bluuebunny/crossref_metadata_2025_split huggingface dataset:
Collagen Mimetic Peptides as Probes for Bacterial Infection
Authors: Ellison Aubrey , Dempwolff Felix , Kearns Daniel , Raines Ronald 
Published: November 2023

Collagen is the most abundant protein in humans and comprises a major structural component of the extracellular matrix (ECM). In wounds, collagen triple helices suffer damage. As collagen prefers to form a triple helix, we can take advantage of the damaged collagen and introduce collagen mimetic peptides (CMPs) that will adhere to the wound surface. These invasive CMPs can be used to deliver a payload to the collagen surface of a wound. Nature may also use this invasive strand mechanism as a form of host infection. Invasion of host tissue can be mediated by the interaction of bacterial surface proteins and the ECM. Group A Streptococcus (GAS) displays cell‐surface proteins that resemble human collagen. We hypothesize that the collagen‐like strands of GAS form triple helices with denatured collagen in a wound bed. The ensuing adherence could be a basis for infection by GAS. To test this hypothesis, we are using fluorophore‐labeled CMPs to detect collagen strands on the surface of live GAS cells. We are also evaluating knock‐in expression of collagen‐like strands, Scl 1 and Scl 2, on the surface of B. subtilis to transfer the ability to anneal to our CMPs. With these tools we hope to understand and ultimately antagonize infections by GAS.Support or Funding InformationThis work is supported by Grant R01 AR044276 (NIH).
Photosynthetic Apparatus and Biochemical Parameters in Tomato and Squash Crops Influenced by Cucumber Mosaic Virus (CMV) Infection
Authors: Montasser Magdy S. , Nayef Nourah Y , Afzal Mohammed 
Published: November 2023

This study was aimed to compare the influence of two cucumber mosaic virus (CMV) strains (CMV‐KU1 and CMV‐16) on photosynthetic apparatus and different biochemical parameters with emphasis on carotenoids, fatty acids and phenolic compounds in both squash and tomato plants. Squash plants, infected with CMV‐16, showed a decrease in β‐carotene content with a concomitant increase in lutein by which the ratio of lutein/β‐carotene significantly increased by 62% (p<0.05) compared with the control plants. However, the change in lutein/β‐carotene ratio was less pronounced in tomato plants. In response to CMV‐16 infection, the desaturation index indicated by unsaturated/saturated fatty acids (UFA/SFA) increased in both squash and tomato plants, indicating that stress in test plants. Phenolic content in squash plants were significantly changed in response to CMV‐16 inoculation. In CMV‐16 infected squash plants, phenolic accumulation increased sharply indicating that plant tolerance for the viral infection. CMV‐16 in tomato had weaker impact on phenolic content compared with squash plants. This might be due to a possible involvement of symptom development and defense mechanisms due to plant‐virus interactions. All biochemical parameters studied were not significantly influenced in test plants infected with CMV‐KU1 compared with the severe CMV‐16. Satellite RNA in the CMV‐KU1 may have protected plants against infection caused by virulent strains. Our results indicated that CMV‐KU1 is benign to crops compared to the severe viral strain of CMV‐16.This research work was funded by the Research Administration (Research Project # YS01/14)and supported by the College of Graduate Studies, Univ. of Kuwait, Kuwait.Support or Funding InformationResearch Project # YS01/14, University of Kuwait, Kuwait College of Graduate studies, University of Kuwait
Chemical and Genetic Analysis of Hopped Meads
Authors: Halmo Jason R. , Wolyniak Michael J. , Mueller Paul H. 
Published: November 2023

Hops (Humulus lupulus) have been used in alcoholic beverages for centuries to enhance the aroma and provide a bitter flavor. The rise of homebrewing and craft beers has provided a resurgence of interest in understanding ideal hop usage. While hopped beer is well known and understood, the medieval drink Mead is gaining in popularity and is relatively not as well known. The aroma characteristics of commonly used hops are widely known, but much less is understood about the aroma effects in meads. This study aims to provide information on Volatile Organic Compounds (VOCs), which make up the aroma of the drink, found in the Head Space (HS) of six different homebrewed meads: S. cerevisiae, S. cerevisiae with Citra hops, S. cerevisiae with Williamette hops, S. bayanus, S. bayanus with Citra hops, S. bayanus with Williamette Hops.Additionally, common strains of Baker's (S. cerevisiae) and Wine (S. bayanus) yeast have been used to produce commercially lucrative food and drink products. Despite their heavy usage, a great deal remains to be understood how the fermentation pathway can be maximized. The emergence of RNA‐seq allows for rapid detection of changes in RNA during fermentation. This study aims to explore changes in gene expression of the aforementioned yeast during fermentation conditions mimicking that of mead.
Response of the Energetic Metabolism of Saccharomyces cerevisiae to Different Nutritional Conditions of Carbon and Nitrogen
Authors: Olivares‐Marin Ivanna Karina , Madrigal‐Pérez Luis Alberto , Canizal‐Garcia Melina , González‐Hernández Juan Carlos , Regalado‐González Carlos 
Published: November 2023

The energetic metabolism of Saccharomyces cerevisiae is oxidative/fermentative, and its balance can be altered by different factors such as oxygen supply and nutrient homeostasis. Carbon (C) is known as the main nutrient affecting alcoholic fermentation in S. cerevisiae, allowing fermentation as the principal pathway for energy production even in the presence of oxygen when high levels of fermentable sources are available (Crabtree effect). In addition, nitrogen (N) starvation can lead to sluggish or stuck fermentation, and the presence of certain N sources may enhance sugars consumption, associating in this way nutritional status with alcoholic fermentation. However, little is known about nutrients interactions and their effect on fermentation. The objective of this work was to investigate the impact of different C and N sources and their concentration, on the fermentative growth of S. cerevisiae. Fermentative and respiratory phenotypes of S. cerevisiae BY4742 was studied using the doubling time (Dt) to discriminate among phenotypes from 81 different conditions of N and C in duplicate, using five independent experiments. We used synthetic‐complete (SC) medium supplemented with glucose, sucrose or galactose used as C source, and proline, glutamate and ammonium as N source. Our results showed that the energetic metabolism of S. cerevisiae is directed toward fermentation or respiration depending on the type of carbon and nitrogen source and their concentrations. As expected, glucose supplementation resulted in a large number of conditions with a fermentative phenotype (19%), followed by sucrose utilization (17%). Cultures supplemented with galactose showed a fermentative phenotype only at 2% (w/v) when proline or glutamate was used as N donor (4%). The best N source was proline, irrespective of its concentration and the C source used in the culture media. Ammonium showed cellular toxicity when a concentration of 5% (w/v) was used in the cultures, and galactose supplementation showed more severe toxicity. Glutamate showed an intermediate number of fermentative phenotypes relative to proline and ammonium, despite of its quality as N donor. Our findings suggested a possible energetic role for proline that could be affecting fermentation induction.Support or Funding InformationThis worked was supported by a grant of the Consejo Nacional de Ciencia y Tecnología [grant number 427081] to IKOM.
Decreased Insulin Signaling Causes Loss of PFK‐2 and Impaired Glycolysis in the Heart
Authors: Humphries Kenneth , Bockus Lee , Eyster Craig 
Published: November 2023

The heart has a dynamic capacity to orchestrate energy production with contractile demand. Normally, beta‐adrenergic signaling works through the cAMP‐dependent protein kinase (PKA) pathway to coordinate moment‐to‐moment changes in both contraction and metabolism. The main metabolic target of PKA is phosphofructose kinase‐2 (PFK‐2), which generates fructose‐2,6‐bisphosphate in response to PKA mediated phosphorylation. This metabolite is a potent allosteric activator of PFK‐1 and serves to increase glycolysis. We have previously found that PFK‐2 is unresponsive to PKA activation in the diabetic heart and we hypothesize that this may contribute to metabolic inflexibility. Despite the central role of PFK‐2 in cardiac metabolism it is unknown how its content and activity changes in either the healthy or diabetic heart. We have recently found that in the absence of insulin signaling there is a decrease in cardiac PFK‐2 content. This is true in types 1 and 2 diabetic models and with fasted animals, suggesting turnover of PFK‐2 is a normal glucose‐sparing response. Functionally, metabolomics studies have revealed that the loss of PFK‐2 is accompanied by an increase in glycolytic products upstream of PFK‐1, and a decrease of products downstream of PFK‐1. Ongoing mechanistic studies in primary adult mouse cardiomyocytes have identified that PFK‐2 levels are regulated by multiple means. In the absence of insulin PFK‐2 is rapidly degraded by both proteasomal and chaperone mediated autophagy mechanisms. Thus, the loss of PFK‐2 content as a result of reduced insulin signaling impairs its ability to dynamically regulate glycolysis. Although this may be beneficial in the fasted state to conserve systemic glucose, it represents a potential pathological impairment in diabetes.Support or Funding InformationThis work is supported by the National Institutes of Health grant R01HL125625.
Protein Modifying Enzyme Ate1 Controls Cellular Warburg Effects
Authors: Jiang Chunhua , Birnbaum Michael , Patel Devang , Kumar Akhilesh , Morgan William , Lampidis Theodore , Fontanesi Flavia , Barrientos Antonio , Zhang Fangliang 
Published: November 2023

Protein arginylation by arginyl‐transfer RNA protein transferase (Ate1) is a post‐translational modification that targets a number of metabolic enzymes. However, the mechanisms and downstream effects of this modification in cellular metabolism are unknown.In this study, wild type mouse embryonic fibroblast cells (MEF‐WT) and Ate1 knockout mouse embryonic fibroblast cells (MEF‐KO) were used to measure several key metabolic parameters including glucose uptake, glucose starvation sensitivity, lactate production, cellular oxygen consumption rate (OCR). Ate1 is also down‐regulated by shRNA to repeat some of the above experiments. The results showed that Ate1‐KO MEF is more sensitive to glucose starvation than MEF‐WT, and that KO cells have significant higher glucose uptake and lactate production than MEF‐WT. Conversely, Ate1‐KO cells have lower cellular OCR than MEF‐WT. While the WT and Ate1‐KO cells have similar levels of cellular ATP, a significantly larger proportion of ATP in KO cells are derived from the glycolysis pathway. We further showed that this phenomenon can be repeated when Ate1 is down‐regulated by shRNA in WT cells, and that this phenotype can also be reversed when a recombinant Ate1 protein is reintroduced in the KO cells.CONCLUSIONOur data suggest that knockout of Ate1 in MEF shift cellular metabolic pathways from mitochondrial oxidative phosphorylation to aerobic glycolysis, which is the sign of the Warburg effect.Support or Funding Information

NIGMS (NIH), R01, # GM107333.
DoD (CDMRP), Idea Award, PC140622
DoD (CDMRP), Exploratory Grant, PC141013
Genetic and Functional Characterization of the Enzymes of Nicotinic Acid Degradation in Bacillus niacini
Authors: To Tsun Ki Jerrick , Snider Mark J. 
Published: November 2023

N‐Heteroaromatic compounds (NHACs) are byproducts of fuel processing and are common components of herbicides, pesticides and pharmaceuticals that have been identified as environmental contaminants. A current approach to removing NHAC contaminants is bioremediation, which involves the use of bacteria and their degradation systems. Optimizing bioremediation efforts requires the understanding of different degradation strategies that have evolved in bacteria. The microbial degradation of nicotinic acid serves as a model system, the details of which can be translated to improving bioremediation of NHACs. Analysis of the recently sequenced genome of Bacillus niacini has putatively identified two gene clusters that collectively code for a distinct degradation pathway of nicotinic acid. This study describes the genetic characterization of key enzymes involved in the B. niacini pathway following the initial hydroxylation steps of the pyridine ring through gene knockouts and complementation studies. Further, reaction assays of the enzymes catalyzing the decarboxylation‐hydroxylation and the tripyridol ring‐opening steps will be established to confirm reaction substrates and products and to provide the platform for future mechanistic studies of these novel reactions.Support or Funding InformationThis work was supported by the Department of Chemistry and the Henry J. Copeland Fund for Independent Study at The College of Wooster.
Administration of NaoXinTong to db/db mice inhibits the development of diabetic nephropathy
Authors: Yang Shu , Liu Mengyang , Su Peng , Han Jihong 
Published: November 2023

Buchang NaoXinTong capsule (NXT), a Chinese Materia Medica standardized product extracted from 16 various kinds of Chinese traditional herbal medicines including Salvia miltiorrhiza, Angelica sinennsis, Astragali Radix, is clinically used for treatment of patients with cerebrovascular and cardiovascular diseases. Clinically, it has been observed that NXT can demonstrate anti‐diabetic properties with unclear mechanisms. In this study, we used a pro‐diabetic animal model, db/db mice, to investigate if NXT can inhibit the development of diabetic nephropathy. The type 2 diabetic mice (~6‐week‐old) were randomly divided into two groups (10 mice/group), and started feeding normal chow and normal chow containing NXT, respectively, for 14 weeks. We collected blood and urine samples during the treatment, and kidney, adipose tissue and liver samples at the end of the experiment, respectively, for determination of serum glucose or lipid levels, renal functions as well as the involved mechanisms. We found that NXT reduced diabetes‐increased glucose, total and LDL‐cholesterol and triglyceride levels in the serum. NXT also reduced urinary protein levels. In the kidney, we determined that NXT inhibited mesangial matrix expansion, expression of vascular endothelial growth factor A (VEGFA), fibronectin and advanced glycation end (AGE) products while it repaired the diabetes‐induced podocyte injury and dysfunction by increasing expression of WT‐1 and nephrin. In addition, NXT inhibited renal accumulation of extracellular matrix (ECM) proteins by increasing matrix metalloproteinases (MMPs) expression. Mechanistically, we determined that NXT inhibited TGFβ/Smad signaling pathway and CTGF expression in kidney. Furthermore, we observed that NXT improved glucose metabolism in the liver and increase FGF21 expression in both liver and white adipose tissue, which is accompanied by increased expression of genes responsible for energy metabolism in the liver. Taken together, our study demonstrates that NXT inhibits the development of diabetic nephropathy by ameliorating glucose metabolism, maintaining kidney tissue structure and blocking the diabetes‐induced renal dysfunction. Our study further suggests the potential application of NXT for diabetes treatment in clinic.Support or Funding InformationThe National Science Foundation of China Grants 81473204 to J Han and 81573427 to Y Duan
Identifying a Source of Beta‐Alanine and its Broader Implications in Arabidopsis thaliana by GC/MS
Authors: Perrett Morgan , Gothard Megan , Ludwig Andrea , Rouhier Kerry A 
Published: November 2023

β‐alanine, a naturally occurring non‐protein amino acid, serves as a precursor for the formation of vitamin B5 and, ultimately, coenzyme A in plants. The synthesis of β‐alanine has not been explored extensively in plants despite interest in the development of alternative methods for producing natural compounds. Previous work in plants showed that β‐alanine could be synthesized from propionyl‐CoA. Our lab studies the degradation of branched‐chain amino acids (BCAAs) ‐ valine, leucine, and isoleucine ‐ in Arabidopsis thaliana and the degradation of valine and isoleucine are direct sources of propionyl‐CoA. Therefore, we proposed that valine and isoleucine could serve as a source of β‐alanine via the production of propionyl‐CoA. Using metabolic tracing with radiolabeled precursors measured by Gas Chromatography/Mass Spectrometry (GC/MS), we were able to measure β‐alanine via isoleucine but not valine. However, valine treatment of young seedlings did result in increased levels of β‐alanine, which suggested an indirect link through amino acid homeostasis. Additionally, we used a mutant seedline that lacks expression of an enzyme necessary for valine and propionyl‐CoA degradation (mmsd‐1) to further emphasize the link between β‐alanine and propionyl‐CoA by shifting the equilibrium towards β‐alanine production. Here, we found that seeds had significantly high levels of β‐alanine compared to wild‐type seeds.Support or Funding InformationThis project was funded by the Jean Dreyfus Boissevain Lectureship for Undergraduate Institutions and Kenyon College.
Time‐resolved analysis of amino acid deprivation responses reveals dynamic relationship between GCN2 and mTORC1
Authors: Nikonorova Inna A , Goudie Michael P , Mirek Emily T , Wang Yongping , Anthony Tracy G 
Published: November 2023

In higher eukaryotes, sensing of amino acids by liver is critical for fine tuning of whole body metabolism according to nutrient availability. Amino acid (AA) depletion activates General Control Nonderepressible 2 (GCN2, or eIF2AK4) kinase and consequential phosphorylation of eukaryotic initiation factor 2 (eIF2). Phosphorylated eIF2 allows for preferential translation of specific mRNAs, such as activating transcription factor 4 (ATF4). AA depletion also reduces the activity of another AA sensor, mammalian target of rapamycin complex 1 (mTORC1), a major regulator of cell growth. The GCN2 pathway inhibits mTORC1 activity, but how remains unclear. Our study aimed to define the role of GCN2 in the regulation of mTORC1 activity to AA depletion in vivo. We used the anti‐cancer drug asparaginase (ASNase) as a molecular tool to induce AA depletion in wild type (WT) and Gcn2−/− mice. Following a single injection of ASNase, hepatic signaling via GCN2 and mTORC1 was analyzed. In this experimental setup we addressed three types of possible regulation: 1) immediate protein‐protein interactions (15–30 min), 2) early translational changes (1–3 h) and 3) long term transcriptional alterations (6–18 h). We found that genetic disruption of GCN2 lead to hyperactivation of hepatic mTORC1 at 15–30 min following ASNase. This indicates that GCN2 modulates hepatic mTORC1 activity via protein‐protein interaction(s). Examination of translational changes via polyribosome profiling revealed enhanced translation of ATF4 in WT, but not Gcn2−/− livers, at 1h. This suggests that: 1) translational induction of ATF4 by ASNase requires GCN2 and 2) hyperactivation of mTORC1 per se is not enough to induce ATF4 synthesis. Analysis of transcriptional changes induced by ATF4 revealed that Sestrin2, an inhibitor of mTORC1, is induced at a much later time point,12–18 h following ASNase, and is not involved in immediate or early control. Taken together, our data provide a mechanistic framework for dynamic interaction of the GCN2 pathway with mTORC1 during amino acid stress.Support or Funding InformationThis work was supported by NIH grant RO1HD070487 to T.G.A. and NIH K12 grant IRACDA New Jersey‐New York for Science Partnerships in Research and Education to I.A.N.
Hormonal Regulation of Glycine Metabolism And Its Potential Role in Diabetes Susceptibility
Authors: Jog Ruta , Wang Jian , Leff Todd 
Published: November 2023

Type II diabetes (T2D) is characterized by insulin resistance, β cell dysfunction and impaired glucose tolerance. Multiple large‐scale metabolomics studies have demonstrated that diabetes is accompanied by alterations in amino acid metabolism. Interestingly, in both humans and animal models, circulating glycine levels are strongly reduced in obesity, glucose intolerance and T2D. These observations identify glycine as an important biomarker of T2D, and raise the possibility that altered glycine metabolism may play an active role in the development of the disease. The goals of our study are to determine if altered glycine metabolism plays a role in the etiology of diabetes, and to characterize the regulatory pathways that control plasma glycine levels. Glycine cleavage system (GCS), a multimeric enzyme complex, represents the only biochemical route that degrades glycine in human body. Human genetic evidences indicate that loss‐of‐function mutations of GCS cause hyperglycinemia and neurodevelopmental disorders resulting in early death. Given the key role of GCS in control of circulating level of glycine, we hypothesize that during progression of T2D, GCS‐mediated glycine catabolism may be altered in main metabolic organs including liver. Here, we show that in hepatoma cell lines both insulin and glucocorticoids strongly stimulate transcription of glycine decarboxylase (GLDC) gene that encodes the rate‐limiting component of GCS. We also show that the insulin responsive transcription factor sterol‐regulatory element binding protein‐1c (SREBP‐1c) regulates GLDC gene transcription and likely mediates the stimulatory effect of insulin. SREBP‐1c is known to mediate insulin's stimulatory effect on lipogenesis genes even in the presence of hepatic insulin resistance. These observations strengthen a working model that insulin‐mediated stimulation of GLDC, even in insulin resistant states, increases the activity of the glycine cleavage system and contributes to the low levels of glycine observed in T2D.Support or Funding InformationMichigan Diabetes Research and Training Center Pilot/Feasibility Grant