Review
Gastroenterology & Hepatology
Djesia Arnone, Caroline Chabot, Anne-Charlotte Heba, Tunay Kokten, Benedicte Caron, Franck Hansmannel, Natacha Dreumont, Ashwin N. Ananthakrishnan, Didier Quilliot, Laurent Peyrin-Biroulet
Summary: Excessive sugar consumption is linked to the rising incidence of diseases such as diabetes, cardiovascular diseases, and cancer. It can disrupt the intestinal barrier and increase susceptibility to infections.
CLINICAL GASTROENTEROLOGY AND HEPATOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Elisabet Alacid, Nicholas A. T. Irwin, Vanessa Smilansky, David S. Milner, Estelle S. Kilias, Guy Leonard, Thomas A. Richards
Summary: This study reveals sequence variation in the SLTS system across the Perkinsozoa, specifically in the parasite Parvilucifera sinerae. The results show that the transcriptome of P. sinerae is segregated based on different spliced-leader exons, suggesting functional differentiation. Furthermore, the SLTS system marks a subsection of the transcriptome with increased mRNA abundance and includes genes necessary for SLTS function.
Article
Agriculture, Dairy & Animal Science
Katherine M. Halloran, Emily C. Hoskins, Claire Stenhouse, Robyn M. Moses, Kathrin A. Dunlap, M. Carey Satterfield, Heewon Seo, Gregory A. Johnson, Guoyao Wu, Fuller W. Bazer
Summary: The study demonstrated that administration of exogenous progesterone in early pregnancy influenced the expression of selected genes for nutrient transporters and a protein involved in polyamine synthesis on day 125 of pregnancy, suggesting a 'programming' effect of progesterone on gene expression that affected the composition of nutrients in fetal-placental fluids.
JOURNAL OF ANIMAL SCIENCE AND BIOTECHNOLOGY
(2021)
Editorial Material
Neurosciences
Jessica T. Y. Yue, Frank A. Duca, Tony K. T. Lam
Summary: A recent study found that the duodenum can distinguish between sugar and sweeteners, but the specific cells involved in this process remain unknown. Researchers engineered a flexible optic fiber for optogenetic manipulation of gut cells in mice, and found that silencing CCK cells in the duodenum reduced the preference for sugar and increased the intake of sweeteners. This study suggests that gut optogenetics may provide insights into how the gut-brain axis regulates feeding and glucose homeostasis.
NATURE NEUROSCIENCE
(2022)
Article
Nutrition & Dietetics
Elena Chiarello, Mattia Di Nunzio, Gianfranco Picone, Giorgia Antonelli, Francesco Capozzi, Alessandra Bordoni
Summary: This study examined the metabolism and absorption of glucose, fructose, and sucrose in enterocytes. The results suggest that fructose is taken up and catabolized more quickly than glucose, and the metabolism of these sugars differs in the cells. Further research is needed to confirm these findings and to explore specific transporters and enzymes involved in sugar metabolism.
Article
Biotechnology & Applied Microbiology
Qiang Tang, Fulei Nie, Juanjuan Kang, Wei Chen
Summary: An innovative method called mRNALocater was proposed to detect the subcellular localization of eukaryotic mRNA by adopting a model fusion strategy. The method utilizes electron-ion interaction pseudopotential and pseudo k-tuple nucleotide composition to encode sequences and employs correlation coefficient filtering algorithm and feature forward search technology to mine hidden feature information, improving prediction accuracy. Results from independent dataset tests show promising performances for predicting eukaryotic mRNA sub-cellular localizations, making mRNALocater a powerful tool in practical applications.
Article
Plant Sciences
Wenyu Xiong, Jie Chen, Junqiang He, Meifang Xiao, Xiaoyu He, Bin Liu, Feng Zeng
Summary: CGSGCG exhibits anti-diabetic effects by reducing blood glucose, improving gut microbiota, and regulating relevant signaling pathways.
PLANT FOODS FOR HUMAN NUTRITION
(2022)
Article
Biochemistry & Molecular Biology
Inaki Milton-Laskibar, Amanda Cuevas-Sierra, Maria P. Portillo, J. Alfredo Martinez
Summary: The study demonstrates that resveratrol administration can improve non-alcoholic fatty liver disease through modulating gut microbiota composition. Resveratrol effectively reduces liver weight and serum cholesterol levels while increasing HDL cholesterol levels. It also prevents obesogenic diet-induced liver damage by improving liver steatosis and inflammation. The results of gut microbiota sequencing show a complex relationship between certain bacteria from the Ruminococcaceae family and hepatic markers.
Article
Multidisciplinary Sciences
Gerda Kildisiute, Waleed M. Kholosy, Matthew D. Young, Kenny Roberts, Rasa Elmentaite, Sander R. van Hooff, Clarissa N. Pacyna, Eleonora Khabirova, Alice Piapi, Christine Thevanesan, Eva Bugallo-Blanco, Christina Burke, Lira Mamanova, Kaylee M. Keller, Karin P. S. Langenberg-Ververgaert, Philip Lijnzaad, Thanasis Margaritis, Frank C. P. Holstege, Michelle L. Tas, Marc H. W. A. Wijnen, Max M. van Noesel, Ignacio Del Valle, Giuseppe Barone, Reinier van der Linden, Catriona Duncan, John Anderson, John C. Achermann, Muzlifah Haniffa, Sarah A. Teichmann, Dyanne Rampling, Neil J. Sebire, Xiaoling He, Ronald R. de Krijger, Roger A. Barker, Kerstin B. Meyer, Omer Bayraktar, Karin Straathof, Jan J. Molenaar, Sam Behjati
Summary: The neuroblastoma cancer cells resemble fetal sympathoblasts, indicating a pan-neuroblastoma cancer cell state that could potentially be targeted for novel treatment strategies. The findings highlight the importance of understanding the phenotype of neuroblastoma cells for the development of immunotherapeutic and targeted avenues.
Article
Gastroenterology & Hepatology
David C. Montrose, Ryohei Nishiguchi, Srijani Basu, Hannah A. Staab, Xi Kathy Zhou, Hanhan Wang, Lingsong Meng, Melanie Johncilla, Juan R. Cubillos-Ruiz, Diana K. Morales, Martin T. Wells, Kenneth W. Simpson, Shiying Zhang, Belgin Dogan, Chen Jiao, Zhangjun Fei, Akihiko Oka, Jeremy W. Herzog, R. Balfour Sartor, Andrew J. Dannenberg
Summary: Excessive dietary fructose consumption exacerbates colitis by altering the composition, distribution, and metabolic function of resident enteric microbiota, leading to increased access of gut luminal microbes to the colonic mucosa, reduced protective commensal microbes, and increased luminal conjugated bile acids, all of which worsen colitis.
CELLULAR AND MOLECULAR GASTROENTEROLOGY AND HEPATOLOGY
(2021)
Article
Biology
Johan Reimegard, Marcel Tarbier, Marcus Danielsson, Jens Schuster, Sathishkumar Baskaran, Styliani Panagiotou, Niklas Dahl, Marc R. Friedlander, Caroline J. Gallant
Summary: The SPARC method combines single-cell RNA sequencing with proximity extension assays to measure global mRNA and 89 intracellular proteins simultaneously in individual cells. Results show that mRNA expression does not accurately reflect protein abundance, with protein levels of transcription factors better predicting downstream effects. Overall, protein expression variation is lower than mRNA variation in single cells, but relative protein variation does not correlate with mRNA level.
COMMUNICATIONS BIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Anoop T. Ambikan, Hong Yang, Shuba Krishnan, Sara Svensson Akusjarvi, Soham Gupta, Magda Lourda, Maike Sperk, Muhammad Arif, Chenq Zhang, Hampus Nordqvist, Sivasankaran Munusamy Ponnan, Anders Sonnerborg, Carl Johan Treutiger, Liam O'Mahony, Adil Mardinoglu, Rui Benfeitas, Ujjwal Neogi
Summary: This study used system-wide network-based system biology analysis to identify potential determinants of COVID-19 severity at personalized and group levels. The results indicated the significant role of mononuclear phagocytes in coordinating immune cells and identified certain genes and metabolites that could play a crucial role in COVID-19 severity. The study also suggested metabolic perturbations targeting the central metabolic pathway as an alternative treatment strategy for severe COVID-19.
Article
Biotechnology & Applied Microbiology
Anna A. Feitzinger, Anthony Le, Ammon Thompson, Mehnoor Haseeb, Mohan Koumar Murugesan, Austin M. Tang, Susan E. Lott
Summary: Overall, maternal transcripts are more conserved while zygotic transcripts evolve at a higher rate. Within-population variation in transcript abundance is greater than between populations, and expression variation is highest post-MZT between African lines.
Article
Multidisciplinary Sciences
Dillion M. Fox, Kim M. Branson, Ross C. Walker
Summary: The study investigates the potential impact of using quantum computing technology for codon optimization, demonstrating that a Quantum Annealer is competitive in identifying optimal solutions. The utility of gate-based systems is also evaluated, suggesting that future generation devices may be highly efficient.
Article
Biochemistry & Molecular Biology
Lin Lyu, Xue Li, Ru Feng, Xin Zhou, Tuhin K. Guha, Xiaofei Yu, Guo Qiang Chen, Yufeng Yao, Bing Su, Duowu Zou, Michael P. Snyder, Lei Chen
Summary: We developed an analysis pipeline called spatial metatranscriptome (SMT) that extracts microbial sequences from spatial transcriptomic (ST) data, assigns taxonomic labels, and generates a spatial microbial abundance matrix. The pipeline was applied to human and murine intestinal sections and validated with alternative assays. This work provides biological insights into host-microbe interactions at different spatial scales and demonstrates the feasibility of SMT analysis.
Article
Biochemistry & Molecular Biology
Jinki Yeom, Eduardo A. Groisman
Summary: In times of nutrient scarcity, microorganisms like Salmonella enterica serovar Typhimurium can preserve functional proteins by inhibiting their degradation, allowing for a rapid return to growth once nutrients become available. This strategy is conserved across different microbial species and facilitates quick recovery from slow-growth states.
Article
Genetics & Heredity
Hubert Salvail, Jeongjoon Choi, Eduardo A. Groisman
Summary: Operon organization can lead to the concerted transcription of genes, with some operons producing two mRNAs but only allowing translation of certain genes. In the case of a bicistronic operon involving the novel gene ugtS and the virulence gene ugtL in Salmonella enterica serovar Typhimurium, only the longer mRNA permits translation of both genes. The small protein UgtS plays a role in regulating the virulence program by controlling the phosphorylation kinetics of the master virulence regulator PhoP.
Article
Multidisciplinary Sciences
Jeongjoon Choi, Matias Schmukler, Eduardo A. Groisman
Summary: Horizontal gene transfer drives bacterial evolution, and H-NS proteolysis is a mechanism essential for derepressing foreign genes and colonization of mammalian hosts.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Biochemistry & Molecular Biology
Weiwei Han, Bee-Zen Peng, Chunyan Wang, Guy E. Townsend II, Natasha A. Barry, Frank Peske, Andrew L. Goodman, Jun Liu, Marina Rodnina, Eduardo A. Groisman
Summary: Protein synthesis is a vital cellular process that requires a significant amount of energy. However, cells can sustain protein synthesis under starvation conditions through the use of a bacterial elongation factor called EF-C2, which promotes translocation without hydrolyzing GTP. EF-G2, a variant of EF-C2, is crucial for bacterial gut colonization and can sustain protein synthesis at slower rates. EF-G2 is more abundant than canonical EF-C1 and specifically accumulates during carbon starvation. A unique 26-residue region in EF-G2 is essential for protein synthesis, dissociation from the ribosome, and the absence of GTPase activity. These findings provide insights into how cells minimize energy consumption while maintaining protein synthesis in fluctuating nutrient environments.
Article
Multidisciplinary Sciences
Jennifer L. Modesto, Victoria H. Pearce, Guy E. Townsend
Summary: The presence of distinct glycans in heterogeneous mixtures is challenging to detect due to structural complexity and diversity. In this study, the authors exploit the sensing abilities of gut microbes to develop quantitative glycan biosensors. They couple the bacterial detection machinery with an optimized luciferase reporter to indicate the presence and abundance of compositionally similar, yet structurally distinct glycans. These tools can greatly enhance our understanding of the mammalian gut environment and identify host-microbial interactions critical for human health.
NATURE COMMUNICATIONS
(2023)
Article
Multidisciplinary Sciences
Emilia Krypotou, Guy E. Townsend, Xiaohui Gao, Shoichi Tachiyama, Jun Liu, Nick D. Pokorzynski, Andrew L. Goodman, Eduardo A. Groisman
Summary: Therapeutic manipulation of the gut microbiota has great potential for human health. Bacteria in the gut use phase separation to enhance their fitness and this mechanism can be targeted for clinical intervention. The intrinsically disordered region (IDR) of the transcription termination factor Rho is crucial for phase separation and gene regulation in the gut. Phase separation is vital for host-commensal bacteria interactions and has implications for novel clinical applications.
Article
Biochemistry & Molecular Biology
Eduardo A. A. Groisman, Jeongjoon Choi
Summary: Horizontal gene transfer plays a significant role in bacterial evolution. Enteric bacteria such as Salmonella Typhimurium and Escherichia coli break down the silencing effect of H-NS protein on horizontally acquired genes by using the same protease, Lon, in different environments. Anti-silencing proteins displace H-NS from AT-rich DNA, making H-NS susceptible to degradation and decreasing its overall amounts. The conservation of amino acid sequences in the Lon protease and H-NS cleavage site suggests a common mechanism for exploiting horizontally acquired genes in diverse bacteria.
Review
Microbiology
Nick D. Pokorzynski, Eduardo A. Groisman
Summary: Cells adjust growth and metabolism to nutrient availability. Facultative intracellular pathogens must efficiently prioritize carbon utilization in order to survive in their animal hosts. Bacterial regulators of carbon metabolism control virulence programs, while signals controlling virulence regulators may impact carbon source utilization. Intestinal inflammation and disruption of the gut microbiota can also influence the availability of carbon sources. Coordination between virulence factors and carbon utilization determinants allows pathogens to adopt metabolic pathways that promote antimicrobial resistance and overcome nutrient deprivation imposed by the host.
MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS
(2023)
Article
Gastroenterology & Hepatology
Victoria H. Pearce, Eduardo A. Groisman, Guy E. Townsend II
Summary: The mammalian gut microbiota plays a crucial role in human health and has therapeutic potential for treating various diseases. Dietary factors, particularly simple sugars, can alter the composition of gut microbiota and lead to pathogenic outcomes. This study reveals a molecular pathway through which dietary sugars can silence a key regulator of carbohydrate utilization in gut microbiota, highlighting the potential for targeted interventions in modulating microbial populations for therapeutic purposes.
Correction
Multidisciplinary Sciences
R. J. L. Townshend
Correction
Microbiology
Alexandre Duprey, Eduardo A. Groisman