Algorithms and software tools for ordering clone libraries: application to the mapping of the genome of Schizosaccharomyces pombe.

A complete set of software tools to aid the physical mapping of a genome has been developed and successfully applied to the genomic mapping of the fission yeast Schizosaccharomyces pombe. Two approaches were used for ordering single-copy hybridisation probes: one was based on the simulated annealing algorithm to order all probes, and another on inferring the minimum-spanning subset of the probes using a heuristic filtering procedure. Both algorithms produced almost identical maps, with minor differences in the order of repetitive probes and those having identical hybridisation patterns. A separate algorithm fitted the clones to the established probe order. Approaches for handling experimental noise and repetitive elements are discussed. In addition to these programs and the database management software, tools for visualizing and editing the data are described. The issues of combining the information from different libraries are addressed. Also, ways of handling multiple-copy probes and non-hybridisation data are discussed.     

Quantitative Evaluation of Erotactin Secretion in Eggs of Hormosira banksii (Fucales,Phaeophyceae)

The release of the C₁₁-hydrocarbon spermatozoid attractant hormosirene by eggs of the Australian fucoid Hormosira banksii has been determined quantitatively using a closed-loop extraction technique. The eggs secrete erotactin for more than 2 weeks with an exponentially decreasing rate. The initial secretion rate was estimated to be 75 fmol h^?1 egg^?1 and the total amount of hormosirene produced per egg to be 2.35 pmol (0.35 ng). The results were used to calculate the threshold range for spermatozoid chemotaxis in the pheromone gradient around eggs.     

The reproductive biology of Cyclops vicinus

Investigations of the reproductive biology of Cyclops vicinusrevealed that mated females oscillate between gravid and nongravidreproductive conditions. The gravid condition can be dividedin two recognizable phases: gravid/nonovigerous and gravid/ovigerous,the former phase being shortest. The maturation of new oocytestakes place when the old egg sacs are still being carried; thisensures a rapid clutch succession. Females which remain unmated,extrude few eggs, in no case complete egg sacs, and remain gravidthus conserving oocytes. Females which mate only once, showa similar reproductive pattern (clutch size and clutch succession)to those which remain combined with males, and thus have theopportunity to remate, but tend to produce fewer clutches. Malesare able to fertilize 3–4 females day^–1. Matingcapacity of males is possibly limited by the time needed tofill a new spermatophore. Short-term starvation (5 days) lengthenedclutch-to-clutch periods and diminished clutch size. When thestarvation period started in the gravid/ovigerous phase, a normalclutch was extruded but no new oocytes matured during starvation,indicating that the energy for egg maturations is provided inthe first part of the reproductive cycle.     

Some notes on the ecology of a GermanBranchipus schaefferi population (Crustacea: Anostraca)

Habitat preference, seasonal occurrence, starvation resistance, hatching eggs ofBranchipus schaefferi, and effects of predation onB. schaefferi were studied.Branchipus was only present in turbid, unvegetated ponds and absent in ponds which contain higher aquatic vegetation and theSpirogyra sp. The first individuals ofB. schaefferi appeared in April when water temperature was 10 °C and the last adults in November at a water temperature of 3.5 °C. Up to 6 reproducing generations were observed during this period. Abundance ofB. schaefferi was higher in temporary ponds than in permanent ponds. Sex ratio was close to unity for most of the year. Body size ofB. schaefferi males and females was significantly positively correlated with pond volume. Without foodB. schaefferi could survive for 1.5 to 2 days at 20 °C and 4 to 5 days at 10 °C. Hatching success of eggs decreased when eggs were dried for 7 months. Freezing of eggs had no effect on hatching success. From] the predators tested,Chaoborus sp. larvae clearly selected smallB. schaefferi; one consumed approximately 6Branchipus d–1 at a density of 6 to 12 prey 1–1. The other predators, dragonfly larvae, and larvae and adults ofTriturus alpestris selected alternative prey types, for exampleTubifex sp. and ostracods.     

Twintrons are not unique to the Euglena chloroplast genome: structure and evolution of a plastome cpn60 gene from a cryptomonad

Introns within introns (twintrons) are known only from the Euglena chloroplast genome. Twintrons are group II or III introns, into which another group II or III intron has been transposed. In this paper we describe a non-Euglena twintron structure within a plastid-encoded chaperone gene (cpn60) of the cryptomonad alga Pyrenomonas salina. In addition, the evolutionary relationships between members of the Cpn60 protein family are determined. Our findings permit the inclusion of cryptomonad plastomes in phylogenetic studies of intron evolution and present further evidence for the origin of modern plastids from a cyanobacterial ancestor.This paper is dedicated to Prof. Dr. Peter Sitte on the occasion of his 65th birthday     

A monoclonal antibody extends the half-life of an anti-HIV oligodeoxynucleotide and targets it to CD4+ cells.

An approach was sought to increase the half-life and target cell specificity of antisense oligodeoxynucleotides (oligos). A monoclonal antibody (MAb) was derived from mice immunised with an oligo complementary to a region (1-20) of the HIV genome. This MAb exerts a protective effect on the oligo from the degradation induced by plasma exonucleases in vitro and in vivo. Moreover the anti-oligo MAb dissociates from the oligo in the presence of its complementary sequence to allow hybridization of the two complementary strands. To direct the oligo to CD4+ cells the anti-oligo MAb was cross-linked to an anti-CD4 MAb. The heteroaggregate determines a 5-fold increase in the cellular membrane binding of the oligo to CD4+ lymphocytes. These findings suggest a new approach to enhancing the therapeutic action and the target specificity of antisense oligodeoxynucleotides useful for the selective inhibition of HIV replication in vivo.     

Innate colour preferences of flower visitors

Freshly emerged flower visitors exhibit colour preferences prior to individual experience with flowers. The understanding of innate colour preferences in flower visitors requires a detailed analysis, as, on the one hand, colour is a multiple-signal stimulus, and, on the other hand, flower visits include a sequence of behavioural reactions each of which can be driven by a preferential behaviour. Behavioural reactions, such as the distant approach, the close-range orientation, the landing, and the extension of mouthparts can be triggered by colour stimuli. The physiological limitations of spectral sensitivity, the neuro-sensory filters, and the animals' different abilities to make use of visual information such as brightness perception, wavelength-specific behaviour and colour vision shape colour preferences. Besides these receiverbased factors, there are restrictions of flower colouration due to sender-based factors such as the absorption properties of floral pigments and the dual function of flower colours triggering both innate and learned behaviour. Recordings of the spectral reflection of coloured objects, which trigger innate colour preferences, provide an objective measure of the colour stimuli. Weighting the spectral reflection of coloured objects by the spectral composition of the ambient light and the spectral sensitivity of the flower visitors' photoreceptors allows the calculation of the effective stimuli. Perceptual dimensions are known for only a few taxa of flower visitors.     

Nitrogenase — hydrogenase relationships in Rhizobium japonicum

The conditions necessary for coordinate derepression of nitrogenase and O₂-dependent hydrogenase activities in free-living cultures of Rhizobium japonicum were studied. Carbon sources were screened for their ability to support nitrogenase, and then hydrogenase activities. There was a positive correlation between the level of nitrogenase and corresponding hydrogenase activities among the various carbon substrates. The carbon substrate -ketoglutarate was able to support the highest levels of both nitrogenase and hydrogenase activities. When cells were incubated in -ketoglutarate-containing medium, without added H₂ but in the presence of acetylene (to block H₂ evolution from nitrogenase) significant hydrogenase activity was still observed. Complete inhibition of nitrogenase-dependent H₂ evolution by acetylene was verified by the use of a Hup^- mutant. Hydrogen is therefore not required to induce hydrogenase. The presence of 10% acetylene inhibited derepression of hydrogenase. Constitutive (Hup^c) mutants were isolated which contained up to 9 times the level of hydrogenase acitivity than the wild type in nitrogenase induction medium. These mutants did not have greater nitrogenase activities than the wild type.This is contribution number 1254 from the Department of Biology and the McCollum-Pratt Institute Abbreviations: -Ketoglutarate-containing medium (LOKG) and pre-adaptation medium (SRM) as described in Materials and methods     

CMP-N-acetylneuraminic acid hydrolase, an ectoenzyme distributed unevenly over the hepatocyte surface.

The regional localization of CMP-N-acetylneuramic acid hydrolase at the hepatocyte surface was studied by using plasma membranes and hepatocytes isolated from rat liver. 1. By homogenization of the rat liver plasma membrane preparations and subsequent discontinuous sucrose gradient centrifugation, one light and two heavy membrane fractions were obtained. The origin of these three subfractions is discussed based on the specific activities in the three fractions of 5'-nucleotidase, alakaline phosphatase and Mg2+-ATPase and on electron microscopic examination of the fractions. Evidence is given suggesting that the light fraction is derived from the bile canalicular surface of the plasma membrane, and that the heavy fractions are derived predominantly from the sinusoidal and lateral surfaces of the liver cell membrane. CMP-AcNeu hydrolase was present at highest specific activity in one of the heavy subfractions. Therefore it is concluded that CMP-AcNeu hdyrolase is located preferentially in the sinusoidal and/or lateral plasma membrane parts of the liver cell. 2. Experiments with intact and disintegrated hepatocytes isolated from rat liver indicated that CMP-AcNeu hydrolase is located at the surface of the cell membrane, with its functional group directed to the outside.     

Rhizobium japonicum mutants that are hypersensitive to repression of H2 uptake by oxygen.

The synthesis of an H2 oxidation system in free-living Rhizobium japonicum wild-type strain SR is repressed by oxygen. Maximal H2 uptake rates were obtained in strain SR after derepression in 11 microM or less dissolved oxygen. Oxygen levels above 45 microM completely repressed H2 uptake in strain SR. Five R. japonicum mutant strains that are hypersensitive to repression or H2 oxidation by oxygen were derived from strain SR. The mutants were obtained by screening H2 uptake-negative mutants that retained the ability to oxidize H2 as bacteroids from soybean nodules. As bacteroids, the five mutant strains were capable of H2 oxidation rates comparable to that of the wild type. The mutants did not take up H2 when derepressed in 22 microM dissolved oxygen, whereas strain SR had substantial activity at this oxygen concentration. The O2 repression of H2 uptake in both the wild-type and two mutant strains, SR174 and SR200, was rapid and was similar to the effect of inhibiting synthesis of H2 uptake system components with rifampin. None of the mutant strains was able to oxidize H2 when the artificial electron acceptors methylene blue or phenazine methosulfate were provided. The mutant strains were not sensitive to killing by oxygen, they took up O2 at rates similar to strain SR, and they did not produce an H2 uptake system that was oxygen labile. Cyclic AMP levels were comparable in strain SR and the five mutant strains after subjection of the cultures to the derepression conditions.