Comparative genomics: methods and applications

Interpreting the functional content of a given genomic sequence is one of the central challenges of biology today. Perhaps the most promising approach to this problem is based on the comparative method of classic biology in the modern guise of sequence comparison. For instance, protein-coding regions tend to be conserved between species. Hence, a simple method for distinguishing a functional exon from the chance absence of stop codons is to investigate its homologue from closely related species. Predicting regulatory elements is even more difficult than exon prediction, but again, comparisons pinpointing conserved sequence motifs upstream of translation start sites are helping to unravel gene regulatory networks. In addition to interspecific studies, intraspecific sequence comparison yields insights into the evolutionary forces that have acted on a species in the past. Of particular interest here is the identification of selection events such as selective sweeps. Both intra- and interspecific sequence comparisons are based on a variety of computational methods, including alignment, phylogenetic reconstruction, and coalescent theory. This article surveys the biology and the central computational ideas applied in recent comparative genomics projects. We argue that the most fruitful method of understanding the functional content of genomes is to study them in the context of related genomic sequences. In particular, such a study may reveal selection, a fundamental pointer to biological relevance.     

疏浚物中有机锡的生物累积效应研究

于1998年6月在塘沽港附近水域采集贻贝（Mytilus edulis），经试验室培养驯化后作为试验材料，研究了三丁基氯化锡（TBTC0和三苯基氯化锡（TPTC）的累积效应及其对贻贝的毒性影响。结果表明，在累积效应试验中，TBTC及TPTC对贻贝的半致死浓度LC50分别为3．5μg/dm^3和5．0μg/dm^3，当TBTC浓度达2．0μg/dm^3时，贻贝的成活率开始降低，实验还表明，TPT对贻贝的毒性效应与TBT相近。     

Portrait of an Asian stalk-eyed fly

Diopsid flies have eyes set on stalks which are in some cases so long that the distance between the eyes exceeds the body length. These conspicuous structures have given rise to much speculation about their adaptive value, but there are very few actual observations by which to judge these hypotheses.Cyrtodiopsis whitei Curran lives in the tropical rainforest of Malaysia. We describe a number of aspects of its morphology and biology, some functional properties of the eye, and the ritualized fights between males, by which harems are acquired. The evolutionary significance of the eyestalks is discussed: they represent structures subjected to a double selection pressure; they are an adaptation by which a sensory system is better matched to the special problems encountered in a densely structured habitat (in that the field of view is extended and the ability to estimate distance and size and to identify objects at a large distance is improved), also they act as key stimulus for species recognition and as releaser for intraspecific behaviour.     

A unique strategy of host colony exploitation in a parasitic ant: workers of<Emphasis Type="Italic"> Polyrhachis lama</Emphasis> rear their brood in neighbouring host nests

The formicine ant Polyrhachis lama is a social parasite, exploiting its ponerine host ant species Diacamma sp. In most social parasitic associations, the parasitic species are closely related to their host species group, evolving directly from independent ancestors of the host species. However, in the Polyrhachis lama–Diacamma sp. association, the associated species belong to different ant subfamilies. Based on preliminary field surveys, we had presumed that P. lama might have given up its reproductive division of labour, i.e. workers would be able to produce males as well as workers and females parthenogenetically. In this study, this hypothesis was disproved: Polyrhachis lama workers cannot be fertilized and are only able to produce males. In the host–parasite association originating from nests possessing a P. lama queen, workers penetrate surrounding Diacamma sp. nests, carrying brood for rearing within these satellite nests. In this peculiar way, a single P. lama colony is able to exploit several Diacamma sp. colonies simultaneously.     

The influence of serum screening on the amniocentesis rate in women of advanced maternal age

We investigated the effect of maternal serum screening on the amniocentesis (AC) rate in women of advanced maternal age. The AC rate after maternal serum screening was compared in two groups of women with a singleton pregnancy, 855 women of 30–35 years and 98 of 36 years and older. In our population, 34·1 per cent of the women of 36 years or older were ‘screen-positive’ for Down syndrome. Only 41·2 per cent of these women chose to undergo AC as opposed to 88·2 per cent in the younger age group. Within the older age group, the tendency to avoid AC increased with increasing age. Maternal serum screening led to a significant decrease in the AC rate in the older women. In this group, a comparison between the ‘a priori’ and the calculated risk might have had more influence on the decision to undergo AC than being screen-positive or screen-negative as such. We conclude that maternal serum screening had a major effect on the AC rate in women of advanced maternal age. This is of importance in a society in which the average maternal age is steadily increasing.     

Feeding ecology of the three juvenile phases of the spiny lobster<Emphasis Type="Italic"> Panulirus argus</Emphasis> in a tropical reef lagoon

The three juvenile phases of the spiny lobster Panulirus argus (algal phase: 5-15 mm carapace length, CL; postalgal phase: 15-45 mm CL, and subadults: 45-80 mm CL) occur in the reef lagoon at Puerto Morelos, Mexico. The algal phase abounds in this lagoon, which is covered by extensive seagrass-algal meadows, but the density of postalgal and subadult juveniles is low, owing to the scarcity of crevice-type shelters suitable for these phases. The feeding ecology of the three juvenile phases was investigated to examine whether spatial or temporal differences in food intake, diet composition, or nutritional condition occurred among phases and could partially account for the low abundance of the larger juveniles. Juveniles were collected by divers at night, from January to November 1995, throughout the mid-lagoon and back-reef zones. Percent stomach fullness, relative weight of the digestive gland (RWDG, an index of nutritional condition), percent frequency of occurrence and percent volume of food categories in the diet were compared between sexes, juvenile phases, molt stages (postmolt, intermolt, premolt), seasons, and sampling zones (mid-lagoon and back-reef zones). Significant differences in stomach fullness occurred only among molt stages, mainly because postmolt individuals had emptier stomachs. The main food categories in all juvenile phases were crustaceans (mostly hermit crabs and brachyurans) and gastropods, but the food spectrum was wide, including many other animal taxa as well as plant matter. In June 1995, the epibenthic macrofauna was sampled in five sites in the lagoon that differed in their amount of vegetation. The most abundant taxa in all sites were decapods and gastropods, but density and diversity measures showed that the distribution of these potential prey taxa for juvenile P. argus was rather patchy. Diet overlap in juvenile lobsters was high between sexes, juvenile phases, sampling zones, seasons, and molting stages, indicating that all juveniles fed on the same general food categories throughout time. The only factor that affected the RWDG was the juvenile phase. RWDG was significantly lower in subadults than in algal and postalgal phases, suggesting a poorer nutritional condition in the largest juveniles. This may be related to the scarcity of suitable shelters for large juveniles throughout the lagoon, which may preclude subadults from exploiting food resources in areas of the lagoon where shelter is limited.     

Larvae of deep-sea fishes (Stomiatoidea) from Biscayne Bay,Florida, USA,and their ecological significance

Twenty stomiatoid fish larvae (3.1 to 21,9 mm) belonging to the genera Bathophilus, Cyclothone, and Stomias were collected in plankton nets from surface waters over depths of 3 to 4 m from Biscayne Bay, Florida, USA. The adults are mesopelagic in the open water of the Florida Current and, therefore, these larvae were presumably advected in parcels of high salinity water into the shallows of Biscayne Bay by winds, tides, or currents. The presence of these larvae suggest that sewage discharged into the Florida Current may be recycling into coastal waters as well as into Biscayne Bay.Scientific Contribution No. 1403, University of Miami, Rosenstiel School of Marine and Atmospheric Science. The support of Environmental Protection Agency Contract FW QA 18050 DIU, Water Quality Office, Division of Water Quality Research is gratefully acknowledged.     

A preliminary approach to epidermal antimicrobial defense in the Delphinidae

In three delphinid species (Pacific spotted dolphin, Stenella attenuata; common dolphin, Delphinus delphis; harbor porpoise, Phocoena phocoena) the enzyme lysozyme and the peptide group -defensins are demonstrated for the first time in cetaceans as products of the thick integument. Lysozyme was found between the lamellae of the stratum corneum, in the cells of the stratum spinosum, free cells of the dermis, and in endothelial cells of dermal blood vessels. -defensins (especially type 3) were clearly located in cells of the upper stratum spinosum, and concentrated between the upper five or six layers of the stratum corneum. The occurrence and localization of such substances that may serve as a non-specific defense against bacteria, fungi, algae, and ectoparasites, was known until now only for haired marine mammals with typical skin glands, like in pinnipeds.Communicated by O. Kinne, Oldendorf/Luhe     

贺词

环境预防战略,无论是清洁生产、生态效益还是污染防治,是改变不可持续生产和消费方式的最佳战略.自从它被引入《21世纪议程》后,政府和工商业越来越多地采用了清洁生产观念,并且为完善这一概念做出了巨大的努力.