Amelioration of Bacterial Genomes: Rates of Change and Exchange

Although bacterial species display wide variation in their overall GC contents, the genes within a particular species' genome are relatively similar in base composition. As a result, sequences that are novel to a bacterial genome—i.e., DNA introduced through recent horizontal transfer—often bear unusual sequence characteristics and can be distinguished from ancestral DNA. At the time of introgression, horizontally transferred genes reflect the base composition of the donor genome; but, over time, these sequences will ameliorate to reflect the DNA composition of the new genome because the introgressed genes are subject to the same mutational processes affecting all genes in the recipient genome. This process of amelioration is evident in a large group of genes involved in host-cell invasion by enteric bacteria and can be modeled to predict the amount of time required after transfer for foreign DNA to resemble native DNA. Furthermore, models of amelioration can be used to estimate the time of introgression of foreign genes in a chromosome. Applying this approach to a 1.43-megabase continuous sequence, we have calculated that the entire Escherichia coli chromosome contains more than 600 kb of horizontally transferred, protein-coding DNA. Estimates of amelioration times indicate that this DNA has accumulated at a rate of 31 kb per million years, which is on the order of the amount of variant DNA introduced by point mutations. This rate predicts that the E. coli and Salmonella enterica lineages have each gained and lost more than 3 megabases of novel DNA since their divergence. Received: 7 July 1996 / Accepted: 27 September 1996     

Sequence analysis of lacZ- mutations induced by ion beam irradiation in double-stranded M13mp18DNA

While M13mp18 double-stranded DNA was irradiated with ion beam, and transfected intoE. coli JM103, a decrease of transfecting activity was discovered. The lacZ^- mutation frequency at 20% survival could reach (3.6–16.8) × 10⁴, about 2, 3–10 times that of unirradiated M13DNA. Altogether, 27 IacZ^-mutants were selected, 10 of which were used for sequencing. 7 of the sequenced mutants show base changes in 250-bp region examined (the remaining 3 mutants probably have base changes outside the regions sequenced). 5 of the base-changed mutants contain more than one mutational base sites (some of them even have 5–6 mutational base sites in 250-bp region examined); this dense distribution of base changes in polysites has seldom been seen in X-rays, Y-rays or UV induced DNA mutations. Our experiments also showed that the types of base changes include transitions(50%), transversions (45%) and deletion (5%); no addition or duplication was observed. The transitions were mainly C→T and A→G; the transversions were mainly C→A and C→G. The mutations involving cytosine residue (in the template strand) constitute about 60% of all the base changes observed. In comparison with the surrounding sequences of mutational base sites, the base located between TG and CT is found to be easily substituted.     

Identification of the Sites for Suppressor Mutations on the Hemagglutinin Molecule to Temperature-Sensitive Phenotype of the Influenza Virus

A temperature-sensitive (ts) mutant of the influenza virus A/WSN/ 33 strain, ts-134, possessed a defect in intracellular transport at the nonpermissive temperature and marked thermolability of hemagglutinin (HA) activity at 51 C. These were caused by a change at amino acid residue 157 from tyrosine to histidine in the HA protein. We isolated 37 spontaneous revertant clones from ts-134 at the nonpermissive temperature and determined their HA sequences. The deduced amino acid sequences demonstrated that one was a true revertant and the others were revertants with suppressor mutations, each of which had an additional amino acid change besides those of ts-134. The changed amino acids were located at 14 positions on the HA molecule, and eight of them were found in multiple revertants. These were located in five to six distinct regions on the three-dimensional structure of the HA molecule. However, the heat stability of HAs in the revertants was recovered differently depending on the sites of the changed amino acids. The kinetics of transport of the HA protein in the revertants were slightly delayed compared to the wild-type both at permissive and nonpermissive temperatures.     

S－美芬妥英羟化代谢多态性的分子机制研究进展

人群中存在着Ｓ－美芬妥英羟化代谢多态性。从人肝微粒体已分离出Ｓ－美芬妥英羟化酶。在基因克隆研究中已分离出与该羟化酶活性有关的Ｐ４５０ｃＤＮＡ,属Ｐ４５０２Ｃ１９。最近报道,人肝中Ｐ４５０２Ｃ１９的含量和催活Ｓ－美芬妥英羟化活性密切相关,其弱代谢者主要由于ＣＹＰ２Ｃ１９的外显子５单碱基对（Ｇ→Ａ）的变异,使核苷酸序列错位而产生无功能的Ｐ４５０蛋白的结果。     

Resolving genetic relationships with microsatellite markers: a parentage testing system for the swallow Hirundo rustica

Eight polymorphic microsatellite markers from the swallow were isolated and characterized. Extraordinary variability was revealed at the HrU6 locus with 45 different alleles scored among 46 unrelated individuals. The probability that the same genotype combination would occur in two random and unrelated individuals at six selected loci was as low as 1.3 × 10^-8 and the combined exclusion probability was 0.9996. Stable Mendelian inheritance was observed in about 1000 meioses. No significant linkage was revealed and for almost all combinations of marker-pairs, linkage closer than 5 cM could be excluded. At two loci, null (nonamplifying) alleles were encountered. Thirteen (30%) extra-pair offspring were identified in 5 (56%) broods when applying the marker set on a nearly complete swallow colony. We were able to identify a single male from the other families in the colony as the most likely father for nine of the 13 extra-pair offspring.     

Effects of diet on growth, fecundity and duration of tethered flight of Nezara viridula

The effects of diet during the fifth stadium on performance of adult N. viridula were determined through comparing growth, fecundity, and duration of tethered flight of insects reared on four axenic diets: fresh green bean, raw-shelled peanut, a combination of the two and soaked soybean seed. Females reared on the combination diet were heavier than those reared on green beans and oviposited more than those reared on peanuts. Three-day-old adult females reared on peanuts flew longer than those reared on green beans. More females reared on diets containing mature seed showed a capacity for extended flight and had larger fat bodies at 34-days postemergence. Thus, inadequate diet during the fifth stadium irreversibly affected growth, development, reproduction and flight capacity.

---

Résumé Les effets du régime alimentaire pendant le 5ème stade sur les performances imaginales de N. viridula ont été déterminés en comparant la croissance, la fécondité, la durée du vol captif, et l'accumulation de corps gras chez des insectes élevés sur 4 régimes stérilisés. A partir de la formation des larves de 5ème stade, elles ont été alimentées sur haricots verts et arachides, ou transférées sur un régime formé exclusivement d'arachides, ou de haricots verts, ou de graines de soja trempées, cependant la durée du 5ème stade. Les insectes ont été transférés sur un régime de haricots verts et arachides à leur émergence.Les femelles élevées continuellement de haricots verts et arachides étaient plus lourdes (P<0,01) à l'émergence (161,6 mg) que celles élevées sur haricots verts (146,3 mg) pendant le 5ème stade, et pondent plus d'oeufs (P<0,08) pendant une durée de 34 jours (100,9 oeufs) que celles élevées sur arachides (54,7 oeufs). Plus de femelles élevées sur haricots verts et arachides (76,2%) pondent que celles élevées sur arachides (61,1%), soja trempé (62,5%), ou haricots verts (60,9%).Les femelles élevées sur arachides volaient plus longtemps (P < 0,01) (42,9 mn) que celles élevées sur haricots verts (19,8 mn) pendant des vols captifs le 3ème jour après l'émergence. 78% de toutes les femelles élevées sur arachides volaient >-30 mn, contre 50% pour celles élevées sur haricots verts et arachides, ou soja trempé, et 35% pour celles élevées sur haricots verts. Seulement 7% des femelles élevées sur haricots verts volaient à la 60ème minute à la fin du test, contre 25% pour les femelles soja trempé, 33% pour les femelles haricots verts et arachides, et 47% pour celles élevées sur arachides. Les femelles ont été disséquées 34 jours après l'émergence pour déterminer l'importance du corps gras. Les indices de corps gras (Kiritani, 1963) montraient que les femelles élevées sur arachides (1,8) et graines de soja (1,7) ont apparemment un corps gras plus développé que celles élevées sur haricots verts et arachides (1,5), our haricots verts (1,2), pendant le 5ème stade.Ces résultats montrent que l'alimentation pendant le dernier stade larvaire de N. viridula affecte irréversiblement la croissance, la fécondité et l'aptitude au vol des femelles. En estimant que des résultats semblables auraient été obtenus avec des insectes élevés sur ces 4 aliments depuis l'éclosion, haricots verts et arachides constituent le meilleur aliment pour l'élevage de N. viridula. Ce régime fournit une graine mûre, vraisemblablement nécessaire pour l'accumulation d'un corps gras suffisant et une aptitude au vol migratoire, et une plante verte qui fournit les aliments apparement essentiels à l'ovogenèse.

     

Short-term variations in catches of the pea moth,Cydia nigricana, in interacting pheromone traps

Short-term variations in the relative catch in each of two or three interacting pheromone traps for the pea moth,Cydia nigricana (F.), were investigated for traps aligned along the wind. The proportional catch in each trap varied widely, although the mean values accorded with previous estimates. Over consecutive short intervals during a single trapping period the proportion caught in the centre trap of a three-trap line was constant. The proportion caught in the upwind trap of two-and three-trap lines showed trends in time. These trends differed between trapping periods, but two lines of traps operated simultaneously gave similar results to each other. It is suggested that these results, which are predicted by a model based on various components of moth orientation behaviour, are caused by changes in systematic behavioural processes, not random effects. Possible mechanisms are discussed.

---

Variations à court terme des captures deCydia nigricana dans des pièges à phéromones en interaction

Résumé Des données antérieures concernant les interactions entre des pièges à phéromone alignés le long du vent ont été utilisées pour déduire les caractéristiques du comportement d'orientation deC. nigricana. Ces données ont été introduites dans un modèle de simulation quantitative qui prédisait que quand les captures totales sur une ligne ont été regroupées sur une période globale de piégage, la proportion capturée dans chaque piège devrait aussi avoir des valeurs moyennes semblables, mais varie plus largement que précédemment indiqué. Les simulations concernant des intervalles consécutifs beaucoup plus courts pendant la même période de piégage ont suggéré une forme spécifique de cette variation.Cette note signale des variations à court terme dans la proportion capturée au piège qui confirment ces prédictions. Nous montrons que sur des intervalles consécutifs brefs pendant une simple période de piégage, la proportion capturée dans le piège central d'une ligne de 3 pièges est contstante, bien que sa valeur change suivant les périodes de piégage. La proportion capturée dans le piège face au vent de 2 ou 3 lignes de pièges suit cette tendance dans le temps, ce qui est généralement bien représenté avec des courbes simples. Ces tendances changent suivant les périodes de piégage, mais des lignes de pièges fonctionnant simultanément fournissaient des résultats similaires. On suggère que ces résultats sont dus à des changements dans des processus comportementaux systématiques et non à des effects aléatoires. Les mécanismes possibles sont discutés.

     

Oviposition deterring pheromone influences dispersal distance in tephritid fruit flies

We tested the hypothesis that Rhagoletis pomonella females exhibit a greater propensity for engaging in long distance (i.e.1000 m) flight following encounters with egg-infested oviposition-deterring-pheromone (ODP) marked host fruit than similar females that encounter uninfested, clean (i.e. no ODP) fruit. Female flies which were first tethered to flight mills were presented with and permitted to explore (a) ODP-marked or (b) clean fruit and then stimulated to fly. Results showed that females that had encountered a high rate of infested, ODP-marked fruit displayed long distance flight more frequently and flew greater average distances than females that had searched uninfested fruit. We discuss there results in light of contemporary foraging theory.

---

Résumé La réponse d'insectes à leurs phéromones de dissuasion (ODP) est examinée généralement à un seul niveau de prospection, c'est-à-dire celui de la ressource individuelle elle-même. Ces marqueurs chimiques peuvent, cependant, fournir aussi des informations au prospecteur sur la disponibilité en ressources, tant au niveau de l'inflorescence qu'au niveau de l'habitat. Une telle information influence vraisemblablement le comportement de prospection à différents niveaux.Dans cette note, nous vérifions l'hypothèse que la rencontre avec des hôtes marqués par ODP influence la tendance de Rhagoletis pomonella (Dipt: Tephrit) à entreprendre des vols importants (c'est-à-dire interhabitats). Nous avons montré dans des expériences de laboratoire que les femelles lors de trois rencontres consécutives avec des fruits marqués par ODP: 1) entreprenaient plus fréquemment (19 cas sur 81 contre 6 sur 81) un vol à longue distance (c'est-à-dire 1000 m) et 2) parcourient des distances moyennes supérieures à celles couvertes par des femelles ayant eu la possibilité de prospecter successivement trois fruits propres (sans ODP).Nous engageons le lecteur à examiner nos résultats d'un point de vue qualitatif. Nous ne pouvons nous attendre à ce qu'un vol à longue distance se produise aussi facilement dans la nature qu'au laboratoire, étant donné le plus grand nombre de variables (par exemple, la taille de l'arbre) qui peuvent y modifier le vol réel.Pour terminer, nous discutons les coûts et bénéfices potentiels qui peuvent résulter de ce comportement.

     

Mutant hemoglobin stability depends upon location and nature of single point mutation

The temperature dependence of the rates of heme release from the beta subunits of methemoglobin A and 5 beta mutant methemoglobins has been determined. The rates were largest for two hemoglobins with mutations distal to heme, previously known to be unstable. The other 3 mutants also released heme faster than A. These hemoglobins, with single point mutations at the alpha 1/beta 2 interface, were previously thought to be stable. The low reported yields of the 5 mutant proteins covaries with the relative rates of heme release from the met species.     

A missense mutation (G197→A) in theα-l-fucosidase gene of fucosidosis patients leads to loss ofα-l-fucosidase

Fucosidosis is an autosomal recessive lysosomal storage disease resulting from the absence of -l-fucosidase activity. Two natural missense mutations (G¹⁹⁷A) and (A⁸⁶⁰G) within the -l-fucosidase gene have been reported to be homozygous in four patients with fucosidosis. Expression of wild-type and mutated -l-fucosidase cDNAs in COS-1 cells revealed complete deficiency of -l-fucosidase for the G¹⁹⁷A transition and a normal level of enzyme for A⁸⁶⁰G. We therefore conclude that the change of G¹⁹⁷A is responsible for fucosidosis in the patients while A⁸⁶⁰G is a normal polymorphic variant of -l-fucosidase.