bluuebunny/crossref_metadata_2025 huggingface dataset:
Environmental intervention in carryouts increases sales of healthy menu items in low‐income urban setting
Authors: Lee Seung Hee , Kim Hyunju , Yong Rachel , Hamouda Mohamed , Shon Jiwon , Park Joo Hye , Gittelsohn Joel
Published: June 2021

Low‐income urban populations are disproportionately exposed to prepared food sources (PFSs) that provide few or no healthy options. In Baltimore, the most prevalent PFSs are carryouts, yet virtually no work has been conducted to intervene in these settings. We conducted an 8‐month pilot trial in 8 carryouts (4 intervention, 4 control) using a quasi‐experimental study design.

Formative research such as focus groups, customer and owner interviews, and conjoint analyis led to the development of intervention strategies. The multi‐phase intervention included: healthy menu labeling with point‐of‐purchase (POP) promotions, increase of healthy sides, and promotion of affordable healthy combination meals. Receipts were collected weekly and total sales were tracked for all carryouts. Sales of healthy menu items significantly increased across all intervention carryouts, while foods that were not promoted either decreased or stayed the same. Comparison carryouts did not show any significant changes in sales of healthy menu items. Our findings suggest that a combination of environmental and POP changes can be a part of a successful community‐based approach that positively impacts the sales and availability of healthy items in PFSs in low‐income urban areas.

Grant Funding Source: The Diabetes Research and Training Center and the Center for a Livable Future, Johns Hopkins University
Making a head: diverse craniofacial outcomes in disease
Authors: Richtsmeier Joan Therese , Martinez-Abadias Neus , Heuze Yann , Percival Christopher J , Motch Susan , Hill Cheryl A , Ryan Timothy M , Wang Yingli , Aldridge Kristina , Jabs Ethylin W
Published: June 2021

A recent proposal of tight coupling between evolution of fibroblast growth factor (FGF) signaling and evolution of the vertebrate head underscores the importance of FGFs and their receptors (FGFRs) in cranial variation. Mutations in FGFRs cause achondroplasia and some craniosynostosis syndromes, establishing an essential role for FGF signaling in endochondral and intramembranous bone development. But there is more to the vertebrate head than the skull, and many tissues undergo dramatic change during head evolution and morphogenesis although the association of FGF signaling with variation in other cranial tissues is less well understood. Our objective is to estimate pattern and magnitude of variation in the skull and other head tissues produced by several craniosynostosis syndrome‐causing FGFR2 and FGFR3 mutations to produce hypotheses about their role in head evolution. We use 3D micro‐CT imaging and magnetic resonance microscopy to estimate variation in cranial tissues of mouse models for human craniosynostosis syndromes and identify local effects of these mutations on neural, epithelial and osseous cranial tissues. Our results reveal strong parallels between mouse and human phenotypes carrying corresponding FGFR mutations emphasizing the conservation of FGF/FGFR function in development and suggesting mechanisms of head evolution. Supported by NIH/NIDCR grants 5 R01 DE018500, ‐02S1, ‐02S2.
In‐silico organogenesis: measuring and modelling vertebrate limb development
Authors: Sharpe James
Published: June 2021

Organogenesis is a dynamical multi‐scale process in which large‐scale features (such as the geometric conformation of the tissue) directly feeds back onto the regulation of molecular‐scale events such as gene regulation. Our attempts to capture this process must therefore focus as much on morphometry as molecular biology. Here I will describe our work to transform a classical model of developmental biology – the developing vertebrate limb bud – into a quantitative model system for systems biology and multiscale modeling. In particular, we have developed: (a) 3D and 4D quantitative data‐capture tools[1], and (b) new multiscale simulation software. This integrated approach is allowing us to combine two of the primary questions of organogenesis: mechanical morphogenesis (the active cellular movements which lead to shaping of the tissue [2,3]), and molecular patterning (the spatial regulatory networks which control gene expression ‐ [3] and unpublished work).
The Phenogenomics of Craniofacial Shape
Authors: Hallgrimsson Benedikt , Jamniczky Heather A. , Martínez-Abadías Neus , Young Nathan M. , Marcucio Ralph S.
Published: June 2021

Developmental biology has only recently begun to focus on the mechanisms that generate variation within species. Addressing this difficult question can inform our understanding of dysmorphology. It is also central to the developmental basis for evolvability. Here we review our work on the developmental determinants of shape and size variation in the vertebrate craniofacial complex. We present analyses of the Collaborative Cross founder strains and crosses, mouse mutants and human cranial and facial morphometric data to show that variation in the mammalian skull tends to be structured along axes of covariation. Such axes relate to variation in key developmental processes such as chondrocranial or brain growth, the outgrowth of the facial prominences, and the allometric effects of overall cranial growth. Identifying such key developmental processes is an important first step towards unraveling the complex developmental‐genetic determinants of phenotypic variation. Proceeding beyond this point requires complementary strategies. One is the development of methods for quantitative integration across levels of the genotype‐phenotype map. Another is the use of predictive simulation of complex developmental processes. We present our progress towards these goals and how these strategies can inform our understanding of the developmental basis for phenotypic variation in the vertebrate craniofacial complex.
Alpha2A and Alpha2C Adrenergic Receptors are involved in the regulation of Bone Growth, Structure and Function
Authors: Gouveia Cecilia H , Martins Gisele M , Teixeira Marilia B , Costa Cristiane C , Brum Patricia C
Published: June 2021

Sympathetic nervous system (SNS) activation causes osteopenia via β2 adrenoceptor (β2AR). We showed that sympathetic hyperactivity due to double knockout (KO) of adrenoceptors (AR) that inhibit norepinephrine release, α2A and α2C AR (α2A/α2CAR−/−), leads to an unexpected phenotype of high bone mass. It suggests that β2AR is not the single AR involved in bone mass regulation and that α2‐AR may also mediate the skeletal SNS actions. To investigate the role α2ARs in bone, the skeleton phenotype of 120 day old female α2AAR and α2CAR single KO mice (α2AAR−/− andα2CAR−/−), which exhibit normal sympathetic tone, was evaluated. α2AAR−/−mice shows decreased femur (9%, p<0,001) and tibia (5%, p<0,01) length and α2CAR−/− shows decreased femur length (4%, p<0,001). This is in agreement with α2AAR and α2CAR protein expression in the epiphyseal growth plates. Surprisingly, a microtomography analysis showed that α2CAR−/−mice present 15% decrease (p<0,01) in the femural trabecular bone volume, while there are no differences between wild‐type and α2AAR−/−mice. Accordingly, the three‐point bending test showed 35% decrease in the tibia maximum load in α2CAR−/−, but not in α2AAR−/−mice. These data suggest that α2AAR and α2CAR are involved in the longitudinal bone growth and that α2CAR may positively affect bone structure and function, while α2AAR may negatively regulate these parameters when sympathetic tone is elevated.
CELLULAR PATTERNS OF BAT (CAROLLIA) FORELIMB SKELETOGENESIS AND THEIR BIOMECHANICAL CONSEQUENCES
Authors: Cooper Lisa Noelle , Jast John , Behringer Richard , Rasweiler John J , Sears Karen E.
Published: June 2021

To achieve powered flight, bats altered the architecture of their long bones by reducing mineral concentrations and altering cross‐sectional geometries. This study quantifies differences in adult bone architecture of the short‐tailed bat (Carollia) relative to terrestrial rodents (Mus, Peromyscus). By integrating nanoindentation tests with whole bone bending tests, and visualization of cross‐sectional areas, this study documents architectural differences in limb bones of aerial and terrestrial mammals. Nanoindentation tests revealed that metacarpals of bats are 40% as stiff and 36% as hard as that of rodents. Whole bone bending tests revealed that the bat and mouse humerus are roughly equivalent in stiffness, however the bat radius was much more compliant, suggesting a decreased mineral content. Micro‐CT scans showed that the humeral, femoral, and tibial cross‐sectional geometries are equivalent in both bats and mice; however, distal bones of the bat displayed 8–40% larger medullary cavities compared rodents. In comparing rates of long bone ossification, bats delays appositional ossification relative to mice, but begins diaphyseal longitudinal growth earlier. At late fetal stages, bats rapidly elongate the diaphysis. These findings further our understanding of the microstructural properties of chiropteran bone biology.
Effect of dietary advanced glycation end products on mouse liver
Authors: Patel Raza A. , Baker Susan S. , Liu Wensheng , Desai Sonal , Alkhouri Razan , Kozielski Rafal , Mastrandrea Lucy , Sarfraz Adil , Cai Weijing , Vlassara Helen , Patel Mulchand S. , Baker Robert D. , Zhu Lixin
Published: June 2021

The exact pathophysiology of non‐alcoholic steatohepatitis (NASH) is not known. Previous studies suggest that dietary advanced glycation end products (AGEs) can cause oxidative stress in liver. We aim to study the effects of dietary AGEs on liver health and their possible role in the pathogenesis of NASH. Two groups of mice were fed the same diet except the AGE content varied. One group was fed a high AGE diet and the second group was fed a regular AGE diet. Liver histology, ALT, AST, fasting glucose, fasting insulin, insulin resistance and glucose tolerance were assessed. Histology revealed that neutrophil infiltration occurred in the livers of the high AGE group at week 26; steatosis was not found with the inflamed livers. At week 39 livers from both groups exhibited steatosis, yet no inflammation was detected. Higher insulin levels were detected in the regular AGE group at week 26 (P=0.034), compared to the high AGE group. At week 39, the regular AGE group showed higher levels of ALT (P<0.01) and AST (P=0.02) than those of the high AGE group. We demonstrate that a high AGE diet can cause liver inflammation in the absence of steatosis. Our results are the first to show that dietary AGE can contribute to the pathogenesis of NASH.
Touring the Protein Energy Landscape: The View Depends on Where and How You Look
Authors: Marqusee Susan
Published: June 2021

Decoding the information in the primary sequence of a protein is one of the most fundamental challenges in modern biology. A protein's sequence encodes more than just the native structure; it encodes the entire energy landscape – an ensemble of conformations whose energetics and dynamics are finely tuned. I will present developments in both our single molecule and ensemble studies probing high‐energy fluctuations on the energy landscape. In particular, we have use a novel method to explore the mechanical stability of single protein molecules in the low force regime of the laser tweezers. The low spring constant of the laser tweezers enables us to directly monitor low force refolding events and fluctuations between different molecular structures at quasi‐equilibrium conditions. Using this approach we have been able to identify and monitor novel events on the conformational energy landscape. Our recent results on the differences in mechanical compliance between the molten globule and native states and force‐dependent changes in the unfolding pathway of proteins have important implications for mechanical processes in the cell. I will also present our development of a thiol‐exchange method that allows partitioning of fluctuations and partially unfolded conformations to either side of the rate limiting step for unfolding.
microRNA regulation in stem cells and cancer
Authors: Gregory Richard I
Published: June 2021

Lin28A and Lin28B, two developmentally regulated RNA‐binding proteins selectively inhibit the maturation of let‐7 family microRNAs (miRNAs) in embryonic stem cells and certain cancer. Lin28 recognizes the terminal loop region of let‐7 precursors and recruits the activity of a 3′ terminal uridylyl transferase (TUTase), Zcchc11 (TUT4) to repress let‐7 biogenesis. Unlike Lin28A, Lin28B represses let‐7 processing through a Zcchc11‐independent mechanism. Lin28B functions in the nucleus by sequestering primary let‐7 transcripts and inhibiting their processing by the Microprocessor. Accordingly, the inhibitory effects of Zcchc11 depletion on the tumorigenic capacity and metastatic potential of human cancer cells and xenografts is restricted to Lin28A‐expressing tumors. Overall our results illuminate the distinct mechanisms by which Lin28A and Lin28B function, and have implications for the development of new strategies for cancer therapy. Our most recent progress in understanding these miRNA regulatory pathways will be presented.
Cellular Mechanisms of Triplet Repeat Maintenance: Helicase Requirements for Replication through DNA Structure Barriers
Authors: Freudenreich Catherine H. , Anand Ranjith P , Nguyen Jennifer
Published: June 2021

Natural replication barriers are ubiquitous in genomes, and failure to bypass these barriers during replication results in various forms of genome instability. We found previously that the Srs2 helicase is important for replication though triplet repeat DNA that can form DNA hairpin structures. At an expanded CAG repeat, Srs2 is needed to allow fork reversal and prevent chromosome fragility, as well as to prevent aberrant recombination that increases CAG instability. At CGG repeats, Srs2 facilitates replication through DNA hairpins that stall replication, thereby preventing chromosome fragility. The Srs2 protein has multiple functions, including unwinding activity, DNA translocation, and Rad51 displacement, and may also work in conjunction or competition with other helicases during replication. Data will be presented on the role of Srs2 and other related helicases during replication of DNA structure barriers, and the consequences for repeat instability and chromosome fragility.
Biogenesis of mycobacterial cell envelope glycoconjugates
Authors: Jackson Mary , Dhouib Rabeb , Skovierova Henrieta , Larrouy-Maumus Gerald , Angala Shiva K , Wheat William H , Pham Ha , Gilleron Martine , Brennan Patrick J , Puzo Germain , Nigou Jerome
Published: June 2021

The arabinogalactan (AG) of slow‐growing pathogenic Mycobacterium spp. is characterized by the presence of galactosamine (GalN) modifying some of the interior branched arabinosyl residues. We investigated the biosynthetic origin of this substituent and its role(s) in the physiology and pathogenicity of mycobacteria.

We report on the discovery of the polyprenyl‐phospho‐N‐acetyl‐galactosaminyl synthase (PpgS) and the glycosyltransferase (GT) Rv3779 from Mycobacterium tuberculosis (M. tb) required, respectively, for providing and transferring the GalN substrate for the modification of AG. Disruption of either ppgS (Rv3631) or Rv3779 totally abolished the synthesis of the GalN substituent of AG in M. tb H37Rv. The identification of Rv3779 ‐ which we previously had characterized as a polyprenyl‐phospho‐mannose synthase ‐ as the GalN(Ac)transferase of the system indicates that this GT‐C enzyme is endowed with at least two distinct enzymatic activities and highlights the complexity of the GT‐C enzymes responsible for much of the biosynthesis of mycobacterial cell wall polysaccharides. Interestingly, the catalytic activity of PpgS was increased 40‐ to 50‐fold when co‐expressed with Rv3632, the encoding gene of a small putative transporter. Studies aimed at comparing the virulence and immune responses triggered by the wild‐type and GalN‐deficient strains of M. tb H37Rv are in progress.
Memory performance is related to dietary, metabolic, and inflammatory parameters in older adults
Authors: Ballantyne Danielle Lynn , Shidler Marcelle D. , Krikorian Robert , Lee Seung-Yeon
Published: June 2021

To examine the association of cognitive function to dietary intake and serum insulin and inflammatory markers, we collected data from 38 older adults (72.5±4.9 yrs) with mild cognitive impairment. More than half were females (57.9%), 94.7% were White Americans, and 89.4% had some college or above. Cognitive function was assessed using the Verbal Paired Associate Learning Test (V‐PAL) and California Verbal Learning Test (CVLT). Three day food records were entered into the Nutrition Data System for Research and nutrient intake and glycemic index were calculated. Fasting blood samples were obtained to assay serum insulin, C‐reactive protein, TNF‐α, IL‐1 β, and IL‐6. Regression analyses were conducted using SPSS 19. Vitamin D intake (p<0.001), TNF‐α (p<0.001), and glycemic index (p<0.001) explained 48.4% variance of the V‐PAL total learning score. With respect to the CVLT, the total number of intrusion errors was predicted by insulin (p<0.05, r2=11.2%) and long‐delay free recall was predicted by age (p<0.05, r2=14.2%). These preliminary findings suggest that nutritional and metabolic status may be related to cognitive function in older adults. These associations need to be examined with a larger sample.

NIH/National Institute on Aging grant # R01 AG034617 and the US Highbush Council
Fatigability as a function of physical activity energy expenditure: proof of concept
Authors: Buchowski Maciej , Whitaker Lauren , Powers James , Chen Kong , Schnelle John
Published: June 2021

Increased fatigue is a predictor of morbidity and mortality in older adults. Fatigability defines a change in performance or self‐reported fatigue in response to physical activity (PA). Changes in performance, fatigue, and energy expenditure (EE) were measured simultaneously in 17 adults (11 females, 74–94‐year‐old) performing 8 standardized PA tasks with various EE requirements in a whole‐room indirect calorimeter. Change in performance was measured using a PA movement monitor and change in fatigue was self‐reported on a 7‐point scale for each task. Performance and perceived fatigability severity scores were calculated as a ratio of change in performance and fatigue, respectively, and PAEE. Change in both objective performance and self‐reported fatigue were associated with EE (Spearman rho= −0.72 and −0.68, p<0.001) on a task requiring relatively high level of EE. The performance and perceived fatigability severity scores were significantly correlated (rho=0.77, p< 0.001) and were related to PAEE‐induced fatigue on tasks requiring relatively high EE level. We conclude that fatigability severity is a valid measure of PAEE induced fatigue in older adults.
Grape seed extract modifies insulin resistance induced by a high fat/carbohydrate meal in metabolic syndrome patients
Authors: Edirisinghe Indika , Randolph Jody , Cheema Mandeep , Park Eunyoung , Burton-Freeman Britt , Kappagoda Tissa
Published: June 2021

Insulin resistance is a characteristic feature of metabolic syndrome (MS) and is known to be associated with a relatively high postprandial plasma glucose concentration. We have shown previously that consumption of a meal that is high in readily available carbohydrates/fat causes a postprandial increase in markers of oxidative stress and insulin resistance. The present investigation was undertaken to determine whether a grape seed extract (GSE‐Meganatural© Gold) that is rich in antioxidants would modify these post‐prandial responses in individuals with the MS. After an overnight fast, twelve subjects with MS (6 men and 6 women) consumed a high‐carbohydrate, moderate‐fat meal in a cross‐over design. A GSE (300 mg) or placebo capsule was administrated 1 h before the meal. Postprandial changes in plasma insulin, glucose, oxidative stress and inflammatory markers were measured hourly for 6 h. Postprandial plasma glucose concentrations (area under the curve over 6 hr) were significantly lower when the meal was preceded by GSE compared with placebo (P=0.04). Postprandial insulin concentrations remained unchanged (P>0.05). Meal‐induced increases in oxidized LDL were attenuated with GSE capsule (P<0.05), whereas IL‐6 and TNF‐α concentrations were unchanged after the two treatments (P>0.05). These data suggested that GSE enhances postprandial insulin sensitivity in subjects with the MS. Study was supported by Polyphenolic Inc. Madera, CA
Heavy metal scavenger metallothionein mitigates deep hypothermia induced myocardial contractile anomalies:Role of autophagy
Authors: Jiang Shasha , Ren Jun
Published: June 2021

Metallothionein is a cysteine‐rich, low molecular weight heavy metal scavenger with potent cardioprotective properties. Deep hypothermia, if sustained, increased the risk of cardiovascular morbidity and mortality although the underlying mechanism is unclear. This study was designed to examine the impact of cardiac overexpression of metallothionein on deep hypothermia (4°C)‐induced myocardial contractile dysfunction, if any, and the underlying mechanism involved with a special focus on autophagy. Sustained deep hypothermia (4°C for 3 weeks) increased left ventricular end systolic and diastolic diameter, suppressed fractional shortening and perfused heart contractility, the effect of which was attenuated or ablated by metallothionein. Levels of autophagy marker LC3B, Atg7 and Beclin‐1, the autophagy adaptor protein p62 were increased following hypothermia. Fluorescence‐immunohistochemistry also revealed autophagy in murine hearts. Furthermore, sustained hypothermia triggered overtly reduced phosphorylation of the autophagy inhibitory signaling molecules Akt and mTOR (without affecting that of p70s6 kinase). Protein expression of pan Akt, mTOR and p70sk was unchanged. These hypothermia‐induced changes in autophagy and autophagic signaling were mitigated by metallothionein. Collectively, these data suggested that the heavy metal scavenger may protect against hypothermia‐induced cardiac anomalies through attenuation of cardiac autophagy.

This research is supported by Wyoming INBRE (P20RR016474).
Precancerous and Cancerous Predictive Signatures Using a Custom Designed Novel Gene Expression Assay
Authors: Vase Hollie Francesca , Drew Janice , Farquharson Andrew , Ross Ruth , Carey Frank , Steele Robert
Published: June 2021

Cancers exhibit a range of abnormal gene expression signatures associated with disease initiation and progression characterised by specific biomarkers. Identification of these biomarkers has improved cancer screening, detection, drug development and selection of appropriate drug therapies for individual patients. Typically only very small amounts of tissue are available from patient samples for analysis. A custom designed GeXP (Beckman) multiplex gene expression assay, the hCellMarkerPlex, was developed. Total RNA (50ng) from human colon normal, adenoma and carcinoma tissue samples (n=20) was assayed by hCellMarkerPlex. Predictive hCellMarkerPlex signatures of epithelial (EZR, KRT18, SLC9A2), proliferation (PCNA, CCND1, MS4A12), differentiation (B4GANLT2, CDX1, CDX2), apoptotic (CASP3, NOX1, NTN1), fibroblast (FSP1, COL1A1), structural (ACTG2, CNN1, DES), gene transcription (HDAC1), stem cell (LGR5), endothelial (VWF) and mucin production (MUC2) markers were established. GeXP technology identified gene signatures distinguishing normal, adenoma and carcinoma tissue and identified cellular processes showing abnormal activity associated with pathological status. The resulting biomarker profiles will be of medical use to inform on diagnosis, disease progression and monitoring treatments for colon cancer.
Molecular Analysis of Genetic Variation in Prions of Saccharomyces cerevisiae
Authors: Kelly Amy , Shewmaker Frank , Wickner Reed
Published: June 2021

Several proteins in the yeast Saccharomyces cerevisiae act as prions, forming infectious amyloids that are transmissible to other cells during division and outcrossed mating. The parallel in‐register β‐sheet structure of yeast prions such as [PSI+] and [RNQ+] provides a template for conversion of normally unstructured prion domains into a β‐sheet with folds at sites determined by the template on the ends of the filament. Prion propagation is highly sequence specific, and polymorphisms can disrupt templating and abrogate prion transmission. To investigate intra‐species barriers for prion transmission in yeast, we sequenced prion genes of 80 wild isolates from a diverse array of geographic locations and ecological niches. Molecular population genetics was used to quantify nucleotide diversity and examine the evolutionary basis for heterogeneity of prion alleles. An array of indels, SNPs and premature stop codons were detected in wild isolates. Many novel prion haplotypes were characterized, and several variants blocked prion propagation, resulting in barriers to transmission between strains. Almost half of the wild strains analyzed were heterozygous at one or more loci, suggesting that outcrossed mating occurs quite frequently in yeast. It is possible that the observed prion sequence heterogeneity is a consequence of natural selection against prion infections in wild yeast populations.
Imaging functional anatomy in the brain of mouse models of human disease
Authors: Bearer Elaine L , Gallagher Joseph J , Gonzales Aaron , Jacobs Russell E
Published: June 2021

Defects in axonal transport have been implicated in a number of neurodegenerative diseases, from the poly‐Q diseases like Huntingtonˈs disease, to Alzheimerˈs disease. The temporal sequence by which a pathological process unfolds is often unknown because our detection system relies on fixed tissue. Magnetic resonance imaging (MRI), a non‐destructive imaging modality, allows longitudinal studies inside opaque structures in live animals. We use manganese‐enhanced MRI (MEMRI) to witness axonal transport within the living brain of animal models of Alzheimerˈs disease. Mn2+ enters neurons and is transported by endogenous axonal transport. Thus MEMRI allows us for the first time to measure transport dynamics in the living brain. We find that in mice deleted for amyloid precursor protein (APP), a cargo‐receptor for transport whose product is the main component of senile plaques, transport of Mn2+ is decreased in the optic nerve and in the important memory circuit from hippocampus to forebrain. Older mice over‐expressing mutant APP also display decreased transport, demonstrating a bimodal effect of APP on transport dynamics. Using statistical parametric mapping of genotypic cohorts, sensitive quantitative measurements of transport are possible. Structural MRI also reveals volumetric changes over time. We conclude that MEMRI reveals pathological progression of disease processes in the living brain.
TDP‐43/TBPH enhances neurotoxicity in a Drosophila model relevant to Alzheimerˈs disease
Authors: Norton Zarina , Feany Mel B.
Published: June 2021

Neurodegenerative diseases affect more than 7 million Americans. Our laboratory has developed models of the most prevalent human neurodegenerative disorder, Alzheimer's disease (AD), in Drosophila so that we can use the genetic tools available in these simple model organisms to study proteins and pathways regulating disease pathogenesis. Recently it has been suggested that TAR DNA‐binding protein 43 (TDP‐43), a DNA/RNA binding protein, may play a role in neurodegenerative disease, due to its presence in large aggregates in neurons of patients with frontal temporal lobar dementia and amyotrophic lateral sclerosis, as well as many cases of AD. Despite aggregation and deposition of TDP‐43 in AD brains, the functional role of TDP‐43 in the pathogenesis of AD is currently unclear. We investigated the role of TDP‐43 in AD‐related neurodegeneration by reducing levels of the Drosophila homolog of TDP‐43, TBPH, in control and AD model flies. Our data demonstrates that reducing the level of TBPH in transgenic flies expressing human Abeta1‐42 in retinal cells increases the severity of Abeta toxicity. Importantly, the equivalent reduction of TBPH in the absence of transgenic Abeta has no clear effect on the retina. The worsening of retinal pathology with decreased levels of TBPH suggests TDP‐43 as a candidate disease modifier in AD.
Cell therapy: intravenous renal cell transplantation for acute and chronic renal failure
Authors: Kelly Katherine J , Dominguez Jesus H.
Published: June 2021

Acute kidney injury (AKI), chronic kidney disease (CKD) and end‐stage renal disease (ESRD) are major health problems that lack good solutions. We tested the hypothesis that kidney cells from one donor male rat given iv, could regenerate female rat kidneys with AKI or CKD. Isolated rat renal tubules were transfected with empty vector (A) or with SAA cDNA encoding tubulogenic serum amyloid A1 protein (B) and grown. Kidney cells were infused to rats with severe AKI from 50 min of bilateral renal ischemia or CKD from 3 cisplatin injections. Serum creatinine was 3.9 ± 0.7 in A rats and 1.0 ± in B rats after 48 hr. post‐ischemia (mg/dl, mean ± SE, p ≤ 0.05), and renal inflammation and fibrosis were significantly improved. Donor cell engraftment was documented up to 30 days in recipient kidneys. CKD was induced by cisplatin (1.5 mg/Kg), and 3 weeks later rats were infused with either A cells (7 rats) or B cells (7 rats). Twelve days later blood urea nitrogen (BUN) was 101 ± 4 in A rats and 38 ± 18 in B rats (mg/dl, p ≤ 0.05). Renal fibrosis and tubular atrophy was improved in B rats. We also removed one kidney of 6 rats with cisplatin CKD, and auto‐transplanted these cells iv with correction of BUN after 12 days: 53 ± 5 (n = 6 p ≤0.05). We conclude that renal cell transplantation with kidney primary cells restores function and structure in AKI and CKD.
Chronic high fat diet changes gene expression within the brain reward system: critical periods and sex differences
Authors: Reyes Teresa M , Carlin JesseLea
Published: June 2021

Both the overconsumption of palatable foods and chronic drug use can result in a state of “reward hypofunction”. Previously, we have shown that chronic consumption of a high fat (HF) diet in mice alters dopaminergic and opioid gene expression within the central reward circuitry in a pattern consistent with reward hypofunction. The goal of the present study was to examine whether animals exposed during early life, adolescence or as adults would differ in their responsiveness to the high fat diet, with the prediction that early life exposure would be more potent. Three groups of mice were fed HF diet at birth, 3 weeks, or 6 weeks of age (n=6/group). After 12 weeks, target gene expression was measured in the ventral tegmental area, nucleus accumbens and prefrontal cortex. Contrary to our hypothesis, adult exposure and early exposure to the HF diet both altered gene expression within the central reward circuitry. The pattern of changes differed across regions and timepoints and varied by sex in important ways. The functional implications of these differences will be presented. In sum, we identified changes in the reward circuitry in response to HF diet exposure that parallel neuroadaptations seen in chronic drug use. These changes occur with both early life and adult exposure to HF diet, and vary by sex

Funding to TMR: MH087978, MH091372
Decoupling of sexual dimorphism in the human bony pelvis and its relationship to differential selective pressures
Authors: Brown Kirsten M.
Published: June 2021

Obstetrics and locomotion have opposing demands on the form of the human bony pelvis. Previous work has identified sexual dimorphism in the posterior spaces (PS) and non‐dimorphism in the anterior spaces (PS). This study tests the hypothesis that the AS is more influenced by locomotion, and the PS is more influenced by obstetrics. Landmarks (k = 43) were collected on articulated male (N=102) and female (N=104) pelves. Euclidean Distance Matrix Analysis was used to define distances in each space. MANCOVAs were used to test for effects of sex and body mass for each space. A significant effect of sex and a non‐significant effect of body mass would indicate that the distances are influenced more by obstetrics, while the reverse would indicate that distances are influenced by locomotion.

Results from the MANCOVAs on both the AS and PS distances identified highly significant effects of both sex (p<0.001), and body mass (p<0.001), demonstrating that there are morphological adaptations related to locomotion and obstetrics in both spaces. However, a comparison of the relative proportion of variance attributed to sex and body mass demonstrated that there was a stronger influence of sex in the PS, and a stronger influence of body mass in the AS. These results suggest that decoupling of sexual dimorphism in the human bony pelvis facilitates morphological adaptations related to differential selective pressures within the pelvis.

Grant Funding Source : NSF DDIG (#0925468), Sigma Xi GIAR (#G2009100302)
Teaching students to use social media to do scientific research
Authors: Krontiris-Litowitz Johanna
Published: June 2021

Social media are a set of internet applications that create and exchange user‐generated information. They are valuable tools for scientists especially when utilized to create and exchange scientific data, ideas, hypotheses, etc. The objective of this project was to teach Neuroanatomy students to use a WIKI to work collaboratively to perform a research project. Students were shown an experimental protocol and then asked to use the WIKI to to develop a hypothesis and protocol, perform the experiment, develop consensus on the conclusions, and write a lab report. In this way students learned to use social media to disseminate information, advocate positions, contest claims, evaluate the contributions of collaborators, and work collectively on a common goal. The Project assessed the social media skills of the students in 3 conditions: an exchange of information on the WIKI, an evaluation of peer contributions to the WIKI, and ad hoc discussion about the design and performance of the experiment. All students (n=8) posted ideas in the information exchange but only 87.5% evaluated peer contributions. All students contributed postings to the ad hoc discussion board and postings (1–4 per student) appeared as needed for project progress. While 62.5% of the students initiated topics or questions essential to the progress of the project only 25% of the students summarized contributions, or posted a consensus decision.
The Role of CD 44+ Cells in Human Heart Valve Development
Authors: Votteler Miriam , Berrio Daniel Alexandro Carvajal , Bonin Micheal , Horke Alexander , Brockbank Kelvin , Schenke-Layland Katja
Published: June 2021

Background

Versican is a structural and function proteoglycan found in the extracellular matrix (ECM) of heart valve leaflets. CD44 is a well‐known cell membrane receptor for binding proteoglycans including versican. In our study, we analyzed the expression of CD44 during the late human fetal valvulogenesis.

Methods

For gene expression analyses, we used formalin‐fixed paraffin‐embedded (FFPE) human semilunar heart valve leaflets and performed a comparison of four age groups: group I – first trimester; group II – second trimester; group III – 14 to 19 years, group IV – 50 to 55 years. In addition, we analyzed protein expression using immunohistological staining. We employed antibodies for CD44 and versican using FFPE‐aortic heart valve tissues of the different developmental stages.

Results

We revealed that the transcription of CD44 starts in the first trimester of human fetal development. We also identified that CD44‐positive cells in developing leaflets (first, second and third trimester) are located in a very distinct anatomical site at the junction between vascular wall and leaflet. In contrast, in mature valves, CD44‐positive cells are spread throughout the entire leaflet.

Conclusion

In this study, we demonstrate that CD44‐positive cells represent a distinct cell population present in developing valve leaflets that is crucial for proper human valve development.

Grant Funding Source: Attract 692263 Fraunhofer‐Gesellschaft
How do undergraduate students study for anatomy, and does it matter?
Authors: Barger John Bradley
Published: June 2021

In an undergraduate anatomy class at Indiana University (A215) students are given many suggestions for methods of studying course content outside of class time. There are lists of study strategies in the syllabus and lab guides, and the course instructors spend part of the first several lecture and lab meetings discussing additional study strategies. But which of the strategies do students use most, and which yield the best results on course exams? To answer this question, we administered a survey to the class of nearly 400 undergraduates. The survey questions asked about the amount of time students spent on a variety of specific strategies. These strategies ranged from passive studying (reading text, reviewing figures) to more active approaches (drawing figures, making tables). It was found that differences in study strategies do exist between students, and that there are correlations between strategies and grades. Students that reported the most use of self‐produced study materials showed the greatest success on exams. Those students that used the fewest different types of study methods and spent the least amount of time on the material showed lower scores on exams. The pedagogical implications of these findings indicate that instructors should continue to encourage as many, and as varied, methods of revision as possible.

Grant Funding Source : ‐
More than Meets the Eye: An Interactive 3D Model of the Eye for Enhanced Learning of the Oculomotor System
Authors: Allen Lauren Kathleen , Bhattacharyya Siddhartha , Wilson Timothy D
Published: June 2021

The functional anatomy of the oculomotor system is conceptually difficult for novice students. This is problematic given that the extraocular muscles represent a common site of clinical intervention in the treatment of ocular motility disorders and other diseased states. This study was designed to develop a novel, three‐dimensional (3D) model that is paired with an electronic interface, creating an interactive 3D learning module of the human oculomotor system. Development of the 3D model utilized the Visible Human Project (VHP) Female data set and was refined using multiple forms of 3D software. Undergraduate anatomy students will be exposed to the learning module in a randomized pseudo‐crossover design. Quantitative post‐experience testing of the 3D learning module will be compared to equivalent two‐dimensional (2D) learning materials. Qualitative Likert‐scale questionnaires will be used to assess subjective opinions towards the different learning resources. It is hypothesized that the 3D learning module will enhance students’ spatial and functional comprehension on post‐test measures as well as maintain a higher level of interest, when compared to equivalent traditional 2D educational materials.

Grant Funding Source: Western Graduate Scholarship
Innovation in Education: Histology and Physiology Integration
Authors: Shaw Phyllis , Hanss Basil
Published: June 2021

In Physiology and Histology there are many areas of thematic overlap. The courses were integrated to enhance the educational value of Histology and Physiology with optimal reinforcement of course materials (structure and function). Achievement of this goal included, integration of lectures, change in format of both courses, addition of hours, and change in sequence of specific topics; changes were as follows:

Histology/Physiology ended on the same day.

Exams were administered concomitantly; one more exam was added.

Exams were restructured. Previously there were 6 hrs of exams for physiology and 6 hrs for histology. In 2011, there were 3 exams of 5 hrs each (3 hrs combined multiple choice questions (MCQ), 1 hr histology practical, 1 hr physiology essay).

Combined MCQ exam contained 20% integrated histology/physiology questions.

Histology lectures and labs preceded similar topics in Physiology, and in some cases, histology and physiology lectures were fully integrated (kidney module and GI module).

In those cases where lectures were presented separately, both histology and physiology lecturers consulted with each other to integrate their material as closely as possible (Respiratory System and Female Reproductive System).

The Course Directors feel that the GI System, Urinary System and the Female Reproductive System worked well. Student evaluations support this: GI = 4.12/5.0, Kidney = 3.76/5.0).
Identification of Potential Enhancers in Intron 5 of the RUNX1 Gene
Authors: Gutierrez Soraya Elisa , Alarcon Ricardo , Rebolledo Boris , Fernandez Valentina , Javed Amjad
Published: June 2021

Human RUNX1 gene is the most frequent target for chromosomal translocations associated with acute myeloid leukemia (AML) and acute lymphoid leukemia (ALL). The highest prevalence in AML is noted with (8;21) translocation; which represent s 12 to 15% of all AML cases. Interestingly, all the breakpoints mapped to date in t(8;21) are clustered in intron 5 of the RUNX1 gene and intron 1 of the ETO gene. No homologous sequences have been found at the recombination regions; but DNaseI hypersensitive sites (DHS) have been mapped to the areas of the genes involved in t(8;21). Presence of DHS sites is commonly associated with regulatory elements such as promoters, enhancers, silencers, etc. In this study we used a combination of comparative genomics, chromatin analysis and transfection studies to evaluate potential regulatory elements located in intron 5 of the RUNX1 gene. Our genomic analysis identified nine potential enhancer regions that are evolutionarily conserved. Analysis of histone modification status of these regions in myeloid cells shows a high association of marks characteristic of enhancer modules. Two of these regions were cloned in front of a reporter gene and their effect on transcriptional regulation was evaluated. Taken together our results identified two conserved non coding sequence in intron 5 of the RUNX1 gene that can regulate transcription expression of a reporter gene.

FONDECYT 1100670
Hypoxia sensing by Fe2+/α‐KG dependent dioxygenases regulate hmU synthesis in trypanosome DNA, chromatin structure and Pol II transcription
Authors: sabatini robert , cliffe laura , ekanayake dilrukshi , Hirsch Gwen
Published: June 2021

We have recently demonstrated that O‐linked glucosylation of thymine (base J) in trypanosome DNA regulates Pol II transcription initiation in organisms previously thought to lack transcriptional regulation. Trypanosome cruzi cell lines with reduced levels of base J following the deletion of the thymidine hydroxylase (JBP1) involved in J synthesis resulted in genome‐wide changes in gene expression and increased parasite virulence. Addressing the mechanism of base J function, we now find that the loss of base J coincides with decreased nucleosome abundance, increased histone acetylation and increased Pol II occupancy at promoter regions.

In vivo analysis suggest the thymidine hydroxylases (JBP1 and JBP2) belong to the Fe2+/α‐KG dependent dioxygenase superfamily where hydroxylation is driven by the oxidative decarboxylation of αKG, forming succinate and CO2. We now demonstrate that recombinant JBP1 can hydroxylate synthetic DNA substrates in a Fe2+, α‐KG and oxygen dependent manner. Growth of T. cruzi in hypoxic conditions (<1% oxygen) results in a significant reduction in J levels, which is rapidly restored upon re‐exposure to oxygen, and increased parasite virulence as seen in the JBP KO's. The influence of environment upon J biosynthesis, via JBP, has exciting implications for the regulation of gene expression and parasite survival and adaptation to different host environments.

Supported by NIH.
Dcm‐mediated cytosine DNA methylation is conserved in Escherichia coli and influences the expression of ribosomal protein genes
Authors: Militello Kevin Thomas , Simon Robert D , Qureshi Mehr , Maines Robert , VanHorne Michelle L , Hennick Stacy M , Jayakar Sangeeta K , Pounder Sarah
Published: June 2021

In Escherichia coli, cytosine DNA methylation is catalyzed by the Dcm (DNA cytosine methylase) protein and occurs at the second cytosine in the sequence 5′CCWGG3′. Although the presence of cytosine DNA methylation was reported over 35 years ago, the biological role of 5‐methylcytosine in E. coli remains unclear. There is data indicating that Dcm can protect the genome against attack by a restriction enzyme that cleaves the same sequence, yet DNA methyltransferases in eukaryotes often influence gene expression. In order to gain insight into the potential roles of cytosine DNA methylation in E. coli, we: (a) screened 162 strains including laboratory strains, pathogens, and recently isolated environmental samples for the presence of the full‐length dcm gene using the polymerase chain reaction; (b) examined the same strains for the presence of 5‐methylcytosine at 5′CCWGG3′ sites using a restriction enzyme isoschizomer digestion assay; and (c) quantified the levels of 5‐methyl‐2′‐deoxycytidine in selected strains using liquid chromatography tandem mass spectrometry. Dcm‐mediated cytosine DNA methylation is conserved in all 162 strains examined, and the level of 5‐methylcytosine ranges from 0.8–1.2% of the cytosines. We also tested the hypothesis that Dcm influences gene expression. Gene expression in wild‐type and dcm knockout cells was compared via qPCR. We focused on ribosomal protein genes, as they have been previously demonstrated to contain numerous 5′CCWGG3′ sites. We demonstrate that Dcm represses expression of ribosomal protein genes during stationary phase, and this may explain the ubiquitous presence of this DNA modification pathway. Support for this work was provided by the Geneseo Foundation and NIH grant R15AI074035‐01.
A Novel Role for the MRN‐CtIP complex in Schizosaccharomyces pombe Non‐Homologous End‐Joining (NHEJ)
Authors: Li Yanhui , Runge Kurt
Published: June 2021

Objective

To elucidate the mechanisms for that allow Hermes transposon excision from the S. pombe genome.

Results

MRN (Mre11‐Rad50‐Nbs1) ‐CtIP complexes are key players in double‐strand break repair from yeasts to humans. The role of MRN‐CtIP in NHEJ is unclear owing to the differing results in Saccharomyces cerevisiae and S. pombe: while both yeasts require Ku and DNA ligase IV to join the ends of transfected linear plasmids, only S. cerevisiae requires its MRN‐CtIP complex. The excision of the hAT transposon Hermes uncovered a role for MRN‐CtIP in S. pombe NHEJ. hAT transposons produce an 8 bp target site duplication (TSD) upon insertion, and excise by forming DNA hairpins on each side of the chromosomal break. In Maize and Drosophila, hAT transposon excision yields NHEJ repair events that retain both TSDs, while S. cerevisiae events have much larger deletions. In S. pombe, excision yields repair events that retain both TSDs, and efficient repair requires Ku70, DNA ligase IV and each component of MRN‐CtIP. Mutants that eliminate Mre11 dimerization, but not those that eliminate Mre11 nuclease activities, also greatly reduce repair.

Conclusion

S. pombe does utilize its MRN‐CtIP complex for NHEJ, and the Mre11 dimerization domain plays an important role. Repair events in S. pombe are more similar to those in metazoans compared to the events in S. cerevisiae, which show a greater amount of resection prior to end‐joining.

Source of research support: NIH R01GM050752 and NIH R01AG019960