bluuebunny/crossref_metadata_2025_split huggingface dataset:
What fruit flies teach us about RNA silencing.
Authors: Zamore Phillip D 
Published: June 2021

RNA silencing is remarkably similar between fruit flies and man. Like humans, flies have three distinct RNA‐guided mechanisms to silence genes: the microRNA (miRNA), the siRNA‐guided RNA interference (RNAi), and Piwi‐interacting RNA (piRNA) pathways (1). These three classes of small RNAs are produced by different pathways from different types of precursor RNAs, but each functions as a sequence‐specific guide for a member of the Argonaute family of proteins (2). Much of what we know about these three types of small silencing RNAs was learned through biochemical and genetic studies in the model organism, Drosophila melanogaster (3‐5). For each pathway, the fundamental mechanisms for small RNA biogenesis and function were discovered first in flies, then in man. In flies, each pathway serves a unique and largely non‐overlapping function. We know that miRNAs regulate the expression of protein coding genes, RNAi defends against viral infection and transposons in the soma, and piRNAs protect the germ line from selfish genetic elements such as transposons. New functions for small silencing RNAs continue to be discovered.What are the lessons taught us by flies and how can we apply them to develop robust RNAi strategies for drug‐target discovery and human therapy? Finally, what discoveries in flies remain to be translated into improvements in triggering RNA silencing in mammals?
Small RNA metabolism and function in Arabidopsis
Authors: Chen Xuemei 
Published: June 2021

The transcriptome of plants includes diverse species of 21‐24 nucleotide small RNAs, which are composed of microRNAs (miRNAs) and endogenous small interfering RNAs (siRNAs). miRNAs regulate target mRNAs through transcript cleavage or translational inhibition and play crucial roles in various developmental and physiological processes. Endogenous siRNAs trigger and maintain DNA and histone methylation leading to heterochromatin formation.We have been studying the biogenesis, degradation, and function of small RNAs in Arabidopsis. We showed that plant small RNAs are 2′‐O‐methylated by the small RNA methyltransferase HEN1 on the 3' terminal ribose and that the methyl group protects small RNAs from a 3′‐5' exonuclease that degrades small RNAs and from a so‐called uridylation activity that adds a short U tail to small RNAs. Subsequently, animal siRNAs and piRNAs were found to be 2′‐O‐methylated by HEN1 homologs. We have also identified a family of exonucleases that degrades small RNAs and demonstrated that small RNA turnover is crucial for plant development. Finally, we studied the developmental function of one miRNA, miR172, and revealed that it plays a crucial role in the temporal regulation of floral stem cells. These findings in small RNA metabolism and function will be discussed.
Independent, combined, and duration‐dependent effects of diet and exercise on WAT inflammation and metabolic disturbances in obese C57/BL6 mice
Authors: Vieira Victoria Jeanne , Valentine Rudy J , Natao Nirav , Young Virginia , Woods Jeffrey A 
Published: June 2021

White adipose tissue (WAT) inflammation causes insulin resistance (IR) and hepatic steatosis (HS). Exercise training (EX) may decrease inflammation in WAT thereby ameliorating these disturbances, even in the absence of fat loss.This study compared low‐fat diet (LFD) and EX on WAT inflammation, IR, and HS in obese mice.Mice (n=109) fed a 45% fat diet (HFD) for 6 wks were randomly assigned to EX (treadmill, 5d/wk; 40 min/d; 65%VO2max) or sedentary (SED) groups. Mice remained on HFD or switched to a 10% fat diet (LFD). After 6 or 12 wks, WAT and liver were weighed and relative fat (rFat) was calculated. HS was assessed by total liver TG, and IR by HOMA. Rt‐PCR was used to determine WAT gene expression (MCP‐1, F480, TNF‐α, IL1ra, leptin). Comparisons were made using 2‐way (EX, LFD, EXxLFD) ANOVA covarying for rFat.EX and LFD reduced rFat and leptin, which improved when combined. Improvements in IR and HS were explained by reduced rFat at 6 wks. By 12 wks, MCP‐1, F480, TNF‐α, and IL1ra were reduced by EX and LFD. Regression analyses revealed EX, rFat, and WAT inflammation predicted reductions in IR (R2=.75; p<0.01); rFat and LFD predicted improvements in HS (R2=.51; p<0.01). From 6 to 12 wks, EX attenuated increases in rFat, HS, and WAT inflammation, but LFD decreased IL1ra.Unique metabolic consequences of SED and HFD are evident long‐term, highlighting the importance of both EX and LFD in preventing obesity‐related metabolic disturbances.Grant Funding SourceNIH T32 DK59802
Leucine contents of isonitrogenous protein sources predict post prandial skeletal muscle protein synthesis in rats fed a complete meal
Authors: Norton Layne Eiseman , Wilson Gabriel J , Rupassara Indu , Garlick Peter J , Layman Donald K 
Published: June 2021

Leucine (leu) is recognized as a nutrient signal for regulation of muscle protein synthesis (MPS), however previous research has been limited primarily to acute studies with free amino acids (J. Nutr. 133:1553S‐6S, 2005). It is unclear if isonitrogenous protein sources containing different levels of leu will produce differential MPS responses in animals adapted to meal feeding. This study examined 4 different protein sources: wheat (supplemented with lysine), soy, egg, and whey, (containing 6.8, 8.0, 8.8, and 10.9% leu respectively) on the potential to activate initiation factors and MPS. Male rats (250g) were trained for 14d to eat 3 meals/d consisting of 16/54/30% of energy from protein, carbohydrates and fats. Rats were sacrificed after 13hr fast or 90min after consuming their normal breakfast. Measurements included plasma insulin, glucose and amino acids, MPS via D5‐Phe incorporation, and phosphorylation of initiation factors 4E‐BP1 and S6K. Wheat and soy did not stimulate MPS above fasted levels whereas egg and whey significantly increased MPS with whey greater than egg. MPS responses were closely related with changes in plasma leu and phosphorylation of 4E‐BP1 and S6K. These findings suggest that leu content of protein sources is a critical factor in determining protein quality as it relates to changes in post prandial MPS responses. Supported by National Dairy Council, Egg Nutrition Center, Illinois CFAR.Grant Funding SourceEgg Nutrition Center and National Dairy Council
Signaling Networks in Chemotaxis and Cytokinesis
Authors: Devreotes Peter N. , Borleis Jane , Cai Huaqing , Franca‐Koh Jonathan , Swaney Kristen , Kamimura Yoichiro , Long Yu , Rahdar Meghdad , Tang Michelle , Willard Stacey 
Published: June 2021

The mechanisms of sensing shallow gradients of extracellular signals is remarkably similar in Dictyostelium amoebae and mammalian leukocytes. An extensive series of studies have indicated that the upstream components and reactions in the signaling pathway are quite uniform while downstream responses such as PIP3 accumulation and actin polymerization are sharply localized towards the high side of the gradient.We have recently shown that activation of TorC2 and PKB occurs at the leading edge of chemotaxing cells and plays a critical role in directed cell migration. Within seconds of stimulation of chemotactically sensitive cells, two PKB homologs, PKBA and PKBR1, transiently phosphorylate at least 10 proteins. The enzymes are activated by phosphorylation of their hydrophobic motifs (HMs) through TorC2. Cells deficient in both PKBs or TorC2 lack most of the phosphorylated substrates and are specifically impaired in directional sensing. Activation of PKBA requires PIP3 while activation of PKBR1 is independent of PIP3. This redundant circuit explains previous observations on the role of PIP3 in chemotaxis. In cells lacking PTEN, high levels of PIP3 overactivate PKBA and impair chemotaxis by triggering many extraneous pseudopodia. In the absence of PIP3, chemotaxis can occur almost normally because PKBR1 is activated by TorC2 independently of PIP3.
Regulation of Substrate Processing by the Proteasome
Authors: Finley Daniel 
Published: June 2021

The proteasome, a large protease, recognizes the target protein via its ubiquitin chain, unfolds the protein, removes the chain, and injects the unfolded protein through a narrow gated channel into the large interior chamber of its 28‐subunit core particle, where it will be degraded.Ubiquitin‐dependent protein degradation is essential for cells to survive many environmental stresses. Stress regulates the proteasome by changing its composition. In one example, we identified a response to deficient ubiquitin levels, or "ubiquitin stress." Ubiquitin stress does not upregulate proteasomes. Instead, ubiquitin stress alters proteasome composition. The gene encoding deubiquitinating enzyme Ubp6, which associates with the proteasome, is induced when ubiquitin levels fall. Enhanced loading of proteasomes with Ubp6 alters proteasome function. Ubp6 spares ubiquitin from proteasomal degradation via its deubiquitinating activity and probably also because of its capacity to inhibit the proteasome noncatalytically. This pathway, originally described in yeast, seems to function comparably in mammals.Ubp6 works in tension with the proteasome‐associated ubiquitin ligase Hul5. Ubp6 attenuates chains while Hul5 extends them. When Hul5 is missing, the proteasome works with impaired fidelity, perhaps because chain extension is needed to prolong the substrate's association with the proteasome. Unlike Ubp6, Hul5 is not induced by ubiquitin stress. Thus, when proteasomes are remodeled under some stress conditions, the ratio of Ubp6 to Hul5 is changed.
The NIH supported Virtual Human Embryo (VHE) Project: educational and research resources for human embryology
Authors: Cork R. John , Gasser Raymond F. 
Published: June 2021

The Carnegie Collection that is housed at the Human Developmental Anatomy Center (HDAC) in Washington DC is considered by many to be the best collection of human embryos in the world. The overall aim of the VHE project that began in 2000 is to make the best representative examples from each of the 23 Carnegie stages available to embryology researchers and educators, either on disks or online. To date, we have completed databases for 20 embryos (stages 1 ‐ 15 & 23) and are presently working on stages 16, 17, 18 & 20. The project will be completed within the next two years depending on continued funding from NIH. Each of the databases includes: a complete set of labeled sections viewable at three or four levels of magnification, a 3D computer model of the embryo, animations and other documents and figures related to the specimen. The disks have recently been revised to include an overview of each stage, a consistent format and the most current terminology for labels. We will show how these resources are freely available for educators to incorporate into presentations and/or class work and will give some examples of how the databases are being used for research into human embryology.Supported by NIH grants RO1 HD 37811 and RO1 LM 7591
Identification of differentially expressed genes in early inner ear development
Authors: Paxton Christian Nephi , Chapman Susan C. , Schoenwolf Gary C. 
Published: June 2021

To understand the etiology of congenital hearing loss, we must gain a comprehension understanding of the molecular genetic mechanisms underlying normal ear development. Our lab is identifying genes and their mechanisms of action that lead to inner ear initiation and development. Using Agilent microarrays, we compared the differential expression of the pre‐otic placodal domain with an adjacent rostral control tissue (a domain that is competent, but not specified, to form otic tissue). We identified 1,261 transcripts differentially expressed between the two tissues at a change of 2‐fold or greater: 463 were up regulated in the pre‐otic domain, and 798 were upregulated in the control tissue. We have validated the pre‐otic expression of several signaling molecules and transcription factors identified in this array using in situ hybridization. Furthermore, the expression patterns of this group of genes were explored in detail to determine how the timing of their expression relates to specific events of otic induction and development. In conclusion, a number of novel candidate genes for otic placode induction have been identified. Funded by the Deafness Research Foundation and the NIH.Grant Funding SourceDeafness Research Foundation and NIH
Hypoxia as an Environmental Cause of Holoprosencephaly
Authors: Smith Francis Joel , Marcucio Ralph S 
Published: June 2021

Holoprosencephaly is a complex congenital malformation of the forebrain and face. Recent clinical evidence shows a correlation between hypoxia and holoprosencephaly. We examined the role of hypoxia in causing holoprosencephaly in chick embryos. Chicken eggs were incubated in 13% O2 (hypoxia) or in 20% O2 (normoxic control). Embryos were collected on days 4, 5, 6, and 10. Embryos were photographed for morphologic analysis, sectioned in paraffin, and H&E stained for histologic analysis. 56% of hypoxic embryos (days 4‐6) survived, and 50% survived to day 10. These embryos were mildly or severely developmentally delayed. Malformations included severe cephalic, facial and eye anomalies, and absence of the upper jaw anlage. Another group of eggs were incubated in normoxia to day 7 and transferred to hypoxia. These embryos were collected on day 12 and photographed for morphologic analysis. All the postnormoxic hypoxic embryos (day 12) survived and showed a wide range of stages, compared to normal 12‐day‐old embryos. Malformations included midfacial hypoplasia, midline clefting, and eye anomalies. Hypoxia leads to high mortality, developmental delay, and craniofacial and cephalic malformations resembling holoprosencephaly in chick embryos. Future work will be done to examine the molecular mechanisms of these defects in hypoxia.Grant Funding SourceNIH
Cadaver Computed Tomography: Virtual dissection as a tool for teaching anatomy
Authors: Ellozy Sharif H , Lerner Susan M , Reidenberg Joy S , Weintraub Joshua L , Lefkovitz Zvi , Marin Michael L , Laitman Jeffrey T 
Published: June 2021

Traditionally, cadaver dissection has been the mainstay of anatomy instruction. However, as clinical medicine becomes more image driven, familiarity with cross‐sectional anatomy is crucial. Additionally, introducing clinical correlates in the preclinical years of medical education is essential in generating student enthusiasm. In order to facilitate these goals high resolution computed tomography was performed on all cadavers used in the first year anatomy class. Axial, sagittal, coronal and 3D volume rendered reconstructions were performed. Specific reconstructions of bony structures, aerodigestive tract, and vascular system were also done. All of the CT scans were read by a radiologist and findings recorded. Students were then given access to all of the studies and instructed on how to use a DICOM viewer. Images from reconstructions were included on their examinations, and part of the students' final grade came from a team building exercise using the CT images. The applicability of this tool to clinical medicine is twofold: 1) it introduces students to cross sectional imaging; and 2) it allows students to identify variant anatomy, post‐surgical changes, and pathology prior to dissection. Unlike other anatomy correlates such as the Visible Human, these reconstructions are of the students' own cadaver, and provide a permanent resource to the student long after the dissection is completed.Grant Funding Sourcen/a
Transcriptional Regulation of N‐Acetyl Glutamate Synthase
Authors: Kirsch Sandra Beth , Marino‐Ramirez Leonardo , Tuchman Mendel , Caldovic Ljubica 
Published: June 2021

The urea cycle converts ammonia, a toxic product of protein metabolism, to urea in mammalian livers. N‐acetyl glutamate synthetase (NAGS) catalyzes the formation of N‐acetyl glutamate, an essential cofactor of carbamylphosphate synthetase I (CPSI). By providing an essential activator of CPSI, the first and rate‐limiting enzyme in the urea cycle, NAGS helps regulate urea production and may function as a nitrogen load sensor.Methods to identify transcription start sites, conserved regulatory regions, and cis‐acting regulatory motifs for NAGS included 5' RACE, multiple sequence alignment of several mammalian species upstream non‐coding sequences, Cis‐element OVERrepresentation software & Chromatin Immunoprecipitation (ChIP). Regions of high conservation were identified immediately upstream and 3kb upstream of the translation start codon. Several transcription factor binding motifs, including Sp1, AR & CREB, were conserved within the putative promoter while a TATA box motif was absent. ChIP analysis verified binding of Sp1 to the NAGS promoter. These data indicate NAGS transcription is regulated through Sp1 and hormone signalling pathways including glucocorticoids and cAMP, similar to regulation of urea cycle enzymes ASS, ASL & arginase I. These finding suggest regulation of NAGS occurs through metabolite sensing pathways and that NAGS could be the first nitrogen load sensor.NIH # 2R01DK064913‐05A1
N‐3 fatty acid treatment and plasma transthyretin in patients with Alzheimer's disease
Authors: Faxen Irving Gerd , Freund‐Levi Yvonne , Eriksdotter‐Jönhagen Maria , Basun Hans , Palmblad Jan , Vedin Inger , Wahlund Lars‐Olof , Cederholm Tommy 
Published: June 2021

BackgroundTransthyretin (TTR) binds Abeta and may reduce brain Abeta, a key pathogenetic feature in Alzheimer's disease (AD). N‐3 fatty acids (FA), i.e. DHA and EPA, increase TTR transcription in rat brain. We studied the effects of n‐3 FAs on plasma TTR levels in patients with AD. Methods: 204 outpatients with AD were randomised to DHA/EPA (80/20%), 4 g/d during 6 mo (EPAX, Pronova AS) or placebo (n‐6 FA). After 6 mo all patients received EPAX for another 6 mo. Cognitive function was assessed by MMSE and ADASCog.ResultsBaseline plasma TTR was 260[plusmn]80 in the EPAX‐group (89 pat, 75 y, 57% w) and 264[plusmn]55 mg/l in the controls (85 pat, 75 y, 46% w) (ns). After 6 mo TTR levels was 250[plusmn]59 and 229[plusmn]51 in the EPAX and control groups, respectively (p<0.015). Repeated measures ANOVA indicated an increase in TTR by EPAX treatment (P=0.04), most evident in the men. From 6 to 12 mo TTR increased significantly in both groups. MMSE correlated to TTR at 12 mo (r=0.16, P=0.03) and inversely to ADAS‐Cog (r=‐0.2, P=0.01). In multiple regression analyses increased TTR at 6 mo was independently related to n‐3 treatment (OR 2.1, 95% CI 1.01‐4.2)ConclusionN3 FA treatment in patients with AD appeared to increase TTR. Since n3 FA may prevent cognitive decline, and TTR may decrease Abeta deposition, the results warrant further exploration. & [beta] & [plusmn]
N‐3 polyunsaturated fatty acids do not alter immune and inflammation measures in endurance athletes
Authors: Henson Dru A. , Nieman David C. , McAnulty Steve , Jin Fuxia , Maxwell Kendra 
Published: June 2021

We tested the influence of 2.4 g/day n‐3 polyunsaturated fatty acids (n‐3 PUFA) over 6 weeks on exercise performance, inflammation, and immune measures in 23 trained cyclists before and after a 3‐day period of intensified exercise. Subjects were randomized to n‐3 PUFA (N=11) (2,000 mg eicosapentaenoic acid, EPA, 400 mg docosahexaenoic acid, DHA) or placebo (N=12) groups, and ingested supplements under double blinded methods for 6 weeks prior to and during a 3‐d period in which subjects cycled for 3 h/day at ~57% Wattsmax with 10‐km time trials iduring the final 15 minutes of each 3‐h bout. Blood and saliva were collected before and after the 6‐week supplementation period, immediately following the 3‐h exercise bout on the third day, and 14‐h post‐exercise. Supplementation with n‐3 PUFA significantly increased plasma EPA and DHA, but had no effect on 10‐km time trial performance, pre‐exercise measures, and exercise‐induced increases in plasma cytokines, myeloperoxidase, blood total leukocytes, serum C‐reactive protein, and creatine kinase, or the decrease in the salivary IgA:protein ratio. In conclusion, 6 weeks supplementation with n‐3 PUFAs increased plasma EPA and DHA, but had no effect on exercise performance or in countering measures of inflammation and immunity before or after a 3‐day period of nine hours of heavy exertion.Supported by a grant from Cooper Complete, The Cooper Aerobics Center, Dallas TX
The Effect of Whey Protein on Post‐Meal Blood Glucose and Insulin
Authors: Akhavan Tina , Luhovyy Bohdan L , Anderson Harvey G 
Published: June 2021

Dairy protein ingestion is associated with satiety and the reduction of blood glucose (BG) in response to carbohydrate. The objective of this experiment was to examine the effect of whey protein on pre‐ and post‐meal glucose and insulin. Healthy normal weight adult males (n = 10) and females (n = 8) were provided whey protein (5, 10, 20 and 40 g) and hydrolyzed whey protein (10 g) in 300 ml of water or water alone 30 min prior to a pizza meal (12 kcal/kg body weight). Insulin and BG were measured by finger prick at baseline and at intervals pre‐and post‐meal for 170 min. Pre‐ (0‐30 min) and post‐ (30‐170 min) meal areas under the curve (AUCs) for BG and insulin were calculated. Sex (p <0.05) and whey protein (p <0.001) affected BG and insulin responses. Females had higher post‐meal BG and insulin AUCs than males (n =18, p < 0.05). Whey protein (10 g to 40 g) increased pre‐meal insulin and BG but reduced post‐meal BG and insulin AUCs (n = 18, p <0.05). The lower post‐meal BG AUC after whey protein was not associated with a higher insulin AUC compared with the control suggesting that whey protein treatments improved post‐meal insulin sensitivity. We concluded that the ingestion of whey protein prior to a meal resulted in lower post‐meal BG and insulin and reduced the amount of insulin required for the post‐meal glucose response.Grant Funding SourceNatural Sciences and Engineering Research Council of Canada (NSERC) and Kraft Ins.
The Impact of Egg Consumption on Heart Health using the NHANES III Follow‐up Survey
Authors: Scrafford Carolyn , Tran Nga , Barraj Leila 
Published: June 2021

The association between egg consumption and heart health was evaluated using the NHANES III (1988‐94) Follow‐up Survey and FFQ. Egg consumption was obtained from the 30‐day FFQ administered to participants within the NHANES III survey. Adults 17 years and older were followed for mortality from all causes. There were 366 deaths from CHD and 137 deaths due to stroke among 14,946 subjects included in the analysis. Estimated rate ratios (RR) of death from CHD or stroke associated with categories of egg consumption were estimated using Cox proportional hazards regression. Multivariate models show no increased risk of death from CHD with increased egg consumption (Males: RR = 1.40, 95% CI 0.83‐2.85; Females: RR = 0.93, 95% CI 0.30‐2.84). There was a slight reduction in risk of mortality from stroke in males among consumers of 1 to 6 eggs/week compared to <1 egg/week consumers (RR = 0.93, 95% CI 0.87 ‐ 0.996). Females showed a significant reduction in risk of stroke among consumers of 1 to 6 eggs/week (RR = 0.89, 95% CI 0.83 ‐ 0.95) and 1 or more egg/day (RR = 0.84, 95% CI 0.71 ‐ 0.99). These results showing no association between egg consumption and increased risk of death from CHD or stroke agree with the conclusions in previous studies using the NHANES I Follow‐up Survey, the Health Professionals and Nurses' Health Study.Funding sources: Egg Nutrition Center and NIH Training Grant T32HD046405.Grant Funding SourceT32HD046405