Absorption changes of P-700 reversible in milliseconds at low temperature in Triton-solubilized Photosystem I particles

Triton-solubilized Photosystem I particles from spinach chloroplasts exhibit largely reversible P-700 absorption changes over the temperature range from 4.2 K to room temperature. For anaerobic samples treated with dithionite and neutral red at pH 10 and illuminated during cooling, a brief (1 μs) saturating flash produces absorption changes in the long wavelength region that decay in 0.95 ± 0.2 ms from 4.2 to 50 K. Above 80 K a faster (100 ± 30 μs) component dominates in the decay process, but this disappears again above about 180 K. The major decay at temperatures above 200 K occurs in about 1 ms. The difference spectrum of these absorption changes between 500 and 900 nm closely resembles that of P-700. Using ascorbate and 2,6-dichlorophenolindophenol as the reducing system with a sample of Photosystem I particles cooled in darkness to 4.2 K, a fully reversible signal is seen upon both the first and subsequent flashes. The decay time in this case is 0.9 ± 0.3 ms.     

MS2Rescore: Data-Driven Rescoring Dramatically Boosts Immunopeptide Identification Rates

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Relative Quantification of Proteins in Formalin-Fixed Paraffin-Embedded Breast Cancer Tissue Using Multiplexed Mass Spectrometry Assays

The identification of clinically relevant biomarkers represents an important challenge in oncology. This problem can be addressed with biomarker discovery and verification studies performed directly in tumor samples using formalin-fixed paraffin-embedded (FFPE) tissues. However, reliably measuring proteins in FFPE samples remains challenging. Here, we demonstrate the use of liquid chromatography coupled to multiple reaction monitoring mass spectrometry (LC-MRM/MS) as an effective technique for such applications. An LC-MRM/MS method was developed to simultaneously quantify hundreds of peptides extracted from FFPE samples and was applied to the targeted measurement of 200 proteins in 48 triple-negative, 19 HER2-overexpressing, and 20 luminal A breast tumors. Quantitative information was obtained for 185 proteins, including known markers of breast cancer such as HER2, hormone receptors, Ki-67, or inflammation-related proteins. LC-MRM/MS results for these proteins matched immunohistochemistry or chromogenic in situ hybridization data. In addition, comparison of our results with data from the literature showed that several proteins representing potential biomarkers were identified as differentially expressed in triple-negative breast cancer samples. These results indicate that LC-MRM/MS assays can reliably measure large sets of proteins using the analysis of surrogate peptides extracted from FFPE samples. This approach allows to simultaneously quantify the expression of target proteins from various pathways in tumor samples. LC-MRM/MS is thus a powerful tool for the relative quantification of proteins in FFPE tissues and for biomarker discovery.     

A Computational Approach to Developing Mathematical Models of Polyploid Meiosis

Mathematical models of meiosis that relate offspring to parental genotypes through parameters such as meiotic recombination frequency have been difficult to develop for polyploids. Existing models have limitations with respect to their analytic potential, their compatibility with insights into mechanistic aspects of meiosis, and their treatment of model parameters in terms of parameter dependencies. In this article I put forward a computational approach to the probabilistic modeling of meiosis. A computer program enumerates all possible paths through the phases of replication, pairing, recombination, and segregation, while keeping track of the probabilities of the paths according to the various parameters involved. Probabilities for classes of genotypes or phenotypes are added, and the resulting formulas are simplified by the symbolic-computation system Mathematica. An example application to autotetraploids results in a model that remedies the limitations of previous models mentioned above. In addition to the immediate implications, the computational approach presented here can be expected to be useful through opening avenues for modeling a host of processes, including meiosis in higher-order ploidies.     

Fluctuating selection: the perpetual renewal of adaptation in variable environments

Darwin insisted that evolutionary change occurs very slowly over long periods of time, and this gradualist view was accepted by his supporters and incorporated into the infinitesimal model of quantitative genetics developed by R. A. Fisher and others. It dominated the first century of evolutionary biology, but has been challenged in more recent years both by field surveys demonstrating strong selection in natural populations and by quantitative trait loci and genomic studies, indicating that adaptation is often attributable to mutations in a few genes. The prevalence of strong selection seems inconsistent, however, with the high heritability often observed in natural populations, and with the claim that the amount of morphological change in contemporary and fossil lineages is independent of elapsed time. I argue that these discrepancies are resolved by realistic accounts of environmental and evolutionary changes. First, the physical and biotic environment varies on all time-scales, leading to an indefinite increase in environmental variance over time. Secondly, the intensity and direction of natural selection are also likely to fluctuate over time, leading to an indefinite increase in phenotypic variance in any given evolving lineage. Finally, detailed long-term studies of selection in natural populations demonstrate that selection often changes in direction. I conclude that the traditional gradualist scheme of weak selection acting on polygenic variation should be supplemented by the view that adaptation is often based on oligogenic variation exposed to commonplace, strong, fluctuating natural selection.     

Correlation of general anesthetic potency with solubility in membranes

Recently (Franks, N.P. and Lieb, W.R. (1978) Nature 274, 339–342) it has been claimed that the traditional correlation between anesthetic potency and vegetable oil solubility breaks down when the alkanols are compared to other volatile anesthetics. Lately, however, new information on the partitioning of anesthetics into lipid bilayers has become available. In this report the potency of twenty-one structurally diverse anesthetic agents is shown to correlate well with their ability to partition into phosphatidylcholine bilayers. Thus the original Meyer-Overton oil solubility hypothesis accomodates a wider range of anesthetics, including alkanols, volatile and gaseous agents, and barbiturates, when lipid bilayer solubility is substituted for oil solubility.     

Determination of proteoglycan dimer geometry by electric birefringence

Proteoglycan solutions contain a certain amount of dimer whose presence may be of significance in arthrotic disorders. By measuring the multicomponent electric birefringence transients of these solutions, and analysing the rotary diffusion coefficients in terms of a recently published theory for bent rod-like molecules, the geometry of the dimer has been determined.