TASK DEFINITION: In this task, you're given a paragraph from the research paper and your task is to generate a suitable title for the research paper based on the given paper. Under 100 words is a good title length.
PROBLEM: Sixteen longSAGE libraries from four different clinical stages of cervical intraepithelial neoplasia have enabled us to identify novel cell-surface biomarkers indicative of CIN stage. By comparing gene expression profi les of cervical tissue at early and advanced stages of CIN, several genes are identifi ed to be novel genetic markers. We present fi fty-six cell-surface gene products differentially expressed during progression of CIN. These cell surface proteins are being examined to establish their capacity for optical contrast agent binding. Contrast agent visualization will allow real-time assessment of the physiological state of the disease process bringing vast benefi t to cancer care. The data discussed in this publication have been submitted to NCBIs Gene Expression Omnibus (GEO, http://www.ncbi.nlm.nih.gov/geo/) and are accessible through GEO Series accession number GSE6252.

SOLUTION: Using LongSAGE to Detect Biomarkers of Cervical Cancer Potentially Amenable to Optical Contrast Agent Labelling

PROBLEM: Background: Nonadditivity in fitness effects from two or more mutations, termed epistasis, can result in compensation of deleterious mutations or negation of beneficial mutations. Recent evidence shows the importance of epistasis in individual evolutionary pathways. However, an unresolved question in molecular evolution is how often and how significantly fitness effects change in alternative genetic backgrounds. Results: To answer this question, we quantified the effects of all single mutations and double mutations between all positions in the IgG-binding domain of protein G (GB1). By observing the first two steps of all possible evolutionary pathways using this fitness profile, we were able to characterize the extent and magnitude of pairwise epistasis throughout an entire protein molecule. Furthermore, we developed a novel approach to quantitatively determine the effects of single mutations on structural stability (DDG U ). This enabled determination of the importance of stability effects in functional epistasis. Conclusions: Our results illustrate common biophysical mechanisms for occurrences of positive and negative epistasis. Our results show pervasive positive epistasis within a conformationally dynamic network of residues. The stability analysis shows that significant negative epistasis, which is more common than positive epistasis, mostly occurs between combinations of destabilizing mutations. Furthermore, we show that although significant positive epistasis is rare, many deleterious mutations are beneficial in at least one alternative mutational background. The distribution of conditionally beneficial mutations throughout the domain demonstrates that the functional portion of sequence space can be significantly expanded by epistasis.

SOLUTION: Article A Comprehensive Biophysical Description of Pairwise Epistasis throughout an Entire Protein Domain

PROBLEM: A membrane (M), protein-based ELISA was developed to detect porcine epidemic diarrhea virus (PEDV). The M gene of PEDV was expressed in Escherichia coli. The purified recombinant M protein was used to immunize rabbits to generate a polyclonal antibody. Immunofluorescence analysis indicated that the anti-PEDV-M antibody reacted with PEDV-infected cells. The antibody was utilized to develop an indirect ELISA to detect PEDV. Other viruses, porcine transmissible gastroenteritis coronavirus, avian infectious bronchitis coronavirus, porcine reproductive and respiratory syndrome virus, classic swine fever virus and porcine pseudorabies virus, were unreactive.

SOLUTION:
Development of a porcine epidemic diarrhea virus M protein-based ELISA for virus detection