Refining spectral library searching

Spectral library searching has many advantages over sequence database searching, yet it has not been widely adopted. One possible reason for this is that users are unsure exactly how to interpret the similarity scores (e.g., “dot products” are not probability‐based scores). Methods to create decoys have been proposed, but, as developers caution, may produce proxies that are not equivalent to reversed sequences. In this issue, Shao et al. (Proteomics 2013, 13, 3273–3283) report advances in spectral library searching where the focus is not on improving the performance of their search engine, SpectraST, but is instead on improving the statistical meaningfulness of its discriminant score and removing the need for decoys. The results in their paper indicate that by “standardizing” the input and library spectra, sensitivity is not lost but is, surprisingly, gained. Their tests also show that false discovery rate (FDR) estimates, derived from their new score, track better with “ground truth” than decoy searching. It is possible that their work strikes a good balance between the theory of library searching and its application. And as such, they hope to have removed a major entrance barrier for some researchers previously unwilling to try library searching.     

Orthogonal polarization spectral imaging

The microcirculation plays a crucial role in the interaction between blood and tissues both in physiological and pathophysiological states. Despite its critical role in numerous diseases including diabetes, hypertension, sepsis or multiple organ failure, methods for direct visualization and quantitative assessment of human microcirculation at the bedside are limited. Orthogonal polarization spectral (OPS) imaging is a relatively new noninvasive method for assessment of human microcirculation without using fluorescent dyes. Recent clinical studies using OPS imaging in various pathological states have shown a wide spectrum of different clinical applications with evident impact on the diagnosis, treatment or prognosis assessment. Thus, there is a great effort to validate OPS imaging for various clinical purposes. The principles of OPS imaging, validation studies, its advantages, limitations, methods of quantitative assessment and current experience in clinical practice are discussed.     

Quantitative spectral comparison by weighted spectral difference for protein higher order structure confirmation

Previously, different approaches of spectral comparison were evaluated, and the spectral difference (SD) method was shown to be valuable for its linearity with spectral changes and its independence on data spacing (Anal. Biochem. 434 (2013) 153–165). In this note, we present an enhancement of the SD calculation, referred to as the “weighted spectral difference” (WSD), by implementing a weighting function based on relative signal magnitude. While maintaining the advantages of the SD method, WSD improves the method sensitivity to spectral changes and tolerance for baseline inclusion. Furthermore, a generalized formula is presented to unify further development of approaches to quantify spectral difference.     

Associations between adult spectral tarsiers

While anecdotal observations of gregarious behavior in nocturnal prosimian primates are common, most anthropologists continue to refer to them as solitary, perhaps based on the assumption that the occasional social interactions observed via ad libitum methods represent random chance encounters and not patterned social interactions. In this paper, I test the null hypothesis that nocturnal encounters between spectral tarsier (Tarsius spectrum) group members, outside of the sleeping tree, are the result of chance. Three male‐female pairs were radio‐collared and observed over a 4‐month period, using continuous focal animal sampling at the Tangkoko Nature Reserve (Sulawesi, Indonesia). Using Waser's random gas model, I found that spectral tarsiers spent more time in proximity to other group members than expected by chance, given the size of their home range and nightly path length. Adult group members spent 11% of the night in physical contact and an additional 17% of the night within a 10‐m radius of one another. Spectral tarsiers were also observed to significantly increase the amount of time spent foraging when located less than 10 m from another group member. Individuals foraging in proximity to another adult group member had lower insect capture rates compared to individuals who were not foraging in proximity to another adult group member. If living in a group is costly to these tarsiers' foraging efficiency, then why don't they actively avoid one another when foraging? One situation in which it might benefit tarsiers to be gregarious is high predation pressure. Preliminary results suggest that predation pressure by snakes may be the most likely factor selecting for the tarsiers to forage in proximity. Am J Phys Anthropol 128:74‐83, 2005. © 2005 Wiley‐Liss, Inc.     

The effect of spectral light deprivation on the spectral sensitivity of the honey bee

Summary The spectral sensitivity of spontaneous phototactic behavior was tested in short wavelength deprived bees and in control bees kept outdoors. Tests were performed with a y-maze with one branch illuminated, the other dark. The relative sensitivities for the control group were: green to blue to UV = 10.272.14. Short wavelength deprived bees show a distinct decrease in their sensitivity to short wavelengths. The relation green to blue to UV here was 10.220.27. Forager bees from outdooors, short wavelength deprived for 10 days, showed a relation of green to blue to UV of 10.261.04. Electrophysiological investigation of the compound eye using electroretinogram recordings showed no difference between deprived and control animals.     

Solid-state spectral perturbations in square-planar complexes

A brief overview of color changes of square-planar complexes upon crystallization is presented along with selected spectra and theoretical spectral modeling results. In general, brilliant colored crystals of several square-planar complexes develop from colorless solution. The systems include Magnus’ green salt, tetracyanometallates, and bis(dimethylglyoximato)nickel(II). It is generally accepted that the transition responsible for a spectral red shift and increase in intensity is from an uppermost filled orbital with a large metal d_z² component to a low-lying empty metal-based p_z orbital. Since these orbitals are largely oriented out of plane, they interact most strongly when the planes are aggregated. Experimental data from selected single-crystal polarized specular reflectance spectra and ZINDO calculations on several systems are reviewed.     

The behavior of wild spectral tarsiers

Field data are presented from a 15-month study of spectral tarsiers in North Sulawesi, Indonesia, based on over 300 sightings of animals in the wild and supplemented by observations from other parts of the island. Animals in study area were caught in mist nets and marked with colored plastic bird rings so that tarsiers followed at night could be individually recognized. Ecological data presented cover the locomotion, use of forest strata, and diet of tarsiers. Although clearly specialized for vertical clinging and leaping, the spectral tarsier is less specialized than the western tarsier, occupying a wider range of habitats and using a wider range of vegetation strata and locomotor patterns. Diet is mostly insects collected both on the ground and in trees. Spectral tarsiers were found to be monogamous and territorial. Families regularly slept at the same sites each day and gave loud duet songs as they congregated at sleeping sites each dawn. Sometimes similar songs were given in the night during territorial conflicts. Family home ranges were plotted and average about 1 ha. Observations are included on mating, the development of young tarsiers, and the dispersion of juveniles. Tarsier young are very precocious and may travel independently as little as 23 days after birth. Tarsiers regularly scent marked their ranges by rubbing branches with urine and special epigastric glands. In addition, they have a varied repertoire of calls and the main vocalizations are described.     

Inhomogeneous broadening in spectral bands of carbonmonoxymyoglobin. The connection between spectral and functional heterogeneity.

The rebinding kinetics of CO to myoglobin after flash photolysis is nonexponential in time below approximately 180 K; the kinetics is governed by a distribution of enthalpic barriers. This distribution results from inhomogeneities in the protein conformation, referred to as conformational substates. Hole-burning experiments on the Soret and IR CO-stretch bands test the assumption that an inhomogeneous distribution of conformational substates results in inhomogeneously broadened spectra. CO was slowly photolyzed at different wavelengths in the Soret band at 10 K. Both the Soret band and the CO-stretch band A1, centered at 1,945 cm-1, shift during photolysis, demonstrating that different wavelengths excite different parts of the distributed population. We have also done kinetic hole-burning experiments by measuring peak shifts in the Soret and A1 bands as the CO molecules rebind. The shifts indicate that the spectral and enthalpic distributions are correlated. In the A1 band, the spectral and enthalpic distributions are highly correlated while in the Soret the correlation is weak. From the peak shifts in the spectral and kinetic hole-burning experiments the inhomogeneous broadening is estimated to be approximately 15% of the total width in the Soret band and approximately 60% in A1. We have previously measured the tilt angle alpha between the bound CO and the heme normal (Ormos, P., D. Braunstein, H. Frauenfelder, M. K. Hong, S.-L. Lin, T. B. Sauke, and R. D. Young. 1988. Proc. Natl. Acad. Sci. USA. 85:8492-8496) and observed a wave number dependence of the tilt angles within the CO-stretch A bands. Thus the spectral and enthalpic distributions of the A bands are coupled to a heterogeneity of the structure.     

Increment-threshold spectral sensitivity in the rabbit

Summary Increment threshold measurements in wild rabbits give rise to spectral sensitivity curves that are unimodal or bimodal in nature, depending on the background luminance. We propose a model that explains the shape of these curves on the basis of synergistic and antagonistic interaction of blue cones (_max = 425 nm), green cones (_max = 523 nm) and rods (_max = 498 nm).     

Phylogenetic analysis based on spectral methods

Whole-genome or multiple gene phylogenetic analysis is of interest since single gene analysis often results in poorly resolved trees. Here, the use of spectral techniques for analyzing multigene data sets is explored. The protein sequences are treated as categorical time series, and a measure of similarity between a pair of sequences, the spectral covariance, is based on the common periodicity between these two sequences. Unlike the other methods, the spectral covariance method focuses on the relationship between the sites of genetic sequences. By properly scaling the dissimilarity measures derived from different genes between a pair of species, we can use the mean of these scaled dissimilarity measures as a summary statistic to measure the taxonomic distances across multiple genes. The methods are applied to three different data sets, one noncontroversial and two with some dispute over the correct placement of the taxa in the tree. Trees are constructed using two distance-based methods, BIONJ and FITCH. A variation of block bootstrap sampling method is used for inference. The methods are able to recover all major clades in the corresponding reference trees with moderate to high bootstrap support. Through simulations, we show that the covariance-based methods effectively capture phylogenetic signal even when structural information is not fully retained. Comparisons of simulation results with the bootstrap permutation results indicate that the covariance-based methods are fairly robust under perturbations in sequence similarity but more sensitive to perturbations in structural similarity.     

Isolation and spectral characterization of phycobiliproteins

Several phycobiliproteins were prepared chromatographically pure and their absorption, fluorescence-emission, fluorescence-excitation and fluorescence-excitation polarization spectra determined. Changes in these spectra with ionic strength of the aqueous medium and chromoprotein concentration were interpreted in terms of interchromophore energy transfer and protein subunit equilibria. The complexity of the polarization spectra confirms the presence of different types of chromophore, designated sensitizing (;s') and fluorescing (;f'), in a single protein.