Assessment of Survival and Body Size Variation of Culicoides imicola (Diptera: Ceratopogonidae) as Functions of “Candidatus Cardinium” (Bacteroidetes) Infection Status

“Candidatus Cardinium hertigii” (Bacteroidetes) is a maternally inherited endosymbiont known from several arthropods. Its mechanisms for persistence in host populations are mostly reproductive manipulation, though it has been occasionally reported to improve fitness parameters in several hosts. In Culicoides (Diptera: Ceratopogonidae) biting midges, the prevalence of “Candidatus Cardinium” infection was documented as moderate, with no detectable sex bias. We therefore investigated whether “Candidatus Cardinium” affects important fitness parameters, such as survival and body size, in Culicoides imicola, a dominant vector species. Field-collected midges were trapped and analyzed for survival under different environmental conditions and antibiotic treatment, taking into account “Candidatus Cardinium” infection status and parity status (i.e., parous or nulliparous). Additionally, wing lengths were measured as a proxy parameter for body size and analyzed together with “Candidatus Cardinium” infection data. The findings revealed no difference in survival of Culicoides infected with “Candidatus Cardinium” and that of uninfected midges in both parity states and under all tested conditions: optimal, starvation, heat, and antibiotic treatment. Beyond survival, no wing length difference was found for “Candidatus Cardinium”-infected versus uninfected midges. In aggregate, these findings support our conclusion that “Candidatus Cardinium” does not have an overt effect on the survival and size of adult C. imicola midges. “Candidatus Cardinium” may affect immature stages or may alter adult reproductive performance.     

Computer Simulation of Radial Immunodiffusion: II. Selection of an Algorithm for the Antibody-Antigen Reaction in Gels

An algorithm needed for computer simulation of immunodiffusion has been deduced from existing theories of the in vitro reaction between antibody and antigen. The “Goldberg most probable polymer distribution” theory provides a formula that gives the amount of free antibody, free antigen, and diffusible complexes from extreme antibody excess through extreme antigen excess for any valences of antibody and antigen. As is shown here, that formula can be used even for those reactions producing complexes, cyclical or otherwise, that may precipitate as well as for those reactions involving heterogeneity of binding avidities. It is necessary, however, to specify an extent of reaction parameter. Five limiting expressions for this parameter are proposed as options for the basic algorithm. These are identified as: (a) the “Heidelberger-Kendall complete reaction” option, (b) the “Singer-Campbell constant avidity” option, (c) the “Hudson extensive antibody heterogeneity” option, (d) a new “extensive antigen heterogeneity” option, and (e) the “Goldberg critical extent of reaction” option. Literature data showing need for the various options are presented.     

Induction of "pore" formation in plant cell membranes by toluene

Treatment with aqueous toluene-ethanol has been shown to induce “pore” formation in plant cell membranes. The evidence is as follows: [List: see text]

While the principal experimental material was roots of Atriplex nummularia Lindl., the fact that similar results were also observed with leaves of Pisum sativum L. and with the alga Chlorella pyrenoidosa Chik. suggests that the phenomenon is general.

Although the phenomenon of pore induction is qualitatively similar to that in microorganisms, the pores induced appear to be smaller. It is proposed that induced leakage could be the basis for the development of simple and rapid methods for plant biochemical studies.

     

Infection Dynamics of the Tick-Borne Pathogen “Candidatus Neoehrlichia mikurensis” and Coinfections with Borrelia afzelii in Bank Voles in Southern Sweden

The tick-borne bacterium “Candidatus Neoehrlichia mikurensis” has recently been recognized as a human pathogen. Together with Borrelia afzelii, it is one of the most common pathogens found in the tick Ixodes ricinus. Here, we compared the epidemiologies of “Ca. Neoehrlichia mikurensis” and B. afzelii by longitudinal sampling from May to September in one of their most abundant vertebrate hosts, the bank vole (Myodes glareolus), using real-time PCR for detection and quantification. The prevalences of “Ca. Neoehrlichia mikurensis” and B. afzelii were determined to be 19% (50/261) and 22% (56/261), respectively. The prevalence of “Ca. Neoehrlichia mikurensis” increased significantly during the sampling season. The clearance rate of “Ca. Neoehrlichia mikurensis” was significantly higher than that of B. afzelii. We found a high frequency of double infections; 46% of all samples infected with “Ca. Neoehrlichia mikurensis” also had a coinfection with B. afzelii. The frequency of coinfections was significantly higher than expected from the prevalence of each pathogen. The high level of coinfections can be caused by interactions between the pathogens or might reflect variation in general susceptibility among voles.     

Frequency-domain order parameters for the burst and spike synchronization transitions of bursting neurons

We are interested in characterization of synchronization transitions of bursting neurons in the frequency domain. Instantaneous population firing rate (IPFR) R(t), which is directly obtained from the raster plot of neural spikes, is often used as a realistic collective quantity describing population activities in both the computational and the experimental neuroscience. For the case of spiking neurons, a realistic time-domain order parameter, based on R(t), was introduced in our recent work to characterize the spike synchronization transition. Unlike the case of spiking neurons, the IPFR R(t) of bursting neurons exhibits population behaviors with both the slow bursting and the fast spiking timescales. For our aim, we decompose the IPFR R(t) into the instantaneous population bursting rate R_b(t) (describing the bursting behavior) and the instantaneous population spike rate R_s(t) (describing the spiking behavior) via frequency filtering, and extend the realistic order parameter to the case of bursting neurons. Thus, we develop the frequency-domain bursting and spiking order parameters which are just the bursting and spiking “coherence factors” β_b and β_s of the bursting and spiking peaks in the power spectral densities of R_b and R_s (i.e., “signal to noise” ratio of the spectral peak height and its relative width). Through calculation of β_b and β_s, we obtain the bursting and spiking thresholds beyond which the burst and spike synchronizations break up, respectively. Consequently, it is shown in explicit examples that the frequency-domain bursting and spiking order parameters may be usefully used for characterization of the bursting and the spiking transitions, respectively.     

Alpha-pheromone-induced "shmooing" and gene regulation require white-opaque switching during Candida albicans mating

A 14-mer α-pheromone peptide of Candida albicans was chemically synthesized and used to analyze the role of white-opaque switching in the mating process. The α-pheromone peptide blocked cell multiplication and induced “shmooing” in a/a cells expressing the opaque-phase phenotype but not in a/a cells expressing the white-phase phenotype. The α-pheromone peptide induced these effects at 25°C but not at 37°C. An analysis of mating-associated gene expression revealed several categories of gene regulation, including (i) MTL-homozygous-specific, pheromone stimulated, switching-independent (CAG1 and STE4); (ii) mating type-specific, pheromone-induced, switching-independent (STE2); and (iii) pheromone-induced, switching-dependent (FIG1, KAR4, and HWP1). An analysis of switching-regulated genes revealed an additional category of opaque-phase-specific genes that are downregulated by α-pheromone only in a/a cells (OP4, SAP1, and SAP3). These results demonstrate that α-pheromone causes shmooing, the initial step in the mating process, only in a/a cells expressing the opaque phenotype and only at temperatures below that in the human host. These results further demonstrate that although some mating-associated genes are stimulated by the α-pheromone peptide in both white- and opaque-phase cells, others are stimulated only in opaque-phase cells, revealing a category of gene regulation unique to C. albicans in which α-pheromone induction requires the white-opaque transition. These results demonstrate that in C. albicans, the mating process and associated gene regulation must be examined within the context of white-opaque switching.     

Ross Sea Mollusca from the Latitudinal Gradient Program: R/V Italica 2004 Rauschert dredge samples

Information regarding the molluscs in this dataset is based on the Rauschert dredge samples collected during the Latitudinal Gradient Program (LGP) on board the R/V “Italica” in the Ross Sea (Antarctica) in the austral summer 2004. A total of 18 epibenthic dredge deployments/samplings have been performed at four different locations at depths ranging from 84 to 515m by using a Rauschert dredge with a mesh size of 500μm. In total 8,359 specimens have been collected belonging to a total of 161 species. Considering this dataset in terms of occurrences, it corresponds to 505 discrete distributional records (incidence data). Of these, in order of abundance, 5,965 specimens were Gastropoda (accounting for 113 species), 1,323 were Bivalvia (accounting for 36 species), 949 were Aplacophora (accounting for 7 species), 74 specimens were Scaphopoda (3 species), 38 were Monoplacophora (1 species) and, finally, 10 specimens were Polyplacophora (1 species). This data set represents the first large-scale survey of benthic micro-molluscs for the area and provides important information about the distribution of several species, which have been seldom or never recorded before in the Ross Sea. All vouchers are permanently stored at the Italian National Antarctic Museum (MNA), Section of Genoa, enabling future comparison and crosschecking. This material is also currently under study, from a molecular point of view, by the barcoding project “BAMBi” (PNRA 2010/A1.10).     

Growth rate fluctuations in phycomyces sporangiophores

The growth rate of the Phycomyces sporangiophore fluctuates under constant environmental conditions. These fluctuations underlie the well-characterized sensory responses to environmental changes. We compared growth fluctuations in sporangiophores of unstimulated wild type and behavioral mutants by use of maximum entropy spectral analysis, a mathematical technique that estimates the frequency and amplitude of oscillations in a time series. The mutants studied are believed to be altered near the input (“night-blind”) or output (“stiff” and “hypertropic”) of the photosensory transduction chain. The maximum entropy spectrum of wild type shows a sharp drop-off in spectral density above 0.3 millihertz, several minor peaks between 0.3 and 10 millihertz, and a broad maximum near 10 millihertz. Similar spectra were obtained for a night-blind mutant and a hypertropic mutant. In contrast, the spectra of three stiff mutants, defective in genes madD, madE, or madG, had distinctive peaks near 1.6 mHz and harmonics of this frequency. A madF stiff mutant, which is less stiff than madD, madE, and madG mutants, had a spectrum intermediate between wild type and the three other stiff mutants. Our results indicate that alterations in one or more steps associated with growth regulation output cause the Phycomyces sporangiophore to express a rhythmic growth rate.     

Amplification Biases and Consistent Recovery of Loci in a Double-Digest RAD-seq Protocol

A growing variety of “genotype-by-sequencing” (GBS) methods use restriction enzymes and high throughput DNA sequencing to generate data for a subset of genomic loci, allowing the simultaneous discovery and genotyping of thousands of polymorphisms in a set of multiplexed samples. We evaluated a “double-digest” restriction-site associated DNA sequencing (ddRAD-seq) protocol by 1) comparing results for a zebra finch (Taeniopygia guttata) sample with in silico predictions from the zebra finch reference genome; 2) assessing data quality for a population sample of indigobirds (Vidua spp.); and 3) testing for consistent recovery of loci across multiple samples and sequencing runs. Comparison with in silico predictions revealed that 1) over 90% of predicted, single-copy loci in our targeted size range (178–328 bp) were recovered; 2) short restriction fragments (38–178 bp) were carried through the size selection step and sequenced at appreciable depth, generating unexpected but nonetheless useful data; 3) amplification bias favored shorter, GC-rich fragments, contributing to among locus variation in sequencing depth that was strongly correlated across samples; 4) our use of restriction enzymes with a GC-rich recognition sequence resulted in an up to four-fold overrepresentation of GC-rich portions of the genome; and 5) star activity (i.e., non-specific cutting) resulted in thousands of “extra” loci sequenced at low depth. Results for three species of indigobirds show that a common set of thousands of loci can be consistently recovered across both individual samples and sequencing runs. In a run with 46 samples, we genotyped 5,996 loci in all individuals and 9,833 loci in 42 or more individuals, resulting in <1% missing data for the larger data set. We compare our approach to similar methods and discuss the range of factors (fragment library preparation, natural genetic variation, bioinformatics) influencing the recovery of a consistent set of loci among samples.     

Generation of Murine Cardiac Pacemaker Cell Aggregates Based on ES-Cell-Programming in Combination with Myh6-Promoter-Selection

Treatment of the “sick sinus syndrome” is based on artificial pacemakers. These bear hazards such as battery failure and infections. Moreover, they lack hormone responsiveness and the overall procedure is cost-intensive. “Biological pacemakers” generated from PSCs may become an alternative, yet the typical content of pacemaker cells in Embryoid Bodies (EBs) is extremely low. The described protocol combines “forward programming” of murine PSCs via the sinus node inducer TBX3 with Myh6-promoter based antibiotic selection. This yields cardiomyocyte aggregates consistent of >80% physiologically functional pacemaker cells. These “induced-sinoatrial-bodies” (“iSABs”) are spontaneously contracting at yet unreached frequencies (400-500 bpm) corresponding to nodal cells isolated from mouse hearts and are able to pace murine myocardium ex vivo. Using the described protocol highly pure sinus nodal single cells can be generated which e.g. can be used for in vitro drug testing. Furthermore, the iSABs generated according to this protocol may become a crucial step towards heart tissue engineering.     

Optimization of Analytical Parameters for Inferring Relationships among Escherichia coli Isolates from Repetitive-Element PCR by Maximizing Correspondence with Multilocus Sequence Typing Data

Repetitive-element PCR (rep-PCR) is a method for genotyping bacteria based on the selective amplification of repetitive genetic elements dispersed throughout bacterial chromosomes. The method has great potential for large-scale epidemiological studies because of its speed and simplicity; however, objective guidelines for inferring relationships among bacterial isolates from rep-PCR data are lacking. We used multilocus sequence typing (MLST) as a “gold standard” to optimize the analytical parameters for inferring relationships among Escherichia coli isolates from rep-PCR data. We chose 12 isolates from a large database to represent a wide range of pairwise genetic distances, based on the initial evaluation of their rep-PCR fingerprints. We conducted MLST with these same isolates and systematically varied the analytical parameters to maximize the correspondence between the relationships inferred from rep-PCR and those inferred from MLST. Methods that compared the shapes of densitometric profiles (“curve-based” methods) yielded consistently higher correspondence values between data types than did methods that calculated indices of similarity based on shared and different bands (maximum correspondences of 84.5% and 80.3%, respectively). Curve-based methods were also markedly more robust in accommodating variations in user-specified analytical parameter values than were “band-sharing coefficient” methods, and they enhanced the reproducibility of rep-PCR. Phylogenetic analyses of rep-PCR data yielded trees with high topological correspondence to trees based on MLST and high statistical support for major clades. These results indicate that rep-PCR yields accurate information for inferring relationships among E. coli isolates and that accuracy can be enhanced with the use of analytical methods that consider the shapes of densitometric profiles.     

Application of Siderotyping for Characterization of Pseudomonas tolaasii and “Pseudomonas reactans” Isolates Associated with Brown Blotch Disease of Cultivated Mushrooms

Pyoverdine isoelectric focusing analysis and pyoverdine-mediated iron uptake were used as siderotyping methods to analyze a collection of 57 northern and central European isolates of P. tolaasii and “P. reactans.” The bacteria, isolated from cultivated Agaricus bisporus or Pleurotus ostreatus mushroom sporophores presenting brown blotch disease symptoms, were identified according to the white line test (W. C. Wong and T. F. Preece, J. Appl. Bacteriol. 47:401–407, 1979) and their pathogenicity towards A. bisporus and were grouped into siderovars according to the type of pyoverdine they produced. Seventeen P. tolaasii isolates were recognized, which divided into two siderovars, with the first one containing reference strains and isolates of various geographical origins while the second one contained Finnish isolates exclusively. The 40 “P. reactans” isolates divided into eight siderovars. Pyoverdine isoelectric focusing profiles and cross-uptake studies demonstrated an identity for some “P. reactans” isolates, with reference strains belonging to the P. fluorescens biovars II, III, or V. Thus, the easy and rapid methods of siderotyping proved to be reliable by supporting and strengthening previous taxonomical data. Moreover, two potentially novel pyoverdines characterizing one P. tolaasii siderovar and one “P. reactans” siderovar were found.     

Mirrored Prominent Deck B Phenomenon: Frequent Small Losses Override Infrequent Large Gains in the Inverted Iowa Gambling Task

Since Bechara et al. pioneered its development, the Iowa Gambling Task (IGT) has been widely applied to elucidate decision behavior and medial prefrontal function. Although most decision makers can hunch the final benefits of IGT, ventromedial prefrontal lesions generate a myopic choice pattern. Additionally, the Iowa group developed a revised IGT (inverted IGT, iIGT) to confirm the IGT validity. Each iIGT trial was generated from the trial of IGT by multiplying by a “−” to create an inverted monetary value. Thus, bad decks A and B in the IGT become good decks iA and iB in the iIGT; additionally, good decks C and D in the IGT become bad decks iC and iD in the iIGT. Furthermore, IGT possessed mostly the gain trials, and iIGT possessed mainly the loss trials. Therefore, IGT is a frequent-gain–based task, and iIGT is a frequent-loss–based task. However, a growing number of IGT-related studies have identified confounding factors in IGT (i.e., gain-loss frequency), which are demonstrated by the prominent deck B phenomenon (PDB phenomenon). Nevertheless, the mirrored PDB phenomenon and guiding power of gain-loss frequency in iIGT have seldom been reexamined. This experimental finding supports the prediction based on gain-loss frequency. This study identifies the mirrored PDB phenomenon. Frequent small losses override occasional large gains in deck iB of the iIGT. Learning curve analysis generally supports the phenomenon based on gain-loss frequency rather than final outcome. In terms of iIGT and simple versions of iIGT, results of this study demonstrate that high-frequency loss, rather than a satisfactory final outcome, dominates the preference of normal decision makers under uncertainty. Furthermore, normal subjects prefer “no immediate punishment” rather than “final reward” under uncertainty.     

Photosynthesis as a function of short day induction and gibberellic Acid treatment in bougainvillea "san diego red"

Short day induction in Bougainvillea “San Diego Red” increases photosynthetic rates in mature leaves; gibberellic acid treatments, which inhibit flowering, cancel the short day effect. These results lend support of a nutritional hypothesis that suggests that in Bougainvillea assimilate supply to the reproductive axis increases before floral initiation and during flower development.     

Increased Autoimmune Diabetes in pIgR-Deficient NOD Mice Is Due to a "Hitchhiking" Interval that Refines the Genetic Effect of Idd5.4

Selective breeding to introduce a gene mutation from one mouse strain onto the genetic background of another strain invariably produces “hitchhiking” (i.e. flanking) genomic intervals, which may independently affect a disease trait of interest. To investigate a role for the polymeric Ig receptor in autoimmune diabetes, a congenic nonobese diabetic (NOD) mouse strain was generated that harbors a Pigr null allele derived from C57BL/6 (B6) mice. These pIgR-deficient NOD mice exhibited increased serum IgA along with an increased diabetes incidence. However, the Pigr null allele was encompassed by a relatively large “hitchhiking” genomic interval that was derived from B6 mice and overlaps Idd5.4, a susceptibility locus for autoimmune diabetes. Additional congenic NOD mouse strains, harboring smaller B6-derived intervals, confirmed Idd5.4 independently of the other three known susceptibility loci on chromosome 1, and further localized Idd5.4 to an interval proximal to Pigr. Moreover, these congenic NOD mice showed that B6 mice harbor a more diabetogenic allele than NOD mice for this locus. The smallest B6-derived interval encompassing the Pigr null allele may, however, confer a small degree of protection against diabetes, but this protection appears to be dependent on the absence of the diabetogenic B6 allele for Idd5.4. This study provides another example of the potential hidden effects of “hitchhiking" genomic intervals and how such intervals can be used to localize disease susceptibility loci.     

Expression of "Dehydrin-Like" Proteins in Embryos and Seedlings of Zizania palustris and Oryza sativa during Dehydration

Proteins inducible by dehydration and abscisic acid (ABA), termed dehydrins or RAB (Responsive to ABA) proteins, have been identified in a number of species and have been suggested to play a role in desiccation tolerance, particularly during seed development. Seeds (caryopses) of North American wild rice (Zizania palustris var interior [Fassett] Dore) are tolerant of dehydration to <10% moisture content (fresh weight basis) only under restricted dehydration and rehydration conditions. In comparison, seeds of paddy rice (Oryza sativa L.) readily tolerate desiccation to <5% water content. Expression of “dehydrin-like” proteins in Zizania and Oryza seedlings and embryos was examined to investigate the relationship between the presence of such proteins and desiccation tolerance. [³⁵S]Methionine labeling of newly synthesized proteins showed that seedlings (first leaf stage) of both Zizania and Oryza synthesized a novel “heat-stable” protein of apparent molecular weight = 20,000 when dehydrated to <75% of their initial fresh weight. ABA (100 micromolar) induced synthesis of a protein with similar electrophoretic mobility in both species. Western blots using antiserum raised against maize (Zea mays L.) dehydrin detected a protein band from dehydrated Zizania shoots and mature embryonic axes that comigrated with the labeled 20-kilodalton polypeptide. Northern blots using a cDNA for an ABA-responsive protein from Oryza (rab 16a) showed that both seedlings and excised embryonic axes of Zizania accumulated RNA similar in sequence to rab 16a in response to water loss. Zizania seedlings and embryonic axes were also capable of ABA accumulation during dehydration. The intolerance of Zizania seeds to dehydration at low temperature is apparently not due to an absence of dehydrin-like proteins or an inability to accumulate ABA.     

On Spo16 and the Coefficient of Coincidence

spo16 mutants in yeast were reported to have reduced map lengths, a high frequency of nondisjunction in the first meiotic division, and essentially unchanged coefficients of coincidence. Were all crossing over in yeast subject to interference, such data would suggest that the “designation” of recombination events to become crossovers is separable from the “implementation” of that crossing over. In the presence of coexisting interference and noninterference phases of crossing over, however, lack of change in the coefficient of coincidence may show only that spo16 reduces crossing over in the two phases by a similar factor.     

Genome-wide association scan shows genetic variants in the FTO gene are associated with obesity-related traits

The obesity epidemic is responsible for a substantial economic burden in developed countries and is a major risk factor for type 2 diabetes and cardiovascular disease. The disease is the result not only of several environmental risk factors, but also of genetic predisposition. To take advantage of recent advances in gene-mapping technology, we executed a genome-wide association scan to identify genetic variants associated with obesity-related quantitative traits in the genetically isolated population of Sardinia. Initial analysis suggested that several SNPs in the FTO and PFKP genes were associated with increased BMI, hip circumference, and weight. Within the FTO gene, rs9930506 showed the strongest association with BMI (p = 8.6 ×10⁻⁷), hip circumference (p = 3.4 × 10⁻⁸), and weight (p = 9.1 × 10⁻⁷). In Sardinia, homozygotes for the rare “G” allele of this SNP (minor allele frequency = 0.46) were 1.3 BMI units heavier than homozygotes for the common “A” allele. Within the PFKP gene, rs6602024 showed very strong association with BMI (p = 4.9 × 10⁻⁶). Homozygotes for the rare “A” allele of this SNP (minor allele frequency = 0.12) were 1.8 BMI units heavier than homozygotes for the common “G” allele. To replicate our findings, we genotyped these two SNPs in the GenNet study. In European Americans (N = 1,496) and in Hispanic Americans (N = 839), we replicated significant association between rs9930506 in the FTO gene and BMI (p-value for meta-analysis of European American and Hispanic American follow-up samples, p = 0.001), weight (p = 0.001), and hip circumference (p = 0.0005). We did not replicate association between rs6602024 and obesity-related traits in the GenNet sample, although we found that in European Americans, Hispanic Americans, and African Americans, homozygotes for the rare “A” allele were, on average, 1.0–3.0 BMI units heavier than homozygotes for the more common “G” allele. In summary, we have completed a whole genome–association scan for three obesity-related quantitative traits and report that common genetic variants in the FTO gene are associated with substantial changes in BMI, hip circumference, and body weight. These changes could have a significant impact on the risk of obesity-related morbidity in the general population.     

Relationship between the Absorption and Emission Spectra and the "Red Drop" in the Action Spectra of Fluorescence In Vivo

The Stepanov equation, relating the intensity of emission, f_e($\bar{v}$), at a given frequency, and that of absorption, k($\bar{v}$), at the same frequency, is applied, in its modified form (see equation 3 in text) to suspensions of Chlorella, Porphyridium, and Anacystis and to chlorophyll solutions. This application can reveal whether the yield of fluorescence, Φ($\bar{v}$), is constant, or changes with frequency. In Chlorella (green alga) a sharp drop of Φ($\bar{v}$) is indicated towards the lower frequencies (longer waves), beginning around $\bar{v}$ = 1.48 × 10⁴cm^-1 (680 mμ); the Φ($\bar{v}$) function calculated from the Stepanov equation is in fair agreement with the directly determined action spectrum for the excitation of chlorophyll fluorescence in this organism. In Porphyridium (red alga) and Anacystis (blue-green alga) application of the Stepanov equation supports the conclusions, derived from direct measurements, of a much earlier “red drop” of the fluorescence excitation spectra. Direct measurements suggest that the drop in Porphyridium may begin at about 1.53 × 10⁴cm^-1 (654 mμ); in Anacystis, it may begin already above 1.57 × 10⁴cm^-1 (<637mμ). These results confirm the relation, postulated earlier by Duysens and others, between the action spectra of photosynthesis and of chlorophyll a fluorescence in algal cells. The relation of these findings to spectroscopic evidence, suggesting the existence of two main chlorophyll a components in vivo, in green as well as in red and blue-green algae, is discussed.     

The Construction and Use of Log-Odds Substitution Scores for Multiple Sequence Alignment

Most pairwise and multiple sequence alignment programs seek alignments with optimal scores. Central to defining such scores is selecting a set of substitution scores for aligned amino acids or nucleotides. For local pairwise alignment, substitution scores are implicitly of log-odds form. We now extend the log-odds formalism to multiple alignments, using Bayesian methods to construct “BILD” (“Bayesian Integral Log-odds”) substitution scores from prior distributions describing columns of related letters. This approach has been used previously only to define scores for aligning individual sequences to sequence profiles, but it has much broader applicability. We describe how to calculate BILD scores efficiently, and illustrate their uses in Gibbs sampling optimization procedures, gapped alignment, and the construction of hidden Markov model profiles. BILD scores enable automated selection of optimal motif and domain model widths, and can inform the decision of whether to include a sequence in a multiple alignment, and the selection of insertion and deletion locations. Other applications include the classification of related sequences into subfamilies, and the definition of profile-profile alignment scores. Although a fully realized multiple alignment program must rely upon more than substitution scores, many existing multiple alignment programs can be modified to employ BILD scores. We illustrate how simple BILD score based strategies can enhance the recognition of DNA binding domains, including the Api-AP2 domain in Toxoplasma gondii and Plasmodium falciparum.