Article
Multidisciplinary Sciences
Tereza Clarence, Nicolas S. M. Robert, Fatih Sarigol, Xiao Fu, Paul A. Bates, Oleg Simakov
Summary: Animal genomes are organized into conserved chromosomes that form distinct evolutionary units. By using chromosomal modeling, researchers have inferred the three-dimensional topology of animal genomes. They have identified evolutionarily conserved three-dimensional networks and novel interactors associated with known gene linkages. This evidence suggests that the spatial organization of animal genomes, termed spatiosynteny, plays a role in understanding the conservation of chromosomes.
Article
Biochemistry & Molecular Biology
Alessa R. Ringel, Quentin Szabo, Andrea M. Chiariello, Konrad Chudzik, Robert Schopflin, Patricia Rothe, Alexandra L. Mattei, Tobias Zehnder, Dermot Harnett, Verena Laupert, Simona Bianco, Sara Hetzel, Juliane Glaser, Mai H. Q. Phan, Magdalena Schindler, Daniel M. Ibrahim, Christina Paliou, Andrea Esposito, Cesar A. Prada-Medina, Stefan A. Haas, Peter Giere, Martin Vingron, Lars Wittler, Alexander Meissner, Mario Nicodemi, Giacomo Cavalli, Frederic Bantignies, Stefan Mundlos, Michael I. Robson
Summary: Regulatory landscapes play a crucial role in complex developmental gene expression. This study investigated how a specific gene, Zfp42, emerged in an ancient vertebrate topologically associated domain (TAD) without disrupting the expression of its neighboring gene, Fat1. The findings suggest that the independent expression of Zfp42 is driven by chromatin activity and context-dependent DNA methylation.
Article
Agriculture, Dairy & Animal Science
Ema Etchegaray, Corentin Dechaud, Jeremy Barbier, Magali Naville, Jean-Nicolas Volff
Summary: Transposable elements are repeated DNA sequences that can insert into new locations in genomes. Harbinger-like DNA transposons are widespread in plants and vertebrates, but absent from mammalian genomes. This study focuses on the variability in the genomic composition of Harbinger-like sequences in teleost fish and the unique origin of the association between transposase and Myb-like protein.
Article
Multidisciplinary Sciences
Mayank N. K. Choudhary, Kara Quaid, Xiaoyun Xing, Heather Schmidt, Ting Wang
Summary: Transposable elements (TEs), previously considered as junk DNA, contribute to species-specific 3D-genome structure by providing binding sites for CTCF protein. These elements play a role in gene regulation during mammalian evolution.
NATURE COMMUNICATIONS
(2023)
Article
Biology
Zhe Liang, Qian Zhang, Changmian Ji, Guihua Hu, Pingxian Zhang, Yifan Wang, Liwen Yang, Xiaofeng Gu
Summary: This study reveals the changes in three-dimensional spatial organization of the genome in rice under heat stress conditions, including A/B compartment transition, increase in the size of topologically associated domains, and loss of short-range interactions, which influence chromatin accessibility and gene expression. Different rice cultivars show distinct responses to heat stress, with 93-11 exhibiting more dynamic changes in gene expression and chromatin accessibility.
Article
Virology
Spyros Lytras, Gloria Arriagada, Robert J. Gifford
Summary: Research reveals that the incorporation of hepadnaviruses in saurian genomes is exclusive, showing a greater diversity of eHBVs than previously recognized. By characterizing eHBV elements, four distinct subgroups within the Avihepadnavirus genus are identified and their evolution traced through the Cenozoic Era. The study also suggests that metahepadnaviruses originated over 300 million years ago in the Paleozoic Era, infecting a broad range of vertebrates.
Article
Biology
Jeremiah J. Minich, Malia L. Moore, Nicholas A. Allsing, Anthony Aylward, Emily R. Murray, Loi Tran, Todd P. Michael
Summary: This study compares the impact of storage methods on DNA quality and long-read sequencing quality in fish and plant species. It shows that use of 95% ethanol can largely protect against degradation, allowing for the assembly of high-quality reference genomes and reducing the need for cryogenic storage. This is significant for future research in remote sampling.
COMMUNICATIONS BIOLOGY
(2023)
Article
Biology
Geoffrey C. Waldbieser, Shikai Liu, Zihao Yuan, Caitlin E. Older, Dongya Gao, Chenyu Shi, Brian G. Bosworth, Ning Li, Lisui Bao, Mona A. Kirby, Yulin Jin, Monica L. Wood, Brian Scheffler, Sheron Simpson, Ramey C. Youngblood, Mary V. Duke, Linda Ballard, Adam Phillippy, Sergey Koren, Zhanjiang Liu
Summary: This study generated high-quality chromosome level reference genome sequences for channel catfish and blue catfish in the US, and identified three major pericentric inversions on their chromosomes. These reference genome sequences, along with the contrasting chromosomal architecture, can provide guidance for interspecific breeding programs.
Review
Biotechnology & Applied Microbiology
Fei Ke, Qi-Ya Zhang
Summary: Genomic studies of viral diseases in aquaculture have gained increasing attention due to the potential for recombination, mutation, and insertion in the viral genome, which could lead to more severe diseases and widespread infections. This review focuses on aquaculture viruses belonging to Varidnaviria, Duplodnaviria, and Naldaviricetes, and three families: Iridoviridae, Alloherpesviridae, and Nimaviridae. These large DNA viruses with genomes larger than 100 kbp and more than 100 genes have been extensively studied for their replication, transcription, virus-host interactions, and genetic variation.
Article
Engineering, Multidisciplinary
Hongfan Yang, Aimin Wang, Huanxiong Xia, Sihan Wang, Jianhua Liu, Xiaohui Ao, Yaowen Zhang, Jie Shi
Summary: This study developed an efficient hybrid inverse identification method for in-situ measurement of curing shrinkage of adhesives. By combining artificial fish swarm algorithm, finite element method, and 3D digital image correlation technology, the non-contact and non-destructive measurement of curing shrinkage was achieved.
Article
Geography, Physical
Yangzi Cong, Chi Chen, Bisheng Yang, Jianping Li, Weitong Wu, Yuhao Li, Yandi Yang
Summary: This research proposes a novel 3D mapping method based only on LiDAR data to enhance the performance of SLAM-based 3D point cloud map reconstruction. The proposed system consists of a localization module for rapid egomotion estimation and a mapping module for accurate point cloud fusion. Through extensive experiments, the system outperforms existing frameworks and shows improvement in precision compared to high-precision point cloud maps.
ISPRS JOURNAL OF PHOTOGRAMMETRY AND REMOTE SENSING
(2022)
Article
Biochemistry & Molecular Biology
Jiankang Wang, Ryuichiro Nakato
Summary: CohesinDB is a comprehensive multiomics cohesin database that includes data from 530 studies, 2043 datasets, and 176 cell types. By integrating these data, CohesinDB provides information on cohesin binding sites, chromatin loops, and CRMs, serving as a valuable resource for researchers studying cohesin, epigenomics, transcriptional regulation, and chromatin organization.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Ecology
Lipeng Li, Feipeng Shi, Chunxu Wang
Summary: Solving the problem of fish image classification is crucial for preserving fish diversity. This paper proposes a fusion model called Tripmix-Net, which achieves significant accuracy improvement in classifying same-genus fish images with complex backgrounds. The proposed approach serves as a new concept for fine-grained image classification of fish against complex backgrounds.
ECOLOGICAL INFORMATICS
(2022)
Article
Biochemistry & Molecular Biology
Inkyu Park, Bokyung Choi, Hanna Weiss-Schneeweiss, Soonku So, Hyeon-Ho Myeong, Tae-Soo Jang
Summary: This study conducted comparative analyses on the karyotypes of three Iris species in Korea, with an emphasis on the number and localization of 5S and 35S rDNA loci using FISH. The chloroplast genomes of the same individuals were also sequenced and compared. The results provide important insights into the origin of the progenitor species and the genomes of Iris series Chinenses.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Evolutionary Biology
Rodrigo Zeni dos Santos, Rodrigo Milan Calegari, Duilio Mazzoni Zerbinato de Andrade Silva, Francisco J. Ruiz-Ruano, Silvana Melo, Claudio Oliveira, Fausto Foresti, Marcela Uliano-Silva, Fabio Porto-Foresti, Ricardo Utsunomia
Summary: Eukaryotic genomes contain a significant amount of repetitive DNA sequences, such as satellite DNAs, which are highly dynamic and often genus- or species-specific. However, a satellite DNA named CharSat01-52 has been found to be conserved in multiple distantly related species within the Characoidei superfamily. Despite challenging general predictions, CharSat01-52 shows similar levels of intra- and interspecific divergence, with transcriptional activity observed across different species. Arrays of CharSat01-52 have also been identified in single-molecule real-time long reads of Astyanax paranae and A. mexicanus.
GENOME BIOLOGY AND EVOLUTION
(2021)
Article
Chemistry, Multidisciplinary
Tianheng Jiang, Xiaoxun Li, Tenglong Li, Gungun Lin, Huan Liu, Dayong Jin, Lei Jiang
Summary: Fresh popcorn dissolves quickly in the mouth and has a good taste. However, this taste decays rapidly with increased exposure to air, especially humid air. The mechanism of saliva wetting the popcorn is still unknown.
ADVANCED FUNCTIONAL MATERIALS
(2023)
Article
Chemistry, Analytical
Sareh Zhand, Ying Zhu, Hojjatollah Nazari, Mohammad Sadraeian, Majid Ebrahimi Warkiani, Dayong Jin
Summary: In this study, dithiol-modified Subzyme was attached to gold nanoparticles, leading to an improved limit of detection compared to using magnetic microparticles. The method was successfully applied to the detection of exosomal PD-L1 RNA with a limit of detection as low as 50 fM and a reaction time of 8 minutes. This work suggests new potentials for point-of-care testing in clinical applications.
ANALYTICAL CHEMISTRY
(2023)
Article
Chemistry, Analytical
Dan Shao, Fei Su, Xueyu Zou, Jie Lu, Sitong Wu, Ruijun Tian, Dongmei Ran, Zhiyong Guo, Dayong Jin
Summary: Lung adenocarcinoma is the most common type of lung cancer, and pixel-level labeling can assist pathologists in tumor grading. By manually annotating a dataset and using a data stitching strategy, a framework for lung adenocarcinoma pathology analysis was developed, which accurately labels the histologic patterns of lung adenocarcinoma.
ANALYTICAL CHEMISTRY
(2023)
Article
Chemistry, Multidisciplinary
Langping Tu, Kefan Wu, Yongshi Luo, Enhui Wang, Jun Yuan, Jing Zuo, Ding Zhou, Bin Li, Jiajia Zhou, Dayong Jin, Hong Zhang
Summary: Relatively low efficiency is the bottleneck for the application of lanthanide-doped upconversion nanoparticles. The high-level doping strategy realized in recent years has not improved the efficiency as much as expected. This study combines theoretical simulation and spectroscopy to elucidate the role of cross relaxation (CR) in the upconversion process and demonstrates that inhibiting CR significantly improves upconversion efficiency.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
Article
Materials Science, Multidisciplinary
Sajad Razavi Bazaz, Sareh Zhand, Robert Salomon, Elham Hosseini Beheshti, Dayong Jin, Majid Ebrahimi Warkiani
Summary: This study used the ImmunoInertial microfluidics approach to isolate specific subpopulations of cancer-specific small extracellular vesicles (sEVs), demonstrating high efficiency and selectivity. The method has the advantages of high sensitivity, low cost, and ability to process samples of varying volumes, making it a promising strategy for cancer diagnosis and prognosis in liquid biopsies.
APPLIED MATERIALS TODAY
(2023)
Article
Chemistry, Physical
Lin Zhang, Cheng Cao, Szun S. Tay, Chaohao Chen, Alexander Macmillan, Shihui Wen, Dayong Jin, Joshua McCarroll, Martina H. Stenzel
Summary: Polymer-coated inorganic nanoparticles have unique magnetic, optical, and thermal properties that make them promising drug delivery systems. However, the biological behavior of these nanoparticles is affected by various factors such as size, shape, and protein corona. This study focuses on the effect of drug loading amount on the biological activity of inorganic nanoparticles and highlights the importance of optimizing drug loading amounts in order to achieve optimal drug delivery.
CHEMISTRY OF MATERIALS
(2023)
Editorial Material
Biochemical Research Methods
Le Zhang, Dayong Jin
Article
Chemistry, Multidisciplinary
Aditya Tripathi, Anastasiia Zalogina, Jiayan Liao, Matthias Wurdack, Eliezer Estrecho, Jiajia Zhou, Dayong Jin, Sergey S. Kruk, Yuri Kivshar
Summary: We demonstrate the effect of spin-momentum locking on upconversion photoluminescence emitted from rare-earth doped nanocrystals coupled to a phase-gradient dielectric metasurface. Different directionalities for left and right circular polarized light are observed, which can be attributed to the photonic Rashba effect that leads to a spin-dependent splitting of emitted light in momentum space.
Article
Chemistry, Multidisciplinary
Yongtao Liu, Jiajia Zhou, Shihui Wen, Fan Wang, Hongjun Wu, Qian Chen, Chao Zuo, Dayong Jin
Summary: Multiphoton upconversion super-resolution microscopy (MPUM) is a promising imaging modality that achieves increased resolution and penetration depth through the use of nonlinear near-infrared emission light. However, high excitation power is required for emission saturation, leading to increased phototoxicity. In this study, the authors propose a simple on-chip mirror design that allows for nonlinear saturation emission under low excitation power. This method significantly decreases the excitation power and enables a lateral resolution of around 35 nm in imaging single nanoparticles on-chip. The findings offer a straightforward solution for enhancing super-resolution imaging using pre-designed on-chip devices.
Article
Biochemical Research Methods
Shuang Fu, Wei Shi, Tingdan Luo, Yingchuan He, Lulu Zhou, Jie Yang, Zhichao Yang, Jiadong Liu, Xiaotian Liu, Zhiyong Guo, Chengyu Yang, Chao Liu, Zhen-li Huang, Jonas Ries, Mingjie Zhang, Peng Xi, Dayong Jin, Yiming Li
Summary: We propose a deep-learning method for precise localization of spatially variant point emitters, covering the full chip of a modern sCMOS camera. By using a graphic processing unit-based vectorial point spread function fitter, we accurately model the spatially variant PSF of a high numerical aperture objective in the entire field of view. Combined with deformable mirror-based optimal PSF engineering, we demonstrate high-accuracy three-dimensional single-molecule localization microscopy over a large volume, enabling imaging of mitochondria and nuclear pore complexes in entire cells without hardware scanning, with a 100-fold increase in throughput compared to existing techniques.
Editorial Material
Optics
Xin Chen, Yiwei Hou, Peng Xi
Summary: Principal component analysis (PCA), a common dimensionality reduction method, is used in SIM to accurately identify the frequency vectors and pattern phases of the illumination pattern. It offers precise subpixel accuracy, fast speed, and noise-robustness, making it promising for real-time and long-term live-cell imaging.
LIGHT-SCIENCE & APPLICATIONS
(2023)
Review
Optics
Xin Chen, Suyi Zhong, Yiwei Hou, Ruijie Cao, Wenyi Wang, Dong Li, Qionghai Dai, Donghyun Kim, Peng Xi
Summary: Structured illumination microscopy (SIM) has become the standard for next-generation wide-field microscopy, offering ultrahigh imaging speed, superresolution, a large field-of-view, and long-term imaging. Advanced reconstruction algorithms are necessary to unlock the full potential of SIM system hardware. This article introduces the theory and implementation modalities of two SIM algorithms, optical sectioning SIM (OS-SIM) and superresolution SIM (SR-SIM), and provides an overview of existing processing algorithms and the development of reconstruction algorithms for different SIM techniques. Comparison of off-the-shelf SIM systems and future perspectives are also discussed.
LIGHT-SCIENCE & APPLICATIONS
(2023)
Article
Chemistry, Analytical
Gungun Lin, Jawairia Umar Khan, Sareh Zhand, Yuan Liu, Dayong Jin
Summary: This study presents a modular hydrogel membrane carrier incorporated with composite DNAzymes for rapid and highly sensitive detection of pathogenic bacteria gene targets. The composite DNAzymes are incorporated into polyethylene glycol diacrylate polymer networks, allowing for the cleavage of RNA substrate components to generate fluorescence. By modulating the morphology, composition, and microporous structures of the DNAzyme carriers, quantitative assay performance is achieved. This work represents an important advancement in the development of a generic, isothermal, and protein enzyme-free pathogenic bacteria testing platform technology.
ANALYTICAL CHEMISTRY
(2023)
Article
Engineering, Biomedical
Fu Zou, Yuanhua Liu, Zelyu Chen, Zhanghao Karl, Dayong Jin
Summary: This paper introduces a lightweight network FRUNet based on U-Net, which combines the advantages of Fourier Channel Attention (FCA Block) and Residual unit to improve image segmentation accuracy. FCA Block automatically assigns the weight of learned frequency information to the spatial domain, paying more attention to the precise high-frequency information of diverse biomedical images. The combination of FCA and U-Net is studied, with the skip connection of U-Net fusing encoder information with the decoder. Extensive experimental results show that FRUNet outperforms other advanced medical image segmentation methods in terms of network parameters and accuracy, particularly excelling in pathological section segmentation of nuclei and glands.
IEEE JOURNAL OF TRANSLATIONAL ENGINEERING IN HEALTH AND MEDICINE
(2023)
Article
Chemistry, Multidisciplinary
Zayakhuu Gerelkhuu, Haribalan Perumalsamy, Mahnaz Maddahfar, Dayong Jin, Jaewoo Song, Tae Hyun Yoon
Summary: In order to promote the use of lanthanide-doped upconversion nanoparticles (UCNPs) in various biomedical applications, it is important to assess their toxicity comprehensively, including their cellular association and interactions with human immune cells. Recent advancements in high-throughput single-cell technologies have enabled us to gain a better understanding of the complex interactions between nanoparticles and human immune cells. In this study, we used a single-cell based mass cytometry technique to investigate the heterogeneous interactions of Yb3+/Er3+-doped NaYF4 UCNPs with human peripheral blood mononuclear cells (hPBMCs). The study demonstrated a new innovative approach to understanding the heterogeneous interactions of conventional nanomaterials with complex human immune systems, which will facilitate the safe implementation of nanomaterials in biomedical applications.
ENVIRONMENTAL SCIENCE-NANO
(2023)