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Whole-genome shotgun sequencing of mitochondria from ancient hair shafts (2007)

M. T. Gilbert ; L. P. Tomsho ; S. Rendulic ; [et al.]

American Association for the Advancement of Science (AAAS)

In: Science. 317(5846): 1927-30. doi: 10.1126/science.1146971.

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Publication Date: 2007-09-29

Description: Although the application of sequencing-by-synthesis techniques to DNA extracted from bones has revolutionized the study of ancient DNA, it has been plagued by large fractions of contaminating environmental DNA. The genetic analyses of hair shafts could be a solution: We present 10 previously unexamined Siberian mammoth (Mammuthus primigenius) mitochondrial genomes, sequenced with up to 48-fold coverage. The observed levels of damage-derived sequencing errors were lower than those observed in previously published frozen bone samples, even though one of the specimens was 〉50,000 14C years old and another had been stored for 200 years at room temperature. The method therefore sets the stage for molecular-genetic analysis of museum collections.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Gilbert, M Thomas P -- Tomsho, Lynn P -- Rendulic, Snjezana -- Packard, Michael -- Drautz, Daniela I -- Sher, Andrei -- Tikhonov, Alexei -- Dalen, Love -- Kuznetsova, Tatyana -- Kosintsev, Pavel -- Campos, Paula F -- Higham, Thomas -- Collins, Matthew J -- Wilson, Andrew S -- Shidlovskiy, Fyodor -- Buigues, Bernard -- Ericson, Per G P -- Germonpre, Mietje -- Gotherstrom, Anders -- Iacumin, Paola -- Nikolaev, Vladimir -- Nowak-Kemp, Malgosia -- Willerslev, Eske -- Knight, James R -- Irzyk, Gerard P -- Perbost, Clotilde S -- Fredrikson, Karin M -- Harkins, Timothy T -- Sheridan, Sharon -- Miller, Webb -- Schuster, Stephan C -- HG002238/HG/NHGRI NIH HHS/ -- New York, N.Y. -- Science. 2007 Sep 28;317(5846):1927-30.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Centre for Ancient Genetics, University of Copenhagen, Universitetsparken 15, DK-2100 Copenhagen, Denmark.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17901335" target="_blank"〉PubMed〈/a〉

Keywords: Animals ; Bone and Bones/chemistry ; DNA Damage ; DNA, Mitochondrial/chemistry/genetics/*history ; Elephants/*genetics ; Genes, Mitochondrial ; *Genome ; *Hair/chemistry/ultrastructure ; History, Ancient ; Mitochondria/*genetics ; Molecular Sequence Data ; Preservation, Biological ; *Sequence Analysis, DNA ; Siberia ; Temperature

Print ISSN: 0036-8075

Electronic ISSN: 1095-9203

Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics

Published by American Association for the Advancement of Science (AAAS)

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RING1A and BMI1 bookmark active genes via ubiquitination of chromatin-associated proteins (2016)

Arora, M., Packard, C. Z., Banerjee, T., Parvin, J. D.

Oxford University Press

In: Nucleic Acids Research

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Publication Date: 2016-03-19

Description: During mitosis the chromatin undergoes dramatic architectural changes with the halting of the transcriptional processes and evacuation of nearly all transcription associated machinery from genes and promoters. Molecular bookmarking of genes during mitosis is a mechanism of faithfully transmitting cell-specific transcription patterns through cell division. We previously discovered chromatin ubiquitination at active promoters as a potential mitotic bookmark. In this study, we identify the enzymes involved in the deposition of ubiquitin before mitosis. We find that the polycomb complex proteins BMI1 and RING1A regulate the ubiquitination of chromatin associated proteins bound to promoters, and this modification is necessary for the expression of marked genes once the cells enter G1. Depletion of RING1A, and thus inactivation of mitotic bookmarking by ubiquitination, is deleterious to progression through G1, cell survival and proliferation. Though the polycomb complex proteins are thought to primarily regulate gene expression by transcriptional repression, in this study, we discover that these two polycomb proteins regulate the transcription of active genes during the mitosis to G1 transition.

Print ISSN: 0305-1048

Electronic ISSN: 1362-4962

Topics: Biology

Published by Oxford University Press

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A pandemic reconstrued (1993)

R. M. Packard

American Association for the Advancement of Science (AAAS)

In: Science. 259(5094): 539. doi: 10.1126/science.259.5094.539.

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Publication Date: 1993-01-22

Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Packard, R M -- New York, N.Y. -- Science. 1993 Jan 22;259(5094):539.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17734177" target="_blank"〉PubMed〈/a〉

Print ISSN: 0036-8075

Electronic ISSN: 1095-9203

Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics

Published by American Association for the Advancement of Science (AAAS)

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Availability of water affects organ growth in prenatal and neonatal snapping turtles (Chelydra serpentina) (2000)

Packard, G. C. ; Packard, M. J. ; Birchard, G. F.

Springer

Journal of comparative physiology 170 (2000), S. 69-74

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ISSN: 1432-136X

Keywords: Key words Development ; Embryo ; Organ growth ; Turtle ; Water

Source: Springer Online Journal Archives 1860-2000

Topics: Biology , Medicine

Notes: Abstract We manipulated the amount of water that was available to prenatal and neonatal snapping turtles (Chelydra serpentina) in order to assess the impact of water on growth by different organs in these animals. Three treatments were used: (1) turtles that completed their incubation on a wet substrate, (2) turtles that completed their incubation on a dry substrate, and (3) turtles that spent a few days in water after completing incubation on a dry substrate. Turtles hatching on a dry substrate (treatment 2) were smaller than animals in the other two treatments (which did not differ in size), so data for mass of different organs were adjusted by ANCOVA to remove effects of body size. Scaled masses of liver, stomach, lungs, kidneys, and small intestine did not differ between turtles emerging in wet environments and those hatching in dry environments, but hearts of turtles hatching in dry settings were substantially larger than those of animals hatching in wet ones. Thus, the mass of most organs in turtles developing in wet and dry environments scaled to body size, whereas the heart was hypertrophied in embryos developing in dry environments. Turtles that spent a few days in water after hatching from eggs in dry environments grew rapidly in size, and the increase in body size was accompanied by disproportionately rapid growth in the liver, stomach, lungs, kidneys, and small intestine. The heart did not increase in size during this period, despite the substantial increase in body mass over that at hatching. The enlarged heart of turtles hatching on dry substrates may have been caused by a circulatory hypovolemia late in incubation; the rapid growth of organs other than the heart when these animals were placed in water may reflect a release from constraints on growth once circulatory volume was restored.

Type of Medium: Electronic Resource

URL: http://dx.doi.org/10.1007/s003600050009

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Water loss from eggs of domestic fowl and calcium status of hatchlings (1993)

Packard, M. J. ; Packard, G. C.

Springer

Journal of comparative physiology 163 (1993), S. 327-331

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ISSN: 1432-136X

Keywords: Chicken embryo ; Calcium metabolism ; Water loss ; Egg, Domestic fowl

Source: Springer Online Journal Archives 1860-2000

Topics: Biology , Medicine

Notes: Abstract Water balance in eggs of domestic fowl was manipulated by drilling holes (each 3 mm in diameter) through the calcareous layer into the air cell on day 10 of incubation. Water loss between days 0 and 18 averaged 6 g for eggs in the control group (no hole) but increased to 8, 12, and 15 g for eggs with 1, 2, or 3 holes, respectively. Hatching success was 79–87% for eggs with 0–2 holes through the eggshell but only 43% for eggs with three holes. Live mass of hatchlings declined as the number of holes drilled in the eggshell increased, but dry mass of carcasses was unaffected by the treatments. The quantity of Ca2+, Mg2+, and phosphorus in residual yolks and yolk-free carcasses of hatchlings was not influenced by the amount of water lost from eggs. Plasma Ca2+ and Mg2+ were elevated in hatchlings from eggs with high rates of water loss. The inability to regulate plasma Ca2+ may be a negative consequence of excessive water loss and could contribute to increased mortality of embryos.

Type of Medium: Electronic Resource

URL: http://dx.doi.org/10.1007/BF00347783

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Accumulation of lactate by supercooled hatchlings of the painted turtle (Chrysemys picta): implications for overwinter survival (2000)

Hartley, L. M. ; Packard, M. J. ; Packard, G. C.

Springer

Journal of comparative physiology 170 (2000), S. 45-50

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ISSN: 1432-136X

Keywords: Key wordsChrysemys picta ; Lactic acidosis ; Anaerobic metabolism ; Supercooling

Source: Springer Online Journal Archives 1860-2000

Topics: Biology , Medicine

Notes: Abstract Hatchlings of the North American painted turtle (Chrysemys picta) typically spend their first winter of life inside the shallow, subterranean nest where they completed embryogenesis the preceding summer. Neonates at northern localities consequently may be exposed during winter to subzero temperatures and frozen soil. Hatchlings apparently survive exposure to such conditions by supercooling, but the physiological consequences of this adaptive strategy have not been examined. We measured lactate in hatchling painted turtles after exposure to each of three temperatures (0 °C, −4 °C, and −8 °C) for three time periods (5 days, 15 days, and 25 days) to determine the extent to which overwintering hatchlings might rely on anaerobic metabolism to regenerate ATP. Whole-body lactate increased with increasing duration of exposure and decreasing temperature, and the highest levels were associated with the group that experienced the highest mortality. These results indicate that animals may develop a considerable lactic acidosis during a winter in which temperatures fall below 0 °C for weeks or months and that accumulation of lactate may contribute to mortality of overwintering animals.

Type of Medium: Electronic Resource

URL: http://dx.doi.org/10.1007/s003600050006

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Hatchling painted turtles (Chrysemys picta) survive exposure to subzero temperatures during hibernation by avoiding freezing (1993)

Packard, G. C. ; Packard, M. J.

Springer

Journal of comparative physiology 163 (1993), S. 147-152

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ISSN: 1432-136X

Keywords: Cold tolerance ; Freeze avoidance ; Supercooling ; Reptilia ; Turtle Chrysemys picta

Source: Springer Online Journal Archives 1860-2000

Topics: Biology , Medicine

Notes: Abstract Hatchling painted turtles (Chrysemys picta) were placed individually into artificial nests constructed in jars of damp soil and then were cooled slowly to temperatures between-7.7 and-12.7 °C. Distinct exotherms were recorded in all jars when water in the soil began to freeze at temperatures between-0.9 and-2.4 °C. A second (animal) exotherm was subsequently detected in some of the jars when water in hatchlings also began to freeze. An animal exotherm occurred in the temperature records for all 23 hatchlings that died in tests terminating at temperatures between-7.7 and-10.8 °C, but no such exotherm was apparent in the temperature records for the 23 turtles that survived these treatments. Moreover, the 4 hatchlings that produced exotherms in tests terminating between-11.5 and-12.7 °C failed to survive, but 5 of 7 hatchlings that produced no exotherm in these tests also died. Thus, turtles that die at subzero temperatures above-11 °C apparently succumb to freezing when ice propagates across their integument from the frozen soil, but animals that die at temperatures below-11 °C generally perish from some other cause. These findings indicate that hatchling painted turtles overwintering inside their shallow, subterranean nests survive exposure to subzero temperatures by avoiding freezing instead of by tolerating freezing.

Type of Medium: Electronic Resource

URL: http://dx.doi.org/10.1007/BF00263600

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