Conformational stability of factor VIIa: biophysical studies of thermal and guanidine hydrochloride-induced denaturation

The binding of the multidomain protein factor VIIa (fVIIa) to tissue factor provides the interprotein communication necessary to make fVIIa an efficient catalyst of the initial event in the extrinsic pathway of blood coagulation. We have investigated the stability of individual domains in fVIIa and the influence of Ca2+ and an irreversible active-site inhibitor (FFR-chloromethyl ketone). Equilibrium guanidine hydrochloride (GuHCl)-induced unfolding monitored by tryptophan fluorescence and far-UV circular dichroism (CD) demonstrated that the gamma-carboxyglutamic acid (Gla) domain unfolds at 0.3 M GuHCl and the serine protease (SP) domain at 3 M GuHCl and that Ca2+ is a prerequisite for the formation of an ordered, compact structure in the Gla domain. The loss of amidolytic activity coincides with the first transition, which is stabilized by the active-site inhibitor, and a change in the environment of the active site is demonstrated using a fluorescent inhibitor (DEGR-chloromethyl ketone). Thermal unfolding monitored by differential scanning calorimetry (DSC) reveals that Ca2+ stabilizes the SP domain slightly, increasing the unfolding temperature by 2.7 degrees C. In addition, Ca2+ is required for a large enthalpy change concomitant with unfolding of the Gla domain, and this unfolding enthalpy is only detectable in the presence of the SP domain, indicating some kind of interaction between these domains. Thermal unfolding measured by CD indicates secondary structural changes at the same temperature as the heat absorption in the DSC but only when both the Gla domain and the SP domain are present together with Ca2+ ions. Taken together, these results indicate a Ca2+-dependent interaction between the Gla domain and the SP domain, implying a high degree of flexibility of the domains in free fVIIa. It is also shown that the epidermal growth factor-like domains are stable at elevated temperatures and high GuHCl concentrations. Moreover, already at physiological temperature, subtle structural changes take place which influence the overall shape of fVIIa and are detrimental to its enzymatic activity.     

Measurement of histamine release from human lung tissue ex vivo by microdialysis technique

OBJECTIVE AND DESIGN: Currently no method is available for measurement of mediator release from intact human lung. In this study, a microdialysis technique was used to measure histamine release from mast cells in human lung tissue ex vivo. MATERIAL: Microdialysis fibers of 216 microm were inserted into lung tissue and perfused with Krebs Ringer buffer at a rate of 3 microl/min. After a 15 min period of steady-state perfusion, anti-IgE and vehicle were injected into the lung tissue above individual fibers. Samples from each fibre were collected for 20 min at 2 min intervals. Histamine was assayed fluorometrically. RESULTS: Anti-IgE concentrations of 40-40,000 U/ml dose-dependently released histamine, significant histamine release being demonstrated with anti-IgE concentrations of 400 U/ml and greater. The kinetics of histamine release showed peak values 2-8 min after the injection. Great individual responses were observed but data could be reproduced within individual donors. Monocyte chemoattractant protein-1, a potent basophil secretagogue, did not induce histamine release in lung tissue which indicated mast cells to be the histamine source. Substance P did not release histamine in the lung tissue. CONCLUSIONS: The microdialysis technique allowed measurements of histamine release from mast cells in intact lung ex vivo. The method may prove useful since a number of experiments can be performed in a few hours in intact lung tissue without any dispersion or enzymatic treatment.     

An improved PCR-based method for site directed mutagenesis using megaprimers

The antimicrobial activity of a combination of lactic acid and whey permeate fermented by a nisin-producing Lactococcus lactis strain was tested by the agar diffusion method using bacteria isolated from fish as test organisms. Lactic acid inhibited all bacterial strains studied, but nisin whey permeate inhibited Gram-positive bacteria only. The combination was more effective than lactic acid alone against Pseudomonas fluorescens and Staphylococcus hominis isolated from fish, and Pseudomonas aeruginosa ATCC9721 and Micrococcus luteus ATCC9341.     

Using Survey Data and Mathematical Modeling to Prioritize Water Interventions in Developing Countries

Water Resources Management - A traditional cost-benefit analysis of potential water interventions in a given locality is a laborious and time-intensive process. To help decision makers identify...     

Uncertainty modeling and robust minimax LQR control of multivariable nonlinear systems with application to hypersonic flight

For a class of multi‐input and multi‐output nonlinear uncertainty systems, a novel approach to design a nonlinear controller using minimax linear quadratic regulator (LQR) control is proposed. The proposed method combines a feedback linearization method with the robust minimax LQR approach in the presence of time‐varying uncertain parameters. The uncertainties, which are assumed to satisfy a certain integral quadratic constraint condition, do not necessarily satisfy a generalized matching condition. The procedure consists of feedback linearization of the nominal model and linearization of the remaining nonlinear uncertain terms with respect to each individual uncertainty at a local operating point. This two‐stage linearization process, followed by a robust minimax LQR control design, provides a robustly stable closed loop system. To demonstrate the effectiveness of the proposed approach, an application study is provided for a flight control problem of an air‐breathing hypersonic flight vehicle (AHFV), where the outputs to be controlled are the longitudinal velocity and altitude, and the control variables are the throttle setting and elevator deflection. The proposed method is used to derive a linearized uncertainty model for the longitudinal motion dynamics of the AHFV first, and then a robust minimax LQR controller is designed, which is based on this uncertainty model. The controller is synthesized considering seven uncertain aerodynamic and inertial parameters. The stability and performance of the synthesized controller is evaluated numerically via single scenario simulations for particular cruise conditions as well as a Monte‐Carlo type simulation based on numerous cases. It is observed that the control scheme proposed in this paper performs better, especially from the aspect of robustness to large ranges of uncertainties, than some controller design schemes previously published in the literature. Copyright © 2011 John Wiley and Sons Asia Pte Ltd and Chinese Automatic Control Society     

Carcass characteristics and composition of Brahman, angus and Brahman x Angus steers fed for different times-on-feed

Twenty-five steers of each of three breedtypes (Angus, Brahman and F(1) Brahman x Angus) were sorted by frame size and muscle thickness, assigned to groups (five steers of each breedtype) to be fed for 0, 56, 112, 168 or 224 days, slaughtered and compared for various carcass traits. Steers of each breedtype had similar dressing percentages. Carcasses from all three breedtypes merited similar USDA quality and yield grades; breedtypes differences in quality grade were slight. Differences were found in the fat deposition patterns exhibited by the three breedtypes. Brahman steers tended to deposit more of their total fat as subcutaneous fat early in the feeding period. Angus steers had more (P < 0·05) seam fat as a percentage of carcass weight at all five feeding periods and more (P < 0·05) kidney, pelvic and heart fat at two of the five feeding periods than Brahman steers. Brahman steers had a higher percentage of their separable lean in the muscles of the round than did steers of the other breedtypes.     

The T Cell Repertoires from Nickel Sensitized Joint Implant Failure Patients

Nickel (Ni²⁺) is one of the most common allergens, affecting around 10–15% of the general population. As the demand for orthopedic implant surgery rises, the number of surgical revisions due to joint implant failure also increases. There is evidence that some patients develop joint failure due to an immune response to a component of the implant, and we have found that Ni²⁺ is an especially important cause. Hence, understanding the mechanisms by which Ni²⁺ allergy induces joint implant failure becomes a critical research question. The structural basis of Ni²⁺ activation of pathogenic T cells is still not clear. The purpose of this study was to characterize Ni²⁺-reactive T cell repertoires derived from the peripheral blood of joint failure patients due to Ni²⁺ sensitization using single-cell sequencing techniques. We stimulated the proliferation of Ni²⁺ -reactive T cells from two implant failure patients in vitro, and sorted them for single-cell VDJ sequencing (10× genomics). We identified 2650 productive V-J spanning pairs. Both TCR α chains and β chains were enriched. TRBV18 usage is the highest in the P7 CD4+ population (18.1%), and TRBV5-1 usage is the highest in the P7 CD8+ population (12.1%). TRBV19 and TRBV20-1 segments are present in a high percentage of both P7 and P9 sequenced T cells. Remarkably, the alpha and beta chain combination of TRAV41-TRBV18 accounts for 13.5% of the CD4+ population of P7 patient. Compared to current Ni specific T cell repertoire studies of contact dermatitis, the Vα and Vβ usages of these joint implant failure patients were different. This could be due to the different availability of self-peptides in these two different tissues. However, TRBV19 (Vβ17) was among frequently used TCR β chains, which are common in previous reports. This implies that some pathogenic T cells could be similar in Ni²⁺ hypersensitivities in skin and joints. The alignment of the TCR CDR3β sequences showed a conserved glutamic acid (Glu) that could potentially interact with Ni²⁺. The study of these Ni²⁺ specific TCRs may shed light on the molecular mechanism of T cell activation by low molecular weight chemical haptens.     

Hemi- and Homozygous Loss-of-Function Mutations in DSG2 (Desmoglein-2) Cause Recessive Arrhythmogenic Cardiomyopathy with an Early Onset

About 50% of patients with arrhythmogenic cardiomyopathy (ACM) carry a pathogenic or likely pathogenic mutation in the desmosomal genes. However, there is a significant number of patients without positive familial anamnesis. Therefore, the molecular reasons for ACM in these patients are frequently unknown and a genetic contribution might be underestimated. Here, we used a next-generation sequencing (NGS) approach and in addition single nucleotide polymor-phism (SNP) arrays for the genetic analysis of two independent index patients without familial medical history. Of note, this genetic strategy revealed a homozygous splice site mutation (DSG2–c.378+1G>T) in the first patient and a nonsense mutation (DSG2–p.L772X) in combination with a large deletion in DSG2 in the second one. In conclusion, a recessive inheritance pattern is likely for both cases, which might contribute to the hidden medical history in both families. This is the first report about these novel loss-of-function mutations in DSG2 that have not been previously identi-fied. Therefore, we suggest performing deep genetic analyses using NGS in combination with SNP arrays also for ACM index patients without obvious familial medical history. In the future, this finding might has relevance for the genetic counseling of similar cases.     

Structural Basis for The Recognition of Deaminated Nucleobases by An Archaeal DNA Polymerase

With increasing temperature, nucleobases in DNA become increasingly damaged by hydrolysis of exocyclic amines. The most prominent damage includes the conversion of cytosine to uracil and adenine to hypoxanthine. These damages are mutagenic and put the integrity of the genome at risk if not repaired appropriately. Several archaea live at elevated temperatures and thus, are exposed to a higher risk of deamination. Earlier studies have shown that DNA polymerases of archaea have the property of sensing deaminated nucleobases in the DNA template and thereby stalling the DNA synthesis during DNA replication providing another layer of DNA damage recognition and repair. However, the structural basis of uracil and hypoxanthine sensing by archaeal B-family DNA polymerases is sparse. Here we report on three new crystal structures of the archaeal B-family DNA polymerase from Thermococcus kodakarensis (KOD) DNA polymerase in complex with primer and template strands that have extended single stranded DNA template 5’-overhangs. These overhangs contain either the canonical nucleobases as well as uracil or hypoxanthine, respectively, and provide unprecedented structural insights into their recognition by archaeal B-family DNA polymerases.