91 Works

Genomic and transcriptomic data for the frog Platyplectrum ornatum

Scott Edwards, Sangeet Lamichhaney, Renee Catullo, Scott Keogh, Simon Clulow & Tariq Ezaz
The diversity of genome sizes across the tree of life is of key interest in evolutionary biology. Various correlates of variation in genome size, such as accumulation of transposable elements or rate of DNA gain and loss, are well known, but the underlying molecular mechanisms that drive or constrain genome size are poorly understood. Here we study one of the smallest genomes among frogs characterized thus far, that of the ornate burrowing frog (Platyplectrum ornatum)...

Deletion of Polyamine Transport Protein PotD Exacerbates Virulence in Glaesserella (Haemophilus) parasuis in the Form of Non-biofilm-generated Bacteria in a Murine Acute Infection Model

Ke Dai, Zhen Yang, Xiaoyu Ma, Yung-Fu Chang, Sanjie Cao, Qin Zhao, Xiaobo Huang, Rui Wu, Yong Huang, Jing Xia, Qigui Yan, Xinfeng Han, Xiaoping Ma, Xintian Wen & Yiping Wen
Polyamines are small, polycationic molecules with a hydrocarbon backbone and multiple amino groups required for optimal cell growth. The potD gene, belonging to the ABC (ATP-binding cassette) transport system potABCD, encodes the bacterial substrate-binding subunit of the polyamine transport system, playing a pivotal role in bacterial metabolism and growth. The swine pathogen Glaesserella parasuis possesses an intact pot operon, and the studies presented here mainly examined the involvement of PotD in Glaesserella pathogenesis. A potD-deficient...

Quasispecies of SARS-CoV-2 revealed by single nucleotide polymorphisms (SNPs) analysis

Rongsui Gao, Wenhong Zu, Yang Liu, Junhua Li, Zeyao Li, Yanling Wen, Haiyan Wang, Jing Yuan, Lin Cheng, Shengyuan Zhang, Yu Zhang, Shuye Zhang, Weilong Liu, Xun Lan, Lei Liu, Feng Li & Zheng Zhang
New SARS-CoV-2 mutants have been continuously indentified with enhanced transmission ever since its outbreak in early 2020. As an RNA virus, SARS-CoV-2 has a high mutation rate due to the low fidelity of RNA polymerase. To study the single nucleotide polymorphisms (SNPs) dynamics of SARS-CoV-2, 158 SNPs with high confidence were identified by deep meta-transcriptomic sequencing, and the most common SNP type was C > T. Analyses of intra-host population diversity revealed that intra-host quasispecies’...

Evolutionary tradeoffs between male secondary sexual traits revealed by a phylogeny of the hyperdiverse tribe Eumaeini (Lepidoptera: Lycaenidae)

Wendy A. Valencia-Montoya, Tiago B. Quental, João Filipe R. Tonini, Gerard Talavera, James D. Crall, Gerardo Lamas, Robert C. Busby, Ana Paula S. Carvalho, Ana B. Morais, Nicolás Oliveira Mega, Helena Piccoli Romanowski, Marjorie A. Liénard, Shayla Salzman, Melissa R. L. Whitaker, Akito Y. Kawahara, David J. Lohman, Robert K. Robbins & Naomi E. Pierce
Male butterflies in the hyperdiverse tribe Eumaeini possess an unusually complex and diverse repertoire of secondary sexual characteristics involved in pheromone production and dissemination. Maintaining multiple sexually selected traits is likely to be metabolically costly, potentially resulting in trade-offs in the evolution of male signals. However, a phylogenetic framework to test hypotheses regarding the evolution and maintenance of male sexual traits in Eumaeini has been lacking. Here, we infer a comprehensive, time-calibrated phylogeny from 379...

Estimating the Net Value of Treating Hepatitis C Virus Using Newly Available Direct-Acting Antivirals in India (Supporting Datasets)

David Bloom, Alex Khoury & V. Srinivasan
Recently developed direct-acting antiviral (DAA) treatments for hepatitis C virus (HCV) have been groundbreaking for their high efficacy across disease genotypes and lack of severe side effects. This study uses a cost-of-illness (COI) approach to estimate the net value conferred by this class of drugs using the cost and efficacy of one of these novel drug combinations, sofosbuvir and velpatasvir (SOF/VEL), recently licensed for generic manufacture in India. This study considers COI of lifetime earnings...

Phytogeographic history of the Tea family inferred through high-resolution phylogeny and fossils

Yujing Yan, Charles Davis, Dimitar Dimitrov, Zhiheng Wang, Carsten Rahbek & Michael Borregaard
The tea family (Theaceae) has a highly unusual amphi-Pacific disjunct distribution: most extant species in the family are restricted to subtropical evergreen broadleaf forests in East Asia, while a handful of species occur exclusively in the subtropical and tropical Americas. Here we used an approach that integrates the rich fossil evidence of this group with phylogenies in biogeographic analysis to study the processes behind this distribution pattern. We first combined genome-skimming sequencing with existing molecular...

Antioxidant and antibacterial activities of 13 ornamental herbaceous peony cultivars: a comparative study with stems and leaves

Lei Liu, Yingdan Yuan & Jun Tao
Paeonia lactiflora is an important ornamental and medicinal plant, but after the flowering period, the above-ground parts of ornamental cultivars are often discarded as waste. When considering the development of medicinal plant resources, attention should be paid to the comprehensive development and utilisation of the plant. In this study, 13 ornamental herbaceous peony cultivars were selected, and their stems and leaves were analysed for antioxidant and antibacterial activities. The results showed that total phenolic content...

Data for: Ecology and behavior predict an evolutionary trade-off between song complexity and elaborate plumages in antwrens (Aves, Thamnophilidae)

Renata Beco, Luís Fábio Silveira, Elizabeth Derryberry & Gustavo Bravo
The environment can impose constraints on signal transmission properties such that signals should evolve in predictable directions (Sensory Drive Hypothesis). However, behavioral and ecological factors can limit investment in more than one sensory modality leading to a trade-off in use of different signals (Transfer Hypothesis). In birds, there is mixed evidence for both sensory drive and transfer hypothesis. Few studies have tested sensory drive while also evaluating the transfer hypothesis, limiting understanding of the relative...

Dataset S1 - Noelaerhabdaceae organic carbon isotope culture data compilation

Samuel Phelps, Gwenn Hennon, Sonya Dyhrman, María Hernández-Limón, Olivia Williamson & Pratigya Polissar
The carbon isotope fractionation in algal organic matter (Ep), including the long-chain alkenones produced by the coccolithophorid family Noelaerhabdaceae, is used to reconstruct past atmospheric CO2 levels. The conventional proxy linearly relates Ep to changes in cellular carbon demand relative to diffusive CO2 supply, with larger Ep values occurring at lower carbon demand relative to supply (i.e. abundant CO2). However, the response of Gephyrocapsa oceanica, one of the dominant alkenone producers of the last few...

Vachellia drepanolobium nutrient translocation in response to smoke

Katherine Angier, Richard Rabideau-Childers, Brendan Dean, Meghan Blumstein, Walker Darling, Annina Kennedy-Yoon, Clayton Ziemke, Christian Perez-Martinez, Donghao Wu, Wenqing Ye, Inam Yekwayo, Duncan Kimuyu, Dino Martins & Naomi Pierce
1. Fire is a major selective force on arid grassland communities, favoring traits such as the smoke-induced seed germination response seen in a wide variety of plant species. However, little is known about the relevance of smoke as a cue for plants beyond the seedling stage. 2. We exposed a fire-adapted savanna tree, Vachellia (=Acacia) drepanolobium, to smoke and compared nutrient concentrations in leaf and root tissues to unexposed controls. Experiments were performed on three...

Three periods of gold mineralization in the Liaodong Peninsula, North China Craton

Peng Zhang, Linlin Kou & Yang Zhao
The Liaodong gold province includes voluminous gold deposits, which occur in an Archean gneiss complex, Paleoproterozoic metamorphic rocks, and Mesozoic granite. However, the ore-forming age, the genesis, and the geodynamic setting of the gold deposits are not well constrained. In this study, we have summarized previous geochronology data, H-O-S-Pb isotopes, and He-Ar isotopic compositions of the gold deposits. Based on geochronology data, the gold mineralization was divided into Late Triassic, Early Jurassic, and Early Cretaceous....

Dataset female gregariousness in bonobos and chimpanzees

Martin Surbeck
Spatial association between females often mirrors pattern and strength of social relationships and cooperation within groups. Here we test for proposed differences in female-female associations and the role of sexual signaling between the two species of the genus Pan that have been linked to difference in female cooperation. Unlike previous studies, we found only limited evidence for a higher female-female gregariousness in bonobos. While bonobo females exhibited a slightly higher average number of females in...

Beneficial worm allies warn plants of parasite attack belowground and reduce aboveground herbivore preference and performance

Shokoofeh Kamali, Ali Javadmanesh, Lukasz Stelinski, Tina Kydnt, Alireza Seifi, Mojtaba Hosseini, Mehyar Heydarpour, Javad Asili & Javad Karimi
We investigated responses of tomato (Solanum lycopersicum) to two functional guilds of nematodes - plant parasite (Meloidogyne javanica) and entomopathogens (Heterorhabditis bacteriophora, Steinernema feltiae belowground, and S. carpocapsae) - as well as a leaf mining insect (Tuta absoluta) aboveground. Our results indicate that entomopathogenic nematodes (EPNs): 1) induced plant defense responses, 2) reduced root knot nematode (RKN) infestation belowground and 3) reduced herbivore (T. absoluta) host preference and performance aboveground. Concurrently, we investigated the plant...

Deletion of the sodium/hydrogen exchanger 6 causes low bone volume in adult mice

Fuster Daniel, Daniela Schnyder, Giuseppe Albano, Patrycja Kucharczyk, Silvia Dolder, Mark Siegrist, Manuel Anderegg, Ganesh Pathare, Willy Hofstetter, Roland Baron & Daniel G. Fuster
The sodium/hydrogen exchanger 6 (NHE6) localizes to recycling endosomes, where it mediates endosomal alkalinization through K+/H+ exchange. Mutations in the SLC9A6 gene encoding NHE6 cause severe X-linked mental retardation, epilepsy, autism and corticobasal degeneration in humans. Patients with SLC9A6 mutations exhibit skeletal malformations, and a previous study suggested a key role of NHE6 in osteoblast-mediated mineralization. The goal of this study was to explore the role of NHE6 in bone homeostasis. To this end, we...

BMI1 promotes steroidogenesis through maintaining redox homeostasis in mouse MLTC-1 and primary Leydig cells

Tingting Gao, Meng Lin, Binbin Shao, Qiao Zhou, Yufeng Wang, Xia Chen, Dan Zhao, Xiuliang Dai, Cong Shen, Hongbo Cheng, Shenmin Yang, Hong Li, Bo Zheng, Xingming Zhong, Jun Yu, Li Chen & Xiaoyan Huang
In males, aging is accompanied by decline in serum testosterone levels due to impairment of testicular Leydig cells. The polycomb protein BMI1 has recently been identified as an anti-aging factor. In our previous study, BMI1 null mice showed decreased serum testosterone and Leydig cell population, excessive oxidative stress and p16/p19 signaling activation. However, a cause-and-effect relationship between phenotypes and pathways was not investigated. Here, we used the rescue approach to study the role of oxidative...

Evaluation of cesarean delivery rates in different levels of hospitals in Jiangsu Province, China, using the 10-Group classification system

Ning Gu, Yimin Dai, Dan Lu, Tingmei Chen, Muling Zhang, Tao Huang, Yalan Qi, Xinning Han, Lihua Xie, Jishi Yang, Chengling Fan, Yunhua Yan, Anhong Zhang, Xiaoping Weng, Huiling Zhang, Li Su, Yingyan Li & Yali Hu
To compare cesarean delivery (CD) rates in referral and non-referral hospitals in Maternal Safety Collaboration in Jiangsu province, China. Sixteen participants (4 referral hospitals, 12 non-referral hospitals) from Drum Tower Hospital Collaboration for Maternal Safety reported CD rates in 2019 using ten-group classification system and maternal/neonatal morbidity and mortality. A total of 22,676 CDs were performed among 52,499 deliveries and the average CD rate was 43.2% (range 34.8–69.6%). CD rate in non-referral hospitals (44.7%) was...

A novel fusion circular RNA F-circBA1 derived from the BCR-ABL fusion gene displayed an oncogenic role in chronic myeloid leukemia cells

Yuan Tan, Zhenglan Huang, Xin Wang, Hongdan Dai, Guoyun Jiang & Wenli Feng
The BCR-ABL fusion gene plays a crucial role in the leukemogenesis of chronic myeloid leukemia (CML). The BCR-ABL oncoprotein encoded by this fusion gene has been extensively studied. However, research on whether BCR-ABL also affects circular RNAs (circRNAs) is limited. This study aimed to explore the new fusion circRNAs produced by BCR-ABL and their role in CML cells. In this study, we identified a novel fusion circRNA, named F-circBA1, originating from BCR-ABL in K562 and...

A seven-gene signature and the C–C motif chemokine receptor family genes are the sarcoma-related immune genes

Jiarui Chen, Tuo Liang, Jiemei Cen, Jie Jiang, Shixin Pan, Shengsheng Huang, Liyi Chen, Xuhua Sun, Hao Li, Tianyou Chen, Wei Liang, Shian Liao, Chaojie Yu, Yuanlin Yao, Zhen Ye, Wuhua Chen, Hao Guo, Xinli Zhan & Chong Liu
Cells of the tumor microenvironment exert a vital influence on sarcoma prognosis. This study aimed to analyze and identify differentially expressed genes (DEGs) related to immunity and their significance as immune biomarkers for the accurate prediction of overall survival of patients with sarcoma. The Cancer Genome Atlas was adopted for obtaining sarcoma gene microarray and corresponding clinical information. ESTIMATE algorithm was used to calculate tumor immune microenvironment indices. Immune-associated DEGs were identified using the limma...

Special electromagnetic field-treated water and far-infrared radiation alleviates lipopolysaccharide-induced acute respiratory distress syndrome in rats by regulating haptoglobin

Changyong Luo, Yan Li, Xu Liang, Yifan Chen, Qiao Zou, Yurong Kong, Zhengguang Guo, Wei Sun & Xin Wang
Special electromagnetic field-treated water (SEW) and far-infrared radiation (FIR) can reduce acute respiratory distress syndrome (ARDS) in rats inflicted by lipopolysaccharides (LPSs). However, little is known about its underlying molecular mechanism. Differentially expressed proteins (DEPs) of SEW and FIR interventions were obtained from a proteomics database. A total of 89 DEPs were identified. Enrichment analysis of DEPs was performed using the Database for Annotation, Visualization, and Integrated Discovery. These DEPs were associated with the responses...

Long non-coding RNA RP11-283G6.5 confines breast cancer development through modulating miR-188-3p/TMED3/Wnt/β-catenin signaling

Jing Pei, Shengquan Zhang, Xiaowei Yang, Chunguang Han, Yubo Pan, Jun Li, Zhaorui Wang, Chenyu Sun & Jing Zhang
The contributions of long non-coding RNAs (lncRNAs) and microRNAs (miRNAs) to breast cancer are critical areas of investigation. In this study, we identified a novel lncRNA RP11-283G6.5 which was lowly expressed in breast cancer and whose low expression was correlated with poor overall survival and disease-free survival of breast cancer patients. Functional experiments revealed that ectopic expression of RP11-283G6.5 confined breast cancer cellular growth, migration, and invasion, and promoted cellular apoptosis. Conversely, RP11-283G6.5 silencing facilitated...

Deletion of Polyamine Transport Protein PotD Exacerbates Virulence in Glaesserella (Haemophilus) parasuis in the Form of Non-biofilm-generated Bacteria in a Murine Acute Infection Model

Ke Dai, Zhen Yang, Xiaoyu Ma, Yung-Fu Chang, Sanjie Cao, Qin Zhao, Xiaobo Huang, Rui Wu, Yong Huang, Jing Xia, Qigui Yan, Xinfeng Han, Xiaoping Ma, Xintian Wen & Yiping Wen
Polyamines are small, polycationic molecules with a hydrocarbon backbone and multiple amino groups required for optimal cell growth. The potD gene, belonging to the ABC (ATP-binding cassette) transport system potABCD, encodes the bacterial substrate-binding subunit of the polyamine transport system, playing a pivotal role in bacterial metabolism and growth. The swine pathogen Glaesserella parasuis possesses an intact pot operon, and the studies presented here mainly examined the involvement of PotD in Glaesserella pathogenesis. A potD-deficient...

A dataset of ovariole number from more than 2,000 insect species

Samuel H. Church, Bruno A. S. De Medeiros, Seth Donoughe, Nicole L. Márquez Reyes & Cassandra G. Extavour
The number of offspring an organism can produce is a key component of its evolutionary fitness and life-history. This number differs widely between organisms, and its variation is the foundation for several hypotheses about life-history evolution, including the prediction that there is an evolutionary trade off between the number of offspring and their size. In insects, the number of egg-producing compartments in the ovary, called ovarioles, has been used as a proxy for potential offspring...

Data for: Phylogenomic analyses reveal non-monophyly of the antbird genera Herpsilochmus and Sakesphorus (Thamnophilidae), with description of a new genus for Herpsilochmus sellowi

Gustavo Bravo, Bret Whitney, Ricardo Belmonte-Lopes, Marcos Bornschein, Natalia Aristizabal, Renata Beco, Jaqueline Battilana, Luciano Naka, Alexandre Aleixo, Marcio Pie, Luis Silveira, Elizabeth Derryberry & Robb Brumfield
The family Thamnophilidae is a species-rich Neotropical radiation of passerine birds. Current classification of its 235 species is mostly based on morphological similarities, but recent studies integrating comprehensive phenotypic and phylogenetic data have redefined taxonomic limits of several taxa. Here, we assess generic relationships of Herpsilochmus, Sakesphorus, Thamnophilus, Biatas, and Dysithamnus using DNA sequences from the mitochondrion, nuclear exons, and ultraconserved elements (UCEs), with further attention to interspecific relationships within Herpsilochmus. We show that Herpsilochmus...

Triennial migration and philopatry in the critically endangered soupfin shark (Galeorhinus galeus)

Andrew Nosal, Daniel Cartamil, Arnold Ammann, Lyall Bellquist, Noah Ben-Aderet, Kayla Blincow, Echelle Burns, Eric Chapman, Ryan Freedman, Peter Klimley, Ryan Logan, Christopher Lowe, Brice Semmens, Connor White & Philip Hastings
Globally, one-quarter of shark and ray species is threatened with extinction due to overfishing. Effective conservation and management can facilitate population recoveries; however, these efforts depend on robust data on movement patterns and stock structure, which are lacking for many threatened species, including the Critically Endangered soupfin shark (Galeorhinus galeus), a circumglobal coastal-pelagic species. Using passive acoustic telemetry, we continuously tracked 34 mature female soupfin sharks, surgically implanted with coded acoustic transmitters, for seven years...

Shorter distal forelimbs benefit bipedal walking and running mechanics: implications for hominin forelimb evolution

Andrew Yegian, Yanish Tucker, Stephen Gillinov & Daniel Lieberman
This file provides the data from the manuscript "Shorter distal forelimbs benefit bipedal walking and running mechanics: implications for hominin forelimb evolution" sin the American Journal of Physical Anthropology. Objectives: Brachial index is a skeletal ratio that describes the relative length of the distal forelimb. Over the course of hominin evolution, a shift towards smaller brachial indices occurred. First, Pleistocene australopiths yield values between extant chimpanzees and humans, with further evolution in Pliocene Homo to...

Registration Year

  • 2021

Resource Types

  • Dataset


  • Harvard University
  • Chinese Academy of Medical Sciences & Peking Union Medical College
  • Capital Medical University
  • Shanghai Jiao Tong University
  • Fudan University
  • Sun Yat-sen University
  • Sichuan University
  • Nanjing Medical University
  • Southern Medical University
  • Huazhong University of Science and Technology