Going the Distance for Protein Function Prediction: A New Distance Metric for Protein Interaction Networks

In protein-protein interaction (PPI) networks, functional similarity is often inferred based on the function of directly interacting proteins, or more generally, some notion of interaction network proximity among proteins in a local neighborhood. Prior methods typically measure proximity as the shortest-path distance in the network, but this has only a limited ability to capture fine-grained neighborhood distinctions, because most proteins are close to each other, and there are many ties in proximity. We introduce diffusion state distance (DSD), a new metric based on a graph diffusion property, designed to capture finer-grained distinctions in proximity for transfer of functional annotation in PPI networks. We present a tool that, when input a PPI network, will output the DSD distances between every pair of proteins. We show that replacing the shortest-path metric by DSD improves the performance of classical function prediction methods across the board.     

人体基因组D14S13位点限制性片段长度多态性的研究

应用pCE1.2探针,分析了296个无关个体基因组D14S13位点Haelll酶解的限制性片段长度多态性（RFLP）,进行了等位基因频率的分布统计,发现至少含有66个等位基因,位点杂合性大于93％,在对8个家系93名相关个体的分析中,没有发现突变发生,此RFLP分析方法已初步应用于法医学的个人识别和亲权鉴定中,并对准确度进行了计算。》     

THE FLORAL AND EXTRA-FLORAL NECTARIES OF PASSIFLORA. II. THE EXTRA-FLORAL NECTARY

Extra-floral nectaries of nine species of Passiflora were studied with light and electron microscopy prior to and during secretion. There is no evidence of ER or Golgi participation in the secretion of nectar. The vascular tissue supplying the nectary is characterized by companion and phloem parenchyma cells which are usually larger than the sieve elements, a configuration similar to that found in leaf minor veins. In the petiolar nectaries, large masses of membrane-bound protein are commonly found in these cells. This protein is absent in laminar nectaries.     

Bacteriophage of Haemophilus influenzae III. Morphology, DNA Homology, and Immunity Properties of HP1c1, S2, and the Defective Bacteriophage from Strain Rd

The phages HP1c1 and S2 and a defective phage of Haemophilus influenzae have been compared. The morphology of the phages and the mol wt of their DNAs are similar, although the defective phage appears to have a different tail plate region. Electron microscope observation indicates that the defective phage does not attach to the cell surface, and its DNA appears to lack cohesive ends. The homology of the DNAs of the phages has been measured by hydridization. DNA from the defective phage shows little or no homology with the other phage DNAs. HP1c1 and S2 DNAs show a high level of homology. Each of these phages can form plaques on lawns of the lysogen of the other phage but at reduced plating efficiencies, suggesting that the two phages have related but not identical immunity systems.     

Relationship Between Prophage Induction and Transformation in Haemophilus influenzae

The interaction between transformation and prophages of HP1c1, S2, and a defective phage of Haemophilus influenzae has been investigated by measurement of (i) the effect of prophage on transformation frequency and (ii) the effect of transformation on phage induction. The presence of any of the prophages does not appreciably alter transformation frequencies in various Rec(+) and Rec(-) strains. However, exposure of competent lysogens to transforming deoxyribonucleic acid (DNA) may induce phage but only in Rec(+) strains, which are able to integrate transforming DNA into their genome. Transformation of Rec(+) lysogens with DNA irradiated with ultraviolet (UV) light causes the production of even more phage than results from unirradiated DNA, but this indirect UV induction is not as effective as direct induction by UV irradiation of lysogens. Both types of UV induction are influenced by the repair capacity of the host. Wild-type cells contain a prophage and can be induced by transformation to produce a defective phage, which kills a small fraction of the cells. Defective phage in wild-type cells are also induced by H. parainfluenzae DNA, and a much larger fraction of the cells is killed. Strain BC200, which is highly transformable but is not inducible for defective phage, is not killed by H. parainfluenzae DNA, suggesting that wild-type cells are killed by killed by this DNA because of phage induction. A minicell-producing mutant, LB11, has been isolated. Some phage induction occurs in this strain when the cells are made competent, unlike the wild type. A large majority of LB11 cells surviving the competence regime are killed by exposure to transforming DNA.     

Evidence against the reversion of mutation in the Haemophilus influenzae phage HP1c1 by preinfection treatment of host cells or phage with MNNG.

N-Methyl-N'-nitrosoguanidine (MNNG) causes reversion of a temperature-sensitive mutation in a bacteriophage of Haemophilus influenzae if exposure to the mutagen takes place after infection but before lysis. However, neither pre-infection treatment of the phage DNA, host cells, or both will cause reversion. The reasons for this are discussed in relation to the somewhat different results in the Escherichia coli lambda phage system and in relation to error-prone repair and replication processes.