bluuebunny/crossref_metadata_2025_split huggingface dataset:
Structural Studies of ATP‐dependent chromatin remodeling
Authors: Leschziner Andres , Isaac Berith , Clapier Cedric R , Cairns Bradley R 
Published: June 2021

ATP‐dependent chromatin remodeling complexes (“remodelers”) are large macromolecular assemblies that use ATP hydrolysis to non‐covalently alter the structure of nucleosomes. Remodelers, conserved from yeast to humans, can be classified into different families based on the identity of their ATPase subunit. The diversity in their composition beyond the ATPase is reflected in the variety of outcomes of which they are capable both in vitro and in vivo: sliding of nucleosomes along DNA, ejection of histone dimers or octamers and histone dimer exchange.How do remodelers remodel chromatin? How are different products generated? Are they the result of fundamentally different mechanisms or rather of the relative fine‐tuning of a common one? We are taking a structural approach to addressing these questions, using three‐dimensional electron microscopy (3D EM), a technique well suited to the study of large, conformationally flexible complexes.Our model system is the remodeler RSC from S.cerevisiae, a ~ 1MDa 15‐subunit complex. We have obtained 3D reconstructions of RSC and have shown that it is conformationally flexible. We have proposed that a large cavity seen in the structure is the binding site for the nucleosome as it accounts for a number of biochemical observations. Our immediate goals are to map the location of RSC components as well as the actual binding site of the nucleosome in our reconstruction.
Biochemical characterization of the cellular biosynthesis and trafficking of Caspr2
Authors: Falivelli Giulia , Davide Comoletti , Dubi Noga , De Jaco Antonella , Wilson Jennifer , Taylor Palmer 
Published: June 2021

Recent genetic studies have linked mutations of Contactin‐associated Protein‐like 2 (Caspr2), a gene product of CNTNAP2, in neurodevelopmental conditions such as autism and epilepsy. Although little information is currently available for the role of this protein in the human brain, recent lines of evidence suggest that Caspr2 is a key molecule in cell‐cell interactions important for normal neuronal function and cortical development. Here, we investigate the processing and trafficking of Caspr2 wild type and several mutants using biochemical and cell biological approaches. Through analysis of glycosylation processing in HEK293 cells, we show that some of the mutations impair Caspr2’s trafficking to its cellular location. Furthermore, analyses of confocal immunofluorescence co‐localization with chaperons like calreticulin demonstrate that certain mutants have increased retention in the endoplasmic reticulum and retarded transport of newly synthesized proteins to the cell surface. These observations promise to yield critical insights into congenital processes that give rise brain abnormalities in neuronal connectivity.This work was supported by: USPHS Grant R37 GM‐18360 and NIEHS to PT, and Autism Speaks #2617 to DC
A novel vision to the process of ERpahgy in yeast
Authors: Liu Ang‐Yu , Ho Kung‐Hsien , Huang Wei‐Pang 
Published: June 2021

Under oxidative stresses, accumulation of misfolded protein in the endoplasmic reticulum (ER) activates downstream pathway ‐ the unfolded protein response (UPR) to protect cells. Autopahgy, on the other hand, is another protective response to cope with cellular stresses in eukaryotes, which involves in the degradation of cytosolic proteins and defective organelles. It is known that the ER‐selective autophagy, or ERphagy, will be induced during ER stresses and serve a protective role to maintain cell survival. However, the correlation of ERphagy with other type of autophagy is not clear. Here, we show that ERphagy is a selective process distinct from the cytoplasm‐to‐vacuole targeting (Cvt) pathway and the non‐selective macroautophagy. We found that under the dithiothreitol (DTT)‐induced ER stress, the ER‐containing autophagosomes (ERAs) would tend to accumulate in cytoplasm rather than fuse with vacuoles rapidly. However, soon after DTT is removed, ERAs will start to fuse with vacuoles and be degraded. We also discovered that the Cvt pathway would be partially inhibited at the vesicle forming stage during ERphagy, causing the delayed maturation phenotype of prApe1. Nevertheless, ERphagy seems to have limited effect on the process of the starvation–induced macroautophagy, and starvation treatment would not promote the clearance of accumulated ERAs in cytoplasm either. Taken these together, ERphagy as a selective process may compete with the Cvt pathway for utilizing the share of common regulatory machinery, but not preferable to the starvation‐induced macroautophagy.NSC96‐2311‐B‐002‐012‐MY3
Involvement of protein kinase Cα in invadopodia formation in Src‐3T3 cells
Authors: O'Neill Audrey Kathleen , Gallegos Lisa Leon , Newton Alexandra C. 
Published: June 2021

Dynamic structures termed podosomes or invadopodia take the form of actin puncta or rings and are involved in extracellular matrix remodeling, adhesion, and invasion. Though various protein kinase C (PKC) isoforms are known to affect these structures, the precise role of PKCα in signaling upstream of invadopodia in transformed cells remains unclear. We have begun to analyze the role of PKCα in NIH 3T3 fibroblasts transformed with active Src (Src‐3T3 cells). PKCα colocalizes with actin and the invadopodia marker Tks5 at rosettes, and inhibition of conventional PKC isoforms interferes with PKCα localization and rosette formation. The target of PKC that is responsible for invadopodia formation is unknown; however, one possible candidate is Discs Large 1 (DLG1), which we show is a substrate of PKC. DLG1 is present at numerous actin‐based structures including invadopodia and is involved in motility and invasion. Strikingly, coexpression of DLG1 and PKCα in COS‐7 epithelial cells causes formation of actin‐based rosettes (in a cPKC‐dependent manner), suggesting that phosphorylated DLG is sufficient for establishment of these structures.This work was supported by NIH P01 DK54441 and NIH GM43154.
Elg1 (Enhanced level of genome instability 1) has an essential role in early development and suppressing tumorigenesis
Authors: Sikdar Nilabja , Myung Kyungjae 
Published: June 2021

IntroductionHigh levels of chromosome rearrangements known as gross chromosomal rearrangements (GCRs) such as translocations, deletion of chromosome arm, interstitial deletions, inversions and gene amplification, have been reported in many cancers. Multiple pathways, such as S‐phase checkpoints, DNA replication, chromatin remodeling, and telomere maintenance suppress the GCR formation. Elg1 was discovered during the genome wide screening of yeast S. cerevisiae as a suppressor of GCR formation. Elg1 is a suppressor of genomic instability and functions in DNA repair in yeast and human.ObjectivesTo investigate whether the loss of Elg1 in mouse a in vivo model system causes any genomic disorder and null Elg1 MEF cells shows any Genomic instability phenotypes.ResultsAbsence of Elg1 in mice caused early embryonic lethality and zebra fish Elg1 MO embryos also has developmental problem suggesting Elg1 has an essential role during early development. This embryonic developmental defect rescued in absence of p53 in zebrafish and developed normal. The heterozygous mice developed tumors including sarcoma, carcinoma, and adenoma in various organs from 11 month after birth. The Elg1+/mMEFs and Elg1+/− chicken DT 40 cells show high level of DN A damage sensitivity as well as chromosomal instability in respond to DNA damage. High levels of genomic rearrangements were observed in tumors developed in the Elg1+/mmice by comparative genome hybridization. The microarray and pathway analysis of tumors from the Elg1 heterozygous mice showed the upregulation of Smad independent Tgf‐β pathway.ConclusionsTaken together, Elg1 has an essential role in early development that appears to have a close link to suppress genomic instability and ultimately tumorigenesis.
Epigenetic marks of nuclear‐encoded mitochondrial genes by DNA methylation
Authors: Takasugi Masaki , Hirabayashi Keiji , Yagi Shintaro , Shiota Kunio 
Published: June 2021

Mitochondria are semi‐self‐replicating organelles with it's intrinsic mitochondrial DNA (mtDNA). mtDNA is not under epigenetic regulation and, thus, unable to confer tissue or cell type dependent information in mammalian cells. However, of approximately 1,200 proteins in mitochondria, only 13 proteins are encoded by mtDNA. To investigate whether there are differences of epigenetic information of nuclear mitochondrial genes depending on tissues, we studied on tissue‐dependent and differentially methylated regions (T‐DMRs) in the promoters of nuclear mitochondrial genes. We analyzed methylation status of all known mitochondrial genes in mouse liver, brain, and heart. More than 200 mitochondrial genes were identified to have T‐DMRs which are specifically hypomethylated in one of the tissues. The mitochondrial genes with T‐DMRs were related to various mitochondrial functions. We also found that liver‐specific transcription factor binding site were enriched in the genes with liver‐hypomethylated T‐DMR. In conclusion, each tissue examined has inherent DNA methylation pattern of mitochondrial genes, and epigenetic regulation underlies the tissue‐dependent functions of mitochondria.This work was supported by grant from NIBIO.
Comparative analysis of genome‐scale metabolic models for Mycoplasma genitalium, Ureaplasma parvum, and Mycoplasma hominis reveals novel routes through the Pentose Phosphate Pathway
Authors: DeJongh Matthew , Poel Nathan B. , Best Aaron A. , Henry Christopher S. 
Published: June 2021

We have recently developed a high‐throughput computational pipeline for generating genome‐scale metabolic models. To test this pipeline, we have generated models for three mollicutes: Mycoplasma genitalium G‐37 (Mg), Ureaplasma parvum serovar 3 (Up), and Mycoplasma hominis (Mh). All three genomes lack an annotated transaldolase (TAL) gene, resulting in incomplete pentose phosphate pathways (PPP). However, all three organisms require production of phospho‐ribose‐diphosphate (PRPP), a key product of the PPP. To meet this demand, all three models predict novel routes through the PPP. The route predicted in the Mg and Up models relies on secondary activities of the phosphofructokinase (PFK) and fructose‐bisphosphate aldolase (FBA) enzymes to cope with the accumulation of sedoheptulose 7‐phosphate. This PPP bypass was recently discovered in an E. coli mutant lacking the TAL gene. Because Mh lacks a gene for PFK, the Mh model predicts a different route, reversing the activity of FBA and postulating the presence of Sedoheptulose‐1,7‐bisphosphatase. There is no genomic evidence for the presence of known forms of this enzyme in Mh; in this case, the model reveals the necessity of clarifying the pathway of PRPP production in Mh. Our study highlights the potential for comparative analysis of metabolic models to predict novel biochemistry and suggest testable hypotheses in prokaryotic metabolism.NSF MCB 0745100
Biomarker discovery by stable isotope labeling and quantitative proteomics
Authors: Filiou Michaela D. , Zhang Yaoyang , Teplytska Larysa , Reckow Stefan , Frank Elisabeth , Kessler Melanie S. , Maccarrone Giuseppina , Hambsch Boris , Landgraf Rainer , Turck Christoph W. 
Published: June 2021

In order to identify protein biomarkers for anxiety disorders we have compared the synaptosome proteomes of high (HAB), normal (NAB) and low (LAB) anxiety‐related behavior mice using 15N metabolic labeling and quantitative mass spectrometry.For accurate mass spectrometric‐based relative quantification, mice were metabolically labeled with a 15N‐enriched diet achieving 92% 15N incorporation in brain tissue. To detect phenotype‐related differences unlabeled HAB and LAB synaptosomes were compared with synaptosomes from 15N‐labeled NAB mice. We have found differentially expressed proteins between HAB and LAB synaptosomes involved in energy metabolism, transport and phosphorylation processes. Selected candidate biomarkers were validated with immunochemical and enzymatic assays. The identified biomarkers provide important information on pathways involved in disease mechanisms and shed light on anxiety pathophysiology.This work was supported by a BMBF QuantPro grant and the Max Planck Society.
Fluorescent intercalator displacement as a tool for RNA‐ligand discovery
Authors: Asare‐Okai Papa Nii , Chow Christine S 
Published: June 2021

Fluorescent intercalator displacement (FID) is a useful tool for identifying new nucleic‐acid‐binding ligands. The success of this method is based on the fact that it can be fashioned into a versatile high‐throughput assay, which can then be used to assess relative binding affinities of compounds to nucleic acids in a simple and efficient manner. FID is becoming an increasingly attractive method because it is a tag‐less approach; neither the nucleic acid nor the small molecule under investigation has to be modified. In this study, a modified FID method for screening RNA‐binding ligands was established, using 3‐methyl‐2‐((1‐(3‐(trimethylammonio)propyl)‐4‐quinolinylidene)methyl)benzothiazolium (TO‐PRO) as the fluorescent intercalator. Electrospray ionization mass spectrometry (ESI‐MS) was employed to investigate the FID mechanism. Our results provide molecular evidence that correlates a reduction in fluorescence intensity in the FID assay with displacement of the TO‐PRO dye molecule from structured RNA. The FID assay was then used to screen a variety of RNA‐binding ligands. With FID, it is possible to differentiate ligands that bind to a variety of RNA constructs from the ribosome and HIV (A‐site, h31, H69, and TAR) with moderate selectivity.This work is supported by the National Institute of Health (NIH)
Phosphate‐dependent physiological changes during short‐term dietary phosphorus deficiency with or without a dietary phosphorus binder
Authors: Bobeck Elizabeth A , Cook Mark E 
Published: June 2021

Patients with end‐stage renal failure are susceptible to increased plasma phosphate; hence, animal models to rapidly screen strategies to prevent dietary phosphate absorption are needed. The objective of this experiment was to evaluate a short‐term animal feeding model for estimating the effectiveness of a phosphate binder to limit dietary phosphate absorption. Nutrient‐adequate chicks (10 days of age) were either maintained on a phosphorus (P) adequate diet (0.70% total P, or 0.45% available P) or switched to a P deficient (0.35% total P) diet with or without 1% inclusion of the phosphate binder sevelamer hydrochloride (Sev) (n=15/trt). Body weight gain from 10–13d of age, plasma phosphate, and dry fat‐free tibiotarsus ash were determined on day 13. When chicks were placed on the P deficient diet, bone ash and plasma phosphate, but not body weight, were reduced (9% and 26%, respectively) within 3 days (p<0.05, main effect of P). The addition of Sev to the diet (main effect) had no effect on plasma phosphate or ash, but reduced body weight 22%. Since there was no interaction between P and Sev, these data would suggest, within the limits of this model, that Sev was unable to interfere with phosphate absorption even when animals were clearly deficient. These data also suggest body weight was reduced through a mechanism other than phosphate deficiency. This work was supported by the Wisconsin Alumni Research Foundation (WARF).Grant Funding Source: WARF
Vitamin D status of elderly Mayan residents of the western highlands of Guatemala
Authors: Bermudez Odilia I. , Sud Sohil , Montenegro‐Bethancourt Gabriela , Heaney Robert , Armas Laura , Solomons Noel W. 
Published: June 2021

IntroductionWhile the prevalence of various chronic diseases is known to be high among elderly Guatemalan Mayans, and research linking vitamin D (VitD) deficiency to such conditions continues to advance, little is known about vitD concentrations in older adults.ObjectivesTo assess 25(OH)D in Mayans, 60y or older, from the highland province of Quetzaltenango, Guatemala.MethodsBlood samples were collected and analyzed (for serum 25(OH)D concentrations) from 108 subjects (mean age=69y, 50% men, 78% rural).ResultsMean 25(OH)D values were 53±15 nmol/L. As ages rose, 25(OH)D declined (r=−0.28, p=0.004). Values for 25(OH)D were optimal (>80 nmol/L) in 4%, suboptimal (50–80 nmol/L) in 50%, and deficient (<50 nmol/L) in 46% of subjects. Men had higher VitD than women (58±17 vs. 48±12 nmol/L, p=0.001). VitD was higher although non‐significant in urban vs. rural elders (55±15 vs 47±12 nmol/L, p=0.23). Traditional dress allows 6 to 13% solar exposure of skin.ConclusionsDespite their optimal geographic location for adequate sunlight exposure, most elderly Guatemalan Mayans had suboptimal or deficient levels of VitD. Age, sex and skin exposure seemed to play a role on it.
Effect of peanut skin phenolics on pancreatic amylase activity and fructose‐mediated albumin glycation
Authors: Garner Pamela L. , Hargrove James L. , Hartle Diane K. , Pegg Ronald B , Greenspan Phillip 
Published: June 2021

Peanut skins, a by‐product of the peanut industry, have not been incorporated into the human food supply in the United States. This high protein product contains a high concentration of polyphenolics; the majority of the phenolics are proanthocyanidins or condensed tannins, but lower molecular weight phenolics (catechin and epicatechin) are also present. This present study was designed to examine the bioactivity of peanut skin phenolics on two biological processes relevant to the development of diabetes and its complications. Extracts of peanut skins inhibited porcine pancreatic α‐amylase by 90% at approximately 2 μg peanut skin phenolics/ml. The 90% level of inhibition of fructose‐mediated glycation of albumin was observed at approximately 20 μg peanut phenolics/ml. The difference in the degree of inhibition between these two biological processes may well be due to the differences in the mechanism of inhibition. Peanut skin proanthocyanidins probably inhibit α‐amylase activity by binding directly to the enzyme. However, since there is 10 mg albumin/ml in the protein glycation assay, the inhibition observed with peanut skins probably reflects its intrinsic antioxidant and/or metal‐ion chelating activity.Support provided by the State of Georgia Food Industry Partnership.
Effects of fermented soy food containing natural S‐equol on tail skin temperature in ovariectomized rat.
Authors: Yoneda Takeshi , Ueno Tomomi , Iwashita Soh , Uchiyama Shigeto 
Published: June 2021

Equol has been reported to have greater estrogenic activity, decreasing risks of osteoporosis, menopausal symptoms and hyperlipidemia in menopausal women. We succeeded in industrial production of a fermented soy food containing natural S‐equol (FSE) using equol‐producing lactic acid bacteria, Lactococcus 20–92. It was reported that ovariectomized (OVX) rat increase tail skin temperature (TST) like hot flashes in postmenopausal women. We examined the effects of FSE on TST in OVX rat, and compared with Premarin (conjugated estrogen drug).The study groups were consisted of sham, control, Premarin and FSE groups. Sham and control groups were administered vehicle, Premarin group were administered Premarin 6 mg/kg BW and FSE group were administered FSE as equol 12 mg/kg BW for 4 weeks. TST was evaluated at 3rd and 4th week after OVX operation. Uterine weight was measured at 4th week.TST was significantly higher in control group compared with sham group, and significantly lower in Premarin and FSE groups compared with control group at 3rd and 4th week. Premarin group significantly increased the uterine weight reduced after OVX operation, but FSE group did not.These results suggest that FSE is capable to improve hot flashes without effect on reproductive organs in postmenopausal women. Therefore, natural S‐equol might be expected to have activity as a selective estrogen receptor modulators.
Abrogation of TCDD Induced Epigenetic Silencing of BRCA‐1 by Resveratrol
Authors: Papoutsis Andreas , Romagnolo Donato , Selmin Ornella 
Published: June 2021

BRCA‐1 protein is involved in repair of DNA damage. Mutations of the BRCA‐1 gene confer a high risk of developing breast cancer. In sporadic breast cancers BRCA‐1 is silenced in the absence of mutations. 2,3,7,8 tetrachlorodibenzene(p)dioxin (TCDD) is a ligand of the aryl hydrocarbon receptor (AhR) that contributes to this etiology. Resveratrol is a dietary ligand of the AhR with potential protective effects. Activation of the AhR leads to its association with xenobiotic responsive elements (XRE) harbored in the BRCA‐1 promoter. The results of DNA binding studies in MCF‐7 breast cancer cells documented that TCDD induced the association of the AhR to the XRE which was reduced by cotreatment with resveratrol. Western blot analysis revealed that TCDD reduced BRCA‐1 protein expression and that this effect was counteracted by resveratrol. Epigenetic modifications investigated by chromatin immunoprecipitation assays (ChIP) indicated that TCDD facilitated, whereas resveratrol antagonized the recruitment of DNA methyltransferase 1 (DNMT1) and histone deaceytlase 1 (HDAC1). These findings support a model in which resveratrol prevents the assembly of a co‐repressive complex responsible for transcriptional inactivation of BRCA‐1. We are currently investigating changes in DNA methylation induced by TCDD at the BRCA‐1 promoter and the preventative effects of resveratrol.Susan G. Komen Breast Cancer for the Cure
A legume enriched diet facilitates weight loss and improves biomarkers of insulin resistance and inflammation
Authors: Zhang Zhiying , Lanza Elaine , Mitchell Diane , Mentor‐Marcel Roycelynn , Colburn Nancy , Hartman Terryl 
Published: June 2021

The LIFE Study tested the effects of a legume enriched, low‐glycemic index, weight maintenance diet on biomarkers of insulin resistance and inflammation among males at high risk for colorectal cancer (n=64). The study included an optional 4‐wk period (n=44) where men continued on the diet with consistent legume consumption but dietary guidance was provided and weight loss encouraged. Mean body weight and BMI significantly decreased by 4.4% (−4.0±0.4 S.E.M. kg) and 1.3 (±0.1 kg/m2), respectively. Levels of serum total cholesterol (TC), LDL‐C, TG, C‐peptide, and fasting plasma glucose, insulin, and C‐reactive protein were all significantly reduced. Compared to the weight maintenance diet, the weight loss diet was lower energy (−770.3 ± 397.0 S.D. kcal/d) and energy density (0.70 vs 1.15, P<0.001). Subjects consumed less total fat (31 vs 34% energy, P<0.001), saturated fat (10 vs 12%, P=0.007), and cholesterol (62.3 vs 70 mg/1000 kcal/d, P=0.0255). After energy adjustment they ate more vegetables (2.6 vs 2.2 serv./1000 kcal/d, P=0.0133) and legumes (1.9 vs 1.5 serv./1000 kcal/d, P=0.0009) during the weight loss phase, and consumed more total carotenoids (10759 vs 8799 μg/1000 kcal/d, P=0.0014), vitamin C (74.0 vs 61.8 mg/1000 kcal/d, P=0.0202), and folate (559.7 vs 444.1μg/1000 kcal/d, P<0.001). These results indicated that a high legume diet may facilitate weight loss and improve the aforementioned biomarkers.Grant Funding Source: National Institute of Health