Protein Phosphorylation Site Prediction via Feature Discovery Support Vector Machine

Protein phosphorylation/dephosphorylation is the central mechanism of post-translational modification which regulates cellular responses and phenotypes. Due to the efficiency and resource constraints of the in vivo methods for identifying phosphorylation sites, there is a strong motivation to computationally predict potential phosphorylation sites. In this work, we propose to use a unique set of features to represent the peptides surrounding the amino acid sites of interest and use feature selection support vector machine to predict whether the serine/threonine sites are potentially phosphorylable, as well as selecting important features that may lead to phosphorylation. Experimental results indicate that the new features and the prediction method can more effectively predict protein phosphorylation sites than the existing state of the art methods. The features selected by our prediction model provide biological insights to the in vivo phosphorylation.     

Effects of 2,4-D on a Populus tremuloides community in the western United States-22 years after treatment

Normal 0 false false false EN-US X-NONE X-NONE MicrosoftInternetExplorer4 st1\:*{behavior:url(#ieooui) } /* Style Definitions */ table.MsoNormalTable {mso-style-name:"Table Normal"; mso-tstyle-rowband-size:0; mso-tstyle-colband-size:0; mso-style-noshow:yes; mso-style-priority:99; mso-style-qformat:yes; mso-style-parent:""; mso-padding-alt:0in 5.4pt 0in 5.4pt; mso-para-margin:0in; mso-para-margin-bottom:.0001pt; mso-pagination:widow-orphan; font-size:11.0pt; font-family:"Calibri","sans-serif"; mso-ascii-font-family:Calibri; mso-ascii-theme-font:minor-latin; mso-fareast-font-family:"Times New Roman"; mso-fareast-theme-font:minor-fareast; mso-hansi-font-family:Calibri; mso-hansi-theme-font:minor-latin; mso-bidi-font-family:"Times New Roman"; mso-bidi-theme-font:minor-bidi;} Quaking aspen ( Populus tremuloides Michx.) stands were accidentally sprayed with 2,4-D in a sagebrush control program in western Wyoming in 1958. We visited the site during the summer of 1981 to evaluate the long-term effect on the aspen trees and the associated vegetation. Initially, some observers believed that the aspen had been “destroyed.” Subsequent data indicate just the opposite—aspen stocking appeared to have been improved by the treatment. On two of the sampled clones, 22 years after spraying, there were approximately 17,000 more suckers/ha on the sprayed than on the unsprayed plots. These are adequate numbers to restock the site to pretreatment densities. Although undergrowth vegetation appeared to be changed as a result of the treatment, this cannot be attributed solely to the herbicide because heavy grazing, mostly by domestic livestock, has occurred on the grazing allotment. A similarity index was calculated between sprayed and unsprayed portions of the same aspen clones. Forbs were still less on the sprayed areas, whereas grasses were similar on the sprayed and unsprayed areas. Spraying apparently does not have as adverse an effect on aspen communities as some conservationists originally thought.        

Observations on Double-crested Cormorants ( Phalacrocorax auritus ) at sportfishing waters in southwestern Utah

Counts of Double-crested Cormorants ( Phalacrocorax auritus ) were made at 13 reservoirs and lakes in southwestern Utah during 1989-91 to determine current abundance of that species. Food habits of cormorants were studied at three of the reservoirs in 1989. Data were also collected on trout abundance during standardized gill-netting to make comparisons between cormorant numbers and trout abundance. Cormorants were observed at all waters studied except one and were generally most numerous during the spring as they migrated through the area. Estimated cormorant abundance ranged from 0 to 34 bird-days per ha and was highest at the larger, lower-elevation reservoirs. Cormorants were summer residents at several of the larger reservoirs and nested successfully at Piute Reservoir. Trout accounted for 24-81% of the diet of cormorants, with Utah chubs constituting most of the remainder of the diet. Estimates of the annual consumption of fish by cormorants ranged from 0 to 15.8 kg per ha. The index of trout abundance was inversely related to cormorant abundance ( P < .01) at the waters studied. Cormorants apparently have increased in numbers and extended their range in southwestern Utah during the past decade. This change may be the result of factors that have led to similar changes throughout North America as well as some factors unique to Utah. Methods to mitigate the impact of predation by piscivorous birds of sportfisheries are discussed. The Utah Division of Wildlife Resources has initiated a new management plan at Minersville Reservoir that incorporates piscivorous birds into sportfish management at that reservoir.     

Distribution and abundance of native Bonneville cutthroat trout ( Oncorhynchus clarki utah ) in southwestern Utah

The Bonneville cutthroat trout ( Oncorhynchus clarki utah ; BCT) was once abundant throughout the Bonneville Basin. In southwestern Utah, however, only 3 local populations of the subspecies were known to exist in 1977, when conservation efforts to protect and replicate them began. By 1995 remnant populations were known in 6 streams, and replicate populations had been established in an additional 16. Populations of BCT in southwestern Utah streams were survey by electrofishing in 1994 and 1995 to describe the subspecies' status. Estimated densities of age-1 and older BCT ranged from 118 to 546 fish per km. Biomass estimates ranged from 8 to 64 kg per ha. Several age groups of BCT were collected at most locations. Six populations were classified as self-sustaining, 9 as expanding through natural recruitment, 6 as new, and 1 as hybridized. Overall status of BCT in southwestern Utah has improved since 1977, but conservation measures must continue to maintain a positive trend.