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 ===== Cold Spring Harbor Laboratory =====
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-June 16, 1904. The [[:Carnegie Institution]] of Washington hosts a gala dedication ceremony on the grounds of the Bio Lab to mark the formal opening of the Station for Experimental Evolution (SEE) at Cold Spring Harbor. The plans for the station had been **suggested by eugenicist** [[:Charles Davenport]], in 1903 (CSHL, 2015). It originally opened for the purposes of studying heredity and evolution, through experiments with plants and animals (CSHL, 2015). The station became a main research centre for American eugenics.
+June 16, 1904. The [[:Carnegie Institution]] of Washington hosts a gala dedication ceremony on the grounds of the Bio Lab to mark the formal opening of the Station for Experimental Evolution (SEE) at Cold Spring Harbor. The plans for the station had been **suggested by eugenicist** [[:Charles Davenport]], in 1903 (CSHL, 2015). It originally opened for the purposes of studying heredity and evolution, through experiments with plants and animals (CSHL, 2015). The station became a main research centre for American [[:eugenics]].
 The Station was located on 9 acres of land, in Cold Spring Harbor. It was leased for 50 years upon the Station's opening, from the Wawepex Society (CSHL, 2014). Davenport served as director of the station, as well as Cold Spring Harbor Laboratory, and in 1910, the [[:Eugenics Record Office]], which would eventually become part of the Department of Genetics (CSHL, 2015).
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 The South Fork of LI is "The Hamptons" with Montauk Point the farthest end. There Gurney’s Inn became and remains an elite escape destination flanked by Hither Hills State Park and beach that protects a strip of land from the Atlantic Ocean to the Bay.
-Between the forks is Shelter Island notorious for bootleggers, gamblers and gangsters. Beyond the tip of the North Fork Orient Point is [[:Plum Island Animal Disease Center]] and BSL4 lab dealing with the most dangerous virus and pathogens. "Since 1954, the DHS S&T Office of National Laboratories (ONL) Plum Island Animal Disease Center (PIADC) has served as the nation's premier defense against accidental or intentional introduction of FADs Foot and Mouth Disease. ((https://web.archive.org/web/20141117102917/https://www.dhs.gov/science-and-technology/plum-island-animal-disease-center))
+Between the forks is Shelter Island notorious for bootleggers, gamblers and gangsters. Beyond the tip of the North Fork's Orient Point is [[:Plum Island]] Animal Disease Center and BSL4 lab dealing with the most dangerous virus and pathogens. "Since 1954, the DHS S&T Office of National Laboratories (ONL) Plum Island Animal Disease Center (PIADC) has served as the nation's premier defense against accidental or intentional introduction of FADs Foot and Mouth Disease. ((https://web.archive.org/web/20141117102917/https://www.dhs.gov/science-and-technology/plum-island-animal-disease-center))
-There are two ferries that leave from Orient Point to New Haven for the public and separate ferry for cleared personnel to Plum Island. If we sail a little past Plum Island there is Fischer's Island that ranks high in the old money exclusive getaway spots and a nice sail from there to Newport.
+There are two ferries that leave from Orient Point, one to New London for the public and separate ferry for cleared personnel to Plum Island. If we sail a little past Plum Island there is Fischer's Island that ranks high in the old money exclusive getaway spots and a nice sail from there to Newport.
 Somewhere between Yale, Plum Island and Cold Spring Harbor Lyme disease appeared spread by ticks & deer who swim quite far.
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 By the late 1960s, the confluence of [[:molecular genetics]], [[:virology]], and animal cell culture was revolutionizing the study of biochemistry of higher cells. Sophisticated methods had been developed to grow mammalian and human cell lines in culture dishes in the manner of bacteria. It had also been demonstrated that certain animal viruses, known as tumor viruses, can "transform" cultured cells into cancerous equivalents. It was thus possible to mimic cancer in a petri dish and to perform controlled experiments on the origin and progression of malignancy.
-A Cold Spring Harbor course taught each summer since 1958 was instrumental in introducing researchers to the new techniques for culturing animal cells and their viruses. The potential power of the tumor virus model system prompted a migration of former phage biologists into the field of basic cancer research. Bacteriophages had provided a means to probe the genetics of bacterial cells; now the tumor viruses made possible a similar approach to mammalian cells.  ((https://web.archive.org/web/20030819170328fw_/http://www.cshl.edu/History/100years-war.html}}
+A Cold Spring Harbor course taught each summer since 1958 was instrumental in introducing researchers to the new techniques for culturing animal cells and their viruses. The potential power of the tumor virus model system prompted a migration of former phage biologists into the field of basic cancer research. Bacteriophages had provided a means to probe the genetics of bacterial cells; now the tumor viruses made possible a similar approach to mammalian cells.  ((https://web.archive.org/web/20030819170328fw_/http://www.cshl.edu/History/100years-war.html))
+==== Experimental Evolution and Genetics Research ====
+Although the staff of the Carnegie Institution’s Station for Experimental Evolution was small at first, important early work was performed both in and around the Main Building. Immediately after receiving his Ph.D. from the [[:University of Chicago]] in 1906 [[:George Shull]] (1874–1954) came to Cold Spring Harbor and began planting maize (Indian corn) in an experimental garden on the east side of the Main Building.
+By 1908 he was reporting in the Carnegie Institution of Washington Yearbook experiments that became world-famous. Shull showed that when two different but carefully inbred strains of [[:corn]] were crossed, the yield was 20% higher than if each strain were allowed to self-pollinate. This phenomenon of “hybrid vigor” that he demonstrated experimentally was later employed in commercial seed production to create high-yielding strains that today make corn the most important agricultural crop in the United States.
+Also in 1908, in the basement of the Main Building, Charles Banta conducted cave experiments aimed at inducing color mutations in tadpoles of the tiger salamander.
+In 1914, the Animal House (now McClintock Laboratory) was completed and the animal breeding experiments at Cold Spring Harbor were moved from the Main Building to this new facility.
+In 1923, [[:Cornell]]-trained biogeneticist [[:Milislav Demerec]] (1895-1966) was appointed to the Carnegie Department of Genetics by assistant director [[:Albert Blakeslee]] (1874–1954). Although trained as a maize geneticist, Demerec soon turned his efforts at Cold Spring Harbor to the fruit fly Drosophila.
+His work was done on the second floor of the Main Building. In the late 1930s Demerec and Calvin Bridges, who was at the [[:California Institute of Technology]], collaborated during the summers on drawing large-scale maps of the four Drosophila chromosomes, which was considered quite a feat in those days. By 1940 the first edition of Demerec’s Drosophila Guide appeared. This classic in its field was destined to go through eight editions, the last appearing in 1969.
+[[:Barbara McClintock]] was a member of the Carnegie staff and the cornfields where she found **evidence of movable genetic switches—“jumping genes”—that can turn genes on and off** were next to the Main Building.
+As early as 1946 it had become apparent that a major new building would be required if the genetics program at Cold Spring Harbor were to have a future in a scientific world in which molecules as well as chromosomes were investigated. The 1905 Main Building and the 1914 Animal House were inadequate for the kinds of research they now wished to do.
+In 1953 the Demerec Laboratory was completed and the Main Building officially became the Carnegie Library. In addition to housing laboratories, the Main Building had long served as the main repository of reference works and journals for both the Carnegie Department of Genetics and the Bio Lab, and this was now its sole function. ((https://web.archive.org/web/20210226064210/https://www.cshl.edu/education/center-for-humanities/carnegie-building/))
+==== Viral Eugenics ====
+{{ ::cold_spring_harbor_study_deadly_omicron_w_bu.png?600|}}
+Role of spike in the pathogenic and antigenic behavior of SARS-CoV-2 BA.1 Omicron
+Da-Yuan Chen, Devin Kenney, Chue-Vin Chin, Alexander H Tavares, Nazimuddin Khan, Hasahn L Conway, GuanQun Liu, Manish C Choudhary, Hans P Gertje, Aoife K OConnell, Darrell N Kotton, Alexandra Herrmann, View ORCID ProfileArmin Ensser, John H Connor, Markus Bosmann, Jonathan Z Li, Michaela U Gack, Susan C Baker, Robert N Kirchdoerfer, Yachana Kataria, Nicholas A Crossland, Florian Douam, Mohsan Saeed
+doi: https://doi.org/10.1101/2022.10.13.512134
+This article is a preprint and has not been certified by peer review
+Abstract
+The recently identified, globally predominant SARS-CoV-2 Omicron variant (BA.1) is highly transmissible, even in fully vaccinated individuals, and causes attenuated disease compared with other major viral variants recognized to date. The Omicron spike (S) protein, with an unusually large number of mutations, is considered the major driver of these phenotypes. We generated chimeric recombinant SARS-CoV-2 encoding the S gene of Omicron in the backbone of an ancestral SARS-CoV-2 isolate and compared this virus with the naturally circulating Omicron variant. The Omicron S-bearing virus robustly escapes vaccine-induced humoral immunity, mainly due to mutations in the receptor binding motif (RBM), yet unlike naturally occurring Omicron, efficiently replicates in cell lines and primary-like distal lung cells. In K18-hACE2 mice, while Omicron causes mild, non-fatal infection, the Omicron S-carrying virus inflicts severe disease with a mortality rate of 80%. This indicates that while the vaccine escape of Omicron is defined by mutations in S, major determinants of viral pathogenicity reside outside of S.
+Competing Interest Statement
+The authors have declared no competing interest. ((https://web.archive.org/web/20221015155327/https://www.biorxiv.org/content/10.1101/2022.10.13.512134v1))
+==== Virus Promoters, DNA Clones and GMO Rice ====
+Discovery of a novel merbecovirus DNA clone contaminating agricultural rice sequencing datasets from Wuhan, China
+Abstract {{ ::gmo_rice_virus_dna_cold_spring_harbor_preprint_feb_2023.png?400|}}
+HKU4-related coronaviruses are a group of betacoronaviruses belonging to the same merbecovirus subgenus as Middle Eastern Respiratory Syndrome coronavirus (MERS-CoV), which causes severe respiratory illness in humans with a mortality rate of over 30%.
+The high **genetic similarity** between HKU4-related coronaviruses and MERS-CoV makes them an attractive subject of research for modeling potential zoonotic spillover scenarios. In this study, we identify a novel [[:coronavirus]] contaminating agricultural rice RNA sequencing datasets from [[:Wuhan]], China.
+The datasets were generated by the [[:Huazhong Agricultural University]] in early 2020. We were able to assemble the complete viral genome sequence, which revealed that it is a novel HKU4-related merbecovirus.
+The **assembled genome is 98.38% identical to the closest known full genome** sequence, Tylonycteris pachypus bat isolate BtTp-GX2012. Using in silico modeling, we identified that the novel HKU4-related coronavirus spike protein likely binds to human dipeptidyl peptidase 4 (DPP4), the receptor used by MERS-CoV. We further identified that the novel HKU4-related coronavirus genome has been inserted into a bacterial artificial chromosome in a format consistent with previously published coronavirus [[:infectious clones]].
+Additionally, we have found a near complete read coverage of the spike gene of the MERS-CoV reference strain HCoV-EMC/2012, and identify the **likely presence of a HKU4-related-MERS chimera in the datasets**.
+Our findings contribute to the knowledge of HKU4-related [[:coronaviruses]] and document the use of a previously unpublished HKU4 reverse genetics system in apparent MERS-CoV related [[:gain-of-function]] research. Our study also emphasizes the importance of improved [[:biosafety]] protocols in sequencing centers and coronavirus research facilities.
+Competing Interest Statement
+The authors have declared no competing interest.
+Paper in collection COVID-19 SARS-CoV-2 preprints from medRxiv and bioRxiv ((https://www.biorxiv.org/content/10.1101/2023.02.12.528210v1))