ALBERT — All Library Books, journals and Electronic Records Telegrafenberg

1

Unknown

Microaerobic steroid biosynthesis and the molecular fossil record of Archean life [Evolution] (2011)

Waldbauer, J. R., Newman, D. K., Summons, R. E.

National Academy of Sciences

In: PNAS - Proceedings of the National Academy of Sciences

add to mindlist on the mindlist

Details

Publication Date: 2011-08-18

Description: The power of molecular oxygen to drive many crucial biogeochemical processes, from cellular respiration to rock weathering, makes reconstructing the history of its production and accumulation a first-order question for understanding Earth’s evolution. Among the various geochemical proxies for the presence of O2 in the environment, molecular fossils offer a unique record of O2 where it was first produced and consumed by biology: in sunlit aquatic habitats. As steroid biosynthesis requires molecular oxygen, fossil steranes have been used to draw inferences about aerobiosis in the early Precambrian. However, better quantitative constraints on the O2 requirement of this biochemistry would clarify the implications of these molecular fossils for environmental conditions at the time of their production. Here we demonstrate that steroid biosynthesis is a microaerobic process, enabled by dissolved O2 concentrations in the nanomolar range. We present evidence that microaerobic marine environments (where steroid biosynthesis was possible) could have been widespread and persistent for long periods of time prior to the earliest geologic and isotopic evidence for atmospheric O2. In the late Archean, molecular oxygen likely cycled as a biogenic trace gas, much as compounds such as dimethylsulfide do today.

Print ISSN: 0027-8424

Electronic ISSN: 1091-6490

Topics: Biology , Medicine , Natural Sciences in General

Published by National Academy of Sciences

Permalink

	Location	Call Number	Expected	Availability

Others were also interested in ...

PAPER CURRENT

S·F·X

Fulltext

2

Unknown

Comprehensive identification of human bZIP interactions with coiled-coil arrays (2003)

J. R. Newman ; A. E. Keating

American Association for the Advancement of Science (AAAS)

In: Science. 300(5628): 2097-101. doi: 10.1126/science.1084648.

add to mindlist on the mindlist

Details

Publication Date: 2003-06-14

Description: In eukaryotes, the combinatorial association of sequence-specific DNA binding proteins is essential for transcription. We have used protein arrays to test 492 pairings of a nearly complete set of coiled-coil strands from human basic-region leucine zipper (bZIP) transcription factors. We find considerable partnering selectivity despite the bZIPs' homologous sequences. The interaction data are of high quality, as assessed by their reproducibility, reciprocity, and agreement with previous observations. Biophysical studies in solution support the relative binding strengths observed with the arrays. New associations provide insights into the circadian clock and the unfolded protein response.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Newman, John R S -- Keating, Amy E -- New York, N.Y. -- Science. 2003 Jun 27;300(5628):2097-101. Epub 2003 Jun 12.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biology, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12805554" target="_blank"〉PubMed〈/a〉

Keywords: Amino Acid Sequence ; Basic-Leucine Zipper Transcription Factors ; Chromatography, High Pressure Liquid ; Circadian Rhythm ; Circular Dichroism ; Cyclic AMP Response Element-Binding Protein/chemistry/metabolism ; DNA-Binding Proteins/chemistry/isolation & purification/*metabolism ; Dimerization ; G-Box Binding Factors ; Humans ; *Leucine Zippers ; Peptides/chemistry/isolation & purification/metabolism ; *Protein Array Analysis ; Protein Binding ; Protein Folding ; Protein Structure, Tertiary ; Signal Transduction ; Temperature ; Thermodynamics ; Transcription Factors/*chemistry/isolation & purification/*metabolism

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)

Permalink

	Location	Call Number	Expected	Availability

Others were also interested in ...

PAPER CURRENT

S·F·X

Fulltext

3

Unknown

Genome-wide analysis in vivo of translation with nucleotide resolution using ribosome profiling (2009)

N. T. Ingolia ; S. Ghaemmaghami ; J. R. Newman ; [et al.]

American Association for the Advancement of Science (AAAS)

In: Science. 324(5924): 218-23. doi: 10.1126/science.1168978.

add to mindlist on the mindlist

Details

Publication Date: 2009-02-14

Description: Techniques for systematically monitoring protein translation have lagged far behind methods for measuring messenger RNA (mRNA) levels. Here, we present a ribosome-profiling strategy that is based on the deep sequencing of ribosome-protected mRNA fragments and enables genome-wide investigation of translation with subcodon resolution. We used this technique to monitor translation in budding yeast under both rich and starvation conditions. These studies defined the protein sequences being translated and found extensive translational control in both determining absolute protein abundance and responding to environmental stress. We also observed distinct phases during translation that involve a large decrease in ribosome density going from early to late peptide elongation as well as widespread regulated initiation at non-adenine-uracil-guanine (AUG) codons. Ribosome profiling is readily adaptable to other organisms, making high-precision investigation of protein translation experimentally accessible.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2746483/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉 〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2746483/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Ingolia, Nicholas T -- Ghaemmaghami, Sina -- Newman, John R S -- Weissman, Jonathan S -- AG10770/AG/NIA NIH HHS/ -- GM080853/GM/NIGMS NIH HHS/ -- P01 AG010770/AG/NIA NIH HHS/ -- P01 AG010770-16/AG/NIA NIH HHS/ -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2009 Apr 10;324(5924):218-23. doi: 10.1126/science.1168978. Epub 2009 Feb 12.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Cellular and Molecular Pharmacology, Howard Hughes Medical Institute, University of California, San Francisco, and California Institute for Quantitative Biosciences, San Francisco, CA 94158, USA. ingolia@cmp.ucsf.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19213877" target="_blank"〉PubMed〈/a〉

Keywords: 5' Untranslated Regions ; *Codon ; Gene Library ; *Genome, Fungal ; Introns ; Peptide Chain Elongation, Translational ; Peptide Chain Initiation, Translational ; *Protein Biosynthesis ; RNA, Fungal/*genetics/metabolism ; RNA, Messenger/*genetics/metabolism ; Ribosomes/*metabolism ; Saccharomyces cerevisiae/*genetics/metabolism/physiology ; Saccharomyces cerevisiae Proteins/*biosynthesis ; Sequence Analysis, DNA

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)

Permalink

	Location	Call Number	Expected	Availability

Others were also interested in ...

PAPER CURRENT

S·F·X

Fulltext

4

Electronic Resource

Effect of Heat Generated during Stressing upon the Tensile Properties of Rubber (1926)

Boone, C. E. ; Newman, J. R.

s.l. : American Chemical Society

Industrial & engineering chemistry 18 (1926), S. 539-540

add to mindlist on the mindlist

Details

ISSN: 1520-5045

Source: ACS Legacy Archives

Topics: Chemistry and Pharmacology , Process Engineering, Biotechnology, Nutrition Technology

Type of Medium: Electronic Resource

URL: http://dx.doi.org/10.1021/ie50197a028

Permalink

	Location	Call Number	Expected	Availability

Others were also interested in ...

Paper (German National Licenses)

Fulltext

5

Electronic Resource

CO2 is the main inorganic C species entering photosynthetically active leaf protoplasts of the freshwater macrophyte Ranunculus penicillatus ssp. pseudofluitans (1999)

Newman, J. R. ; Raven, J. A.

Oxford, UK : Blackwell Science Ltd.

Plant, cell & environment 22 (1999), S. 0

add to mindlist on the mindlist

Details

ISSN: 1365-3040

Source: Blackwell Publishing Journal Backfiles 1879-2005

Topics: Biology

Notes: Submerged aquatic macrophytes growing in water where free CO2 is unavailable (above pH 8·2) must use mechanisms to supply external dissolved inorganic carbon in a form available to chloroplasts (CO2). Active transport of HCO3– across the plasmalemma has not been proven to be widespread in aquatic macrophytes and catalytic conversion of HCO3– to CO2 is the usual supply mechanism in submerged macrophytes. The interaction of leaf form and function in this respect was investigated in the linear, submerged leaves of Ranunculus penicillatus (Dumort.) Bab ssp. pseudofluitans (Syme) S.Webster. Viable protoplasts were isolated using a mixture of cell wall degrading enzymes optimized for this species. Protoplast viabilities greater than 80% after 5 h of isolation were achieved. Photosynthetic rates of isolated protoplasts were comparable with that of intact plant tissue. Results of carbon isotopic disequilibrium experiments showed that CO2 was the preferred species of dissolved inorganic carbon for photosynthesis by protoplasts and that HCO3– which predominates in the plant’s natural environment mainly contributes by supplying CO2 outside the cells.

Type of Medium: Electronic Resource

URL: http://dx.doi.org/10.1046/j.1365-3040.1999.00460.x

Permalink

	Location	Call Number	Expected	Availability

Others were also interested in ...

Paper (German National Licenses)

Fulltext

6

Electronic Resource

Requirement for carbonic anhydrase activity in processes other than photosynthetic Inorganic carbon assimilation (1994)

RAVEN, J. A. ; NEWMAN, J. R.

Oxford, UK : Blackwell Publishing Ltd

Plant, cell & environment 17 (1994), S. 0

add to mindlist on the mindlist

Details

ISSN: 1365-3040

Source: Blackwell Publishing Journal Backfiles 1879-2005

Topics: Biology

Notes: A number of non-green plant tissues have high rates of HCO3−-consuming reactions in the cytosol, i.e. C4 dicarboxylic acid production preceding organic acid anion transport into dicarboxylate consuming compartments in N2-fixing root nodules, in lipogenic tissues, and in thermogenic aroid spadices and, in the case of lipogenic tissues, in acetyl CoA incorporation into lipid in plastid stroma. Since inorganic C supply to the cytosol or stroma by decarboxylation reactions, and by transmembrane fluxes, involves only CO2, the HCO3− consumed in the rapid metabolic processes must originate from hydration (hydroxylation) of CO2. Computations based on the first-order rate constant for uncatalysed conversion of CO2 to HCO3− and the most likely in vivo CO2 concentration show that the uncatalysed reaction is possibly adequate to supply the observed HCO3− requirement in the HCO3−-consuming compartments. However, carbonic anhydrase activity is well established in legume root nodules, and also appears to occur in aroid spadices. In addition to coping with any heterogeneities in HCO3−, consumption in the cytosol, the root nodule activity may be involved in optimizing haemoglobin function. Further work is needed on carbonic anhydrase expression is tissues with rapid HCO3− consumption, especially in view of reports of negligible carbonic anhydrase activity in some non-green plant tissues. Other possible roles of carbonic anhydrase in non-green plant tissues are briefly discussed.

Type of Medium: Electronic Resource

URL: http://dx.doi.org/10.1111/j.1365-3040.1994.tb00275.x

Permalink

	Location	Call Number	Expected	Availability

Others were also interested in ...

Paper (German National Licenses)

Fulltext

7

Electronic Resource

Carbonic anhydrase in Ranunculus penicillatus spp. pseudofluitans: activity, location and implications for carbon assimilation (1993)

NEWMAN, J. R. ; RAVEN, J. A.

Oxford, UK : Blackwell Publishing Ltd

Plant, cell & environment 16 (1993), S. 0

add to mindlist on the mindlist

Details

ISSN: 1365-3040

Source: Blackwell Publishing Journal Backfiles 1879-2005

Topics: Biology

Notes: Levels of carbonic anhydrase activity were determined on a total (60 EUmg−1 protein), external (7.36 EU), internal (50.14 EU) and protoplast (15.63 EU) basis for Ranunculus penicillatus (Dumort.) Bab ssp. pseudofluitans (Syme) S. Webster, a freshwater aquatic macrophyte, by conventional electrometric methods. The site of activity of ‘external’ carbonic anhydrase (CA) has been visualized using 5-Dimethylaminonapthalene-1- sulphonamide (DNSA)-CA fluorescent complex formation, and is postulated to be closely associated with the epidermal cell wall. The photosynthetic rate of R. penicillatus ssp. pseudofluitans at pH 9.0 is in excess of the uncatalysed rate of production of CO2 from HCO−3, and this plant is therefore using HCO−3 for photosynthesis. The possible contribution of CA activity to inorganic carbon assimilation, and specifically to transport of HCO−3, in submerged aquatic plants is discussed.

Type of Medium: Electronic Resource

URL: http://dx.doi.org/10.1111/j.1365-3040.1993.tb00896.x

Permalink