Sugarcane bagasse ash as fertilizer for soybeans: Effects of added residues on ash composition, mineralogy, phosphorus extractability and plant availability

Sugarcane bagasse is commonly combusted to generate energy. Unfortunately, recycling strategies rarely consider the resulting ash as a potential fertilizer. To evaluate this recycling strategy for a sustainable circular economy, we characterized bagasse ash as a fertilizer and measured the effects of co-gasification and co-combustion of bagasse with either chicken manure or sewage sludge: on the phosphorus (P) mass fraction, P-extractability, and mineral P phases. Furthermore, we investigated the ashes as fertilizer for soybeans under greenhouse conditions. All methods in combination are reliable indicators helping to assess and predict P availability from ashes to soybeans. The fertilizer efficiency of pure bagasse ash increased with the ash amount supplied to the substrate. Nevertheless, it was not as effective as fertilization with triple-superphosphate and K₂SO₄, which we attributed to lower P availability. Co-gasification and co-combustion increased the P mass fraction in all bagasse-based ashes, but its extractability and availability to soybeans increased only when co-processed with chicken manure, because it enabled the formation of readily available Ca-alkali phosphates. Therefore, we recommend co-combusting biomass with alkali-rich residues to increase the availability of P from the ash to plants.

Combining diffusive gradients in thin films (DGT) and spectroscopic techniques for the determination of phosphorus species in soils

A wide range of methods are used to estimate the plant-availability of soil phosphorus (P). Published research has shown that the diffusive gradients in thin films (DGT) technique has a superior correlation to plant-available P in soils compared to standard chemical extraction tests. In order to identify the plant-available soil P species, we combined DGT with infrared and P K- and L_2,3-edge X-ray adsorption near-edge structure (XANES) spectroscopy. This was achieved by spectroscopically investigating the dried binding layer of DGT devices after soil deployment. All three spectroscopic methods were able to distinguish between different kinds of phosphates (poly-, trimeta-, pyro- and orthophosphate) on the DGT binding layer. However, infrared spectroscopy was most sensitive to distinguish between different types of adsorbed inorganic and organic phosphates. Furthermore, intermediates of the time-resolved hydrolysis of trimetaphosphate in soil could be analyzed.

Influence of wood ash pre-treatment on leaching behaviour, liming and fertilising potential

In Denmark, increasing amounts of woody biomass are being used for the production of renewable energy, resulting in more wood ashes being generated. While these materials have been mainly landfilled, wood ashes may also be utilised for fertilizing and liming purposes on top of soils. Pre-treatments involving hardening or granulation may be carried out prior to soil application. In this study, two Danish wood ash samples were hardened and/or granulated. Lab-hardening induced rapid changes in the shape of the acid neutralisation capacity curve of the ashes. Up-flow column tests, assuming local equilibrium conditions, were employed to investigate the leaching from pre-treated ashes. Granules and loose ashes demonstrated similar leaching behaviours, indicating that similar geochemical processes were governing their leaching. In comparison with untreated fresh ashes, the hardened ashes demonstrated reduced leaching of Ca, Ba, Pb and Zn with concentration levels generally below or close to the analytical limits of quantification; to the contrary, the leaching of As, P, Sb, Si, V and Mg was enhanced in the hardened ashes. The release of alkalinity was reduced by hardening. In general, all granules were barely breakable by finger-pinching and they could withstand one month of continuous leaching, preserving their overall shape. The solubility of phosphorous in neutral ammonium citrate indicated that about 30-51% of the total P content in the ash samples was released, suggesting that the ashes could be potentially valuable as P-fertiliser if applied onto soil.

Combined disc pelletisation and thermal treatment of MSWI fly ash

An environmentally friendly and cost efficient way for the management of municipal solid waste incineration (MSWI) fly ash represents its thermal co-treatment together with combustible waste. However, the safe introduction and storage of MSWI fly ash in the waste bunker is challenging and associated with severe problems (e.g. dust emissions, generation of undefined lumps and heat in case of moistened MSWI fly ash). Therefore, the aim of this study is to investigate the suitability of pelletisation as a pretreatment of MSWI fly ash. In particular, MSWI fly ash was characterised after sampling, pelletisation and thermal treatment and the transfer of constituents to secondary fly ash and flue gas was investigated. For this purpose, MSWI fly ash pellets with a water content of about 0.15 kg/kg and a diameter of about 8 mm have been produced by disc pelletiser and treated in an electrically heated pilot-scale rotary kiln at different temperatures, ranging from 450 °C to 1050 °C. The total contents of selected elements in the MSWI fly ash before and after thermal treatment and in the generated secondary fly ash have been analysed in order to understand the fate of each element. Furthermore, leachable contents of selected elements and total content of persistent organic pollutants of the thermally treated MSWI fly ash were determined. Due to the low total content of Hg (0.7 mg/kg) and the low leachate content of Pb (<0.36 mg/kg), even at the lowest treatment temperature of 450 °C, thermally treated MSWI fly ash pellets can be classified as non-hazardous waste. However, temperatures of at least 650 °C are necessary to decrease the toxic equivalency of PCDD/F and DL-PCB. The removal of toxic heavy metals like Cd and Pb is significantly improved at temperatures of 850 °C, 950 °C or even 1050 °C. The observed metal removal led to relatively high contents of e.g. Cu (up to 11,000 mg/kg), Pb (up to 91,000 mg/kg) and Zn (up to 21,000 mg/kg) in the secondary fly ash. This metal enriched secondary fly ash might represent a potential raw material for metal recovery (e.g. via acidic leaching). Due to the high content of total dissolved solids observed in the leachate of thermally treated MSWI fly ash pellets, a wet extraction procedure is suggested to enable its safe disposal at non-hazardous waste landfills.

Chemical state of mercury and selenium in sewage sludge ash based P-fertilizers

Phosphorus-fertilizers from secondary resources such as sewage sludge ash (SSA) will become more important in the future as they could substitute conventional fertilizers based on the nonrenewable resource phosphate rock. Thermochemical approaches were developed which remove heavy metals from SSA prior to its fertilizer application on farmlands. We analyzed the chemical state of mercury and selenium in SSA before and after thermochemical treatment under different conditions for P-fertilizer production by X-ray absorption near edge structure (XANES) spectroscopy. In some incineration plants the mercury loaded carbon adsorber from off-gas cleaning was collected together with the SSA for waste disposal. SSAs from those plants contained mercury mainly bound to carbon/organic material. The other SSAs contained inorganic mercury compounds which are most probably stabilized in the SSA matrix and were thus not evaporated during incineration. During thermochemical treatment, carbon-bound mercury was removed quantitatively. In contrast, a certain immobile fraction of inorganic mercury compounds remained in thermochemically treated SSA, which were not clearly identified. HgSe might be one of the inorganic compounds, which is supported by results of Se K-edge XANES spectroscopy. Furthermore, the chemical state of selenium in the SSAs was very sensitive to the conditions of the thermochemical treatment.

Antimony (Sb) and lead (Pb) in contaminated shooting range soils: Sb and Pb mobility and immobilization by iron based sorbents, a field study

Small-arm shooting ranges often receive a significant input of lead (Pb), copper (Cu) and antimony (Sb) from ammunition. The goal of the present study was to investigate the mobility, distribution and speciation of Pb and Sb pollution under field conditions in both untreated and sorbent-amended shooting range soil. Elevated Sb (19-349μgL(-1)) and Pb (7-1495μgPbL(-1)) concentrations in the porewater of untreated soil over the four-year test period indicated a long-term Sb and Pb source to the adjacent environment in the absence of remedial measures. Mixing ferric oxyhydroxide powder (CFH-12) (2%) together with limestone (1%) into the soil resulted in an average decrease of Sb and Pb porewater concentrations of 66% and 97%, respectively. A similar reduction was achieved by adding 2% zerovalent iron (Fe°) to the soil. The remediation effect was stable over the four-year experimental period indicating no remobilization. Water- and 1M NH4NO3-extractable levels of Sb and Pb in field soil samples indicated significant immobilization by both treatments (89-90% for Sb and 89-99% for Pb). Results from sequential extraction analysis indicate fixation of Sb and Pb in less accessible fractions like amorphous iron oxides or even more crystalline and residual mineral phases, respectively. This work shows that amendment with Fe-based sorbents can be an effective method to reduce the mobility of metals both in cationic and anionic form in polluted shooting range soil.

Sewage sludge ash--A promising secondary phosphorus source for fertilizer production

Sewage sludge incineration is extensively practiced in some European countries such as the Netherlands, Switzerland, Austria and Germany. A survey of German sewage sludge ash showed that the recovery potential is high, approx. 19,000 t of phosphorus per year. However, the survey also discovered that the bioavailability of phosphorus in the sewage sludge ash is poor and that more than half of the ashes cannot be used as fertilizers due to high heavy metal content. A new thermochemical process for sewage sludge ash treatment was developed that transforms the ash into marketable fertilizer products. Sewage sludge ash was thermochemically treated with sodium and potassium additives under reducing conditions, whereby the phosphate-bearing mineral phases were transformed into plant available phosphates. High P-bioavailability was achieved with a molar Na/P ratio >1.75 in the starting materials. Sodium sulfate, carbonate and hydroxide performed comparably as additives for this calcination process. Potassium carbonate and -hydroxide have to be added in a molar K/P ratio >2.5 to achieve comparable P-solubility. The findings of the laboratory scale investigations were confirmed by an industrial demonstration trial for an ash treatment with sodium sulfate. Simultaneously, the volatile transition metal arsenic (61% removal) as well as volatile heavy metals such as cadmium (80%), mercury (68%), lead (39%) and zinc (9%) were removed via the off-gas treatment system. The product of the demonstration trial is characterized by high bioavailability and a toxic trace element mass fraction below the limit values of the German fertilizer ordinance, thus fulfilling the quality parameters for a P-fertilizer.

Genetic redundancy strengthens the circadian clock leading to a narrow entrainment range

Circadian clocks are internal timekeepers present in almost all organisms. Driven by a genetic network of highly conserved structure, they generate self-sustained oscillations that entrain to periodic external signals such as the 24 h light-dark cycle. Vertebrates possess multiple, functionally overlapping homologues of the core clock genes. Furthermore, vertebrate clocks entrain to a range of periods three times as narrow as that of other organisms. We asked whether genetic redundancies play a role in governing entrainment properties and analysed locomotor activity rhythms of genetically modified mice lacking one set of clock homologues. Exposing them to non-24 h light-dark cycles, we found that the mutant mice have a wider entrainment range than the wild types. Spectral analysis furthermore revealed nonlinear phenomena of periodically forced self-sustained oscillators for which the entrainment range relates inversely to oscillator amplitude. Using the forced oscillator model to explain the observed differences in entrainment range between mutant and wild-type mice, we sought to quantify the overall oscillator amplitude of their clocks from the activity rhythms and found that mutant mice have weaker circadian clocks than wild types. Our results suggest that genetic redundancy strengthens the circadian clock leading to a narrow entrainment range in vertebrates.

Mathematical modeling in chronobiology

Circadian clocks are autonomous oscillators entrained by external Zeitgebers such as light-dark and temperature cycles. On the cellular level, rhythms are generated by negative transcriptional feedback loops. In mammals, the suprachiasmatic nucleus (SCN) in the anterior part of the hypothalamus plays the role of the central circadian pacemaker. Coupling between individual neurons in the SCN leads to precise self-sustained oscillations even in the absence of external signals. These neuronal rhythms orchestrate the phasing of circadian oscillations in peripheral organs. Altogether, the mammalian circadian system can be regarded as a network of coupled oscillators. In order to understand the dynamic complexity of these rhythms, mathematical models successfully complement experimental investigations. Here we discuss basic ideas of modeling on three different levels (1) rhythm generation in single cells by delayed negative feedbacks, (2) synchronization of cells via external stimuli or cell-cell coupling, and (3) optimization of chronotherapy.

Circadian transcription in liver

Circadian rhythms regulate a wide range of cellular, physiological, metabolic and behavioral activities in mammals. The complexity of tissue- and day-time specific regulation of thousands of clock controlled genes (CCGs) suggests that many transcriptional regulators are involved. Our bioinformatic analysis is based on two published DNA-array studies from mouse liver. We search overrepresented transcription factor binding sites in promoter regions of CCGs using GC-matched controls. Analyzing a large set of CCG promoters, we find known motifs such as E-boxes, D-boxes and cAMP responsive elements. In addition, we find overrepresented GC-rich motifs (Sp1, ETF, Nrf1), AT-rich motifs (TBP, Fox04, MEF-2), Y-box motifs (NF-Y, C/EBP) and cell cycle regulators (E2F, Elk-1). In a subset of system-driven genes, we find overrepresented motifs of the serum response factor SRF and the estrogen receptor ER. The analysis of published ChIP data reveals that some of our predicted regulators (C/EBP, E2F, HNF-1, Myc, MEF-2) target relatively many clock controlled genes. Our analysis of CCG promoters contributes to an understanding of the complex transcriptional regulation of circadian rhythms in liver.

SysBioMed report: advancing systems biology for medical applications

The following report selects and summarises some of the conclusions and recommendations generated throughout a series of workshops and discussions that have lead to the publication of the Science Policy Briefing (SPB) Nr. 35, published by the European Science Foundation. (Large parts of the present text are directly based on the ESF SPB. Detailed recommendations with regard to specific application areas are not given here but can be found in the SPB. Issues related to mathematical modelling, including training and the need for an infrastructure supporting modelling are discussed in greater detail in the present text.)The numerous reports and publications about the advances within the rapidly growing field of systems biology have led to a plethora of alternative definitions for key concepts. Here, with 'mathematical modelling' the authors refer to the modelling and simulation of subcellular, cellular and macro-scale phenomena, using primarily methods from dynamical systems theory. The aim of such models is encoding and testing hypotheses about mechanisms underlying the functioning of cells. Typical examples are models for molecular networks, where the behaviour of cells is expressed in terms of quantitative changes in the levels of transcripts and gene products. Bioinformatics provides essential complementary tools, including procedures for pattern recognition, machine learning, statistical modelling (testing for differences, searching for associations and correlations) and secondary data extracted from databases.Dynamical systems theory is the natural language to investigate complex biological systems demonstrating nonlinear spatio-temporal behaviour. However, the generation of experimental data suitable to parameterise, calibrate and validate such models is often time consuming and expensive or not even possible with the technology available today. In our report, we use the term 'computational model' when mathematical models are complemented with information generated from bioinformatics resources. Hence, 'the model' is, in reality, an integrated collection of data and models from various (possibly heterogeneous) sources. The present report focuses on a selection of topics, which were identified as appropriate case studies for medical systems biology, and adopts a particular perspective which the authors consider important. We strongly believe that mathematical modelling represents a natural language with which to integrate data at various levels and, in doing so, to provide insight into complex diseases: 1. Modelling necessitates the statement of explicit hypotheses, a process which often enhances comprehension of the biological system and can uncover critical points where understanding is lacking. 2. Simulations can reveal hidden patterns and/or counter-intuitive mechanisms in complex systems. 3. Theoretical thinking and mathematical modelling constitute powerful tools to integrate and make sense of the biological and clinical information being generated and, more importantly, to generate new hypotheses that can then be tested in the laboratory.Medical Systems Biology projects carried out recently across Europe have revealed a need for action: 4. While the need for mathematical modelling and interdisciplinary collaborations is becoming widely recognised in the biological sciences, with substantial implications for the training and research funding mechanisms within this area, the medical sciences have yet to follow this lead. 5. To achieve major breakthroughs in Medical Systems Biology, existing academic funding schemes for large-scale projects need to be reconsidered. 6. The hesitant stance of the pharmaceutical industry towards major investment in systems biology research has to be addressed. 7. Leading medical journals should be encouraged to promote mathematical modelling.

Phase response curves elucidating the dynamics of coupled oscillators

Phase response curves (PRCs) are widely used in circadian clocks, neuroscience, and heart physiology. They quantify the response of an oscillator to pulse-like perturbations. Phase response curves provide valuable information on the properties of oscillators and their synchronization. This chapter discusses biological self-sustained oscillators (circadian clock, physiological rhythms, etc.) in the context of nonlinear dynamics theory. Coupled oscillators can synchronize with different frequency ratios, can generate toroidal dynamics (superposition of independent frequencies), and may lead to deterministic chaos. These nonlinear phenomena can be analyzed with the aid of a phase transition curve, which is intimately related to the phase response curve. For illustration purposes, this chapter discusses a model of circadian oscillations based on a delayed negative feedback. In a second part, the chapter provides a step-by-step recipe to measure phase response curves. It discusses specifications of this recipe for circadian rhythms, heart rhythms, neuronal spikes, central pattern generators, and insect communication. Finally, it stresses the predictive power of measured phase response curves. PRCs can be used to quantify the coupling strength of oscillations, to classify oscillator types, and to predict the complex dynamics of periodically driven oscillations.

Is there a bias in proteome research?

Advances in technology have enabled us to take a fresh look at data acquired by traditional single experiments and to compare them with genomewide data. The differences can be tremendous, as we show here, in the field of proteomics. We have compared data sets of protein-protein interactions in Saccharomyces cerevisiae that were detected by an identical underlying technical method, the yeast two-hybrid system. We found that the individually identified protein-protein interactions are considerably different from those identified by two genomewide scans. Interacting proteins in the pooled database from single publications are much more closely related to each other with respect to transcription profiles when compared to genomewide data. This difference may have been introduced by two factors: by a selection process in individual publications and by false positives in the whole-genome scans. If we assume that the differences are a result of false positives in the whole-genome data, the scans would contain 47%, 44%, and 91% of false positives for the UETZ, ITO-core, and ITO-full data, respectively. If, however, the true fraction of false positives is considerably lower than estimated here, the data from hypothesis-driven experiments must have been subjected to a serious selection process.

Spatio-temporal analysis of irregular vocal fold oscillations: biphonation due to desynchronization of spatial modes

This report is on direct observation and modal analysis of irregular spatio-temporal vibration patterns of vocal fold pathologies in vivo. The observed oscillation patterns are described quantitatively with multiline kymograms, spectral analysis, and spatio-temporal plots. The complex spatio-temporal vibration patterns are decomposed by empirical orthogonal functions into independent vibratory modes. It is shown quantitatively that biphonation can be induced either by left-right asymmetry or by desynchronized anterior-posterior vibratory modes, and the term "AP (anterior-posterior) biphonation" is introduced. The presented phonation examples show that for normal phonation the first two modes sufficiently explain the glottal dynamics. The spatio-temporal oscillation pattern associated with biphonation due to left-right asymmetry can be explained by the first three modes. Higher-order modes are required to describe the pattern for biphonation induced by anterior-posterior vibrations. Spatial irregularity is quantified by an entropy measure, which is significantly higher for irregular phonation than for normal phonation. Two asymmetry measures are introduced: the left-right asymmetry and the anterior-posterior asymmetry, as the ratios of the fundamental frequencies of left and right vocal fold and of anterior-posterior modes, respectively. These quantities clearly differentiate between left-right biphonation and anterior-posterior biphonation. This paper proposes methods to analyze quantitatively irregular vocal fold contour patterns in vivo and complements previous findings of desynchronization of vibration modes in computer modes and in in vitro experiments.

Combining frequency and positional information to predict transcription factor binding sites

MOTIVATION

Even though a number of genome projects have been finished on the sequence level, still only a small proportion of DNA regulatory elements have been identified. Growing amounts of gene expression data provide the possibility of finding coregulated genes by clustering methods. By analysis of the promoter regions of those genes, rather weak signals of transcription factor binding sites may be detected.

RESULTS

We introduce the new algorithm ITB, an Integrated Tool for Box finding, which combines frequency and positional information to predict transcription factor binding sites in upstream regions of coregulated genes. Motifs are extracted by exhaustive analysis of regular expression-like patterns and by estimating probabilities of positional clusters of motifs. ITB detects consensus sequences of experimentally verified transcription factor binding sites of the yeast Saccharomyces cerevisiae. Moreover, a number of new binding site candidates with significant scores are predicted. Besides applying ITB on yeast upstream regions, the program is run on human promoter sequences.

AVAILABILITY

ITB is available upon request.

The harmonic-to-noise ratio applied to dog barks

Dog barks are typically a mixture of regular components and irregular (noisy) components. The regular part of the signal is given by a series of harmonics and is most probably due to regular vibrations of the vocal folds, whereas noise refers to any nonharmonic (irregular) energy in the spectrum of the bark signal. The noise components might be due to chaotic vibrations of the vocal-fold tissue or due to turbulence of the air. The ratio of harmonic to nonharmonic energy in dog barks is quantified by applying the harmonics-to-noise ratio (HNR). Barks of a single dog breed were recorded in the same behavioral context. Two groups of dogs were considered: a group of ten healthy dogs (the normal sample), and a group of ten unhealthy dogs, i.e., dogs treated in a veterinary clinic (the clinic sample). Although the unhealthy dogs had no voice disease, differences in emotion or pain or impacts of surgery might have influenced their barks. The barks of the dogs were recorded for a period of 6 months. The HNR computation is based on the Fourier spectrum of a 50-ms section from the middle of the bark. A 10-point moving average curve of the spectrum on a logarithmic scale is considered as estimator of the noise level in the bark, and the maximum difference of the original spectrum and the moving average is defined as the HNR measure. It is shown that a reasonable ranking of the voices is achievable based on the measurement of the HNR. The HNR-based classification is found to be consistent with perceptual evaluation of the barks. In addition, a multiparametric approach confirms the classification based on the HNR. Hence, it may be concluded that the HNR might be useful as a novel parameter in bioacoustics for quantifying the noise within a signal.

Statistical analysis of the DNA sequence of human chromosome 22

We study statistical patterns in the DNA sequence of human chromosome 22, the first completely sequenced human chromosome. We find that (i). the 33.4 x 10(6) nucleotide long human chromosome exhibits long-range power-law correlations over more than four orders of magnitude, (ii). the entropies H(n) of the frequency distribution of oligonucleotides of length n (n-mers) grow sublinearly with increasing n, indicating the presence of higher-order correlations for all of the studied lengths 1<or=n<or=10, and (iii). the generalized entropies H(n)(q) of n-mers decrease monotonically with increasing q and the decay of H(n)(q) with q becomes steeper with increasing n<or=10, indicating that the frequency distribution of oligonucleotides becomes increasingly nonuniform as the length n increases. We investigate to what degree known biological features may explain the observed statistical patterns. We find that (iv). the presence of interspersed repeats may cause the sublinear increase of H(n) with n, and that (v). the presence of monomeric tandem repeats as well as the suppression of CG dinucleotides may cause the observed decay of H(n)(q) with q.

Irregular vocal-fold vibration--high-speed observation and modeling

Direct observations of nonstationary asymmetric vocal-fold oscillations are reported. Complex time series of the left and the right vocal-fold vibrations are extracted from digital high-speed image sequences separately. The dynamics of the corresponding high-speed glottograms reveals transitions between low-dimensional attractors such as subharmonic and quasiperiodic oscillations. The spectral components of either oscillation are given by positive linear combinations of two fundamental frequencies. Their ratio is determined from the high-speed sequences and is used as a parameter of laryngeal asymmetry in model calculations. The parameters of a simplified asymmetric two-mass model of the larynx are preset by using experimental data. Its bifurcation structure is explored in order to fit simulations to the observed time series. Appropriate parameter settings allow the reproduction of time series and differentiated amplitude contours with quantitative agreement. In particular, several phase-locked episodes ranging from 4:5 to 2:3 rhythms are generated realistically with the model.

Optimization of coding potentials using positional dependence of nucleotide frequencies

We study the coding potential of human DNA sequences, using the positional asymmetry function (D(p)) and the positional information function (I(q)). Both D(p)and I(q)are based on the positional dependence of single nucleotide frequencies. We investigate the accuracy of D(p)and I(q)in distinguishing coding and non-coding DNA as a function of the parameters p and q, respectively, and explore at which parameters p(opt)and q(opt)both D(p)and I(q)distinguish coding and non-coding DNA most accurately. We compare our findings with classically used parameter values and find that optimized coding potentials yield comparable accuracies as classical frame-independent coding potentials trained on prior data. We find that p(opt)and q(opt)vary only slightly with the sequence length.

Information content of protein sequences

The complexity of large sets of non-redundant protein sequences is measured. This is done by estimating the Shannon entropy as well as applying compression algorithms to estimate the algorithmic complexity. The estimators are also applied to randomly generated surrogates of the protein data. Our results show that proteins are fairly close to random sequences. The entropy reduction due to correlations is only about 1%. However, precise estimations of the entropy of the source are not possible due to finite sample effects. Compression algorithms also indicate that the redundancy is in the order of 1%. These results confirm the idea that protein sequences can be regarded as slightly edited random strings. We discuss secondary structure and low-complexity regions as causes of the redundancy observed. The findings are related to numerical and biochemical experiments with random polypeptides.

Nonlinear phenomena in the natural howling of a dog-wolf mix

It was reported to the first author that a female dog-wolf mix showed anomalously rough-sounding vocalization. Spectral analysis of recordings of the vocalization revealed frequency occurrences of subharmonics, biphonation (two independent pitches) and chaos. Since these nonlinear phenomena are currently widely discussed as integral to mammalian vocalization [Wilden et al., Bioacoustics 9, 171-196 (1988)] or as indicators of vocal pathologies [Herzel et al., J. Speech Hearing Res. 37, 1008-1019 (1994); Riede et al., Z. Sgtkde 62 Suppl: 198-203 (1997)], we sought to understand the production mechanism of the observed vocal instabilities. First the frequency of nonlinear phenomena in the calls was determined for the female and four additional individuals. It turned out that these phenomena appear, but much less frequently in the repertoire of the four other animals. The larynges of the female and two other individuals were dissected post mortem. There was no apparent asymmetry of the vocal folds but a slight asymmetry of the arytenoid cartilages. The most pronounced difference, however, was an upward extension of both vocal folds of the female. This feature is reminiscent of "vocal lips" (syn. "vocal membranes") in some primates and bats. Spectral analysis of the female's voice showed clear similarities with an intensively studied voice of a human who produces biphonation intentionally. Finally, the possible communicative relevance of nonlinear phenomena is discussed.

Are noncoding sequences of Rickettsia prowazekii remnants of "neutralized" genes?

It has been hypothesized that a large fraction of 24% noncoding DNA in R. prowazekii consists of degraded genes. This hypothesis has been based on the relatively high G+C content of noncoding DNA. However, a comparison with other genomes also having a low overall G+C content shows that this argument would also apply to other bacteria. To test this hypothesis, we study the coding potential in sets of genes, pseudogenes, and intergenic regions. We find that the correlation function and the chi(2)-measure are clearly indicative of the coding function of genes and pseudogenes. However, both coding potentials make almost no indication of a preexisting reading frame in the remaining 23% of noncoding DNA. We simulate the degradation of genes due to single-nucleotide substitutions and insertions/deletions and quantify the number of mutations required to remove indications of the reading frame. We discuss a reduced selection pressure as another possible origin of this comparatively large fraction of noncoding sequences.

Average mutual information of coding and noncoding DNA

One basic problem in the analysis of DNA sequences is the recognition of protein-coding genes. Computer algorithms to facilitate gene identification have become important as genome sequencing projects have turned from mapping to large-scale sequencing, resulting in an exponentially growing number of sequenced nucleotides that await their annotation. Many statistical patterns have been discovered that are different in coding and noncoding DNA, but most of them vary from species to species, and hence require prior training on organism-specific data sets. Here, we investigate if there exist species-independent statistical patterns that are different in coding and noncoding DNA. We introduce an information-theoretic quantity, the average mutual information (AMI), and we find that the probability distribution functions of the AMI are significantly different in coding and noncoding DNA, while they are almost identical for different species. This finding suggests that the AMI might be useful for the recognition of protein-coding regions in genomes for which training sets do not exist.

Normalization strategies for cDNA microarrays

Multiple Arabidopsis thaliana clones from an experimental series of cDNA microarrays are evaluated in order to identify essential sources of noise in the spotting and hybridization process. Theoretical and experimental strategies for an improved quantitative evaluation of cDNA microarrays are proposed and tested on a series of differently diluted control clones. Several sources of noise are identified from the data. Systematic and stochastic fluctuations in the spotting process are reduced by control spots and statistical techniques. The reliability of slide to slide comparison is critically assessed within the statistical framework of pattern matching and classification.

Species independence of mutual information in coding and noncoding DNA

We explore if there exist universal statistical patterns that are different in coding and noncoding DNA and can be found in all living organisms, regardless of their phylogenetic origin. We find that (i) the mutual information function [symbol: see text] has a significantly different functional form in coding and noncoding DNA. We further find that (ii) the probability distributions of the average mutual information [symbol: see text] are significantly different in coding and noncoding DNA, while (iii) they are almost the same for organisms of all taxonomic classes. Surprisingly, we find that [symbol: see text] is capable of predicting coding regions as accurately as organism-specific coding measures.

10-11 bp periodicities in complete genomes reflect protein structure and DNA folding

MOTIVATION

Completely sequenced genomes allow for detection and analysis of the relatively weak periodicities of 10-11 basepairs (bp). Two sources contribute to such signals: correlations in the corresponding protein sequences due to the amphipatic character of alpha-helices and the folding of DNA (nucleosomal patterns, DNA supercoiling). Since the topological state of genomic DNA is of importance for its replication, recombination and transcription, there is an immediate interest to obtain information about the supercoiled state from sequence periodicities.

RESULTS

We show that correlations within proteins affect mainly the oscillations at distances below 35 bp. The long-ranging correlations up to 100 bp reflect primarily DNA folding. For the yeast genome these oscillations are consistent in detail with the chromatin structure. For eubacteria and archaea the periods deviate significantly from the 10.55 bp value for free DNA. These deviations suggest that while a period of 11 bp in bacteria reflects negative supercoiling, the significantly different period of thermophilic archaea close to 10 bp corresponds to positive supercoiling of thermophilic archaeal genomes.

AVAILABILITY

Protein sets and C programs for the calculation of correlation functions are available on request from the authors (see http://itb.biologie.hu-berlin.de).

Modeling the role of nonhuman vocal membranes in phonation

Although the mammalian larynx exhibits little structural variation compared to sound-producing organs in other taxa (birds or insects), there are some morphological features which could lead to significant differences in acoustic functioning, such as air sacs and vocal membranes. The vocal membrane (or "vocal lip") is a thin upward extension of the vocal fold that is present in many bat and primate species. The vocal membrane was modeled as an additional geometrical element in a two-mass model of the larynx. It was found that vocal membranes of an optimal angle and length can substantially lower the subglottal pressure at which phonation is supported, thus increasing vocal efficiency, and that this effect is most pronounced at high frequencies. The implications of this finding are discussed for animals such as bats and primates which are able to produce loud, high-pitched calls. Modeling efforts such as this provide guidance for future empirical investigations of vocal membrane structure and function, can provide insight into the mechanisms of animal communication, and could potentially lead to better understanding of human clinical disorders such as sulcus vocalis.

Sequence periodicity in complete genomes of archaea suggests positive supercoiling

The topological state of genomic DNA is of importance for its replication, recombination and transcription. The wrapping of the DNA around nucleosomes is associated with sequence periodicities (Trifonov and Sussman, Proc. Natl. Acad. Sci. USA, 77, pp. 3816-20). Recently, also the negative supercoiling of eubacterial DNA was related to 11 base pair (bp) periodicity (Herzel et al. Physica A, 249, pp. 449-59). Archaeal plasmids and a virus-like particle from Sulfolobus are positively supercoiled, but the superhelical conformation of archaeal genomic DNA is still uncertain. The problem of superhelicity can now be addressed via a comparative statistical analysis of the available complete genomes. For this purpose one has to look for periodicities which are in phase with the helical repeat of 10-11 bp. Similar periodicities are induced, however, by the amphipatic character of alpha-helices of encoded proteins (Zhurkin, Nucl. Acids Res., 9, pp. 1963-71). We show that these protein-induced periodicities are extended over a few periods only. The periods of additional long-ranging oscillations deviate significantly from the value for free DNA. A period of 11 bp in Eubacteria reflects negative supercoiling, whereas the significantly different period of thermophilic Archaea close to 10 bp suggests positive supercoiling of archaeal genomes.

Phonation onset: vocal fold modeling and high-speed glottography

Phonation onset is discussed in the framework of dynamical systems as a Hopf bifurcation, i.e., as a transition from damped to sustained vocal fold oscillations due to changes of parameters defining the underlying laryngeal configuration (e.g., adduction, subglottal pressure, muscular activity). An analytic envelope curve of the oscillation onset is deduced by analyzing the Hopf bifurcation in mathematical models of the vocal folds. It is governed by a single time constant which can be identified with the physiological parameter phonation onset time. This parameter reflects the laryngeal state prior to phonation and can be used as a quantitative classification criterion in order to assess the phonation onset in clinical diagnosis. The extraction of the phonation onset time from simulated time series using a simplified two-mass model and from digital high-speed videos is described in detail. It shows a good agreement between theory and measurement.

Correlations in protein sequences and property codes

Correlation functions in large sets of non-homologous protein sequences are analysed. Finite size corrections are applied and fluctuations are estimated. As symbol sequences have to be mapped to sequences of numbers to calculate correlation functions, several property codes are tested as such mappings. We found hydrophobicity autocorrelation functions to be strongly oscillating. Another strong signal is the monotonously decaying alpha-helix propensity autocorrelation function. Furthermore, we detected signals corresponding to an alteration of positively and negatively charged residues at a distance of 3-4 amino acids. To look beyond the property codes gained by the methods of physical chemistry, mappings yielding a strong correlation signal are sought for using a Monte Carlo simulation. The mappings leading to strong signals are found to be related to hydrophobicity of alpha-helix propensity. A cluster analysis of the top scoring mappings leads to two novel property codes. These two property codes are gained from sequence data only. They turn out to be similar to known property codes for hydrophobicity or polarity.

Estimating the entropy of DNA sequences

The Shannon entropy is a standard measure for the order state of symbol sequences, such as, for example, DNA sequences. In order to incorporate correlations between symbols, the entropy of n-mers (consecutive strands of n symbols) has to be determined. Here, an assay is presented to estimate such higher order entropies (block entropies) for DNA sequences when the actual number of observations is small compared with the number of possible outcomes. The n-mer probability distribution underlying the dynamical process is reconstructed using elementary statistical principles: The theorem of asymptotic equi-distribution and the Maximum Entropy Principle. Constraints are set to force the constructed distributions to adopt features which are characteristic for the real probability distribution. From the many solutions compatible with these constraints the one with the highest entropy is the most likely one according to the Maximum Entropy Principle. An algorithm performing this procedure is expounded. It is tested by applying it to various DNA model sequences whose exact entropies are known. Finally, results for a real DNA sequence, the complete genome of the Epstein Barr virus, are presented and compared with those of other information carriers (texts, computer source code, music). It seems as if DNA sequences possess much more freedom in the combination of the symbols of their alphabet than written language or computer source codes.

Whistle register and biphonation in a child's voice

This paper deals with high-pitched vocalizations of a normal healthy child. In the transition region between whistle register and falsetto frequency jumps and coexisting pitches ('biphonation') are observed. The recorded signals are compared to simulations of an asymmetric two-mass model of vocal fold vibrations. As a possible mechanism of the whistle register vortex-induced vibrations are discussed.

Phase dependencies of the human baroreceptor reflex

We studied the influence of respiratory and cardiac phase on responses of the cardiac pacemaker to brief (0.35-s) increases of carotid baroreceptor afferent traffic provoked by neck suction in seven healthy young adult subjects. Cardiac responses to neck suction were measured indirectly from electrocardiographic changes of heart period. Our results show that it is possible to separate the influences of respiratory and cardiac phases at the onset of a neck suction impulse by a product of two factors: one depending only on the respiratory phase and one depending only on the cardiac phase. This result is consistent with the hypothesis that efferent vagal activity is a function of afferent baroreceptor activity, whereas respiratory neurons modulate that medullary throughput independent of the cardiac phase. Furthermore, we have shown that stimulus broadening and stimulus cropping influence the outcome of neck suction experiments in a way that makes it virtually impossible to obtain information on the phase dependency of the cardiac pacemaker's sensitivity to vagal stimulation without accurate knowledge of the functional shape of stimulus broadening.

[Endoscopic imaging of vocal cord vibrations. Digital high speed recording with various systems]

Vocal fold vibration patterns during phonation are presented with different digital imaging systems. With newly developed technical equipment color images up to 1000 digital images/s were obtained without light intensifying enhancement techniques via rigid and flexible endoscopy. With this color high-speed system, morphologic structures, such as small blood vessels, were visualized in high-resolution quality as a result of additional color information. In another system, zooming of endoscopic pictures via pixel interpolation algorithms provided full-monitor presentation of vocal fold vibratory patterns. This system allows PC-based synchronization with microphone and electroglottographic signals in a frame-by-frame technique. Although only processing gray scale images, analyses of dynamic changes in modes of vibration were facilitated by the higher frame rate recording of up to 2000 frames/s and, in addition, they display corresponding analog signals. Both methods provide clinically important information. Furthermore, we demonstrated irregular vocal fold vibration patterns in a healthy adult volunteer. In this experiment, the irregular vibratory modes were induced by voluntarily applying asymmetric vocal fold tension. The asymmetric vocal fold vibration pattern resulted in (functionally induced) roughness of the voice as predicted by computer models of asymmetric vocal fold vibration. Digital high-speed cinematography proved to be a highly promising technique in the analysis of dysphonia and provided physiological examples that could be compared with models of coupled nonlinear oscillators.

Bifurcations in excised larynx experiments

Bifurcation analysis was applied to vocal fold vibration in excised larynx experiments. Phonation onset and vocal instabilities were studied in a parameter plane spanned by subglottal pressure and asymmetry of either vocal fold adduction or elongation. Various phonatory regimes were observed, including single vocal fold oscillations. Selected spectra demonstrated correspondence between these regimes and vocal registers noted in the literature. To illustrate the regions spanned by the various phonatory regimes, two-dimensional bifurcation diagrams were generated. Many instabilities or bifurcations were noted in the regions of coexistence, i.e., regions in which the phonatory regimes overlap. Bifurcations were illustrated with spectrograms and fundamental frequency contours. Where possible, results from these studies were related to clinical observations.

The modular structure of informational sequences

It is shown that DNA sequences can be decomposed into smaller units much the same as texts can be decomposed into syllables, words, or groups of words. Those smaller units (modules) are extracted from DNA sequences according to statistical criteria. Tests with sequences of known modular structure (two novels and a FORTRAN source code) were performed. The rate to which DNA sequences can be decomposed into modules (modularity) turns out to be a very sensitive measure to distinguish DNA sequences from random sequences.

Bifurcations in an asymmetric vocal-fold model

A two-mass model of vocal-fold vibrations is analyzed with methods from nonlinear dynamics. Bifurcations are located in parameter planes of physiological interest (subglottal pressure, stiffness of the folds). It is shown that a sufficiently large tension imbalance of the left and right vocal fold induces bifurcations to subharmonic regimes, toroidal oscillations, and chaos. The corresponding attractors are characterized by phase portraits, spectra, and next-maximum maps. The relevance of these simulations for voice disorders such as laryngeal paralysis is discussed.

Analysis of vocal disorders with methods from nonlinear dynamics

Several authors have recently demonstrated the intimate relationship between nonlinear dynamics and observations in vocal fold vibration (Herzel, 1993; Mende, Herzel, & Wermke, 1990; Titze, Baken, & Herzel, 1993). The aim of this paper is to analyze vocal disorders from a nonlinear dynamics point of view. Basic concepts and analysis techniques from nonlinear dynamics are reviewed and related to voice. The voices of several patients with vocal disorders are analyzed using traditional voice analysis techniques and methods from nonlinear dynamics. The two methods are shown to complement each other in many ways. Likely physiological mechanisms of the observed nonlinear phenomena are presented, and it is shown how much of the terminology in the literature describing rough voice can be unified within the framework of nonlinear dynamics.