bluuebunny/crossref_metadata_2025_split huggingface dataset:
The histone H2A N‐terminal tail regulates H2B monoubiquitylation and H3 K4 methylation via a novel trans tail pathway
Authors: Zheng Suting , Reese Joseph C 
Published: June 2021

The roles of the histone H3 and H4 N‐terminal tails in regulating chromatin structure and gene transcription have been extensively studied. However, very little is known about the functions of the H2A N‐terminal tail in transcription regulation. We analyzed multiple histone modifications associated with active transcription in the absence of the histone H2A tail. Our results reveal a novel trans‐tail regulation between the H2A tail and H2BK123 monoubiquitylation (H2BK123ub). Deletion of the H2A tail, or as little as four amino acids (a.a. 16–20), leads to a significant decrease in H2BK123ub, followed by a global reduction in H3K4 methylation by COMPASS. COMPASS complex purified from a H2A tail deletion strain lacks the Cps35 subunit, similar to the complex purified from a RAD6 deletion mutant. Rad6, which is responsible for ubiquitylating H2B K123, is still capable of being targeted to genes in the absence of the H2A tail, suggesting a type of post‐recruitment regulation. Deletion of the H2A tail causes a lag in the induction time of the GAL1 gene compared to wild type. Additionally, we show that deleting the Ubp8 and Ubp10 deubiquitylases not only restores the normal rate of induction of GAL1, but also restores H2BK123ub and H3K4me3 levels within the cell. Our analysis uncovers a role for the H2A tail in regulating transcription by maintaining a proper level of H2BK123 ubiquitylation and H3K4 methylation.This research was supported by funds from National Institutes of Health (GM58672) to J.C.R.
Identification and maturation of newly synthesized fungal histone H3
Authors: Waterborg Jakob Harm 
Published: June 2021

Reversed‐phase hplc of histone H3 in Ustilago maydis, Saccharomyces cerevisiae and Schizosaccharomyces pombe revealed the existence of a distinct form, ~5–20% of total histone H3 depending on strains and culture conditions, with delayed column elution, i.e. a more hydrophobic character. This form was more highly labeled by methionine than bulk H3, consistent with increased levels of lysine methylation and protein hydrophobicity. It does not contain non‐acetylated histone H3 and, in U.maydis, and has higher steady‐state acetylation levels than bulk H3. In asynchronous cultures, acetylation of replacement and of replication‐dependent H3 variants was more than 3‐, and 2‐fold higher, respectively, than bulk H3. Lysine pulse label incorporated exclusively into this form, identifying it as newly synthesized histone H3. Consistent with this, its abundance decreased in cycloheximide. Cell fractionation demonstrated that it does not represent a cytoplasmic pool. Lysine pulse‐chase labeling in U.maydis demonstrated a discrete chase into bulk, mature histone H3 with a half‐life of 30 min, complete within the 150 min cell doubling time. Western blotting and mass spectrometry are used to identify sites of acetylation and methylation in new H3 and changes during histone H3 maturation.Research supported by Missouri Life Sciences Research Board #13254
Non‐canonical inteins: Alternate mechanisms for protein splicing
Authors: Mills Kenneth V. , Reitter Julie N. , Duffee Lauren R. , York Daniel J. , Dorval Deirdre M. , Lewandowski Katherine T. 
Published: June 2021

Protein splicing involves the post‐translational excision of an intervening polypeptide (the intein) from flanking domains (the exteins), as well as ligation of the exteins. The first step of splicing is an amide‐ester rearrangement of the peptide bond that links the N‐terminal extein and intein. However, the intein that interrupts a putative phage terminase in C. thermocellum lacks an N‐terminal nucleophile and should not be able to promote this step. We show that this intein can splice, and have examined the influence of conserved residues on efficient splicing. The third step of splicing is cyclization of Asn coupled to peptide bond cleavage. However, the PolII intein from P. abyssi has a C‐terminal Gln and can still promote splicing. We compare the effects of C‐terminal Asn and Gln on splicing efficiency, as well as the influence of conserved residues on the catalysis of splicing.This material is based upon work supported by the National Science Foundation under Grant No. 0320824 and CAREER grant No. 0447647.
Site‐directed mutagenesis of a novel secondary alcohol dehydrogenase from M. luteus WIUJH20
Authors: Shoger Nicholas , Huang Jenq‐Kuen , Wen Lisa 
Published: June 2021

A novel secondary alcohol dehydrogenase (2o‐ADH) has been characterized in this lab previously. This 2o‐ADH is categorized as secondary alcohol dehydrogenase based on its biochemical reactions, but it belongs to NAD+‐dependent short‐chain L‐3‐hydroxyacyl‐CoA dehydrogenase (SCADH) based on amino acid sequence homology. In literatures, 2o‐ADH and SCADHs are distinguished in term of their primary structure and substrate specificities. SCADH has tight substrate specificity; it only catalyzes L‐3‐hydroxyacyl‐CoAs with various hydrocarbon chain‐length. In comparison the 2o‐ADH has low substrate specificity; it can catalyze hydroxy fatty acids with hydroxyl group in either D or L form on a number of carbon positions. However, the enzyme can not use hydroxyacyl‐CoA as a substrate. This 2o‐ADH is an excellent model system to study structure‐function relationship and determine what distinguishes their substrate specificity. We report here generation of single and double amino acid substitution mutants (D60S, A67K, and D60S + A67K) of 2o‐ADH in order to probe substrate functional group specificity.The research was supported in part by Western Illinois University Foundation.
A possible mechanism for the regulation of IRES‐mediated expression by eIF2A
Authors: Merrick William C. , Reineke Lucas C. , Cao Yu , Baus Diane 
Published: June 2021

We have shown that eIF2A has the capability of repressing expression from the URE2 IRES in vivo.1 Current studies are addressing how this down regulation might be achieved. There are now five pieces of evidence that allow for the postulation of a model for this regulation:
the eIF2A mRNA disappears within 2–3 minutes with essentially any stress
eIF2A protein may or may not show enhanced degradation depending on the stress
eEF1A binds to the URE2 IRES element
by pull down experiments, eEF1A and eIF2A reciprocally bind each other
it appears that the interaction between eEF1A and eIF2A is through the C‐terminal regions of each protein
In the model to be presented, it is anticipated that the binding of eEF1A to the URE2 IRES‐element facilitates the binding of eIF2A (and Met‐tRNA) and that the resulting complex at the level of the 80S ribosome is slow to convert to an elongating ribosome. With the down‐regulation of eIF2A protein and/or activity, eIF2 is presumed to direct Met‐tRNA binding in a more efficient manner allowing for a 10‐fold increase in expression.Preliminary evidence indicates that the regulation of IRES‐mediated expression is not exclusive to the URE2 IRES element but that eIF2A down‐regulates expression from several other IRES elements as well (identified by Gilbert et al.2).
Lipid rafts determine association of Orai1, STIM1 and the TRPC1 and TRPC6 proteins
Authors: ROSADO JUAN A , GALAN CARMEN , SALIDO GINES M 
Published: June 2021

Different laboratories have shown that proteins involved in Ca2+ entry are localized in discrete plasma membrane lipid rafts, cholesterol and sphingolipid‐enriched membrane domains that scaffold certain signaling molecules while excluding others. Lipid rafts have been shown to determine targeting of STIM1 clusters to endoplasmic reticulum‐plasma membrane junctions upon store depletion, facilitating the interaction of STIM1 with TRPC1 and the activation of store‐operated Ca2+ entry (SOCE). The aim of the study was to investigate the role of lipid rafts in SOCE and the association between Orai1, STIM1 and TRPCs. Treatment of HEK293 cells with thapsigargin (TG; 1 μM) results in association of Orai1 with STIM1, TRPC1 and TRPC6. TG‐induced association of these proteins was significantly attenuated by preincubation for 30 min with 10 mM methyl‐β‐cyclodextrin (CD; p<0.05; Student's t‐test), which depletes cells of cholesterol and disrupts lipid rafts domains, without altering the association of Orai1 with STIM1 or the TRPCs in non‐stimulated cells. Preincubation with CD significantly reduced TG‐induced Ca2+ entry by 20% (p<0.05) without having any effect on Ca2+ release. In conclusion, here we show that lipid raft domains are necessary for the formation of Ca2+ signalling complexes, involving Orai1, TRPCs and STIM1, which are important for SOCE.Supported by MEC grant BFI2007‐60104 and Junta de Extremadura.
AHR (Acute hypoxia responsive element) As a New Tool Detecting Acute Hypoxia
Authors: CILEK Mehmet Zeynel , HIROHATA Satoshi , HATIPOGLU Omer Faruk , NINOMIYA Yoshifumi 
Published: June 2021

ObjectivePreviously we reported an interesting gene that transiently induced in the endothelium in myocardial infarction which may be a hypoxia‐inducible gene expressed by endothelial cells. Its expression was limited to a few hours’ hypoxia. We tested if this switch element (we named this sequence as AHR (Acute hypoxia responsive element) for this induction can be used for detecting acute hypoxia.MethodsWe prepared several different constructs with different length of AHR promoter then performed luciferase assay in hypoxic cells. We identified the responsible AHR activated by acute hypoxia. We made green fluorescence protein (GFP) expressing construct (AHR‐GFP) under the control of AHR. We transfected AHR‐GFP construct into human umbilical vein endothelial cells (HUVECs), and examined GFP production under 30 minutes, 1, 3, 6, 12 or 24 hours of hypoxia respectively. After incubation, cells were fixed with 4% paraformaldehyde (PFA) and observed under the fluorescence microscope.ResultsWhen AHR‐GFP –transfected HUVEC was cultured in normoxic condition, GFP was very slightly observed. In contrast to this, the number of GFP‐positive HUVEC increased at 3h (~10‐fold compared to normoxia) under hypoxic stimulation. The induction of AHR under hypoxia returned to the normoxic level at 24h of hypoxia.ConclusionsAHR works under acute hypoxia and may be used as a specific tool for detecting acute hypoxia.
The effect of bee venom against glutamate toxicity in microglial cells
Authors: Lee Sang Min , Yang Eun Jin 
Published: June 2021

Bee venom (BV) extracted from honey bee has been used in a traditional Korean medical therapy. Several research groups demonstrated the anti‐inflammation effects of BV in immune‐related diseases in vivo and in vitro.Glutamate is predominant excitatory neurotransmitter in the central nervous system (CNS). Prolonged exposure of glutamate receptors to high or persistently increased concentrations of glutamate leads the cell death. In addition, changes in glutamate release, uptake and activity of glutamate transporters have been reported in many neurodegenerative diseases such as Huntington¡s disease, Parkinsons¡s disease, Alzheimer¡s disease, and amyotrophic lateral sclerosis (ALS). However, BV is not clear whether BV has a protective effect against glutamate‐mediated cell death. To assess whether BV affords protection against glutamate mediated cell death, we examined the cell viability and signal transduction regarding cell survival with glutamate‐treated microglial cells in either the presence or absence of BV. First of all, we confirmed glutamatergic toxicity on microglial cells. Then, we found that BV had an inhibitory effect against the glutamatergic toxicity. As a result of it, our results showed that BV inhibited significantly the cell toxicity against glutamate and activation of proteins such as Akt, JNK, Erk and p38 were altered by exposure of glutamate time dependent manner.
Nuclear Pore Complex [NPC] and Epigenetic Regulator Proteins Share Conserved Domains for Interaction with Functional Non‐Coding ncRNA
Authors: Wissler Joerg E. 
Published: June 2021

OBJECTIVEFunctional small hairpin ncRNA may address defined homologous helix‐nucleating domains shared in epigenetic regulator proteins entangled in growth, metabolic syndromes, vascular, cancer, epi‐ and genetic information indexing of the epigenome. Whether they may also participate in nucleocytoplasmic transport was investigated by searching conserved interaction domains in nuclear [epigenome] and NPC proteins [Mol. Biol. Cell 20 Suppl, 534, 2009; Ann. N.Y. Acad. Sci. 1137: 316–342, 2008].RESULTSEdited, modified, redox‐ and metalloregulated functional small hairpin ncRNA [<200n] as bioaptamers in RNP complexes were obtained from transcriptional RNA output of cells activated by extrinsic [environmental] factors. Several components of chromatin formation modulation and NPC were found having conserved homologous helix‐nucleating structural [proteomic] domains in terms of K/RxxxH [K/R3H], i.e.‐t/s/xK/R/q/n/hxxxH/y/n/q/e/d/r/kx7‐9h/xx7–9h/xx5–20K/R/q/n/e/h‐with accessory canonical basic [R/K]n, R/K‐zipper, SR/K/RS, EF‐hand and/or HxxxH/y/n/q segments. They include nucleosomal assembly, histone deacetylase, DNA‐C5‐methyltransferase, sirtuin, hypoxia‐inducible factor, nuclear pore complex, nucleoporin, importin, exportin and nuclear transport factor protein families. By redox‐ and metalloregulated multivalent interaction with molecular imprints in protein components, such ncRNA may display functions in NPC, its transfer or shuttle factors in synergism with indexing of the nuclear epigenome.CONCLUSIONSThe results suggest that in the “terra incognita” of molecular dynamics of NPC and orchestration with genomic and nucleocytoplasmic processes, new functions associated with epigenetic imprinting and inheritance await discovery.
Poly(A)‐specific ribonuclease (PARN): Molecular mechanisms of mRNA cap and poly(A) tail recognition
Authors: Virtanen Anders , Henriksson Niklas , Nilsson Per , Wu Mousheng , Song Haiwei 
Published: June 2021

PARN is a homodimeric, processive, and cap‐interacting 3′ exoribonuclease that degrades mRNA poly(A) tails. To reveal mechanisms by which PARN recognizes cap and poly(A) we have performed a structural and functional study of PARN. A crystal structure and subsequent mutational analysis revealed that amino acid residues involved in cap recognition were crucial for cap‐stimulated deadenylation activity and poly(A) hydrolysis. A detailed kinetic analysis showed that PARN harbors specificity for adenosine recognition in its active site. We propose that two binding pockets, which interact with the nucleotides surrounding the scissile bond, play a pivotal role in providing specificity towards adenosine recognition. Interestingly, the binding pocket required for recognition of the penultimate adenosine residue is also required for cap binding and efficient hydrolysis. We conclude that the cap‐binding site partially overlaps with the active site of PARN.This work was supported by the Swedish Research Council, the Linneus Support from the Swedish Research Council to the Uppsala RNA Research Centre and the Lennanders Foundation at Uppsala University. H.S. acknowledges financial support from the Biomedical Research Council of A*STAR (Agency for Science, Technology, and Research) in Singapore.
How HIV‐1 Rev Gets its Groove On
Authors:   Galileo SMART team, Colton Shannon , Herman Tim , Giles Kurt , Koo Ben , Jeske Sabine , Fernandes Jason , DeBella Stan 
Published: June 2021

HIV‐1 Rev is an essential viral regulatory protein. Rev is responsible for nuclear export of partially and unspliced viral RNAs; these viral RNAs are required for the production of essential late‐stage viral proteins such as Gag and Env, and also serve as genomic RNAs for virion packaging. Rev's structure is key to understanding its function. Rev has several major domains, including an arginine rich RNA binding domain. This domain forms a marginally stable alpha helix that binds a major groove in the viral RNA. We have built physical 3D models of Rev as well as a portion of the HIV‐1 RNA that Rev recognizes, the Rev Response Element (RRE). These models allow us to visually illustrate the details of this important RNA‐protein interaction. A better understanding this interaction could allow for novel anti‐HIV therapies that target this essential interaction.The SMART (Students Modeling A Research Topic) program was established by the Center of BioMolecular Modeling at the Milwaukee School of Engineering and involves partnerships between university researchers and local high schools. This work is funded by NIH‐NCRR‐SEPA and HHMI.
Association Between 5‐HT Receptor Gene Promoter Polymorphism and Obesity
Authors: Hemimi Neveen Salah El Din , El Salam Mona Mohamed Abd , Khalil Marwa Mahmoud , Ahmad Heba Mohamed Galal El Din 
Published: June 2021

BackgroundSerotonin has an integral role in appetite control, sexual and social behaviour, and stress response and these all form part of the individual susceptibility to obesity. AA genotype of 5‐HT2A gene promoter polymorphism was associated with increase receptor expression and binding.AimTo study the relation between the G1438A polymorphism of the 5‐HT2A gene and the susceptibility to obesity.Material& Method69 individuals with BMI < 25 Kg/m2 and 120 individuals with BMI ≥ 25 Kg/m2 were enrolled in the study. The G1438A polymorphism of the 5‐HT2A gene was detected by restriction fragment length polymorphism polymerase chain reaction (RFLP‐PCR) of peripheral blood DNA samples. Analysis of data was done by using SPSS program.ResultsGenotype frequencies for AA and GA& GG were 25% and 75% respectively in the group with BMI ≥ 25 Kg/m2 compared to 52.2% and 47.8% in the normal BMI group. Carriers of GA& GG genotype were at a significant high risk of developing obesity when compared with carrier of AA genotype (OR=3.3, 95%CI= 1.7–6.1). Moreover, the mean energy intake per day was significantly increased among carriers of GA&GG genotype when compared to AA genotype (p< 0.05).ConclusionG allele was a risk factor for obesity.Source of Fund: Ain Shams University.
ANTIBACTERIAL ACTIVITY OF Co(II) COMPLEXES WITH SOME HETEROCYCLIC COMPOUNDS
Authors: Govori Sevdije R , Ajvazi Njomza , Buza Aida , Haziri Arben , Rifati Arleta 
Published: June 2021

The antibacterial activity of cobalt (II) complexes with some heterocyclic derivatives were investigated in vitro against Staphylococcus aureus, Escherichia coli and Enterochoaco. Applying the disc method we mesasured diameters of the inhibition zone around disc which are previously wetted with N,N‐DMF solution of compounds (1 – 5) in concentration 1mg/l, 0.5mg/l and 0.1mg/l.Comparing the inhibitory activities of the tested complexes, it was found that these complexes were more active than heterocyclic compounds (A – E).
Effect of Phospholipids on the Stability and Absorption of Açaí Anthocyanins
Authors: Cardona Jorge Alfredo , Talcott Stephen T , Mertens‐Talcott Susanne U 
Published: June 2021

The purposes of this study were to determine the efficacy of phospholipids as aiding agents in the absorption of anthocyanins isolated from açaí on a monolayer from human Caco‐2 colon cancer cells and to evaluate their effect on anthocyanin stability. Transepithelial electrical resistance (TEER) was monitored to check cell confluence and integrity. Cells remained in culture for 18–21 days to guarantee enterocytic cell differentiation and P‐gp expression. Anthocyanin content was determined spectrophotometrically and by HPLC‐MS analysis. Açaí contained two anthocyanins, cyanindin‐3‐glucoside (C3G) and cyanidin‐3‐rutinoside (C3R). C3G and C3R alone were poorly absorbed (1.6% and 1.7% respectively). The presence of phospholipids (5000 mg/kg) significantly increased the absorption of C3G and C3R (5.66% and 10.2% respectively). Color degradation followed first‐order kinetics. Anthocyanin degradation was similar within treatments at every temperature illustrating that the presence of phospholipids did not affect anthocyanins degradation kinetics. In contrast, effects of temperature were evident. Higher temperatures resulted in higher losses of anthocyanins and reduced shelf life of the samples. Refrigeration (5 °C) resulted in an average half life of 97.7 days whereas higher temperatures (25 °C and 37 °C) resulted in reductions of 43% and 59% in half life respectively.Grant Funding Source: ASN
Antioxidants induced cytokine alterations indicative of a better prognosis after ACL surgery
Authors: Barker Tyler , Martins Thomas B. , Hill Harry R. , Kjeldsberg Carl R. , Trawick Roy H. , Leonard Scott W. , Walker James A. , Traber Maret G. 
Published: June 2021

Following anterior cruciate ligament (ACL) surgery, muscle weakness is commonly observed and may be potentiated by pro‐inflammatory cytokines. Because vitamins E and C (AO) reportedly modulate cytokines, the purpose of this study was to evaluate the influence of AO supplements on cytokines pre‐ and post‐ACL surgery. A randomized, double‐blind, placebo‐controlled study was conducted in men undergoing ACL surgery, who were supplemented with AO or placebos (PL; n = 10/group). Supplementation began ~2‐w prior to and concluded 3‐mo after surgery. Fasting plasma AO and cytokines were measured. IL‐6, IL‐10, and IL‐2rα increased (P < 0.05) and PGF2α decreased (P < 0.05) following ACL surgery and during NSAID medication. AO supplementation ameliorated (P < 0.05) the increase in IL‐10. Thus, despite standard of care NSAID medication, a systemic cytokine response occurred post‐surgery, and AO protected against the increase in IL‐10. By 3‐mo post‐surgery and after the discontinuation of NSAIDs, IL‐1β increased (P < 0.05), but for a given increase in IL‐1β, AO potentiated the increase (P < 0.05) in IL‐4. The AO potentiated increase in IL‐4 may limit the systemic release of IL‐1β and protect against the adverse sequelae of inflammatory responses. In conclusion, AO supplementation induced immunological alterations after ACL surgery indicative of a better prognosis.Source of support: USANA Health Sciences, Inc., SLC, UT.
Association of dietary and serum folate in a cohort of asymptomatic HIV+ patients in Botswana
Authors: Marlink Richard , Bussmann Hermann , Masmouie Hoda , Burns Patricia J , Tsalaile Lesedi , Raesi Mpho , Makhema Joseph , Campa Adriana , Baum Marianna K 
Published: June 2021

ObjectiveDeficiency of folate is common in HIV infection and is associated with increased risk for cardiovascular disease, hypertension and anemia. We determined the variables associated with risk for folate deficiency in HIV infected antiretroviral naïve HIV infected adults in Botswana.MethodsAfter consenting, 140 HIV+ adults were administered medical, physical activity and 24‐hour recall questionnaires. Clinical exams were performed. Blood was drawn for CD4 cell count, viral load and serum folate levels.ResultsThe mean age was 34.0±8.21, 48% (n=67) were male and 15.2% had low serum folate (<5 ng/mL). Serum folate was significantly correlated with physical activity (r=0.244, p=0.011), BMI (r=−0.255, p=0.004), and female gender (r=−0.560, p<0.001). CD4 cell count and viral load were not significantly related to serum folate. Total folate intake was predictive of serum folate levels (β= 2.476, p=0.015) in a dose‐response relationship after controlling for physical activity, smoking, hypertension and gender.ConclusionFolate intake is reflected in serum levels in a dose response manner and is a good marker of folate intake from diet and from supplements in HIV+ adults. Serum folate levels may be used as an index of adherence in micronutrient supplementation trials that contain folate.Funded by NIDA