A non-metric sequence alignment program

An algorithm for nucleic acid and protein sequence alignment is presented. It is a non-metric local similarity minimal-difference algorithm and in the current implementation, assembles the matching regions found into a pseudo-global format. Its strengths are its speed of execution and the especially convenient presentation of its output. The algorithm is intended for use in sequence melding and local (small-region) similarity searching. It is not designed to replace a metric Needleman-Wunsch-Sellers-type similarity algorithm. The program is written in FORTRAN and is designed to be easily transportable to a variety of computer systems.     

Discrimination by male ring-tailed Lemurs (Lemur catta) between the scent marks of male and those of female conspecifics

Olfaction plays an important role in the social communication of all prosimians. (The experiment reported in this paper forms part of an intensive chemobehavioral study of olfaction in Lemur catta (ring-tailed lemur) being carried out in this laboratory.) Five male Lemur cattawere tested on their behavioral responses to paired scent stimuli. Responses measured were (1) total investigation time, (2) arm-marking, (3) ABO/BO rubbing, and (4) flehmen. Males showed a strong discrimination between the scent stimuli,giving higher levels of response to female scent on measures 1, 3, and 4. This response suggests an olfactory-related preference by males for female scent under controlled conditions. This preference may be a consequence of the females’ dominance over males and the brevity of estrus in L. catta,both of which would favor such choice behavior.     

Changes in Respiratory Metabolism during Aging in Seeds and Isolated Axes of Soybean

Cyanide-sensitive O₂ uptake was observed in the isolated embryonicaxis of soybean [Glycine max L. merr. cv. ‘Essex’]within 5 min after wetting and the O₂ uptake rate during thefirst h of imbibition was directly proportional to axis moisturecontent. Within 10 min after wetting, O₂ uptake was lower inaged low vigor (LV) axes than in high vigor (HV) axes imbibedeither in water (LV axes sustain imbibition injury) or in 30%w/v polyethylene glycol (LV axes do not sustain imbibition injury).Mitochondria isolated from LV axes after 4- and 24-h imbibitionwere characterized by lower O₂ uptake, ADP:O, and respiratorycontrol ratios relative to HV mitochondria. A plot of O₂ uptakevs temperature between 10 and 25?C revealed a break in the slopebetween 13 and 16?C for HV, but not LV, axes. Since LV axessustained water uptake injury at all temperatures tested, whereasHV axes sustained chilling injury only below 16?C, the dataindicate two temperature-O₂ uptake relationships: one for injuredtissues and one for non-injured tissues. We conclude that deteriorationper se involves impairment of respiratory metabolism in thesoybean embryonic axis. Chilling (10?C; HV and LV axes) andimbibitional (25?C; LV axes) injuries during the initial minof inbibition further disrupt respiratory metabolism and interferewith subsequent mitochondrial development and axis growth. ¹Scientific Articles No. A-3548, Contribution No. 6623 of theMaryland Agricultural Experiment Station. (Received May 25, 1983; Accepted September 28, 1983)     

Besondere Haarstrukturen der Soricidae (Mammalia,Insectivora) und ihre taxonomische Deutung

Zusammenfassung Die vorliegende Untersuchung befaßt sich mit besonderen Haarfeinstrukturen der Soricidae, wobei geklärt werden soll, ob dem H-förmigen Haarquerschnitt-Profil eine taxonomische Bedeutung zukommt. Wir überprüften deshalb die betreffenden Haarstrukturen mit Hilfe des REM in 8 Gattungen.Das besondere Haarprofil, das auf das Terminalsegment der Grannenhaare beschränkt ist, findet sich bei folgenden Gattungen:Sorex, Neomys, Blarina undCryptotis, alles Vertreter der Subfamilie Soricinae. Sämtliche untersuchten Vertreter der Subfamilie Crocidurinae, d.h.Crocidura, Praesorex, Suncus undSylvisorex weisen ein einfaches Haarprofil auf.Das H-Profil wird als Synapomorphie der Soricinae angesehen und charakterisiert diese als monophyletische Gruppe. Die haarmorphologischen Kriterien ergänzen somit die osteologischen Kriterien von Repenning (1967) und sprechen für die Beibehaltung der von vielen Autoren abgelehnten Subfamilien.

---

Special hair structures in Soricidae (Mammalia, Insectivora) and their taxonomic interpretation

Summary The following study should clear up the structures of the H-shaped profile found in the hairs of some shrews and show if it has a taxonomic signification. Therefore we studied the concerned hair structures by scanning electron microscopy in 8 genera.The special hair-shape, which is confined to the terminal segment of guard hairs, is found in the species of the following genera:Sorex, Neomys, Blarina andCryptotis, all members of the subfamily Soricinae. All the examined members of the subfamily Crocidurinae, i.e.Crocidura, Praesorex, Suncus andSylvisorex show a simple hair shape.The H-shaped hair characterizes the Soricinae as a monophyletic unity. Yet, the morphological criteria of hair complete the osteological criteria of Repenning (1967) an plead for the validitiy of the often refuted subfamilies.

---

---

Mit Unterstützung des Schweizerischen Nationalfonds zur Förderung der wissenschaftlichen Forschung (Nr. 3.515.71, 3.821.72, 3.413-0.74)

---

Unser Dank gilt Herrn Prof. N. Schönenberger, Herrn Prof.R. Krstic und Frau C. Regamey, die uns bei der histologischen Präparation behilflich waren, insbesondere auch Herrn Dr. T. Jalanti, der uns in die REM-Technik einführte. Kostbares Material wurde uns von Frau A. Geraets (Bonn), Herrn Prof. U. Rahm (Basel) und Herrn Dr. V. Aellen (Genf) zur Verfügung gestellt; auch ihnen sei hierfür herzlich gedankt.     

Evaluation Of Eight Fluorochrome Combinations For Simultaneous Dna-Protein Flow Analyses

Eight fluorescent dye combinations for simultaneous DNA-protein staining have been evaluated spectroscopically and flow microfluoromctrically: propidium iodide (PI) with fluorescein-isothiocyanate (FITC), fluorescamine (FC), and dansylchloride (DANS); diamidinophenylindole (DAPI) with sulphorhodamin (SR101), tetramethylrhodamin isothiocyanate (TRITC), and nitroben-zodiazole (NBD); acriflavine (AF) with stilbene isothiocyanate sulphonic acid (SITS), and DAPI. Three different experimental tumor cell lines have been employed in the investigations. Simultaneous DNA-protein analyses have been carried out with the newly developed HEIFAS instrument. Spectroscopically two groups of dyes were distinguishable according to their excitation maximum below 400 nm and above 450 nm respectively. DANS and NBD were found to be unsatisfactory with respect to their protein distributions obtained by flow analysis. The remaining stains involved in the dye combinations revealed comparable flow distributions of the cellular DNA and protein content. With respect to preparation time and number of centrifugal steps involved in the staining protocols, and in connection with the stability of the dye used, the DAPI-SR101 method proved to be fastest and easiest With this combination DNA and protein flow analysis can be performed simultaneously within 30 min.     

Hydrogen-ion binding by tobacco-mosaic-virus protein polymers.

Hydrogen ion titration curves of tobacco mosaic virus protein have been measured in various conditions of protein concentration, temperature, ionic strength, and rate of pH change. The polymers present at each stage are deduced from turbidity and sedimentation data, plus published information. A simple semi-quantitative analysis of the curves is given, and the pK values of the two abnormal carboxylates in single helix are estimated as 6.4 and about 7.0. Disks, and some faster-forming unknown polymers in the same size range, have been abnormal carboxylate with pK 6.9. These results are most easily interpreted in terms of electrostatic interactions between carboxylates, probably at the axial ends of the protein subunits.     

Small-angle X-ray-scattering investigation and structural-model study of the fatty-acid synthetase from pig liver (author's transl)

The structure of the fatty acid synthetase from pig liver was studied on models based upon structural and functional properties selected from pertinent results available from numerous investigations carried out with fatty acid synthetases from this and other sources. When comparing small-angle X-ray-scattering curves calculated with these models and curves obtained from small-angle X-ray-scattering experiments carried out with the pig-liver enzyme, we tried to select a model which would lead to an acceptable correlation between the calculated and the experimental curves and at the same time fulfil the known structural and functional requirements. The comparison of the curves was started with a model of low complexity. The observed discrepancy, together with arguments from the structural and the functional properties, helped decide which is the next most reasonable model to be considered. This procedure was repeated for five models of increasing complexity. In the model which led to the best fit the multienzyme complex is composed of two halves in an assymetric conformation including hollow spaces. This highly anisotropic model would imply that the two halves change their conformation each time a synthetic cycle is completed and that the growing fatty acid is handed over from one half to the other.     

Localization of N6-methyladenosine in the Rous sarcoma virus genome.

The 10,000-nucleotide RNA genome of the Prague strain, subgroup B (PR-B) of Rous sarcoma virus, was found to contain 11.6 ± 0.5 residues of m⁶Ap by quantitative analysis of ³²P-labeled virion RNA after complete RNAase digestion. Approximately ten of the m⁶Ap residues are located, without obvious clustering, in that region of the genome between 500 and 4000 nucleotides from the 3′ poly(A) end. The src gene, which is required for transformation, and part of the env gene, which codes for the major viral envelope glycoprotein, have previously been mapped in this region of the viral genome. A transformation-defective deletion mutant of PR-B Rous sarcoma virus, which lacks the src gene, has 7.0 ± 0.2 m⁶Ap residues per RNA subunit. This supports our mapping of a portion of the m⁶A residues in src and suggests that this methylation is specific to certain regions of the genome. The possible significance of this result for Rous sarcoma virus RNA processing and translation is discussed.