Article
Biochemistry & Molecular Biology
Pauline Francois, Hugo Arbes, Stephane Demais, Agnes Baudin-Baillieu, Olivier Namy
Summary: Ribosome profiling, a powerful tool for studying translation regulation, suffers from a lack of standardization in the bioinformatics part, hindering result reproducibility. A unique tool has been proposed to standardize the general steps of RiboSeq analysis, aiming to unify bioinformatics pipelines for translation research.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2021)
Article
Biotechnology & Applied Microbiology
Soma Jana, Partha P. Datta
Summary: The study found that the pI values of translation factors are related to the translation event, where initiation factors are mainly basic, while elongation and release factors are strictly acidic. Among all translation factors, initiation factor 2 (IF2) and ribosome recycling factor (RRF) showed variable pI values that are linked to the order of phylogeny.
Article
Microbiology
Xuejing Fan, Tianyu Bao, Huaxi Yi, Zongcai Zhang, Kenan Zhang, Xin Liu, Xue Lin, Zhen Zhang, Zhen Feng
Summary: The translation efficiency of Lactobacillus rhamnosus under osmotic stress was found to be regulated through co-regulation of differentially expressed genes involved in various metabolic pathways at the translation and transcription levels. This balance between survival and growth of cells was controlled by transcription and translation mechanisms.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Heleen M. van 't Spijker, Emily E. Stackpole, Sandra Almeida, Olga Katsara, Botao Liu, Kuang Shen, Robert J. Schneider, Fen-Biao Gao, Joel D. Richter
Summary: GGGGCC (G(4)C(2)) repeat expansion in the first intron of C9ORF72 leads to amyotrophic lateral sclerosis and frontotemporal dementia. The repeated RNA is translated into neurotoxic DPR proteins. It was found that there are three translation initiation sites in the intron upstream of the (G(4)C(2)) repeats, and ribosomes are stalled on the repeats during translocation. Additionally, the translation process is inhibited by a uORF in the preceding exon.
Article
Biotechnology & Applied Microbiology
Xiaoyu Yang, Bo Song, Jie Cui, Lina Wang, Shuoshuo Wang, Linlin Luo, Lei Gao, Beixin Mo, Yu Yu, Lin Liu
Summary: This study reveals that translational reprogramming plays an important role in rice's response to salt stress, with the salt-tolerant cultivar SR86 adopting a more flexible translational adaptive strategy compared to the salt-sensitive cultivar NB. The differences in translational dynamics under salt stress between NB and SR86 may be due to their varying levels of ribosome stalling.
Article
Cell Biology
Isabella N. Brown, M. Carmen Lafita-Navarro, Maralice Conacci-Sorrell
Summary: The nucleolus plays a crucial role in protein synthesis by producing new ribosomes. In cancer, nucleolar activity is heightened due to increased demand for protein synthesis. The transcription factor MYC promotes nucleolar activity and understanding and potentially inhibiting aberrant nucleolar activity in cancer cells could lead to novel therapeutics.
Review
Biochemistry & Molecular Biology
Vandana Yadav, Inayat Ullah Irshad, Hemant Kumar, Ajeet K. Sharma
Summary: This passage discusses the methods used to extract translation rate parameters from ribosome profiling data and their applications in deciphering the regulation of gene expression. The accurate rate parameters may provide new insights into the kinetic control of the process of gene expression.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2021)
Review
Cell Biology
Marianne Mercer, Seoyeon Jang, Chunyang Ni, Michael Buszczak
Summary: Regulation of mRNA translation is crucial for germ cell development and function across species, involving specific RNA binding proteins. These proteins are conserved and play similar roles in germ cells of various species, highlighting the importance of understanding the mechanisms controlling mRNA translation in germ cells.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2021)
Review
Microbiology
Elizabeth B. B. Sawyer, Teresa Cortes
Summary: Ribosome profiling, a recent addition to the -omics toolkit, provides insights into the process and regulation of translation. In the case of mycobacteria, this method has led to new discoveries about translational regulation and expanded our understanding of canonical translation mechanisms.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Tomoya Fujita, Takeshi Yokoyama, Mikako Shirouzu, Hideki Taguchi, Takuhiro Ito, Shintaro Iwasaki
Summary: This study investigated ribosome pause sites in Escherichia coli using different ribosome profiling strategies, revealing remarkable differences compared to eukaryotes. The identified pause sites were biochemically validated and provided a useful resource for ribosome stalling sites in bacteria.
Article
Biochemistry & Molecular Biology
Tomoya Fujita, Takeshi Yokoyama, Mikako Shirouzu, Hideki Taguchi, Takuhiro Ito, Shintaro Iwasaki
Summary: In this study, ribosome pause sites in Escherichia coli were surveyed using monosome and disome profiling strategies. Compared to eukaryotes, ribosome collisions in bacteria showed remarkable differences, and the identified pause sites were biochemically validated and showed puromycin resistance.
Article
Biochemical Research Methods
Hailin Hu, Xianggen Liu, An Xiao, YangYang Li, Chengdong Zhang, Tao Jiang, Dan Zhao, Sen Song, Jianyang Zeng
Summary: Riboexp is a novel deep reinforcement learning-based framework that successfully models the uneven distribution of ribosomes on mRNA during translation elongation, outperforming existing methods in predicting ribosome density. The application of Riboexp in codon optimization significantly increases protein production, while also providing meaningful biological insights through in-depth analyses.
BRIEFINGS IN BIOINFORMATICS
(2021)
Article
Biochemistry & Molecular Biology
Ravi Tharakan, Ceereena Ubaida-Mohien, Yulan Piao, Myriam Gorospe, Luigi Ferrucci
Summary: As human muscle ages, the translation of proteins related to oxidative phosphorylation, especially those encoded by the mitochondrial genome, decreases, potentially leading to reduced strength and function in old skeletal muscle.
Article
Biochemical Research Methods
Aditi Jain, Arvind Kumar Gupta
Summary: We propose a deterministic mathematical model, called the ribosome flow model with extended objects and abortions (RFMEOA), to describe the flow of ribosomes along a mRNA. The model takes into account important cellular features, including ribosomes covering multiple codons and detachments from various regions due to realistic biological situations like ribosome-ribosome collisions. We prove that the ribosome density profile and protein production rate in the RFMEOA converge to a unique steady-state. Simulations show that an increase in the initiation rate may sometimes lead to a decrease in the production rate, which is a surprising result. We believe this model can provide insight into the effects of premature termination on protein expression and be helpful for understanding and re-engineering the translation process.
IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS
(2023)
Article
Cell Biology
Saisai Wei, Wenhao Guo, Yu Qian, Jie Xiang, Kangli Liu, Xiang-Jing Gao, Xiangwei Gao, Yicheng Chen
Summary: Our study reveals that zinc oxide nanoparticles (ZnO NPs) affect the transcription of 78 genes and translation of 1,448 genes in A549 human lung cancer cells within one hour of exposure. The mitogen-activated protein kinase (MAPK) pathway is up-regulated upon ZnO NP treatment, and upstream open reading frame (uORF) plays a crucial role in the induction of up-regulated genes such as TLNRD1 and CCNB1IP1, which in turn reduces ZnO NP-induced cytotoxicity. This study characterizes the landscape of translational alteration under ZnO NPs treatment and identifies potential targets to enhance the anticancer effect of ZnO NPs.
Article
Nutrition & Dietetics
Abrar M. Babateen, Oliver M. Shannon, Gerard M. O'Brien, Edward Okello, Anmar A. Khan, Sofia Rubele, Emma Wightman, Ellen Smith, Nicholas McMahon, Dilara Olgacer, Christina Koehl, William Fostier, Ines Mendes, David Kennedy, John C. Mathers, Mario Siervo
Summary: The study found that prolonged consumption of beetroot juice is feasible in older overweight and obese adults, leading to increased nitric oxide production and improved health outcomes. Compliance with the interventions was high, indicating potential benefits of nitrate-rich foods on vascular and brain functions.
Article
Biochemistry & Molecular Biology
Hasmik Jasmine Samvelyan, John Cummings Mathers, Timothy Michael Skerry
Summary: The study suggests that fasting/feeding interventions can enhance bone response to mechanical loading in young mice, but not in older mice. The endocrine responses to feeding timing differ between older and young mice, which may affect bone adaptation to loading.
Article
Oncology
Solange Parra-Soto, Fiona C. Malcomson, Frederick K. Ho, Jill P. Pell, Linda Sharp, John C. Mathers, Carlos Celis-Morales
Summary: This study found that ABSI is associated with an increased risk of lung, liver, esophagus, colorectal, and breast cancers, as well as all cancers combined, independently of BMI. Cancer risk prediction improves with the combination of ABSI and BMI.
CANCER EPIDEMIOLOGY BIOMARKERS & PREVENTION
(2022)
Article
Endocrinology & Metabolism
Stella Panagio Breininger, Laura Sabater, Fiona Caroline Malcomson, Sorena Afshar, Jelena Mann, John Cummings Mathers
Summary: Obese individuals show differential microRNA expression in the rectal mucosa compared to non-obese individuals, and weight loss following surgery may normalize this expression. The dysregulated microRNAs in obesity and following weight loss are implicated in pathways related to inflammation, obesity, and cancer.
INTERNATIONAL JOURNAL OF OBESITY
(2022)
Article
Nutrition & Dietetics
Abrar M. Babateen, Oliver M. Shannon, Gerard M. O'Brien, Edward Okello, Ellen Smith, Dilara Olgacer, Christina Koehl, William Fostier, Emma Wightman, David Kennedy, John C. Mathers, Mario Siervo
Summary: The pilot study found that prolonged consumption of nitrate-rich beetroot juice did not significantly affect cognitive function and cerebral blood flow in overweight and obese older participants. Larger studies using more sophisticated imaging methods are needed to confirm these findings and determine the potential influence of prolonged dietary nitrate supplementation on brain function in older overweight individuals.
Editorial Material
Nutrition & Dietetics
John C. Mathers
NUTRITION BULLETIN
(2022)
Article
Oncology
John C. Mathers, Faye Elliott, Finlay Macrae, Jukka-Pekka Mecklin, Gabriela Moslein, Fiona E. McRonald, Lucio Bertario, D. Gareth Evans, Anne-Marie Gerdes, Judy W. C. Ho, Annika Lindblom, Patrick J. Morrison, Jem Rashbass, Raj S. Ramesar, Toni T. Seppala, Huw J. W. Thomas, Harsh J. Sheth, Kirsi Pylvanainen, Lynn Reed, Gillian M. Borthwick, D. Timothy Bishop, John Burn
Summary: The CAPP2 trial found that daily intake of 30 g resistant starch (RS) has a substantial protective effect against non-colorectal cancer for patients with Lynch syndrome (LS).
CANCER PREVENTION RESEARCH
(2022)
Article
Environmental Sciences
Baoya Shang, Shanshan Wang, Lingxia Lu, Huanhuan Ma, Aiqi Liu, Anze Zupanic, Ling Jiang, Aml S. Elnawawy, Yadong Yu
Summary: The reutilization of eggshell waste has gained increasing attention for manufacturing antimicrobial materials to address the public health crisis caused by drug-resistant bacteria. Research has also found that eggshells can be used as raw materials for calcium sources, such as calcium oxide and hydroxyapatite.
JOURNAL OF ENVIRONMENTAL MANAGEMENT
(2022)
Review
Nutrition & Dietetics
Laura Haigh, Colette Kirk, Khalil El Gendy, Jennifer Gallacher, Linda Errington, John C. Mathers, Quentin M. Anstee
Summary: This study synthesized data from randomized and clinical controlled trials to explore the effects of Mediterranean Diet and Calorie Restriction interventions on surrogate markers of non-alcoholic fatty liver disease (NAFLD) in adults. The results showed that these dietary interventions reduced liver function markers and had positive effects on liver steatosis and stiffness. There was a dose-response relationship between the degree of calorie restriction and improvements in liver function and weight loss.
CLINICAL NUTRITION
(2022)
Letter
Oncology
John C. Mathers, Faye Elliott, D. Timothy Bishop, John Burn
CANCER PREVENTION RESEARCH
(2023)
Article
Biochemistry & Molecular Biology
Paula N. Brandao-Lima, Gabrielli B. de Carvalho, Tanyara B. Payolla, Flavia M. Sarti, Regina M. Fisberg, Fiona C. Malcomson, John C. Mathers, Marcelo M. Rogero
Summary: This study evaluated the levels of 21 miRNAs in plasma according to MetS components and sex in adults. The results showed that miR-16 and miR-363 levels were reduced in women with MetS, while men with one or more risk factors showed higher levels of miR-let-7c and miR-30a. Individuals with raised waist circumference, blood pressure, low HDL-cholesterol concentrations, and high fasting plasma glucose and/or insulin resistance exhibited specific miRNA patterns in plasma. These findings suggest that plasma miRNA levels may serve as early biomarkers for the cardiometabolic components of MetS and highlight sex differences in individuals with MetS.
Article
Nutrition & Dietetics
John C. Mathers
Summary: This paper reviews the progress in research on dietary fibre and human health over the past fifty years. The findings indicate that diets low in dietary fibre are associated with increased risk of common non-communicable diseases. Advances in microbiome research have allowed for better understanding of the associations between dietary fibre, the gut microbiome, and human health. The challenge now lies in determining the characteristics of a healthy gut microbiome and implementing interventions to increase dietary fibre intake.
PROCEEDINGS OF THE NUTRITION SOCIETY
(2023)
Article
Nutrition & Dietetics
Longgang Zhao, Michael D. Wirth, Fanny Petermann-Rocha, Solange Parra-Soto, John C. Mathers, Jill P. Pell, Frederick K. Ho, Carlos A. Celis-Morales, James R. Hebert
Summary: Diet can affect the incidence and severity of COVID-19. Analysis of data from the UK biobank found that higher dietary inflammatory index (DII) scores were associated with an increased risk of COVID-19 and greater disease severity. Approximately one-quarter of the positive associations between DII and COVID-19 outcomes were mediated by body mass index.
Article
Biochemistry & Molecular Biology
F. C. Malcomson, J. C. Mathers
Summary: Personalised and precision nutrition uses individual characteristics and responses to nutrients, foods, and dietary patterns to develop targeted nutritional advice for improving health. This approach is moving away from the 'one size fits all' model and may have potential for better population health and disease prevention. While most efforts have focused on obesity and cardiovascular diseases, there is a need to apply personalised and precision nutrition approaches in cancer prevention and for cancer survivors, taking advantage of the understanding of dietary factors, genetics, and the microbiome.
Article
Endocrinology & Metabolism
Khalil Elgendy, Fiona C. Malcomson, Sorena Afshar, Michael D. Bradburn, John C. Mathers
Summary: This study was conducted to investigate the effects of weight loss induced by bariatric surgery on DNA methylation in obese patients. The results showed that bariatric surgery reversed DNA methylation in the rectal mucosa to levels similar to those in individuals without obesity. These findings suggest that bariatric surgery can potentially reduce the risk of cancer and other diseases by reversing DNA methylation.
INTERNATIONAL JOURNAL OF OBESITY
(2023)