The Integration of Proteome-Wide PTM Data with Protein Structural and Sequence Features Identifies Phosphorylations that Mediate 14-3-3 Interactions.

14-3-3s are abundant proteins that regulate essentially all aspects of cell biology, including cell cycle, motility, metabolism, and cell death. 14-3-3s work by docking to phosphorylated Ser/Thr residues on a large network of client proteins and modulating client protein function in a variety of ways. In recent years, aided by improvements in proteomics, the discovery of 14-3-3 client proteins has far outpaced our ability to understand the biological impact of individual 14-3-3 interactions. The rate-limiting step in this process is often the identification of the individual phospho-serines/threonines that mediate 14-3-3 binding, which are difficult to distinguish from other phospho-sites by sequence alone. Furthermore, trial-and-error molecular approaches to identify these phosphorylations are costly and can take months or years to identify even a single 14-3-3 docking site phosphorylation. To help overcome this challenge, we used machine learning to analyze predictive features of 14-3-3 binding sites. We found that accounting for intrinsic protein disorder and the unbiased mass spectrometry identification rate of a given phosphorylation significantly improves the identification of 14-3-3 docking site phosphorylations across the proteome. We incorporated these features, coupled with consensus sequence prediction, into a publicly available web app, called "14-3-3 site-finder". We demonstrate the strength of this approach through its ability to identify 14-3-3 binding sites that do not conform to the loose consensus sequence of 14-3-3 docking phosphorylations, which we validate with 14-3-3 client proteins, including TNK1, CHEK1, MAPK7, and others. In addition, by using this approach, we identify a phosphorylation on A-kinase anchor protein-13 (AKAP13) at Ser2467 that dominantly controls its interaction with 14-3-3.

Emergency management of corneal injuries.

UNLABELLED: Corneal injuries account for a significant proportion of the ophthalmic workload of most emergency departments. Although the vast majority of cases are relatively minor, accurate diagnosis and appropriate management are vital to prevent potentially sight-threatening sequelae. We present a survey of corneal injury cases at a general emergency department. INTRODUCTION: Corneal injuries are very common in both the adult and paediatric population and account for a significant proportion of the workload of most emergency departments. This survey assesses management of corneal injury cases at a general emergency department. MATERIALS AND METHODS: A retrospective case study was performed of 100 patients consecutively diagnosed with a corneal abrasion by slit lamp examination at the emergency department of the Chelsea and Westminster Hospital, London. Each case was assessed to determine documentation of set criteria including visual acuity (VA), treatment and grade of examiner. RESULTS: The commonest cause of injury was direct minor trauma (64% of cases) with contact lens related problems accounting for 12% of presentations. VA was documented correctly in 85 adult patients (90.4% of adults), incorrectly in 2 cases, and not documented at all in 7 adults (7.4%). VA was not recorded in paediatric cases. All cases were treated with topical chloramphenicol drops although frequency of treatment ranged from 2 to 5 times daily and duration of treatment ranged between 3 and 5 days and for 7 days. 6 cases (6%) were assessed by an emergency nurse practitioner and the remaining number were seen by a casualty officer. DISCUSSION: VA must be accurately documented in all adult cases and should be documented in children of school age. A pinhole test should be performed in cases where VA is below 6/9. For analgesia, the use of topical nonsteroidal anti-inflammatory drugs, lubricants and bandage contact lens should be considered. Emergency nurse practitioners and general practitioners are ideally placed to follow-up uncomplicated cases.

Comparison of trans- and intra-abdominal duplex examinations of the splanchnic circulation.

To evaluate the influence of the technical problems experienced when scanning transabdominally, a comparison was made between transabdominal and intra-abdominal Doppler parameters of the aorta and the splanchnic arteries. Peroperative color duplex sonography of the abdominal aorta and the splanchnic arteries was performed on 25 patients who were undergoing abdominal vascular reconstructive surgery under stabilized standardised anaesthesia. Doppler samples and diameter measurements were taken of the aorta, celiac, common hepatic, splenic, superior and inferior mesenteric arteries, both trans- and intra-abdominally. Significantly higher velocities were recorded in the celiac artery during intra-abdominal examinations. There was a trend toward higher recorded velocities in the other vessels. There was also a significant difference in the diameter measurements of most of the vessels. The trans- and intra-abdominal results were not always equivalent. The differences were not due to technical aspects. Transabdominal duplex sonography is difficult and may not be completely accurate in detecting quantitative flow parameters in the splanchnic arteries.

The periodontally-involved root surface.

Recent years have seen much research on the periodontally-involved root surface. Many of these studies have produced results which suggest that plaque contaminants of the root surface are only superficially placed, and capable of being removed by gentle means. Further research has attested to the difficulties in rendering periodontally-involved root surfaces free of calculus deposits by instrumentation, yet clinical studies show that periodontal disease can be managed by root planing. It is concluded that root surface debridement is best assessed on the basis of the healing response and that it should aim to disrupt plaque on and remove plaque from the periodontally-involved root surface rather than to remove part of the root surface itself.