bluuebunny/crossref_metadata_2025_split huggingface dataset:
Systematic Characterization and Conservation of Adjacent Gene Co‐Regulation in Fungi
Authors: Eldabagh Reem , Foley Jay , Arnone James 
Published: June 2021

It is essential that cells orchestrate gene expression, which oftentimes requires regulated expression of large gene sets. Previously it has been observed that spatial positioning influences transcription, including in rRNA and ribosome biogenesis (RRB) and ribosomal protein (RP) regulons. Both include a disproportionate number of immediately adjacent gene pairs, which results in tighter transcriptional coordination among adjacent paired genes compared to unpaired genes. This non‐random genomic distribution has been seen in a handful of functionally related gene families and many of these pairings are conserved across divergent fungal lineages. To date, the significance of these observations has not been extended in a systematic way to characterize how prevalent and significant the role of adjacent gene co‐regulation is in transcriptional regulation. Therefore, we statistically analyzed genome‐wide expression profile data under five stressors for the RP, nitrogen metabolism, carbohydrate metabolism, toxin response and heat shock regulons, using Python to compute Pearson's correlation coefficient values. Surprisingly, it seems there is not an overall transcriptional advantage to functional pairing of genes in S. cerevisiae – although there are specific conditions that this pairing appears advantageous for, which could be the driving force behind this arrangement. Divergent fungal lineages were similarly analyzed to allow for comparison of newer evolved pairings to ancestral pairings. Our results demonstrate that the longer two genes have co‐existed as neighbors, the tighter their transcriptional response is to broad stress and nutritional conditions. Moreover, we systematically characterized the genomic distribution of the 140 gene families defined by the G.O. Slim designation, where we found that ~25% of these functional groupings can be found as functionally related, immediately adjacent gene pairs. This suggests that adjacent gene co‐regulation is much more wide‐spread than previously realized. Moreover, hypergeometric distribution analyses of gene expression were conducted, enabling the identification of potentially influential histone remodelers on the adjacent gene pairs in S. cerevisiae. Such analyses have been completed on the RP, nitrogen metabolism, heat shock, and toxin response regulons. Future work will focus on extending this analysis to genes of other regulons to better understand gene expression, and verifying these results experimentally using knockout strains of yeast.Support or Funding InformationThis research was supported by funding from the Garden State Louis Stokes Alliance for Minority Progress. The GS‐LSAMP is supported by a grant from the National Science Foundation. It was also supported by the Center for Research and ART at William Paterson University of New Jersey.This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Kinetic Studies of 2‐(2′‐hydroxyphenyl)benzenesulfinate desulfinase substrate analogs
Authors: Kedir Dean Reshad , Watkins Linette M. 
Published: June 2021

2‐(2′‐hydroxyphenyl)benzenesulfinate desulfinase (DszB) is an enzyme that catalyzes the cleavage of the carbon‐sulfur bond as the final step of the desulfurization of 2‐(2′‐hydroxyphenyl)benzenesulfinate (HPBS) producing sulfite and 2‐hydroxybiphenyl (HBP). This reaction is used to study the biodesulfurization of dibenzothiophene, the major organosulfur compound found in fossil fuels/petroleum. Previous studies in the Watkins lab suggested that halogenated analogs of HPBS are competitive inhibitors of DszB, so a coupled assay was used to test their effect on kinetic activity. The relative activity of these analogs was tested measure both products of the reaction. The rate of HBP formation was monitored using a fluorometric assay with an excitation at 288 nm and measuring emission at 414 nm. The rate of sulfite product formation was measured in the coupled assay with Sulfite Oxidase (SOX) by analyzing a change in absorbance at 540 nm. When testing the analogs HPBS‐Cl and HPBS‐Br for activity, no product was detected. When measuring enzyme activity in the presence of the halogenated analogs and the substrate HPBS, an increase in DszB activity was observed, with HPBS‐Cl and HPBS‐Br showing an increase product formation of 475% and 213%, respectively. Individually these HPBS analogs did not act as catalytic substrates or competitive inhibitors, however when coupled with HPBS the analogs acted as activators. Based on these results, we are exploring the structure of DszB to further understand how HPBS analogs can affect the desulfinase kinetics.Support or Funding InformationNSF CHE‐1757874This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Reduced amino acids: the placenta after maternal vertical sleeve gastrectomy in the rat
Authors: Welch Bradley , Himel Alexandra , Duncan Brittany , Spann Redin , Grayson Bernadette E 
Published: June 2021

Vertical sleeve gastrectomy (VSG) is a surgical weight loss procedure used to reduce the comorbidities of Metabolic Syndrome improving obesity, diabetes and heart disease. Both in humans and rodents, maternal bariatric surgery prior to pregnancy results in challenges during pregnancy including increased small‐for‐gestational age offspring that we have shown in the rodent model of VSG develop greater metabolic disease later in life compared to obese controls. A common gestational cause of poor growth in utero is maternal protein deficiency. Previously, we published that VSG dams had normal levels of plasma amino acids in the fasting condition and following a protein shake gavage. We did not find any gross abnormalities in plasma amino acids under these conditions. In the current work, we hypothesized that the maternal levels were sufficient and that the transporters within the placenta may be differentially transporting amino acids to the fetus. Using gestational day 19 placenta from pregnant Lean, Obese and post‐VSG dams, we performed analysis of the amino acid content of the placenta and prepared placental mRNA for quantitative PCR analysis of genes associated with amino acid transport. Aliphatic Amino acids: isoleucine, leucine, proline and valine were statistically reduced in comparison to Lean dam levels (p< 0.05). Phenylalanine, aspartic acid and glutamic acid, arginine, histidine and methionine were also significantly reduced (p< 0.05). Furthermore, amino acid transporter SLC38A1 (SNAT1) and SLC38A4 (SNAT4) showed trends towards reductions in both VSG and Obese dams. On the contrary, SLC38A2 (SNAT2) and SLC7a7 (LAT1) was significantly elevated (p< 0.05) in VSG in comparison to Lean and Obese. Collectively, these data suggest that despite healthy ingestion of proteins by the mother, alterations in amino acid availability to the fetus may be obstructed by the placenta after bariatric surgery. More work is needed in order to determine the relevance of these findings to the human condition.Support or Funding InformationThe research reported in this publication was supported by the National Institute of General Medical Sciences of the National Institutes of Health under Award Number 1P20GM121334‐01, and BEG is also supported DOD contract W81XWH‐16‐1‐0387.This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Sequence specificity of amyloid propagation in the yeast model
Authors: Chernoff Yury O , Chen Buxin , Gyoneva Stefka , Romanyuk Andrey V 
Published: June 2021

Amyloids are highly ordered homogenous fibrous aggregates produced by many proteins in vitro and associated with some diseases in vivo. Self‐perpetuating amyloids (prions) cause infectious neurodegenerative diseases in mammals and transmit heritable traits in yeast. The ability of a yeast protein to generate and propagate an amyloid state is controlled by a specific region of the protein termed prion domain (PrD). Amyloid propagation is a sequence‐specific process. Divergence of PrD sequences impairs transmission of amyloid state to the orthologous proteins from other species in some combinations, leading to so‐called “species barrier” in prion transmission. Such a barrier is detected even between prion proteins of the closely related species of Saccharomyces yeast. These proteins are capable of coaggregating, thus demonstrating that conversion to a prion state does not represent a mechanical consequence of coaggregation and requires a higher level of sequence identity. Moreover, slight sequence differences may result in “poisoning” of amyloid growth by a divergent protein. Amyloids of different species exhibit differential patterns both in vivo and in vitro. Detailed analysis of the yeast prion protein Sup35 revealed that specific changes within different amino acid stretches of Sup35 PrD are responsible for the species barrier in different cross‐species combinations.(Supported by NSF.)
Targeting Mutant V600EB‐Raf in Melanoma Interrupts Immunoediting of Leukocyte Functions and Melanoma Extravasation
Authors: Liang Shile , Peng Hsin‐Hsin , Robertson Gavin P , Dong Cheng 
Published: June 2021

Previous studies have shown that neutrophils (PMNs) could facilitate melanoma transendothelial migration mediated by endogenously produced chemokine interleukin 8 (IL‐8) from the tumor microenvironment. The objective of this study was to investigate the role of B‐Raf, the most mutated gene in malignant melanomas, in this process. Using short interfering RNA (siRNA) to reduce expression/activity of mutant V600EB‐Raf in melanoma, we showed knockdown of mutant V600EB‐Raf inhibited melanoma cell extravasation in vitro and subsequent lung metastasis development in vivo. Mechanistic studies showed that inhibition of V600EB‐Raf significantly reduced the constitutive secretion of IL‐8 from melanoma cells, as well as the capacity of endogenous IL‐8 production from the melanoma‐PMN microenvironment. Furthermore, a reduction in ICAM‐1 expression on melanoma cells was detected following mutant V600EB‐Raf knockdown. Together, these results suggest that targeting mutant V600EB‐Raf reduces melanoma cell extravasation by decreasing IL‐8 production and interruption of ICAM‐1‐β2 integrin binding of melanoma cell to the endothelium mediated by PMNs in the microcirculation, which provides a rationale and mechanistic basis for targeting mutant V600EB‐Raf to inhibit melanoma extravasation and subsequent metastasis development.This study was supported by NIH CA‐97306, NSF BES‐0138474 and American Cancer Society RSG‐04‐053‐01‐GMC.
Reliability and validity of a wearable heart rate and respiratory rate sensor system
Authors: Tharion William J. , Buller Mark J. , Karis Anthony J. , Mullen Stephen P. 
Published: June 2021

Purpose: To determine if heart rate (HR) and respiration rate (RR) of the wearable Hidalgo Vital Sign Detection System (VSDS) were reliable and valid.Methods: 8 men performed activities of varying intensity; low (e.g., lying prone & supine) medium (e.g., treadmill walking) and high (treadmill running). VSDS HR and RR were compared to reference standard (RS) HR (Schiller AT‐6 ECG) and RR (SensorMedics 2900 metabolic cart). Reliability was assessed by (1) mean between trials and (2) intraclass R. Validity was assessed by (1) mean between VSDS and RS, (2) Pearson r, and (3) Bland‐Altman (BA) plots. Acceptability of VSDS of HR measures was set a priori to be within 2 bpm (low activities) and 6 bpm (high activities) and RR to be within 1 breath per min (brpm) (low activities) and 3 brpm (high activities) of RS measures.Results: HR showed no significant differences between trials. Intraclass R's ranged from 0.60 to 0.97; R for all activities: 0.88 (p<0.01). There was no significant difference between VSDS and RS HR. RR reliability showed no differences between trials except for pushups (mean Δ = −3.1 brpm; p<0.05). Intraclass R's ranged from 0.52 to 0.97; R for all activities: 0.90 (p<0.01). RR validity estimates showed differences between VSDS and RS (range: 1.9 brpm to − 10.4 brpm). Pearson r values ranged from 0.23 to 0.82.Conclusion: VSDS HR data was both reliable and valid. RR was reliable but did not meet the validity criterion. This work was supported by U.S. Army Medical Research and Materiel Command.
A Na‐dependent fructose co‐transporter in lobster hepatopancreas
Authors: Ahearn Gregory A. , Sterling Kenneth M. , Cheeseman Christopher I. 
Published: June 2021

3H‐Fructose (Fru) and 3H‐Glucose (Glc) transport were determined in brush‐border membrane vesicles (BBMV), baso‐lateral membrane vesicles (BLMV) and isolated cells (E, R, F, B) of lobster, Homarus americanus, hepatopancreas (HP). Glc transport was Na‐dependent in BBMV and not affected by a ten‐fold excess of Fru, indicating the presence of an apparent SGLT‐1‐like transporter. Glc uptake by BLMV was facilitative and was not inhibited by a ten‐fold excess of Fru. Fru uptake by BBMV was hyperbolic, Na‐dependent, and not inhibited by Glc. Fru uptake by BLMV was Na‐dependent and not inhibited by Glc. Hepatopancreatic E, F and B cells showed Na‐dependent uptake of Fru, while R cells did not. Na‐dependent Fru uptake by E cells was not inhibited by Glc or mannose (Man). Glucose uptake by E cells was facilitative. Western blot analysis of BBMV, BLMV and E, R, F and B cells with antibodies for mammalian GLUT‐2, GLUT‐4, GLUT‐5, SGLT‐1 and SGLT‐4 indicated the presence of the respective lobster HP orthologous proteins. A GLUT‐2‐like protein (∼50 kD) was present in all four cell types and only in BLMV. A GLUT‐4‐like protein (∼50 kD) was localized to BLMV. A 50 kD, GLUT‐5‐like protein, was present in F and B cells and in BLMV. An SGLT‐1‐like protein (∼75 kD) was detected in R, F and B cells; the signal was strongest in F cells. The SGLT‐1‐like protein was limited to BBMV. An SGLT‐4‐like protein was present in E, R, and F cells; the strongest signal was from E cells. Comparison of Fru and Glc uptake by BBMV, BLMV, and cells, indicated distinct Na‐dependent cotransporters for each sugar.Supported by NSF grant IBN04‐21986.
A novel prolactin receptor (PRLR2) in tilapia (Oreochromis mossambicus) is involved in the sea water acclimation response
Authors: Fiol Diego Fernando , Sanmarti Enio , Lim Andreana , Kültz Dietmar 
Published: June 2021

A novel prolactin receptor (OmPRLR2) was identified and cloned in the euryhaline fish Oreochromis mossambicus using the suppression subtractive hybridization approach based on its response to hyperosmotic stress. OmPRLR2 protein has 55% identity with a known tilapia PRLR and 50% identity with human PRLR. Expression of OmPRLR2 was detected mainly in osmoregulatory organs (gills, intestine and kidney) but also in brain and muscle. Expression of the two tilapia PRLR differs in response to osmotic stress; OmPRLR1 expression is augmented during hypoosmotic stress but OmPRLR2 expression increased during hyperosmotic stress. Expression levels and tissue distribution of OmPRLR2 protein were quantified using specific antibodies, confirming its overexpression during hyperosmotic stress in gill cells. Stably transfected HEK‐293 cell lines overexpressing Tet‐inducible OmPRLR1 and OmPRLR2 were established. Receptors were functionally characterized using a casein promoter reporter system and through the analysis of expression of different prolactin (PRL) and growth hormone (GH) responsive genes. Specific responses of tilapia PRL177, tilapia PRL188, ovine PRL and tilapia GH were analyzed and show strong specificities for the ligands and resulting in activation of different signal transduction pathways. Additionally, cell lines expressing OmPRLR2 have increased tolerance to hyperosmotic media. Our results indicate that OmPRLR2 is a novel receptor contributing to osmosensory signal transduction in euryhaline fish.This work was supported by a grant from the National Science Foundation (IOB‐0542755).
Long–Term Effects of High‐and Low‐Glycemic Load Energy‐Restricted Diets on Metabolic Adaptation and the Composition of Weight Loss
Authors: Das Sai Krupa , Gilhooly Cheryl H. , Golden Julie K. , Pittas Anastassios G. , Fuss Paul J. , Dallal Gerard E. , Saltzman Edward , Roberts Susan B. 
Published: June 2021

The effects of high glycemic load (HG) and low glycemic load (LG) diets on resting metabolic rate (RMR) and body composition changes in response to caloric restriction (CR) remains controversial. Objective To examine the effects of two CR diets differing primarily in glycemic load on RMR and the % of weight lost as fat and fat free mass (FFM). Methods One year randomized controlled trial of HG and LG diets at 30% CR in 29 healthy overweight adults (mean±SD, age 35±5y; BMI 27.5±1.5 kg/m2). All food was provided for 6 mo, and self‐administered for the next 6 mo. Outcome measures included RMR, fat and FFM. Results There was no significant effect of diet on change in RMR after accounting for the decreases in body fat and FFM, at any time point (p=0.51 at 3 mo, p=0.56 at 6 mo and p=0.85 at 12 mo). In the subgroup of individuals who lost >5% body weight the LG diet group had a significantly higher percentage of weight loss as fat and a significantly lower percentage of weight loss as FFM compared to the HG group (p<0.05). Conclusions This study found no evidence for differential RMR response to weight loss between the HG and LG diets. However, for a given weight loss, the LG diet resulted in greater fat loss and less FFM loss.Support NIH grants NGA‐3U01‐AG20480, K23DK61506, #H150001; USDA 58‐1950‐4‐401
Engineering Tryptophan Residues into Glyoxysomal Malate Dehydrogenase
Authors: Johnson Adam , Bell Ellis 
Published: June 2021

Glyoxysomal Malate Dehydrogenase, which normally lacks any tryptophans, has been engineered to contain a single tryptophan in a variety of different locations both in or near the active site, at sites distant from the active site and at sites near the dimer interface. These mutants have been used to probe conformational flexibility in regards to local conformation changes around the engineered tryptophan residues. This represents a significant tool in the ability to ascertain conformational integrity in mutants and conformational changes induced by allosteric ligands binding to distinct sites in the oligomer. Specifically studied in here are two mutations one distant and one near the subunit interface, L229W and I319W respectively. Mutants were expressed and purified using Ni‐NTA Affinity chromatography. These mutants have been characterized by initial rate kinetics, MALDI‐TOF and fluorescence spectroscopy, and used in both guanidine hydrochloride unfolding experiments and KI collisional quenching experiments in the presence or absence of various coligands to probe differential effects of ligands on conformational accessibility and stability. Studies are underway to construct a “dead” tryptophan subunit with a native subunit to monitor if the tryptophans report on conformational communication across the subunit interface.Supported by NSF Grant MCB 0448905 to Ellis Bell
Proteomic Approaches to Defining Avian Natural Killer Cell Surface Proteins
Authors: Zhang Lei , Katselis George S. , Goto Ronald M. , Goebel Thomas W. , Yokoyama Wayne M. , Lee Terry D. , Miller Marcia M. 
Published: June 2021

Receptor/ligand interactions that dominate the control of natural killer (NK) cell activity likely differ in detail among vertebrate species as the result of natural selection. We are interested in innate immune responses in the avian species that serve as alternate hosts for pathogens causing human disease. We would like to link the challenge of pathogens to the genetics of NK cell activity. We are applying a largely unbiased high throughput proteomic approach to identify components of the surface of chicken NK cells. Our goal is to develop methods for preparing membrane fractions in abundance so that rare proteins, e.g. NK cell receptors, can be detected by mass spectrometry. We are comparing different fractionation methods for the capacity to provide membrane proteins from embryonic spleen cells that exhibit natural cytotoxic activity. We found it necessary to enhance the yield of membrane proteins since simpler methods are inadequate. We are now comparing methods incorporating fractionation by relative hydrophobicity and by shotgun glycopeptides capture. NK cell surface proteins identified by molecular biology serve as controls in evaluating purification.Supported in part by NSF MCB‐0524167
Effects of Nucleotides on Changes in Flexibility & Allosteric Interactions in Glutamate Dehydrogenase
Authors: Scheel Carolyn , Bell Ellis 
Published: June 2021

Higher eukaryotic glutamate dehydrogenases exhibit complex homo and hetero tropic regulation involving subunit interactions and ligand induced conformational changes. Previous have shown that the amino acid substrates, glutamate or norvaline have differential effects on local and global stability of the protein. To investigate the effects of nucleotide cofactors [NAD(H) and NADP(H)] and the allosteric regulators ADP and GTP similar approaches, using Limited proteolysis, Differential Scanning Calorimetry, Dynamic Light Scattering have been used in combination with Isothermal Titration Calorimetry to study ligand induced changes in local flexibility and stability. Overall these studies indicate that both activity and allosteric regulation of this complex enzyme are linked to changes in conformational flexibility rather than discrete ligand induced changes in conformation.This research is supported by a Grant from the National Science Foundation: MCB 0448905 to EB
Systemic Characterization of Immune Suppression from Battlefield‐like Stress
Authors: Muhie Seid , Hammamieh Rasha , Cummings Christiano , Yang David , Jett Marti 
Published: June 2021

This study was designed to determine impact of battlefield‐like stress on the immune response using whole genome profiling and computational analyses. We collected whole blood samples from 15 US Army Ranger Training Battalion cadets before, and after 5 and 8 weeks training. Genome wide transcriptomes were analyzed using oligo‐nucleotide arrays representing ~24,700 human genes. More than 2300 differentially regulated genes were identified at both time points. Ontological enrichment showed suppression of transcripts important in microbial pattern recognition, inflammation, chemotaxis, and antigen preparation and presentations. Profiled genes and pathways were confirmed using both quantitative real time PCR arrays and high throughput ELISAs. Our computational analyses (for regulatory motifs and networks) identified the stress response site (STRE) as common regulatory motif of a number of profiled genes. Though, population of mono‐nuclear cells was not changed significantly, in vitro exposure of leucocytes to Staphylococcus enterotoxin B, a pyrogenic toxin, showed no response, and they seemed anergic. This may mean a highly compromised protective immune response. Suppression of most molecules involved in antigen presentation and lymphocytes' activation pathways may explain why individuals or animal models exposed to chronic stress show poor response towards proteineous antigen based vaccines.We are grateful to DTRA for funding.