Multiple DNA and protein sequence alignment on a workstation and a supercomputer

This paper describes a multiple alignment method using a workstationand supercomputer. The method is based on the alignment of aset of aligned sequences with the new sequence, and uses a recursiveprocedure of such alignment. The alignment is executed in areasonable computation time on diverse levels from a workstationto a supercomputer, from the viewpoint of alignment resultsand computational speed by parallel processing. The applicationof the algorithm is illustrated by several examples of multiplealignment of 12 amino acid and DNA sequences of HIV (human immunodeficiencyvirus) env genes. Colour graphic programs on a workstation andparallel processing on a supercomputer are discussed. Received on April 26, 1988; accepted on July 7, 1988     

Ergot—a blessing and a scourge

Ergot, the black mass of a particular fungus on cereal grains, especially rye, was the cause of frightful epidemics in Europe more than a thousand years ago, and the ingested contaminated grain has occasioned disease in Russia as late as 1927 and in the United States a generation earlier. Medicinally administered, however, it provides a very important drug in the science of obstetrics.     

Carotenoids in floral parts of a narcissus, a daffodil and a tulip

1. The qualitative and quantitative distribution of carotenoids of the floral parts of three monocotyledons, the narcissus Scarlet Elegance, the daffodil King Alfred and the tulip Golden Harvest, were studied. β-Carotene, lutein or epoxy-β-carotenes were usually the main pigments, depending on the floral part and on the flower. When β-carotene was the major pigment there were only small amounts of, or sometimes no, epoxycarotenes. 2. Anthers, stigmas and styles of the three flowers did not possess any specific carotenoids but in some cases contained appreciable amounts of epoxycarotenoids. The possibility that these take part in reproduction is discussed. 3. The generalization that yellow flowers contained large amounts of xanthophylls and only traces of carotenes, whereas deep-orange flowers seemed to be characterized by the presence of large amounts of one carotene, was not always the correct one. It is suggested that the floral parts are yellow or orange depending on what carotenoids are present, which is the major one and the amount of total carotenoids, and also on the presence of other non-carotenoid pigments. 4. Two new probable isomers of 5,6:5′,6′-diepoxy-β-carotene were isolated and found together in various floral parts of the tulip Golden Harvest.     

Needle aspiration cytology of a benign and a malignant schwannoma

The histologic and cytologic features of an uncommon solitary, malignant schwannoma and a benign schwannoma are presented. The benign tumor revealed characteristic interlacing fascicles of spindle-shaped cells on both histology and cytology. The malignant schwannoma produced a variable histologic pattern that was selectively sampled from a recurrence in a scar; only obviously malignant, undifferentiated, spindle-shaped cells not capable of further characterization were seen on cytology. Preliminary experience with immunoperoxidase staining for the neural crest marker S-100 protein has been encouraging and may permit identification of these tumors on aspiration smears.     

Aquatic and terrestrial locomotory energetics in a toad and a turtle: a search for generalisations among ectotherms

Murray short-necked turtles were trained to walk on a motorised treadmill and to swim in a recirculating flume. Through filmed records, the frequency of limb movement and the time that thrust was directed against the substrate were measured. The animals wore masks when walking and accessed air when swimming from a ventilated capsule placed on top of the water surface. Measurement of the exhalant O(2) and CO(2) levels from these devices enabled the measurement of metabolic rates. Equivalent data were obtained from swimming and hopping cane toads, although repeatable measures of limb frequency and contact times were not obtained due to the intermittent form of locomotion in this species. Comparing the cost of transport, the energy required to transport a mass of animal over a unit distance, with other animals showed that toads do not have a cheap form of terrestrial locomotion, but turtles do; turtles use half the cost predicted from their body mass. This economy of locomotion is consistent with what is known about turtle muscle, the mechanics of their gait, and the extremely long contact time for a limb with the substrate. Swimming in toads is energetically expensive, whereas turtles, on the basis of mass, use about the same energy to transport a unit mass as an equivalent-size fish. The data were compared with the predictions of the Kram-Taylor hypothesis for locomotory scaling, and walking turtles were found to provide a numerical fit. The data show that both terrestrial and aquatic locomotory energetics in toads are generally higher than predictions on the basis of mass, whereas in turtles they are lower.     

Comparison of a potentiometric and a micromechanical triglyceride biosensor

Sensitive biosensors for detection of triglyceride concentration are important. In this paper we report on two types of silicon based triglyceride sensors: an electrolyte-insulator-semiconductor capacitor (EISCAP) which is a potentiometric device and a polysilicon microcantilever. The detection principle for both sensors is based on the enzymatic hydrolysis of triglyceride though the sensing mechanisms are different: electronic for the EISCAP and mechanical for the microcantilever. The characteristics and performances of the two sensors are critically compared. The EISCAP sensor necessitates the presence of a buffer for stable measurements which limits the sensitivity of the sensor at low concentrations of the bioanalyte to 1mM. The cantilever sensor works without a buffer which improves the lower level of sensitivity to 10 microm. Both sensors are found to give reproducible and reliable results.     

Strain while skiing and hauling a sledge or carrying a backpack

Eight soldiers on skis transported three loads of different weights on the level, uphill and downhill. The load was placed either on a cargo sledge or in a backpack or divided between the sledge and the backpack. The sledge had a new type of haulage-shaft, which was fixed to both sides of the pelvis. A service belt spread the pull over the whole upper body. The physical stain of different transport methods and the serviceability of the sledge was studied by measuring heart rate (HR), oxygen consumption, ventilation, and perceived exertion. The results indicate that both absolute and relative strain were systematically lower when pulling the load on the sledge than when carrying it in the backpack and on the sledge. HR when pulling a load equal to the human body weight on the sledge was on average 133 beats X min-1; HR was significantly higher 144 beats X min-1 when the load was divided between backpack and sledge. At the lower load level the differences between the transport methods were not significant for HR, oxygen consumption or ventilation. Uphill travel increased oxygen consumption by about 50% over that on the level. Perceived exertion at all load levels was significantly lower with the sledge than with the backpack alone or in combination. The estimated maximal allowable working time emphasized the advantage of the sledge and the importance of high physical working capacity. The maneuverability of the sledge with the new haulage shaft was good and the braking mechanisms worked well.(ABSTRACT TRUNCATED AT 250 WORDS)     

Simultaneous force and fluorescence measurements of a protein that forms a bond between a living bacterium and a solid surface

All microbial biofilms are initiated through direct physical contact between a bacterium and a solid surface, a step that is controlled by inter- and intramolecular forces. Atomic force microscopy and confocal laser scanning microscopy were used simultaneously to observe the formation of a bond between a fluorescent chimeric protein on the surface of a living Escherichia coli bacterium and a solid substrate in situ. The chimera was composed of a portion of outer membrane protein A (OmpA) fused to the cyan-fluorescent protein AmCyan. Sucrose gradient centrifugation and fluorescent confocal slices through bacteria demonstrated that the chimeric protein was targeted and anchored to the external cell surface. The wormlike chain theory predicted that this protein should exhibit a nonlinear force-extension "signature" consistent with the sequential unraveling of the AmCyan and OmpA domains. Experimentally measured force-extension curves revealed a unique pair of "sawtooth" features that were present when a bond formed between a silicon nitride surface (atomic force microscopy tip) and E. coli cells expressing the OmpA-AmCyan protein. The observed sawtooth pair closely matched the wormlike chain model prediction for the mechanical unfolding of the AmCyan and OmpA substructures in series. These sawteeth disappeared from the measured force-extension curves when cells were treated with proteinase K. Furthermore, these unique sawteeth were absent for a mutant stain of E. coli incapable of expressing the AmCyan protein on its outer surface. Together, these data show that specific proteins exhibit unique force signatures characteristic of the bond that is formed between a living bacterium and another surface.     

Between a rock and a hard place: arthropod trackways and ichnotaxonomy

Several challenges exist in ichnotaxonomy: overcoming the perceived distinction between invertebrate and vertebrate ichnotaxonomy, standardizing terminology, rationalizing the plethora of ichnotaxa already in existence, and developing principles for diagnosing new ichnotaxa. Ichnotaxa should be based on morphology, and this morphology incorporates three key components; the behaviour expressed, the producer, and the substrate. Invertebrate and vertebrate ichnotaxa can both be accommodated within this framework, but they differ in the relative contributions of these components. The key to justifying the synonymy of existing ichnotaxa is the recognition of intergrading specimens. However, this is only the case for minor morphological variants (i.e. those representing minor differences in behaviour, such as gait parameters or stance; or minor differences in preservation, such as undertrack fallout or slight differences in substrate conditions). Intergrading specimens should not be used to justify synonymy between major morphological variants (i.e. those representing major behavioural differences, defined herein as ethological categories; or major differences in preservation, such as formation in soup, soft and firmgrounds), and such specimens should be denoted as hybrids (e.g. Cruziana × Rusophycus ). New ichnotaxa should ideally be based on observations of large samples of material, so that recurrence is demonstrable, and morphological continuums, or subset relationships, representing minor morphological variation, are identified. Ichnotaxa may only be erected on the basis of limited material if they truly represent a unique morphology. These principles have been developed with arthropod trackways in mind, but it is hoped that they will be of more general utility.     

利用δ声波场和近红外光实现乳腺肿瘤的精确定位

本文提出一种利用δ声波场和近红外光漫射理论实现球形乳腺肿瘤精确定位的新颖思路。通过构建一个δ波形的声波场,作用到乳腺组织中从而改变组织内某一点的光学特性参数,这种改变对组织表面光分布的影响可以视为微扰,通过控制其作用点在深度上扫描,测得一系列乳腺组织表面一级微扰光分布,从中提取肿瘤与正常组织的差异特性,实现乳腺肿瘤的精确定位和大小测定。该方法具有广泛的临床医学应用前景,为乳腺癌的早期检测提供一种全新思路。     

Hypolithic microbial communities: between a rock and a hard place

Drylands are the largest terrestrial biome on Earth and a ubiquitous feature is desert pavement terrain, comprising rocks embedded in the mineral soil surface. Quartz and other translucent rocks are common and microbial communities termed hypoliths develop as biofilms on their ventral surfaces. In extreme deserts these represent major concentrations of biomass, and are emerging as key to geobiological processes and soil stabilization. These highly specialized communities are dominated by cyanobacteria that support diverse heterotrophic assemblages. Here we identify global-scale trends in the ecology of hypoliths that are strongly related to climate, particularly with regard to shifts in cyanobacterial assemblages. A synthesis of available data revealed a linear trend for colonization with regard to climate, and we suggest potential application for hypoliths as 'biomarkers' of aridity on a landscape scale. The potential to exploit the soil-stabilizing properties of hypolithic colonization in environmental engineering on dryland soils is also discussed.     

Respiratory and behavioral effects of ozone on a lizard and a frog

Ozone at concentrations found in urban air pollution is known to have significant physiological effects on humans and other mammals. Exposure of the lizard, Sceloporus occidentalis, to 0.6 ppm ozone for 4 h at 25 degrees C induced 1.6 degrees C of behavioral hypothermia immediately following exposure, but selected body temperature recovered to control 35.3 degrees C the next day. Lizards exposed at 35 degrees C to 0.6 ppm ozone for 4 h selected body temperatures 1.9 degrees C below controls after exposure, and the behavioral hypothermic response persisted and increased to 3.3 degrees C the following day. Four-hour exposures of the frog, Pseudacris cadaverina, to 0.2 to 0.8 ppm ozone resulted in concentration-dependent alterations of respiration including depression of lung ventilation and oxygen consumption and the adoption of a low profile posture that reduced the exposed body surface. Ozone levels in wilderness habitats downwind of urban sources can potentially have stressful physiological effects on wildlife. Defensive physiological and behavioral reactions to ozone exposure may interfere with routine activities, and oxidant air pollution may be in part responsible for observed wildlife population declines.     

一株携带质粒的人两歧双歧杆菌的分离与鉴定

目的:分离携带天然质粒的人双歧杆菌.方法:用自制的改良型Blb双歧杆菌选择培养基,从人新鲜粪便分离双歧杆菌,对初步质粒检测阳性的单菌落通过糖发酵试验、(G C)mol%测定和16S rDNA序列分析,进行菌株鉴定.结果:筛选到一株携带天然质粒的人双歧杆菌,编号B200304,在1.0%琼脂糖凝胶上,测得质粒的相对分子质量约为22 kb.通过对该菌株的形态学观察和糖发酵试验等生理生化特征研究,证明该菌株为两歧双歧杆菌(Bifidobacterium bifidum);HPLC法测得其(G C)mol%为55.6,16SrDNA序列分析进一步证实该菌株为两歧双歧杆菌.结论:分离得到一株携带天然质粒的人两歧双歧杆菌新菌株.     

Tools and methodologies capable of isolating and identifying a target molecule for a bioactive compound

Elucidating the mechanism of action of bioactive compounds, such as commonly used pharmaceutical drugs and biologically active natural products, in the cells and the living body is important in drug discovery research. To this end, isolation and identification of target protein(s) for the bioactive compound are essential in understanding its function fully. And, development of reliable tools and methodologies capable of addressing efficiently identification and characterization of the target proteins based on the bioactive compounds accelerates drug discovery research. Affinity-based isolation and identification of target molecules for the bioactive compounds is a classic, but still powerful approach. This paper introduces recent progress on affinity chromatography system, focusing on development of practical affinity matrices and useful affinity-based methodologies on target identification. Beneficial affinity chromatography systems with using practical tools and useful methodologies facilitate chemical biology and drug discovery research.     

Asymmetric plant-mediated cross-effects between a herbivorous insect and a phytopathogenic fungus

• 1 Cross‐effects between a herbivorous insect and a phytopathogenic fungus on their common host plant were examined. Specifically, we addressed the questions whether (i) infection of Chinese cabbage leaves by the fungus Alternaria brassicae affects the development and host selection behaviour of the leaf beetle Phaedon cochleariae and (ii) whether herbivory influences host suitability of Chinese cabbage for A. brassicae.
• 2 Feeding on fungus‐infected leaves prolonged larval development and reduced pupal weight of P. cochleariae. Adult beetles avoided feeding and egg deposition on fungus‐infected leaves. In contrast to these local effects, no systemic effect of phytopathogenic infection on the herbivore was detected.
• 3 Herbivory did not influence fungal growth neither locally nor systemically.
• 4 Thus, our results demonstrate an asymmetric relationship between herbivore and fungus. Whereas herbivory had no visible impact on fungal growth, fungal infection of the plant induced local resistance against P. cochleariae.

     

Development of a method to evaluate caspase-3 activity in a single cell using a nanoneedle and a fluorescent probe

A method to detect an enzymatic reaction in a single living cell using an atomic force microscope equipped with an ultra-thin needle (a nanoneedle) and a fluorescent probe molecule was developed. The nanoneedle enables the low-invasive delivery of molecules attached onto its surface directly into a single cell. We hypothesized that an enzymatic reaction in a cell could be profiled by monitoring a probe immobilized on a nanoneedle introduced into the cell. In this study, a new probe substrate (NHGcas546) for caspase-3 activity based on fluorescent resonance energy transfer (FRET) was constructed and fixed on a nanoneedle. The NHGcas546-modified nanoneedle was inserted into apoptotic cells, in which caspase-3 is activated after apoptosis induction, and a change in the emission spectrum of the immobilized probe could be observed on the surface of the nanoneedle. Thus, we have developed a successful practical method for detecting a biological phenomenon in a single cell. We call the method MOlecular MEter with Nanoneedle Technology (MOMENT).     

SEQGEL: a versatile and comfortable DNA editor which supports a special keyboard and a speech synthesizer

A DNA editor for an Apple II is described which contains manyadditional functions apart from just editing sequences. Thedata files are normal ASCII text or binary files and can thusbe used easily by other programs. The program supports a specialkeyboard which greatly facilitates typing of DNA sequences.Furthermore a speech synthesizer is supported by the editor.The speech feedback, together with the special keyboard, reducestyping errors to a minimum. ; accepted on March 10, 1986     

Isolation and characterization of a protein-tyrosine kinase and a phosphotyrosine-protein phosphatase from Klebsiella pneumoniae

Two proteins of Klebsiella pneumoniae, termed Yor5 and Yco6, were analyzed for their capacity to participate in the reversible phosphorylation of proteins on tyrosine. First, protein Yco6 was overproduced from its specific gene and purified to homogeneity by affinity chromatography. Upon incubation in the presence of radioactive adenosine triphosphate, it was found to effectively autophosphorylate. Two-dimensional analysis of its phosphoamino acid content revealed that it was modified exclusively at tyrosine. Second, protein Yor5 was also overproduced from the corresponding gene and purified to homogeneity by affinity chromatography. It was shown to contain a phosphatase activity capable of cleaving the synthetic substrate p-nitrophenyl phosphate into p-nitrophenol and free phosphate. In addition, it was assayed on individual phosphorylated amino acids and appeared to dephosphorylate specifically phosphotyrosine, with no effect on phosphoserine or phosphothreonine. Such specificity for phosphotyrosine was confirmed by the observation that Yor5 was able to dephosphorylate protein Yco6 previously autophosphorylated. Together, these data demonstrate that similarly to other bacterial species including Acinetobacter johnsonii and Escherichia coli, the cells of K. pneumoniae contain both a protein-tyrosine kinase and a phosphotyrosine-protein phosphatase. They also provide evidence that this phosphatase can utilize the kinase as an endogenous substrate, which suggests the occurrence of a regulatory mechanism connected with reversible protein phosphorylation on tyrosine. Since Yco6 and Yor5 are both involved in the synthesis of capsular polysaccharide and since capsules are essential to the virulence of K. pneumoniae, we suggest that reversible protein phosphorylation on tyrosine may be part of the cascade of reactions that determine the pathogenicity of bacteria.     

Plant-mediated competition facilitates a phoretic association between a gall mite and a psyllid vector

Phoretic associations between mites and insects commonly occur in patchy and ephemeral habitats. As plants provide stable habitats for herbivores, herbivorous mites are rarely dependent on other animals for phoretic dispersal. However, a phoretic gall mite, Aceria pallida, which is found on plants, seasonally attaches to a herbivorous insect, Bactericera gobica, for overwintering survival. After detachment, the gall mite shares a habitat with its vector and is likely to compete with this vector for plant resources. However, excessive competition works against the sustainability of the seasonal phoretic association. How the gall mite, as an obligate phoretic mite, balances this relationship with its vector during the growing season to achieve phoresy is unknown. Here, the plant-mediated interspecific interaction between the gall mite and the psyllid after detachment was studied in the laboratory and field. The laboratory results showed that infestation by the gall mite had detrimental effects on the survival and development of psyllid nymphs. Meanwhile, the mite population and the gall size were also adversely affected. The results from the field showed that the mean densities of the mite galls and psyllids were lower in the mixed-species infestation treatment than in the single-species infestation treatment across the investigation period. However, the interspecific interaction between the gall mite and the psyllid decreased rather than accelerated leaf abscission caused by the psyllid, which promoted the persistence of the psyllid population and then indirectly contributed to phoretic association. Our results suggest that the plant-mediated competition between the phoretic gall mite and its vector after detachment facilitates the maintenance of the phoretic association.