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941.
Yves Frank Tomas Hruz Thomas Tschager Valentin Venzin 《Algorithms for molecular biology : AMB》2018,13(1):14
Background
Liquid chromatography combined with tandem mass spectrometry is an important tool in proteomics for peptide identification. Liquid chromatography temporally separates the peptides in a sample. The peptides that elute one after another are analyzed via tandem mass spectrometry by measuring the mass-to-charge ratio of a peptide and its fragments. De novo peptide sequencing is the problem of reconstructing the amino acid sequences of a peptide from this measurement data. Past de novo sequencing algorithms solely consider the mass spectrum of the fragments for reconstructing a sequence.Results
We propose to additionally exploit the information obtained from liquid chromatography. We study the problem of computing a sequence that is not only in accordance with the experimental mass spectrum, but also with the chromatographic retention time. We consider three models for predicting the retention time and develop algorithms for de novo sequencing for each model.Conclusions
Based on an evaluation for two prediction models on experimental data from synthesized peptides we conclude that the identification rates are improved by exploiting the chromatographic information. In our evaluation, we compare our algorithms using the retention time information with algorithms using the same scoring model, but not the retention time.942.
Frank H. Gleason Steve K. Schmidt Agostina V. Marano 《Extremophiles : life under extreme conditions》2010,14(5):417-425
Zoosporic true fungi are thought to be ubiquitous in many ecosystems, especially in cool, moist soils and freshwater habitats which are rich in organic matter. However, some of the habitats where these fungi are found may periodically experience extreme conditions, such as soils in extremely dry, hot and cold climates, acidic and alkaline soils, polluted rivers, anaerobic soil and water, saline soil and water, periglacial soils, oligotrophic soils, tree canopies and hydrothermal vents. It is clear that many ecotypes of zoosporic true fungi have indeed adapted to extreme or stressful environmental conditions. This conclusion is supported by studies in both the field and in the laboratory. Therefore, in our opinion, at least some true zoosporic fungi can be considered to be extremophiles. 相似文献
943.
Frank Petrigliano David McAllister Santiago Miriuka Denis A. Evseenko 《Cell biochemistry and function》2013,31(4):271-280
Mesenchymal stem or stromal cells (MSCs) were initially isolated from the bone marrow and received their name on the basis of their ability to differentiate into multiple lineages such as bone, cartilage, fat and muscle. However, more recent studies suggest that MSCs residing in perivascular compartments of the small and large blood vessels play a regulatory function supporting physiologic and pathologic responses of parenchymal cells, which define the functional representation of an organ or tissue. MSCs secrete or express factors that reach neighbouring parenchymal cells via either a paracrine effect or a direct cell‐to‐cell interaction promoting functional activity, survival and proliferation of the parenchymal cells. Previous concept of ‘epithelial–stromal’ interactions can now be widened. Given that MSC can also support hematopoietic, neuronal and other non‐epithelial parenchymal lineages, terms ‘parenchymal–stromal’ or ‘parenchymal–mesenchymal’ interactions may better describe the supportive or ‘trophic’ functions of MSC. Importantly, in many cases, MSCs specifically provide supportive microenvironment for the most primitive stem or progenitor populations and therefore can play a role as ‘stem/progenitor niche’ forming cells. So far, regulatory roles of MSCs have been reported in many tissues. In this review article, we summarize the latest studies that focused on the supportive function of MSC. This thread of research leads to a new perspective on the interactions between parenchymal and mesenchymal cells and justifies a principally novel approach for regenerative medicine based on co‐application of MSC and parenchymal cell for the most efficient tissue repair. Copyright © 2013 John Wiley & Sons, Ltd. 相似文献
944.
The influence of fruit ingestion by the bat, Sturnira lilium, on germination of the seeds of the tree Solanum riparium was studied in a secondary rain forest in northwestern Argentina. Bat frequencies in disturbed areas were analyzed by mist net captures. Germination rates were determined for seeds collected from trees and bat feces. S. lilium was the most abundant fruit bat in the study area. Fruit digestion and the passage of seeds through the intestine did not significantly affect germination in S. riparium. In this case the fruit bats, therefore, probably provide only seed dispersal. 相似文献
945.
Frank Adolf Alexia Herrmann Andrea Hellwig Rainer Beck Britta Brügger Felix T. Wieland 《Traffic (Copenhagen, Denmark)》2013,14(8):922-932
Intracellular transport and maintenance of the endomembrane system in eukaryotes depends on formation and fusion of vesicular carriers. A seeming discrepancy exists in the literature about the basic mechanism in the scission of transport vesicles that depend on GTP‐binding proteins. Some reports describe that the scission of COP‐coated vesicles is dependent on GTP hydrolysis, whereas others found that GTP hydrolysis is not required. In order to investigate this pivotal mechanism in vesicle formation, we analyzed formation of COPI‐ and COPII‐coated vesicles utilizing semi‐intact cells. The small GTPases Sar1 and Arf1 together with their corresponding coat proteins, the Sec23/24 and Sec13/31 complexes for COPII and coatomer for COPI vesicles were required and sufficient to drive vesicle formation. Both types of vesicles were efficiently generated when GTP hydrolysis was blocked either by utilizing the poorly hydrolyzable GTP analogs GTPγS and GMP‐PNP, or with constitutively active mutants of the small GTPases. Thus, GTP hydrolysis is not required for the formation and release of COP vesicles. 相似文献
946.
Feng Liu Leona Bessonova Thomas H. Taylor Argyrios Ziogas Frank L. Meyskens Jr. Hoda Anton‐Culver 《Pigment cell & melanoma research》2013,26(1):128-135
Using US SEER17 Registry data, age‐specific melanoma incidence rates were calculated and comparisons were made between males and females. Relative Risk (RR) for males and females in each age group was computed and compared with that from Nordic Cancer Registry data set and to that for non‐melanoma skin cancer (NMSC). For age groups 44 and younger, females showed higher incidence rates, with a peak difference at age 20–24 (RR = 2.01, 95% CI = 1.21–3.33). Males exhibited higher incidence rates after age 44. The same bimodal gender difference was confirmed by the Nordic Cancer Registry data set, but it was not observed for NMSC, which is known to be strongly associated with cumulative exposure to solar UV radiation. We conclude that exposure to solar ultraviolet (UV) radiation is the major causative factor for melanoma at older age (>44 yr), but that other factors may play a role in early onset melanomas, particularly in females. 相似文献
947.
Hyphae of filamentous Ascomycota consist of compartments that are connected via septal pores. To avoid a dramatic loss of cellular content after wounding, fungi developed mechanisms to occlude their septal pores. In most Pezizomycotina, so‐called Woronin bodies are anchored in proximity to the pore. This is a prominent example for precise spatial positioning of organelles, but so far the underlying molecular organization has remained largely unknown. Using the pathogenic mould Aspergillus fumigatus, we provide evidence that Woronin bodies are important for stress resistance and virulence. Furthermore the molecular machinery anchoring them at the septum is described. Namely, we have identified Lah as the tethering protein and provide evidence that the Woronin body protein HexA binds to the septal pore in a Lah‐dependent manner. Moreover, we demonstrate that a striking poly‐histidine motif targets HexA to the septal cell wall. Thus, the axis HexA‐Lah is an excellent candidate for the tether linking Woronin bodies to the septum. This model applies to A. fumigatus, but most likely also to the vast majority of the Pezizomycotina. Our findings shed light on the evolution of Woronin body anchoring and provide a basis for the development of novel strategies to combat fungal pathogens like A. fumigatus. 相似文献
948.
Gang Fang Robert Friesen Frank Lanfermeijer Anja Hagting Bert Poolman Wil N. Konings 《Molecular membrane biology》2013,30(4):297-304
The di-tripeptide transport system (DtpT) of Lactococcus lactis was purified to apparent homogeneity by pre-extraction of crude membrane vesicles with octaethylene glycol monodecyl ether (C10E8), followed by solubilization with n-dodecyl-beta-D-maltoside (DDM) and chromatography on a Ni-NTA resin. The DtpT protein was reconstituted into detergent-destabilized preformed liposomes prepared from E. coli phospholipid/ phosphatidylcholine. A variety of detergents were tested for their ability to mediate the membrane reconstitution of DtpT and their effectiveness to yield proteoliposomes with a high transport activity. The highest activities were obtained with TX100, C12E8 and DM, whereas DDM yielded relatively poor activities, in particular when this detergent was used at concentrations beyond the onset of solubilization of the preformed liposomes. Parallel with the low activity, significant losses of lipid were observed when the reconstitution was performed at high DDM concentrations. This explained at least part of the reduced transport activity as the DtpT protein was highly dependent on the final lipid-to-protein ratios in the proteoliposomes. Consistent with the difference in mechanism of DDM- and TX100-mediated membrane protein reconstitution, the orientation of the DtpT protein in the membrane was random with DDM and inside-in when T100 was used. The methodology to determine the orientation of membrane-reconstituted proteins from the accessibility of cysteines for thiol-specific reagents is critically evaluated. 相似文献
949.
Cécile Breyton Ali Flayhan Frank Gabel Mathilde Lethier Grégory Durand Pascale Boulanger Mohamed Chami Christine Ebel 《The Journal of biological chemistry》2013,288(42):30763-30772
Within tailed bacteriophages, interaction of the receptor-binding protein (RBP) with the target cell triggers viral DNA ejection into the host cytoplasm. In the case of phage T5, the RBP pb5 and the receptor FhuA, an outer membrane protein of Escherichia coli, have been identified. Here, we use small angle neutron scattering and electron microscopy to investigate the FhuA-pb5 complex. Specific deuteration of one of the partners allows the complete masking in small angle neutron scattering of the surfactant and unlabeled proteins when the complex is solubilized in the fluorinated surfactant F6-DigluM. Thus, individual structures within a membrane protein complex can be described. The solution structure of FhuA agrees with its crystal structure; that of pb5 shows an elongated shape. Neither displays significant conformational changes upon interaction. The mechanism of signal transduction within phage T5 thus appears different from that of phages binding cell wall saccharides, for which structural information is available. 相似文献
950.
Frank Rattay Thomas Potrusil Cornelia Wenger Andrew K. Wise Rudolf Glueckert Anneliese Schrott-Fischer 《PloS one》2013,8(11)