Article
Environmental Sciences
Clara Lopes, Catia Figueiredo, Miguel Baptista, Miguel Caetano, Miguel M. Santos, Joana Raimundo
Summary: This study found that the sunfish population in the southern waters of Portugal is exposed to microplastic pollution, with most of the ingested microplastics being fragments and fibers, and blue being the most prevalent color. These findings emphasize the need for effective management policies to address plastic pollution in marine ecosystems.
MARINE ENVIRONMENTAL RESEARCH
(2023)
Article
Environmental Sciences
Miguel Baptista, Catia Figueiredo, Olga M. Azevedo, Maria T. Pina Rodrigues, Tania Costa, Marta Tiago Santos, Nuno Queiroz, Rui Rosa, Joana Raimundo
Summary: Trace elements can be critical contaminants in aquatic environments, especially for fish at higher trophic levels. However, data on the elemental composition of less commercially important marine species are lacking. A study on juvenile ocean sunfish showed that zinc and arsenic were the elements with the highest concentrations in body tissues, with significant variability between tissues and between white and red muscles.
Article
Ecology
Slavomir Stasiov, Marek Ciliak, Michal Wiezik, Marek Svitok, Adela Wiezikova, Andrea Diviakova
Summary: The study showed that larger and medium-sized pitfall traps were more effective in capturing harvestmen and millipedes compared to small traps. Larger traps and traps filled with NaCl solution tended to capture larger individuals more frequently. The combination of larger traps and formaldehyde was most effective, although formaldehyde has the disadvantage of being toxic.
ECOLOGY AND EVOLUTION
(2021)
Article
Multidisciplinary Sciences
Mark Pagel, Ciara O'Donovan, Andrew Meade
Summary: Macroevolution poses challenges to evolutionary theory due to abrupt changes and long stagnation periods. This study introduces a statistical model that considers directional changes and evolvability changes to account for this uneven evolutionary landscape. In mammals, both processes independently contribute to macroevolution, with increased evolvability being more common than reduced evolutionary potentials. Large or sudden phenotypic changes can be statistically explained as biased random walks, bridging the gap between macroevolution and gradualist microevolution. This study emphasizes the importance of considering multiple evolutionary processes simultaneously.
NATURE COMMUNICATIONS
(2022)
Article
Ecology
Itsumi Nakamura, Morihiko Yamada
Summary: The study demonstrates that ocean sunfish have the ability to adjust their behavior and heat exchange rate in response to changes in environmental temperature, suggesting their capability to prevent heat loss through cooling during thermoregulation.
JOURNAL OF EXPERIMENTAL MARINE BIOLOGY AND ECOLOGY
(2022)
Article
Biology
Tim Janicke, Salome Fromonteil
Summary: The study found that sexual size dimorphism (SSD) based on length measurements was correlated with the sex difference in the opportunity for sexual selection but showed a weak and statistically non-significant relationship with the sex difference in the Bateman gradient. This suggests that pre-copulatory sexual selection plays a limited role in the evolution of SSD across a broad phylogenetic context.
Article
Ecology
Sigurd Einum, Tim Burton
Summary: An individual's fitness cost associated with environmental change depends on the rate of adaptive phenotypic plasticity. However, understanding of plasticity rates in an ecological and evolutionary context remains limited. A quantitative synthesis of existing plasticity rate data reveals considerable variation in plasticity rates among species, with different rates observed among higher taxa.
Article
Evolutionary Biology
Neil Brocklehurst, David P. Ford, Roger B. J. Benson
Summary: The divergence in macroevolutionary patterns between synapsids and reptiles laid the foundation for subsequent evolutionary events and may be critical in understanding the substantial differences between mammals and reptiles today. The early burst of evolution in amniotes resulted in the early origins of morphologically distinctive subgroups, with reptiles showing more constrained evolution compared to synapsids. The differences in rates and constraints of morphological evolution provide insights into the evolutionary history and potential explanations for the biological differences between these two groups.
SYSTEMATIC BIOLOGY
(2022)
Article
Ecology
Tao Zhu, Xin Qi, Yu Chen, Liang Wang, Xueze Lv, Weifang Yang, Jianwei Zhang, Kaiyang Li, Zhonghua Ning, Zhihua Jiang, Lujiang Qu
Summary: Domestication of ducks has led to significant phenotypic, genetic, and physiological differences compared to wild ancestors. Study of genomic and transcriptomic data has revealed that genes related to skeletal development were strongly selected during domestication, resulting in changes in skeletal systems and affecting digestive, immune, and metabolic functions.
BMC ECOLOGY AND EVOLUTION
(2021)
Article
Multidisciplinary Sciences
Jaim Sivan, Itay Tesler, Shlomo Hadad, Abraham Allan Degen, Eli Geffen, Michael Kam
Summary: The morphological constraint hypothesis suggests that male snakes usually have longer tails than females to accommodate reproductive organs. In this study, the hypothesis was tested intraspecifically on Cerastes vipera, showing that males have relatively longer tails due to the length of the hemipenes pocket. This is the first report to support the MCH intraspecifically, and further studies are needed to determine if these relations are widespread among snake families or specifically within C. vipera.
SCIENTIFIC REPORTS
(2023)
Article
Ecology
Yiming Hu, Brett Scheffers, Xinyuan Pan, Huijian Hu, Zhixin Zhou, Dan Liang, Cheng Wenda, Zhixin Wen, Luke Gibson
Summary: The study in the Himalayas-Hengduan Mountains of China shows a significant positive correlation between species abundance and elevational range size, while weak correlations were found with body size and elevational range center. An interesting finding is the gradual weakening of the abundance-elevational range size relationship from temperate to subtropical ecosystems. This study highlights the importance of investigating abundance relationships across different environmental variables to reveal underlying mechanisms behind patterns.
JOURNAL OF ANIMAL ECOLOGY
(2021)
Article
Biology
Shengnan Chen, Ying Jiang, Long Jin, Wenbo Liao
Summary: Testis asymmetry in anuran species was studied to test the packaging and compensation hypotheses. The results showed a positive correlation between testes size asymmetry and livers mass, supporting the packaging hypothesis; and a positive relationship between postcopulatory sperm competition and the degree of testes asymmetry, supporting the role of sexual selection. However, no effect of developmental stress on testes size asymmetry was found, inconsistent with the compensation hypothesis.
Article
Environmental Sciences
Ryan F. Heneghan, Jason D. Everett, Julia L. Blanchard, Patrick Sykes, Anthony J. Richardson
Summary: Using a trait-based marine ecosystem model, the study reveals that future oceans, especially in tropical regions, will favor food webs dominated by carnivorous and gelatinous filter-feeding zooplankton, which will partially offset the decline in phytoplankton biomass and increase in carnivorous zooplankton. However, this shift will result in decreased carrying capacity for future fish communities and less nutritious food, exacerbating projected declines in small pelagic fish biomass in tropical regions by 2100.
NATURE CLIMATE CHANGE
(2023)
Article
Genetics & Heredity
Jason Bertram
Summary: The study develops a new theoretical approach that uncovers a previously undocumented genome-wide signature of selection and finds that selection has substantial effects on much of the genome in Drosophila populations. It also reveals that selective allele frequency divergence is substantially elevated at intermediate allele frequencies, potentially explained by positive selection.
Article
Ecology
Talita Ferreira Amado, Pablo Ariel Martinez, Daniel Pincheira-Donoso, Miguel Angel Olalla-Tarraga
Summary: The research found that the shape of body size distributions of anurans is related to diversification rates and influenced by the environment. Skewed body size distributions may result from species formation and extinction biased towards different sizes, while environmental factors also play a significant role in shaping the distribution patterns.
GLOBAL ECOLOGY AND BIOGEOGRAPHY
(2021)
Correction
Multidisciplinary Sciences
Yilong Li, Nicola D. Roberts, Jeremiah A. Wala, Ofer Shapira, Steven E. Schumacher, Kiran Kumar, Ekta Khurana, Sebastian Waszak, Jan O. Korbel, James E. Haber, Marcin Imielinski, Joachim Weischenfeldt, Rameen Beroukhim, Peter J. Campbell
Correction
Multidisciplinary Sciences
Esther Rheinbay, Morten Muhlig Nielsen, Federico Abascal, Jeremiah A. Wala, Ofer Shapira, Grace Tiao, Henrik Hornshoj, Julian M. Hess, Randi Istrup Juul, Ziao Lin, Lars Feuerbach, Radhakrishnan Sabarinathan, Tobias Madsen, Jaegil Kim, Loris Mularoni, Shimin Shuai, Andres Lanzos, Carl Herrmann, Yosef E. Maruvka, Ciyue Shen, Samirkumar B. Amin, Pratiti Bandopadhayay, Johanna Bertl, Keith A. Boroevich, John Busanovich, Joana Carlevaro-Fita, Dimple Chakravarty, Calvin Wing Yiu Chan, David Craft, Priyanka Dhingra, Klev Diamanti, Nuno A. Fonseca, Abel Gonzalez-Perez, Qianyun Guo, Mark P. Hamilton, Nicholas J. Haradhvala, Chen Hong, Keren Isaev, Todd A. Johnson, Malene Juul, Andre Kahles, Abdullah Kahraman, Youngwook Kim, Jan Komorowski, Kiran Kumar, Sushant Kumar, Donghoon Lee, Kjong-Van Lehmann, Yilong Li, Eric Minwei Liu, Lucas Lochovsky, Keunchil Park, Oriol Pich, Nicola D. Roberts, Gordon Saksena, Steven E. Schumacher, Nikos Sidiropoulos, Lina Sieverling, Nasa Sinnott-Armstrong, Chip Stewart, David Tamborero, Jose M. C. Tubio, Husen M. Umer, Liis Uuskuela-Reimand, Claes Wadelius, Lina Wadi, Xiaotong Yao, Cheng-Zhong Zhang, Jing Zhang, James E. Haber, Asger Hobolth, Marcin Imielinski, Manolis Kellis, Michael S. Lawrence, Christian von Mering, Hidewaki Nakagawa, Benjamin J. Raphael, Mark A. Rubin, Chris Sander, Lincoln D. Stein, Joshua M. Stuart, Tatsuhiko Tsunoda, David A. Wheeler, Rory Johnson, Jueri Reimand, Mark Gerstein, Ekta Khurana, Peter J. Campbell, Nuria Lopez-Bigas, Joachim Weischenfeldt, Rameen Beroukhim, Inigo Martincorena, Jakob Skou Pedersen, Gad Getz
Article
Medicine, Legal
Shengjie Gao, Bowen Li, Likai Mao, Wenfeng Wang, Dan Zou, Jianchao Zhng, Mi Zhou, Simin Yu, Feixue Zheng, Ye Yin, Shi Qiang Liu, Huanming Yang, Hongqi Wang
Summary: There is an increasing demand for prenatal paternity testing in forensic applications. A proposed methodology called the Prenatal paternity Test Analysis System (PTAS) utilizes Next-Generation Sequencing (NGS)-based SNP genotyping to accurately determine paternity in both early-pregnancy and mid-to-late pregnancy samples, making a significant breakthrough in NIPPT theory.
FORENSIC SCIENCE INTERNATIONAL
(2023)
Article
Biochemistry & Molecular Biology
Xin Jin, Yanqun Wang, Jinjin Xu, Yimin Li, Fanjun Cheng, Yuxue Luo, Haibo Zhou, Shanwen Lin, Fei Xiao, Lu Zhang, Yu Lin, Zhaoyong Zhang, Yan Jin, Fang Zheng, Wei Chen, Airu Zhu, Ye Tao, Jingxian Zhao, Tingyou Kuo, Yuming Li, Lingguo Li, Liyan Wen, Rijing Ou, Fang Li, Long Lin, Yanjun Zhang, Jing Sun, Hao Yuan, Zhen Zhuang, Haixi Sun, Zhao Chen, Jie Li, Jianfen Zhuo, Dongsheng Chen, Shengnan Zhang, Yuzhe Sun, Peilan Wei, Jinwei Yuan, Tian Xu, Huanming Yang, Jian Wang, Xun Xu, Nanshan Zhong, Yonghao Xu, Kun Sun, Jincun Zhao
Summary: This study investigates the potential of plasma cell-free DNA fragmentation patterns in assessing tissue injury and monitoring treatment effectiveness in COVID-19 patients. The findings show that these DNA fragmentation characteristics reflect patient-specific physiological changes during treatment, and reveal frequent tissue injuries in COVID-19 patients.
MOLECULAR GENETICS AND GENOMICS
(2023)
Article
Multidisciplinary Sciences
Yang Dong, Shengchang Duan, Qiuju Xia, Zhenchang Liang, Xiao Dong, Kristine Margaryan, Mirza Musayev, Svitlana Goryslavets, Goran Zdunic, Pierre-Francois Bert, Thierry Lacombe, Erika Maul, Peter Nick, Kakha Bitskinashvili, Gyorgy Denes Bisztray, Elyashiv Drori, Gabriella De Lorenzis, Jorge Cunha, Carmen Florentina Popescu, Rosa Arroyo-Garcia, Claire Arnold, Ali Ergul, Yifan Zhu, Chao Ma, Shufen Wang, Siqi Liu, Liu Tang, Chunping Wang, Dawei Li, Yunbing Pan, Jingxian Li, Ling Yang, Xuzhen Li, Guisheng Xiang, Zijiang Yang, Baozheng Chen, Zhanwu Dai, Yi Wang, Arsen Arakelyan, Varis Kuliyev, Gennady Spotar, Nabil Girollet, Serge Delrot, Nathalie Ollat, Patrice This, Cecile Marchal, Gautier Sarah, Valerie Laucou, Roberto Bacilieri, Franco Roeckel, Pingyin Guan, Andreas Jung, Michael Riemann, Levan Ujmajuridze, Tekle Zakalashvili, David Maghradze, Maria Hohn, Gizella Jahnke, Erzsebet Kiss, Tamas Deak, Oshrit Rahimi, Sariel Hubner, Fabrizio Grassi, Francesco Mercati, Francesco Sunseri, Jose Eiras-Dias, Anamaria Mirabela Dumitru, David Carrasco, Alberto Rodriguez-Izquierdo, Gregorio Munoz, Tamer Uysal, Cengiz Ozer, Kemal Kazan, Meilong Xu, Yunyue Wang, Shusheng Zhu, Jiang Lu, Maoxiang Zhao, Lei Wang, Songtao Jiu, Ying Zhang, Lei Sun, Huanming Yang, Ehud Weiss, Shiping Wang, Youyong Zhu, Shaohua Li, Jun Sheng, Wei Chen
Summary: We investigate the evolution and domestication of grapevines by studying 3525 cultivated and wild varieties worldwide. Harsh climate in the Pleistocene led to the separation of wild grape ecotypes due to habitat fragmentation. Domestication occurred around 11,000 years ago in Western Asia and the Caucasus, giving rise to table and wine grapevines. The domesticates from Western Asia dispersed into Europe, hybridizing with ancient wild ecotypes and diversifying into muscat and unique western wine grape ancestries as human migration took place in the late Neolithic. Analysis of domestication traits also provides insights into the selection for berry palatability, hermaphroditism, muscat flavor, and berry skin color. These findings demonstrate the significance of grapevines in the early development of agriculture across Eurasia.
Article
Multidisciplinary Sciences
Ziqi Gao, Chenran Jiang, Jiawen Zhang, Xiaosen Jiang, Lanqing Li, Peilin Zhao, Huanming Yang, Yong Huang, Jia Li
Summary: This article presents a new computational model, HIGH-PPI, for predicting protein-protein interactions (PPIs) and extrapolating molecular details. The model uses a double-viewed hierarchical graph learning approach, considering both the interactions between proteins and the structure-function relationship within proteins. Experimental results demonstrate that HIGH-PPI achieves high accuracy and robustness in PPI prediction.
NATURE COMMUNICATIONS
(2023)
Article
Multidisciplinary Sciences
Xiaoqian Lin, Tongyuan Hu, Jianwei Chen, Hewei Liang, Jianwei Zhou, Zhinan Wu, Chen Ye, Xin Jin, Xun Xu, Wenwei Zhang, Xiaohuan Jing, Tao Yang, Jian Wang, Huanming Yang, Karsten Kristiansen, Liang Xiao, Yuanqiang Zou
Summary: The authors present an expanded version of the Cultivated Genome Reference (CGR), termed CGR2, which includes 3324 high-quality draft genomes based on gut bacterial isolates from Chinese individuals. They classify 527 species from 8 phyla, including 179 previously unidentified species, and provide information on secondary metabolite biosynthetic gene clusters and gut phage-bacteria interactions.
NATURE COMMUNICATIONS
(2023)
Article
Multidisciplinary Sciences
Xiaomin Liu, Leying Zou, Chao Nie, Youwen Qin, Xin Tong, Jian Wang, Huanming Yang, Xun Xu, Xin Jin, Liang Xiao, Tao Zhang, Junxia Min, Yi Zeng, Huijue Jia, Yong Hou
Summary: Although the association between human microbiome, especially gut microbiota, and longevity has been revealed in recent studies, the causality between them is still unclear. This study used bidirectional two-sample Mendelian randomization (MR) analyses to assess the relationship between the human microbiome (gut and oral microbiota) and longevity. The findings suggest that certain disease-protected gut microbiota and probiotics are associated with increased odds of longevity, while other gut microbiota are negatively associated with longevity.
SCIENTIFIC REPORTS
(2023)
Article
Biotechnology & Applied Microbiology
Xiangwei Hu, Kai Xia, Minhui Dai, Xiaofeng Han, Peng Yuan, Jia Liu, Shiwei Liu, Fuhuai Jia, Jiayu Chen, Fangfang Jiang, Jieyao Yu, Huanming Yang, Jian Wang, Xun Xu, Xin Jin, Karsten Kristiansen, Liang Xiao, Wei Chen, Mo Han, Shenglin Duan
Summary: Intermittent fasting is a promising weight loss method that modulates the gut microbiota. A three-week IF program resulted in an average weight loss of 3.67 kg and improved clinical parameters, regardless of initial BMI and gut microbiota status.
NPJ BIOFILMS AND MICROBIOMES
(2023)
Article
Ecology
Yang Zhou, Xiaoyu Zhan, Jiazheng Jin, Long Zhou, Juraj Bergman, Xuemei Li, Marjolaine Marie C. Rousselle, Meritxell Riera Belles, Lan Zhao, Miaoquan Fang, Jiawei Chen, Qi Fang, Lukas Kuderna, Tomas Marques-Bonet, Haruka Kitayama, Takashi Hayakawa, Yong-Gang Yao, Huanming Yang, David N. Cooper, Xiaoguang Qi, Dong-Dong Wu, Mikkel Heide Schierup, Guojie Zhang
Summary: A comparative analysis of Y chromosomes in 29 primate species reveals rapid evolution and different patterns of evolution in different regions. The Y chromosome plays a critical role in determining male sex and has unique sequence classes that have experienced distinct evolutionary trajectories. By generating and analyzing 19 new primate sex chromosome assemblies, along with 10 existing ones, this study reports the rapid evolution of the primate Y chromosome. Different primate lineages exhibit varying rates of gene loss, structural changes, and chromatin modifications on their Y chromosomes. The study also highlights the contribution of selection on Y-linked genes to the evolution of male traits across primates.
NATURE ECOLOGY & EVOLUTION
(2023)
Article
Biochemistry & Molecular Biology
Xiaoying Zhao, Kunli Qu, Benedetta Curci, Huanming Yang, Lars Bolund, Lin Lin, Yonglun Luo
Summary: Recent progress in CRISPR gene editing tools has expanded the possibilities for treating devastating genetic diseases. In this study, three methods of gene editing (NHBEJ, HDR, and PE) were compared for correcting loss-of-function mutations in Duchenne Muscular Dystrophy. The highest efficiency was achieved with NHBEJ, followed by HDR and PE2. The correction efficiency was increased with the use of PE3. This study demonstrates the potential for highly efficient correction of DMD mutations using CRISPR gene editing.
Article
Chemistry, Multidisciplinary
Zhiming Li, Yanmei Ju, Jingjing Xia, Zhe Zhang, Hefu Zhen, Xin Tong, Yuzhe Sun, Haorong Lu, Yang Zong, Peishan Chen, Kaiye Cai, Zhen Wang, Huanming Yang, Jiucun Wang, Jian Wang, Yong Hou, Xin Jin, Tao Zhang, Wenwei Zhang, Xun Xu, Liang Xiao, Ruijin Guo, Chao Nie
Summary: This study used deep-shotgun sequencing to analyze 450 facial samples and 2069 publicly available skin metagenomic datasets, and constructed a Unified Human Skin Genome (UHSG) catalog containing 813 prokaryotic species. The core functions of the skin microbiome were described based on the UHSG, and differences in amino acid metabolism, carbohydrate metabolism, and drug resistance functions among different phyla were identified. Additionally, analysis of near-complete genomes revealed 1220 putative novel secondary metabolites. The UHSG provides a convenient reference database for studying the role of skin microorganisms in the skin.
Article
Biology
Xi Dai, Honglian Shao, Nianqin Sun, Baiquan Ci, Jun Wu, Chuanyu Liu, Liang Wu, Yue Yuan, Xiaoyu Wei, Huanming Yang, Longqi Liu, Weizhi Ji, Bing Bai, Zhouchun Shang, Tao Tan
Summary: This study applied scATAC-seq technology to investigate the chromatin status of in vitro cultured cynomolgus monkey embryos. The findings provide insights into the chromatin reorganization and transcriptional regulatory mechanisms during early post-implantation development in primates, including the identification of regulatory factors and lineage specification.
Article
Cell Biology
Chentao Yang, Yang Zhou, Yanni Song, Dongya Wu, Yan Zeng, Lei Nie, Panhong Liu, Shilong Zhang, Guangji Chen, Jinjin Xu, Hongling Zhou, Long Zhou, Xiaobo Qian, Chenlu Liu, Shangjin Tan, Chengran Zhou, Wei Dai, Mengyang Xu, Yanwei Qi, Xiaobo Wang, Lidong Guo, Guangyi Fan, Aijun Wang, Yuan Deng, Yong Zhang, Jiazheng Jin, Yunqiu He, Chunxue Guo, Guoji Guo, Qing Zhou, Xun Xu, Huanming Yang, Jian Wang, Shuhua Xu, Yafei Mao, Xin Jin, Jue Ruan, Guojie Zhang
Summary: Since the release of the complete human genome, efforts in human genomic study have shifted towards closing gaps in ethnic diversity. In this study, a fully phased diploid human genome from a Han Chinese male individual (CN1) was presented, achieving the telomere-to-telomere (T2T) level. Comparisons with the CHM13 haploid T2T genome revealed significant variations in the centromere and numerous novel structural variations outside the centromere. CN1 outperformed CHM13 as a reference genome for the East Asian population, impacting rare SNP calling and uncovering East Asian specific introgression sequences.
Article
Ophthalmology
Wei Li, Xiang-Dong He, Zheng-Tao Yang, Dong-Ming Han, Yan Sun, Yan-Xian Chen, Xiao-Tong Han, Si-Cheng Guo, Yu-Ting Ma, Xin Jin, Huan-Ming Yang, Ya Gao, Zhuo-Shi Wang, Jian-Kang Li, Wei He
Summary: The aim of this study was to investigate the genetic characteristics and genotype-phenotype associations in a trio-based cohort of inherited eye diseases (IEDs). Through retrospective analysis of a large cohort of Chinese proband-parent trios, the researchers identified 108 IED-causative genes and found that the top 24 genes explained two-thirds of the genetically solved trios. The study also revealed the significant role of de novo mutations (DNMs) in IEDs and its association with paternal age at reproduction.
INVESTIGATIVE OPHTHALMOLOGY & VISUAL SCIENCE
(2023)