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Yale University

Yale University

Private research university in new haven, connecticut, united states

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Continental Who's Who
June 18, 2021
www.prnewswire.com:443
/PRNewswire/ -- William McBride, Ph.D., is being recognized by Continental Who's Who as a Top Educator for his remarkable contributions to the field of...
June 17, 2021
BioSpace
Lunaphore Appoints Dr. Carlo Bifulco to Scientific Advisory Board - read this article along with other careers information, tips and advice on BioSpace
City of New Haven
June 10, 2021
www.prnewswire.com:443
/PRNewswire/ -- Mayor Justin Elicker joined Governor Ned Lamont, Congresswoman Rosa DeLauro, Senator Richard Blumenthal, City officials, Alders, project...
Katherine Kornei
June 3, 2021
www.nytimes.com
Analysis of the fossil record shows a mysterious mass extinction that decimated the diversity of sharks in the world's oceans, and they've never fully recovered.
Bloomberg
May 26, 2021
@bsindia
No consensus has emerged on long-haul diagnosis, therapies
BioSpace
May 20, 2021
BioSpace
Cybrexa Therapeutics, an oncology-focused biotechnology company developing a new class of therapeutics through its alphalexTM Peptide Drug Conjugate (PDC) tumor targeting platform, today announced that it has appointed pharmaceutical and financial services veteran Stephen Basso as Chief Financial Officer.
GS1 US
May 18, 2021
www.prnewswire.com:443
/PRNewswire/ -- GS1 US has appointed the following executives to the GS1 US Board of Governors: Sam Heyworth, vice president, consumables, Amazon; and Brad...
BioSpace
May 17, 2021
BioSpace
AavantiBio, a gene therapy company focused on transforming the lives of patients with rare genetic diseases, announced the appointment of Jessie Hanrahan, Ph.D. as Chief Regulatory Officer.
Mike Dorning
May 15, 2021
phys.org
Eleven Madison Park, a top Manhattan restaurant, is going meatless. The Epicurious cooking site stopped posting new beef recipes. The Culinary Institute of America is promoting "plant-forward" menus. Dozens of colleges, including Harvard and Stanford, are shifting toward "climate-friendly" meals.
Carl Zimmer and Apoorva Mandavilli
May 14, 2021
www.nytimes.com
The country has managed to avoid a variant-fueled spike in coronavirus cases. Scientists say we were lucky.
Nadine Jolie Courtney
May 12, 2021
Business Insider
Here are 16 hotels for your first post-pandemic trip if you're vaccinated or comfortable traveling, based on expert advice on safety and amenities.
BioSpace
May 10, 2021
BioSpace
Yale University, in partnership with Boehringer Ingelheim, today announced the launch of a Biomedical Data Science Fellowship program designed to attract and support some of the brightest and most innovative minds in data science from around the world.
BioSpace
May 10, 2021
BioSpace
Yale University, in partnership with Boehringer Ingelheim, today announced the launch of a Biomedical Data Science Fellowship program designed to attract and support some of the brightest and most innovative minds in data science from around the world.
Andrew Ross Sorkin, Jason Karaian, Sarah Kessler, Michael J. de la Merced, Lauren Hirsch and Ephrat Livni
May 7, 2021
www.nytimes.com
Employers are debating the pros and cons of mandating workers to get vaccinated.
Geraldine Fabrikant
May 6, 2021
www.nytimes.com
At Yale, a colleague said, he showed "there was a way to compete hard and well in financial markets, but to have our lives be about something that mattered more."
Science X staff
May 6, 2021
phys.org
The bulging, equator-belted midsection of Earth currently teems with a greater diversity of life than anywhere else--a biodiversity that generally wanes when moving from the tropics to the mid-latitudes and the mid-latitudes to the poles.
Grome, M. W., Isaacs, F. J.
April 30, 2021
Science
Genomic DNA is composed of four standard nucleotides, each with a different nucleobase: adenine (A), thymine (T), cytosine (C), and guanine (G). These nucleobases form the genetic alphabet, ATCG, which is conserved across all domains of life. However, in 1977, the DNA virus cyanophage S-2L was discovered with all instances of A substituted with 2-aminoadenine (Z) throughout its genome ([ 1 ][1], [ 2 ][2]), forming the genetic alphabet ZTCG. Studies revealed interesting properties of Z-substituted DNA (dZ-DNA) ([ 3 ][3]-[ 6 ][4]), but little of Z synthesis was understood. On pages 516 and 512 of this issue, Sleiman et al. ([ 7 ][5]) and Zhou et al. ([ 8 ][6]), respectively, characterize viral Z biosynthesis. On page 520, Pezo et al. ([ 9 ][7]) identify a Z-specific DNA polymerase that is responsible for assembling dZ-DNA from nucleotides. All three studies identify additional "Z-genomes" in diverse bacteriophages (viruses that infect bacteria), which may have offered evolutionary advantages alongside standard ATCG DNA since life began. The nucleobases within standard DNA interact to form A:T and G:C base pairs. Two DNA single strands with complementary base sequences can recognize one another, form hydrogen bonds between matching base pairs, and zipper into a double helix. Notably, A:T forms two hydrogen bonds between bases, whereas G:C forms a stronger, more stable pair with three bonds. Within RNA, the nucleobase uracil (U) is substituted for T, forming A:U, but this does not alter the bond number. Within dZ-DNA, Z:T base pairs form with three hydrogen bonds, increasing bond number and thus stability compared with A:T ([ 2 ][2], [ 5 ][8]). This makes Z the first instance of a nonstandard nucleobase that naturally alters canonical base pairing. Although research on dZ-DNA has been scant, three studies in the late 1980s characterized synthetic and genomic dZ-DNA, confirming three major property enhancements over standard DNA: thermal stability: dZ-DNA is more stable at higher temperatures ([ 5 ][8]); sequence specificity: a single dZ-DNA strand is more accurate in binding complementary DNA sequences ([ 4 ][9]); and nuclease resistance: dZ-DNA is resistant to degradation by nucleases that recognize and cut specific DNA sequences containing A ([ 3 ][3], [ 4 ][9]). Since those studies, the mechanical properties of helical dZ-DNA were examined ([ 6 ][4]), revealing increased rigidity, thermal and force stability, and a propensity to adopt a nonstandard helical form. These features may offer evolutionary advantages in a world dominated by standard DNA. Bacteriophages (such as cyanophage S-2L) reproduce by injecting their genomic DNA into bacteria, hijacking host cellular machinery and manufacturing viral proteins to copy, build, and package new viral genomes inside the cell. To defend against infection, bacteria use a variety of mechanisms such as nucleases to destroy viral DNA. However, dZ-DNA could provide resistance to nucleases, evading host defenses. Additionally, the increased stability of dZ-DNA may permit viral persistence in extreme conditions to infect a broader range of hosts. Despite research into dZ-DNA, little was known about the origin of Z or how it incorporates into the virus genome. Sleiman et al. and Zhou et al. used protein characterizations and metagenomic database analyses to identify key proteins of interest, determine mechanisms of action, and track sequence similarities within proteins across divergent evolutionary lineages (viruses, bacteria, and archaea). Although the entire mechanism of Z-genome replication remains unknown, two major proteins were found to be responsible for Z synthesis: PurZ (2-amino adenylosuccinate synthetase), a virus-encoded protein that assembles a Z precursor dSMP (N6-succino-2-amino-2′-deoxyadenylate) from cellular dGMP (2′-deoxyguanosine-5′-monophosphate), and PurB (adenylosuccinate lyase), a bacterial protein that completes the synthesis of Z nucleotide dZMP (2-amino-2′-deoxyadenosine-5′-monophosphate) from dSMP (see the figure). Processing by host guanylate or nucleoside diphosphate kinases is needed to convert dZMP into dZTP (2-mino-2′-deoxyadenosine-5′-triphosphate) for DNA incorporation ([ 7 ][5], [ 8 ][6]). Searching genomic databases for similar PurZ sequences, a diverse set of 50 to 100 putative PurZ-containing genomes were identified, predominantly from bacteriophages, but also several archaea and bacteria. Putative bacteriophage hosts vary widely in environment, geography, and phylogeny (evolutionary relation), spanning actinobacteria, cyanobacteria, and proteobacteria ([ 7 ][5]-[ 9 ][7]). Further testing confirmed two additional Z-genome bacteriophages: Vibrio phage PhiVC8 ([ 7 ][5]) and Acinetobacter phage SH-Ab 15497 ([ 8 ][6]). When examined alongside cyanophage S-2L, other major Z-associated proteins were discovered, including a putative Z-specific DNA polymerase, DpoZ, which is considered responsible for Z-genome DNA assembly. Characterization of DpoZ by Pezo et al. confirmed not only its efficiency in assembling dZ-DNA but also its capacity to discriminate between A and Z during assembly: incorporating Z while excluding A. This ability contrasts the structurally analogous bacterial DNA polymerase-I Klenow fragment that has been shown to indiscriminately incorporate both nucleotides A and Z efficiently ([ 9 ][7]). The selective nature of DpoZ may ensure exclusion of A from Z-genomes. Whether Z is incorporated into bacterial genomes is an open question worthy of exploration. Diving deeper into phylogenetics, the viral PurZ was identified as an analog to archaeal PurA (adenylosuccinate synthetase), a protein responsible for A biosynthesis ([ 7 ][5]). This distant evolutionary connection raises questions of whether Z-specific proteins arose from bacterial host genes co-opted and adapted by viruses or are remnants of a preliminary biology, where Z-genomes existed in much greater frequency, perhaps even within cells. Phylogenetic analyses reveal that PurZ and DpoZ are often inherited together, suggesting that Z-genomes may have existed alongside canonical DNA since early evolution, before the divergence of actinobacteria, cyanobacteria, and proteobacteria ∼3.5 billion years ago ([ 9 ][7]). Furthermore, a 2011 chemical analysis of a 1969 Antarctic carbonaceous meteorite revealed a composition of standard and noncanonical nucleobases of likely abiogenic extraterrestrial origin within the rock, including some deemed exceedingly rare on Earth: Z base ([ 10 ][10]). Origin-of-life researchers frequently explore meteorite compositions to gain insight into prebiotic chemical conditions on Earth, raising a potential role for Z in early forms of life. ![Figure][11] Z nucleotides in viral genomesGRAPHIC: N. DESAI/ SCIENCE With capacity to synthesize dZ-DNA, researchers can harness the properties of Z directly for applications in DNA technologies. Setting the stage, a 1988 study ([ 4 ][9]) revealed that dZ-DNA probes recognize and strongly bind specific genomic sequences in certain conditions better than standard DNA. Decades later, structural DNA nanotechnology uses hundreds of synthetic DNA strands that self-assemble into three-dimensional nano-scale structures in a test tube but typically suffer from low yields and instability ([ 11 ][12]). Incorporating Z into DNA strands may offer improved thermal stability, resistance to endonucleases, structural rigidity, and greater assembly yields from enhanced sequence specificity, advancing manufacturing of personalized, injectable drug-delivery vehicles or nanoscale scaffolding for nanomachines. For synthetic biology, the enhanced properties of Z could improve the targeting capabilities and longevity of designer DNA or RNA strands used in antisense DNA and gene-targeting therapies, along with genome engineering and synthesis technologies for improved safety and efficacy ([ 12 ][13]). Researchers have long recognized the applications of expanding genetic alphabets in cells: incorporating nonstandard bases into DNA to enhance cell manufacturing capabilities, genetic isolation of strains, and biocontainment, among others ([ 13 ][14], [ 14 ][15]). Although researchers have incorporated noncanonical bases into DNA, they have yet to extend this technology to whole genomes. Z is a natural case that may provide insight into this endeavor. However, before knowledge of Z-genomes can be fully applied, many questions remain. For example, with the selective nature of DpoZ, a cell could theoretically build a Z-genome, but it is not known whether dZ-DNA is compatible with most DNA-interacting cellular machinery. Many proteins interact with genomic DNA to maintain a healthy, functioning cell. As Z-substitution alters DNA structure, many proteins may require reengineering to accommodate dZ-DNA. Another question is whether Z-genomes encode Z-specific RNA polymerases, making Z-substituted RNA. Cellular translation machineries recognize RNA nucleotides to assemble proteins. If Z replaces A, this changes the code, and re-engineering of cellular machinery might be required to recognize Z and assemble protein. However, if feasible, engineered cellular machinery that recognizes Z, alongside natural machinery recognizing A, could incorporate synthetic protein subunits into natural protein production to make unnatural designer proteins for therapeutics and biomaterials or to engineer dependencies on synthetic molecules for biocontainment ([ 15 ][16]). Renewed interest in Z should spark investigations into Z-genome biology and spur new innovations in materials and biotechnology. 1. [↵][17]1. M. D. Kirnos, 2. I. Y. Khudyakov, 3. N. I. Alexandrushkina, 4. B. F. Vanyushin , Nature 270, 369 (1977). [OpenUrl][18][CrossRef][19][PubMed][20][Web of Science][21] 2. [↵][22]1. I. Y. Khudyakov, 2. M. D. Kirnos, 3. N. I. Alexandrushkina, 4. B. F. Vanyushin , Virology 88, 8 (1978). [OpenUrl][23][CrossRef][24][PubMed][25] 3. [↵][26]1. M. Szekeres, 2. A. V. Matveyev , FEBS Lett. 222, 89 (1987). [OpenUrl][27][CrossRef][28][PubMed][29][Web of Science][30] 4. [↵][31]1. A. Chollet, 2. E. Kawashima , Nucleic Acids Res. 16, 305 (1988). [OpenUrl][32][CrossRef][33][PubMed][34][Web of Science][35] 5. [↵][36]1. C. Cheong, 2. I. Tinoco Jr., 3. A. Chollet , Nucleic Acids Res. 16, 5115 (1988). [OpenUrl][37][CrossRef][38][PubMed][39][Web of Science][40] 6. [↵][41]1. M. Cristofalo et al ., Biophys. J. 116, 760 (2019). [OpenUrl][42][CrossRef][43][PubMed][44] 7. [↵][45]1. D. Sleiman et al ., Science 372, 516 (2021). [OpenUrl][46][Abstract/FREE Full Text][47] 8. [↵][48]1. Y. Zhou et al ., Science 372, 512 (2021). [OpenUrl][49][Abstract/FREE Full Text][50] 9. [↵][51]1. V. Pezo et al ., Science 372, 520 (2021). [OpenUrl][52][Abstract/FREE Full Text][53] 10. [↵][54]1. M. P. Callahan et al ., Proc. Natl. Acad. Sci. U.S.A. 108, 13995 (2011). [OpenUrl][55][Abstract/FREE Full Text][56] 11. [↵][57]1. N. Seeman, 2. H. F. Sleiman , Nat. Rev. Mater. 3, 17068 (2018). [OpenUrl][58] 12. [↵][59]1. W. Zhang, 2. L. A. Mitchell, 3. J. S. Bader, 4. J. D. Boeke , Annu. Rev. Biochem. 89, 77 (2020). [OpenUrl][60] 13. [↵][61]1. D. Malyshev et al ., Nature Lett 509, 385 (2014). [OpenUrl][62] 14. [↵][63]1. Z. Yang et al ., Nucleic Acids Res. 35, 4238 (2007). [OpenUrl][64][CrossRef][65][PubMed][66][Web of Science][67] 15. [↵][68]1. A. J. Rovner et al ., Nature 518, 89 (2015). [OpenUrl][69][CrossRef][70][PubMed][71] Acknowledgments: We are supported by the NIH (R01GM140481, R01GM125951, R01GM117230, U54CA209992), NSF (EF-1935120, IOS-1923321), and US Department of Energy (BER). 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{openurl}?query=rft.jtitle%253DScience%26rft.stitle%253DScience%26rft.aulast%253DSleiman%26rft.auinit1%253DD.%26rft.volume%253D372%26rft.issue%253D6541%26rft.spage%253D516%26rft.epage%253D520%26rft.atitle%253DA%2Bthird%2Bpurine%2Bbiosynthetic%2Bpathway%2Bencoded%2Bby%2Baminoadenine-based%2Bviral%2BDNA%2Bgenomes%26rft_id%253Dinfo%253Adoi%252F10.1126%252Fscience.abe6494%26rft.genre%253Darticle%26rft_val_fmt%253Dinfo%253Aofi%252Ffmt%253Akev%253Amtx%253Ajournal%26ctx_ver%253DZ39.88-2004%26url_ver%253DZ39.88-2004%26url_ctx_fmt%253Dinfo%253Aofi%252Ffmt%253Akev%253Amtx%253Actx [47]: /lookup/ijlink/YTozOntzOjQ6InBhdGgiO3M6MTQ6Ii9sb29rdXAvaWpsaW5rIjtzOjU6InF1ZXJ5IjthOjQ6e3M6ODoibGlua1R5cGUiO3M6NDoiQUJTVCI7czoxMToiam91cm5hbENvZGUiO3M6Mzoic2NpIjtzOjU6InJlc2lkIjtzOjEyOiIzNzIvNjU0MS81MTYiO3M6NDoiYXRvbSI7czoyMjoiL3NjaS8zNzIvNjU0MS80NjAuYXRvbSI7fXM6ODoiZnJhZ21lbnQiO3M6MDoiIjt9 [48]: #xref-ref-8-1 "View reference 8 in text" [49]: 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Gwyn Topham Transport correspondent
April 29, 2021
the Guardian
Airline cites research that suggests overseas holidays would have little impact on hospital admissions
BioSpace
April 29, 2021
BioSpace
Repertoire Immune Medicines, a clinical-stage biotech company decoding the immune synapse to create novel immune therapies for cancer, immune disorders, infectious disease, and other serious diseases, today announced a new collaboration with Yale University focused on understanding the basis of cellular immunity of multiple sclerosis (MS) by determining what types of antigens are activating T cells in patients.
April 27, 2021
BioSpace
Susan Hockfield, Ph.D., MIT President Emerita, Joins Repertoire Immune Medicines Board of Directors - read this article along with other careers information, tips and advice on BioSpace
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