bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identification of regulatory mechanisms and RNA targets of human Pumilio proteins
Authors: VanEtten Jamie , Schagat Trista , Bhasi Ashwini , McEachin Richard , Goldstrohm Aaron 
Published: June 2021

Proper gene expression requires a balance between synthesis, modification, and degradation of mRNAs. PUF proteins are a conserved family of RNA binding proteins that regulate specific mRNAs to control many biological processes including development and proliferation. PUFs bind specific sequence elements in the 3′ UTRs of specific mRNAs via an RNA binding domain. PUFs in model organisms repress targets via deadenylation and degradation and/or direct inhibition of translation. The mechanisms by which human PUFs repress their mRNA targets as well as their physiological targets remain unclear. Humans have two related PUFs, PUM1 and PUM2. We found that human PUFs employ a conserved mechanism of repression via direct recruitment of the CCR4‐NOT deadenylase complex to target mRNAs, leading to translational inhibition and accelerated mRNA degradation. Further, PUMs could repress a non‐adenylated mRNA; therefore, PUMs exhibit a second deadenylation independent repression mechanism.Few specific mRNAs regulated by PUMs have been identified. To better ascertain the roles of human PUMs, we sought to identify mRNAs regulated by them. We depleted PUMs from human cells and measured changes in mRNA expression levels by RNA‐Seq. We identified more than of 200 PUM target RNAs meeting the following criteria: >;1.5‐fold change, >;1 PUM site, and FDR = 0.05. Our results begin to reveal PUM regulated pathways in human networks.University of Michigan internal grant
Conformational changes of the carbon‐fixing enzyme CODH/ACS revealed by electron microscopy
Authors: Thompson Samuel M. , Brignole Edward J. , Ragsdale Stephen W. , Drennan Catherine L. 
Published: June 2021

Carbon monoxide dehydrogenase/acetyl‐CoA synthase (CODH/ACS) is a 310 kDa bifunctional enzyme involved in the anaerobic fixation of atmospheric carbon (CO2) by the acetogenic bacterium Moorella thermoacetica. The CODH subunit reduces CO2 to CO, which transfers through a central hydrophobic tunnel to the active site of ACS. ACS contains a dinickel iron‐sulfur site where CO combines with a methyl group supplied by corrinoid iron‐sulfur protein (CFeSP) and coenzyme A (CoA). Conformational changes of ACS have been hypothesized as the structural mechanism regulating access of methylated‐CFeSP and CoA to the proximal nickel in the active site. However, the conformations of CODH/ACS that have been observed crystallographically are insufficient to accommodate methyltransfer from CFeSP to ACS. To examine the conformations of CODH/ACS we used single‐particle electron microscopy (EM). Because CODH/ACS contains O2 sensitive metallocofactors, we developed a method for preparing negatively stained EM specimens in an anaerobic chamber. The resulting structures of CODH/ACS reveal a dramatic hinge‐like opening of the ACS subunit that can accommodate methyl transfer from CFeSP to CODH/ACS and gives new insight into the catalytic mechanism of this environmentally relevant enzyme.This work is supported by funding from the NIH. Samuel Thompson is supported by the MIT Undergraduate Research Opportunities Program.
Effects of fetal alcohol exposure on zinc homeostasis in the newborn pulmonary alveolar macrophage
Authors: Konomi Juna , Brown Lou Ann 
Published: June 2021

Since zinc is essential for innate and adaptive immunity, zinc deficiency increases susceptibility to infection and magnifies existing infections. To examine the effects of in utero alcohol exposure, C57BL/6 female mice were fed the Lieber DeCarli liquid diet with 25% ethanol derived calories or with 25% maltose dextrin derived calories during preconception and pregnancy. At delivery, alveolar macrophages (AMs) from dams and pups were isolated and treated with FluoZin‐3AM to measure AM zinc and FITC‐labeled inactive Staph. aureus to measure phagocytosis. AMs from pregnant ethanol‐fed dams had lower intracellular zinc (p=0.007) and decreased phagocytic function (p<0.05), when compared to pregnant controls. AMs isolated from pups with fetal ethanol exposure displayed lower zinc levels (p=0.078) and AM function (p=0.041) than unexposed pups. Additionally, protein expression of the zinc transporter, ZnT1, was significantly lower in exposed pups than unexposed pups (p=0.003). Chronic alcohol exposure in adults or chronic in utero exposure decreases pulmonary AM function via decreased zinc availability which may contribute to an increased risk of respiratory infections.Funding: NIH/NIAAA P50 AA135757(LAB)
Secreted products from human adipose tissue decrease mitochondrial function of colon cancer cells
Authors: Schwartz Betty , Yehuda‐Shnaidman Einav , Nimri Lili 
Published: June 2021

Obesity is linked to increased risk of colon cancer, the third most common cancer. Adipose tissue (AT) from obese differs from AT of lean in their immunogenic profile, body fat distribution and metabolic profile. AT from obese release free fatty acids (FFAs), and many pro‐inflammatory chemokines, factors known to play a key role in regulating malignant transformation or cancer progression.Mitochondria are important organelles in cellular processes, including cellular respiration and energy expenditure, and programmed cell death (apoptosis). The metabolic networks that confer tumor cells oncogenic and metastatic properties, such as increased proliferation and the ability to avoid apoptosis, are still not well understood. Our goal in this study is to identify key molecular signals and interactions between adipocytes and colon cancer cells that may foster the genesis and growth of the latter.We tested the effect of 24 hours exposure of conditioned media (CM) isolated from AT of obese vs. non obese subjects on the metabolic profile of colon cancer cell lines. We found that CM from obese subjects led to a reduction of basal and maximal oxygen consumption rates and to changes in the gene expression of mitochondrial proteins, with no effect on glycolytic proteins. This metabolic approach may lead to a more complete picture relating obesity to colon cancer.
Influence of dietary protein upon the development of obesity, insulin resistance (IR) and energy metabolism (EM) in malnourished mice fed a high fat diet (HFD)
Authors: Camargo Rafael Ludemann , Batista Thiago Martins , Branco Renato Chaves Souto , Gonçalves Vanessa dos Santos , Boschero Antônio Carlos , Carneiro Everardo Magalhães 
Published: June 2021

AimTo determine the influence of the dietary protein content upon obesity, IR and EM in malnourished mice fed a normal‐protein (NP‐HFD) or a low‐protein HFD diet (LP‐HFD).MethodsWeaned male C57BL/6 mice were fed a protein‐restricted diet (6% protein ‐ R). After 6 weeks one group received a NP‐HFD (35% fat and 14% protein – RH) or LP‐HFD (35% fat and 6% protein – RRH).ResultsRH group had increased body weight (BW) (R=21.4±0.8; RH=30.7±1.0g) and perigonadal fat pad (R=1.6±0.08; RH=3.0±0.3%BW). RRH mice had lower BW (RRH=27.1±0.9g). RRH mice were protected from the hyperglycemia (R=65.8±3.1; RH=83.4±4.3; RRH=77.5±6.9mg/dL) and hyperinsulinemia (R=0.1±0.02; RH=0.3±0.03; RRH=0.1±0.03ng/mL) observed in RH mice. RH mice became glucose and insulin‐intolerant, which was improved in RRH mice (R=25.1±1.8; RH=40.7±3.2; RRH=29.9±3.1mg/dL.min/103/R=3.0±0.2; RH=4.3±0.3; RRH=3.3±0.3 mg/dL.min/103, respectively). Calorie intake was increased in HFD mice (R=10.1±0.79; RH=13.2±0.9; RRH=12.4±0.6kcal/day). During the dark period RH mice showed decreased energy expenditure which was prevented in RRH mice (R=136.7±4.0; RH=107.3±5.5; RRH=120.9±6.5 kcal/day/kg^0.75/103), despite the decreased ambulatory activity (R=24.3±2.8; RRH=16.2±0.9 arbitrary number/103) in this group.ConclusionRH mice became obese, hyperglycemic and IR, which was attenuated in RRH mice, possibly by regulation of the basal EM. Financial Support: FAPESP
Longitudinal evaluation of estimated calorie and protein intake in patients on ketogenic therapy for seizures
Authors: Lennon Dylan J , Allen Hannah J , Giurcanu Mihai C , Borum Peggy R 
Published: June 2021

BackgroundKetogenic therapy (KT) is prescribed as a ratio of grams of fat to carbohydrate plus protein. Prescribed Calories (Cals) and protein (Pro) describe total dietary energy recommendations (Recs) and should support each patient's nutritional state.ObjectivesTo compare Cal and Pro intake with prescribed Cal and Pro and with national Recs for healthy children.Methods24 hour diet records were entered into Nutrition Data System for Research. Cal (kcal/day) and Pro (g/day) intake was determined up to the first year of available data. Cal Recs were calculated from Estimated Energy Requirements for actual height, weight, age, gender, and physical activity. Pro Recs were calculated from DRIs for age and gender.ResultsDiet records were evaluated for intake as percent of prescribed Cals, Pro, recommended Cals, and DRI for Pro.

Intake of Prescribed (%)
Intake of Recommended (%)

Cal
Pro
Cal
Pro

(M=mean, SD=Stdev)

Month
n
M±SD
M±SD
M±SD
M±SD

1–3
16
97±8
99±8
95±17
124±22

4–6
15
98±17
99±17
93±15
120±24

7–9
14
96±10
99±10
91±18
119±16

10–12
14
95±5
97±5
87±16
113±14

ConclusionWhen monitored regularly, parameters of diet intake reflect adherence to KT diet prescription, which is altered based on nutritional needs that may differ from those expected for a population of healthy children.Supported in part by the National Institutes of Health (NIH) and National Center for Research Resources (NCRR) CTSA grant 1UL1RR029890
Reversal of Progress against Malnutrition in Egypt
Authors: Zaghloul Sahar 
Published: June 2021

ObjectiveTo assess trends and determinants of stunting, a monitoring indicator for economic and human development in Egypt, where marked economic and social changes have taken place.MethodsWHO global database, Food and Agriculture Organization Food balance sheet and World Bank indicators were used to describe trends in childhood growth, food availability and economic development.ResultsNeonatal, infant and under five mortality rates decreased between 1995 and 2010. Prematurity and congenital anomalies among children < 5 years of age increased (20% and 30% respectively). Stunting decreased from 35% to 20.3% between 1990 and 2003 and bounced back to 30.7% by 2010. Moreover, the onset of stunting is now earlier (< 6 month of age). Iron deficiency anemia increased from 30 to 60% and from 30 to 46% among preschool girls and boys respectively. Gross domestic product per capita increased and inflation rate decreased between 1990 and 2011. A reverse pattern occurred between 2003 and 2004.Daily calorie availability per capita did not change between 1995 and 2009 while calories from animal sources increased from 6.6% to 8.6%. Per capita protein from milk, eggs, poultry and pulses revealed a marked shortage compared to recommendations for 2–5 year old children.ConclusionStunting reflects the cumulative effects of inadequate food intake, poor health conditions and projects low levels of human development and economic growth.Congenital anomalies and prematurity may explain the early onset of stunting predicated by maternal poor health. Egypt, post Arab Spring, has a window of opportunity to reform its subsidy food and social programs to target improvement of maternal nutrition, strengthen breastfeeding and develop complementary feeding.
Effect of ketogenic therapy on seizure load score, medication load score, and response score in patients with intractable epilepsy
Authors: Allen Hannah J , Lennon Dylan J , Giurcanu Mihai C , Borum Peggy R 
Published: June 2021

BackgroundThe goal of ketogenic therapy (KT) for intractable epilepsy (IE) is to eliminate seizures and the need for medication.ObjectiveUse Seizure Load Score (SLS), Medication Load Score (MLS), and Response Score (RS) to determine response to KT of patients with IE.MethodsSeizure variables were ranked (1–5) to determine the Seizure Load (SL). Prescribed antiepileptic drug (AED) dose/kg was divided by the minimum recommended AED dose/kg to determine Medication Load (ML). SLS and MLS represent a % change in SL or ML from baseline (BL) at 100%. RS is the mean of SLS and MLS for specified time periods on KT. SLS, MLS, and RS were determined for patients on KT for the following time periods: 1–3, 3–6, and 6–12 months.ResultsPatients were stratified using SLS in the table below: Group 1 (SLS 50% better than BL), Group 2 (SLS better than BL, not 50% better), and Group 3 (SLS worse than BL). MLS and RS were determined for each group and time period on KT.ConclusionPatients can be stratified into response groups using SLS. MLS and RS provide additional information about the response to KT so that progress toward eliminating seizures and the need for medication can be assessed.Supported in part by the National Institutes of Health (NIH) and National Center for Research Resources (NCRR) CTSA grant 1UL1RR029890
Ionizing radiation differentially modulates Wnt pathway components through ILK in normal and tumor bone cell lineages
Authors: Naves Marcelo Andery , Nogueira‐Pedro Amanda , Peres Giovani B. , Giordani Adelmo , Segreto Helena , Teixeira Vicente P.C. 
Published: June 2021

Osteosarcoma (OS) frequently invades, mestastasizes, relapses and is characteristically radioresistent. Integrin‐linked kinase (ILK) modulates cell survival, death and radiosensibility. It can also interact with Wnt signaling pathway that is essential to skeletal development and may also play an important role in OS progression.Murine pre‐osteoblast (MC3T3‐E1), rat OS (UMR‐106) and human OS (MG63) lineages were irradiated using a 60Co radiation source (2 and 6 Gy for 24 e 72 hr). We analyzed cell viability (MTT assay), adhesion (crystal violet assay), apoptosis, ILK, βcatenin, p‐GSK‐3β and p‐Akt protein expression (flow cytometry) and gelatinolytic activity (zymography).Osteoblastic cells presented a substantial decrease in viability and cell adhesion. Apoptosis was reduced in MC3T3 groups irradiated with 6Gy dose. OS cells were less viable (except MG63 cells at 24 hr) and less adherent. Apoptosis increased in irradiated groups. ILK, p‐GSK‐3β, β‐catenin and p‐Akt expressions were significantly increased in all irradiated cell lineages, except in MC3T3 cells treated for 72 hr that showed a decrease in those protein expressions. Irradiation didn't modify cell gelatinolytic activity.Ionizing radiation differentially modulated the cellular biology aspects of osteoblasts and OS lineages. This was probably accomplished by modulation of canonical Wnt signaling pathway through ILK.
Angiotensin II induced skin fibrosis in mice is associated with vascular injury
Authors: Stawski Lukasz , Haines Paul , Trojanowska Maria 
Published: June 2021

We recently reported that Ang II induces skin fibrosis in mice (Stawski et al, 2012). The goal of this study was to further investigate the mechanisms involved in skin fibrosis induced by Ang II as a model for the pathogenic mechanisms of Scleroderma. Ang II was administered to mice for 7 and 14 days by subcutaneous osmotic pump. TUNEL and cleaved Caspase 3 staining showed increased number of apoptotic cells present in the vessels and in the connective tissue in Ang II treated mice. IHC staining showed increased number of Mmp12‐positive cells, including ECs in Ang II infused mice. MMP12 protein level was increased in Ang II treated human MVECs in a dose dependant manner. Pdgfrb‐positive cells were observed around the vessels in control mice, but were increased in all skin layers in Ang II mice. Real‐time PCR analysis showed a statistically significant increase in the levels of vascular injury markers: Angpt2 at day 7, Mmp12 and Thbs1 at day 14 and pericyte marker Adam12 at day 7 in the skin of Ang II infused mice.These observations together with the previously reported data strongly suggest that the Ang II model closely reproduces one of the key features of SSc ‐ vascular injury. Moreover, persistent defect of endothelial cells in this model may lead to development of a chronic fibrogenic environment resulting in activation of peri‐endothelial cells that leads to fibrosis.
Gene expression patterns through oral squamous cell carcinoma development
Authors: Oliveira‐Costa Joao Paulo , Carvalho Alex Fiorini , Silveira Giorgia Gobbi , Carraro Dirce Maria , Soares Fernando Augusto , Ribeiro‐Silva Alfredo 
Published: June 2021

Oral squamous cell carcinoma (OSCC) development is still a poorly understood phenomenon, in terms of gene expression profiles which might be involved in alterations leading to high invasiveness and aggressive behavior. Using 36 samples of OSCC cases, we performed cDNA and lincRNA microarrays, comprising whole human genome, in order to identify gene profiles with similar behavior throughout T1 to T4 tumor staging. We found 4 different gene expression profiles, either with a rise in expression levels, or decrease in expression levels, between T1, T2, T3 and T4 TNM staging. The four different gene expression profiles showed 58 differentially expressed genes, including an increased expression of RUNX family genes, and decreased expression of zinc finger proteins. Our study shows the existence of several genes with similar expression patterns during OSCC development, and also points to novel genes, which has not yet been implicated in oral carcinogenesis, providing new potential targets in oral cancer research.Sponsored by FAPESP (2010/08637–0 and 2010/08400–0)
Circulating 15‐hydroxyeicosatetraenoic acid levels are Elevated in a Mouse Model of Inflammatory disorders following High fat diet Administration.
Authors: Kaimi Nika , Vakili Ladan , Haghnegahdar Maryam , Farahmand foozhan , Sedigh farhad , Safar sheila , Meshkat arash , Niknam Daniel 
Published: June 2021

ObjectiveTo determine the plasma levels of the inflammatory marker 15‐hydroxyeicosatetraenoic acid in ApoE deficient mouse treated wit high fat diet.Introduction15‐hydroperoxyeicosatetraenoic acid (15‐HPETE) is a product of oxidation of arachidonic acid (C20:4). HPETEs are potent prooxidant molecules that can lead to stimulation of several metabolic pathways resulting in an inflammatory condition in many organs and systems. Fortunately our organism has evolved to use mechanisms to convert the potent 15‐HPETE to a lesser active molecule 15‐ hydroxyeicosatetraenoic acid, 15‐HETE. Still elevated levels of 15‐HETE are undesirable in most circumstances. We sought to determine the effect of a high fat diet in an animal model of inflammation namely ApoE deficient mouse. Using SepPak columns and a Q 4000 mass spectrometer, the plasma levels of 15‐HETE were determined. The data was analyzed using the software supplied by the manufacturer and statistical significance determined using ANOVA through Prism application.Resultsfeeding a high fat diet amplified the circulating levels of 15‐HETE (p = 0.021 vs. the control group) which in turn can activate pathways that produce inflammatory molecules.Conclusionreducing fat consumption can lead to reduced level of plasma oxidized fatty acids which in turn can help alleviate the inflammatory pressure.
Effect of acute hypoxia on phenotype and plasticity of M1 and M2 macrophages
Authors: Malyshev Igor , Kalish Sergey , Mantulin Nikita 
Published: June 2021

Federation Pathogenetic roles of hypoxia may be related with influences on immunity. The aim of study was to investigate the effect of hypoxia on the macrophage phenotype and plasticity in C57/BL mice, which have the pro‐inflammatory M1 macrophage phenotype, and in BALB/c mice, which have the anti‐inflammatory M2 one.MethodsHypoxia was produced in an altitude chamber. After hypoxia, macrophages were isolated from peritoneal lavage. NO production, inducible NO synthase content and cell shape were used as phenotype markers. To determine the phenotypic plasticity, we quantified the capability of macrophages for changing the phenotype to M1 and to M2.Results1) The response of macrophages to hypoxia has two successive phases, the immediate, anti‐inflammatory phase, and the delayed, pro‐inflammatory phase. These phases were more pronounced in Ñ57/BL6 M1 macrophages than in ÂÀLB/c M2 macrophages; 2) the effect of hypoxia on macrophage phenotypic plasticity depends on the genetically predetermined macrophage phenotype. Hypoxia increased the capability of macrophages for changing to the pro‐inflammatory M1 phenotype, while their capability for changing to the anti‐inflammatory M2 phenotype remained virtually unaffected.ConclusionEffects of hypoxia involve immune responses and depend on the genetically predetermined macrophage phenotype. This study was supported by the RFBR (12–04‐01191‐a)
Oral Infection augments the production of Inflammatory Markers of Atherogenesis.
Authors: Meshkat Arash , Hamidi Homa , Mobayen Shirin , Vakili Ladan , Karimi Nika , Navab Kaveh , Kalantari Ryan , Farazmand Maryam , Haghnegahdar Maryam 
Published: June 2021

ObjectiveTo determine if oral infection will result in an increase in markers of inflammation that are known to augment atherogenesis.IntroductionIt is known that patients with inflammation or infection of the oral cavity have a higher risk of acquiring susceptibility and being in a state of systemic inflammation increasing their risk of having vascular abnormalities. In the present study we sought to examine if infection of the oral cavity would result in an increase in the levels of markers of atherogenesis.MethodsFour month old female Apo E mice were treated with P. Gingivitis or with vehicle for 10 days. Plasma was prepared using heparinized capillary tubes and plasma separators and was cryopreserved. Circulating levels of interleukin 6 and 13‐HODE were determined using a commercially available ELISA kit and LC‐ESIMS/MS employing a Q4000 Quadrupole system. The data were analyzed using one way ANOVA taking advantage of GraphPad Prism application.ResultsIn mice receiving the P. Gingivitis treatment the levels of circulating IL‐6 and 13‐HODE were significantly higher (p=0.011 and p=0.031, respectively). There was no difference in the levels of 20‐ HETE which is known not to increase in inflammation.ConclusionThe present study indicates that oral infection with P. Gingivitis results in increases in the levels of circulating inflammatory molecules that are known to contribute to vascular dysfunction and increased vulnerability to atherogenic reactions.
Dynamic Model of Platelet Lifespan in Adult and Newborn Mice
Authors: Ait‐Oudhia Sihem , Mager Donald E. , Liu Zhi‐Jian , Veng‐Pedersen Peter , Sola‐Visner Martha 
Published: June 2021

ObjectiveTo develop a mathematical model of platelet survival (PLT‐S) in newborn and adult mice and identify factors controlling differences in PLT lifespan (PLT‐L) between these groups.MethodsPLT‐S profiles were obtained from 23 mice (16 newborn and 7 adult) by measuring biotinylate labeled (LBL) and total PLT count (PLTtot=LBL+non‐LBL) using flow cytometry. Non‐LBL endogenous PLT were described with three transit‐compartments and a zero‐order production rate. In newborns, PLT‐L model parameters were time‐dependent and approached the constant values in adults. Biotinylation efficiency was assumed complete, and LBL and PLTtot were simultaneously analyzed using population‐based modeling. Between‐animal variability (BAV) was estimated.ResultsThe final model well described LBL and PLTtot in all animals. Parameters were estimated with good precision. At time=0, PLT‐L was fitted at 4.92 and 3.76 days in newborn and adult mice. After 14 days, PLT‐L for all animals was constant at 3.76 days. PLT production was estimated to be similar between groups at 12.4 and 11.9 (103 cells/μL/h). BAV for PLT‐L parameters were below 30%.ConclusionNeonatal PLT‐L is greater than adults by 1 day, but PLT production rates are similar. Unlike traditional models assuming steady‐state, our dynamic PLT‐L model captured data well and allowed for accurate estimation of factors governing PLT counts. Grants HL046925 & GM 57980.