trauma to the cochlea induces expression of TGF‐β. We hypothesize that TGF‐β1 co‐operates with the Wnt/β‐catenin pathway to elicit fibrosis. TGF‐β is known to activate the PI3K pathway, which can stabilize β‐catenin.

Methods

Cochleae from 3 days rat pups were divided into: 1) Control untreated; 2) TGF‐β1; 3) TGF‐β3; 4) LY294002 (LY); 5) EIT; 6) EIT+ TGF‐β1; 7) EIT+ TGF‐β3; 8) EIT+ LY. mRNA levels of Axin2; Wnt4, Wnt5b and CTGF were measured. Confocal studies for α‐SMA), presence of stress fibers, and expression of SOX2 were carried out in organ of Corti (oC) explants and lateral wall tissues (LW) after 96h of incubation.

Results

EIT upregulated CTGF expression in oC and LW tissues. Axin2 mRNA levels were increased in oC explants treated with TGF‐β1 or 3. EIT downregulated Wnt5b expression in oC explants. Increase of SOX2 levels ocurred near the wound area and in LY treated explants. EIT induced expression of α‐SMA and actin stress fibers in oC explants. TGF‐β1 induced expression of α‐SMA. LY treatment reduced α‐SMA levels and the presence of stress fibers, however many apoptotic bodies were present in these explants.

Conclusion

Induction of EIT in the cochlea triggers a fibrogenic response as part of the wound healing process, in which TGF‐βs assume a key role. oC and LW cells respond differently to a mechanical trauma induced by an electrode. Our results suggest increased activation of the Wnt/β‐catenin pathway by EIT in oC explants, exacerbated by TGF‐β1 treatment, which leads to cell growth and differentiation. Wnt pathways do not appear to participate in the fibrotic response initiated in the LW tissues.
Effect of Pathway‐Interconnectors in SEB‐Induced Apoptosis Related Events in Human PBMCs
Authors: Banwarth Emily Anne , McAllister Erin , Rothschadl Kendra , Wampfler Ashlynne , Mendis Chanaka , Jett Marti
Published: June 2021

Staphylococcus enterotoxin B (SEB) is produced by the bacterium Staphylococcus aureus. SEB is the most common cause of food poisoning often accompanied with nausea, diarrhea, and intestinal cramping. The purpose of this study is to further investigate human peripheral blood mononuclear cells (PBMCs) in order to better understand the apoptosis related events induced by SEB. C‐Jun N‐Terminal Kinase (JNK) has been previously identified to be induced by SEB, and has demonstrated that it inter‐connects multiple signaling cascades. As a crucial pathway inter‐connector in SEB‐induced human PBMCs, we believe that JNK may possess inhibitory effects of SEB‐induced apoptosis. We will further evaluate the utilization of the intrinsic (caspase 3, MCLR1, BAX, etc.), extrinsic (caspase 8, caspase 10) pathways, and gene expression profile using RT and PCR. Protein expression patterns of some genes will be examined through ELISA. We believe that our work will allow us to better understand the complex interactions of multiple signal transduction pathways induced by SEB.
“An inexplicable disease”‐ Prion disease as a ‘choose‐your‐own‐ experiment’ case to introduce students to scientific inquiry
Authors: Hines Justin K. , Serrano Antonio , Miller Sarah
Published: June 2021

The study objective was to develop and test a case study which simulates scientific inquiry within the limits of a single course period and which can be used in large lecture‐format courses. Students unknowingly take the roles of the initial investigators of the Kuru epidemic of Papua New Guinea in 1957 and work in groups to iteratively conduct simulated investigations, evaluate the results, and form hypotheses regarding the nature of the disease. The activity culminates in a mock‐scientific conference, in which student groups collaborate by sharing findings, mirroring real events which led to the discovery of prion diseases. Learning goals focus on student opinions, attitudes and skills related to the nature of science, causes of disease epidemics, and prions as atypical infectious agents. The activity has been implemented successfully at five schools in seven courses which span five fields: biology, microbiology, genetics, zoology, and biochemistry. We present aggregated data from five courses measuring cognitive and affective learning gains. In addition to positive content learning gains and overwhelmingly positive affective responses from students, we were successful in using a modified CLASS‐BIO survey to measure objective changes in attitudes toward biology as a result of the activity alone. We hope that both the activity and approach can be used broadly by life sciences educators.
Vitamin D deficiency in tropical country, not related to adipocyte status
Authors: Sari Dina Keumala , Al Rasyid Harun
Published: June 2021

Background

Low circulating 25‐hydroxyvitamin D [25(OH)D] serum may increase risk of morbidity and mortality, especially in obese women and vitamin D deficiency are considered new markers for obesity and diabetes mellitus.

Objective

We investigated whether deficiency vitamin D occur in normoweight and overweight‐obese women who lived in abundant sunlight exposures area such Indonesia

Design

This was a cross‐sectional study, we include healthy normoweight women subjects (n=41) and overweight‐obese women with no other disease subjects (n=41), we investigated by ethnicity, age, sunlight exposure, way of dressed, using sunscreen, whitening, and nutrient intake. We included other parameters such systolic and diastolic pressure, Body Mass Index (BMI), waist circumference, fat distribution, 25‐hydroxyvitamin D, and calcium serum.

Results

There are no different between two group in ethnicity, sunlight exposure, sunscreen and whitening using, and nutrient intake, but there are significant different in systolic (p=0.0012) and diastolic pressure (p=0.019), BMI (p=0.000), waist circumference (p=0.000), and fat distribution (p=0.000) between two group. Interestingly, there are no significant different in 25‐ hydroxyvitamin D (p=0.140) and calcium serum (p=0.464) between two group.

Conclusions

The results indicate that vitamin D deficiency can be found in tropical countries and there is no different between non‐obese and obese women, and it is important to decide the requirement for different population. Many factors can influenced the deficiency such vitamin D intake and lifestyle to not avoid sunlight exposure to much. This should be attention in preventing diabetes mellitus.
Dietary patterns associated with hypertension among the low income urban population in Pakistan
Authors: Safdar Nilofer Fatimi , Bertone‐Johnson Elizabeth , Cordeiro Lorraine , Jafar Tazeen , Cohen Nancy
Published: June 2021

Hypertension affects 33% of the adult population in Pakistan. Various studies have shown the critical role of specific dietary patterns in the prevention and management of hypertension. However, the dietary determinants of hypertension in Pakistan remain unknown. In this study we aimed to identify dietary patterns from baseline food frequency data and assess their associations with hypertension in 5491 subjects from the Control of Hypertension and Risk Attenuation (COBRA) study, 2004. Factor analysis was used to identify the “fat and sweet”, “fruit and vegetable” and “seafood and yogurt” patterns with 20% variance in food intake. Associations between dietary patterns and subject characteristics were assessed using ANOVA and chi square tests. Odds of hypertension were higher in women and increased with age and BMI in both genders (<0.001). When adjusted for covariates, the seafood and yogurt (OR= 0.72: 95% CI: 0.61,0.84; p‐value <0.001) and fruit and vegetable (OR =0.89: 95% CI: 0.80,0.99; p‐value= 0.039) patterns were inversely related with hypertension, whereas no significant association was seen for the fat and sweet pattern. Our findings suggests that specific dietary patterns may have a role in regulating blood pressure in this population, however, more prospective studies are needed.
Profiles from assessment of amount, source, and cost of egg consumption by low‐income women inform nutrition education intervention planning
Authors: Wei Cheng‐Hsin , Lohse Barbara
Published: June 2021

Egg intake of females (n=155; 85% 18 – 50 y; 55% white; 59% SNAP) in federally funded nutrition education was examined for amount, source and cost based on findings from 3‐day telephone diet recalls. Mean egg intake for the 81% reporting any intake was 27.6 ± 25.5 g; range: 0.2–108.6 g. Four egg intake categories were identified: egg alone (25%), egg white alone (4%), visual egg (17%), hidden egg (54%). Ranked prices (n=224) were highest for visual and hidden egg sources; visual egg consumers had most kcal (p=.005), fat (p=.001), and sodium (p=.003). Food security was not associated with price rank or other egg intake factors. Egg intake was positively associated with kcal (p<0.001), protein (p<0.001), fat (P<0.001) even when age (which was inversely associated with kcals and fat) was controlled. Eating competence (EC) was associated (P=.049) with lower consumption of visual egg dishes, which are higher in fat and kcals and cost more. Two‐step cluster analysis revealed 2 clusters differentiated by education level, SNAP participation, food security and EC. The cluster with lower income, education, food security, and eating competence consumed more eggs (P=.05) and more visual egg dishes (P=0.039); but not when kcals were controlled. Results suggest nutrition education intervention focus on transitioning egg intake from visual to whole egg sources and suggest a benefit to including EC concepts. Funded by American Egg Board.

Grant Funding Source: American Egg Board
The role of the temporal environment in shaping Dominican women's food routines in New York City and the Santo Domingo, D.R.
Authors: Weisberg Pamela , Devine Carol
Published: June 2021

In the US, foreign born individuals adopt food behaviors that are associated with higher risk of chronic disease. However, the mechanism of change in food behaviors is not well understood. The purpose of this research was to explore food behaviors in Dominican women living in New York City (NYC) and Santo Domingo (SD) in order to better understand the process of change. Qualitative interviews addressed social, cultural, environmental and personal influences on food behavior in twelve Dominican women. Study findings revealed that women constructed food routines that characterized the way in which they procured, prepared and consumed food. Household temporal environment, which is the perceived time available to procure, prepare and consume food, shaped food routines. In SD, the day was structured around the main meal, allowing for a leisurely food routine. In NYC, temporal environment varied and women developed a range of food routines including, a) maintenance of home cooked family meals, b) reliance on fast food and maintenance of family meals c) abandonment of cooking and family meals. While Latino neighborhoods may provide access to traditional foods, the temporal environment may necessitate dietary change. It is important for health professionals to consider the temporal environment when planning policies and interventions. Supported by Cornell University DNS, LALSP, GS

Grant Funding Source: Cornell University DNS, LALSP, Grad School