46 Works

Genomic changes underlying repeated niche shifts in an adaptive radiation

David A. Marques, Felicity C. Jones, Federica Di Palma, David M. Kingsley & Thomas E. Reimchen
In adaptive radiations, single lineages rapidly diversify by adapting to many new niches. Little is known yet about the genomic mechanisms involved, i.e. the source of genetic variation or genomic architecture facilitating or constraining adaptive radiation. Here, we investigate genomic changes associated with repeated invasion of many different freshwater niches by threespine stickleback in the Haida Gwaii archipelago, Canada, by re-sequencing single genomes from one marine and 28 freshwater populations. We find 89 likely targets...

The oldest unvaccinated Covid-19 survivors in South America

Mateus V. de Castro, Monize V. R. Silva, Michel S. Naslavsky, Marilia O. Scliar, Kelly Nunes, Maria Rita Passos-Bueno, Erick C. Castelli, Jhosiene Y. Magawa, Flávia L. Adami, Ana I. S. Moretti, Vivian L. de Oliveira, Silvia B. Boscardin, Edecio Cunha-Neto, Jorge Kalil, Emmanuelle Jouanguy, Paul Bastard, Jean-Laurent Casanova, Mauricio Quiñones-Vega, Patricia Sosa-Acosta, Jéssica S. de Guedes, Natália P. de Almeida, Fábio C. S. Nogueira, Gilberto B. Domont, Keity S. Santos & Mayana Zatz
Abstract Background Although older adults are at a high risk of severe or critical Covid-19, there are many cases of unvaccinated centenarians who had a silent infection or recovered from mild or moderate Covid-19. We studied three Brazilian supercentenarians, older than 110 years, who survived Covid-19 in 2020 before being vaccinated. Results Despite their advanced age, humoral immune response analysis showed that these individuals displayed robust levels of IgG and neutralizing antibodies (NAbs) against SARS-CoV-2....

A haplotype-resolved genome assembly of the Nile rat facilitates exploration of the genetic basis of diabetes

Huishi Toh, Chentao Yang, Giulio Formenti, Kalpana Raja, Lily Yan, Alan Tracey, William Chow, Kerstin Howe, Lucie A. Bergeron, Guojie Zhang, Bettina Haase, Jacquelyn Mountcastle, Olivier Fedrigo, John Fogg, Bogdan Kirilenko, Chetan Munegowda, Michael Hiller, Aashish Jain, Daisuke Kihara, Arang Rhie, Adam M. Phillippy, Scott A. Swanson, Peng Jiang, Dennis O. Clegg, Erich D. Jarvis … & Yury V. Bukhman
Abstract Background The Nile rat (Avicanthis niloticus) is an important animal model because of its robust diurnal rhythm, a cone-rich retina, and a propensity to develop diet-induced diabetes without chemical or genetic modifications. A closer similarity to humans in these aspects, compared to the widely used Mus musculus and Rattus norvegicus models, holds the promise of better translation of research findings to the clinic. Results We report a 2.5 Gb, chromosome-level reference genome assembly with...

Additional file 1 of A haplotype-resolved genome assembly of the Nile rat facilitates exploration of the genetic basis of diabetes

Huishi Toh, Chentao Yang, Giulio Formenti, Kalpana Raja, Lily Yan, Alan Tracey, William Chow, Kerstin Howe, Lucie A. Bergeron, Guojie Zhang, Bettina Haase, Jacquelyn Mountcastle, Olivier Fedrigo, John Fogg, Bogdan Kirilenko, Chetan Munegowda, Michael Hiller, Aashish Jain, Daisuke Kihara, Arang Rhie, Adam M. Phillippy, Scott A. Swanson, Peng Jiang, Dennis O. Clegg, Erich D. Jarvis … & Yury V. Bukhman
Additional file 1: Figure S1. Venn diagram of gene lists linked to type 2 diabetes by different types of evidence. Figure S2. Heterozygosity inferred by comparing the paternal and maternal scaffolded contigs, shown on the paternal scaffolds. Figure S3. Length distributions of structural variants. Figure S4. Functional classification of duplicated genes. Figure S5. Sequence alignment of Nile rat Gckr proteins to 113 mammalian orthologs. Figure S6. Missing Nile rat Hadh gene present in alternate haplotype...

Additional file 4 of Integrative analyses of maternal plasma cell-free DNA nucleosome footprint differences reveal chromosomal aneuploidy fetuses gene expression profile

Min Zhang, Kun Li, Shoufang Qu, Zhiwei Guo, Yuanli Wang, Xu Yang, Junhua Zhou, Guojun Ouyang, Rongtao Weng, Fenxia Li, Yingsong Wu & Xuexi Yang
Additional file 4: Table S4. Differential promoter coverage genes and GO, KEGG enrichment analysis results of differential genes for pregnant women with trisomy 13.

Additional file 1 of Bacteriomes in lesions of pulmonary tuberculosis and its association with status of Mycobacterium tuberculosis excretion

Weili Du, Yingli Zhao, Li Zhang, Jialu Che, Zichen Liu, Kun Li & Nanying Che
Additional file 1: Supplemental Table 1. Values of bacterial MetaCyc pathways of all TB lesions (40 TB-E and 42 TB-NE).

Additional file 2 of Bacteriomes in lesions of pulmonary tuberculosis and its association with status of Mycobacterium tuberculosis excretion

Weili Du, Yingli Zhao, Li Zhang, Jialu Che, Zichen Liu, Kun Li & Nanying Che
Additional file 2: Supplemental Table 2. Bacterial metabolic pathways that are significantly down/up regulated in TB-E compared to TB-NE.

Periodic spatial patterning with a single morphogen

Sheng Wang, Jordi Garcia-Ojalvo & Michael B. Elowitz
Data and code repository for paper "Periodic spatial patterning with a single morphogen"

Conserved structural elements specialize ATAD1 as a membrane protein extraction machine

Lan Wang, Hannah Toutkoushian, Vladislav Belyy, Claire Kokontis & Peter Walter
The mitochondrial AAA protein ATAD1 (in humans; Msp1 in yeast) removes mislocalized membrane proteins, as well as stuck import substrates from the mitochondrial outer membrane, facilitating their re-insertion into their cognate organelles and maintaining mitochondria’s protein import capacity. In doing so, it helps to maintain proteostasis in mitochondria. How ATAD1 tackles the energetic challenge to extract hydrophobic membrane proteins from the lipid bilayer and what structural features adapt ATAD1 for its particular function has remained...

Ground truth data used to train the synapse classifier used in Lillvis et al., 2022 for ExLLSM circuit reconstruction

Joshua Lillvis
Brain function is mediated by the physiological coordination of a vast, intricately connected network of molecular and cellular components. The physiological properties of network components can be quantified with high throughput; the ability to assess many animals per study has been key to relating physiological properties to behavior. Conversely, detailed anatomical properties (e.g., the synaptic connectivity of molecularly-defined cell types across an entire circuit) are presently quantifiable only with low throughput; thus we know very...

Additional file 6 of Integrative analyses of maternal plasma cell-free DNA nucleosome footprint differences reveal chromosomal aneuploidy fetuses gene expression profile

Min Zhang, Kun Li, Shoufang Qu, Zhiwei Guo, Yuanli Wang, Xu Yang, Junhua Zhou, Guojun Ouyang, Rongtao Weng, Fenxia Li, Yingsong Wu & Xuexi Yang
Additional file 6: All additional figures.

Additional file 6 of Integrative analyses of maternal plasma cell-free DNA nucleosome footprint differences reveal chromosomal aneuploidy fetuses gene expression profile

Min Zhang, Kun Li, Shoufang Qu, Zhiwei Guo, Yuanli Wang, Xu Yang, Junhua Zhou, Guojun Ouyang, Rongtao Weng, Fenxia Li, Yingsong Wu & Xuexi Yang
Additional file 6: All additional figures.

Integrative analyses of maternal plasma cell-free DNA nucleosome footprint differences reveal chromosomal aneuploidy fetuses gene expression profile

Min Zhang, Kun Li, Shoufang Qu, Zhiwei Guo, Yuanli Wang, Xu Yang, Junhua Zhou, Guojun Ouyang, Rongtao Weng, Fenxia Li, Yingsong Wu & Xuexi Yang
Abstract Background Chromosomal aneuploidy is the most common birth defect. However, the developmental mechanism and gene expression profile of fetuses with chromosomal aneuploidy are relatively unknown, and the maternal immune changes induced by fetal aneuploidy remain unclear. The inability to obtain the placenta multiple times in real-time is a bottleneck in research on aneuploid pregnancies. Plasma cell-free DNA (cfDNA) carries the gene expression profile information of its source cells and may be used to evaluate...

Additional file 1 of Integrative analyses of maternal plasma cell-free DNA nucleosome footprint differences reveal chromosomal aneuploidy fetuses gene expression profile

Min Zhang, Kun Li, Shoufang Qu, Zhiwei Guo, Yuanli Wang, Xu Yang, Junhua Zhou, Guojun Ouyang, Rongtao Weng, Fenxia Li, Yingsong Wu & Xuexi Yang
Additional file 1: Table S1. Differential promoter coverage genes and GO, KEGG enrichment analysis results of differential genes for all pregnant women with trisomy.

Bacteriomes in lesions of pulmonary tuberculosis and its association with status of Mycobacterium tuberculosis excretion

Weili Du, Yingli Zhao, Li Zhang, Jialu Che, Zichen Liu, Kun Li & Nanying Che
Abstract Background Bacteria in lung play an important role in sustaining lung health. Understanding the characteristics of bacteriomes in lesions of pulmonary tuberculosis (TB) patients, who excrete Mycobacterium tuberculosis (MTB), is important for TB prevention and effective treatment. Methods In this study, bacteriomes in lesions from TB patients excreting bacteria (TB-E) and those from TB patients not excreting bacteria (TB-NE) with matched normal lung tissues (NT) were compared by 16S rRNA sequencing. Bacterial MetaCyc functions...

Systematic characterization of wing mechanosensors that monitor airflow and wing deformations

Joseph Fabian, Igor Siwanowicz, Myriam Uhrhan, Masateru Maeda, Richard Bomphrey & Huai-Ti Lin
Animal wings deform during flight in ways that can enhance lift, facilitate flight control, and mitigate damage. Monitoring the structural and aerodynamic state of the wing is challenging because deformations are passive, and the flow fields are unsteady; it requires distributed mechanosensors that respond to local airflow and strain on the wing. Without a complete map of the sensor arrays, it is impossible to model control strategies underpinned by them. Here, we present the first...

Additional file 5 of Integrative analyses of maternal plasma cell-free DNA nucleosome footprint differences reveal chromosomal aneuploidy fetuses gene expression profile

Min Zhang, Kun Li, Shoufang Qu, Zhiwei Guo, Yuanli Wang, Xu Yang, Junhua Zhou, Guojun Ouyang, Rongtao Weng, Fenxia Li, Yingsong Wu & Xuexi Yang
Additional file 5: Table S5. Immunity genes with differential promoter coverage in all trisomic pregnant women.

Integrative analyses of maternal plasma cell-free DNA nucleosome footprint differences reveal chromosomal aneuploidy fetuses gene expression profile

Min Zhang, Kun Li, Shoufang Qu, Zhiwei Guo, Yuanli Wang, Xu Yang, Junhua Zhou, Guojun Ouyang, Rongtao Weng, Fenxia Li, Yingsong Wu & Xuexi Yang
Abstract Background Chromosomal aneuploidy is the most common birth defect. However, the developmental mechanism and gene expression profile of fetuses with chromosomal aneuploidy are relatively unknown, and the maternal immune changes induced by fetal aneuploidy remain unclear. The inability to obtain the placenta multiple times in real-time is a bottleneck in research on aneuploid pregnancies. Plasma cell-free DNA (cfDNA) carries the gene expression profile information of its source cells and may be used to evaluate...

Additional file 2 of Bacteriomes in lesions of pulmonary tuberculosis and its association with status of Mycobacterium tuberculosis excretion

Weili Du, Yingli Zhao, Li Zhang, Jialu Che, Zichen Liu, Kun Li & Nanying Che
Additional file 2: Supplemental Table 2. Bacterial metabolic pathways that are significantly down/up regulated in TB-E compared to TB-NE.

Additional file 1 of Integrative analyses of maternal plasma cell-free DNA nucleosome footprint differences reveal chromosomal aneuploidy fetuses gene expression profile

Min Zhang, Kun Li, Shoufang Qu, Zhiwei Guo, Yuanli Wang, Xu Yang, Junhua Zhou, Guojun Ouyang, Rongtao Weng, Fenxia Li, Yingsong Wu & Xuexi Yang
Additional file 1: Table S1. Differential promoter coverage genes and GO, KEGG enrichment analysis results of differential genes for all pregnant women with trisomy.

Additional file 2 of Integrative analyses of maternal plasma cell-free DNA nucleosome footprint differences reveal chromosomal aneuploidy fetuses gene expression profile

Min Zhang, Kun Li, Shoufang Qu, Zhiwei Guo, Yuanli Wang, Xu Yang, Junhua Zhou, Guojun Ouyang, Rongtao Weng, Fenxia Li, Yingsong Wu & Xuexi Yang
Additional file 2: Table S2. Differential promoter coverage genes and GO, KEGG enrichment analysis results of differential genes for pregnant women with trisomy 21.

Additional file 2 of A haplotype-resolved genome assembly of the Nile rat facilitates exploration of the genetic basis of diabetes

Huishi Toh, Chentao Yang, Giulio Formenti, Kalpana Raja, Lily Yan, Alan Tracey, William Chow, Kerstin Howe, Lucie A. Bergeron, Guojie Zhang, Bettina Haase, Jacquelyn Mountcastle, Olivier Fedrigo, John Fogg, Bogdan Kirilenko, Chetan Munegowda, Michael Hiller, Aashish Jain, Daisuke Kihara, Arang Rhie, Adam M. Phillippy, Scott A. Swanson, Peng Jiang, Dennis O. Clegg, Erich D. Jarvis … & Yury V. Bukhman
Additional file 2: Supplementary Table 1. TOGA status of 18430 ancestral placental mammal genes in muroid rodent genome assemblies. Supplementary Table 2. Positively selected genes and their mutation tolerance in humans according to gnomAD.

Periodic spatial patterning with a single morphogen

Sheng Wang, Jordi García-Ojalvo & Michael B Elowitz
Data and code repository for paper "Periodic spatial patterning with a single morphogen"

Additional file 2 of Integrative analyses of maternal plasma cell-free DNA nucleosome footprint differences reveal chromosomal aneuploidy fetuses gene expression profile

Min Zhang, Kun Li, Shoufang Qu, Zhiwei Guo, Yuanli Wang, Xu Yang, Junhua Zhou, Guojun Ouyang, Rongtao Weng, Fenxia Li, Yingsong Wu & Xuexi Yang
Additional file 2: Table S2. Differential promoter coverage genes and GO, KEGG enrichment analysis results of differential genes for pregnant women with trisomy 21.

Additional file 1 of The oldest unvaccinated Covid-19 survivors in South America

Mateus V. de Castro, Monize V. R. Silva, Michel S. Naslavsky, Marilia O. Scliar, Kelly Nunes, Maria Rita Passos-Bueno, Erick C. Castelli, Jhosiene Y. Magawa, Flávia L. Adami, Ana I. S. Moretti, Vivian L. de Oliveira, Silvia B. Boscardin, Edecio Cunha-Neto, Jorge Kalil, Emmanuelle Jouanguy, Paul Bastard, Jean-Laurent Casanova, Mauricio Quiñones-Vega, Patricia Sosa-Acosta, Jéssica S. de Guedes, Natália P. de Almeida, Fábio C. S. Nogueira, Gilberto B. Domont, Keity S. Santos & Mayana Zatz
Supplementary Material 1

Registration Year

  • 2022
    46

Resource Types

  • Dataset
    24
  • Text
    12
  • Collection
    10

Affiliations

  • Howard Hughes Medical Institute
    46
  • Chinese Academy of Sciences
    32
  • Lanzhou Veterinary Research Institute
    26
  • Heilongjiang Provincial Academy of Agricultural Sciences
    26
  • Sichuan University
    26
  • Capital Medical University
    26
  • Southern Medical University
    26
  • Chinese Academy of Medical Sciences & Peking Union Medical College
    26
  • Shandong University of Finance and Economics
    26
  • First Affiliated Hospital of Soochow University
    26