Tag: human

Posted on

Earth Week keynote speaker discusses human dimensions of landscape architecture | Campus

Landscape architect David Rubin mentioned human-centered, sustainable and resilient urban structure at Purdue’s 2022 Earth Week lecture collection in the Course of 1950 Wednesday night time.

Rubin is the founder of DAVID RUBIN Land Collective, a landscape architecture, city structure and planning studio. In his presentation “Integrated Infrastructure: A Methods Tactic To Sustainability, Empathy, and Resiliency,” he explained how the Land Collective facilities the human working experience into its operate.

Rubin mentioned landscape is for everybody, and it can be utilised to positively notify communities.

“Landscape is the most equitable setting,” he reported. “Everybody stands on it, so you can positively carry up everyone by means of the manipulation of our surroundings.”

Emily Twomey, a sophomore in the Faculty of Engineering, stated Rubin’s presentation changed the way she imagined about landscape.

“I believe it genuinely opened my horizons, looking at my limited point of view (as) an engineering major,” she explained.

Rubin talked over the Grand Junction Plaza challenge in Westfield, Indiana, and a few initiatives in Washington, D.C., which ended up Canal Park, Potomac Park Flood Levee and Franklin Park.

He explained each individual of these tasks in fantastic element to display how the Land Collective viewed as the holistic requires of people and the atmosphere, and these examples demonstrate how Purdue’s landscape could enjoy a job in establishing a much more sustainable campus tradition, also.

“It’s so important to be working here at Purdue to inform the high-quality and character of the campus, since it informs all people: pupils, college, alumni, administration (and) guests,” Rubin reported. “Everybody walks by means of the campus group.”

Olivia Miller, a sophomore in the College or university of Engineering, mentioned she was intrigued in listening to Rubin’s presentation due to the fact she is a member of PurdueTHINK, a student consulting firm which is at the moment hunting into more out of doors, sustainable hangout spots on campus.

When doing work on a undertaking, it is really crucial to the Land Collective to make every person sense comfortable in their areas, Rubin claimed.

“In all of our drawings, we are generally representing every single member of the constituency, which includes the unhomed,” he mentioned.

The Land Collective engages with neighborhood communities by actively listening to men and women enduring homelessness and other marginalized groups describing their activities in these conversations.

“Empathy is the root of our mission,” he explained.

In addition to empathy, accessibility was a different essential expression in Rubin’s Earth 7 days presentation.

“Accessibility is about conquering physical challenges, but, additional importantly, accessibility is about the invitation to take part,” Rubin reported. “Designing available landscapes in the context of sustainable gestures is the only way to tactic a holistic reaction.”

Editor’s Be aware: This reporting is supported by Carbon Neutral Indiana, a nonprofit serving to “individuals and firms cleanse up their carbon footprints.”

Posted on

The mutational landscape of human somatic and germline cells

  • 1.

    Martincorena, I. & Campbell, P. J. Somatic mutation in cancer and normal cells. Science 349, 1483–1489 (2015).

    ADS 
    CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar     

  • 2.

    Rouhani, F. J. et al. Mutational history of a human cell lineage from somatic to induced pluripotent stem cells. PLoS Genet. 12, e1005932 (2016).

    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar     

  • 3.

    Coorens, T. H. H. et al. Extensive phylogenies of human development reveal variable embryonic patterns. Preprint at bioRxiv https://doi.org/10.1101/2020.11.25.397828 (2020).

  • 4.

    Blokzijl, F. et al. Tissue-specific mutation accumulation in human adult stem cells during life. Nature 538, 260–264 (2016).

    ADS 
    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar     

  • 5.

    Bae, T. et al. Different mutational rates and mechanisms in human cells at pregastrulation and neurogenesis. Science 359, 550–555 (2018).

    ADS 
    CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar     

  • 6.

    Osorio, F. G. et al. Somatic mutations reveal lineage relationships and age-related mutagenesis in human hematopoiesis. Cell Rep. 25, 2308–2316.e4 (2018).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar     

  • 7.

    Martincorena, I. et al. Somatic mutant clones colonize the human esophagus with age. Science 362, 911–917 (2018).

    ADS 
    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar     

  • 8.

    Lee-Six, H. et al. The landscape of somatic mutation in normal colorectal epithelial cells. Nature 574, 532–537 (2019).

    ADS 
    CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar     

  • 9.

    Moore, L. et al. The mutational landscape of normal human endometrial epithelium. Nature 580, 640–646 (2020).

    ADS 
    CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar     

  • 10.

    Zhu, M. et al. Somatic mutations increase hepatic clonal fitness and regeneration in chronic liver disease. Cell 177, 608–621.e12 (2019).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar     

  • 11.

    Schmitt, M. W. et al. Detection of ultra-rare mutations by next-generation sequencing. Proc. Natl Acad. Sci. USA 109, 14508–14513 (2012).

    ADS 
    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar     

  • 12.

    Abascal, F. et al. Somatic mutation landscapes at single-molecule resolution. Nature 593, 405–410 (2021).

    ADS 
    CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar     

  • 13.

    Rahbari, R. et al. Timing, rates and spectra of human germline mutation. Nat. Genet. 48, 126–133 (2016).

    CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar     

  • 14.

    Goldmann, J. M. et al. Parent-of-origin-specific signatures of de novo mutations. Nat. Genet. 48, 935–939 (2016).

    CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar     

  • 15.

    Kong, A. et al. Rate of de novo mutations and the importance of father’s age to disease risk. Nature 488, 471–475 (2012).

    ADS 
    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar     

  • 16.

    Lynch, M. Rate, molecular spectrum, and consequences of human mutation. Proc. Natl Acad. Sci. USA 107, 961–968 (2010).

    ADS 
    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar     

  • 17.

    Milholland, B. et al. Differences between germline and somatic mutation rates in humans and mice. Nat. Commun. 8, 15183 (2017).

    ADS 
    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar     

  • 18.

    Visvader, J. E. & Clevers, H. Tissue-specific designs of stem cell hierarchies. Nat. Cell Biol. 18, 349–355 (2016).

    CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar     

  • 19.

    Jónsson, H. et al. Parental influence on human germline de novo mutations in 1,548 trios from Iceland. Nature 549, 519–522 (2017).

    ADS 
    Article 
    CAS 

    Google Scholar     

  • 20.

    Ozturk, S. Telomerase activity and telomere length in male germ cells. Biol. Reprod. 92, 53 (2015).

    PubMed 
    Article 
    CAS 
    PubMed Central 

    Google Scholar     

  • 21.

    Demanelis, K. et al. Determinants of telomere length across human tissues. Science 369, eaaz6876 (2020).

    PubMed 
    PubMed Central 
    Article 

    Google Scholar     

  • 22.

    Fryxell, K. J. & Zuckerkandl, E. Cytosine deamination plays a primary role in the evolution of mammalian isochores. Mol. Biol. Evol. 17, 1371–1383 (2000).

    CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar     

  • 23.

    Alexandrov, L. B. et al. Clock-like mutational processes in human somatic cells. Nat. Genet. 47, 1402–1407 (2015).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar     

  • 24.

    Alexandrov, L. B. et al. The repertoire of mutational signatures in human cancer. Nature 578, 94–101 (2020).

    ADS 
    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar     

  • 25.

    Boot, A. et al. In-depth characterization of the cisplatin mutational signature in human cell lines and in esophageal and liver tumors. Genome Res. 28, 654–665 (2018).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar     

  • 26.

    Forbes, S. A. et al. COSMIC: somatic cancer genetics at high-resolution. Nucleic Acids Res. 45, D777–D783 (2017).

    CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar     

  • 27.

    Pleguezuelos-Manzano, C. et al. Mutational signature in colorectal cancer caused by genotoxic pks+ E. coli. Nature 580, 269–273 (2020).

    ADS 
    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar     

  • 28.

    Li, X. C. et al. A mutational signature associated with alcohol consumption and prognostically significantly mutated driver genes in esophageal squamous cell carcinoma. Ann. Oncol. 29, 938–944 (2018).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar     

  • 29.

    Nik-Zainal, S. et al. Mutational processes molding the genomes of 21 breast cancers. Cell 149, 979–993 (2012).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar     

  • 30.

    Alexandrov, L. B. et al. Mutational signatures associated with tobacco smoking in human cancer. Science 354, 618–622 (2016).

    ADS 
    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar     

  • 31.

    Di Persio, S. et al. Spermatogonial kinetics in humans. Development 144, 3430–3439 (2017).

    PubMed 
    Article 
    CAS 
    PubMed Central 

    Google Scholar     

  • 32.

    Scally, A. Mutation rates and the evolution of germline structure. Phil. Trans. R. Soc. B 371, 20150137 (2016).

    PubMed 
    PubMed Central 
    Article 

    Google Scholar     

  • 33.

    Frigola, J. et al. Reduced mutation rate in exons due to differential mismatch repair. Nat. Genet. 49, 1684–1692 (2017).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar     

  • 34.

    Rodriguez-Galindo, M., Casillas, S., Weghorn, D. & Barbadilla, A. Germline de novo mutation rates on exons versus introns in humans. Nat. Commun. 11, 3304 (2020).

    ADS 
    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar     

  • 35.

    GTEx Consortium. The GTEx Consortium atlas of genetic regulatory effects across human tissues. Science 369, 1318–1330 (2020).

    Article 
    CAS 

    Google Scholar     

  • 36.

    Karczewski, K. J. et al. The mutational constraint spectrum quantified from variation in 141,456 humans. Nature 581, 434–443 (2020).

    ADS 
    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar     

  • 37.

    Xia, B. et al. Widespread transcriptional scanning in the testis modulates gene evolution rates. Cell 180, 248–262.e21 (2020).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar     

  • 38.

    Koren, A. et al. Differential relationship of DNA replication timing to different forms of human mutation and variation. Am. J. Hum. Genet. 91, 1033–1040 (2012).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar     

  • 39.

    Francioli, L. C. et al. Genome-wide patterns and properties of de novo mutations in humans. Nat. Genet. 47, 822–826 (2015).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar     

  • 40.

    Chen, C., Qi, H., Shen, Y., Pickrell, J. & Przeworski, M. Contrasting determinants of mutation rates in germline and soma. Genetics 207, 255–267 (2017).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar     

  • 41.

    .Walsh, C. et al. Somatic mutations in single human cardiomyocytes demonstrate accelerated age-related DNA damage and cell fusion. Preprint at Research Square https://doi.org/10.21203/rs.3.rs-84503/v1 (2020).

  • 42.

    Kirkwood, T. B. Evolution of ageing. Nature 270, 301–304 (1977).

    ADS 
    CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar     

  • 43.

    Sakkas, D., Ramalingam, M., Garrido, N. & Barratt, C. L. R. Sperm selection in natural conception: what can we learn from Mother Nature to improve assisted reproduction outcomes? Hum. Reprod. Update 21, 711–726 (2015).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar     

  • 44.

    Brunner, S. F. et al. Somatic mutations and clonal dynamics in healthy and cirrhotic human liver. Nature 574, 538–542 (2019).

    ADS 
    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar     

  • 45.

    Lawson, A. R. J. et al. Extensive heterogeneity in somatic mutation and selection in the human bladder. Science 370, 75–82 (2020).

    ADS 
    CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar     

  • 46.

    Olafsson, S. et al. Somatic evolution in non-neoplastic IBD-affected colon. Cell 182, 672–684.e11 (2020).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar     

  • 47.

    Ellis, P. et al. Reliable detection of somatic mutations in solid tissues by laser-capture microdissection and low-input DNA sequencing. Nat. Protoc. 16, 841–871 (2021).

    CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar     

  • 48.

    Li, H. Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. Preprint at arXiv https://arxiv.org/abs/1303.3997v2 (2013).

  • 49.

    Tischler, G. & Leonard, S. biobambam: tools for read pair collation based algorithms on BAM files. Source Code Biol. Med. 9, 13 (2014).

    PubMed Central 
    Article 

    Google Scholar     

  • 50.

    Jones, D. et al. cgpCaVEManWrapper: simple execution of CaVEMan in order to detect somatic single nucleotide variants in NGS data. Curr. Protoc. Bioinformatics 56, 15.10.1–15.10.18 (2016).

    Article 

    Google Scholar     

  • 51.

    Coorens, T. H. H. et al. Lineage-independent tumors in bilateral neuroblastoma. N. Engl. J. Med. 383, 1860–1865 (2020).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar     

  • 52.

    Yoshida, K. et al. Tobacco smoking and somatic mutations in human bronchial epithelium. Nature 578, 266–272 (2020).

    ADS 
    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar     

  • 53.

    Raine, K. M. et al. cgpPindel: identifying somatically acquired insertion and deletion events from paired end sequencing. Curr. Protoc. Bioinformatics 52, 15.7.1–15.7.12 (2015).

    Article 

    Google Scholar     

  • 54.

    Slater, G. S. C. & Birney, E. Automated generation of heuristics for biological sequence comparison. BMC Bioinformatics 6, 31 (2005).

    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar     

  • 55.

    Suzuki, M. et al. Late-replicating heterochromatin is characterized by decreased cytosine methylation in the human genome. Genome Res. 21, 1833–1840 (2011).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar     

  • 56.

    Coorens, T. H. H. et al. Embryonal precursors of Wilms tumor. Science 366, 1247–1251 (2019).

    ADS 
    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar     

  • 57.

    Blokzijl, F., Janssen, R., van Boxtel, R. & Cuppen, E. MutationalPatterns: comprehensive genome-wide analysis of mutational processes. Genome Med. 10, 33 (2018).

    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar     

  • 58.

    Stamatoyannopoulos, J. A. et al. Human mutation rate associated with DNA replication timing. Nat. Genet. 41, 393–395 (2009).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar     

  • 59.

    Potten, C. S., Kellett, M., Rew, D. A. & Roberts, S. A. Proliferation in human gastrointestinal epithelium using bromodeoxyuridine in vivo: data for different sites, proximity to a tumour, and polyposis coli. Gut 33, 524–529 (1992).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar     

  • 60.

    Heller, C. G. & Clermont, Y. Spermatogenesis in man: an estimate of its duration. Science 140, 184–186 (1963).

    ADS 
    CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar     

  • 61.

    Farmery, J. H. R., Smith, M. L., NIHR BioResource – Rare Diseases & Lynch, A. G. Telomerecat: a ploidy-agnostic method for estimating telomere length from whole genome sequencing data. Sci. Rep. 8, 1300 (2018).

    ADS 
    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar     

  • 62.

    Martincorena, I. et al. Universal patterns of selection in cancer and somatic tissues. Cell 171, 1029–1041.e21 (2017).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar