Analysis of Combinatorial Gene Regulation with Thermodynamic Models

Immunologic monitoring in transplantation revisited

PURPOSE OF REVIEW

Tailoring immunosuppressive drugs to an individual's needs is crucial to improve long-term outcomes of organ transplant patients. The purpose of this review is to summarize the data on promising biomarkers able to detect the risk of acute or chronic rejection and to discuss the potential issues for their implementation in the clinic.

RECENT FINDINGS

Multiple publications have indicated that circulating antibodies targeting human leukocyte antigen (HLA) and non-HLA antigens as well as donor-specific memory T cells are associated with accelerated graft failure. Other studies published within the year show that specific genomic and proteomic signatures obtained from urine, blood, and graft tissue correlate with acute rejection in kidney and heart transplant patients.

SUMMARY

The development of reliable biomarkers is crucial for individualizing therapy aimed at extending allograft survival and improving patient health. Emerging data indicate that monitoring assays, likely used in panels, have the potential to be diagnostic and possibly predictive of long-term outcome. In addition to ongoing discovery efforts, progress in the field will require multicenter validation, assay standardization, and commercialization so as to efficiently deliver reliable testing strategies to the practicing clinician.

On multi-strain model for Hepatitis C

In this paper we present a multi-strain model for hepatitis C virus (HCV) including an immune response term. The model is presented and discussed. Also we argue that the added multi-strain term represents some basic properties of the immune system and that it should be included to study longer term behavior of the disease.

Accuracy of functional surfaces on comparatively modeled protein structures

Identification and characterization of protein functional surfaces are important for predicting protein function, understanding enzyme mechanism, and docking small compounds to proteins. As the rapid speed of accumulation of protein sequence information far exceeds that of structures, constructing accurate models of protein functional surfaces and identify their key elements become increasingly important. A promising approach is to build comparative models from sequences using known structural templates such as those obtained from structural genome projects. Here we assess how well this approach works in modeling binding surfaces. By systematically building three-dimensional comparative models of proteins using MODELLER: , we determine how well functional surfaces can be accurately reproduced. We use an alpha shape based pocket algorithm to compute all pockets on the modeled structures, and conduct a large-scale computation of similarity measurements (pocket RMSD and fraction of functional atoms captured) for 26,590 modeled enzyme protein structures. Overall, we find that when the sequence fragment of the binding surfaces has more than 45% identity to that of the template protein, the modeled surfaces have on average an RMSD of 0.5 Å, and contain 48% or more of the binding surface atoms, with nearly all of the important atoms in the signatures of binding pockets captured.

Solid organ allograft survival improvement in the United States: the long-term does not mirror the dramatic short-term success

Organ survival in the short-term period post-transplant has improved dramatically over the past few decades. Whether this has translated to a long-term survival benefit remains unclear. This study quantifies the progression of nonrenal solid organ transplant outcomes from 1989 to 2009 in liver, lung, heart, intestine and pancreas transplants. Long-term graft survival was analyzed using data on adult solid organ transplant recipients from the UNOS/SRTR database and is reported as organ half-life and yearly attrition rates. Liver, lung, heart, intestine and pancreas half-lives have improved from 5.8 to 8.5, 1.7 to 5.2, 8.8 to 11, 2.1 to 3.6 and 10.5 to 16.7 years, respectively. Long-term attrition rates have not shown the same consistent improvement, with the yearly attrition rate 5-10 years post-transplant for liver, lung, heart and pancreas changing from 4.7 to 4.3, 10.9 to 10.1, 6.4 to 5.1 and 3.3 to 4.2, respectively. Attrition rates for intestine and pancreas transplantation alone display more variability due to smaller sample size but exhibit similar trends of improved first-year attrition and relatively stagnant long-term attrition rates. With first-year survival and attrition rates almost at a pinnacle, further progress in long-term survival will come from targeting endpoints beyond first-year rejection and survival rates.