Article
Biochemistry & Molecular Biology
Zhen Li, Sheng Hu Qian, Fan Wang, Hany Mohamed, Guangfu Yang, Zhen-Xia Chen, Dengguo Wei
Summary: G-quadruplexes in viral genomes can be targeted for antiviral therapies. This study identified putative quadruplex-forming sequences (PQSs) in viral genomes and analyzed their abundance, structural stability, and conservation. A database was constructed to collect details of each viral PQS. The results showed an enrichment of G(2)-PQS in both eukaryotic and prokaryotic viruses, while G(3)-PQS was only enriched in eukaryotic viruses and depleted in prokaryotic viruses. Structural stability of PQSs was lower in prokaryotic viruses compared to eukaryotic viruses.
JOURNAL OF GENETICS AND GENOMICS
(2022)
Article
Multidisciplinary Sciences
Max E. Schon, Vasily V. Zlatogursky, Rohan P. Singh, Camille Poirier, Susanne Wilken, Varsha Mathur, Juergen F. H. Strassert, Jarone Pinhassi, Alexandra Z. Worden, Patrick J. Keeling, Thijs J. G. Ettema, Jeremy G. Wideman, Fabien Burki
Summary: This study utilized single-cell genomics and phylogenomics to infer the evolutionary origin of the plastid-lacking phylum Picozoa, revealing that they belong to the Archaeplastida and altering our understanding of plastid evolution.
NATURE COMMUNICATIONS
(2021)
Article
Geosciences, Multidisciplinary
Bess G. Koffman, Matthew B. Osman, Alison S. Criscitiello, Sofia Guest
Summary: Collaboration with other women is a key factor in closing gender gaps in ice core science, as it increases the number of women co-authors and exceeds the estimated proportion of women in the field.
Article
Biology
Emma M. Templeton, Luke J. J. Chang, Elizabeth A. Reynolds, Marie D. Cone D. LeBeaumont, Thalia Wheatley
Summary: When people feel connected, short gaps between turns in conversation are created. Long gaps between strangers indicate disconnection, but between friends, they signal moments of increased connection. Long gaps between strangers are perceived as awkward, while those between friends involve more genuine laughter and less topic changes, suggesting they allow space for enjoyment and mutual reflection. This study highlights the meaningful differences in turn-taking dynamics between friends and strangers.
PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2023)
Article
Plant Sciences
Chi Zhang, Qianshi Lin, Jiayin Zhang, Zihao Huang, Peng Nan, Linfeng Li, Zhiping Song, Wenju Zhang, Ji Yang, Yuguo Wang
Summary: This study investigates the adaptation strategies and evolution of organelle genomes in the holoparasitic plant Christisonia kwangtungensis. By comparing the plastid genome and transcriptome of C. kwangtungensis with its closely related species, the study reveals differences in gene loss and gene expression, indicating different pathways to the loss of photosynthetic genes in these species. The study also discovers horizontally transferred genes of plastid origin in the mitochondrial genome, which may indicate historical hosts. This research provides insights into the evolution of parasitism in Orobanchaceae.
Article
Environmental Sciences
Xu Zhang, Jinbao Li, Qianjin Dong, Zifeng Wang, Han Zhang, Xiaofeng Liu
Summary: This study develops an empirical hydrological model to bridge the temporal gap between GRACE and GRACE-FO products and successfully reconstructs global terrestrial water storage anomalies (TWSA). The model performs similarly to previous studies but does not require detrending or deseasonalizing transformations, improving the physical understanding of TWSA.
SCIENCE OF THE TOTAL ENVIRONMENT
(2022)
Article
Chemistry, Applied
Ji-Qiang Jin, Wei-Dong Dai, Chen-Yu Zhang, Zhi Lin, Liang Chen
Summary: This study systematically investigated the phylogenetic relationships, morphological traits, and metabolite profiles of 27 typical tea accessions, revealing the diversification of genetic, morphological, and chemical characteristics of tea plants and leading to a better understanding of wild tea plants.
JOURNAL OF FOOD COMPOSITION AND ANALYSIS
(2022)
Article
Mechanics
Zhiwei Song, Lin Lu, Liang Cheng, Yong Liu, Guoqiang Tang, Xiaofan Lou
Summary: This study numerically investigates two-dimensional wave-induced fluid oscillations in two narrow gaps, focusing on the initial transient and final quasi-steady states. The amplitude and phase analyses reveal the characteristics of the transient and quasi-steady responses, and the roles of radiation damping and time-dependent period-averaged phase adjustment in establishing dynamic equilibrium. Simplified formulas are derived based on the intrinsic synchronization modes of quasi-steady oscillations to predict resonant and anti-resonant frequencies of the two-gaps system. The effects of incident wave amplitudes on the fluid responses and higher-order harmonics are highly dependent on frequency bands. Fourier transformations analysis explains the contributions of higher-order harmonics on overall responses.
Article
Surgery
Nathalie Sela, Blaire L. Anderson, Alexandra M. Moulton, Arika L. Hoffman
Summary: Despite an increase in research activity among female physicians in the transplantation field over time, gender disparities persist in publication amount and authorship positions, with male medical physicians being more productive.
JOURNAL OF SURGICAL RESEARCH
(2021)
Article
Computer Science, Information Systems
Chengxiang Yin, Jian Tang, Tongtong Yuan, Zhiyuan Xu, Yanzhi Wang
Summary: This paper presents a novel real-time model, Sem2Ins, for instance segmentation. It leverages conditional generative adversarial networks, deep supervision, and weighted fusion layer to generate instance boundaries based on semantic segmentation. Experimental results demonstrate that Sem2Ins performs well in terms of both speed and accuracy, outperforming state-of-the-art solutions and comparable to powerful detect-and-segment approaches.
IEEE TRANSACTIONS ON MULTIMEDIA
(2022)
Article
Engineering, Civil
Bao Zhang, Yibin Yao, Yulin He
Summary: This study evaluated different methods to fill the data gap in Greenland and its six sub-regions, with the results showing that the BPNN method outperformed others, especially in terms of accuracy for the whole of Greenland, helping to re-estimate the ice mass change in the region.
JOURNAL OF HYDROLOGY
(2022)
Article
Chemistry, Inorganic & Nuclear
Duomei Xue, Di Wu, Zeren Chen, Ying Li, WeiMing Sun, Jingyao Liu, Zhiru Li
Summary: The Zintl cluster Ge9Be has been identified as a potential member of the superatom family due to its similarity to chalcogen elements. It has the ability to form stable ionic compounds and covalent compounds with multiple valence superatoms. Utilizing solid Zintl clusters, stable superatom motifs can be designed and synthesized for specific characteristics-oriented applications.
INORGANIC CHEMISTRY
(2021)
Article
Biodiversity Conservation
Jing Li, Yiyan Sun, Li Wang, Yuan Wang
Summary: The study identifies priority conservation areas in Anhui Province based on systematic conservation planning theory and suggests expanding the protected area network to enhance conservation benefits for biodiversity and key ecosystem services.
ECOLOGICAL INDICATORS
(2023)
Article
Computer Science, Information Systems
Kai Huang, Houdong Liang, Chongchong Yao, Xi Zhao, Yue Cui, Yao Tian, Ruiyuan Zhang, Xiaofang Zhou
Summary: This demonstration introduces a novel VQI system called VISUALNEO, which enables efficient subgraph querying in large graph databases. It inherits advanced features from recent VQIs and connects to generic Neo4j databases through a database manager module, providing aesthetic query result exploration.
PROCEEDINGS OF THE VLDB ENDOWMENT
(2023)
Article
Computer Science, Artificial Intelligence
Yilin Niu, Fei Huang, Wei Liu, Jianwei Cui, Bin Wang, Minlie Huang
Summary: Semantic parsing maps natural language questions into logical forms. Data synthesis methods can hardly cover the diverse structures in natural languages, leading to a large gap in sentence structure between synthetic and natural questions. The proposed decomposition-based method unifies the sentence structures to improve generalization. It not only enhances the semantic parser's accuracy but also benefits other semantic understanding tasks like sentence embedding learning and retrieval.
TRANSACTIONS OF THE ASSOCIATION FOR COMPUTATIONAL LINGUISTICS
(2023)
Article
Multidisciplinary Sciences
Hiroto Kaneko, Romain Blanc-Mathieu, Hisashi Endo, Samuel Chaffron, Tom O. Delmont, Morgan Gaia, Nicolas Henry, Rodrigo Hernandez-Velazquez, Canh Hao Nguyen, Hiroshi Mamitsuka, Patrick Forterre, Olivier Jaillon, Colomban de Vargas, Matthew B. Sullivan, Curtis A. Suttle, Lionel Guidi, Hiroyuki Ogata
Summary: There is a significant association between viral community composition and carbon export efficiency on a global scale, with viruses predicted to infect ecologically important hosts playing a crucial role in this process. These findings suggest that viruses likely act in the carbon pump process at a large scale in a manner dependent on their hosts and ecosystem dynamics.
Article
Microbiology
Anthony C. C. Woo, Morgan Gaia, Julien Guglielmini, Violette Da Cunha, Patrick Forterre
Summary: Double-stranded DNA viruses of the realm Varidnaviria share homologous major capsid proteins (MCPs) and packaging ATPases (pATPases) and infect hosts from the three domains of life, suggesting a common ancestor. The evolutionary history of Varidnaviria shows complex characteristics, with Sphaerolipoviridae exhibiting divergent MCPs and pATPases grouping with Bamfordvirae. The grouping of Bamfordvirae infecting archaea with those infecting bacteria, in contradiction with the cellular tree of life, presents questions on the validity of Adenoviridae and Helvetiavirae ranking.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Violette Da Cunha, Morgan Gaia, Hiroyuki Ogata, Olivier Jaillon, Tom O. Delmont, Patrick Forterre
Summary: This study reveals the presence and expression of actin-related genes in viral genomes, suggesting that viruses recruited these genes from ancient protoeukaryotic hosts and transferred them to give rise to eukaryotic actins, which could have contributed to the emergence of the modern eukaryotic cytoskeleton.
MOLECULAR BIOLOGY AND EVOLUTION
(2022)
Article
Biochemistry & Molecular Biology
Paul Villain, Violette da Cunha, Etienne Villain, Patrick Forterre, Jacques Oberto, Ryan Catchpole, Tamara Basta
Summary: Research shows that expressing bacterial gyrase from Thermotoga maritima in the archaeon Thermococcus kodakarensis can induce negative supercoiling and impact gene expression and chromosomal topology. However, this artificially introduced supercoiling activity did not significantly affect the growth rate of the archaeon.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Biology
Ammara Manzoor, Saira Amir, Farzana Gul, Muhammad Abubakar Sidique, Masood Ur Rehman Kayani, Syed Shujaat Ali Zaidi, Sundus Javed, Syed Tahir Abbas Shah, Arshan Nasir
Summary: This study describes the microbial composition of the gastrointestinal and reproductive tracts of married Pakistani couples. It reveals differences in microbial diversity and composition between fertile and infertile couples, providing a foundation for future research on the association between the human microbiome and infertility.
Article
Biochemistry & Molecular Biology
Paul Villain, Ryan Catchpole, Patrick Forterre, Jacques Oberto, Violette da Cunha, Tamara Basta
Summary: This study reveals the evolutionary history of DNA gyrase in Archaea using phylogenomic approaches and sequence datasets. The results suggest that DNA gyrase was introduced into Euryarchaeal group II through horizontal gene transfer from bacterial ancestors. Furthermore, DNA gyrase has spread to other Archaea lineages through rare horizontal gene transfers. The study also shows the co-evolution of DNA gyrase and Topoisomerase VI in Archaea.
MOLECULAR BIOLOGY AND EVOLUTION
(2022)
Article
Biochemistry & Molecular Biology
Suzanne M. Scheaffer, Diana Lee, Bradley Whitener, Baoling Ying, Kai Wu, Chieh-Yu Liang, Hardik Jani, Philippa Martin, Nicholas J. Amato, Laura E. Avena, Daniela Montes Berrueta, Stephen D. Schmidt, Sijy O'Dell, Arshan Nasir, Gwo-Yu Chuang, Guillaume Stewart-Jones, Richard A. Koup, Nicole A. Doria-Rose, Andrea Carfi, Sayda M. Elbashir, Larissa B. Thackray, Darin K. Edwards, Michael S. Diamond
Summary: Bivalent vaccines induce broad immune responses against SARS-CoV-2 and its variants, offering a customizable approach to protect against COVID-19 as new strains emerge.
Article
Multidisciplinary Sciences
Celine Molinaro, Maelle Benefice, Aurore Gorlas, Violette Da Cunha, Hadrien M. L. Robert, Ryan Catchpole, Laurent Gallais, Patrick Forterre, Guillaume Baffou
Summary: In this article, the authors introduce a method for studying thermophilic microorganisms at high temperatures using microscale laser heating with gold nanoparticles as light absorbers. The method is demonstrated with two species and offers a simple and safe way to observe thermophiles using current microscopy tools.
NATURE COMMUNICATIONS
(2022)
Article
Multidisciplinary Sciences
Marie-Claire Daugeron, Sophia Missoury, Violette Da Cunha, Noureddine Lazar, Bruno Collinet, Herman van Tilbeurgh, Tamara Basta
Summary: The synthesis of t(6)A, a universal tRNA modification, is catalyzed by the KEOPS complex in Archaea and Eukaryotes. A fifth subunit, Gon7, is found only in Fungi and Metazoa. In this study, a fifth KEOPS subunit, Pcc2, is identified in Archaea and it is structurally and functionally similar to eukaryotic Gon7. Pcc2 regulates the oligomeric state of the KEOPS complex, which is conserved from Archaea to Eukaryotes.
NATURE COMMUNICATIONS
(2023)
Article
Microbiology
Maria Batool, Ciara Keating, Sundus Javed, Arshan Nasir, Muhammad Muddassar, Umer Zeeshan Ijaz
Summary: Antimicrobial resistance (AMR) is a global public health concern, particularly affecting low- and middle-income countries. This study aimed to link microbial assembly and covariates to gut microbiome structure and evaluate antimicrobial gene prevalence using PICRUSt2. The researchers analyzed the microbial profiles of healthy adults in Pakistan and found that drinking tap water was the main contributor to increased AMR signatures in the Pakistani cohort. They also observed abnormal gut microbial signatures in smokers and identified smoking and age as factors impacting the microbial community structure in this cohort.
Article
Multidisciplinary Sciences
Morgan Gaia, Lingjie Meng, Eric Pelletier, Patrick Forterre, Chiara Vanni, Antonio Fernandez-Guerra, Olivier Jaillon, Patrick Wincker, Hiroyuki Ogata, Mart Krupovic, Tom O. Delmont
Summary: DNA viruses have a significant impact on the ecology and evolution of cellular organisms, but their overall diversity and evolutionary paths are still unclear. This study discovered plankton-infecting relatives of herpesviruses in the sunlit oceans, which belong to a new phylum named Mirusviricota. These mirusviruses exhibit chimaeric attributes connecting them to both herpesviruses and giant eukaryotic viruses, and they play a lasting role in the ecology of marine ecosystems and the evolution of eukaryotic DNA viruses.
Article
Microbiology
Ryan J. Catchpole, Valerie Barbe, Ghislaine Magdelenat, Evelyne Marguet, Michael Terns, Jacques Oberto, Patrick Forterre, Violette Da Cunha
Summary: A conjugative plasmid isolated from Thermococcus enables the transfer of DNA between Archaea, regardless of their natural competence or the temperature, through type IV secretion systems. This is the first self-transmissible plasmid identified in a Euryarchaeon and it is also found in other Thermococcales species. The plasmid is a bona fide conjugative plasmid that requires cell-to-cell contact and is dependent on plasmid-encoded type IV secretion system-like genes. It can transfer to various Thermococcales species and propagate at temperatures of up to 100 degrees C. It has also been used to develop a genetic toolkit for modifying Archaeal genomes and has allowed targeted genome modification in previously untransformable Thermococcales species and interphylum transfer to a Crenarchaeon.
NATURE MICROBIOLOGY
(2023)
Article
Virology
Julien Guglielmini, Morgan Gaia, Violette Da Cunha, Alexis Criscuolo, Mart Krupovic, Patrick Forterre
Summary: Type II DNA topoisomerases of the family A (Topo IIAs) are present in all Bacteria and eukaryotes. The origin of eukaryotic Topo IIA remains mysterious, but they have close homologs in large viruses and may have been acquired from them. This highlights the important role of viruses in eukaryogenesis and suggests early proto-eukaryotes used a different type of topoisomerase to solve DNA topological problems.
