bluuebunny/crossref_metadata_2025_split huggingface dataset:
Characterization of the Epigenomic Status of the US OEF/OIF War Veterans: A Pilot Clinical Study
Authors: Chakraborty Nabarun , Muhie Seid , Yang Ruoting , Gautam Aarti , Donohue Duncan , Daigel Bernie , Zhang Yuanyang , Amara Duna Abu , Flory Jannie , Yehuda Rachel , Doyle Frank , Hammamieh Rasha , Marmar Charles , Jett Marti 
Published: November 2023

Management of post‐traumatic stress disorder (PTSD) is complicated by the overlapping symptoms of its co morbidities and the diagnostic reliance on self‐report and time consuming psychological evaluation. A more comprehensive understanding of molecular pathophysiology of PTSD could facilitate an unbiased biomarker‐driven next‐generation intervention strategy. Herein, we cast light on the epigenomic consequences of combat elicited PTSD. In this study, hypermethylated genes were investigated as to the implications for behavior, immune response, nervous system development, and relevant PTSD co‐morbidities such as cardiac health and diabetes.52 PTSD‐positive male veterans of US Operation Iraqi Freedom (OIF) and Operation Enduring Freedom (OEF) were matched to 52 controls by age and ethnicity. PTSD diagnosis was determined by a clinician‐administered PTSD scale (CAPS), score >40, while the control group demonstrated a CAPS <10. Methylation status of DNA extracted from whole blood was assayed using high density arrays (Agilent, Inc.). 5,000 probes were statistically differentially methylated (FDR < 0.1), representing approximately 3,600 unique genes.Chromosome 4 and 18 imprints a significantly large portion of the methylated probes, including those which control emotional and cognition process, and glucocorticoid deficiency. Interestingly, a significant number of genes facilitating telomere maintenance and insulin reception were hypermethylated at both promoter and gene body sites; therefore the DNA methylation status in these genes could be prevailing. Nearly 85% of the differentially methylatedprobes were hypermethylated in PTSD patients. The majority of these probes encode the candidate proteins responsible for transcription regulation and enzymaticactions. Genes involved in memory consolidation, emotion/aggressive behavior, and perturbed circadian rhythm were preferentially hypermethylated. PTSD epigenetically perturbed both the cellular and humoral immune system; in addition the morphologies of two brain regions known to control PTSD symptoms, namely cerebral cortex and hippocampus were perturbed. Genes involved in several PTSD comorbidities, such as cardiomyopathy and poor insulin management, were also hypermethylated. Integration of the epigenomic observations with other omics outcomes is underway, as well as validation of these findings in an independent cohort.
Structural And Functional Analysis Of Acetylcholinesterase Complexes With “In Situ Click‐Chemistry” Inhibitors
Authors: MARCHOT Pascale , SHARPLESS K. Barry , TAYLOR Palmer , BOURNE Yves 
Published: November 2023

Ligand binding sites on acetylcholinesterase (AChE) comprise the active center, buried at the base of a deep and narrow gorge lined by aromatic residues, and the peripheral anionic site, located at the gorge entry. These features propelled AChE as an initial reaction vessel suited for in situ click‐chemistry synthesis of high‐affinity syn‐TZ2PA6 and TZ2PA5 inhibitors, forming a central syn‐triazole upon cycloaddition within the gorge from alkyne and azide reactants bound to the active site and peripheral site, respectively [1,2]. Subsequent crystallographic analyses of mouse AChE or its Tyr337Ala mutant in complexes with the syn‐and anti‐TZ2PA6 regioisomers demonstrated that association of the syn product is accompanied by distinctive side chain positions, freezing‐in‐frame a conformation distinct from an unbound state or an anti complex [3,4]. To correlate the inhibitor dimensions with reactivity and explore whether cycloaddition can occur in a crystalline template, we developed crystal‐soaking procedures and solved structures of AChE complexes with the two TZ2PA5 regioisomers and their TZ2 and PA5 precursors [5]. These new structures, complementary to those of the preformed TZ2PP6 complexes, point to yet undescribed motions in the active site and at the gorge mouth associated with TZ2 binding and reveal coordinated side chain motions that guide the enzyme toward a state favoring syn‐triazole formation. We will present the rationale of the work, describe those molecular determinants that dictate, in a rate‐limiting step, proper alignment of the azide and alkyne reactants to form the triazole product within the gorge, and compare our data with those from other in situ click chemistry studies.Support or Funding InformationSupported by grants RO‐1‐GM18360‐41 and UO1‐NS 058046 (to PT) and by CNRS grants “Action CNRS/USA” and “PICS” (to PM and YB)
Evolution of Phospholipases A2 in Catalysis and Allosteric Regulation by Membranes
Authors: Mouchlis Varnavas D , McCammon J. Andrew , Dennis Edward A 
Published: November 2023

Defining the molecular details and consequences of the association of water‐soluble proteins with membranes is fundamental to understanding protein–lipid interactions and membrane functioning.1 Phospholipase A2 (PLA2) enzymes, which catalyze the hydrolysis of phospholipid substrates that comprise the membrane bilayer, provide the ideal system for studying protein–lipidinteractions.2 Our current study focuses on understanding the catalyticcycle of two different recombinant human intracellular PLA2s: the GIVA cPLA2 and GVIA iPLA2, which are responsible forarachidonic acid release for eicosanoid signaling and for membrane phospholipidre modeling, respectively. Molecular dynamics (MD) simulations, guided by hydrogen/deuterium exchange mass spectrometric (DXMS)3 experimental data, were used to show that the channel to the active sites of these PLA2s are opened upon all ostericinteraction of the enzyme surface with the membrane to facilitate entry of the substrate phospholipid. This constitutes the first detailed study describing the binding and the interaction mechanism of intracellular PLA2s with the membrane bilayer as well as how they bind a single phospholipid molecule in the catalytic site. These enzymes are implicated in many diseases, and understanding their detailed mechanism of action will aid in the discovery of new therapeutics.Support or Funding InformationAcknowledgementsThis work was supportedby NIH Grant GM20501
Coevolution and Disease‐Causing Mutations in Glucose‐6‐Phosphate Dehydrogenase (G6PD)
Authors: Cunningham Anna , Colavin Alexandre , Huang KC , Mochly‐Rosen Daria 
Published: November 2023

Glucose‐6‐phosphate dehydrogenase (G6PD) is essential for protection against oxidative stress. Over 160 different missense mutations in G6PD reduce the activity and/or stability of the enzyme, causing G6PD deficiency, which results in anemia and neonatal jaundice, and contributes to many other diseases. Severity of G6PD deficiency is categorized into four clinical classes based on G6PD activity in patient blood samples; however, the structural location and class of a mutation do not fully predict its biochemical effects. The goal of this work is to further understand how mutations affect different parameters of G6PD function.Towards this goal, sequence coevolution analysis (SCA) was used to identify coevolving groups (sectors) of G6PD residues. Previous applications of SCA to protein domains have identified coevolving sectors that control distinct parameters of protein function. Application of a novel SCA algorithm to G6PD identified several sectors that were enriched in disease‐causing mutations. Overall, the sectors select for known G6PD‐deficiency‐causing mutations and exclude predicted non‐phenotypic mutations.G6PD mutants from several sectors, as well as mutants not associated with any sectors, were biochemically characterized. Principal component analysis of the biochemical data showed that the mutants do not cluster by sector, but do cluster by clinical classification. We conclude that coevolution may be a good predictor of whether a G6PD mutation causes G6PD deficiency, but coevolving sectors do not correlate to specific biochemical parameters of G6PD.Support or Funding InformationNSF Graduate Research Fellowship ProgramStanford Interdisciplinary Graduate Fellowship (SIGF)Stanford Child Health Research Institute (CHRI)NIH
Understanding the Ability of Heavily Contaminated Soil to Sustain Enzyme Function
Authors: LeRoux Danielle 
Published: November 2023

Liberty State Park (LSP) in Jersey City, NJ was a flourishing industrial rail yard and as a result has various types of contamination, particularly high heavy metal concentrations. Now, the park sustains a flourishing and diverse ecosystem. LSP has successfully produced the enzymes that catalyze ecological reactions necessary for forest growth. In fact, preliminary data show that the site with the highest heavy metal concentrations at LSP has the highest enzyme activity compared to sites with little to no heavy metal contamination. This presents an interesting anomaly because research typically shows that high concentrations of heavy metals are detrimental to the health of organisms.This project aims to understand the unprecedented ability of the contaminated soil to foster growth. Three locations were used in our analysis of these characteristics: LSP 14/16 which has the highest concentrations of metals, LSP 43 which has intermediate levels, and Hutcheson Memorial Forest (HMF), located in Franklin Township, NJ was used as the control site with no history of heavy metal contamination. All three sites have the same natural succession.Properties of the soil such as the exchangeable metal concentrations, phosphatase activity, percent organic matter, and surface area were measured. These characteristics were analyzed with respect to distinct particle sizes: coarse sand (425 – 2000 μm), fine sand (75 – 425 μm), silt (2 – 75 μm) and clay (< 2 μm). Exchangeable metals are the metals that are loosely bound to the soil and the concentrations are determined with an ICP‐MS. Organic matter is essential for the health and productivity of the soil. It is measured by loss‐on‐ignition. Surface area is typically directly correlated with other characteristics and is measured using a particle size analyzer.Exchangeable metals from this experiment show similar values to previous measurements, but they have decreased over the period of several years. The organic matter is at healthy levels in HMF but is nearly eight times as much in LSP. Finally, the surface area of the soil in HMF is larger than the surface area of the soil in LSP. The results have led us to conclude that the surface area does not play a role in the anomaly and more experiments need to be conducted on the organic matter.
Regulation of Tyrosine Hydroxylase Studied by Fluorescence Anistotropy and Fluorescent Resonance Energy Transfer
Authors: Daubner Susan Colette , Teran Leonel , Rodriguez Augustin , Cruz Eduardo 
Published: November 2023

Tyrosine hydroxylase (TyrH) is regulated by feedback inhibition and activation by multiple phosphorylation at three different serine residues in its N‐terminal regulatory (R) domain. TyrH phosphorylated at serine19 and 40 may be stabilized by 14‐3‐3 protein binding. We have cloned the rat brain 14‐3‐3 proteins, and have variants of TyrH that allow cAMP‐dependent protein kinase (PKA) to phosphorylate both serine19 and ‐40 residues (TyrHA17R) or just serine19 (TyrHA17R‐S40A). Wild‐type TyrH is phosphorylated only at serine40 by PKA. These variants are fully active and can be fully phosphorylated at the targeted serine residues using PKA. Using fluorescence anisotropy we are studying the interaction between several of the seven isoforms of 14‐3‐3 and TyrH in its different phosphorylation states. After tagging the 14‐3‐3 proteins with DANSYL‐Cl, titration is performed with unlabeled, once‐phosphorylated, and doubly phosphorylated TyrH. This protocol gives increases in anisotropy as complexation occurs. Preliminary experiments including dansylated zeta 14‐3‐3 and TyrHA17RpS19pS40 gave a saturation curve with a Kd value of 3 μM.To study the movements of the N‐terminal regulatory (R) domain of TyrH we are using Fluorescent Resonance Energy Transfer, FRET, to measure changing distances between the catalytic (C) and R domains. A TyrH variant with all but one tryptophan mutated to phenylalanine, leaving tryptophan233 in the C domain, and all the three exposed cysteine residues mutated to alanine, has been made and called TyrHW2FC3A. Using TyrHW2FC3A as template, a series of variants was made with new cysteine residues in the N‐terminus (Q10C, E20C, T30C, I35C, and A45C). These cysteine residues are tagged with IAEDANS, and energy transfer between tryptophan233 and the new cysteines is measured. These variants have been overexpressed and purified and are active. KM values for tetrahydropterin for the TyrHE20C‐, TyrHT30C‐, and TyrHI35CW2FC3A variants are 60, 90, and 30 μM, comparable to the value for wild‐type TyrH of 40 μM.
Structural Basis for Weight Loss in Patients with Chronic Obstructive Pulmonary Disease: Modeling of Gly80 and Ser80 Variants of Human Group IID Phospholipase A2 and their Receptor Complexes
Authors: Hariprasad Gururao , Ethayathulla Abdul Samarth , Khan Mohd Imran 
Published: November 2023

Weight loss is a well known systemic manifestation of Chronic Obstructive Pulmonary Disease. a Gly80Ser mutation on human group IID secretory phospholipase A2 enhances expression of cytokines that are responsible for weight loss. In this study, we seek to establish the structural correlation of wild type and foresaid mutation with its function. Secretory phospholipase A2 with glycine and serine at eightieth positions and M‐type receptor were modeled. The enzymes were docked to the receptor and molecular dynamics was carried out to 40ns. Structural analysis shows the enzymes to be comprising of three helices (HI‐H3), two short helices (SH1 and SH2), five loops including a calcium binding loop (L1‐L5), and stabilized by seven disulfide bonds. The overall back bone folds of the two models are very similar with main chain RMSD of less than 1Å. Active site within the substrate binding channel shows catalytic triad of water‐His67‐ Asp112 which show hydrogen bonded network. The major structural differences between wild and mutant enzymes are: (1) loop‐L3 between H2 and H3 that bears the residue Gly80 in the wild type is flexible, being completely exposed to solvent and forms three hydrogen bonded interactions: (a) main chain nitrogen of Gly80 with hydroxyl group of Tyr86; (b) Oδ2 of Asp84 with amide nitrogen of Tyr82, and (c) polar contact between main chain oxygen atom of Gly80 and water molecule. Whereas, in the mutant enzyme the loop region between residues Ser80 and Arg87 adopts a relatively closed conformation with respect to the channel opening, where it is more rigid and stabilized by five hydrogen bonded interactions and two salt bridges. This along with the loss of hydrogen bond between Ser80 and Tyr86 provides flexibility to the loop; (2) conformation of loop in sPLA2‐Ser80 makes interfacial binding surface more planar thereby increasing compactness of the enzyme as indicated by decrease of volume by 2nm3, and (3) interfacial binding surface contact area and quality of interactions of the mutant enzyme is better with the receptor as compared to the wild type. Therefore, the structural differences delineated in this study are potential biophysical factors that determine the potency of wild and mutant enzymes with macrophage receptors, for respective functions of cytokine release resulting in clinical scenario of cachexia.Support or Funding InformationThis research was supported by Department of Science and Technology, Govt. of India: SR/FT/18.
Structural Insights into Novel Esterase
Authors: RHEE SANGKEE , KIM SANGHOON 
Published: November 2023

Chloramphenicol (Cm) and florfenicol (Ff) are broad‐spectrum antibiotics that inhibit protein synthesis. Both antibiotics are a bacteriostat but differ in their chemical structure in that a fluoro group is attached to C3 of Ff. Specifically, both antibiotics prevent a formation of the peptide bond by irreversibly binding to a receptor site on the 50S subunit of the bacterial ribosome. It is well established that chloramphenicol acetyltransferase inactivates Cm by first recognizing the hydroxyl group of C3 in Cm and then specifically acetylating the hydroxyl group. Due to this specificity, Ff cannot serve as a substrate of chloramphenicol acetyltransferase. Interestingly, a novel esterase, which was recently characterized by metagenome screening, inactivates both antibiotics possibly by hydrolysis of those antibiotics, suggesting that this esterase could be a novel enzyme in inactivating both Cm and Ff. Sequence analysis indicates that its sequence is highly similar to those of microbial hormone senstive lipase. Consistent with this comparison, a newly identified esterase contains Ser156 in the GxSxG motif and Asp252 and His282, the catalytic triad conserved in the family of microbial hormone sensitive lipase. In order to understand this novel enzymatic feature, we are carrying out X‐ray crystallographic analysis. Our studies will provide structural insights into antibiotics hydrolysis.Support or Funding InformationThis work was supported by a grant from the Next‐Generation BioGreen 21 Program, Rural Development Administration, KOREA.
Correlating Gene Expression Profiles to Lipid Induction in the Microalga Chlorella protothecoides
Authors: Maggard Rachel Susanne Jolly , Waikel Rebekah L. 
Published: November 2023

Microalgae are a promising source for sustainable biofuel production, but large‐scale production can be cost‐prohibitive. An understanding of the relationship between algal genome and metabolic pathways could serve to decrease cost and increase commercial viability. In this study, we examine the relationship between gene expression and lipid induction in Chlorella protothecoides. Using NextGen sequencing, we identified candidate genes, which were differentially expressed in algae grown in nitrogen sufficient (low lipid production) and nitrogen deficient (high lipid production) conditions. Using TaqMan real‐time PCR, differential expression was confirmed and quantified for each candidate gene in algae grown in media of varying nitrogen concentrations, and patterns of expression were defined. Systematic alterations were then made in pH, light, and micronutrients, and new expression profiles were generated. These expression profiles were correlated with cellular concentrations of lipids measured by lipid stain and flow cytometry to establish a distinct gene expression profile for lipid producing C. protothecoides. These expression profiles provide insight into C. protothecoides specific lipid production pathways. In addition, these lipid induction profiles are currently being used to rapidly assess the impact of environmental factors on lipid production days before detectable lipid production would be quantified.Support or Funding InformationResearch Scholars Program, Kentucky NSF EPScOR
Tissue Engineering: Simple Versus Complex Organs
Authors: Taylor Doris 
Published: November 2023

To date only “simple” bioengineered tissues have been FDA approved and are currently on the market. These tissues typically lack either vasculature or nerve innervation and are simple tubular or balloon‐like structures. In order to move forward with bioengineered organs, the challenges of developing sustainable vasculature and/or innervation still have to be overcome.Current success include engineered bladder, trachea, esophagus, and urethra. I will discuss the engineering of these “simpler” organs versus that of a complex tissue such as heart, one of the most complex organs to be bioengineered.Our approach involves the use of biologic matrices. Cardiac extracellular matrix (ECM) is a complex architecturally‐organized mixture of proteins glycoamino‐, and proteo‐glycans that contains an embedded vascular network. In fact, during cardiac development, cell‐matrix interactions give rise to regional cell fate specifications. We hypothesize that ECM plays a critical role in stem cell fate, localization and function after tissue injury.We will show that decellularized ECM (dECM) composition and architecture provides physical, mechanical and biochemical cues that direct stem or progenitor cell fate – and that age, sex, and disease state can alter those biologic cues.
Antiproliferative Effects of Hinute‐AM in Human Breast Cancer Cell Lines
Authors: Mukherjee Shyamali , Mitra Piyali , Ratna Anuradha , Maebuchi Motohiro , Furuta Hitoshi , Das Salil K 
Published: November 2023

Breast cancer is a debilitating disease that affects women worldwide. In the United States, breast cancer is the second leading cause of cancer‐related deaths in women. Diet is an important factor in the development of numerous diseases, including breast cancer. We reported earlier that the consumption of soy protein controlled not only the proliferation of dimethylbenz [a] anthracene (DMBA)‐induced breast cancer cells in rats but also its aggressiveness. Soy protein is hydrolyzed in the gut to small peptides which are easily absorbed and are involved in various cellular functions. Fuji Oil Company, Osaka, Japan, has commercially marketed a soy protein hydrolysate, termed Hinute‐AM, composed of primarily di‐ and tripeptides, to be used as a health food. This product was found to have anti‐inflammatory property. It is possible that the antiproliferative effects of soy protein on breast cancer in rats may be mediated by its hydrolysis in the small intestine to small peptides. Hence, we hypothesized that the beneficial effect of soy protein in breast cancer development may be mediated by its hydrolysis product as peptides. Several normal (MCF 10A, 12A, and 184 A1), triple negative (MDA–MB‐231, BT‐549 and HCC‐1806) and steroid receptor positive (T47D and MCH 7) breast cancer cell lines were treated with different concentrations of Hinute‐AM for 24 h. Hinute‐AM at both low and high concentrations did not have any significant effect on proliferation of normal cells. However, while it inhibited proliferation of all breast cancer cell lines at low concentration (0.02–0.10 mg/ml), at high concentration (0.5–2.0 mg/ml), it had no effect. Furthermore, while Hinute‐AM had no effect on the levels of Ki‐67 and cyclin D1 levels in normal cells, it significantly decreased their levels in all breast cancer cell lines. The mechanism by which Hinute‐AM inhibits proliferation of breast cancer cell lines is under investigation.Support or Funding Information(Supported by grants from Fuji Oil Company, Osaka, Japan and NIH 5U54MD007593)