Paircoil2: improved prediction of coiled coils from sequence

We introduce Paircoil2, a new version of the Paircoil program, which uses pairwise residue probabilities to detect coiled-coil motifs in protein sequence data. Paircoil2 achieves 98% sensitivity and 97% specificity on known coiled coils in leave-family-out cross-validation. It also shows superior performance compared with published methods in tests on proteins of known structure.     

Immunohistochemical analysis of Bin1/Amphiphysin II in human tissues: diverse sites of nuclear expression and losses in prostate cancer

The Bin1/Amphiphysin II gene encodes at least seven alternately spliced adapter proteins that have been implicated in membrane dynamics and nuclear processes. Nuclear localized Bin1 polypeptides have tumor suppressor and proapoptotic activities, suggesting that Bin1 may suppress cancer in tissues where nuclear expression may occur. One question is the extent to which human tissues express nuclear Bin1 isoforms. A secondary issue has been the need for a specific antibody that can detect all the splice isoforms expressed by the human, mouse, and rat Bin1 genes. Using a novel mouse monoclonal antibody with these characteristics, we performed an immunohistochemical analysis of Bin1 expression in a panel of normal human tissues. We also compared the expression profile of Bin1 in normal or malignant tissues derived from human prostate, where Bin1 is a candidate tumor suppressor gene. In brain, a distinct nuclear staining pattern overlapped with a cytosolic staining pattern present in certain layers of the cerebral cortex and cerebellum. Bone marrow cells displayed mainly nuclear localization whereas peripheral lymphoid cells exhibited mainly cytosolic localization. In several epithelial tissues, nuclear or nucleocytosolic staining patterns were displayed by basal cells in skin, breast, or prostate, whereas cytosolic or plasma membrane-associated staining patterns were noted in gastrointestinal cells. Interestingly, a striking gradient of expression was observed in gastrointestinal epithelia, particularly in the large intestine, with the strongest staining displayed by cells destined to undergo apoptosis at the villus tip. In prostate, Bin1 staining was frequently absent in cases of primary prostate adenocarcinoma. This study used a novel reagent to document the extent of expression of nuclear Bin1 isoforms, which exhibit cancer suppression and proapoptotic activity in human cells.     

Ultrasonographic measurements of accessory sex glands,ampullae, and urethra of normal stallions of various size types

For the purpose of establishing clinical reference values, this paper reports results of ultrasonographic examination and measurement of accessory sex glands, ampullae, and the pelvic urethra of 102 mature, healthy breeding stallions (2-29 years of age) of various size types (7 Miniature Horses, 27 small ponies, 53 light horses and 15 heavy horses). Examinations were done per rectum in mostly unsedated stallions using an Aloka 210 scanner with a 7.5 MHz linear veterinary transrectal transducer (Corometrics Medical Systems, Inc., North Wallingford, CT, USA). Most measures of accessory sex glands, ampullae and the urethra were larger in horses of larger sizes. Except for vesicular glands, the majority of the measures for all glands were smaller for Miniature Horses and ponies than for light horses and heavy horses (P < 0.05). For vesicular glands, measures for heavy horses were greater than for those of other groups (P < 0.05). Measures were similar for Miniature Horses and ponies, and for light horses and heavy horses. For all measures, differences between left and right paired glands were not different (P > 0.10). The lumen diameter of vesicular glands and ampullae as well as prostate lobe thickness showed the greatest asymmetry. Although there were too few representatives of various breeds for statistical comparison, among the light horse breeds Arabian stallions had the smallest mean values for the majority of the measures. Among stallions, echogenic characteristics of accessory sex glands, particularly vesicular glands, varied widely, possibly related to variation in recent sexual activity. For some stallions, echogenic character, particularly that of vesicular glands, varied remarkably from left to right gland within stallions. For ampullae, there was also wide variation in lumen contents between stallions. These data are generally consistent with previous reports with smaller numbers of stallions, as well as consistent with in vitro measures in previous studies. The results provide useful clinical guidelines for size measures of accessory sex glands in horses.     

Analysis of the RNASEL gene in familial and sporadic prostate cancer

The RNASEL gene on chromosome 1q25 was recently identified as a candidate gene for hereditary prostate cancer (PC). To confirm these findings, we screened 326 patients from 163 families with familial PC for potential germline mutations, by use of conformation-sensitive gel electrophoresis, followed by direct sequence analysis. A total of six variants were identified, including one intronic and five exonic changes (three missense and two silent alterations). There were no unequivocal pathogenic changes. To further test for potential associations between genes and increased risk for disease, the three missense polymorphisms (Ile97Leu, Arg462Gln, and Glu541Asp) were genotyped in 438 patients with familial PC and in 510 population-based control subjects. Association testing revealed no significant differences between patients and control subjects for either the Leu97 variant (chi(2) trend test = 1.42; P=.23) or the Asp541 variant (chi2=1.52; P=.22). However, significant differences were detected for the Arg462Gln genotypes (chi2=5.20; P=.02; odds ratio [OR] = 0.54; 95% confidence interval [CI] 0.32-0.91) when the genotype Gln/Gln was compared with Arg/Arg. In subset analyses, associations were also observed in the younger group (age at diagnosis 相似文献   

BIRD-DISPERSAL OF PHYTOLACCA AMERICANA L. AND THE INFLUENCE OF FRUIT REMOVAL ON SUBSEQUENT FRUIT DEVELOPMENT

Characteristics of fruits, seeds, and ripening of Phytolacca americana were studied in New Jersey, USA to assess their importance in the dispersal strategy of this species. Removal by birds was directly related to the percent of ripe fruits available on a raceme. Fruit removal from a raceme resulted in lower fruit pulp and seed weights for fruits developing on the same raceme, but these differences probably do not influence probability for dispersal by birds. We demonstrate that characteristics of the fruit pulp may decrease seed availability for the primary seed predator, Peromyscus leucopus, and increase the time fruits are available for dispersal. We speculate on the significance of the sequential fruiting in Phytolacca and the relationship to availability of dispersal agents and high-lipid fruits. Sequential ripening and protection from predation result in seed dispersal from late August to early December.