Site-specific sequence-stratigraphic section benchmark charts are key to regional chronostratigraphic systems tract analysis in growth-faulted basins

AAPG Bulletin ◽  
2005 ◽  
Vol 89 (6) ◽  
pp. 715-724 ◽  
Author(s):  
L. Frank Brown ◽  
Robert G. Loucks ◽  
Ramón H. Treviño
Keyword(s):  
Specific Sequence ◽  
Site Specific ◽  
Sequence Stratigraphic ◽  
Stratigraphic Section

scholarly journals An Integrated Model of Phenotypic Trait Changes and Site-Specific Sequence Evolution

2017 ◽  
Vol 66 (6) ◽  
pp. 917-933 ◽  
Author(s):  
Eli Levy Karin ◽  
Susann Wicke ◽  
Tal Pupko ◽  
Itay Mayrose
Keyword(s):  
Integrated Model ◽  
Phenotypic Trait ◽  
Sequence Evolution ◽  
Specific Sequence ◽  
Site Specific

Amino-Functionalized 5′ Cap Analogs as Tools for Site-Specific Sequence-Independent Labeling of mRNA

2017 ◽  
Vol 28 (7) ◽  
pp. 1978-1992 ◽  
Author(s):  
Marcin Warminski ◽  
Pawel J. Sikorski ◽  
Zofia Warminska ◽  
Maciej Lukaszewicz ◽  
Anna Kropiwnicka ◽  
...  
Keyword(s):  
Specific Sequence ◽  
Site Specific

CLUSTERING OF CALIBRATED RADIOCARBON DATES: SITE-SPECIFIC CHRONOLOGICAL SEQUENCES IDENTIFIED BY DENSE RADIOCARBON SAMPLING

Radiocarbon ◽  
2020 ◽  
pp. 1-10
Author(s):  
Peter Demján ◽  
Peter Pavúk
Keyword(s):  
Bronze Age ◽  
Statistical Significance ◽  
Real Life ◽  
Simulated Data ◽  
Hierarchical Cluster ◽  
Specific Sequence ◽  
Radiocarbon Dates ◽  
Site Specific ◽  
Archaeological Data ◽  
A Site

ABSTRACT Calibrated radiocarbon (14C) determinations are commonly used in archaeology to assign calendar dates to a site’s chronological phases identified based on additional evidence such as stratigraphy. In the absence of such evidence, we can perform dense 14C sampling of the site to attempt to identify periods of heightened activity, separated by periods of inactivity, which correspond to archaeological phases and gaps between them. We propose a method to achieve this by hierarchical cluster analysis of the calibrated 14C dates, followed by testing of the different clustering solutions for consistency based on silhouette coefficient and statistical significance using randomization. Separate events identified in such a way can then be regarded as evidence for distinct phases of activity and used to construct a site-specific sequence. This can be in turn used as a Bayesian prior to further narrow down the distributions of the calibrated 14C dates. We assessed the validity of the method using simulated data as well as real-life archaeological data from the Bronze Age settlement of Troy. A Python implementation of the method is available online at https://github.com/demjanp/clustering_14C.

Large-cluster and combined fluorescent and gold immunoprobes

1996 ◽  
Vol 54 ◽  
pp. 892-893
Author(s):  
Richard D. Powell ◽  
James F. Hainfeld ◽  
Carol M. R. Halsey ◽  
David L. Spector ◽  
Shelley Kaurin ◽  
...  
Keyword(s):  
Metal Cluster ◽  
Sulfonyl Chloride ◽  
Gel Filtration ◽  
Cross Linking ◽  
Site Specific ◽  
Fab Fragments ◽  
Cluster Label ◽  
Covalently Linked ◽  
Texas Red ◽  
Fold Excess

Two new types of covalently linked, site-specific immunoprobes have been prepared using metal cluster labels, and used to stain components of cells. Combined fluorescein and 1.4 nm “Nanogold” labels were prepared by using the fluorescein-conjugated tris (aryl) phosphine ligand and the amino-substituted ligand in the synthesis of the Nanogold cluster. This cluster label was activated by reaction with a 60-fold excess of (sulfo-Succinimidyl-4-N-maleiniido-cyclohexane-l-carboxylate (sulfo-SMCC) at pH 7.5, separated from excess cross-linking reagent by gel filtration, and mixed in ten-fold excess with Goat Fab’ fragments against mouse IgG (obtained by reduction of F(ab’)2 fragments with 50 mM mercaptoethylamine hydrochloride). Labeled Fab’ fragments were isolated by gel filtration HPLC (Superose-12, Pharmacia). A combined Nanogold and Texas Red label was also prepared, using a Nanogold cluster derivatized with both and its protected analog: the cluster was reacted with an eight-fold excess of Texas Red sulfonyl chloride at pH 9.0, separated from excess Texas Red by gel filtration, then deprotected with HC1 in methanol to yield the amino-substituted label.

The challenge of detecting modifications on proteins

2020 ◽  
Vol 64 (1) ◽  
pp. 135-153 ◽  
Author(s):  
Lauren Elizabeth Smith ◽  
Adelina Rogowska-Wrzesinska
Keyword(s):  
Mass Spectrometry ◽  
Protein Function ◽  
Chemical Properties ◽  
Lysine Acetylation ◽  
Mass Determination ◽  
Post Translational Modifications ◽  
Site Specific ◽  
The Common

Abstract Post-translational modifications (PTMs) are integral to the regulation of protein function, characterising their role in this process is vital to understanding how cells work in both healthy and diseased states. Mass spectrometry (MS) facilitates the mass determination and sequencing of peptides, and thereby also the detection of site-specific PTMs. However, numerous challenges in this field continue to persist. The diverse chemical properties, low abundance, labile nature and instability of many PTMs, in combination with the more practical issues of compatibility with MS and bioinformatics challenges, contribute to the arduous nature of their analysis. In this review, we present an overview of the established MS-based approaches for analysing PTMs and the common complications associated with their investigation, including examples of specific challenges focusing on phosphorylation, lysine acetylation and redox modifications.

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