Comparing extraction method efficiency for high-throughput palaeoproteomic bone species identification.

High-throughput proteomic analysis of archaeological skeletal remains provides information about past fauna community compositions and species dispersals in time and space. Archaeological skeletal remains are a finite resource, however, and therefore it becomes relevant to optimize methods of skeletal proteome extraction. Ancient proteins in bone specimens can be highly degraded and consequently, extraction methods for well-preserved or modern bone might be unsuitable for the processing of highly degraded skeletal proteomes. In this study, we compared six proteomic extraction methods on Late Pleistocene remains with variable levels of proteome preservation. We tested the accuracy of species identification, protein sequence coverage, deamidation, and the number of post-translational modifications per method. We find striking differences in obtained proteome complexity and sequence coverage, highlighting that simple acid-insoluble proteome extraction methods perform better in highly degraded contexts. For well-preserved specimens, the approach using EDTA demineralization and protease-mix proteolysis yielded a higher number of identified peptides. The protocols presented here allowed protein extraction from ancient bone with a minimum number of working steps and equipment and yielded protein extracts within three working days. We expect further development along this route to benefit large-scale screening applications of relevance to archaeological and human evolution research.

Influence of CD68+ macrophages and neutrophils on anastomotic healing following laparoscopic sigmoid resection due to diverticulitis.

BACKGROUND: The aim of this prospective study was to evaluate the predictive value of a potential preexisting low-grade inflammation regarding the incidence of anastomotic leakage in elective laparoscopic sigmoid resection due to diverticulitis. METHODS: Patients with either chronically recurrent diverticulitis or sigmoid stenosis caused by chronic diverticulitis were included in this study. All patients with acute local or systemic inflammation were excluded. Detailed patient information (e.g. American Society of Anesthesiologists (ASA) grade, comorbidities, duration of hospital stay, and anastomotic leakage) was prospectively recorded. CD68(+) macrophages, neutrophils, CD3(+) T-lymphocytes, CD11c(+) dendritic cells, MHCII, TNFR1, and NF-κB were evaluated by immunohistochemistry within the acquired sample of colonic bowel wall tissue. Clinical and immunohistochemical data was compared between groups (leakage vs. no leakage). Additionally, a matched-pair analysis was performed due to the widely heterogeneous groups concerning the number of patients and to minimize the effect of extraneous variables. RESULTS: A total of 83 patients were included in the study, of which 7 patients suffered an anastomotic leakage. Neither the clinical nor the immunohistochemical parameters were significantly different between the groups. The matched-pair analysis revealed a nonsignificant increase in mean duration of hospital stay for the group with anastomotic leakage and a significantly higher percentage of CD68(+) macrophages and neutrophils in the colonic wall obtained at the index operation in both the mucosal and submucosal layers for the leakage group. CONCLUSIONS: A preexisting low-grade inflammation represented by infiltrates of macrophages and neutrophils is a predictor for increased risk of developing colon anastomotic leakage.