Article
Biochemical Research Methods
Klairton Lima Brito, Alexsandro Oliveira Alexandrino, Andre Rodrigues Oliveira, Ulisses Dias, Zanoni Dias
Summary: Most existing mathematical models for genome rearrangement problems consider only gene order, but recent research has started to incorporate more information such as intergenic region sizes. This study investigates a new variation where the target intergenic region sizes have a range of acceptable values, allowing flexibility in transforming gene order while considering variations in intergenic regions. The authors present approximation algorithms and an NP-hardness proof for the problem, relying on the Flexible Weighted Cycle Graph.
IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS
(2023)
Article
Multidisciplinary Sciences
Dimitrios Vitsios, Ryan S. Dhindsa, Dorota Matelska, Jonathan Mitchell, Xuequing Zou, Joshua Armenia, Fengyuan Hu, Quanli Wang, Ben Sidders, Andrew R. Harper, Slave Petrovski
Summary: Large reference datasets have allowed us to determine germline genetic variation intolerance in genes and genic subregions. We introduced a new metric, OncMTR, which identified genic subregions enriched with cancer-driving mutations that are depleted of germline variation. OncMTR significantly predicted driver mutations in hematologic malignancies and improved genetic signals for these diseases.
Article
Computer Science, Interdisciplinary Applications
Gabriel Siqueira, Alexsandro Oliveira Alexandrino, Zanoni Dias
Summary: Genome rearrangement distance problems estimate the evolutionary distance between genomes. This study introduces a new model considering intergenic regions and multiple copies of genes. It proposes a series of problems and approximation algorithms, and demonstrates their effectiveness through experimental tests.
JOURNAL OF COMBINATORIAL OPTIMIZATION
(2023)
Article
Clinical Neurology
Jaeyoon Chung, Anjali Das, Xinyu Sun, Debora R. Sobreira, Yuk Yee Leung, Catherine Igartua, Sahar Mozaffari, Yi-Fan Chou, Sam Thiagalingam, Jesse Mez, Xiaoling Zhang, Gyungah R. Jun, Thor D. Stein, Brian W. Kunkle, Eden R. Martin, Margaret A. Pericak-Vance, Richard Mayeux, Jonathan L. Haines, Gerard D. Schellenberg, Marcelo A. Nobrega, Kathryn L. Lunetta, Jayant M. Pinto, Li-San Wang, Carole Ober, Lindsay A. Farrer
Summary: Variants in the MGMT gene are associated with the development of Alzheimer's disease (AD), particularly in women. Multi-omics analyses suggest that this association may be mediated by the regulation of MGMT expression.
ALZHEIMERS & DEMENTIA
(2023)
Article
Biochemical Research Methods
Alexsandro Oliveira Alexandrino, Andre Rodrigues Oliveira, Ulisses Dias, Zanoni Dias
Summary: The genome rearrangement field focuses on minimizing the number of genome rearrangements through pairwise genome comparisons. Models should consider gene order, intergenic regions, and types of rearrangement events.
JOURNAL OF BIOINFORMATICS AND COMPUTATIONAL BIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Pirro G. Hysi, Massimo Mangino, Paraskevi Christofidou, Mario Falchi, Edward D. Karoly, Robert P. Mohney, Ana M. Valdes, Tim D. Spector, Cristina Menni
Summary: This study conducted a genome-wide association study on the levels of circulating metabolites in European subjects, identifying 202 unique genomic regions associated with 478 different metabolites. The replication study confirmed the robustness of these associations and discovered 74 novel genomic regions not previously associated with any metabolites.
Article
Agronomy
Amrit Kumar Nayak, C. Anilkumar, Sasmita Behera, Rameswar Prasad Sah, Gera Roopa Lavanya, Awadhesh Kumar, Lambodar Behera, Muhammed Azharudheen Tp
Summary: The new cgSSR markers associated with grain size traits have a significant impact on practical plant breeding to increase the number of causative alleles for these traits through marker aided rice breeding programs.
Article
Clinical Neurology
Line Skotte, Joao Fadista, Jonas Bybjerg-Grauholm, Vivek Appadurai, Michael S. Hildebrand, Thomas F. Hansen, Karina Banasik, Jakob Grove, Clara Albinana, Frank Geller, Carmen F. Bjurstrom, Bjarni J. Vilhjalmsson, Matthew Coleman, John A. Damiano, Rosemary Burgess, Ingrid E. Scheffer, Ole Birger Vesterager Pedersen, Christian Erikstrup, David Westergaard, Kaspar Rene Nielsen, Erik Sorensen, Mie Topholm Bruun, Xueping Liu, Henrik Hjalgrim, Tune H. Pers, Preben Bo Mortensen, Ole Mors, Merete Nordentoft, Julie W. Dreier, Anders D. Borglum, Jakob Christensen, David M. Hougaard, Alfonso Buil, Anders Hviid, Mads Melbye, Henrik Ullum, Samuel F. Berkovic, Thomas Werge, Bjarke Feenstra
Summary: This study conducted a genome-wide association study of febrile seizures and discovered seven new loci, as well as confirmed four previously reported loci, all related to genes associated with central fever response, neuronal excitability, and epilepsy. The findings also showed positive genetic correlations with epilepsy and a lower polygenic risk in febrile seizure patients with neuropsychiatric disease.
Article
Agriculture, Multidisciplinary
Ren Yun, Chen Dan, Li Wen-jie, Tao Luo, Yuan Guo-qiang, Cao Ye, Li Xue-mei, Deng Qi-ming, Wang Shi-quan, Zheng Ai-ping, Zhu Jun, Liu Huai-nian, Wang Ling-xia, Li Ping, Li Shuang-cheng
Summary: This study conducted pedigree-based analysis of the elite backbone parent rice variety SH527 to identify key genomic regions for hybrid rice breeding, revealing the unique contributions of progenitors to SH527 and the conserved key genomic regions within all its derivatives. These findings provide insights into hybrid rice breeding and highlight the importance of certain genomic regions for rice yield.
JOURNAL OF INTEGRATIVE AGRICULTURE
(2021)
Article
Food Science & Technology
Jinxin Li, Hao Zhang, Xijuan Yang, Ling Zhu, Gangcheng Wu, Xiguang Qi, Hui Zhang
Summary: This study investigated the carbonyl trapping activity of bound-polyphenol rich insoluble dietary fiber (BP-IDF) from different whole grains and its underlying mechanism. The black highland barley BP-IDF showed significant effects in scavenging carbonyls, particularly for methylglyoxal, glyoxal, acrolein, and malondialdehyde. Even after gastrointestinal digestion, the black highland barley BP-IDF still retained considerable trapping activity. The presence of bound polyphenols was found to contribute to the carbonyl scavenging capacity.
FOOD RESEARCH INTERNATIONAL
(2022)
Article
Biotechnology & Applied Microbiology
Ruiqi Zhang, Fusheng Yao, Xue Cheng, Mengyuan Yang, Zhonghua Ning
Summary: This study determined the phenotype and heritability of egg yolk water content and conducted a genome-wide association study (GWAS) to understand the molecular mechanism underlying egg yolk moisture content. The results identified a series of single nucleotide polymorphisms (SNPs), candidate genes, and candidate regions related to egg yolk moisture content, providing insights on its molecular mechanism and potential for developing new egg traits.
Article
Biochemical Research Methods
Gabriel Siqueira, Alexsandro Oliveira Alexandrino, Andre Rodrigues Oliveira, Zanoni Dias
Summary: The rearrangement distance is a method for comparing genomes of different species by determining the number of rearrangement events needed to transform one genome into another. This study explores the effects of transposition and reversal events on genome representation, considering gene repetition and intergenic regions. Practical experiments on simulated genomes show that using partitions can improve distance estimates.
ALGORITHMS FOR MOLECULAR BIOLOGY
(2021)
Article
Plant Sciences
Aixia Yang, Xiaolei Ding, Yuan Feng, Ruiwen Zhao, Jianren Ye
Summary: This study compared the reproductivity and genetic variations of different strains of B. xylophilus in Liaoning Province and other parts of China. It found that the Liaoning isolates have higher reproductive ability at low temperatures and showed significant genetic differentiation from other isolates. Genome-wide association analysis identified SNPs closely related to low-temperature tolerance in genes responsible for environmental adaptation. These findings contribute to a better understanding of the prevalence and diffusion status of B. xylophilus in China.
FRONTIERS IN PLANT SCIENCE
(2023)
Article
Plant Sciences
Jessica Delfini, Vania Moda-Cirino, Jose dos Santos Neto, Douglas Mariani Zeffa, Alison Fernando Nogueira, Luriam Aparecida Brandao Ribeiro, Paulo Mauricio Ruas, Paul Gepts, Leandro Simoes Azeredo Goncalves
Summary: This research aimed to identify Quantitative Trait Nucleotides (QTNs) associated with common bean productivity by evaluating ten morpho-agronomic traits in 178 Mesoamerican common bean domesticated accessions. They identified 64 stable QTNs detected by multiple methods or in multiple environments, with 39 showing significant phenotypic differences between their alleles. The accumulation of favorable alleles resulted in reduced plant height and increased nodules, seed weight, yield, pod insertion height, and number of pods per plant.
FRONTIERS IN PLANT SCIENCE
(2021)
Article
Psychiatry
Weichen Song, Guan Ning Lin, Shunying Yu, Min Zhao
Summary: This study confirms the existence of a shared genetic basis between schizophrenia, smoking, and cannabis usage, and identifies specific genes associated with this relationship. These findings have important implications for the clinical prevention and intervention of psychosis.
PSYCHIATRY RESEARCH
(2022)
Article
Clinical Neurology
Domenico D'Amico, Olivier Biondi, Camille Januel, Cynthia Bezier, Delphine Sapaly, Zoe Clerc, Mirella El Khoury, Venkat Krishnan Sundaram, Leo Houdebine, Thibaut Josse, Bruno Della Gaspera, Cecile Martinat, Charbel Massaad, Laure Weill, Frederic Charbonnier
Summary: This study reveals that the IRE1 alpha/XBP1 branch of the unfolded protein response is disrupted in spinal muscular atrophy (SMA), with a depletion of XBP1s contributing to SMA pathogenesis. Rebalancing XBP1s expression can induce SMN expression and protect spinal motor neurons in severe SMA-like mice.
NEUROPATHOLOGY AND APPLIED NEUROBIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Matthieu Rousset, Sandrine Humez, Cyril Laurent, Luc Buee, David Blum, Thierry Cens, Michel Vignes, Pierre Charnet
Summary: Mutations on voltage-gated calcium channels can cause neurological disorders and contribute to various conditions. By transplanting membrane preparations of these channels into Xenopus oocytes, their activity can be conserved, allowing for the study of calcium signaling.
Article
Biotechnology & Applied Microbiology
Liling Delila, Ouada Nebie, Nhi Thao Ngoc Le, Lassina Barro, Ming-Li Chou, Yu-Wen Wu, Naoto Watanabe, Masayasu Takahara, Luc Buee, David Blum, David Devos, Thierry Burnouf
Summary: This study evaluated the virus removal properties of a nanofiltration process on human platelet lysates (HPL) and found that it effectively reduced viral and procoagulant risks while preserving the neuroprotective and anti-inflammatory properties of HPL.
BIOENGINEERING & TRANSLATIONAL MEDICINE
(2023)
Article
Hematology
Steve Raoul Noumegni, Cecile Tromeur, Clement Hoffmann, Raphael Le Mao, Emmanuelle Le Moigne, Claire de Moreuil, Vincent Mansourati, Bahaa Nasr, Jean-Christophe Gentric, Marie Guegan, Elise Poulhazan, Luc Bressollette, Karine Lacut, Romain Didier, Francis Couturaud
Summary: Patients with first episodes of VTE are at increased risk of recurrent VTE and ATE during and after anticoagulation. Risk factors include age, cancer-associated VTE, and unprovoked VTE.
SEMINARS IN THROMBOSIS AND HEMOSTASIS
(2023)
Article
Oncology
Thomas Rico, Marine Denechaud, Raphaelle Caillierez, Thomas Comptdaer, Eric Adriaenssens, Luc Buee, Bruno Lefebvre
Summary: The role of Tau in genome protection and repair suggests that Tau expression in cancer cells could affect their response to DNA-damaging anti-cancer treatments. Knockdown of Tau in breast cancer cell lines improved the cellular response to DNA damage and reduced tumor volume in mouse-xenograft models. Tau facilitates the translocation of 53BP1 to the nucleus in response to DNA damage by regulating microtubule protein trafficking.
Article
Radiology, Nuclear Medicine & Medical Imaging
Mahdi Ghazal, Corentin Scholaert, Corentin Dumortier, Camille Lefebvre, Nicolas Barois, Sebastien Janel, Mehmet Cagatay Tarhan, Morvane Colin, Luc Buee, Sophie Halliez, Sebastien Pecqueur, Yannick Coffinier, Fabien Alibart, Pierre Yger
Summary: Recently, there has been rapid development in electronic devices that can record the electrical activities of multiple neurons simultaneously, allowing for new possibilities in interfacing and decoding neuronal activity. This study used EDOT electropolymerization to optimize the cell/electrode interface of these devices. The results showed improved signal-to-noise ratio, better biocompatibility, and detection of a higher number of neurons compared to gold electrodes.
BIOMEDICAL PHYSICS & ENGINEERING EXPRESS
(2023)
Article
Dermatology
Kevin Serror, Lauren Ferrero, Francoise Boismal, Maxime Sintes, Manuel Thery, Benoit Vianay, Emilie Henry, David Gentien, Pierre DE LA Grange, David Boccara, Maurice Mimoun, Jean-David Bouaziz, Armand Benssussan, Laurence Michel
Summary: Keloid scars are hypertrophic and proliferating pathological scars with no tendency to regression. There is heterogeneity in keloid morphologies, as well as within a keloid itself, particularly in the expression of ECM-associated genes, proliferation, migration, and traction forces of fibroblasts. This heterogeneity leads to a better understanding of keloid pathophysiology and treatment adaptation.
EXPERIMENTAL DERMATOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Marie Tautou, Florian Descamps, Paul-Emmanuel Larchanche, Luc Buee, Jamal El Bakali, Patricia Melnyk, Nicolas Sergeant
Summary: This study demonstrates the potential of a polyaminobiaryl-based compound, PEL24-199, in treating Alzheimer's disease by targeting both amyloid plaques and neurofibrillary tangles. The compound showed pharmacologic activity by modulating beta-secretase and resulted in the restoration of spatial memory and reduction of neuroinflammation.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Neurosciences
Agathe Launay, Ouada Nebie, Jhenkruthi Vijaya Shankara, Thibaud Lebouvier, Luc Buee, Emilie Faivre, David Blum
Summary: Adenosine signals through four receptors and plays a crucial role in regulating various brain functions. Dysfunction of A2ARs is observed in AD patients and contributes to synaptic loss, impaired communication, and memory deficits. Targeting A2ARs with adenosine drugs shows potential for treating AD and related disorders.
Article
Cell Biology
Romain Perbet, Valentin Zufferey, Elodie Leroux, Enea Parietti, Jeanne Espourteille, Lucas Culebras, Sylvain Perriot, Renaud Du Pasquier, Severine Begard, Vincent Deramecourt, Nicole Deglon, Nicolas Toni, Luc Buee, Morvane Colin, Kevin Richetin
Summary: Tau protein accumulation in astrocytes is involved in neurodegenerative disorders. The origins of 3R and 4R isoforms of tau in astrocytes remain unclear. This study demonstrates that neurons with accumulated 3R or 4R tau have the ability to transfer tau to astrocytes through extracellular vesicles (EVs). Tau-containing EVs disrupt the mitochondrial system of astrocytes and the damage is more severe with 3R tau-containing EVs. EVs from the brain fluid of tauopathy patients also affect mitochondrial function in astrocytes derived from human induced pluripotent stem cells (iPSCs).
Article
Nutrition & Dietetics
Thibaut Gauvrit, Hamza Benderradji, Alexandre Pelletier, Soulaimane Aboulouard, Emilie Faivre, Kevin Carvalho, Aude Deleau, Emmanuelle Vallez, Agathe Launay, Anna Bogdanova, Melanie Besegher, Stephanie Le Gras, Anne Tailleux, Michel Salzet, Luc Buee, Fabien Delahaye, David Blum, Didier Vieau
Summary: Early-life exposure to high-fat diets (HF) can program metabolic and cognitive alterations in adult offspring. The hippocampus plays a crucial role in memory and metabolic homeostasis, and maternal HF during lactation can have effects on physiological, metabolic, and cognitive parameters in young adult offspring mice. A multi-omics strategy revealed sex-specific transcriptomic and proteomic modifications in the hippocampus, with mitochondria and synapses identified as the main targets of maternal HF.
Article
Cell Biology
David Gentien, Elnaz Saberi-Ansari, Nicolas Servant, Ariane Jolly, Pierre de la Grange, Fariba Nemati, Geraldine Liot, Simon Saule, Aurelie Teissandier, Deborah Bourc'his, Elodie Girard, Jennifer Wong, Julien Masliah-Planchon, Erkan Narmanli, Yuanlong Liu, Emma Torun, Rebecca Goulancourt, Manuel Rodrigues, Laure Villoing Gaude, Cecile Reyes, Mateo Bazire, Thomas Chenegros, Emilie Henry, Audrey Rapinat, Mylene Bohec, Sylvain Baulande, Radhia M'kacher, Eric Jeandidier, Andre Nicolas, Giovanni Ciriello, Raphael Margueron, Didier Decaudin, Nathalie Cassoux, Sophie Piperno-Neumann, Marc-Henri Stern, Johan Harmen Gibcus, Job Dekker, Edith Heard, Sergio Roman-Roman, Joshua J. Waterfall
Summary: Through comprehensive multi-omics characterization, we identified genomic instability as a hallmark of uveal melanoma (UM) and confirmed the recurrent deletion in the BAP1 promoter associated with high risk of metastasis in UM patients. We also discovered the upregulation of PRAME as an independent prognostic biomarker and a potential therapeutic target in UM.
Article
Oncology
Fariba Nemati, Leanne de Koning, David Gentien, Franck Assayag, Emilie Henry, Khadija Ait Rais, Gaelle Pierron, Odette Mariani, Michele Nijnikoff, Gabriel Champenois, Andre Nicolas, Didier Meseure, Sophie Gardrat, Nicolas Servant, Philippe Hupe, Maud Kamal, Christophe Le Tourneau, Sophie Piperno-Neumann, Manuel Rodrigues, Sergio Roman-Roman, Didier Decaudin, Pascale Mariani, Nathalie Cassoux
Summary: This study investigated the feasibility of using patient-derived xenografts (PDXs) to screen for potential therapies for uveal melanoma. The results showed that PDX models demonstrated consistency with patient samples in terms of morphology, gene mutations, and chromosome status. PDXs could serve as a valid tool for selecting personalized treatment options.
Proceedings Paper
Computer Science, Artificial Intelligence
Aurelien Olivier, Clement Hoffmann, Ali Mansour, Luc Bressollette, Benoit Clement
Summary: This study aimed to predict the occurrence of pulmonary embolism in patients with deep venous thrombosis using clinical data and ultrasound images. Promising results were obtained using a deep learning model that combined images and clinical factors as input, with increased accuracy observed when using smaller models.
2023 IEEE STATISTICAL SIGNAL PROCESSING WORKSHOP, SSP
(2023)