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.     

Enhancing disease resistances of Super Hybrid Rice with four antifungal genes

A plant expression vector harboring four antifungal genes was delivered into the embryogenic calli of ‘9311’, an indica restorer line of Super Hybrid Rice, via modified biolistic particle bombardment. Southern blot analysis indicated that in the regenerated hygromycin-resistant plants, all the four anti-fungal genes, including RCH10, RAC22, β-Glu and B-RIP, were integrated into the genome of ‘9311’, co-transmitted altogether with the marker gene hpt in a Mendelian pattern. Some transgenic R1 and R2 progenies, with all transgenes displaying a normal expression level in the Northern blot analysis, showed high resistance to Magnaporthe grisea when tested in the typical blast nurseries located in Yanxi and Sanya respectively. Furthermore, transgenic F₁ plants, resulting from a cross of R₂ homozygous lines with high resistance to rice blast with the non-transgenic male sterile line Peiai 64S, showed not only high resistance to M. grisea but also enhanced resistance to rice false smut (a disease caused by Ustilaginoidea virens) and rice kernel smut (another disease caused by Tilletia barclayana).     

Constrained sequence alignment

This paper presents a dynamic programming algorithm for aligning two sequeces when the alignment is constrained to lie between two arbitrary boundary lines in the dynamic programming matrix. For affine gap penalties, the algorithm requires onlyO(F) computation time andO(M+N) space, whereF is the area of the feasible region andM andN are the sequence lengths. The result extends to concave gap penalties, with somewhat increased time and space bounds. K.-M. C. and W. M. were supported in part by grant R01 LM05110 from the National Library of Medicine. R. C. H. was supported by PHS grant R01 DK27635.     

’Forrest’ resistance to the soybean cyst nematode is bigenic: saturation mapping of the Rhg1and Rhg4 loci

Field resistance to cyst nematode (SCN) race 3 (Heterodera glycines I.) in soybean [Glycine max (L.) Merr.] cv ’Forrest’ is conditioned by two QTLs: the underlying genes are presumed to include Rhg1 on linkage group G and Rhg4 on linkage group A2. A population of recombinant inbred lines (RILs) and two populations of near-isogenic lines (NILs) derived from a cross of Forrest×Essex were used to map the loci affecting resistance to SCN. Bulked segregant analysis, with 512 AFLP primer combinations and microsatellite markers, produced a high-density genetic map for the intervals carrying Rhg1 and Rhg4. The two QTLs involved in resistance to SCN were strongly associated with the AFLP marker E_ATGM_CGA87 (P=0.0001, R²=24.5%) on linkage group G, and the AFLP marker E_CCGM_AAC405 (P=0.0001, R² =26.2%) on linkage group A2. Two- way analysis of variance showed epistasic interaction (P=0.0001, R² =16%) between the two loci controlling SCN resistance in Essex×Forrest recombinant inbred lines. Considering the two loci as qualitative genes and the resistance as female index FI <5%, jointly the two loci explained over 98% of the resistance. The locations of the two QTLs were confirmed in the NILs populations. Therefore SCN resistance in Forrest×Essex is bigenic. High-efficiency marker-assisted selection can be performed using the markers to develop cultivars with stable resistance to SCN. Received: 5 November 2000 / Accepted: 23 January 2001     

Abstract biological systems as sequential machines: Behavioral reversibility

Rosen’s identification of abstract biological systems, called (M,R)-systems, with sequential machines is formally characterized. It is then shown that the determination of environmental alterations of (M,R)-systems from a knowledge of the response sequence and the structure of the system, which we call behavioral reversibility, can be interpreted as information-losslessness of sequential machines. Applying this relationship, necessary conditions for behavioral reversibility are derived. It is further shown that, similar to Rosen’s work on structural reversibility, (M,R)-systems are behaviorally reversible only if the number of physically realizable mappings are restricted.     

Contributions to relational biology

The principle of biotopological mapping (Rashevsky, 1954,Bull. Math. Biophysics,16, 317–48) is given a generalized formulation, as the principle of relational epimorphism in biology. The connection between this principle and Robert Rosen’s representation of organisms by means of categories (1958,Bull. Math. Biophysics,20, 317–41) is studied. Rosen’s theory of (M,R)-systems, (1958,Bull. Math. Biophysics,20, 245–60) is generalized by dropping the assumption that only terminalM _i components are sending inputs into theR _i components. It is shown that, if the primordial organism is an (M,R)-system, then the higher organisms, obtained by a construction well discussed previously (1958,Bull. Math. Biophysics,20, 71–93), are also (M,R)-systems. Several theorems about such derived (M,R)-systems are demonstrated. It is shown that Rosen’s concept of an organism as a set of mappings throws light on phenomena of synesthesia and also leads to the conclusion that Gestalt phenomena must occur not only in the fields of visual and auditory perception but in perceptions of any modality.     

Conflicting results in EEG alpha feedback studies

Success or failure of EEG feedback training for alpha enhancement can depend on how alpha activity is quantified and fed back. Alpha-enhancement failures usually employ a percent time(%) technique; successes typically use amplitude integration(). To dramatize the differences between percent and integration techniques, we derived both measures simultaneously from left occipital(O ₁ ) and left central(C ₃ ) sites for 16 male subjects who were given 5.6 hours of integrated alpha feedback from the midline occipital(O_z ) site. At both the O ₁ and C ₃ sites the integrated and percent measures were not equivalent and not linearly related. Statistically significant differences in the(integrated, percent) correlation coefficients(z-transformed) were observed under the different recording conditions: alpha enhancement, alpha enhancement, alpha suppression, and baselines. Theoretical discussion of integration and percent techniques is given and the adoption of amplitude integration measures and feedback stimuli is strongly advocated.This study was supported by the following grants and contracts: National Institute of Mental Health (NIMH) Predoctoral Fellowship #1 F01 MH51704-01, NIMH General Research Support Grant #LPNI 185, and a Langley Porter Neuropsychiatric Institute Postdoctoral Fellowship (Interdisciplinary Training Program, NIMH #7082) to James V. Hardt, and by NIMH Research Scientist Development Award 2K02 MH38897, NIMH Research Grant #1 R01 MH24820, Office of Naval Research (ARPA) Contract N00014-70-C-0350, and Instruction and Research Funds, Computer Center Accounts (UCSF) #1431 and #1437 to Joe Kamiya.     

The root–soil system of Norway spruce subjected to turning moment: resistance as a function of rotation

The reactions of trees to wind, rockfall, and snow and debris flow depend largely on how strong and deformable their anchorage in the soil is. Here, the resistive turning moment M of the root–soil system as a function of the rotation ϕ at the stem base plays the major role. M(ϕ) describes the behavior of the root–soil system when subject to rotational moment, with the maximum M(ϕ) indicating the anchorage strength M _a of the tree. We assessed M(ϕ) of 66 Norway spruce (Picea abies L. Karst) by pulling them over with a winch. These 45- to 170-year-old trees grew at sites of low and high elevation, with a diameter at breast height DBH = 14–69 cm and a height H = 9–42 m. M(ϕ) displayed a strong nonlinear behavior. M _a was reached at a lower ϕ for large trees than for small trees. Thus overhanging tree weight contributed less to M _a for the large trees. Overturning also occurred at a lower ϕ for the large trees. These observations show that the rotational ductility of the root–soil system is higher for small trees. M _a could be described by four monovariate linear regression equations of tree weight, stem weight, stem volume and DBH ² ·H (0.80 < R ² < 0.95), and ϕ at M _a, ϕ _a, by a power law of DBH²·H (R ² = 0.85). We found significantly higher M _a for the low-elevation spruces than for the high-elevation spruces, which were more shallowly anchored, but no significant difference in ϕ _a. The 66 curves of M(ϕ), normalized (_n) by M _a in M-direction and by ϕ _a in ϕ-direction, yielded one characteristic average curve: . Using and the predictions of M _a and ϕ _a, it is shown that M(ϕ) and the curves associated with M(ϕ) can be predicted with a relative standard error ≤25%. The parameterization of M(ϕ) by tree size and weight is novel and provides useful information for predicting with finite-element computer models how trees will react to natural hazards.     

Biological character of human adipose-derived adult stem cells and influence of donor age on cell replication in culture

To investigate the biological character of human adipose-derived adult stem cells (hADAS cells) when cultured in vitro and the relationship between hADAS cell's replication activity and the donor's age factor, and to assess the stem cells as a new source for tissue engineering, hADAS cells are isolated from human adipose tissue of different age groups (from adolescents to olds ＜20 years old, 21-40years old, 41-60 years old and ＞61 years old groups). The protein markers (CD29, CD34, CD44, CD45,CD49d, HLA-DR, CD106) of hADAS cells were detected by flow cytometry (FCM) to identify the stem cell,and the cell cycle was examined for P20 hADAS cells to evaluate the safety of the subculture in vitro.The generative activity of hADAS cells in different age groups was also examined by MTT method. The formula "TD = t log2/logNt - logN0 "was used to get the time doubling (TD) of the cells. The results showed that the cells kept heredity stabilization by chromosome analysis for at least 20 passages. The TD of these cells increased progressively by ageing, and the TD of the ＜20 years old group was lower than that of the ＞61 years old group (statistical analysis of variance (ANOVA), P=-0.002, P＜0.05). These findings suggested that a higher level of hADAS cells replication activity was found in the younger donators, and they represent novel and valuable seed cells for studies of tissue engineering.     

Cell cycle control at the first restriction point and its effect on tissue growth

Cell cycle is controlled at two restriction points, R ₁ and R ₂. At both points the cell will commit apoptosis if it detects irreparable damage. But at R ₁ an undamaged cell also decides whether to proceed to the S phase or go into a quiescent mode, depending on the environmental conditions (e.g., overpopulation, hypoxia). We consider the effect of this decision at the population level in a spherical tissue {r < R(t)}. We prove that if the cells have full control at R ₁, they can manipulate the size of R(t) to ensure that 0 < c ≤ R(t) ≤ C < ∞; simulations further show that R(t) can be made nearly stationary. In the absence of such control, R(t) will either increase to ∞ or decrease to 0. The mathematical model and analysis involve a system of PDEs in {r < R(t)}.     

Duct,exocrine, and endocrine components of cultured fetal mouse pancreas

Summary Twenty to twenty-two days postcoitum mouse fetal pancreas organ bits were cultured on the dermal surface of irradiated pigskin as a substrate. The medium used for long term culture consisted of Eagle’s Minimum Essential Medium with the addition of 10% bovine serum, 0.02 U/ml insulin, 0.025 μg/ml glucagon, 3.63 μg/ml hydrocortisone, 100 μg/ml soybean trypsin inhibitor or 10⁻⁸ M atropine. When the medium lacked trypsin inhibitor or atropine but contained the three hormones, the pigskin support began to be destroyed after 2 to 4 wk in culture. Thereafter, the cultured cells could not grow and survive on the digested pigskin. When 10⁻⁶ M atropine was added to the medium, amylase secretion from cultured cells and destruction of pigskin were inhibited completely but pancreas cells could not grow or survive. In contrast, 100 μg/ml soybean trypsin inhibitor or 10⁻⁸ M atropine permitted cell growth, permitted amylase secretion from the cultured acinar cells, and prevented the destruction of pigskin. Under these conditions pancreas cells migrated or grew or both from the organ bits onto the surface of the pigskin dermis and organoid aggregations formed. Hydrocortisone was needed to permit growth for more than 2 wk. Glucagon and insulin had additive effects. Light and electron microscopic observations indicated the culture of at least five kinds of cells, i.e., duct, acinar, centroacinar, endocrine, and mesenchymal. The majority of cultured cells were duct cells and acinar cells. There were few mesenchymal cells. Mouse pancreas cells were cultured for at least 12 wk by this method. This investigation was supported by PHS Grant CA 30220 awarded by the National Cancer Institute, DHHS, Grant 1203M awarded by the Council for Tobacco Research, Inc., and Grant RD-65 (for equipment) awarded by the American Cancer Society. Nude mice were provided by Dr. Wendall M. Farrow of Life Sciences, Inc., Resource Laboratory N01, CP6-1005 of the National Cancer Institute.     

Physical mapping of genes on yeast mitochondrial DNA: Localization of antibiotic resistance loci, and rRNA and tRNA genes

Summary We have physically mapped the loci conferring resistance to antibiotics that inhibit mitochondrial protein synthesis (erythromycin, chloramphenicol and paromomycin) or respiration (oligomycin I and II), as well as the 21s and 14s rRNA and tRNA genes on the restriction map of the mitochondrial genome of the yeast Saccharomyces cerevisiae. The mitochondrial genes were localized by hybridization of labeled RNA probes to restriction fragments of grande (strain MH41-7B) mitochondrial DNA (mtDNA)¹ generated by endonucleases EcoRI, HpaI, BamHI, HindIII, SalI, PstI and HhaI. We have derived the HhaI restriction fragment map of MH41-7B mit DNA, to be added to our previously reported maps for the six other endonucleases.The antibiotic resistance loci (ant ^R) were mapped by hybridization of ³H-cRNA transcribed from single marker petite mtDNA's of low kinetic complexity to grande restriction fragments. We have chosen the single Sal I site as the origin of the circular physical map and have positioned the antibiotic loci as follows: C (99.5-1.Ou)-P(27-36.Ou)-O_II (58.3-62u)-O_I (80-84u)-E (94.4-98.4u). The 21s rRNA is localized at 94.4-99.2u, and the 14s rRNA is positioned between 36.2-39.8u. The two rRNA species are separated by 36% of the genome. Total mitochondrial tRNA labeled with ¹²⁵I hybridized primarily to two regions of the genome, at 99.5-11.5u and 34-44u. A third region of hybridization was occasionally detected at 70-76u, which probably corresponds to seryl and glutamyl tRNA genes, previously located to this region by petite deletion mapping.Supported by USPHS Training Grant T32-GM-07197.Supported by USPHS Training Grant 5-T01-GM-0090-19.The Franklin McLean Memorial Research Institute is operated by the University of Chicago for the U. S. Energy Research and Development Administration under Contract EY-76-C-02-0069.     

pORE: a modular binary vector series suited for both monocot and dicot plant transformation

We present a series of 14 binary vectors suitable for Agrobacterium-mediated transformation of dicotyledonous plants and adaptable for biolistic transformation of monocotyledonous plants. The vector size has been minimized by eliminating all non-essential elements from the vector backbone and T-DNA regions while maintaining the ability to replicate independently. The smallest of the vector series is 6.3 kb and possesses an extensive multiple cloning site with 21 unique restriction endonuclease sites that are compatible with common cloning, protein expression, yeast two-hybrid and other binary vectors. The T-DNA region was engineered using a synthetic designer oligonucleotide resulting in an entirely modular system whereby any vector element can be independently exchanged. The high copy number ColE1 origin of replication has been included to enhance plasmid yield in Escherichia coli. FRT recombination sites flank the selectable marker cassette regions and allow for in planta excision by FLP recombinase. The pORE series consists of three basic types; an ‘open’ set for general plant transformation, a ‘reporter’ set for promoter analysis and an ‘expression’ set for constitutive expression of transgenes. The sets comprise various combinations of promoters (P _HPL, P _ENTCUP2 and P _TAPADH), selectable markers (nptII and pat) and reporter genes (gusA and smgfp).     

Iso-lines and inbred-lines confirmed loci that underlie resistance from cultivar ‘Hartwig’ to three soybean cyst nematode populations

Soybean [Glycine max (L.) Merr.] cultivars varied in their resistance to different populations of the soybean cyst nematode (SCN), Heterodera glycines, called HG Types. The rhg1 locus on linkage group G was necessary for resistance to all HG types. However, the loci for resistance to H. glycines HG Type 1.3- (race 14) and HG Type 1.2.5- (race 2) of the soybean cyst nematode have varied in their reported locations. The aims were to compare the inheritance of resistance to three nematode HG Types in a population segregating for resistance to SCN and to identify the underlying quantitative trait loci (QTL). ‘Hartwig’, a soybean cultivar resistant to most SCN HG Types, was crossed with the susceptible cultivar ‘Flyer’. A total of 92 F5-derived recombinant inbred lines (RILs; or inbred lines) and 144 molecular markers were used for map development. The rhg1 associated QTL found in earlier studies were confirmed and shown to underlie resistance to all three HG Types in RILs (Satt309; HG Type 0, P = 0.0001 R ² = 22%; Satt275; HG Type 1.3, P = 0.001, R ² = 14%) and near isogeneic lines (NILs; or iso-lines; Satt309; HG Type 1.2.5-, P = 0.001 R ² = 24%). A new QTL underlying resistance to HG Type 1.2.5- was detected on LG D2 (Satt574; P = 0.001, R ² = 11%) among 14 RILs resistant to the other HG types. The locus was confirmed in a small NIL population consisting of 60 plants of ten genotypes (P = 0.04). This QTL (cqSCN-005) is located in an interval previously associated with resistance to both SDS leaf scorch from ‘Pyramid’ and ‘Ripley’ (cqSDS-001) and SCN HG Type 1.3- from Hartwig and Pyramid. The QTL detected will allow marker assisted selection for multigenic resistance to complex nematode populations in combination with sudden death syndrome resistance (SDS) and other agronomic traits.     

Common loci underlie field resistance to soybean sudden death syndrome in Forrest,Pyramid, Essex,and Douglas

Soybean [Glycine max (L.) Merr.] sudden death syndrome (SDS) caused by Fusarium solani f. sp. glycines results in severe yield losses. Resistant cultivars offer the most-effective protection against yield losses but resistant cultivars such as ’Forrest’ and ’Pyramid’ vary in the nature of their response to SDS. Loci underlying SDS resistance in ’Essex’ × Forrest are well defined. Our objectives were to identify and characterize loci and alleles that underlie field resistance to SDS in Pyramid×’Douglas’. SDS disease incidence and disease severity were determined in replicated field trials in six environments over 4 years. One hundred and twelve polymorphic DNA markers were compared with SDS disease response among 90 recombinant inbred lines from the cross Pyramid×Douglas. Two quantitative trait loci (QTLs) for resistance to SDS derived their beneficial alleles from Pyramid, identified on linkage group G by BARC-Satt163 (261-bp allele, P=0.0005, R²=16.0%) and linkage group N by BARC-Satt080 (230-bp allele, P=0.0009, R²=15.6%). Beneficial alleles of both QTLs were previously identified in Forrest. A QTL for re- sistance to SDS on linkage group C2 identified by BARC-Satt307 (292-bp allele, P=0.0008, R²=13.6%) derived the beneficial allele from Douglas. A beneficial allele of this QTL was previously identified in Essex. Recombinant inbred lines that carry the beneficial alleles for all three QTLs for resistance to SDS were significantly (P≤0.05) more resistant than other recombinant inbred lines . Among these recombinant inbred lines resistance to SDS was environmentally stable. Therefore, gene pyramiding will be an effective method for developing cultivars with stable resistance to SDS. Received: 20 October 1999 / Accepted: 22 May 2001     

Hypoxia tolerance decreases with body size in red drum Sciaenops ocellatus

Mass‐specific oxygen consumption rate, i.e. standard metabolic rate (R_s) and critical oxygen tension (P_crit) of red drum Sciaenops ocellatus were measured and scaled over a 2500‐fold range in mass (M_F; 0·26–686 g). R_s conformed to well established models (R_s = 3·73·91 M_F^?0·21; r² = 0·86) while P_crit increased over the size range (P_crit = 3·15 log₁₀M_F + 16·19; r² = 0·44). This relationship may be ecologically advantageous as it would allow smaller S. ocellatus to better utilize hypoxic zones as habitat and refuge from predators.     

Stability of Hor1-specific YAC-clones and physical mapping of Hor1-loci in barley

 The hordeins are the major class of storage proteins in barley and are encoded by multigene families. Two YAC-clones specific for the C-hordein-coding Hor1-locus of barley (Hordeum vulgare L.) were selected. The clones were constructed with DNA from the cultivars ‘Franka’ and ‘Hockey’ and have insert sizes of 330 kb and 350 kb, respectively. Performing partial digestions and hybridizations with vector-specific probes, a restriction analysis was conducted using restriction enzymes with a 8-bp recognition sequence. Both clones cover the complete region of the Hor1-locus, but exhibit a different pattern of restriction sites reflecting the polymorphic nature of the locus on the scale of long-range restriction mapping. The maximal extent of the regions homologous to the Hor1-specific probe, pBSC5, was 105 kb in the ‘Hockey’-derived YAC and 190 kb in the yeast artificial chromosome constructed with ‘Franka’-DNA. Furthermore the high degree of instability observed with the Hor1-specific YAC-clones is discussed in conjunction with the structure of the Hor1-locus. Received: 19 December 1996 / Accepted: 31 January 1997     

Somatic embryogenesis from stigmas and styles of grapevine

Summary An in vitro protocol has been developed for callus indiction, somatic embryogenesis, and plant regeneration from stigma-style culture of grapevine. Four different grapevine cultivars (Vitis vinifera L.: cvs. ‘Bombino Nero’, ‘Greco di Tufo’, ‘Merlot’, and ‘Sangiovese’) were tested. Exlants were cultured on Nitsch and Nitsch medium (NN) supplemented with various combinations of 6-benzylaminopurine (BA: 4.5 and 9.0 μM) and β-naphthoxyacetic acid (NOA; 5.0 and 9.9 μM). Sucrose (88 mM) was used as the carbon source. Somatic embryogenesis was induced within 3–7 mo. after culture initiation. Even though explants of different origin (unfertilized ovules and anthers) regenerated somatic embryos, the higher embryogenic potential was observed in stigma and style explants, with the exception of ‘Merlot’, which regenerated somatic embryos only from unfertilized ovules. The percentages of stigma-style explants producing somatic embryos was 7% in ‘Bombino Nero’ (cultured on NN medium supplemented 9.0 μM BA and 9.9 μM NOA). 14% in ‘Greco di Tufo’ (4.5 μM BA and 9.9 μM NOA), and 8% in ‘Sangiovese’ (9.0 μM BA and 9.9 μM NOA). The presence of growth regulators (BA and NOA) in the medium was essential for induction of somatic embryogenesis. Plants were regenerated on hormone-free NN medium containing 88 mM sucrose.