Article
Multidisciplinary Sciences
Yoshiaki Kita, Hirozumi Nishibe, Yan Wang, Tsutomu Hashikawa, Satomi S. Kikuchi, U. Mami, Aya C. Yoshida, Chihiro Yoshida, Takashi Kawase, Shin Ishii, Henrik Skibbe, Tomomi Shimogori
Summary: The study introduced a new gene expression profiling system GePS to reveal distinct gene expression patterns in the neonatal marmoset brain compared to mice, and identified potential associations of marmoset-specific genes with different brain regions through gene-ontology analysis. A three-dimensional cortical surface mapping algorithm based on cortical gene expression helped delineate higher-order cortical areas not observable in two-dimensional data.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Biotechnology & Applied Microbiology
Mariana Costa Dias, Cecilio Caldeira, Markus Gastauer, Silvio Ramos, Guilherme Oliveira
Summary: This study aims to explore the molecular adaptive responses of two plant species in the Canga environment in Brazil. Through RNA-seq technology, we identified differentially expressed genes in these two plants grown in Canga and forest substrates, and found that genes involved in light stimulus and the circadian rhythm pathway were altered.
Article
Biotechnology & Applied Microbiology
Irene M. Kaplow, Daniel E. Schaffer, Morgan E. Wirthlin, Alyssa J. Lawler, Ashley R. Brown, Michael Kleyman, Andreas R. Pfenning
Summary: This study proposes a machine learning-based approach to evaluate enhancer conservation, which leverages the combinatorial sequence code of enhancer activity instead of relying on individual nucleotide alignment. The researchers use a convolutional neural network model to predict tissue-specific open chromatin in mammals and demonstrate the model's high accuracy in predicting enhancer conservation and divergence. This framework provides a mechanism to annotate tissue-specific regulatory function across genomes and study enhancer evolution using predicted regulatory differences.
Article
Geriatrics & Gerontology
Natasha L. Pacheco, Nicole Noren Hooten, Yongqing Zhang, Calais S. Prince, Nicolle A. Mode, Ngozi Ezike, Kevin G. Becker, Alan B. Zonderman, Michele K. Evans
Summary: The study revealed sex-specific transcriptional changes in middle-aged frailty, aiding in the understanding of frailty progression and providing potential therapeutic targets for preventing frailty.
Article
Food Science & Technology
Changan Zhu, Min Zhang, Shuwen Wang, Xinhao Gao, Teng Lin, Jingquan Yu, Jinhu Tian, Zhangjian Hu
Summary: This study investigated the presence of phenolic compounds derived from four Solanaceae fruits during gastrointestinal digestion and their effect on human gut microbiota. The results showed that the total phenolic content of all Solanaceae fruits increased during digestion. Different phenolic compound profiles were found among the fruits, with pepino and tamarillo having higher bioaccessibility of phenolic acids and flavonoids, respectively. Goldenberry fruits showed the best effect in decreasing the Firmicutes/Bacteroidetes ratio and tamarillo promoted the growth of Bifidobacterium and short-chain fatty acids production. This study provided valuable information to promote the consumption of Solanaceae fruits as functional foods for gut health.
FOOD RESEARCH INTERNATIONAL
(2023)
Article
Chemistry, Multidisciplinary
Yue Li, Guankui Wang, Lynn Griffin, Nirmal K. Banda, Laura M. Saba, Ernest Groman, Robert Scheinman, S. Moein Moghimi, Dmitri Simberg
Summary: The complement system plays a key role in opsonization and immune clearance of engineered nanoparticles; there are differences in complement opsonization mechanisms and efficiencies in different preclinical species and laboratory strains; nanoparticles with higher C3 deposition in animal sera also show higher deposition in humans.
JOURNAL OF CONTROLLED RELEASE
(2021)
Article
Plant Sciences
Hailong Yang, Kate Nukunya, Queying Ding, Beth E. Thompson
Summary: Differences in cell wall composition and sugar accumulation contribute to growth suppression in the lower floret of maize spikelets. Gene expression analysis reveals that differentially expressed genes in the upper and lower floral meristems are involved in hormone regulation, cell wall, sugar, and energy homeostasis. Additionally, cell wall modifications and sugar accumulation differ between the upper and lower florets. A boundary domain between the upper and lower florets is identified and hypothesized to play a role in floral meristem activity.
Article
Multidisciplinary Sciences
Maohua Yuan, Xianmei Yin, Bixing Gao, Rui Gu, Guihua Jiang
Summary: This study analyzed the chloroplast genomes of several Caragana species and found that they have similar genome structures and repeat sequences. The chloroplast genomes can be used for identification and classification of Caragana species, and they are also useful for further phylogenetic studies.
Article
Multidisciplinary Sciences
Margarete Diaz-Cuadros, Teemu P. Miettinen, Owen S. Skinner, Dylan Sheedy, Carlos Manlio Diaz-Garcia, Svetlana Gapon, Alexis Hubaud, Gary Yellen, Scott R. Manalis, William M. Oldham, Olivier Pourquie
Summary: Animals display inter-species variation in embryonic development rates, with differences in biochemical reaction rates being thought responsible for species-specific rates. This study establishes an in vitro system using pluripotent stem cells to simulate the twofold difference in developmental rates between mouse and human embryos. The mass-specific metabolic rates were found to scale with developmental rate, higher in mouse cells than in human cells. Manipulating metabolic rates could control developmental rate and have translational applications.
Article
Physiology
Chaonan Zhang, Fei Wang, Qiujie Wang, Jixing Zou, Junjie Zhu
Summary: Microplastics have different effects on fish feeding behavior, intestinal morphology, and inflammatory response. By using largemouth bass, grass carp, and Jian carp as model organisms, the study explored the effects of microplastics concentration and size, as well as exposure and depuration times. Histological analysis showed abnormalities in the intestines of all three species after exposure to microplastics. The mRNA abundance of immune-related genes in the intestines fluctuated significantly. The differential gene expressions in response to different sizes and concentrations of microplastics exposure varied among different fish species. The reason for the different effects of microplastics on fishes remains unclear, but it may be related to the differences in the structure and function of the digestive system. These results provide a theoretical basis for further analysis of the mechanism of fish intestinal pathology caused by microplastics.
FRONTIERS IN PHYSIOLOGY
(2023)
Article
Multidisciplinary Sciences
Xiaoyu Tu, Sibo Ren, Wei Shen, Jianjian Li, Yuxiang Li, Chuanshun Li, Yangmeihui Li, Zhanxiang Zong, Weibo Xie, Donald Grierson, Zhangjun Fei, Jim Giovannoni, Pinghua Li, Silin Zhong
Summary: Non-coding cis-regulatory variants play a crucial role in the evolution of transcription regulation and phenotype diversity in animal genomes. However, the dynamics of cistrome in plants are not well understood. This study compares the binding of GLK transcription factors in different plant species and reveals that while the function of GLKs is conserved, their binding sites are mainly species-specific. The study also highlights the importance of quantitative measurement of TF occupancy.
NATURE COMMUNICATIONS
(2022)
Article
Genetics & Heredity
Nancy W. Lin, Cuining Liu, Ivana Yang, Lisa A. Maier, Dawn L. DeMeo, Cheyret Wood, Shuyu Ye, Margaret H. Cruse, Vong L. Smith, Carrie A. Vyhlidal, Katerina Kechris, Sunita Sharma
Summary: This study identified sex-specific differences in miRNA expression during human fetal lung development, which may impact susceptibility to pulmonary diseases later in life.
FRONTIERS IN GENETICS
(2022)
Article
Biochemistry & Molecular Biology
Chao-Jen Wong, Jennifer L. Whiddon, Ashlee T. Langford, Andrea E. Belleville, Stephen J. Tapscott
Summary: Mis-expression of DUX4 in skeletal muscle causes facioscapulohumeral muscular dystrophy (FSHD). Dogs have a DUXC gene that is similar to DUX4 and Dux, and the expression of DUXC in canine cells induces a pluripotent program similar to DUX4 and Dux. The conservation of homeodomains and transcriptional program activation between human DUX4 and canine DUXC suggests the potential use of DUXC-containing mammals for preclinical models of FSHD.
HUMAN MOLECULAR GENETICS
(2022)
Article
Evolutionary Biology
Jiao Wang, Xuyuan Liu, Yue Lan, Tengcheng Que, Jing Li, Bisong Yue, Zhenxin Fan
Summary: This study investigated the methylation patterns of Tibetan macaque, Chinese rhesus macaque, and crab-eating macaque, and compared the differences among them. The results showed differences in methylation and gene expression profiles among the three macaque species, which may be associated with variations in physiology and habitat. Additionally, a potential mechanism through which genomic alterations modulate methylation landscapes and influence the transcriptome was identified.
EVOLUTIONARY APPLICATIONS
(2023)
Article
Biochemistry & Molecular Biology
Sara B. Linker, Inigo Narvaiza, Jonathan Y. Hsu, Meiyan Wang, Fan Qiu, Ana P. D. Mendes, Ruth Oefner, Kalyani Kottilil, Amandeep Sharma, Lynne Randolph-Moore, Eunice Mejia, Renata Santos, Maria C. Marchetto, Fred H. Gage
Summary: Human neurodevelopment is slower than that in other nonhuman primates, a phenomenon referred to as neoteny. The transcription factor GATA3 plays a unique role in human neuronal maturation, and downregulation of GATA3 accelerates the speed of developing action potentials, modulating the human neotenic phenotype.
Article
Oncology
Anthony J. Maxwell, Karen Clements, Bridget Hilton, David J. Dodwell, Andrew Evans, Olive Kearins, Sarah E. Pinder, Jeremy Thomas, Matthew G. Wallis, Alastair M. Thompson
Article
Surgery
Kathryn H. Steele, R. Douglas Macmillan, Graham R. Ball, Malin Akerlund, Stephen J. McCulley
JOURNAL OF PLASTIC RECONSTRUCTIVE AND AESTHETIC SURGERY
(2018)
Article
Urology & Nephrology
Giulia Furini, Nina Schroeder, Linghong Huang, David Boocock, Alessandra Scarpellini, Clare Coveney, Elisa Tonoli, Raghavendran Ramaswamy, Graham Ball, Claudia Verderio, Timothy S. Johnson, Elisabetta A. M. Verderio
JOURNAL OF THE AMERICAN SOCIETY OF NEPHROLOGY
(2018)
Article
Cell Biology
Jayakumar Vadakekolathu, Shaymaa Ismael Kadhim Al-Juboori, Catherine Johnson, Anne Schneider, Magdalena Elzbieta Buczek, Anna Di Biase, Alan Graham Pockley, Graham Roy Ball, Desmond George Powe, Tarik Regad
CELL DEATH & DISEASE
(2018)
Article
Genetics & Heredity
Lu Jiang, Graham Ball, Charlie Hodgman, Anne Coules, Han Zhao, Chungui Lu
Article
Biochemistry & Molecular Biology
Dimitrios Zafeiris, Sergio Rutella, Graham Roy Ball
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2018)
Article
Oncology
Alastair M. Thompson, Karen Clements, Shan Cheung, Sarah E. Pinder, Gill Lawrence, Elinor Sawyer, Olive Kearins, Graham R. Ball, Ian Tomlinson, Andrew Hanby, Jeremy St J. Thomas, Anthony J. Maxwell, Matthew G. Wallis, David J. Dodwell
EUROPEAN JOURNAL OF CANCER
(2018)
Article
Multidisciplinary Sciences
Donald Barron, Graham Ball, Matthew Robins, Caroline Sunderland
Article
Oncology
Shaymaa I. K. Al-Juboori, Jayakumar Vadakekolathu, Sarra Idri, Sarah Wagner, Dimitrios Zafeiris, Joshua R. D. Pearson, Rukaia Almshayakhchi, Michele Caraglia, Vincenzo Desiderio, Amanda K. Miles, David J. Boocock, Graham R. Ball, Tarik Regad
JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH
(2019)
Article
Microbiology
Lav Sharma, Irene Oliveira, Fatima Goncalves, Fernando Raimundo, Rupesh Kumar Singh, Laura Torres, Guilhermina Marques
Summary: This study investigates the impact of soil chemistry on different entomopathogenic fungi (EPF) in Portuguese vine farms. The study found that the occurrence of EPF, such as Beauveria bassiana and Metarhizium robertsii, is influenced by various soil chemical properties, which can help in developing effective biological pest management strategies.
Review
Biology
Vishnu D. Rajput, Harish, Rupesh Kumar Singh, Krishan K. Verma, Lav Sharma, Francisco Roberto Quiroz-Figueroa, Mukesh Meena, Vinod Singh Gour, Tatiana Minkina, Svetlana Sushkova, Saglara Mandzhieva
Summary: Plants rely on a complex grid of antioxidant enzymes to cope with stress conditions, with SOD, CAT, POX, and GPX playing crucial roles in minimizing reactive oxygen species. The interplay of these enzymes is essential for plant health and development, and their manipulation can be useful in developing stress-tolerant transgenic plants.
Meeting Abstract
Oncology
Tarek Mohamed Ahmed Abdel-Fatah, Rebekah Webb, Ruizhe Li, Xin Chen, Elisabetta Giannotti, Dorothee Auer, Jennifer Walker, Paul M. Moseley, A. Graham Pockley, Graham Ball, Ian O. Ellis, Emad Rakhah, Zsolt Hodi, Andrew Lee, Arlene Chan, Stephen Chan
JOURNAL OF CLINICAL ONCOLOGY
(2019)
Article
Hematology
Sarah Wagner, Jayakumar Vadakekolathu, Sarah K. Tasian, Heidi Altmann, Martin Bornhaeuser, A. Graham Pockley, Graham R. Ball, Sergio Rutella
Meeting Abstract
Oncology
Alastair M. Thompson, Karen Clements, Shan Cheung, Sarah E. Pinder, G. Lawrence, Elinor Sawyer, Olive Kearins, Graham R. Ball, Ian Tomlinson, Andrew M. Hanby, Jeremy Thomas, Anthony J. Maxwell, Matthew G. Wallis, David J. Dodwell
Meeting Abstract
Oncology
Patsy Whelehan, Kulsam Ali, Sarah Vinnicombe, Graham Ball, Julie Cox, Paul Farry, Maggie Jenkin, Dimitrios Kapsoulis, Keith Lowry, Stuart McIntosh, Rachel Nutt, Rachel Oeppen, Michael Reilly, Michaela Stahnke, Jim Steel, Yee Ting Sim, Violet Warwick, Louise Wilkinson, Andrew Evans
BREAST CANCER RESEARCH
(2018)