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Stable Isotope Tracing In Vivo Reveals A Metabolic Bridge Linking The Microbiota To Host Histone Acetylation

Peder Lund, Leah Gates, Marylene Leboeuf, Sarah Smith, Lillian Chau, Elliot Friedman, Mariana Lopes, Yedidya Saiman, Min Soo Kim, Christopher Petucci, David Allis, Gary Wu, Benjamin Garcia,

The gut microbiota influences host epigenetics by fermenting dietary fiber into butyrate. Although butyrate could promote histone acetylation by inhibiting histone deacetylases, it may also undergo oxidation to acetyl-CoA, a necessary cofactor for histone acetyltransferases. Here, we find that epithelial cells from germ-free mice harbor a loss of histone H4 ... Read more >>

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Global Microbiota-Dependent Histone Acetylation Patterns Are Irreversible and Independent of Short Chain Fatty Acids.

Yedidya Saiman, Ting-Chin David Shen, Peder J Lund, Victoria M Gershuni, Cholsoon Jang, Shivali Patel, Sunhee Jung, Emma E Furth, Elliot S Friedman, Lillian Chau, Benjamin A Garcia, Gary D Wu,

<h4>Background and aims</h4>Although germ-free mice are an indispensable tool in studying the gut microbiome and its effects on host physiology, they are phenotypically different than their conventional counterparts. While antibiotic-mediated microbiota depletion in conventional mice leads to physiologic alterations that often mimic the germ-free state, the degree to which the ... Read more >>

Hepatology (Hepatology (Baltimore, Md.))
[2021, :]

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FEVER: The Flexed Elbow Valgus External Rotation View for MRI Evaluation of the Ulnar Collateral Ligament in Throwing Athletes-A Pilot Study in Major League Baseball Pitchers.

Pamela J Lund, Gary Waslewski, Ken Crenshaw, Mari Schenk, Graham Munday, Thomas Knoblauch, Alan Rodriguez, Travis Snyder,

<b>Background:</b> Ulnar collateral ligament (UCL) injuries are common in throwing athletes due to repetitive extreme valgus stress during overhead throwing maneuvers. Conventional positioning for elbow MRI provides suboptimal rendering of the UCL. <b>Objective:</b> To perform a prospective pilot study assessing the impact of a flexed elbow valgus external rotation (FEVER) ... Read more >>

AJR Am J Roentgenol (AJR. American journal of roentgenology)
[2021, :]

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Validation of ctDNA Quality Control Materials Through a Precompetitive Collaboration of the Foundation for the National Institutes of Health.

P Mickey Williams, Thomas Forbes, Steven P Lund, Kenneth D Cole, Hua-Jun He, Chris Karlovich, Cloud P Paweletz, Daniel Stetson, Laura M Yee, Dana E Connors, Susan M Keating, Benoit Destenaves, Megan H Cleveland, Christie J Lau, J Carl Barrett, Gary J Kelloff, Robert T McCormack,

We report the results from a Foundation for the National Institutes of Health Biomarkers Consortium project to address the absence of well-validated quality control materials (QCMs) for circulating tumor DNA (ctDNA) testing. This absence is considered a cause of variance and inconsistencies in translating ctDNA results into clinical actions.<h4>Methods</h4>In this ... Read more >>

JCO Precis Oncol (JCO precision oncology)
[2021, 5:]

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Social Normativity of Research Methods and the Methodological Discrepancy between Mainstream Psychological Research and Danish Psychology Students' Master's Thesis Projects.

Thomas Szulevicz, Peter Clement Lund, Rolf Lyneborg Lund,

In this paper, we take a closer look at Danish psychology students' Master's thesis projects. We do this by analysing 4,100 descriptions of all Master's theses in Danish psychology study programs between 2014 and 2019. Via a sentiment analysis of the data material, we identify and categorize the different theses ... Read more >>

Integr Psychol Behav Sci (Integrative psychological & behavioral science)
[2021, :]

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Effect of protein concentrate mixtures and dietary addition of exogenous phytase on major milk minerals and proteins, including casein phosphorylation.

N A Poulsen, G Giagnoni, M Johansen, P Lund, L B Larsen,

Variations in major milk minerals, proteins, and their posttranslational modifications are largely under genetic influence, whereas the effect of nongenetic factors is less studied. Through a controlled feeding experiment (incomplete balanced Latin square design), the effect of concentrate mixtures, based on fava beans, rapeseed meal, or soybean meal as main ... Read more >>

J Dairy Sci (Journal of dairy science)
[2021, :]

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Effect of exogenous dietary phytase and concentrate mixtures based on faba beans, rapeseed meal or soybean meal as main protein source on phytate and total phosphorus excretion in dairy cows

G Giagnoni, P Lund, J Sehested, M Johansen,

The aim of this study was to test the effect of exogenous dietary phytase on in vivo phytate P and total P excretion in dairy cows fed three different concentrate mixtures. Excretion and apparent total tract digestibility (ATTD) of phytate P and total P were measured in 24 Danish Holstein ... Read more >>

Anim Feed Sci Technol (Animal feed science and technology.)
[2021, 276:Not Available]

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Functional, metabolic and transcriptional maturation of stem cell derived beta cells

Diego Balboa, Tom Barsby, Väinö Lithovius, Jonna Saarimäki-Vire, Muhmmad Omar-Hmeadi, Oleg Dyachok, Hossam Montaser, Per-Eric Lund, Mingyu Yang, Hazem Ibrahim, Anna Näätänen, Vikash Chandra, Helena Vihinen, Eija Jokitalo, Jouni Kvist, Jarkko Ustinov, Anni Nieminen, Emilia Kuuluvainen, Ville Hietakangas, Pekka Katajisto, Joey Lau, Per-Ola Carlsson, Sebastian Barg, Anders Tengholm, Timo Otonkoski,

Transplantation of pancreatic islet cells derived from human pluripotent stem cells is a promising treatment for diabetes. Despite progress in stem cell-derived islet (SC-islet) generation, detailed characterization of their functional properties has not been conducted. Here, we generated functionally mature SC-islets using an optimized protocol and comprehensively benchmarked them against ... Read more >>

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Fava beans can substitute soybean meal and rapeseed meal as protein source in diets for lactating dairy cows.

N P Hansen, M Johansen, L Wiking, M Larsen, P Lund, T Larsen, M R Weisbjerg,

The effect of replacing mixtures of wheat and soybean meal and wheat and rapeseed meal by toasted fava beans, and the effect of toasting fava beans on feed intake, milk yield, and composition of milk and feces were investigated using 40 Holstein cows in each of two 4 × 4 ... Read more >>

J Dairy Sci (Journal of dairy science)
[2021, 104(5):5508-5521]

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Reactions to and explanations for the birth of a baby with albinism: a qualitative study in Busoga, Uganda.

Julie Taylor, C Bradbury-Jones, Peter Ogik, Fazira Kawuma, Jane Betts, Patricia Lund,

<h4>Objectives</h4>Babies born with the genetic condition albinism lack pigment in their hair, skin and eyes due to compromised melanin production. This leads to poor vision and the risk of early death due to skin cancer. In Uganda, one of the least developed countries in the world, their lack of pigmentation ... Read more >>

BMJ Open (BMJ open)
[2021, 11(2):e040992]

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Residual carbon dioxide as an index of feed efficiency in lactating dairy cows.

Pekka Huhtanen, Alireza Bayat, Peter Lund, Abdulai Guinguina,

High feed costs make feed conversion efficiency a desirable target for genetic improvement. Residual feed intake (RFI), calculated as the difference between observed and predicted intake, is a commonly used estimate of feed efficiency. However, determination of feed efficiency in dairy herds is challenging due to difficulties in measuring feed ... Read more >>

J Dairy Sci (Journal of dairy science)
[2021, 104(5):5332-5344]

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Impact of UHT treatment and storage on liquid infant formula: Complex structural changes uncovered by centrifugal field-flow fractionation with multi-angle light scattering.

Pernille Lund, Søren Bang Nielsen, Christian Fiil Nielsen, Colin A Ray, Marianne N Lund,

Protein modifications in liquid infant formula (IF) have been widely studied, but distinguishing between heat- and storage-induced structural changes remains challenging. A generic liquid IF was subjected to direct or indirect UHT treatment and stored at 40 °C up to 180 days. Colour and pH were monitored and structural changes were characterised ... Read more >>

Food Chem (Food chemistry)
[2021, 348:129145]

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Mapping the Transcriptional and Fitness Landscapes of a Pathogenic E. coli Strain: The Effects of Organic Acid Stress under Aerobic and Anaerobic Conditions.

Francesca Bushell, John M J Herbert, Thippeswamy H Sannasiddappa, Daniel Warren, A Keith Turner, Francesco Falciani, Peter A Lund,

Several methods are available to probe cellular responses to external stresses at the whole genome level. RNAseq can be used to measure changes in expression of all genes following exposure to stress, but gives no information about the contribution of these genes to an organism's ability to survive the stress. ... Read more >>

Genes (Basel) (Genes)
[2020, 12(1):]

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Improving robustness and accuracy of predicted daily methane emissions of dairy cows using milk mid-infrared spectra.

Amélie Vanlierde, Frédéric Dehareng, Nicolas Gengler, Eric Froidmont, Sinead McParland, Michael Kreuzer, Matthew Bell, Peter Lund, Cécile Martin, Björn Kuhla, Hélène Soyeurt,

<h4>Background</h4>A robust proxy for estimating methane (CH<sub>4</sub> ) emissions of individual dairy cows would be valuable especially for selective breeding. This study aimed to improve the robustness and accuracy of prediction models that estimate daily CH<sub>4</sub> emissions from milk Fourier transform mid-infrared (FT-MIR) spectra by (i) increasing the reference dataset ... Read more >>

J Sci Food Agric (Journal of the science of food and agriculture)
[2021, 101(8):3394-3403]

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Challenges and opportunities to capture dietary effects in on-farm greenhouse gas emissions models of ruminant systems.

Ronaldo Vibart, Cecile de Klein, Arjan Jonker, Tony van der Weerden, André Bannink, Ali R Bayat, Les Crompton, Anais Durand, Maguy Eugène, Katja Klumpp, Björn Kuhla, Gary Lanigan, Peter Lund, Mohammad Ramin, Francisco Salazar,

This paper reviews existing on-farm GHG accounting models for dairy cattle systems and their ability to capture the effect of dietary strategies in GHG abatement. The focus is on methane (CH<sub>4</sub>) emissions from enteric and manure (animal excreta) sources and nitrous oxide (N<sub>2</sub>O) emissions from animal excreta. We identified three ... Read more >>

Sci Total Environ (The Science of the total environment)
[2021, 769:144989]

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Use of a model to understand the synergies underlying the antibacterial mechanism of H2O2-producing honeys.

Maria Masoura, Paolo Passaretti, Tim W Overton, Pete A Lund, Konstantinos Gkatzionis,

Honey has been valued as a powerful antimicrobial since ancient times. However, the understanding of the underlying antibacterial mechanism is incomplete. The complexity and variability of honey composition represent a challenge to this scope. In this study, a simple model system was used to investigate the antibacterial effect of, and ... Read more >>

Sci Rep (Scientific reports)
[2020, 10(1):17692]

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Across kingdom biased CYP-mediated metabolism via small-molecule ligands docking on P450 oxidoreductase

Simon Bo Jensen, Sara Thodberg, Shaheena Parween, Matias Moses, Cecilie Hansen, Johannes Thomsen, Magnus Sletfjerding, Camilla Knudsen, Rita Del Giudice, Philip Lund, Patricia Castaño, Yanet Bustamante, Flemming Jørgensen, Amit Pandey, Tomas Laursen, Birger Lindberg Møller, Nikos Hatzakis,

Metabolic control is mediated by the dynamic assemblies and function of multiple redox enzymes. A key element in these assemblies, the P450 oxidoreductase (POR), donates electrons and selectively activates numerous (>50 in humans and >300 in plants) cytochromes P450 (CYPs) controlling metabolism of drugs, steroids and xenobiotics in humans and ... Read more >>

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Understanding How Microorganisms Respond to Acid pH Is Central to Their Control and Successful Exploitation.

Peter A Lund, Daniela De Biase, Oded Liran, Ott Scheler, Nuno Pereira Mira, Zeynep Cetecioglu, Estefanía Noriega Fernández, Sara Bover-Cid, Rebecca Hall, Michael Sauer, Conor O'Byrne,

Microbes from the three domains of life, <i>Bacteria</i>, <i>Archaea</i>, and <i>Eukarya</i>, share the need to sense and respond to changes in the external and internal concentrations of protons. When the proton concentration is high, acidic conditions prevail and cells must respond appropriately to ensure that macromolecules and metabolic processes are ... Read more >>

Front Microbiol (Frontiers in microbiology)
[2020, 11:556140]

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Lysine and Arginine Protein Post-translational Modifications by Enhanced DIA Libraries: Quantification in Murine Liver Disease.

Aaron E Robinson, Aleksandra Binek, Vidya Venkatraman, Brian C Searle, Ronald J Holewinski, George Rosenberger, Sarah J Parker, Nathan Basisty, Xueshu Xie, Peder J Lund, Gautam Saxena, José M Mato, Benjamin A Garcia, Birgit Schilling, Shelly C Lu, Jennifer E Van Eyk,

Proteoforms containing post-translational modifications (PTMs) represent a degree of functional diversity only harnessed through analytically precise simultaneous quantification of multiple PTMs. Here we present a method to accurately differentiate an unmodified peptide from its PTM-containing counterpart through data-independent acquisition-mass spectrometry, leveraging small precursor mass windows to physically separate modified peptidoforms ... Read more >>

J Proteome Res (Journal of proteome research)
[2020, 19(10):4163-4178]

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Across kingdom biased CYP-mediated metabolism via small-molecule ligands docking on P450 oxidoreductase

Simon Jensen, Sara Thodberg, Shaheena Parween, Matias Moses, Cecilie hansen, Johannes Thomsen, Magnus Sletfjerding, Camilla knudsen, Rita Giudice, Philip Lund, patricia castano, Yanet Bustamante, Flemming Jørgensen, Amit Pandey, Tomas Laursen, Birger Møller, Nikos Hatzakis,

Metabolic control is mediated by the dynamic assemblies and function of multiple redox enzymes. A key element in these assemblies, the P450 oxidoreductase (POR), donates electrons and selectively activates numerous (>50 in humans and >300 in plants) cytochromes P450 (CYPs) controlling metabolism of drugs, steroids and xenobiotics in humans and ... Read more >>

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PROFILING OF Y1 CELLS TREATED WITH FGF-2 REVEALS PARALLELS WITH ONCOGENE-INDUCED SENESCENCE

Peder Lund, Mariana Lopes, Simone Sidoli, Mariel Coradin, Francisca Nathália de Luna Vitorino, Julia Pinheiro Chagas da Cunha, Benjamin Aaron Garcia,

<h4>ABSTRACT</h4> Paradoxically, oncogenes that drive cell cycle progression may also trigger pathways leading to senescence, thereby inhibiting the growth of tumorigenic cells. Along these lines, Y1 cells, which carry an amplification of Ras, become senescent after treatment with the mitogen FGF-2. To understand how FGF-2 promotes senescence, we profiled the ... Read more >>

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AscA (YecA) is a molecular chaperone involved in Sec-dependent protein translocation inEscherichia coli

Tamar Cranford Smith, Max Wynne, Cailean Carter, Chen Jiang, Mohammed Jamshad, Mathew Milner, Yousra Djouider, Emily Hutchinson, Peter Lund, Ian Henderson, Damon Huber,

<h4>ABSTRACT</h4> Proteins that are translocated across the cytoplasmic membrane by Sec machinery must be in an unfolded conformation in order to pass through the protein-conducting channel during translocation. Molecular chaperones assist Sec-dependent protein translocation by holding substrate proteins in an unfolded conformation in the cytoplasm until they can be delivered ... Read more >>

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Application of a Triple-Conducting Heterostructure Electrolyte of Ba0.5Sr0.5Co0.1Fe0.7Zr0.1Y0.1O3-δ and Ca0.04Ce0.80Sm0.16O2-δ in a High-Performance Low-Temperature Solid Oxide Fuel Cell.

Sajid Rauf, Bin Zhu, M A K Yousaf Shah, Zuhra Tayyab, Sanam Attique, Nasir Ali, Naveed Mushtaq, Baoyuan Wang, Changping Yang, Muhammad Imran Asghar, Peter D Lund,

Dual-ion electrolytes with oxygen ion and proton-conducting properties are among the innovative solid oxide electrolytes, which exhibit a low Ohmic resistance at temperatures below 550 °C. BaCo<sub>0.4</sub>Fe<sub>0.4</sub>Zr<sub>0.1</sub>Y<sub>0.1</sub>O<sub>3-δ</sub> with a perovskite-phase cathode has demonstrated efficient triple-charge conduction (H<sup>+</sup>/O<sup>2-</sup>/e<sup>-</sup>) in a high-performance low-temperature solid oxide fuel cell (LT-SOFC). Here, we designed another ... Read more >>

ACS Appl Mater Interfaces (ACS applied materials & interfaces)
[2020, 12(31):35071-35080]

Cited: 2 times

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Short communication: Variation in feed efficiency hampers use of carbon dioxide as a tracer gas in measuring methane emissions in on-farm conditions.

P Huhtanen, A R Bayat, P Lund, A L F Hellwing, M R Weisbjerg,

Breeding cows for low CH<sub>4</sub> emissions requires that the trait is variable and that it can be recorded with low cost from an adequate number of individuals and with high precision, but not necessarily with high accuracy if the trait is measured with high repeatability. The CH<sub>4</sub>:CO<sub>2</sub> ratio in expired ... Read more >>

J Dairy Sci (Journal of dairy science)
[2020, 103(10):9090-9095]

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Between-cow variation in the components of feed efficiency.

A Guinguina, T Yan, P Lund, A R Bayat, A L F Hellwing, P Huhtanen,

A meta-analysis based on an individual-cow data set was conducted to investigate between-cow variations in the components and measurements of feed efficiency (FE) and to explore the associations among these components. Data were taken from 31 chamber studies, consisting of a total of 841 cow/period observations. The experimental diets were ... Read more >>

J Dairy Sci (Journal of dairy science)
[2020, 103(9):7968-7982]

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