Swiftly Computing Center Strings

Background  

The center string (or closest string) problem is a classic computer science problem with important applications in computational biology. Given k input strings and a distance threshold d, we search for a string within Hamming distance at most d to each input string. This problem is NP complete.     

Correlation and Linear Regression if the Random Variables are Subject to Errors or Fluctuations

For the model x=a+e, y=b+d estimators of Pearson's coefficient of correlation and of the line of regression between a and b are presented. The problem of prediction is dealt with.     

<Emphasis Type="SmallCaps">d</Emphasis>-amino acids for the enhancement of a binary biocide cocktail consisting of THPS and EDDS against an SRB biofilm

Biofilms of sulfate reducing bacteria (SRB) are often responsible for Microbiologically Influenced Corrosion (MIC) that is a major problem in the oil and gas industry as well as water utilities and other industries. This work was inspired by recent reports that some d-amino acids may be useful in the control of microbial biofilms. A d-amino acid mixture with equimolar d-tyrosine, d-methionine, d-tryptophan and d-leucine was tested in this work for their enhancement of a biocide cocktail containing tetrakis (hydroxymethyl) phosphonium sulfate (THPS) and ethylenediamine-N,N’-disuccinic acid (EDDS). Desulfovibrio vulgaris (ATCC 7757) was cultured in ATCC 1249 medium. Its biofilm was grown on C1018 carbon steel coupons. Experimental results indicated that the triple biocide cocktail consisting of 30 ppm THPS, 500 ppm EDDS and 6.6 ppm d-amino acid mixture (with equimolar d-tyrosine, d-methionine, d-tryptophan and d-leucine) was far more effective than THPS and EDDS alone and their binary combination. The triple biocide cocktail effectively prevented SRB biofilm establishment and removed the established SRB biofilm. The d-amino acid mixture alone did not show significant effects in the two tasks even at 660 ppm.     

7-Amino-actinomycin D complexes with deoxynucleotides as models for the binding of the drug to DNA

Fluorescence, CD, absorption, and ¹H-nmr studies are reported for complexes of 7-amino-actinomycin D with deoxydinucleotides, deoxytetranucleotides, and poly(dG-dC)· poly(dG-dC). The optical spectra for the 7-amino-actinomycin D complex with pdG-dC, pdG-dC-dG-dC and pdC-dG-dC-dG are similar in shape to the 7-amino-actinomycin D complex with either DNA or poly(dG-dC). The changes in the ¹H chemical shifts of the 7-amino-actinomycin D and the pdG-dC resonances that accompany complex formation show that 7-amino-actinomycin D forms a minature intercalated complex with two pdG-dC molecules. The magnitudes of the induced chemical shifts for the 7-amino-actinomycin D complex formation with pdG-dC are similar to, but slightly different from, the induced chemical shifts which are obtained when actinomycin D forms a minature intercalated complex with two pdG-dC molecules. The pdN-dG dinucleotides (N = C, A, or T) form stacked complexes with 7-amino-actinomycin D. The presence of the 7-amino-group results in a larger dimerization constant (in aqueous solution) for 7-amino-actinomycin D [K_D(6°C) = 4.4 × 10³M^?1], as compared to actinomycin D [K_D(6°C) = 1.7 × 10³M^?1]; the chemical shifts which accompany dimer formation indicate that the chromophores stack in an inverted manner. Intercalation of 7-amino-actinomycin D into minature double helices, as well as into calf thymus DNA, poly(dG-dC)·poly(dG-dC), and poly(dA-dC)·poly(dG-dT), results in an enhancement of the relative fluorescence intensity and a shift in both the absorbance and corrected emission spectra.     

Linear function neurons: Structure and training

Three different representations for a thresholded linear equation are developed. For binary input they are shown to be representationally equivalent though their training characteristics differ.A training algorithm for linear equations is discussed. The similarities between its simplest mathematical representation (perceptron training), a formal model of animal learning (Rescorla-Wagner learning), and one mechanism of neural learning (Aplysia gill withdrawal) are pointed out. For d input features, perceptron training is shown to have a lower bound of 2 ^d and an upper bound of d ^d adjusts. It is possible that the true upper bound is 4 ^d , though this has not been proved. Average performance is shown to have a lower bound of 1.4 ^d . Learning time is shown to increase linearly with the number of irrelevant or replicated features. The (X of N) function (a subset of linearly separable functions containing OR and AND) is shown to be learnable in d ³ time.A method of utilizing conditional probability to accelerate learning is proposed. This reduces the observed growth rate from 4 ^d to the theoretical minimum (for the unmodified version) of 2 ^d . A different version reduces the growth rate to about 1.7 ^d . The linear effect of irrelevant features can also be eliminated. Whether such an approach can be made provably convergent is not known.     

C4 gene polymorphism in primates: evolution,generation, and Chido and Rodgers antigenicity

Eleven new C4d genomic primate sequences of the fourth complement factor (C4) have been obtained. Seven of them belong to five species not yet explored for this gene: Pan paniscus (pygmy chimpanzee), Cercopithecus aethiops (green monkey), Macaca mulatta (rhesus monkey), Macaca fascicularis (cynomolgus), and Saguinus oedipus (cotton top tamarin). The New World monkeys (tamarins, four individuals) sequenced for C4 have a single C4d sequence only, which shows a B isotypic specificity and a Rodgers 3 (Rg3), Chido 1 (Ch1) antigenicity. Rg3 and Ch1 could thus be the oldest Rg/Ch specificity (at least 50 million years old) and Rg1, Rg2, Ch3, and Ch6 could be more recent human-specific antigens. Mechanisms of C4d polymorphism generation were analyzed by compiling all the presently available sequences. Examples of both point mutations and crossing-over events among C4d primate sequences could be detected. The problem of a possible trans-species inheritance of C4d polymorphism was addressed and two apparently contradicting dendrograms were obtained. One of them, constructed by using both exon and intron sequences, does not support trans-species evolution, but supports the proposed theory of extensive homogenization of the C4 genes occurring within each species, because alleles from each primate species cluster together. Another completely different dendrogram, obtained by using exon sequences only, suggests the existence of trans-species evolution for C4d polymorphism, because alleles belonging to different species cluster together in a way similar to that found for HLA class I or II alleles. However, orangutan sequences group together in both kinds of C4d sequence dendrograms and seem to have arisen from an ancestor different from that of chimpanzee, gorilla and man C4d sequences. Finally, further data have been obtained that support trans-species conservation of A-ness and B-ness and the existence of trans-specifically conserved allelic motifs, both in intronic and exonic sequences.     

Identification and characterization of the bacterial <Emphasis Type="SmallCaps">d</Emphasis>-gluconate dehydratase in <Emphasis Type="Italic">Achromobacter xylosoxidans</Emphasis>

Achromobacter xylosoxidans is known to utilize d-glucose via the modified Entner-Doudoroff pathway. Although d-gluconate dehydratase produced from this bacterium was purified and partially characterized previously, a gene that encodes this enzyme has not yet been identified. To obtain protein information on bacterial d-gluconate dehydratase, we partially purified d-gluconate dehydratase in A. xylosoxidans and investigated its biochemical properties. Two degenerate primers were designed based on the N-terminal amino acid sequence of the partially purified d-gluconate dehydratase. Through PCR performed using degenerate primers, a 1,782-bp DNA sequence encoding the A. xylosoxidans d-gluconate dehydratase (gnaD) was obtained. The deduced amino acid sequence of A. xylosoxidans gnaD showed strong similarity with that of proteins belonging to the dihydroxy-acid dehydratase/phosphogluconate dehydratase family (COG0129). This is in contrast to the archaeal d-gluconate dehydratase, which belongs to the enolase superfamily (COG4948). The phylogenetic tree showed that A. xylosoxidans d-gluconate dehydratase is closer to the 6-phosphogluconate dehydratase than the dihydroxy-acid dehydratase. Interestingly, a clade containing A. xylosoxidans enzyme was clustered with proteins annotated as a second and a third dihydroxy-acid dehydratase in the genomes of Clostridium acetobutylicum (Cac_ilvD2) and Streptomyces ceolicolor (Sco_ilvD2, Sco_ilvD3), indicating that the function of these enzymes is the dehydration of d-gluconate.     

Statistical analysis for the spatial validity of a model to forecast the daily number of forest fires

In earlier papers a qualitative and quantitative model was developed for predicting the number of forest fires occurring per day. This model permits the forecast at 00.00 hours Universal Time Convention (UTC) of any day (d), the number of forest fires per day for a range of several days (d tod+5) over a particular region. Input data are the number of forest fires in the region during two preceding days (d–2 andd–1) and the type of day (real and evaluated from radiosonde ford–2,d–1,d and predicted from meteorological medium-range forecasts, i.e. of European Centre, ford+1,d+2,d+3,d+4 andd+5. As this model requires data obtained by radiosonde, particularly temperatures and geopotentials at 850 and 700 hPa and dew points (or specific humidity) at 850 hPa, this study investigates the spatial validity of the model in relation to the distance from the radiosonde station (RS). The highest quality forecast is obtained for the region immediately surrounding the RS, and diminishes with increasing distance from it, this being due to the data obtained from the RS not being representative of the atmospheric column over the region. Hence, the derivation of the critical distance for a particular quality level of measurement. Conversely, fixed quality level implies a specific separation between RS and the region for the prediction, with a higher predictive quality implying a shorter distance.     

Purification and Characterization of NfrA1, a Bacillus subtilis Nitro/flavin Reductase Capable of Interacting with the Bacterial Luciferase

ipa-43d is a hypothetical gene identified by the Bacillus subtilis genome project (Mol. Microbiol. 10, 371-384 1993; Nature 390, 249-256 1997). The ipa-43d protein overexpressed in E. coli was purified to homogeneity and its properties were analyzed biochemically. The ipa-43d protein was found to be tightly associated with FMN and to be capable of reducing both nitrofurazone and FMN effectively. Although the ipa-43d protein catalysis obeys the ping-pong Bi-Bi mechanism, catalysis mode was changed to the sequential mechanism upon coupling with the bioluminescent reaction. Database search showed that B. subtilis possessed four genes (ipa-44d, ytmO, yddN, and yvbT), encoding proteins similar in amino acid sequence to LuxA and LuxB of Photobacterium fischeri, and, in particular, ipa-44d is immediately adjacent to the ipa-43d gene on the chromosome.     

Utilization of d-amino acids by dadR mutants of Salmonella typhimurium

Utilization of d-amino acids being substrates of d-amino acid dehydrogenase of Salmonella typhimurium was examined. The experiments were done with wild type strains and the mutants dadA missing the enzyme activity and dadR in which its synthesis is released from catabolite repression. Growth on d-tryptophan, d-histidine and d-methionine used as precursors of the l-amino acids was faster when the respective auxotrophs carried dadR mutations. The dadR mutants grew faster when d-or l-alanine was present as a sole source of nitrogen. Experiments with d-amino acid dehydrogenase in vitro provided evidence that d-tryptophan is its substrate with a very low affinity to the dehydrogenase.     

A third class I major histocompatibility complex antigen encoded by a gene in the D region of the H-2 d haplotype recognized by cytotoxic T lymphocytes

The D region of the H-2 ^d haplotype contains five class I genes: H-2D ^d , D2 ^d , D3 ^d , D4 ^d and H-2L ^d . Although previous studies have suggested the presence of D-end encoded class I molecules in addition to H-2D^d and H-2L^d, segregation of genes encoding such molecules has not been demonstrated. In this report we have used cãtotoxic T lymphocytes (CTL) to examine the D region of the H-2 ^d haplotype for the presence of additional class I molecules. CTL generated in (C3H × B6.K1)F₁ (K ^k D ^k , K ^b D ^b ) mice against the hybrid class I gene product Q10^d/L^d expressed on L cells cross-react with H-2L^d but not H-2D^d molecules, as determined by lysis of transfected cells expressing H-2L^d but not H-2D^d. Although H-2L^d-specific monoclonal antibodies (mAb) completely inhibit H-2L^d-specific CTL from killing B10.A(3R) (K ^b D ^d L ^d ) target cells, only partial inhibition of anti-Q10 CTL-mediated lysis was observed, suggesting the presence of an additional D-end molecule as a target for these latter CTL. To identify the region containing the gene encoding the Q10 cross-reactive molecule, we show that anti-Q10 CTL lyse target cells from a D-region recombinant strain B10.RQDB, which has H-2D ^d , D2 ^d , D3 ^d , D4 ^d , and H-2D ^b but not the H-2L ^d H-2 ^d , and H-2L ^d (including D2 ^d , D3 ^d , and D4 ^d , lacks this anti-Q10 CTL target molecule. Together, these data demonstrate that a class I gene mapping between H-2D ^d and H-2L ^d encodes an antigen recognozed by anti-Q10 CTL. A likely candidate for this gene is D2 ^d , D3 ^d or D4 ^d .     

Reversion and immobilization of phage Mud1 cts (Apr lac) insertion mutations in Salmonella typhimurium

Summary Phage Mud1 cts (Ap^r lac), or Mud1, insertion mutations may be accompanied by adjacent deletion formation which can complicate use of lac fusions generated with this phage for gene regulatory studies. As for phage Mu insertion mutations, phage Mud1 insertions fail to revert at significant frequency (whether or not accompanied by an adjacent deletion). We describe isolation of revertible (X mutant) derivatives of phage Mud1 in Salmonella typhimurium. The X mutant derivatives allow use of reversion as a simple test to determine whether a Mud1 insertion has occurred precisely without an adjacent deletion that may have fused the lac genes to a promoter outside of the gene of interest. In addition, a simple method for stabilizing Mud1 generated lac fusions against subsequent transposition is described.     

Minimum evolution using ordinary least-squares is less robust than neighbor-joining

The method of minimum evolution reconstructs a phylogenetic tree T for n taxa given dissimilarity data d. In principle, for every tree W with these n leaves an estimate for the total length of W is made, and T is selected as the W that yields the minimum total length. Suppose that the ordinary least-squares formula S _W (d) is used to estimate the total length of W. A theorem of Rzhetsky and Nei shows that when d is positively additive on a completely resolved tree T, then for all W ≠ T it will be true that S _W (d) > S _T (d). The same will be true if d is merely sufficiently close to an additive dissimilarity function. This paper proves that as n grows large, even if the shortest branch length in the true tree T remains constant and d is additive on T, then the difference S _W (d)-S _T (d) can go to zero. It is also proved that, as n grows large, there is a tree T with n leaves, an additive distance function d _T on T with shortest edge ε, a distance function d, and a tree W with the same n leaves such that d differs from d _T by only approximately ε/4, yet minimum evolution incorrectly selects the tree W over the tree T. This result contrasts with the method of neighbor-joining, for which Atteson showed that incorrect selection of W required a deviation at least ε/2. It follows that, for large n, minimum evolution with ordinary least-squares can be only half as robust as neighbor-joining.     

Cloning,Purification and Characterization of an NAD-Dependent <Emphasis Type="SmallCaps">d</Emphasis>-Arabitol Dehydrogenase from Acetic Acid Bacterium, <Emphasis Type="Italic">Acetobacter suboxydans</Emphasis>

d-Xylulose-forming d-arabitol dehydrogenase (aArDH) is a key enzyme in the bio-conversion of d-arabitol to xylitol. In this study, we cloned the NAD-dependent d-xylulose-forming d-arabitol dehydrogenase gene from an acetic acid bacterium, Acetobacter suboxydans sp. The enzyme was purified from A. suboxydans sp. and was heterogeneously expressed in Escherichia coli. The native or recombinant enzyme was preferred NAD(H) to NADP(H) as coenzyme. The active recombinant aArDH expressed in E. coli is a homodimer, whereas the native aArDH in A. suboxydans is a homotetramer. On SDS–PAGE, the recombinant and native aArDH give one protein band at the position corresponding to 28 kDa. The optimum pH of polyol oxidation and ketone reduction is found to be pH 8.5 and 5.5 respectively. The highest reaction rate is observed when d-arabitol is used as the substrate (K _m = 4.5 mM) and the product is determined to be d-xylulose by HPLC analysis.     

d-Mannitol dehydrogenase and d-mannitol-1-phosphate dehydrogenase in Platymonas subcordiformis: some characteristics and their role in osmotic adaptation

d-Mannitol-1-phosphate dehydrogenase (EC 1.1.1.17) and d-mannitol dehydrogenase (EC 1.1.1.67) were estimated in a cell-free extract of the unicellular alga Platymonas subcordiformis Hazen (Prasinophyceae), d-Mannitol dehydrogenase had two activity maxima at pH 7.0 and 9.5, and a substrate specifity for d-fructose and NADH or for d-mannitol and NAD⁺. The K _m values were 43 mM for d-fructose and 10 mM for d-mannitol. d-Mannitol-1-phosphate dehydrogenase had a maximum activity at pH 7.5 and was specific for d-fructose 6-phosphate and NADH. The K _m value for d-fructose 6-phosphate was 5.5 mM. The reverse reaction with d-mannitol 1-phosphate as substrate could not be detected in the extract. After the addition of NaCl (up to 800 mM) to the enzyme assay, the activity of d-mannitol dehydrogenase was strongly inhibited while the activity of d-mannitol-1-phosphate dehydrogenase was enhanced. Under salt stress the K _m values of the d-mannitol dehydrogenase were shifted to higher values. The K _m value for d-fructose 6-phosphate as substrate for d-mannitol-1-phosphate dehydrogenase remained constant. Hence, it is concluded that in Platymonas the d-mannitol pool is derectly regulated via alternative pathways with different activities dependent on the osmotic pressure.Abbreviations Fru6P d-fructose 6-phosphate - Mes 2-(N-morpholino)ethanesulfonic acid - MT-DH d-mannitol-dehydrogenase - MT1P-DH d-mannitol-1-phosphate dehydrogenase - Pipes 1,4-piperazinediethanesulfonic acid - Tris 2-amino-2-(hydroxymethyl)-1,3-propanediol     

d-Mannitol formation from d-glucose in a whole-cell biotransformation with recombinant Escherichia coli

Recently, we reported on the construction of a whole-cell biotransformation system in Escherichia coli for the production of d-mannitol from d-fructose (Kaup B, Bringer-Meyer S, Sahm H (2004) Metabolic engineering of Escherichia coli: construction of an efficient biocatalyst for d-mannitol formation in a whole-cell biotransformation. Appl Microbiol Biotechnol 64:333–339). Supplementation of this strain with extracellular glucose isomerase resulted in the formation of 800 mM d-mannitol from 1,000 mM d-glucose. Co-expression of the xylA gene of E. coli in the biotransformation strain resulted in a d-mannitol concentration of 420 mM from 1,000 mM d-glucose. This is the first example of conversion of d-glucose to d-mannitol with direct coupling of a glucose isomerase to the biotransformation system.     

MICROSATELLITE LOCI REVEAL SEX-DEPENDENT RESPONSES TO INBREEDING AND OUTBREEDING IN RED DEER CALVES

Mean d² is a recently devised microsatellite-based measure that is hypothesised to allow the detection of inbreeding depression and heterosis in free-living populations. Two studies that have investigated the measure have both demonstrated an association between mean d² and traits related to fitness. Here we present an association between mean d¹ and an important component of fitness, first-year overwinter survival, in a population of red deer on the Isle of Rum, Scotland. The association between survival and mean d² differed between males and females. As predicted, outbred female calves (high mean d²) survived better than those that were inbred (low mean d²). However, the association was in the opposite direction in male calves. We suggest that this difference is due to different early growth strategies between the sexes. The association between mean d² and survival was not significantly influenced by any single locus. Decomposition of mean d² into a recent inbreeding component and an outbreeding component showed that it was the degree of outbreeding that influenced survival in males and both the degree of outbreeding and recent inbreeding that influenced survival in females. Our analyses suggest that mean d² is an easy-to-calculate measure of inbreeding and degree of outbreeding that can reveal interesting interactions between genetics and ecology.     

The boxing glove shape of subunit <Emphasis Type="Italic">d</Emphasis> of the yeast V-ATPase in solution and the importance of disulfide formation for folding of this protein

The low resolution structure of subunit d (Vma6p) of the Saccharomyces cerevisiae V-ATPase was determined from solution X-ray scattering data. The protein is a boxing glove-shaped molecule consisting of two distinct domains, with a width of about 6.5 nm and 3.5 nm, respectively. To understand the importance of the N- and C-termini inside the protein, four truncated forms of subunit d (d _11–345, d _38–345, d _1–328 and d _1–298) and mutant subunit d, with a substitution of Cys329 against Ser, were expressed, and only d _11–345, containing all six cysteine residues was soluble. The structural properties of d depends strongly on the presence of a disulfide bond. Changes in response to disulfide formation have been studied by fluorescence- and CD spectroscopy, and biochemical approaches. Cysteins, involved in disulfide bridges, were analyzed by MALDI-TOF mass spectrometry. Finally, the solution structure of subunit d will be discussed in terms of the topological arrangement of the V₁V_O ATPase.     

Vibrational mode frequency calculations of chlorophyll-<Emphasis Type="Italic">d</Emphasis> for assessing (P740<Superscript>+</Superscript>-P740) FTIR difference spectra obtained using photosystem I particles from <Emphasis Type="Italic">Acaryochloris marina</Emphasis>

Acaryochloris marina is an oxygen-evolving organism that utilizes chlorophyll-d for light induced photochemistry. In photosystem I particles from Acaryochloris marina, the primary electron donor is called P740, and it is thought that P740 consist of two chlorophyll-d molecules. (P740⁺-P740) FTIR difference spectra have been produced, and vibrational features that are specific to chlorophyll-d (and not chlorophyll-a) were observed, supporting the idea that P740 consists chlorophyll-d molecules. Although bands in the (P740⁺-P740) FTIR difference spectra were assigned specifically to chlorophyll-d, how these bands shifted, and how their intensities changed, upon cation formation was never considered. Without this information it is difficult to draw unambiguous conclusions from the FTIR difference spectra. To gain a more detailed understanding of cation induced shifting of bands associated with vibrational modes of P740 we have used density functional theory to calculate the vibrational properties of a chlorophyll-d model in the neutral, cation and anion states. These calculations are shown to be of considerable use in interpreting bands in (P740⁺-P740) FTIR difference spectra. Our calculations predict that the 3¹ formyl C–H mode of chlorophyll-d upshifts/downshifts upon cation/anion formation, respectively. The mode intensity also decreases/increases upon cation/anion formation, respectively. The cation induced bandshift of the 3¹ formyl C–H mode of chlorophyll-d is also strongly dependant on the dielectric environment of the chlorophyll-d molecules. With this new knowledge we reassess the interpretation of bands that were assigned to 3¹ formyl C–H modes of chlorophyll-d in (P740⁺-P740) FTIR difference spectra. Considering our calculations in combination with (P740⁺-P740) FTIR DS we find that the most likely conclusions are that P740 is a dimeric Chl-d species, in an environment of low effective dielectric constant (∼2–8). In the P740⁺ state, charge is asymmetrically distributed over the two Chl-d pigments in a roughly 60:40 ratio. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Properties of recombinant <Emphasis Type="Italic">Strep</Emphasis>-tagged and untagged hyperthermophilic D-arabitol dehydrogenase from <Emphasis Type="Italic">Thermotoga maritima</Emphasis>

The first hyperthermophilic d-arabitol dehydrogenase from Thermotoga maritima was heterologously purified from Escherichia coli. The protein was purified with and without a Strep-tag. The enzyme exclusively catalyzed the NAD(H)-dependent oxidoreduction of d-arabitol, d-xylitol, d-ribulose, or d-xylulose. A twofold increase of catalytic rates was observed upon addition of Mg²⁺ or K⁺. Interestingly, only the tag-less protein was thermostable, retaining 90% of its activity after 90 min at 85 °C. However, the tag-less form of d-arabitol dehydrogenase had similar kinetic parameters compared to the tagged enzyme, demonstrating that the Strep-tag was not deleterious to protein function but decreased protein stability. A single band at 27.6 kDa was observed on SDS-PAGE and native PAGE revealed that the protein formed a homohexamer and a homododecamer. The enzyme catalyzed oxidation of d-arabitol to d-ribulose and therefore belongs to the class of d-arabitol 2-dehydrogenases, which are typically observed in yeast and not bacteria. The product d-ribulose is a rare ketopentose sugar that has numerous industrially applications. Given its thermostability and specificity, d-arabitol 2-dehydrogenase is a desirable biocatalyst for the production of rare sugar precursors.