Estimation of restriction maps with known site order using a generalized linear model

A generalized linear model with Gamma errors is used to estimatethe coordinates of a restriction map when the site order isknown. This can be conveniently programmed in a wide range ofstatistical packages (e.g. Genstat 5, Minitab, SAS), and givesmaximum likelihood estimates with their associated optimal properties.Regression diagnostics allow the checking of assumptions andhelp to identify mis–specified, influential or discordantfragment lengths. A specific diagnostic for identifying fragmentlengths causing reversal of restriction site order is derived.Exact ‘fragment’ lengths from DNA sequencing canbe conveniently included in an approximate manner by givingthem a larger weight than observed restriction fragment lengths.Two examples and the Genstat 5 codes used in their analysisare presented.     

Electron Microscopic Studies of Skeletal and Cardiac Muscle of a Benthic Fish. I. Myofibrillar Structure in Resting and Contracted Muscle

SYNOPSIS. Electron microscopic studies are reported on glycerinatedskeletal and cardiac muscle of a benthic fish, Coryphaenoidesspecies. In white skeletal muscle, the sarcomeres have a restinglength of approximately 1.8 µ, with thick filaments 1.4µ and thin filaments 0.75 µ in length. These dimensionsare somewhat shorter than filament lengths of oilier vertebratemuscles, possibly due to the elfect of volume increase duringassembly of thick and thin filaments at high hydrostatic pressure.During ATP-induced contraction of Coryphaenoides muscle fromsarcomere lengths of 1.8 µ to 1.6 µ, there is acharacteristic interdigitation of thick and thin filaments,with decrease in I band length and no change in length of thickor thin filaments. However, in sarcomeres contracted to lengthsof 1.5 µ. to 1.2 µ, there is a slight shorteningof the A band, apparently due to shortening of thick filaments,that occurs despite the presence of residual I band in the samesarcomeres. There is no obvious crumpling or distortion of thickfilaments during contraction to sarcomere lengths as low as1.0 µ, but filament organization undergoes extensive disarrayat sarcomere lengths approaching 0.7 µ. Although effectsfrom heterogeneity of filament length cannot be excluded withcertainty, the present evidence does suggest that contractionot Coryphaenoides muscle from 1.6 µ to 1.0 µ sarcomerelengih is accompanied by shortening of thick filaments consequentto a structural change within the thick filament core.     

MHC-BPS: MHC-binder prediction server for identifying peptides of flexible lengths from sequence-derived physicochemical properties

Major histocompatibility complex (MHC)-binding peptides are essential for antigen recognition by T-cell receptors and are being explored for vaccine design. Computational methods have been developed for predicting MHC-binding peptides of fixed lengths, based on the training of relatively few non-binders. It is desirable to introduce methods applicable for peptides of flexible lengths and trained by using more diverse sets of non-binders. MHC-BPS is a web-based MHC-binder prediction server that uses support vector machines for predicting peptide binders of flexible lengths for 18 MHC class I and 12 class II alleles from sequence-derived physicochemical properties, which were trained by using 4,208∼3,252 binders and 234,333∼168,793 non-binders, and evaluated by an independent set of 545∼476 binders and 110,564∼84,430 non-binders. The binder prediction accuracies are 86∼99% for 25 and 70∼80% for five alleles, and the non-binder accuracies are 96∼99% for 30 alleles. A screening of HIV-1 genome identifies 0.01∼5% and 5∼8% of the constituent peptides as binders for 24 and 6 alleles, respectively, including 75∼100% of the known epitopes. This method correctly predicts 73.3% of the 15 newly published epitopes in the last 4 months of 2005. MHC-BPS is available at .Electronic Supplementary Material Supplementary material is available for this article at and is accessible for authorized users.     

The Length Distribution of Perfect Dimer Repetitive DNA Is Consistent with Its Evolution by an Unbiased Single-Step Mutation Process

We have examined the length distribution of perfect dimer repeats, where perfect means uninterrupted by any other base, using data from GenBank on primates and rodents. Virtually no lengths greater than 30 repeats are found, except for rodent AG repeats, which extend to 35. Comparable numbers of long AC and AG repeats suggest that they have not been selected for special functions or DNA structures. We have compared the data with predictions of two models: (1) a Bernoulli Model in which bases are assumed equally likely and distributed at random and (2) an Unbiased Random Walk Model (URWM) in which repeats are permitted to change length by plus or minus one unit, with equal probabilities, and in which base substitutions are allowed to destroy long perfect repeats, producing two shorter perfect repeats. The source of repeats is assumed to be from single base substutions from neighboring sequences, i.e., those differing from the perfect repeat by a single base. Mutation rates either independent of repeat length or proportional to length were considered. An upper limit to the lengths L≈ 30 is assumed and isolated dimers are assumed unable to expand, so that there are absorbing barriers to the random walk at lengths 1 and L+ 1, and a steady state of lengths is reached. With these assumptions and estimated values for the rates of length mutation and base substitution, reasonable agreement is found with the data for lengths > 5 repeats. Shorter repeats, of lengths ≤ 3 are in general agreement with the Bernoulli Model. By reducing the rate of length mutations for n≤ 5, it is possible to obtain reasonable agreement with the full range of data. For these reduced rates, the times between length mutations become comparable to those suggested for a bottleneck in the evolution of Homo sapiens, which may be the reason for low heterozygosity of short repeats.     

X-Ray Crystal Structure of a Highly Functionalized Thiophene as a New Backbone Amide Linker for Solid-phase Peptide Synthesis. Relationship between Crystal Structure and Reactivity

The development of new linkers (handles) for solid-phase synthesis provides new chemical opportunities for peptide synthesis. To understand the chemical properties of a recently developed backbone amide linker from a structural perspective, the crystal structure of S-((5-formyl-3,4-ethylenedioxy)thiophene-2-yl)-3-thiopropionic acid (T-BAL2) was studied. Specifically, we wished to address whether this highly substituted thiophene retained planarity in the aromatic ring as well as between the aromatic ring and the aldehyde carbonyl. Furthermore, we sought an explanation for the relatively low reactivity in reductive aminations of the thienylaldehyde with amines in solution and on solid phase. Based on the crystal structure of T-BAL2, the thienyl-C (aldehyde) and C–O (aldehyde) bond lengths were applied as measures for the electron-deficiency (electrophilicity) of the aldehyde and compared to similar bond lengths found in previously reported formylated homo- and hetero-aromatic systems, which show significantly higher reactivity towards imine formation. The bond lengths found in the present structure are in accordance with normal C–C single bond and C–O double bond lengths. The high similarity in aldehyde bond lengths in the present system and in the reported systems indicates similar electron distribution in these systems. The lower reactivity of the present system may therefore not be attributed to electronic factors.     

Architectural and functional features of human triceps surae muscles during contraction

Architecturalproperties of the triceps surae muscles were determined in vivo for sixmen. The ankle was positioned at 15° dorsiflexion (15°)and 0, 15, and 30° plantar flexion, with the knee set at 0, 45, and90°. At each position, longitudinal ultrasonic images of the medial(MG) and lateral (LG) gastrocnemius and soleus (Sol) muscles wereobtained while the subject was relaxed (passive) and performed maximalisometric plantar flexion (active), from which fascicle lengths andangles with respect to the aponeuroses were determined. In the passivecondition, fascicle lengths changed from 59, 65, and 43 mm (knee,0°; ankle, 15°) to 32, 41, and 30 mm (knee, 90°ankle, 30°) for MG, LG, and Sol, respectively. Fascicle shorteningby contraction was more pronounced at longer fascicle lengths. MG hadgreatest fascicle angles, ranging from 22 to 67°, and was in a verydisadvantageous condition when the knee was flexed at 90°,irrespective of ankle positions. Different lengths and angles offascicles, and their changes by contraction, might be related todifferences in force-producing capabilities of the muscles and elasticcharacteristics of tendons and aponeuroses.

     

Size-selective grazing of bacteria by Bosmina longirostris--an image-analysis study

Image analyses on the filtering apparatus of Bosmina longirostricshowed that the filter mesh is finer on the gnathobasic filterplates of the second and third trunk limbs (ranges from 0.43to 0.97 µm) and coarser for the outer ones of the thirdlimb (ranges from 0.5 to 1.36 µm), and the intersetulardistances increase with body length. Grazing experiments combinedwith image analysis confirmed the efficient grazing of B.longirostrison natural bacteria with cell lengths equal to or larger thanthe intersetular distances of the gnathobasic filter plates.During the experiments, the animals minimized the average celllength of the bacterioplankton assemblages from 0.77–0.96µm to 0.55–0.68 µm, corresponding to the meanof the filter mesh size on the fine gnathobasic filter platesof the experimental populations. The clearance rates for large,elongated or dividing cells with maximal lengths of 0.88–8.40µm were 2.3–17.7 times higher than those for smallsingle coccoids with a diameter of <0.45 µm. The resultsprovide evidence of a significant differential impact of B.longirostrison the bacterial community structure with respect to the shapeand size of the cells, and demonstrate that the species is amore effective bacterial feeder than considered previously.     

Contribution to the theory of random and biased nets

The probabilistic theory of random and biased nets is further developed by the “tracing” method treated previously. A number of biases expected to be operating in nets, particularly in sociograms, is described. Distribution of closed chain lengths is derived for random nets and for nets with a simple “reflexive” bias. The “island model” bias is treated for the case of two islands and a single axon tracing, resulting in a pair of linear difference equations with two indices. The reflexive bias is extended to multiple-axon tracing by an approximate method resulting in a modification of the random net recursion formula. Results previously obtained are compared with empirical findings and attempts are made to account for observed discrepancies.     

Effect of operational cycle time length on nitrogen removal in an alternating oxidation ditch system

This paper refers to nitrogen removal optimization of an alternating oxidation ditch system through the use of a mathematical model and pilot testing. The pilot system where measurements have been made has a total volume of 120 m³ and consists of two ditches operating in four phases during one cycle and performs carbon oxidation, nitrification, denitrification and settling. The mathematical model consists of one-dimensional mass balance (convection–dispersion) equations based on the IAWPRC ASM 1 model. After the calibration and verification of the model, simulation system performance was made. Optimization is achieved by testing operational cycles and phases with different time lengths. The limits of EU directive 91/271 for nitrogen removal have been used for comparison. The findings show that operational cycles with smaller time lengths can achieve higher nitrogen removals and that an “equilibrium” between phase time percentages in the whole cycle, for a given inflow, must be achieved.     

Photoperiod Responses of Corchorus olitorius L. in Controlled Environments

Controlled environments were used to establish the base-linegrowth and to evaluate the photoperiodic response of two Tossajute (Corchorus olitorius) cultivars. Fresh and dry weightsof shoots and roots, leaf areas and stem lengths were much greaterat long day (LD) 12·5, 11·5 than LD 11·5,12·5 photoperiods for both cultivars. Root lengths weregreater at LD 12·5, 11·5 initially but were longestat LD 11·5, 12·5 at 35 days from emergence. Meanrelative growth rates (MRGR) were similar irrespective of photoperiodor cultivar but declined with plant age. The superior growthof cultivar ‘Yaya’ at LD 12·5, 11·5was due to more growth in the first 7 days, while, for cultivar‘Angbadu’ it was a combination of growth for 7 days,and higher MRGR up to 21 days. Stomatal density was greaterat LD 12·5, 11·5 than LD 11·5, 12·5. Corchorus olitorius L., Tossa jute, photoperiodism, relative growth rate     

Linkage analysis in tetraploid potato and association of markers with quantitative resistance to late blight ( Phytophthora infestans )

We have constructed a partial linkage map in tetraploid potato which integrates simplex, duplex and double-simplex AFLP markers. The map consists of 231 maternal and 106 paternal markers with total map lengths of 990.9 cM and 484.6 cM. The longer of the two cumulative map lengths represents approximately 25% coverage of the genome. In tetraploids, much of the polymorphism between parental clones is masked by `dosage' which significantly reduces the number of individual markers that can be scored in a population. Consequently, the major advantage of using AFLPs – their high multiplex ratio – is reduced to the point where the use of alternative multi-allelic marker types would be significantly more efficient. The segregation data and map information have been used in a QTL analysis of late blight resistance, and a multi-allelic locus at the proximal end of chromosome VIII has been identified which contributes significantly to the expression of resistance. No late blight resistance genes or QTLs have previously been mapped to this location. Received: 1 October 1997 / Accepted: 18 March 1998     

Muscle anatomy is a primary determinant of muscle relaxation dynamics in the lobster (<Emphasis Type="Italic">Panulirus interruptus</Emphasis>) stomatogastric system

We stained sarcomere thin filaments with fluorescently labeled phalloidin, measured sarcomere and muscle length, and calculated sarcomere number in pyloric and gastric mill muscles. A wide range of sarcomere lengths (3.25–12.29 μm), muscle lengths (5.9–21.1 mm), and sarcomere numbers (648–3,036) were observed. Sarcomere number differences occurred both because of changes in sarcomere length and muscle length, and sarcomere and muscle length varied independently. This independence, the wide range of sarcomere numbers present, and the muscles being all ‘slow’, graded muscles allowed us to use these data to test Huxley and Neidergerke’s (1954) hypothesis that muscle dynamics depend on sarcomere number. The time constants of exponential fits to contraction relaxations were used to measure muscle dynamics, and comparison of theoretical predictions and experimental results quantitatively confirm the predicted dependence. The differing dynamics of the various pyloric muscles are likely functionally important, and the dependence of muscle dynamics on sarcomere number implies that sarcomere number is likely closely regulated in these muscles. The stomatogastric system may thus be an excellent model system for studying the mechanisms regulating muscle sarcomere number.     

Loopstructures in synthetic oligonucleotides. Hairpin stability and structure studied as a function of loop elongation

The formation of hairpin structures in the homologous, (partly) self-complementary DNA fragments d(ATCCTAT_nTAGGAT), n = 0–7, was studied by means of nuclear magnetic resonance, T-jump and ultra-violet techniques. It is shown that all compounds in the series may adopt hairpin-like conformations, albeit for n < 3 this only occurs to a significant amount at relatively low concentrations (∼ 10μM). For the present series of oligonucleotides, hairpin formation is accompanied by an apparent loop enthalpy significantly different from zero. The stability of the DNA hairpins turns out to be at its maximum for loop lengths of four or five residues, whereas earlier experiments (Tinocoet al., 1973) indicated that loop lengths of six to seven residues are most favourable for RNA hairpins. This is explained by considering the difference in geometry of A-RNA and B-DNA helices.     

Ultrastructure of the marine predatory flagellate <Emphasis Type="Italic">Metromonas simplex</Emphasis> Larsen et Patterson, 1990 (Cercozoa)

The ultrastructure of the marine predatory flagellate Metromonas simplex Larsen et Patterson was studied. The cell is surrounded by a low-contrast fibrous layer composed of thin hairs covered by a thin bilayer membrane and an outer layer of thin short fibers. The plasmalemma lies under these layers. The predator captures whole cells of the prey, usually bodonids or chrysomonads. The cytostome as a cell pocket is undetectable. The long flagellum bears very thin mastigonemes (hairs) with lengths of 0.8–1.0 μm; the short flagellum is naked and reduced in length. The transitional zone lacks spirals or other additional elements. The transversal plate is elevated on the cell surface. The flagellar root system is very simple and has one microtubular band which originates near the kinetosomes. The latter are parallel to each other and interconnected by fibrous bridges. The vesicular nucleus, Golgi apparatus, and endoplasmic reticulum are of typical structures. The oval mitochondria of 0.6–2.5 μm contain lamellar cristae. The cylindrical extrusomes (trichocysts) found in the cytoplasm have lengths of 1.0–1.4 μm and diameters of 0.12–0.08 μm. The trichocysts have a wheel-shaped structure with 13 spokes visible in cross-sections. The contractile vacuole is absent. The similarity that M. simplex shares with Metopion fluens Larsen et Patterson, cryothecomonads, and other predatory flagellates is discussed.     

The influence of plant growth regulators and storage on root induction and growth in <Emphasis Type="Italic">Pelargonium zonale</Emphasis> cuttings

The effects of post harvest application of ethylene, abscisic acid (ABA), indole-3-butyric acid (IBA) treatments or dark storage on root induction and continued growth of regenerated roots in Pelargonium cuttings were investigated using hydroponics in the greenhouse. Ethylene markedly increased rooting percentage in ‘Greco’ and ‘Surfing’, reduced the number of roots per cutting in ‘Surfing’ and had no effect on the total root lengths in the two cultivars. Ethylene treatment reduced fresh root mass in ‘Surfing’, increased dry root mass and reduced root water content in both cultivars. ABA (50 μM) enhanced rooting percentage in ‘Greco’, reduced the number of roots per cutting, reduced total root lengths and fresh root mass in both cultivars. ABA increased dry root mass and reduced root water content in ‘Surfing’ but this effect was not apparent in ‘Greco’. Storing cuttings in the dark for 4 days had no effect on rooting percentage and number of roots per cutting in ‘Greco’ and ‘Surfing’. However, dark storage reduced total root lengths in ‘Surfing’ and reduced fresh root mass in ‘Greco’. Dark storage had no effect on dry root mass and water content in both cultivars. Applying 4 μl l⁻¹ IBA in the rooting solution induced maximum (100%) root induction in ‘Surfing’. However, IBA reduced the number of roots per cutting in ‘Greco’, reduced total root lengths and fresh root mass in the two cultivars. IBA treatment profoundly increased and reduced dry root mass and root water content, respectively, in ‘Greco’ and ‘Surfing’. The enhanced root induction observed after IBA and ABA applications could be ascribed to their influence on ethylene biosynthesis, since ethylene treatment increased rooting percentage in both cultivars. However, high ABA (100 μM) and IBA (12 μl l⁻¹) levels or dark storage reduced the ability of induced roots to continue growth. We attribute our results to plant stress-response mechanism and ethylene appears to play an important role in the process of root initiation and root growth in Pelargonium cuttings.     

Effects of trace elements on the telomere lengths of hepatocytes L-02 and hepatoma cells SMMC-7721

The effects of selenium, zinc, iron, chromium, and lead on telomere lengths of human cells have not been investigated. This article adopted flow cytometry and fluorescence in situ hybridization to investigate the impact of different elements on cellular apoptosis and telomere lengths of human hepatocytes L-02 and hepatoma cells SMMC-7721. Results showed that these trace elements under the following dosages did not have remarkable effect on cellular apoptosis. However, sodium selenite at doses of 0.5 and 2.5 μmol/L significantly extended the telomere length of hepatocytes L-02; 0.5 μmol/L lead acetate remarkably shortened the telomere length of L-02 cells; 80 μmol/L zinc sulfate, 20 μmol/L ferric chloride, and 200 μmol/L chromic chloride only had slight impact on the telomere length, respectively. Regarding hepatoma cells SMMC-7721, sodium seleite at 0.5 and 2.5 μmol/L had little impact on the telomere length; 80 μmol/L zinc sulfate significantly accelerated the loss of telomere length, whereas 20 μmol/L ferric chloride, 200 μmol/L chromic chloride, and 0.5 μmol/L lead acetate remarkably extended the telomere lengths, respectively. The results revealed differential effects of each trace element on the life-span of human hepatocytes and hepatoma cell lines, which suggested further research on somatic hepatocytes and hepatoma in vivo.     

Nitrogen and phosphorus uptake in two Idaho (USA) headwater wilderness streams

Nitrate and phosphate solutions were released into two reaches of two central Idaho streams to determine within- and between-stream variability in uptake lengths, uptake rates, and mass transfer coefficients. Physical and biotic stream characteristics and periphyton nitrate-uptake rates in recirculating chambers were measured to determine their influence on nutrient dynamics. Phosphate uptake length did not differ among the four reaches. There were no within-stream differences in nitrate uptake lengths but they did differ between the two streams. Long nitrate uptake lengths likely were due to instream concentrations above saturation but also may have been influenced by differences in active surface area and algal abundance. Nitrate and phosphate uptake lengths were longer, and uptake rates higher, than most other published values. However, mass transfer coefficients were comparable to measurements in other streams. Mass transfer coefficients may be a better parameter for temporal and spatial comparisons of instream nutrient dynamics, and for determining the underlying causes of variability in uptake length. Received: 27 May 1998 / Accepted: 11 January 1999     

Characterization of the 16S–23S internal transcribed spacer among 34 higher plants: suitability for interspecific plastid transformation

Biomanufacturing by chloroplast transgene expression has the potential to produce significant amounts of biopharmaceuticals, endow plants with novel commercial or humanitarian capabilities, enhance phytoremediation methods and harden plants against adverse environments. Plastid bioengineering exploits the phenomenon of homologous recombination to specifically integrate heterologous sequences into the plastid genome. Previous research suggests the plastid genome 16S–23S internal transcribed spacer provides an advantageous integration site for transgene expression. To characterize the suitability of the 16S–23S region for interspecific recombination, we developed primers against conserved plastid sequences and amplified ∼2.6 kb from 25 plant species. We analyzed the amplicons with nine species from Genbank for homeology, phylogenetic relationships, potential to form chimeric rDNA elements disruptive to translational/replication systems, and the potential number of recombination events for various minimal essential processing segments (MEPS) lengths. Multiple sequence alignment of the 34 species revealed considerable conservation, with identities exceeding 95% among the angiosperms. Substitutions were statistically clustered, generally in noncoding sites, although proposed functional elements such as the OriA region and 3′ terminus of the 16S rRNA exhibited unexpected variation. The nonrandom distribution of substitutions undermines the established, statistical method of estimating the number of recombination initiation sites. This finding is further substantiated by comparing statistical estimates of the number of MEPS sites to a direct count at three different MEPS lengths. We frame this in silico analysis in terms of the potential of the 16S–23S region as a target for interspecific transformation, and describe a ‘primer-to-plastid’ system to rapidly generate species-specific flanking regions for transformation vectors.     

The style–length of the female florets and their fate in two dioecious species of Xishuangbanna, China

Constraints and evolution are central for the resolution of conflicts between mutualism species and for the stability of mutualisms. Dioecious fig species and their specific pollinators are also in conflict on the use of fig ovaries. Here, our experiments provided some data on the female florets allocation in two dioecious fig trees. The results showed that: (1) there is a bimodal distribution in the style–length of two fig trees’ female florets, moreover, the style–lengths are fairly similar and narrowly distributed in gall figs and more variation seems to occur in seed figs; (2) the styles in seed figs are a little longer than those in gall figs; (3) the pollinator's ovipositor lengths are shorter than the style–lengths in seed figs, but they are very similar to those in gall figs so that pollinators can only lay their eggs into the ovaries of gall figs, but not in seed figs; (4) the stigmas stick together, and the style is curly and flexible in seed syconia of the two fig species studied, so it is very difficult for the pollinators to find suitable ovipositing sites and lay their eggs in seed figs; (5) the variations of style-lengths are bigger in seed figs than gall figs, but they are smaller in dioecious figs than monoecious figs; (6) for Ficus cyrtophylla, about 10% styles are shorter in seed figs than those in gall figs, even shorter than ovipositor. In contrast, about 2% styles in gall figs of Ficus hispida are longer than its corresponding pollinator's ovipositor. In a word, our study suggests that the female floret's fate in these two fig species is mainly dependent on its style–length, but not all. The stigma shape and the floral organization can both also attribute to their fate in the two fig species studied.