Mechanical Signaling on the Single Protein Level Studied Using Steered Molecular Dynamics

Efficient communication between the cell and its external environment is of the utmost importance to the function of multicellular organisms. While signaling events can be generally characterized as information exchange by means of controlled energy conversion, research efforts have hitherto mainly been concerned with mechanisms involving chemical and electrical energy transfer. Here, we review recent computational efforts addressing the function of mechanical force in signal transduction. Specifically, we focus on the role of steered molecular dynamics (SMD) simulations in providing details at the atomic level on a group of protein domains, which play a fundamental role in signal exchange by responding properly to mechanical strain. We start by giving a brief introduction to the SMD technique and general properties of mechanically stable protein folds, followed by specific examples illustrating three general regimes of signal transfer utilizing mechanical energy: purely mechanical, mechanical to chemical, and chemical to mechanical. Whenever possible the physiological importance of the example at hand is stressed to highlight the diversity of the processes in which mechanical signaling plays a key role. We also provide an overview of future challenges and perspectives for this rapidly developing field.     

siMS Score: Simple Method for Quantifying Metabolic Syndrome

Objective

To evaluate siMS score and siMS risk score, novel continuous metabolic syndrome scores as methods for quantification of metabolic status and risk.

Materials and Methods

Developed siMS score was calculated using formula: siMS score = 2*Waist/Height + Gly/5.6 + Tg/1.7 + TA_systolic/130—HDL/1.02 or 1.28 (for male or female subjects, respectively). siMS risk score was calculated using formula: siMS risk score = siMS score * age/45 or 50 (for male or female subjects, respectively) * family history of cardio/cerebro-vascular events (event = 1.2, no event = 1). A sample of 528 obese and non-obese participants was used to validate siMS score and siMS risk score. Scores calculated as sum of z-scores (each component of metabolic syndrome regressed with age and gender) and sum of scores derived from principal component analysis (PCA) were used for evaluation of siMS score. Variants were made by replacing glucose with HOMA in calculations. Framingham score was used for evaluation of siMS risk score.

Results

Correlation between siMS score with sum of z-scores and weighted sum of factors of PCA was high (r = 0.866 and r = 0.822, respectively). Correlation between siMS risk score and log transformed Framingham score was medium to high for age groups 18+,30+ and 35+ (0.835, 0.707 and 0.667, respectively).

Conclusions

siMS score and siMS risk score showed high correlation with more complex scores. Demonstrated accuracy together with superior simplicity and the ability to evaluate and follow-up individual patients makes siMS and siMS risk scores very convenient for use in clinical practice and research as well.     

Metabolic adaptation of endothelial cells to substrate deprivation

Endothelial cells are known to be metabolicallyrather robust. To study the mechanisms involved, porcine aorticendothelial cells (PAEC), cultured on microcarrier beads, were perfusedwith glucose (10 mM) or with substrate-free medium. Substrate-free perfusion for 2 h induced an almost complete loss of nucleoside triphosphates (³¹P-NMR) anddecreased heat flux, a measure of total energy turnover, by >90% inparallel microcalorimetric measurements. Heat flux and nucleosidetriphosphates recovered after addition of glucose. Because proteinsynthesis is a major energy consumer in PAEC, the rate of proteinsynthesis was measured([¹⁴C]leucineincorporation). Reduction or blockade of energy supply resulted in apronounced reduction in the rate of protein synthesis (up to 80%reduction). Intracellular triglyceride stores were decreased by ~60%after 2 h of substrate-free perfusion. Under basal perfusionconditions, PAEC released ~30 pmol purine · mg protein¹ · min¹,i.e., 16% of the cellular ATP per hour, while ATP remained constant. Substrate deprivation increased the release of various purines andpyrimidines about threefold and also induced a twofold rise in purinede novo synthesis([¹⁴C]formate). Theseresults demonstrate that PAEC are capable of recovering from extendedperiods of substrate deprivation. They can do so by a massivedownregulation of their energy expenditure, particularly proteinsynthesis, while at the same time using endogenous triglycerides assubstrates and upregulating purine de novo synthesis to compensate forthe loss of purines.     

Patients' satisfaction with prosthetic devices

The purpose of the paper was to ascertain the factors which affect the satisfaction of patients with the prosthetic therapy. The purpose of the paper was also to ascertain if there are common factors characteristic for patients dissatisfied with the prosthetic therapy although the specialist appraises it as objectively successful. 52 patients of the Clinical Institute for Rehabilitation and Orthopedic Devices were participating in the research, to which, after unsuccessful surgical-prosthetic rehabilitation, reamputation and prosthetic provision was carried out, which was appraised successful by the doctor. It was endeavored to appraise to what extent the appraisal by the doctor corresponds to patient's satisfaction. On the basis of the questionnaire elaborated specifically for this research and the statistical processing, it was concluded that where the doctor appraised the prosthetic therapy as successful, the same opinion was shared by the majority of the patients (92.3%). Patients are similarly satisfied with the function and the esthetic quality of the prosthesis (73%). The reason why 7.7% of patients are dissatisfied in cases when the doctor considers that there are no objective reasons for that should be sought in non-medical factors. The age, the education, the marital status, the income state, the size of the residence and the regional affiliation do not have a significant influence on the satisfaction of patients with the prosthesis (p > 0.05). Patients with a minor handicap achieve satisfaction with the prosthetic therapy faster, as well as the right-handed persons if the prosthesis on the right-hand extremity is in question (p < 0.05). This investigation showed that the responsibility of not wearing prosthetic aids, both orthopedic, and dental prostheses, couldn't be only neuroticism by prosthetic patients, because that connection is not statistically significant (p < 0.09).     

Delivery of a Chlamydial Adhesin N-PmpC Subunit Vaccine to the Ocular Mucosa Using Particulate Carriers

Trachoma, caused by the intracellular bacterium Chlamydia trachomatis (Ct), remains the world’s leading preventable infectious cause of blindness. Recent attempts to develop effective vaccines rely on modified chlamydial antigen delivery platforms. As the mechanisms engaged in the pathology of the disease are not fully understood, designing a subunit vaccine specific to chlamydial antigens could improve safety for human use. We propose the delivery of chlamydia-specific antigens to the ocular mucosa using particulate carriers, bacterial ghosts (BGs). We therefore characterized humoral and cellular immune responses after conjunctival and subcutaneous immunization with a N-terminal portion (amino acid 1–893) of the chlamydial polymorphic membrane protein C (PmpC) of Ct serovar B, expressed in probiotic Escherichia coli Nissle 1917 bacterial ghosts (EcN BGs) in BALB/c mice. Three immunizations were performed at two-week intervals, and the immune responses were evaluated two weeks after the final immunization in mice. In a guinea pig model of ocular infection animals were immunized in the same manner as the mice, and protection against challenge was assessed two weeks after the last immunization. N-PmpC was successfully expressed within BGs and delivery to the ocular mucosa was well tolerated without signs of inflammation. N-PmpC-specific mucosal IgA levels in tears yielded significantly increased levels in the group immunized via the conjunctiva compared with the subcutaneously immunized mice. Immunization with N-PmpC EcN BGs via both immunization routes prompted the establishment of an N-PmpC-specific IFNγ immune response. Immunization via the conjunctiva resulted in a decrease in intensity of the transitional inflammatory reaction in conjunctiva of challenged guinea pigs compared with subcutaneously and non-immunized animals. The delivery of the chlamydial subunit vaccine to the ocular mucosa using a particulate carrier, such as BGs, induced both humoral and cellular immune responses. Further investigations are needed to improve the immunization scheme and dosage.     

Evolution of the clinical presentation and outcomes after radical prostatectomy for patients with clinically localized prostate cancer--changing trends over a ten year period

We demonstrate the evolution of the clinical presentation and outcomes for patients with clinically localized prostate cancer (PC) treated with radical retropubic prostatectomy (RRP) at our department, emphasizing epidemiologic significance of changes during the 10-year period. We assessed the annual trends for changes in patients age, preoperative prostate specific antigen (PSA), preoperative versus postoperative stages and Gleason grades, organ confined status and surgical margin status. A total of 488 RRPs were performed from January 1996 to December 2005 with the annual frequency increased from 8 to 129 (1512.5%). Mean patient age increased from 61.5 to 66.12 years in 2005, with the percentage of men aged more than 70 years increased from 12.5 to 26.5%, respectively. The detection of PC based solely on pathological PSA levels (as indication for prostate biopsy) rose impressively from 25.5 to 70% and the rates of postoperative organ-confined disease also increased significantly from 25 to 74.7%. Mean preoperative PSA decreased from 16.7 to 9.89 ng/mL. On the contrary, there was an increase in percentage of patients with preoperative PSA values ranging from 4 to 10 ng/mL (from 20 to 65.4%). Positive surgical margin rate decreased from 49.4 to 25% and percent of patients receiving neoadjuvant therapy decreased from 78.5 to 5.4%. Proportion of patients who were undergraded decreased from 75.1 to 31.7%. The rates of understaging have remained relatively stable over the years. During the study period, PC was increasingly detected by prostate biopsy on the basis of a pathological PSA level only and shifted significantly to more organ-confined stages with more favourable outcomes for pathological variables due to a more accurate assessment of clinical stage prior to surgery, reduced use of neoadjuvant therapy and improved surgical technique. Our data also argue strongly that routine PSA testing should be expanded and not restricted.     

Weakly supervised learning and interpretability for endometrial whole slide image diagnosis

Fully supervised learning for whole slide image–based diagnostic tasks in histopathology is problematic due to the requirement for costly and time-consuming manual annotation by experts. Weakly supervised learning that utilizes only slide-level labels during training is becoming more widespread as it relieves this burden, but has not yet been applied to endometrial whole slide images, in iSyntax format. In this work, we apply a weakly supervised learning algorithm to a real-world dataset of this type for the first time, with over 85% validation accuracy and over 87% test accuracy. We then employ interpretability methods including attention heatmapping, feature visualization, and a novel end-to-end saliency-mapping approach to identify distinct morphologies learned by the model and build an understanding of its behavior. These interpretability methods, alongside consultation with expert pathologists, allow us to make comparisons between machine-learned knowledge and consensus in the field. This work contributes to the state of the art by demonstrating a robust practical application of weakly supervised learning on a real-world digital pathology dataset and shows the importance of fine-grained interpretability to support understanding and evaluation of model performance in this high-stakes use case.