Sequence comparison with concave weighting functions

We consider efficient methods for computing a difference metric between two sequences of symbols, where the cost of an operation to insert or delete a block of symbols is a concave function of the block's length. Alternatively, sequences can be optimally aligned when gap penalties are a concave function of the gap length. Two algorithms based on the ‘candidate list paradigm’ first used by Waterman (1984) are presented. The first computes significantly more parsimonious candidate lists than Waterman's method. The second method refines the first to the point of guaranteeingO(N ² lgN) worst-case time complexity, and under certain conditionsO(N ²). Experimental data show how various properties of the comparison problem affect the methods' relative performance. A number of extensions are discussed, among them a technique for constructing optimal alignments inO(N) space in expectation. This variation gives a practical method for comparing long amino sequences on a small computer. This work was supported in part by NSF Grant DCR-8511455.     

Approximate matching of regular expressions

Given a sequenceA and regular expressionR, theapproximate regular expression matching problem is to find a sequence matchingR whose optimal alignment withA is the highest scoring of all such sequences. This paper develops an algorithm to solve the problem in timeO(MN), whereM andN are the lengths ofA andR. Thus, the time requirement is asymptotically no worse than for the simpler problem of aligning two fixed sequences. Our method is superior to an earlier algorithm by Wagner and Seiferas in several ways. First, it treats real-valued costs, in addition to integer costs, with no loss of asymptotic efficiency. Second, it requires onlyO(N) space to deliver just the score of the best alignment. Finally, its structure permits implementation techniques that make it extremely fast in practice. We extend the method to accommodate gap penalties, as required for typical applications in molecular biology, and further refine it to search for substrings ofA that strongly align with a sequence inR, as required for typical data base searches. We also show how to deliver an optimal alignment betweenA andR in onlyO(N+logM) space usingO(MN logM) time. Finally, anO(MN(M+N)+N ²logN) time algorithm is presented for alignment scoring schemes where the cost of a gap is an arbitrary increasing function of its length.     

Optimal sequence alignment allowing for long gaps

A new algorithm for optimal sequence alignment allowing for long insertions and deletions is developed. The algorithm requires O((L+C)MN) computational steps, O(LN) primary memory and O(MN) secondary memory storage, whereM andN(M≥N) are sequence lengths,L (typicallyL≤3) is the number of segment specifying the gap weighting function, andC is a constant. We have also modified our earlier traceback algorithm so that it finds all and only the optimal alignments in a compact form of a directed graph. The current versions accept a set of aligned sequences as input, which facilitates multiple sequence alignment by some iterative procedures. Dedicated to Professor Akiyoshi Wada on the occasion of his 60th birthday.     

Pattern matching of biological sequences with limited storage

Existing methods for getting the locally best matched alignmentsbetween a pair of biological sequences require O(N²) computationalsteps and O(N²) storage, where N is the average sequence length.An improved method is presented with which the storage requirementis greatly reduced, while the computational steps remain O(N²).Only a small number of additional steps are required to displayany common sub–sequences with similarity scores greaterthan a given threshold. The aligments found by the algorithmare optimal in the sense that their scores are locally maximal,where each score is a sum of weights given to individual matches/replacements,insertions and deletions involved in the alignment. The algorithmwas implemented in C programming language on a personal computer.Data area of 64 kbytes on random access memory and a few hundredkbytes on a disk is sufficient for comparing two protein ornucleic acid sequences of 2500 residues. The programs are particularlyvaluable when used in combination with fast sequence searchprograms. Received on July 25, 1986; accepted on October 27, 1986     

AnO(N 2 logN) restriction map comparison and search algorithm

We present anO(R logP) time,O(M+P ² ) space algorithm for searching a restriction map withM sites for the best matches to a shorter map withP sites, whereR, the number of matching site pairs, is bounded byMP. As first proposed by Watermanet al. (1984,Nucl. Acids Res. 12, 237–242) the objective function used to score matches is additive in the number of unaligned sites and the discrepancies in the distances between adjacent aligned sites. Our algorithm is basically a sparse dynamic programming computation in which “candidate lists” are used to model the future contribution of all previously computed entries to those yet to be computed. A simple modification to the algorithm computes the distance between two restriction maps withM andN sites, respectively, inO(MN(logM+logN)) time. This author’s work was supported in part by National Library of Medicine Grant R01-LM4960. This author’s work was supported in part by National Library of Medicine Grant R01-LM5110.     

An improved algorithm for statistical alignment of sequences related by a star tree

The insertion-deletion model developed by Thorne, Kishino and Felsenstein (1991, J. Mol. Evol., 33, 114–124; the TKF91 model) provides a statistical framework of two sequences. The statistical alignment of a set of sequences related by a star tree is a generalization of this model. The known algorithm computes the probability of a set of such sequences in O(l ^2k ) time, where l is the geometric mean of the sequence lengths and k is the number of sequences. An improved algorithm is presented whose running time is only O(2^2k l ^k).     

Sequence embedding for fast construction of guide trees for multiple sequence alignment

Background  

The most widely used multiple sequence alignment methods require sequences to be clustered as an initial step. Most sequence clustering methods require a full distance matrix to be computed between all pairs of sequences. This requires memory and time proportional to N ² for N sequences. When N grows larger than 10,000 or so, this becomes increasingly prohibitive and can form a significant barrier to carrying out very large multiple alignments.     

黄土高原冬小麦地N2O排放

从2007年7月1日到2009年6月30日对黄土高原冬小麦地氧化亚氮(N₂O)排放采用静态箱气相色谱法进行了为期2a 的监测。设置2个处理,有小麦田(有小麦生长),无小麦田(出芽初期拔去麦苗)。研究结果表明有小麦田、无小麦田N₂O排放量年际变化不大。有小麦田年均的N₂O 排放量为2.05 kg · N₂O · hm^-2 · a^-1,无小麦田年均的N₂O 排放量为2.28 kg · N₂O · hm^-2 · a^-1 。在冻融交替期,施肥后、翻地后和降雨后无小麦田和有小麦田N₂O排放明显增加,N₂O的季节变化受到这些短期事件的显著影响;有小麦田N₂O排放与地温(P<0.01),气温(P<0.01)和WFPS(P<0.05)显著相关,而无小麦田N₂O排放与这些环境土壤因子都不相关;有小麦田和无小麦田两个处理土壤的WFPS通常都低于60%,可以推断在本地区,硝化反应是N₂O的重要生成源。     

Micropropagation studies inCeropegia SPP

Summary The purpose of this study was to developin vitro techniques for conserving wild and endemic species ofCeropegia by mass multiplication for subsequent reintroduction in their natural habitat. Micropropagation involving a combination of axillary bud culture, shoot multiplication, somatic embryogenesis andin vitro tuber formation forCeropegia jainii, a rare plant of the Indian sub continent,C. bulbosa var.bulbosa andC. bulbosa var.lushii, common species, was developed. Nodal explants from all species were cultured on 0.5 MS medium with 8.8 μM (2 mg·l⁻¹) N⁶-benzyl aminopurine (BA) to regenerate the axillary buds. These produced multiple shoots when transferred to multiplication medium consisting of 0.5 MS medium with 2.2 μM (0.5 mg·l⁻¹) BA, or microtubers when transferred to 0.5 MS medium with 22.2 μM (5 mg·l⁻¹) BA and 23.2 μM (5 mg·l⁻¹) kinetin.In vitro flowering occurred inC. jainii and not in the other two varieties when the plants were cultured on multiplication media with spermine at 0.25 μM (50 μg·l⁻¹) as an additive. Shoot pieces produced callus on MS medium with 9.05 μM (2 mg·l⁻¹) 2,4-dichlorophenoxy acetic acid. Regeneration of the calli by somatic embryogenesis was achieved when they were transferred to 0.5 MS medium with 2.2 μM (0.5 mg·l⁻¹) BA. Rooting of the shoots was possible both byin vitro andex vitro means.     

A Forgotten Chiral Spiro Compound Revisited: 3,3'‐Dimethyl‐3H,3'H‐2,2'‐spirobi[[1,3]benzothiazole]

The title compound was obtained as a side product during dimerization‐oxidation steps of the carbene generated from N‐methylbenzothiazolium iodide. Chromatography on (S,S)‐Whelk O1 column showed on cooling a typical plateau shape chromatogram indicating an exchange between two enantiomers on the column. The thermal barrier to racemization was determined (85 kJ.mol^?1 at 10 °C) by dynamic high‐performance liquid chromatography (DHPLC).The absolute configuration of the first (M) and second eluted (P) enantiomers on the (S, S)‐Whelk O1 column was established by comparing the reconstructed circular dichroism (CD) spectra from the CD detector signal and the calculated CD spectrum of the (P) enantiomer. Mass spectrometry revealed that 3,3'‐dimethyl‐3H,3'H‐2,2'‐spirobi[[1,3]benzothiazole] can be viewed as a masked thiophenate attached to a benzothiazolium framework. Chirality 27:716–721, 2015. © 2015 Wiley Periodicals, Inc.     

Purification and Characterization of Novel N-Acyl-D-aspartate Amidohydrolase from Alcaligenes xylosoxydans subsp. xylosoxydans A-6

Alcaligenes xylosoxydans subsp. xylosoxydans A-6 (Alcaligenes A-6) produced N-acyl-D-aspartate amidohydrolase (D-AAase) in the presence of N-acetyl-D-aspartate as an inducer. The enzyme was purified to homogeneity. The enzyme had a molecular mass of 56 kDa and was shown by sodium dodecyl sulfate (SDS)–polyacrylamide gel electrophoresis (PAGE) to be a monomer. The isoelectric point was 4.8. The enzyme had maximal activity at pH 7.5 to 8.0 and 50°C, and was stable at pH 8.0 and up to 45°C. N-Formyl (K_m=12.5 mM), N-acetyl (K_m=2.52 mM), N-propionyl (K_m=0.194 mM), N-butyryl (K_m=0.033 mM), and N-glycyl (K_m =1.11 mM) derivatives of D-aspartate were hydrolyzed, but N-carbobenzoyl-D-aspartate, N-acetyl-L-aspartate, and N-acetyl-D-glutamate were not substrates. The enzyme was inhibited by both divalent cations (Hg²⁺, Ni²⁺, Cu²⁺) and thiol reagents (N-ethylmaleimide, iodoacetic acid, dithiothreitol, and p-chloromercuribenzoic acid). The N-terminal amino acid sequence and amino acid composition were analyzed.     

Evaluation of chemical methods for estimating available zinc and response of green gram (Phaseolus aureus roxb) to applied zinc in non-calcareous soils

Summary Studies were conducted in 22 non-calcareous soils (India) to evaluate various extractants,viz. (6N HCl, 0.1N HCl, EDTA (NH₄)₂CO₃, EDTA NH₄OAc, DTPA+CaCl₂ and 1M MgCl₂) to find critical levels of soil and plant Zn for green gram (Phaseolus aureus Roxb.). The order of extractability by the different extractants was 6N HCl>0.1N HCl>EDTA (NH₄)₂CO₃<EDTA NH₄OAc DTPA+CaCl₂>1M MgCl₂. Critical levels of 0.48 ppm DTPA × CaCl₂ extractable Zn, 0.80 ppm EDTA NH₄OAc extractable Zn, 0.70 ppm EDTA (NH₄)₂CO₃ extractable Zn, and 2.2 ppm 0.1N HCl extractable Zn were estimated for the soils tested. The critical Zn concentration in 6 weeks old plants was found to be 19 ppm. The 0.1N HCl method gave the best correlation (r=0.588^**) between extractable Zn and Bray's per cent yield, while with DTPA+CaCl₂, it was slightly low (r=0.542^**). The DTPA + CaCl₂ method gave significant (r=0.73^**) correlation with plant Zn concentration. The 0.1N HCl gave the higher correlation with Zn uptake (r=0.661^**) than DTPA (r=0.634^**) 6N HCl and 1M MgCl₂ method gave nonsignificant positive relationship with Bray's per cent yield. For noncalcareous soils apart from the common use of DTPA+CaCl₂, 0.1N HCl can also be used for predicting soil available Zn. The use of 0.1N HCl would be much cheaper than DTPA and other extractants used in the study.     

Excessive use of nitrogen in Chinese agriculture results in high N2O/(N2O+N2) product ratio of denitrification,primarily due to acidification of the soils

China is the world's largest producer and consumer of fertilizer N, and decades of overuse has caused nitrate leaching and possibly soil acidification. We hypothesized that this would enhance the soils' propensity to emit N₂O from denitrification by reducing the expression of the enzyme N₂O reductase. We investigated this by standardized oxic/anoxic incubations of soils from five long‐term fertilization experiments in different regions of China. After adjusting the nitrate concentration to 2 mM, we measured oxic respiration (R), potential denitrification (D), substrate‐induced denitrification, and the denitrification product stoichiometry (NO, N₂O, N₂). Soils with a history of high fertilizer N levels had high N₂O/(N₂O+N₂) ratios, but only in those field experiments where soil pH had been lowered by N fertilization. By comparing all soils, we found a strong negative correlation between pH and the N₂O/(N₂O+N₂) product ratio (r² = 0.759, P < 0.001). In contrast, the potential denitrification (D) was found to be a linear function of oxic respiration (R), and the ratio D/R was largely unaffected by soil pH. The immediate effect of liming acidified soils was lowered N₂O/(N₂O+N₂) ratios. The results provide evidence that soil pH has a marginal direct effect on potential denitrification, but that it is the master variable controlling the percentage of denitrified N emitted as N₂O. It has been known for long that low pH may result in high N₂O/(N₂O+N₂) product ratios of denitrification, but our documentation of a pervasive pH‐control of this ratio across soil types and management practices is new. The results are in good agreement with new understanding of how pH may interfere with the expression of N₂O reductase. We argue that the management of soil pH should be high on the agenda for mitigating N₂O emissions in the future, particularly for countries where ongoing intensification of plant production is likely to acidify the soils.     

Counterselection of GATC sequences in enterobacteriophages by the components of the methyl-directed mismatch repair system

Summary Weak to severe deficit of GATC sequences in the DNA of enterobacteriophages appears to be correlated with their undermethylation during growth indam ⁺ (GATC ade-methylase) bacteria. This observation is corroborated by the sequence analysis showing no evidence for site-specific mutagenicity of 6meAde. The MutH protein of the methyl-directed mismatch repair system recognizes and cleaves the undermethylated GATC sequences in the course of mismatch repair. To enquire whether the MutH function of the methyldirected mismatch repair system participates in counterselection of GATC sequences in enterobacteriophages, we have studied the yield of bacteriophage X174 containing either 0, 1, or 2 GATC sequences, in wild type,dam, andmut (H, L, S, U) Escherichia coli. Following transfection with unmethylated DNA containing two GATC sequences, a net decrease in the yield of infective particles was observed in all bacterialmutH ⁺ dam^– strains, whereas no detectable decrease was observed in bacteria infected by DNA without GATC sequence. This effect of the MutH function is maximum in wild type andmutL andmutS bacteria whereas the effect is not significant inmutU bacteria, suggesting an interaction of the, helicase II with the MutH protein.However, indam ⁺ bacteria, the presence of GATC sequences leads to an increased yield of infective particles. The effect of GATC sequence and its Dam methylation system on phage yield inmutH ^– bacteria reveals that methylated GATC sequences are advantageous to the phage. These results suggest that the methyl-directed mismatch repair system, and in particular its MutH protein, may have participated in severe counterselection of GATC sequences from enterobacteriophages, presumably, by DNA cleavage or by interfering with DNA replication or packaging when GATC sequences are undermethylated. Coevolution of the Dam and MutH proteins could then account for the loss of GATC sequences from DNA of bacteriophages growing indam ⁺ hosts.     

Differential Effects of the KitW Mutation with Other Kit Allelic Combinations on Male Sterility Among Inter- or Intrasubspecific Hybrids in Mice

The combination of the Kit ^W mutation and Kit ^S allele from Mus spretus leads to male hybrid sterility. The effects of other combinations between Kit ^W and Kit ^M from Mus m. molossinus or Kit ^N from Mus m. musculus on male reproductive ability were examined in this study. The Kit ^W/Kit ^M and Kit ^W/Kit ^N males were fertile and showed the normal pattern of spermatogenesis in most seminiferous tubules. There were two amino acid substitutions in the protein deduced from the cDNA sequence coded by the Kit ^M allele sequence and three in the Kit ^M allele compared with the protein from the + Kit allele of C57BL mice. These amino acid exchanges had no effect on the fertility of Kit ^W/Kit ^M and Kit ^W/Kit ^N males. Therefore, comparing the sequence data from cDNA coded by Kit ^M and Kit ^N alleles with that for the Kit ^S allele, we concluded that one or more amino acid exchanges in the extracellular domain would be the cause of male hybrid sterility in the Kit ^W/Kit ^S combination; these substitutions are Phe to Ser at position 72, Thr to Ala at 95, Ser to Arg at 101, Leu to Pro at 123, and Ile to Met at 1303     

Crystal structure,DNA binding studies,nucleolytic property and topoisomerase I inhibition of zinc complex with 1,10-phenanthroline and 3-methyl-picolinic acid

Crystal structure analysis of the zinc complex establishes it as a distorted octahedral complex, bis(3-methylpicolinato-κ² N,O)₂(1,10-phenanthroline-κ² N,N)-zinc(II) pentahydrate, [Zn(3-Me-pic)₂(phen)]·5H₂O. The trans-configuration of carbonyl oxygen atoms of the carboxylate moieties and orientation of the two planar picolinate ligands above and before the phen ligand plane seems to confer DNA sequence recognition to the complex. It cannot cleave DNA under hydrolytic condition but can slightly be activated by hydrogen peroxide or sodium ascorbate. Circular Dichroism and Fluorescence spectroscopic analysis of its interaction with various duplex polynucleotides reveals its binding mode as mainly intercalation. It shows distinct DNA sequence binding selectivity and the order of decreasing selectivity is ATAT > AATT > CGCG. Docking studies lead to the same conclusion on this sequence selectivity. It binds strongly with G-quadruplex with human tolemeric sequence 5′-AG₃(T₂AG₃)₃-3′, can inhibit topoisomerase I efficiently and is cytotoxic against MCF-7 cell line.     

Characterization and Localization of Adenosine A2 Receptors in Bovine Rod Outer Segments

Abstract: Previous work from this laboratory has shown that retinal adenosine A₂ binding sites are localized over outer and inner segments of photoreceptors in rabbit and mouse retinal sections. In the present study, adenosine receptor binding has been characterized and localized in membranes from bovine rod outer segments (ROS). Saturation studies with varying concentrations (10–150 nM) of 5′-(N-[2,8-³H]ethylcarboxamido)adenosine ([³H]NECA) and 100 μg of ROS membrane protein show a single site with a K_D of 103 nM and a B_max of 1.3 pM/mg of protein. Cold Scatchards, which used nonradiolabeled NECA (concentrations ranging from 10 nM to 250 nM) in competition with a fixed amount of [³H]NECA (30 nM), demonstrated the presence of a low-affinity site (K_D, 50 μM) in addition to the high-affinity site. To confirm the presence of A_2abinding sites, saturation analyses with 2-p-(2-[³H]-carboxyethyl)phenylamino-5′-N-ethylcarboxamido adenosine (0–80 nM) also revealed a single population of high-affinity A_2a receptors (K_D, 9.4 nM). The binding sites labeled by [³H]NECA appear to be A₂ receptor sites because binding was displaced by increasing concentrations of 5′-(N-methylcarboxamido)adenosine and 2-chloroadenosine. ROS were fractionated into plasma and disk membranes for localization studies. Receptor binding assays, used to determine specific binding, showed that the greatest concentration of A₂ receptors was on the plasma membranes. Therefore, adenosine A₂ receptors are in a position to respond to changes in the concentration of extracellular adenosine, which may exhibit a circadian rhythm.     

Supramolecular networks of transition metal sulfates templated by piperazine

Syntheses, structural studies from single-crystal X-ray diffraction and thermal behaviour of (C₄H₁₂N₂)[M^II(H₂O)₆](SO₄)₂ with M^II = Mn, Ni, Fe and Cu are reported. All compounds crystallise in monoclinic system, space group P2₁/n. The two isotypical compounds (C₄H₁₂N₂)[Mn(H₂O)₆](SO₄)₂ (I) and (C₄H₁₂N₂)[Ni(H₂O)₆](SO₄)₂ (II), are isostructural with the related cobalt and zinc phases, while the isotypical sulfates (C₄H₁₂N₂)[Fe(H₂O)₆](SO₄)₂ (III) and (C₄H₁₂N₂)[Cu(H₂O)₆](SO₄)₂ (IV) belong to another structure type. The three-dimensional structure networks for the four compounds consist of isolated [M^II(H₂O)₆]²⁺ and (C₄H₁₂N₂)²⁺ cations and (SO₄)²⁻ anions linked by hydrogen-bonds only. The thermal behaviour of the precursors has been studied by powder thermodiffractometry and thermogravimetric analyses. The first stages of dehydration are discussed with respect to the hydrogen bonds within the compounds.     

Ultrastructural observations on effects of different concentrations of calcium and thyroxine in vitro on larval epidermal cells of Rana catesbeiana tadpoles

Summary During anuran metamorphosis dramatic changes in morphogenesis and differentiation of epidermis occur under the influence of thyroid hormones. Modification of ionic calcium concentration also markedly alters the pattern of proliferation and differentiation in amphibian epidermal cells in vitro. The present study was designed to determine the direct effect of low (0.05 mM) and high (0.5mM) calcium (Ca²⁺) in the absence or presence of thyroxine (10⁻⁷ M) on epidermal cells of the body and tail tissue in vitro. When tail fin and body skin explants were maintained in low (0.05 mM) calcium for 48 h, normal ultrastructural morphology and integrity of the cells was observed in both the tissue types. When tissues were exposed to high levels of calcium (0.5mM) in culture medium, tail epidermis showed stratification, and skein cells exhibited apoptosis, both in the presence or absence of thyroid hormones. Under high calcium conditions, the body epidermis showed keratinization of apical cells, apoptosis of skein cells, and increased desmosome formation. These results suggest that (1) optimal Ca²⁺ concentration for larval epidermal cells is quite low (0.05 mM), (2) high Ca²⁺ leads to keratinization only in body epidermis, and (3) apoptosis occurred in skein cells of both the tissues at high Ca²⁺ concentrations (0.5mM). The present study therefore suggests that the extracellular calcium concentration regulates the process of cell death and differentiation inRana catesbeiana larval epidermis, and this effect may be similar to the effect of calcium on mammalian epidermal cells.     

Temporal variation in nitrous oxide (N2O) fluxes from an oil palm plantation in Indonesia: An ecosystem-scale analysis

The rapidly growing areal extent of oil palm (Elaeis guineensis Jacq.) plantations and their high fertilizer input raises concerns about their role as substantial N₂O sources. In this study, we present the first eddy covariance (EC) measurements of ecosystem-scale N₂O fluxes in an oil palm plantation and combine them with vented soil chamber measurements of point-scale soil N₂O fluxes. Based on EC measurements during the period August 2017 to April 2019, the studied oil palm plantation in the tropical lowlands of Jambi Province (Sumatra, Indonesia) is a high source of N₂O, with average emission of 0.32 ± 0.003 g N₂O-N m⁻² year⁻¹ (149.85 ± 1.40 g CO₂-equivalent m⁻² year⁻¹). Compared to the EC-based N₂O flux, average chamber-based soil N₂O fluxes (0.16 ± 0.047 g N₂O-N m⁻² year⁻¹, 74.93 ± 23.41 g CO₂-equivalent m⁻² year⁻¹) are significantly (~49%, p < 0.05) lower, suggesting that important N₂O pathways are not covered by the chamber measurements. Conventional chamber-based N₂O emission estimates from oil palm up-scaled to ecosystem level might therefore be substantially underestimated. We show that the dynamic gas exchange of the oil palm canopy with the atmosphere and the oil palms' response to meteorological and soil conditions may play an important but yet widely unexplored role in the N₂O budget of oil palm plantations. Diel pattern of N₂O fluxes showed strong causal relationships with photosynthesis-related variables, i.e. latent heat flux, incoming photosynthetically active radiation and gross primary productivity during day time, and ecosystem respiration and soil temperature during night time. At longer time scales (>2 days), soil temperature and water-filled pore space gained importance on N₂O flux variation. These results suggest a plant-mediated N₂O transport, providing important input for modelling approaches and strategies to mitigate the negative impact of N₂O emissions from oil palm cultivation through appropriate site selection and management.