Inferring functional modules of protein families with probabilistic topic models

Background  

Genome and metagenome studies have identified thousands of protein families whose functions are poorly understood and for which techniques for functional characterization provide only partial information. For such proteins, the genome context can give further information about their functional context.     

Effectiveness of Short-Distance Translocation and its Effects on Western Rattlesnakes

ABSTRACT Short-distance translocation (SDT) is commonly used to mitigate snake-human interactions, yet little is known about its effectiveness or its effects on behavior and welfare of snakes. Between April 2004 and October 2005, we evaluated SDT as a conservation and management tool by investigating how 500-m SDT affected spatial ecology, body condition, and behavior of western rattlesnakes (Crotalus oreganus) surgically implanted with radiotransmitters in a field study near Osoyoos, British Columbia, Canada. Of 14 rattlesnakes subjected to SDT, 12 (85.7%) returned on ≥1 occasion (range 1–7 times) to the general area they were removed from. Rattlesnakes that underwent SDT showed an increase in total distance moved over an active season compared to non-translocated snakes, but there was no evidence to suggest SDT had an effect on activity range size. There was no evidence to suggest SDT affected body condition, behavior, or mortality rates. Short-distance translocation to high-quality undisturbed habitats was unsuccessful as a long-term solution to snake-human conflict because most translocated snakes returned to conflict areas within a short time (x̄x = 19.9 ± 8.7 days). However, SDT may be an effective short-term tool to manage snake-human conflict in areas where human presence is seasonal or short-lived if careful attention is paid to species-specific biological needs, habitat quality at the release site, and the location of the release site in relation to conflict areas.     

聚酸酐控释制剂的研究进展

聚酸酐材料是一种良好的生物可降解材料,它可以作为药物载体将药物递送入人体的各个器官,如脑、骨骼、血管等,也可作为基因的载体对患者进行基因治疗。聚酸酐的合成工艺简单、成本低廉,可以满足不同的用途。它奇在人体内降解为对人体无害的二元酸而排除体内,具有良好的生物相容性。文中综述了聚酸酐的合成,聚酸酐控释制剂的制备工艺、降解、体内安全性和临床应用方面的研究进展,并提出了今后的发展方向。聚酸酐在医学方面的研究和应用必将日益广泛。     

Cross-hybridizing snake satellite, Drosophila, and mouse DNA sequences may have arisen independently

Previous reports have interpreted hybridization between snake satellite DNA and DNA clones from a variety of distant taxonomic groups as evidence for evolutionary conservation, which implies common ancestry (homology) and/or convergence (analogy) to produce the cross- hybridizing sequences. We have isolated 11 clones from a genomic library of Drosophila melanogaster, using a cloned 2.5-kb snake satellite probe of known nucleotide sequence. We have also analysed published sequence data from snakes, mice, and Drosophila. These data show that (1) all of the cross-hybridization between the snake, fly, and mouse clones can be accounted for by the presence of either of two tandem repeats, [GATA]n and [GACA]n and (2) these tandem repeats are organized differently among the different species. We find no evidence that these sequences are homologous apart from the existence of the simple repeat itself, although their divergence from a common ancestral sequence cannot be ruled out. The sequences contain a variety of homogeneous clusters of tandem repeats of CATA, GA, TA, and CA, as well as GATA and GACA. We suggest that these motifs may have arisen by a self-accelerating process involving slipped-strand mispairing of DNA. Homogeneity of the clusters might simply be the result of a rate of accumulation of tandem repeats that exceeds that of other mutations.      

Evolution of the secondary structures and compensatory mutations of the ribosomal RNAs of Drosophila melanogaster

This paper examines the effects of DNA sequence evolution on RNA secondary structures and compensatory mutations. Models of the secondary structures of Drosophila melanogaster 18S ribosomal RNA (rRNA) and of the complex between 2S, 5.8S, and 28S rRNAs have been drawn on the basis of comparative and energetic criteria. The overall AU richness of the D. melanogaster rRNAs allows the resolution of some ambiguities in the structures of both large rRNAs. Comparison of the sequence of expansion segment V2 in D. melanogaster 18S rRNA with the same region in three other Drosophila species and the tsetse fly (Glossina morsitans morsitans) allows us to distinguish between two models for the secondary structure of this region. The secondary structures of the expansion segments of D. melanogaster 28S rRNA conform to a general pattern for all eukaryotes, despite having highly divergent sequences between D. melanogaster and vertebrates. The 70 novel compensatory mutations identified in the 28S rRNA show a strong (70%) bias toward A-U base pairs, suggesting that a process of biased mutation and/or biased fixation of A and T point mutations or AT-rich slippage-generated motifs has occurred during the evolution of D. melanogaster rDNA. This process has not occurred throughout the D. melanogaster genome. The processes by which compensatory pairs of mutations are generated and spread are discussed, and a model is suggested by which a second mutation is more likely to occur in a unit with a first mutation as such a unit begins to spread through the family and concomitantly through the population. Alternatively, mechanisms of proofreading in stem-loop structures at the DNA level, or between RNA and DNA, might be involved. The apparent tolerance of noncompensatory mutations in some stems which are otherwise strongly supported by comparative criteria within D. melanogaster 28S rRNA must be borne in mind when compensatory mutations are used as a criterion in secondary-structure modeling. Noncompensatory mutation may extend to the production of unstable structures where a stem is stabilized by RNA- protein or additional RNA-RNA interactions in the mature ribosome. Of motifs suggested to be involved in rRNA processing, one (CGAAAG) is strongly overrepresented in the 28S rRNA sequence. The data are discussed both in the context of the forces involved with the evolution of multigene families and in the context of molecular coevolution in the rDNA family in particular.      

Small-subunit ribosomal RNA sequence from Naegleria gruberi supports the polyphyletic origin of amoebas

We have sequenced the small-subunit ribosomal RNA gene of the amoebo- flagellate protozoan Naegleria gruberi. Comparison of this sequence with the rRNA sequences of other eukaryotes resulted in a phylogenetic tree that supports the suggested polyphyletic origin of amoebas and suggests a flagellate ancestry for Naegleria.      

Comparative studies of light leafspot (Pyrenopeziza brassicae) epidemics on the growth and yield of winter oilseed rape

Comparisons of epidemics of light leafspot of differing duration and time of initiation were made in two experiments using a single cultivar of Brassica napus. Fungicide was applied before introduction of disease to prevent infection or some time after inoculation to stop further disease development. In the first experiment, substantial reductions in green leaf area and total plant dry-matter were found at flowering when disease was introduced in the autumn or in January. Plant dry weight at maturity was also greatly reduced in these treatments. The detrimental effect of an epidemic initiated in the autumn was avoided to a large extent if fungicide application began in February. Epidemics initiated in March had only small effects on final dry-matter yield. Seed yield was negatively correlated with the length of the epidemic. In a second experiment, early epidemics initiated in the autumn were halted after different time intervals. Commencing fungicide application even as early as December failed to prevent some loss of dry weight at flowering. At maturity, however, dry weight and seed yield were reduced significantly when fungicide application was delayed until February. Failure to control the disease resulted in a 46% loss of seed yield.