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Paul D. Piehowski Vladislav A. Petyuk John D. Sandoval Kristin E. Burnum Gary R. Kiebel Matthew E. Monroe Gordon A. Anderson David G. Camp II Richard D. Smith 《Proteomics》2013,13(5):766-770
For bottom‐up proteomics, there are wide variety of database‐searching algorithms in use for matching peptide sequences to tandem MS spectra. Likewise, there are numerous strategies being employed to produce a confident list of peptide identifications from the different search algorithm outputs. Here we introduce a grid‐search approach for determining optimal database filtering criteria in shotgun proteomics data analyses that is easily adaptable to any search. Systematic Trial and Error Parameter Selection‐–referred to as STEPS‐–utilizes user‐defined parameter ranges to test a wide array of parameter combinations to arrive at an optimal “parameter set” for data filtering, thus maximizing confident identifications. The benefits of this approach in terms of numbers of true‐positive identifications are demonstrated using datasets derived from immunoaffinity‐depleted blood serum and a bacterial cell lysate, two common proteomics sample types. 相似文献
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Giovanni Monaco Elke Decrock Koen Nuyts Larry E. Wagner II Tomas Luyten Sergei V. Strelkov Ludwig Missiaen Wim M. De Borggraeve Luc Leybaert David I. Yule Humbert De Smedt Jan B. Parys Geert Bultynck 《PloS one》2013,8(8)
The anti-apoptotic Bcl-2 protein is the founding member and namesake of the Bcl-2-protein family. It has recently been demonstrated that Bcl-2, apart from its anti-apoptotic role at mitochondrial membranes, can also directly interact with the inositol 1,4,5-trisphosphate receptor (IP3R), the primary Ca2+-release channel in the endoplasmic reticulum (ER). Bcl-2 can thereby reduce pro-apoptotic IP3R-mediated Ca2+ release from the ER. Moreover, the Bcl-2 homology domain 4 (Bcl-2-BH4) has been identified as essential and sufficient for this IP3R-mediated anti-apoptotic activity. In the present study, we investigated whether the reported inhibitory effect of a Bcl-2-BH4 peptide on the IP 3R1 was related to the distinctive α-helical conformation of the BH4 domain peptide. We therefore designed a peptide with two glycine “hinges” replacing residues I14 and V15, of the wild-type Bcl-2-BH4 domain (Bcl-2-BH4-IV/GG). By comparing the structural and functional properties of the Bcl-2-BH4-IV/GG peptide with its native counterpart, we found that the variant contained reduced α-helicity, neither bound nor inhibited the IP 3R1 channel, and in turn lost its anti-apoptotic effect. Similar results were obtained with other substitutions in Bcl-2-BH4 that destabilized the α-helix with concomitant loss of IP3R inhibition. These results provide new insights for the further development of Bcl-2-BH4-derived peptides as specific inhibitors of the IP3R with significant pharmacological implications. 相似文献
24.
Andy J. Kulikowski II 《Biotropica》2020,52(4):709-716
Ant–hemipteran mutualisms can have positive and negative effects on host plants depending on the level of hemipteran infestation and plant protection conferred by ants against folivory. Differential effects of such mutualisms on plant survival are well documented in undisturbed and ant-invaded systems, but few have explored how anthropogenic disturbance affects interactions between hemipterans and native ant species and what the consequences may be for recovering ecosystems. Within a fragmented landscape in Costa Rica, restored tropical forests harbor a mutualism between the native ant Wasmannia auropunctata and the scale insect Alecanochiton marquesi on the abundant, early-successional tree Conostegia xalapensis. I added A. marquesi scales to C. xalapensis seedlings and either allowed or excluded W. auropunctata to investigate if this mutualism leads to increased scale infestation, decreased scale mortality, and decreased folivory. I also examined whether these effects are mediated by the percentage of remnant forest cover in the landscape. I found that seedlings with ants excluded had fewer scale insects and higher herbivory than plants with ants present. I also found evidence that scale mortality due to fungal attack and parasitism was higher on ant-excluded versus ant-allowed seedlings but only at sites with high surrounding landscape forest cover. Together, these results suggest that mutualisms between scale insects and native ants can promote scale infestation, reduce folivory on native plant species, and potentially disrupt biological control of scale insects in recovering tropical forests. Further, my experiment underscores the importance of remnant tropical forests as sources of biological control in anthropogenically disturbed landscapes. Abstract in Spanish is available with online material. 相似文献
25.
Lesions of the basal forebrain deplete the neocortex of cholinergic fibers. Acetylcholine depletion in the somatosensory cortex of rats results in reduced stimulus-evoked activity in response to whisker stimulation. Previous studies demonstrate that embryonic basal forebrain transplants improve functional activity toward normal. It is not clear if the activity increase is due to cholinergic replacement or other factors present in the graft. In this study, we examined the possibility that nerve growth factor (NGF), a neurotrophin known as a survival factor and a specific protectant for cholinergic basal forebrain neurons, can preserve basal forebrain cells after a lesion and restore functional activity in the somatosensory cortex. We report that NGF alone is capable of restoring functional activity in the barrel cortex of animals with basal forebrain lesions, while vehicle injections of saline do not alter activity. Both high (10 mug) and low (5 mug) doses of NGF unilaterally injected into the lateral ventricle improved stimulus-evoked functional activity during bilateral whisker stimulation. The mechanism of NGF action is not clear since the restoration of functional activity in cortex was not accompanied by increased cholinergic activity as detected by acetylcholinesterase fiber staining. NGF may act directly on cortical neurons, although its site of action is not well defined. 相似文献
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M. A. Matsche K. M. Rosemary H. M. Brundage III J. C. O'Herron II 《Zeitschrift fur angewandte Ichthyologie》2013,29(2):299-309
Non‐lethal sampling techniques were used to document the reproductive structure of the shortnose sturgeon (Acipenser brevirostrum) population at a fish aggregation site (near Bordentown, New Jersey) in the Delaware River. A total of 68 fish were captured using gill nets (100 × 1.8 m, 12.7 or 15.2 cm mesh) and examined laparoscopically in May–June, and 61 additional fish captured and examined in November during 2006–2011. Six stages of reproductive development were identified in females and five stages were identified in males, encompassing differentiation through maturity in both sexes. Fish captured in the spring were predominantly immature with a higher proportion of females (1 : 1.2 M : F sex ratio), while mature males predominated in the autumn (5.7 : 1 M : F), indicating that the Bordentown area serves as an overwintering/pre‐spawn aggregation site. Three distinct forms of intersex were noted in gonads of 11.6% of fish examined: ovo‐testis, consisting of scattered spermatic cysts in predominantly immature ovary (3.9%); testis‐ova, consisting of ovarian lamellae projecting from a predominantly immature testes (4.7%); and zonal distribution, consisting of multiple, nearly‐homogenous pockets of either testicular or ovarian tissues along the gonad (3%). The hormone profile in fish with ovo‐testis was similar to that of immature males, while the hormone profile in fish with testis‐ova was similar to that of immature females. The relatively high prevalence of intersex raises concerns regarding potential reproductive effects and long‐term impacts on shortnose sturgeon in the Delaware River. 相似文献
28.
Phylogenetic studies have demonstrated that Schefflera, the largest genus of Araliaceae, is grossly polyphyletic, comprising five distinct clades within the family. In an effort to establish monophyletic genera among the elements that currently comprise Schefflera, the genus Plerandra is expanded to encompass all of the members of one of these clades. In this synoptical revision, a new infrageneric classification is presented (along with a key) in which six subgenera are recognized. Four of these subgenera are newly described (Plerandra subgenera Canacoschefflera, Costatae, Gabriellarum, and Veilloniorum) and a fifth represents a new combination (Plerandra subg. Dizygotheca). A total of 33 species (one with two subspecies) are accepted, one of which is newly described (P. veilloniorum), and 22 new combinations are made (P. actinostigma, P. baillonii, P. cabalionii, P. costata, P. crassipes, P. elegantissima, P. elongata, P. emiliana, P. gabriellae, P. leptophylla, P. nono, P. osyana, P. osyana subsp. toto, P. pachyphylla, P. pancheri, P. plerandroides, P. polydactylis, P. reginae, P. seemanniana, P. tannae, P. vanuatua, P. veitchii). Neotypes are provided for six accepted names and one heterotypic synonym, and lectotypes are designated for 13 accepted names and 16 heterotypic synonyms. For each accepted species, full synonymy is provided along with geographic range and notes. 相似文献
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Louis Aronne Domenica Rubino Christopher Still Holly Wyatt Colleen Burns Dennis Kim Eduardo Dunayevich for the COR‐II Study Group 《Obesity (Silver Spring, Md.)》2013,21(5):935-943