Editorial Material
Biochemical Research Methods
J. Gray Camp, Ilya Lukonin
Summary: A droplet microfluidic system allows for precise capture, sequencing, and analysis of single-cell transcriptomes from organoids and other small tissue samples.
Article
Ecology
Hugo Robles, Carlos Ciudad, Zeno Porro, Julien Fattebert, Gilberto Pasinelli, Matthias Tschumi, Marta Vila, Martin U. Grueebler
Summary: The study investigates the influence of phenotypic and environmental factors on dispersal movements of juvenile woodpeckers in fragmented landscapes. The results show that larger and healthier individuals tend to emigrate earlier and have shorter transfer durations. Female woodpeckers disperse earlier, move shorter distances, and have longer transfer durations compared to males. Patch size, patch quality, and population density also affect emigration age, transfer duration, and distance. The study highlights the importance of early-life conditions and edge hardness in shaping dispersal behavior and reveals the previously overlooked effect of habitat isolation on sex-biased dispersal.
Article
Biochemical Research Methods
Ajay Subbaroyan, Priyotosh Sil, Olivier C. Martin, Areejit Samal
Summary: Boolean models are a well-established framework for modeling developmental gene regulatory networks (DGRNs) in cell identity acquisition. This study proposes a method for model selection of Boolean DGRNs by leveraging the developmental landscape and using the relative stability of attractors. The novelty of the methodology is rated at 8 out of 10.
BRIEFINGS IN BIOINFORMATICS
(2023)
Article
Biochemistry & Molecular Biology
Camila Ribeiro, Jin Xu, Doron Teper, Donghwan Lee, Nian Wang
Summary: Temporal expression profiles of citrus leaves explain the transition from immature to mature leaves and the differential responses to biotic stress. The gene expression differences between mature and immature leaves contribute to their varying susceptibilities to pathogens and insects, as well as their photosynthetic capacities. The study provides insights into the molecular mechanisms underlying the sink-source transition in citrus leaves and the potential for stage-specific manipulation of citrus traits through gene expression analysis.
PLANT MOLECULAR BIOLOGY
(2021)
Article
Cell Biology
Lautaro Gandara, Albert Tsai, Mans Ekeloef, Rafael Galupa, Ella Preger-Ben Noon, Theodore Alexandrov, Justin Crocker
Summary: This study investigates the effects of hypomethylation on gene expression, morphology, metabolism, behavior, and offspring production in Drosophila melanogaster. The results demonstrate that hypomethylation disrupts gene expression and reduces phenotypic robustness. However, these phenotypic changes are only observed in specific genetic backgrounds or outside of standard laboratory environments.
Article
Cell Biology
Chang Liu, Rui Li, Young Li, Xiumei Lin, Kaichen Zhao, Qun Liu, Shuowen Wang, Xueqian Yang, Xuyang Shi, Yuting Ma, Chenyu Pei, Hui Wang, Wendai Bao, Junhou Hui, Tao Yang, Zhicheng Xu, Tingting Lai, Michael Arman Berberoglu, Sunil Kumar Sahu, Miguel A. Esteban, Kailong Ma, Guangyi Fan, Yuxiang Li, Shiping Liu, Ao Chen, Xun Xu, Zhiqiang Dong, Longqi Liu
Summary: This study used Stereo-seq and scRNA-seq data to analyze the spatially resolved developmental trajectories of cell-fate transitions and molecular changes during zebrafish embryogenesis. Important interactions were identified, providing a fundamental reference for further studies on vertebrate development.
DEVELOPMENTAL CELL
(2022)
Article
Multidisciplinary Sciences
Martin Franke, Elisa De la Calle-Mustienes, Ana Neto, Maria Almuedo-Castillo, Lbai Irastorza-Azcarate, Rafael D. Acemel, Juan J. Tena, Jose M. Santos-Pereira, Jose L. Gomez-Skarmeta
Summary: CTCF plays a critical role in animal development by regulating three-dimensional chromatin structure and enhancer-promoter interactions, essential for controlling the expression of thousands of genes. The architectural protein CTCF mediates chromatin looping and is enriched at the boundaries of topologically associating domains (TADs), impacting gene regulation during development. Loss of CTCF leads to disrupted chromatin structure and affects the expression of developmental regulators, highlighting its essential role in providing structural context for enhancer-promoter interactions.
NATURE COMMUNICATIONS
(2021)
Article
Multidisciplinary Sciences
Dimitra Georgopoulou, Maurizio Callari, Oscar M. Rueda, Abigail Shea, Alistair Martin, Agnese Giovannetti, Fatime Qosaj, Ali Dariush, Suet-Feung Chin, Larissa S. Carnevalli, Elena Provenzano, Wendy Greenwood, Giulia Lerda, Elham Esmaeilishirazifard, Martin O'Reilly, Violeta Serra, Dario Bressan, Gordon B. Mills, H. R. Ali, Sabina S. Cosulich, Gregory J. Hannon, Alejandra Bruna, Carlos Caldas, S. Alon, M. Al Sa'd, S. Aparicio, G. Battistoni, S. Balasubramanian, R. Becker, B. Bodenmiller, E. S. Boyden, Marcel Burger, I. G. Cannell, H. Casbolt, N. Chornay, Y. Cui, A. Dariush, K. Dinh, A. Emenari, Y. Eyal-Lubling, J. Fan, A. Fatemi, E. Fisher, E. A. Gonzalez-Solares, C. Gonzalez-Fernandez, D. Goodwin, W. Greenwood, F. Grimaldi, G. J. Hannon, O. Harris, S. Harris, C. Jauset, J. A. Joyce, E. D. Karagiannis, T. Kovacevic, L. Kuett, R. Kunes, Yoldas A. Kupcu, D. Lai, E. Laks, H. Lee, M. Lee, G. Lerda, Y. Li, A. McPherson, N. Millar, C. M. Mulvey, F. Nugent, C. H. O'Flanagan, M. Paez-Ribes, I. Pearsall, F. Qosaj, A. J. Roth, O. M. Rueda, T. Ruiz, K. Sawicka, L. A. Sepulveda, S. P. Shah, A. Shea, A. Sinha, A. Smith, S. Tavare, S. Tietscher, I. Vazquez-Garcia, S. L. Vogl, N. A. Walton, A. T. Wassie, S. S. Watson, J. Weselak, S. A. Wild, E. Williams, J. Windhager, T. Whitmarsh, C. Xia, P. Zheng, X. Zhuang
Summary: Breast cancer heterogeneity plays a significant role in drug response and resistance. This study utilizes patient-derived tumor xenografts for drug testing and correlation with single-cell proteomic phenotypes revealed by mass cytometry, shedding light on the association between cellular heterogeneity and drug response and resistance.
NATURE COMMUNICATIONS
(2021)
Review
Physiology
Renzo Guerrini, Valerio Conti, Massimo Mantegazza, Simona Balestrini, Aristea S. Galanopoulou, Fabio Benfenati
Summary: Developmental and epileptic encephalopathies (DEEs) are a group of disorders characterized by early-onset severe epileptic seizures, EEG abnormalities, and developmental impairment. DEEs can be caused by genetic and nongenetic factors, with mutations in various genes playing a role. Research in animal models and clinical trials have helped uncover the pathophysiological mechanisms underlying DEEs and explore different treatment options.
PHYSIOLOGICAL REVIEWS
(2023)
Article
Pediatrics
Aviva Eliyahu, Ortal Barel, Lior Greenbaum, Gal Zaks Hoffer, Yael Goldberg, Annick Raas-Rothschild, Amihood Singer, Ifat Bar-Joseph, Vered Kunik, Elisheva Javasky, Orna Staretz-Chacham, Naomi Pode-Shakked, Lily Bazak, Noa Ruhrman-Shahar, Elon Pras, Moshe Frydman, Mordechai Shohat, Ben Pode-Shakked
Summary: The role of lysine methyltransferases and demethylases in chromatin modification regulation is well-established. This study focuses on the association between deleterious variants in the KMT5B gene and developmental disorders such as global developmental delay and intellectual disability. Three unrelated patients with these disorders were found to have distinct de novo mutations in the KMT5B gene. The findings suggest that KMT5B should be considered as a potential gene for the differential diagnosis of neurodevelopmental disorders accompanied by macrocephaly and overgrowth.
FRONTIERS IN PEDIATRICS
(2022)
Article
Genetics & Heredity
Douglas M. Shaw, Hannah P. Polikowsky, Dillon G. Pruett, Hung-Hsin Chen, Lauren E. Petty, Kathryn Z. Viljoen, Janet M. Beilby, Robin M. Jones, Shelly Jo Kraft, Jennifer E. Below
Summary: Developmental stuttering is a speech disorder with a prevalence of 6-12%, but only 0.15% of individuals are diagnosed within electronic health records. A model called PheML was used to identify 9,239 affected individuals for genetic analysis, revealing genetic variants associated with stuttering in ancestry-stratified analysis.
AMERICAN JOURNAL OF HUMAN GENETICS
(2021)
Review
Genetics & Heredity
Sedigheh Delmaghani, Aziz El-Amraoui
Summary: Usher syndrome is a common cause of deaf-blindness in humans. Various treatments are being investigated to restore the function of the inner ear and retinal sensory cells. Consensus on the criteria for diagnosis is important for patient management.
Article
Biology
Yuriria Cortes-Poza, Pablo Padilla-Longoria
Summary: This study models the process of cell fate determination in Arabidopsis thaliana flower using a system of reaction-diffusion equations governed by a potential field. The potential field mimics the flower's epigenetic landscape and is derived from experimental data of the genetic regulatory network. The study shows that the minimal energy solution of the functional corresponds to the observed geometrical features of the flower.
BULLETIN OF MATHEMATICAL BIOLOGY
(2022)
Article
Multidisciplinary Sciences
Natnicha Wankaew, Pajaree Chariyavilaskul, Monpat Chamnanphon, Adjima Assawapitaksakul, Wanna Chetruengchai, Monnat Pongpanich, Vorasuk Shotelersuk
Summary: Differences in drug responses among individuals can be attributed to genetic variations in pharmacogenes, which vary among populations. In this study, genome sequencing of Thai individuals revealed multiple pharmacogenes with variant phenotypes, including several high impact variants not previously reported. These findings provide valuable information for implementing pharmacogenetic testing in Thailand and other Southeast Asian countries, bringing personalized medicine a step closer.
Article
Biochemistry & Molecular Biology
Andrew J. Conith, Sylvie A. Hope, Brian H. Chhouk, R. Craig Albertson
Summary: The study examined the relationship between phenotypic integration and genetic basis, revealing widespread associations among traits at the phenotypic level, but few overlapping genetic regions through QTL analysis. The findings suggest developmental interactions may play a significant role in determining the degree of phenotypic integration among traits.
