Topology is the Principal Determinant in the Folding of a Complex All-alpha Greek Key Death Domain from Human FADD

In order to elucidate the relative importance of secondary structure and topology in determining folding mechanism, we have carried out a phi-value analysis of the death domain (DD) from human FADD. FADD DD is a 100 amino acid domain consisting of six anti-parallel alpha helices arranged in a Greek key structure. We asked how does the folding of this domain compare with that of (a) other all-alpha-helical proteins and (b) other Greek key proteins? Is the folding pathway determined mainly by secondary structure or is topology the principal determinant? Our Φ-value analysis reveals a striking resemblance to the all-beta Greek key immunoglobulin-like domains. Both fold via diffuse transition states and, importantly, long-range interactions between the four central elements of secondary structure are established in the transition state. The elements of secondary structure that are less tightly associated with the central core are less well packed in both cases. Topology appears to be the dominant factor in determining the pathway of folding in all Greek key domains.     

Foraging ecology of a local wild bee community in an abandoned Satoyama system in Kanazawa, Central Japan

Satoyama is a traditional land management system in Japan that emphasizes the importance of a harmonious relationship between humans and their environment. It has been in a state of abandonment and destruction since the late 1960s. In 2000, the Japanese government initiated a new environment policy encouraging the use of Satoyama in biodiversity reservation areas. Before the initiation of active restoration works, an assessment of the potential of the Satoyama system is needed. To assess this potential, a study that focused on the foraging ecology of wild bees in a small abandoned Satoyama terraced paddy was carried out from June to October 2003. A total of 372 foraging bees belonging to 35 species in nine families was collected: two species of social bee ( Apis cerana and Bombus diversus ) and two of solitary bee ( Lasioglossum japonicum and Lasioglossum ohei ) dominated. The foraging activities of wild bees were highly influenced by the requirement of food for the colony and the active time of solitary bees. In the study, most wild bees showed a strong preference for abundant flowering plant species that produced a large number of flowers ( Achyranthes japonica and Polygonum thunbergii ). The results showed that an abandoned Satoyama system was an agricultural system that benefited pollinating bees. Careful and planned restoration practices to increase the diversity of foraging resources, microenvironment diversity and potential nesting areas for wild bees are needed to improve the ability of the Satoyama system to support more diverse and abundant wild bee populations.     

Development of 11 polymorphic microsatellite markers in a macrophyte of conservation concern, Vallisneria americana Michaux (Hydrocharitaceae)

Vallisneria americana Michaux (wild celery) is currently a target of submersed aquatic vegetation restoration efforts in the Chesapeake Bay watershed. To aid these efforts, we have developed 11 polymorphic microsatellite markers to assess the distribution and degree of genetic diversity in both restored and naturally occurring populations in the Chesapeake Bay. In 59 individuals from two populations, we detected two to 10 total alleles per locus. Observed heterozygosity ranged from 0.125 to 0.929, and two loci exhibited significant deviations from Hardy-Weinberg equilibrium in at least one of the populations assayed.     

Isolation and characterization of 11 microsatellite loci from Oropsylla hirsuta, a vector of sylvatic plague

The flea (Oropsylla hirsuta) is an important vector of the plague bacterium, Yersinia pestis, in black-tailed prairie dog (Cynomys ludovicianus) colonies. We developed 11 anonymous microsatellite primers for O. hirsuta using a subtractive hybridization procedure. All primers were polymorphic exhibiting 4-12 alleles.     

Food composition and food niche overlap of three kinds of canidae

The diets of the wolf Canis lupus, red fox Vulpes vulpes and raccoon dog Nyctereutes ussurienusis Matschie were studied in the grassland of eastern Inner Mongolia from August to October in 2007 and from March to July in 2008. Feces were collected from dens and latrines. The frequency of occurrence and the dry weight of the remains of each food item in the feces were calculated. Livestock (50.65% frequency of occurrence) constituted the bulk of the wolf diet, while small rodents (76.31% frequency of occurrence) were most frequently eaten by the foxes. Small rodents (22.69% frequency of occurrence) were important to the raccoon dogs but they also frequently consumed birds (39.81% frequency of occurrence) and insects (26.39% frequency of occurrence). The wolf was the most omnivorous and the red fox was the least omnivorous of these three kinds of canidae according to the diversity index. The food niches of the wolf and the red fox overlapped more than that of the raccoon dog and other species. These three kinds of canidae shared many resources and consequently competition occurred to them. However, their diets also differed to some extent which helped them to avoid competition. Furthermore, raccoon dogs were dormant in winter when food was scarce, which may be the reason why all these species could coexist in a rather unproductive grassland.     

The influence of urea feeding on the bacterial and archaeal community in the forestomach of collared peccary (Artiodactyla, Tayassuidae)

Aims:  This study was carried out to test whether bacterial and archaeal populations, and products of fermentation in each compartment of collared peccary stomach, vary significantly with urea feeding. Bacteria and archaeal population variation among the four stomach compartments were also compared.
Methods and Results:  Archaeal and bacterial communities in the forestomach of four individuals per treatment – peccaries fed diets with and without urea – were analysed at molecular level using PCR followed by denaturing gradient gel electrophoresis. Volatile fatty acids profiles in the three different compartments of the forestomach were also compared. The bacterial community composition varied considerably among each compartment and with urea provision, but no variation was observed between archaeal populations. Differences in bacterial communities between treatments – with and without urea – were greater than amongst stomach compartments. The acetate: propionate proportion decreased with urea provision in diet. Some differences in bacterial but not archaeal community composition were observed in each compartment of the collared peccary forestomach.
Conclusions:  There are some differences in bacterial but not archaeal populations in each compartment of collared peccary stomach. Use of urea in the diet of peccary can substantially modify the profile of volatile fatty acids released in its forestomach, but does not influence the archaeal community composition. Urea has an important effect on bacterial population DGGE profile present in the peccary's forestomach.
Significance and Impact of the Study:  These results demonstrate the ability of the collared peccary to use urea as source of nonprotein nitrogen, and confirm a hypothesis that the collared peccary has a digestive physiology more similar to ruminant than nonruminant animals.     

不同品种金鱼和鲫鱼的分子系统发育关系研究

为探讨不同品种金鱼的系统进化关系,利用PCR技术扩增了金鱼的7个代表品种红龙睛(Red dragongoldfish)、红帽子(Red cap goldfish)、虎头(Tiger head goldfish)、琉金(Gold plating goldfish)、墨龙睛(Black dragongoldfish)、水泡眼(Water vesicle goldfish)、珍珠(Genuine pearl goldfish)的线粒体DNA上细胞色素b的部分核苷酸序列,长度为597 bp.结合GenBank中红鲫、野鲫、日本白鲫、银鲫、鲤鱼的序列进行比较分析,结果显示,这7个金鱼品种之间的同源性都很高,在99.5%～100%之间;7种金鱼和红鲫的同源性也很高,为99.5%～99.8%,与野鲫的同源性在96.8%～97.2%,与日本白鲫、银鲫的同源性为93.1%～94.3%,与鲤鱼的同源性相对较低,为88.3%～88.6%.利用DNAstar软件构建了不同品种金鱼和鲫鱼的分子系统树,从分子水平进一步证实了金鱼起源于野鲫.