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981.
Alessandra Cesano Cheryl L. Willman Kenneth J. Kopecky Urte Gayko Santosh Putta Brent Louie Matt Westfall Norman Purvis David C. Spellmeyer Carol Marimpietri Aileen C. Cohen James Hackett Jing Shi Michael G. Walker Zhuoxin Sun Elisabeth Paietta Martin S. Tallman Larry D. Cripe Susan Atwater Frederick R. Appelbaum Jerald P. Radich 《PloS one》2015,10(4)
Single-cell network profiling (SCNP) data generated from multi-parametric flow cytometry analysis of bone marrow (BM) and peripheral blood (PB) samples collected from patients >55 years old with non-M3 AML were used to train and validate a diagnostic classifier (DXSCNP) for predicting response to standard induction chemotherapy (complete response [CR] or CR with incomplete hematologic recovery [CRi] versus resistant disease [RD]). SCNP-evaluable patients from four SWOG AML trials were randomized between Training (N = 74 patients with CR, CRi or RD; BM set = 43; PB set = 57) and Validation Analysis Sets (N = 71; BM set = 42, PB set = 53). Cell survival, differentiation, and apoptosis pathway signaling were used as potential inputs for DXSCNP. Five DXSCNP classifiers were developed on the SWOG Training set and tested for prediction accuracy in an independent BM verification sample set (N = 24) from ECOG AML trials to select the final classifier, which was a significant predictor of CR/CRi (area under the receiver operating characteristic curve AUROC = 0.76, p = 0.01). The selected classifier was then validated in the SWOG BM Validation Set (AUROC = 0.72, p = 0.02). Importantly, a classifier developed using only clinical and molecular inputs from the same sample set (DXCLINICAL2) lacked prediction accuracy: AUROC = 0.61 (p = 0.18) in the BM Verification Set and 0.53 (p = 0.38) in the BM Validation Set. Notably, the DXSCNP classifier was still significant in predicting response in the BM Validation Analysis Set after controlling for DXCLINICAL2 (p = 0.03), showing that DXSCNP provides information that is independent from that provided by currently used prognostic markers. Taken together, these data show that the proteomic classifier may provide prognostic information relevant to treatment planning beyond genetic mutations and traditional prognostic factors in elderly AML. 相似文献
982.
983.
Sandra Stoppelkamp Kujtim Veseli Katharina Stang Christian Schlensak Hans Peter Wendel Tobias Walker 《PloS one》2015,10(8)
Systemic inflammatory response syndrome (SIRS) is a common complication after cardiovascular surgery that in severe cases can lead to multiple organ dysfunction syndrome and even death. We therefore set out to identify reliable early biomarkers for SIRS in a prospective small patient study for timely intervention. 21 Patients scheduled for planned cardiovascular surgery were recruited in the study, monitored for signs of SIRS and blood samples were taken to investigate biomarkers at pre-assigned time points: day of admission, start of surgery, end of surgery, days 1, 2, 3, 5 and 8 post surgery. Stored plasma and cryopreserved blood samples were analyzed for cytokine expression (IL1β, IL2, IL6, IL8, IL10, TNFα, IFNγ), other pro-inflammatory markers (sCD163, sTREM-1, ESM-1) and response to endotoxin. Acute phase proteins CRP, PCT and pro-inflammatory cytokines IL6 and IL8 were significantly increased (p<0.001) at the end of surgery in all patients but could not distinguish between groups. Normalization of samples revealed significant increases in IL1β changes (p<0.05) and decreased responses to endotoxin (p<0.01) in the SIRS group at the end of surgery. Soluble TREM-1 plasma concentrations were significantly increased in patients with SIRS (p<0.01). This small scale patient study could show that common sepsis markers PCT, CRP, IL6 and TNFα had low predictive value for early diagnosis of SIRS after cardiovascular surgery. A combination of normalized IL1β plasma levels, responses to endotoxin and soluble TREM-1 plasma concentrations at the end of surgery are predictive markers of SIRS development in this small scale study and could act as an indicator for starting early therapeutic interventions. 相似文献
984.
This study investigates how epithelial cells moving together function to coordinate their collective movement to repair a wound. Using a lens ex vivo mock cataract surgery model we show that region-specific reorganization of cell–cell junctions, cytoskeletal networks and myosin function along apical and basal domains of an epithelium mediates the process of collective migration. An apical junctional complex composed of N-cadherin/ZO-1/myosin II linked to a cortical actin cytoskeleton network maintains integrity of the tissue during the healing process. These cells’ basal domains often preceded their apical domains in the direction of movement, where an atypical N-cadherin/ZO-1 junction, linked to an actin stress fiber network rich in phosphomyosin, was prominent in cryptic lamellipodia. These junctions joined the protruding forward-moving lamellipodia to the back end of the cell moving directly in front of it. These were the only junctions detected in cryptic lamellipodia of lens epithelia migrating in response to wounding that could transmit the protrusive forces that drive collective movement. Both integrity of the epithelium and ability to effectively heal the wound was found to depend on myosin mechanical cues. 相似文献
985.
Iris H. Walker Pei-chung Hsieh Paul D. Riggs 《Applied microbiology and biotechnology》2010,88(1):187-197
Maltose-binding protein (MBP) from Escherichia coli has been shown to be a good substrate for protein engineering leading to altered binding (Marvin and Hellinga, Proc Natl
Acad Sci U S A 98:4955–4960, 2001a) and increased affinity (Marvin and Hellinga, Nat Struct Biol 8:795–798, 2001b; Telmer and Shilton, J Biol Chem 278:34555–34567, 2003). It is also used in recombinant protein expression as both an affinity tag and a solubility tag. We isolated mutations in
MBP that enhance binding to maltodextrins 1.3 to 15-fold, using random mutagenesis followed by screening for enhanced yield
in a microplate-based affinity purification. We tested the mutations for their ability to enhance the yield of a fusion protein
that binds poorly to immobilized amylose and their ability to enhance the solubility of one or more aggregation-prone recombinant
proteins. We also measured dissociation constants of the mutant MBPs that retain the solubility-enhancing properties of MBP
and combined two of the mutations to produce an MBP with a dissociation constant 10-fold tighter than wild-type MBP. Some
of the mutations we obtained can be rationalized based on the previous work, while others indicate new ways in which the function
of MBP can be modified. 相似文献
986.
Chiung-Kuang J. Chen Robert E. Berry Tatjana Kh. Shokhireva Marat B. Murataliev Hongjung Zhang F. Ann Walker 《Journal of biological inorganic chemistry》2010,15(2):159-174
CYP102A1 is a highly active, water-soluble, bacterial monooxygenase enzyme that contains both substrate-binding heme and diflavin
reductase subunits, both in a single polypeptide. Recently we developed a procedure which uses the known structure of the
substrate-bound heme domain of CYP102A1 and its sequence homology with a cytochrome P450 of unknown structure, both of which
react with a common substrate but produce different products, to create recombinant enzymes which have substrate selectivity
different from that of CYP102A1, and produce the product of the enzyme of unknown structure. Insect CYP4C7, a terpene hydroxylase
from the cockroach, was chosen as the cytochrome P450 of unknown structure, and farnesol was chosen as the substrate. CYP102A1
oxidizes farnesol to three products (2,3-epoxyfarnesol, 10,11-epoxyfarnesol, and 9-hydroxyfarnesol), whereas CYP4C7 produces
12-hydroxyfarnesol as the major product. In earlier work it was found that the chimera C(78-82,F87L) showed a change in substrate
selectivity from fatty acids to farnesol, and was approximately sixfold more active than wild-type CYP102A1 (Chen et al. in
J Biol Inorg Chem 13:813–824, 2008), but neither it nor any other earlier chimera produced 12-hydroxyfarnesol. In this work we added amino acid residues 327–332,
to create six new full-length, functional chimeric proteins. Four of these, the most active of which was C(78-82,F87L,328-330),
produce 12-hydroxyfarnesol as the major product, with approximately twofold increase in turnover number as compared with wild-type
CYP102A1 toward farnesol. Methylfarnesoate was metabolized to 12-hydroxymethylfarnesoate (70%) and 10,11-epoxymethylfarnesoate
(juvenile hormone III) (30%). The latter is metabolized to 65% 12-hydroxy-10,11-epoxymethylfarnesoate and 35% 15-hydroxy-10,11-epoxymethylfarnesoate.
Substitution of residues 328–330, APA, by VPL was crucial to accomplishing this change in product. 相似文献
987.
Deutscher AT Jenkins C Minion FC Seymour LM Padula MP Dixon NE Walker MJ Djordjevic SP 《Molecular microbiology》2010,78(2):444-458
Bacteriophage T4 is decorated with 155 copies of the highly antigenic outer capsid protein, Hoc. The Hoc molecule (40 kDa) is present at the centre of each hexameric capsomer and provides a good platform for surface display of pathogen antigens. Biochemical and modelling studies show that Hoc consists of a string of four domains, three immunoglobulin (Ig)‐like and one non‐Ig domain at the C‐terminus. Biochemical data suggest that the Hoc protein has two functional modules, a capsid binding module containing domains 1 and 4 and a solvent‐exposed module containing domains 2 and 3. This model is consistent with the dumbbell‐shaped cryo‐EM density of Hoc observed in the reconstruction of the T4 capsid. Mutagenesis localized the capsid binding site to the C‐terminal 25 amino acids, which are predicted to form two β‐strands flanking a capsid binding loop. Mutations in the loop residues, ESRNG, abolished capsid binding, suggesting that these residues might interact with the major capsid protein, gp23*. With the conserved capsid binding module forming a foothold on the virus and the solvent‐exposed module able to adapt to bind to a variety of surfaces, Hoc probably provides survival advantages to the phage, such as increasing the virus concentration near the host, efficient dispersion of the virus and exposing the tail for more efficient contact with the host cell surface prior to infection. 相似文献
988.
989.
Alexandra Pavlova Faith M. Walker Rodney van der Ree Silvana Cesarini Andrea C. Taylor 《Conservation Genetics》2010,11(6):2393-2407
The squirrel glider Petaurus norfolcensis occurs across a broad Australian latitudinal range that includes gaps in distribution and potential biogeographic barriers,
creating the potential for evolution of distinct entities within this species. Because of the species’ threatened status in
the southern part of its range, we tested for the presence of geographically based independent evolutionary units among gliders
sampled from southern, and northern coastal populations, using sequences of mitochondrial cytochrome b DNA (mtDNA) and a set of five nuclear microsatellites in 258 individuals. Our analyses suggest that an initial northward
colonisation in the early- to mid-Pleistocene was followed by isolation by distance and, eventually, divergence between the
sampled coastal and southern populations in the mid- to late-Pleistocene. We propose that the previously large and diverse
southern populations have declined coincidentally with the replacement of wet forests by open sclerophyll woodlands during
the preceding few million years. By contrast coastal populations further north appear to have been expanding and at present
have an effective population size several times greater than southern populations. These results suggest that the two forms
are on different evolutionary trajectories and should be treated separately for conservation purposes. It is highly desirable
that loss of southern populations be prevented to maintain the unique genetic diversity accumulated over a considerable evolutionary
timescale. 相似文献
990.