bluuebunny/crossref_metadata_2025_split huggingface dataset:
Unconventional Protein Secretion and Protein Quality Control
Authors: Ye Yihong , Lee Jin‐Gu 
Published: November 2023

To safeguard proteomic integrity, cells rely on the ubiquitin proteasome system to degrade aberrant polypeptides and autophagy to eliminate protein aggregates. However, it is unclear whether cells can remove defective proteins that escape degradation due to protein quality control (PQC) failure or proteasome dysfunction lest toxic protein aggregates be formed. Here we report a pathway termed Misfolding‐Associated Protein Secretion (MAPS), which utilizes the endoplasmic reticulum (ER)‐associated deubiquitinase USP19 to export aberrant cytosolic proteins that are inefficiently degraded by the proteasome. USP19 possesses both deubiquitinating and chaperone activity, allowing recruitment of misfolded proteins to the ER for deubiquitination, encapsulation into ER‐associated vesicles, and subsequent secretion. USP19 deficient cells are defective in growth after exposing to a proteasome inhibitor, suggesting a critical role in adaptation to proteasome dysfunction. Together, our findings delineate a novel PQC pathway that, unlike degradation‐based mechanism, promotes protein homeostasis by exporting misfolded proteins through an unconventional route.Support or Funding InformationThe research is funded by the intramural research program of NIDDK.
The E3 ligase Listerin/Ltn1 links ribosome‐associated protein quality control and neurodegeneration
Authors: Joazeiro Claudio 
Published: November 2023

We had previously reported that a homozygous mutation in the lister gene leads to neurodegeneration in mice. lister encodes a RING domain E3 ligase, Listerin, which is conserved among eukaryotic organisms and is widely expressed in mouse tissues. To elucidate Listerin's function we took advantage of the genetic and biochemical tractability of S. cerevisiae and discovered that the yeast Listerin ortholog (Ltn1) is a key player in a novel pathway of protein quality control; more specifically, Ltn1 associates with the 60S ribosomal subunit, and acts as the critical E3 ligase mediating degradation of aberrant nascent polypeptides remaining stalled on ribosomes that are unable to either elongate or terminate translation (2, 3). Subsequent work from others revealed that Ltn1 functions together with other factors as part of the Ribosome‐Associated Quality Control (RQC) complex. I will present ongoing work in the lab towards dissecting mechanisms underlying Ltn1 and RQC function.Support or Funding Information
Nature Bank and Drug Leads for TB
Authors: Quinn Ron 
Published: November 2023

Nature Bank is a unique storehouse of nature's chemical diversity. It consists of over 63,000 biota samples of plants, and marine invertebrates sourced from tropical and temperature Australia, China and Papua New Guinea. These samples have been processed using a 2‐step chromatographic procedure to produce over 200,000 fractions, optimised for high throughput screening. In addition, Nature Bank holds a collection of 3250 pure natural products that have been acquired over twenty years of natural product‐based research. Nature Bank is a core resource in the Eskitis Institute's drug discovery platform.Natural product biosynthesis results in a significant number of compounds (~20 000) with molecular weight ≤ 250 Daltons. This set of small natural products contains around 66% of the pharmacophore space of those natural products with MW > 250 Daltons. Natural products with molecular weight ≤ 250 Da can be used in fragment‐based screening.Multiple‐drug resistance tuberculosis is a serious health problem.We have undertaken two orthogonal screening strategies. 1) HTS of the Nature Bank fraction library against Mycobacterium tuberculosis H37Rv. The HTS tested 202,983 natural product fractions, 452 fractions showed confirmed activity following MIC determination in an 11‐point dose response analysis (serial dilution starting at 1 μL of fraction in 40 μL M. tuberculosis broth). Activity was observed as low as 1 in 256 dilution (2 Hits) with 6 Hits at 1 in 128 dilution and 11 Hits at 1 in 64 dilution.2) Fragment‐based screening using direct observation of ligand‐protein complexes in the ICR cell of a FT mass spectrometer. We screened potential TB drug targets and obtained Hits with 10 proteins. We constructed a Network Map to link the natural products with the proteins.The resultant Network Map analysis has provided a novel approach to progress the fragment Hits.Support or Funding InformationThe work was supported by Bill & Melinda Gates Foundation Grand Challenges Explorations Grants OPP1008376 and OPP1035218 and the Australian Research Council (ARC) Linkage Project (LP120100485). We thank the Australian Research Council (ARC) for support toward NMR and MS equipment (Grant LE0668477 and LE0237908).
Arginine Methylation Modulates RNA Biology Of African Trypanosomes
Authors: Read Laurie K. 
Published: November 2023

Kinetoplastid parasites, including Trypanosoma brucei, T. cruzi, and Leishmania spp. share unique biological features. Prominent among these is the lack of transcriptional control. Instead, kinetoplastids regulate gene expression during development and in response to internal and external cues almost entirely by posttranscriptional processes, including mRNA stability and translation. Thus, RNA binding proteins (RBPs) are the key gene regulatory factors in these organisms. Arginine methylation is a posttranslational modification that disproportionately targets RBPs in humans, yeast, and, T. brucei, the causative agent of Human African Trypanosomiasis. To begin to define the impacts of arginine methylation on T. brucei gene expression, we focused on DRBD18, an abundant and essential protein that contains three methylarginine residues between its two RNA binding domains. DRBD18 has opposing effects on the stabilities of two different cohorts of mRNA, such that DRBD18 depletion leads to significant increases and decreases in the abundances of hundreds of mRNAs, including those encoding several kinases, phosphatases, and RBPs. By analysis of DRBD18 knockdown parasites complemented with wild type, hypomethylated (RK), or methylmimic (RF) DRBD18 we demonstrated that methylation promotes the stabilization of those mRNAs that are typically stabilized by DRBD18, whereas hypomethylated DRBD18 is crippled for this function. In direct contrast, destabilization of a different subset of mRNAs relies on hypomethylated DRBD18, and methylmimic DRBD18 cannot perform this function. DRBD18 interacts with the protein arginine methyltransferase, TbPRMT1, and TbPRMT1 knockdown parasites display phenotypes analogous to those of cells complemented with hypomethylated DRBD18, confirming regulation of DRBD18 by methylation. Our data indicate that arginine methylation impacts the association of both mRNAs and effector proteins with DRBD18. For example, RIP/qRT‐PCR revealed differential association of DRBD18(RF) and DRBD18(RK) with target mRNAs. Through tandem affinity purification and mass spectrometry, we isolated several RBPs that interact with hypomethylated or methylmimic DRBD18 in a mutually exclusive manner. Because DRBD18 target mRNAs have unusually long 3′ UTRs, this suggests that methylation regulates association of DRBD18 with other RBPs, which together lead to combinatorial effects on target mRNA fate. In addition, methylmimic and hypomethylated DRBD18 differentially interact with proteins involved in numerous aspects of RNA biology, including RNA transport, deadenylation, and translation. Together, our results demonstrate that arginine methylation acts a molecular switch towards a major trypanosome RBP, DRBD18, highlighting the power of this posttranslational modification to dramatically remodel the transcriptome.Support or Funding InformationThis work was supported by NIH RO1 AI060260
Effects of Acute n‐3 Fatty Acid Administration on Cardiac Lipid Metabolism and Ca2+ Homeostasis during Ischemia‐Reperfusion
Authors: Zirpoli Hylde , Quadri Nosirudeen , O'Shea Karen M , Ananthakrishan Radha , Abdillahi Mariane , Rosario Rosa , Deckelbaum Richard J , Ramasamy Ravichandran 
Published: November 2023

Omega‐3 fatty acids (n‐3 FA) are bioactive nutrients exerting cardioprotective effects. In our previous study, we showed that acute n‐3 FA emulsion administration after myocardial ischemia/reperfusion (I/R) injury provides cardioprotection by preserving cardiac function and decreasing infarct size. To address molecular mechanisms responsible for their cardioprotective effects we focused on two main pathways: lipid metabolism pathways and Ca2+ signaling, both playing a crucial role during early reperfusion in the metabolic and functional recovery of post‐ischemic myocardium.C57BL/6 murine hearts were perfused using Langendorff technique and the administration of n‐3 triglyceride emulsion (300mgTG/100ml) was performed during the reperfusion. We then studied lipid metabolism and Ca2+ signaling.We first investigated whether acute treatment with n‐3 FA emulsion could modulate lipase activity. However, either myocardial ATGL or HSL expression was not altered by n‐3 FA administration during I/R injury, demonstrating that the uptake of n‐3 FA did not involve lipase‐mediated pathways. AMP‐activated protein kinase (AMPK) and peroxisome proliferator‐activated receptor (PPAR) are critical regulators of lipid metabolism. We then examined whether the activities of these molecules were coordinately regulated by n‐3 FA. After ischemic injury, n‐3 FA induced phosphorylation of AMPK (p<0.05); in contrast, PPARα showed no changes in protein expression after n‐3 FA administration.I/R injury also alters Ca2+ homeostasis through several mechanisms. Na+/Ca2+ exchanger (NCX) activity increases cytosolic Ca2+, causing cell damage. Also, in I/R conditions sarco(endo)plasmic reticulum Ca2+‐ATPase (SERCA2a) dysfunction impairs myocardial contractility and Ca2+ handling. Thus, we questioned whether NCX and SERCA2a might be potential targets for n‐3 FA. n‐3 FA administration after ischemic injury increased both mRNA and protein levels of SERCA2a by 60% (p<0.05). n‐3 FA administration significantly decreased protein level of NCX by 50% (p<0.05), with no effect on its transcript level.Our results suggest that n‐3 FA partially affect lipid metabolism by activating AMPK and regulate intracellular Ca2+ homeostasis through their influence on SERCA2a and NCX modulations in I/R conditions.These effects induced by n‐3 FA may contribute to develop new therapeutic approaches in myocardial infarction.
The Portion Control Strategies Trial: a Year‐long Randomized Controlled Trial on the Impact of Portion Control on Weight Change
Authors: Rolls Barbara J. , James Brittany L. , Sanchez Christine E. , Roe Liane S. 
Published: November 2023

Controlling food and beverage portion sizes can help reduce energy intake, but there are few data on the longer‐term effects on body weight. We tested the efficacy of two portion‐control strategies on weight change over one year. In a randomized controlled trial, overweight and obese women were randomly assigned to one of three equally intensive interventions: two focused on portion control and one provided standard weight loss advice. The Portion Selection Group learned to select appropriate portions based on energy density and received tools such as food scales, and the Pre‐portioned Foods Group learned to structure meals around pre‐portioned foods and received vouchers for commercial frozen entrées. The Standard Advice Group learned to manage weight by following the US Dietary Guidelines to eat less and to make nutritious choices. Participants met individually with trained interventionists weekly in Month 1, biweekly in Months 2–5, and monthly in Months 6–12; all groups received the same advice on increasing physical activity and managing behavior change. The participants were 186 women with a mean (±SEM) age of 50±0.8 y and weight of 201±2.1 lb; 19% were overweight and 81% were obese. A total of 151 women (81%) had their weight measured at the end of the trial. Rates of attendance and withdrawal from the trial were similar across groups. Results were analyzed with a statistical model that estimated a weight loss trajectory for all participants regardless of the number of contacts. Participants in all groups lost weight during the first six months (13.0±0.9 lb) and maintained most of this loss during the second six months (11.4±1.2 lb). In the first three months, however, the Pre‐portioned Foods Group lost weight at a greater rate (P<0.01; 11.0±1.1 lb) than the Portion Selection Group (9.1±1.0 lb) and the Standard Advice Group (8.4±1.0 lb), and subsequently regained more weight. At the end of the year, weight loss did not differ significantly across groups; 45% had lost ≥ 5% of body weight and 20% had lost ≥ 10% of body weight. Physical activity (step counts) increased over time but did not differ across groups. Changes in blood pressure over the course of the trial did not differ across groups. In all groups, waist circumference and fasting glucose decreased, HDL cholesterol increased, and LDL cholesterol did not change over the trial. These results show that for all groups, individual instruction on diet and physical activity facilitated weight loss and maintenance of that loss. In addition, limiting exposure to large portions by using pre‐portioned foods enhanced initial weight loss, but this was not sustained in the longer term.Support or Funding InformationNational Institutes of Health grant DK059853
Utilizing Machine Learning Approaches to Understand the Interrelationship of Diet, the Human Gastrointestinal Microbiome, and Health
Authors: Guetterman Heather , Auvil Loretta , Russell Nate , Welge Michael , Berry Matt , Gatzke Lisa , Bushell Colleen , Holscher Hannah 
Published: November 2023

BackgroundA growing body of literature supports the ability of specific foods and nutrients to impact the gastrointestinal microbiome. However, there is a dearth of knowledge on the interplay of dietary components (e.g. foods and nutrients), gastrointestinal bacteria, and bacterial metabolites. Current analytical approaches limit investigation of these complex interrelations; therefore, further research utilizing modern machine learning methods is needed.ObjectiveWe aimed to fill the gap in knowledge about the interrelationship of diet, the gastrointestinal microbiome, and health by utilizing multivariate approaches that address P>>N, many features but few samples to 1) validate results generated by prototype software with previously published results; and 2) identify novel associations among relevant foods, nutrients, bacteria, and bacterial metabolites.MethodsData generated from a human dietary intervention study that included habitual food and nutrient intake patterns (NHANES food frequency questionnaire), daily dietary intake records, breath gas, and fecal bacteria and metabolite data were analyzed using machine learning approaches. Relevant bacteria, bacterial metabolites, foods, and nutrients were identified using Random Forest and relationships among these relevant features were determined using Maximal Information Coefficient.ResultsBreath hydrogen and agave inulin supplementation were predictive of Bifidobacterium abundance. Habitual diet factors were highly relevant in predicting participant body mass index (BMI). Among bacteria, Phascolarctobacterium, Collinsella, and Erysipelotrichacea were important features for predicting BMI. Oscillospira was associated with habitual dietary glycemic load. Phascolarctobacterium and Eubacterium were associated with habitual intake of deep yellow vegetables. Dietary polyunstaruated fatty acids were relevant in predicting Bacteroidetes to Firmicutes ratios. Total fiber and butyrate were highly relevant in predicting Faecalibacterium abundance.ConclusionsFindings revealed similar associations among diet, bacterial genera, and breath hydrogen measures as previously published results, thereby validating the use of these methods in diet‐microbiome studies. BMI, bacterial abundances, dietary fiber intake, glycemic load, and deep yellow vegetable intake were interrelated. As features of a high quality diet were relevant for predicting bacterial abundances and metabolites, additional work is ongoing to calculate healthy eating index scores. These scores will help delineate purported health benefits (or detriments) of dietary components, bacteria, and bacterial metabolites and aid in identifying targets for future diet‐microbiome studies.Support or Funding InformationThis study was partially funded by the Illinois Applied Research Institute.
Trimethylamine‐N‐oxide biomarker response is a function of dietary precursor intake and gut microbiota composition in healthy young men
Authors: Cho Clara E. , Taesuwan Siraphat , Malysheva Olga V. , Bender Erica , Tulchinsky Nathan F. , Yan Jian , Sutter Jessica L. , Caudill Marie A. 
Published: November 2023

Trimethylamine‐N‐oxide (TMAO) has recently emerged as a novel risk factor for chronic diseases but the contribution of diet and gut microbiota to TMAO production has received limited attention. The objective of this study was to compare TMAO biomarker response to foods that contain TMAO (fish) or its dietary precursors, choline and carnitine (eggs and beef), and to determine whether TMAO response was modified by the gut microbiota. As part of a crossover feeding trial with one‐week washout intervals, healthy young men (n = 40) were randomized to study meals representing animal sources of TMAO (i.e., eggs, beef and fish) and a fruit control. Blood and urine samples were collected at baseline and throughout the 6 h study period, and a one‐time baseline stool was provided. TMAO concentrations in plasma and urine were greatly influenced by dietary precursor intake with fish yielding 50–55 times higher TMAO (P < 0.0001), 11–12 times higher trimethylamine (P < 0.0001) and 5–6 times higher dimethylamine (P < 0.0001) than eggs or beef. Notably, circulating TMAO concentrations in response to the fish study meal were increased within 15 min of consumption suggesting that TMAO itself can be absorbed without undergoing processing by the gut microbes. Analysis of 16S rRNA genes indicated that high‐TMAO producers (those with >20% increase in urinary TMAO response to eggs and beef) had more Firmicutes than Bacteroidetes (P = 0.04), and showed less richness (P = 0.03) in gut microbiota composition than low‐TMAO producers (those with <20% increase in TMAO response). Given the inverse relationship between fish consumption and heart disease, the robust increase in circulating TMAO in response to the fish study meal suggests that TMAO may not contribute to the development of heart disease in humans. In addition, TMAO response to dietary TMAO precursors (eggs and beef) appears to be dependent on the gut microbes demonstrating that TMAO may be a biomarker of the gut microbiota composition. Overall, our data raise questions about the utility of lowering circulating concentrations of TMAO, via dietary or pharmaceutical approaches, as a means to improve human health.Support or Funding InformationEgg Nutrition Center, Beef Checkoff through the National Cattlemen's Beef Association, Canadian Institutes of Health Research Postdoctoral Fellowship
Differences in the Infant Gut Microbiota Related to the Fatty Acid Composition of Human Milk: Results from the GEHM Cohort
Authors: Taft Diana H , Dingess Kelly A , Valentine Christina J , Davidson Barbara S , Ollberding Nicholas J , Ward Doyle V , Brenna J Thomas , McMahon Robert J , Morrow Ardythe L 
Published: November 2023

BackgroundThe fatty acid (FA) composition of human milk varies between mothers, influenced by maternal diet. Available evidence suggests a potential influence of dietary FA on the composition of the gut microbiota, but the impact of dietary FAs on gut microbiota are not well characterized, particularly in breastfed infants.ObjectiveWe conducted a pilot study to assess the impact of variation in human milk FA composition on the infant gut microbiota.MethodsHuman milk and infant stool samples were collected at 4 weeks postpartum from 32 mother‐infant pairs; infants were healthy, term singletons. Human milk FAs were measured by a modified Bligh‐Dyer technique and analyzed by gas chromatography. Stool DNA was extracted using a QiaGen kit with bead beating, and the 16s rRNA gene sequenced by Illumina MiSeq. Using weighted UniFrac, non‐metric multidimensional scaling, and ordisurf in QIIME and R, we tested for associations between the infant gut microbiome and 27 different FAs of human milk, presented as both concentration of individual FAs and as proportion of total FA.ResultsHuman milk octadecanoic acid (18:0: common name, stearic acid) concentration and proportion of total FA was associated with the composition of the infant stool microbial community after adjusting for multiple comparisons (p=0.0002 and p=0.0014). The combination of oleic acid and cis‐vaccenic acid (C18:1n9 plus C18:1n7), when analyzed as a proportion of total fatty acid, was also significantly associated with the composition of the infant stool microbiome (p<0.0001). Streptococcus anginosus was more abundant in infants fed milk with lower levels of stearic acid, while Bacillales, Staphylococcaceae, and Staphylococcus levels were higher in infants fed milk with higher levels of stearic acid. Bifidobacteriales, Bifidobacteriaceae, and Bifidobacterium were more abundant in infants fed milk with lower levels of oleic acid and cis‐vaccenic acid, while Actinomycetaceae and Actinomyces were more abundant in infants fed milk with higher levels of oleic acid and cis‐vaccenic acid. Analysis of maternal diet and human milk FA composition is underway.ConclusionsThis pilot project provides initial evidence that variation in the FAs of human milk is associated with differences in infant gut microbiota. Larger studies are needed to test for differences in the microbiota associated with FA.Support or Funding InformationSupported by Mead Johnson Pediatric Nutrition Institute (MJPNI; research contract (#3140)); NICHD P01 HD13021