Addressing trypsin bias in large scale (phospho)proteome analysis by size exclusion chromatography and secondary digestion of large post-trypsin peptides.

In the vast majority of bottom-up proteomics studies, protein digestion is performed using only mammalian trypsin. Although it is clearly the best enzyme available, the sole use of trypsin rarely leads to complete sequence coverage, even for abundant proteins. It is commonly assumed that this is because many tryptic peptides are either too short or too long to be identified by RPLC-MS/MS. We show through in silico analysis that 20-30% of the total sequence of three proteomes (Schizosaccharomyces pombe, Saccharomyces cerevisiae, and Homo sapiens) is expected to be covered by Large post-Trypsin Peptides (LpTPs) with M(r) above 3000 Da. We then established size exclusion chromatography to fractionate complex yeast tryptic digests into pools of peptides based on size. We found that secondary digestion of LpTPs followed by LC-MS/MS analysis leads to a significant increase in identified proteins and a 32-50% relative increase in average sequence coverage compared to trypsin digestion alone. Application of the developed strategy to analyze the phosphoproteomes of S. pombe and of a human cell line identified a significant fraction of novel phosphosites. Overall our data indicate that specific targeting of LpTPs can complement standard bottom-up workflows to reveal a largely neglected portion of the proteome.

An interaction network of the mammalian COP9 signalosome identifies Dda1 as a core subunit of multiple Cul4-based E3 ligases.

The COP9 signalosome (CSN) is an evolutionarily conserved macromolecular complex that interacts with cullin-RING E3 ligases (CRLs) and regulates their activity by hydrolyzing cullin-Nedd8 conjugates. The CSN sequesters inactive CRL4(Ddb2), which rapidly dissociates from the CSN upon DNA damage. Here we systematically define the protein interaction network of the mammalian CSN through mass spectrometric interrogation of the CSN subunits Csn1, Csn3, Csn4, Csn5, Csn6 and Csn7a. Notably, we identified a subset of CRL complexes that stably interact with the CSN and thus might similarly be activated by dissociation from the CSN in response to specific cues. In addition, we detected several new proteins in the CRL-CSN interactome, including Dda1, which we characterized as a chromatin-associated core subunit of multiple CRL4 proteins. Cells depleted of Dda1 spontaneously accumulated double-stranded DNA breaks in a similar way to Cul4A-, Cul4B- or Wdr23-depleted cells, indicating that Dda1 interacts physically and functionally with CRL4 complexes. This analysis identifies new components of the CRL family of E3 ligases and elaborates new connections between the CRL and CSN complexes.

Afatinib versus placebo as adjuvant therapy after chemoradiation in a double-blind, phase III study (LUX-Head & Neck 2) in patients with primary unresected, clinically intermediate-to-high-risk head and neck cancer: study protocol for a randomized controlled trial.

BACKGROUND: Over 50% of patients with head and neck squamous cell carcinoma (HNSCC) present with locoregionally advanced disease. Those at intermediate-to-high risk of recurrence after definitive therapy exhibit advanced disease based on tumour size or lymph node involvement, non-oropharynx primary sites, human papillomavirus (HPV)-negative oropharyngeal cancer, or HPV-positive oropharynx cancer with smoking history (>10-pack-years). Non-surgical approaches include concurrent chemoradiotherapy, induction chemotherapy followed by definitive radiotherapy or chemoradiotherapy, or radiotherapy alone. Following locoregional therapies (including surgical salvage of residual cervical nodes), no standard intervention exists. Overexpression of epidermal growth factor receptor (EGFR), an ErbB family member, is associated with poor prognosis in HNSCC. EGFR-targeted cetuximab is the only targeted therapy that impacts overall survival and is approved for HNSCC in the USA or Europe. However, resistance often occurs, and new approaches, such as targeting multiple ErbB family members, may be required. Afatinib, an irreversible ErbB family blocker, demonstrated antiproliferative activity in preclinical models and comparable clinical efficacy with cetuximab in a randomized phase II trial in recurrent or metastatic HNSCC. LUX-Head & Neck 2, a phase III study, will assess adjuvant afatinib versus placebo following chemoradiotherapy in primary unresected locoregionally advanced intermediate-to-high-risk HNSCC. METHODS/DESIGN: Patients with primary unresected locoregionally advanced HNSCC, in good clinical condition with unfavourable risk of recurrence, and no evidence of disease after chemoradiotherapy will be randomized 2:1 to oral once-daily afatinib (40 mg starting dose) or placebo. As HPV status will not be determined for eligibility, unfavourable risk is defined as non-oropharynx primary site or oropharynx cancer in patients with a smoking history (>10 pack-years). Treatment will continue for 18 months or until recurrence or unacceptable adverse events occur. The primary endpoint measure is duration of disease-free survival; secondary endpoint measures are disease-free survival rate at 2 years, overall survival, health-related quality of life and safety. DISCUSSION: Given the unmet need in the adjuvant treatment of intermediate-to-high-risk HNSCC patients, it is expected that LUX-Head & Neck 2 will provide new insights into treatment in this setting and might demonstrate the ability of afatinib to significantly improve disease-free survival, compared with placebo. TRIAL REGISTRATION: ClinicalTrials.gov NCT01345669.

Outcome of subscapularis muscle release for shoulder contracture secondary to brachial plexus palsy at birth.

Children with unresolved brachial plexus palsy frequently develop a disabling internal rotation contracture of the shoulder. Several surgical options, including soft tissue procedures such as muscle releases and/or transfers, and bone operations such as humeral osteotomy are available to correct this deformity. This study describes the effect of subscapularis muscle release performed in isolation. Thirteen patients (5 boys, 8 girls) were reviewed at an average of 3.5 years after their surgery (range, 2-7 years). Their mean age at operation was 4.7 years (range, 1-8 years). Three children had C5-C6 palsies, 8 had C5-C7 palsies, and 2 had C5-C8 palsies. Postoperatively, patients presented significant gains in shoulder active lateral rotation (+49 degrees, from 5 to 54 degrees), active abduction (+30 degrees, from 63 to 93 degrees), active flexion (+46 degrees, from 98 to 144 degrees), and active extension (+23 degrees, from 7 to 30 degrees). Gains were also observed in passive range of motion, but of a lesser degree. Subscapularis muscle release is a procedure we found to have few significant complications and was highly effective in increasing active range of motion and restoring shoulder function.

Biologie oxydative et implications cliniques du peroxynitrite [Oxidative biology and clinical implications of peroxynitrite]

Peroxynitrite is a strong biological oxidant formed from the reaction between two free radicals, superoxide and nitric oxide. It inflicts serious damages to most biomolecules, including proteins, lipids and nucleic acids, either through direct oxidation or through the secondary generation of highly reactive free radicals. When such damage reaches a critical threshold, cells eventually die by necrosis or apoptosis. An excessive production of peroxynitrite is instrumental in the development of organ damage and dysfunction in conditions such as circulatory shock and ischemia-reperfusion. In such circumstances, various synthetic metalloporphyrins, able to degrade peroxynitrite, disclose important beneficial effects in animal models, and might therefore represent novel pharmacological agents in the future.

One naive T cell, multiple fates in CD8+ T cell differentiation.

The mechanism by which the immune system produces effector and memory T cells is largely unclear. To allow a large-scale assessment of the development of single naive T cells into different subsets, we have developed a technology that introduces unique genetic tags (barcodes) into naive T cells. By comparing the barcodes present in antigen-specific effector and memory T cell populations in systemic and local infection models, at different anatomical sites, and for TCR-pMHC interactions of different avidities, we demonstrate that under all conditions tested, individual naive T cells yield both effector and memory CD8+ T cell progeny. This indicates that effector and memory fate decisions are not determined by the nature of the priming antigen-presenting cell or the time of T cell priming. Instead, for both low and high avidity T cells, individual naive T cells have multiple fates and can differentiate into effector and memory T cell subsets.

Considerations for prenatal counselling of patients with cardiac rhabdomyomas based on their cardiac and neurologic outcomes.

Cardiac rhabdomyomas are benign cardiac tumours with few cardiac complications, but with a known association to tuberous sclerosis that affects the neurologic outcome of the patients. We have analysed the long-term cardiac and neurological outcomes of patients with cardiac rhabdomyomas in order to allow comprehensive prenatal counselling, basing our findings on the records of all patients seen prenatally and postnatally with an echocardiographic diagnosis of cardiac rhabdomyoma encountered from August, 1982, to September, 2007. We analysed factors such as the number and the location of the tumours to establish their association with a diagnosis of tuberous sclerosis, predicting the cardiac and neurologic outcomes for the patients.Cardiac complications include arrhythmias, obstruction of the ventricular outflow tracts, and secondary cardiogenic shock. Arrhythmias were encountered most often during the neonatal period, with supraventricular tachycardia being the commonest rhythm disturbance identified. No specific dimension or location of the cardiac rhabdomyomas predicted the disturbances of rhythm.The importance of the diagnosis of tuberous sclerosis is exemplified by the neurodevelopmental complications, with four-fifths of the patients showing epilepsy, and two-thirds having delayed development. The presence of multiple cardiac tumours suggested a higher risk of being affected by tuberous sclerosis. The tumours generally regress after birth, and cardiac-related problems are rare after the perinatal period. Tuberous sclerosis and the associated neurodevelopmental complications dominate the clinical picture, and should form an important aspect of the prenatal counselling of parents.

A Sufficiency Rating System for Secondary Roads in Iowa, HR-264, Volume I, 1985

County engineers in Iowa face the dual problems of rapidly escalating costs and a decreasing rate of growth of revenues. Various priority systems are in use, ranking projects for inclusion in road improvement programs, but they generally have weaknesses when used to compare one project with another in a different location. The sufficiency rating system has proven to be a useful tool in developing a priority list of projects for primary road systems, but there are none currently in use for secondary road systems. The research reported here was undertaken to develop a sufficiency rating system which could be used for secondary roads in Iowa and to produce the necessary forms and instructions to aid county engineering personnel in their efforts to complete the ratings for roads within their county.

Small RNA-dependent expression of secondary metabolism is controlled by Krebs cycle function in Pseudomonas fluorescens.

Pseudomonas fluorescens CHA0, an antagonist of phytopathogenic fungi in the rhizosphere of crop plants, elaborates and excretes several secondary metabolites with antibiotic properties. Their synthesis depends on three small RNAs (RsmX, RsmY, and RsmZ), whose expression is positively controlled by the GacS-GacA two-component system at high cell population densities. To find regulatory links between primary and secondary metabolism in P. fluorescens and in the related species Pseudomonas aeruginosa, we searched for null mutations that affected central carbon metabolism as well as the expression of rsmY-gfp and rsmZ-gfp reporter constructs but without slowing down the growth rate in rich media. Mutation in the pycAB genes (for pyruvate carboxylase) led to down-regulation of rsmXYZ and secondary metabolism, whereas mutation in fumA (for a fumarase isoenzyme) resulted in up-regulation of the three small RNAs and secondary metabolism in the absence of detectable nutrient limitation. These effects required the GacS sensor kinase but not the accessory sensors RetS and LadS. An analysis of intracellular metabolites in P. fluorescens revealed a strong positive correlation between small RNA expression and the pools of 2-oxoglutarate, succinate, and fumarate. We conclude that Krebs cycle intermediates (already known to control GacA-dependent virulence factors in P. aeruginosa) exert a critical trigger function in secondary metabolism via the expression of GacA-dependent small RNAs.

Roadway Lighting on Secondary Roads in Iowa, HR-251, 1984

There are approximately 800 installations of destination lighting at secondary road intersections in Iowa. Approximately 90% of these have only a single luminaire. The other installations have two luminaires. No warrants currently exist for justifying the use of this type of lighting. Previous research has examined the safety benefits from full lighting of rural intersections that generally serve substantially higher traffic volumes than secondary road intersections in Iowa. However, the safety benefit of destination lighting at intersections carrying relatively low volumes has not been the subject of previous research. The research reported here, sponsored by the Iowa Department of Transportation, was undertaken to identify locations where destination lighting could be expected to improve highway safety. If destination lighting were shown to reduce accident frequency, warrants for its use on secondary roads could be developed. An inventory of secondary road lighting installations in Iowa was assembled. From this inventory, two samples were constituted that would permit two separate comparisons of the accident experience with and without destination lighting. Before and after comparisons were made for the same locations if accident records were available for at least one full year both preceding and following the installation of destination lighting. Accident records for this purpose were available from a statewide computerized record system covering the period from 1977 through 1982. The accident experience at locations having destination lighting installed before 1978 was compared with a sample of comparable locations not having destination lighting. The sample of secondary road intersections used for the before and after comparison included 91 locations. The sample of continuously lighted locations included 102 intersections. Accident experience at these locations was compared with the experience at 102 intersections that were not lighted. The intersections included in these samples averaged only 0.31 accidents per year. The accident rate at secondary road intersections that had destination lighting did not differ significantly from the accident rate at intersections that were not lighted. This conclusion was derived from both comparisons, the before and after experience and the comparison of experience at intersections that were continuously lighted with that at unlighted locations. Furthermore, no significant differences were noted between lighted and unlighted locations in the proportion of accidents that occurred at night. The distribution of accidents by type also did not differ between unlighted intersections and those having destination lighting. It was not possible to formulate warrants for destination lighting since analyses directed toward identifying specific characteristics of an intersection that could be correlated with highway safety did not yield any useful relationships. However, it was noted that the average damages for night accidents that occurred at lighted intersections were lower than for accidents at unlighted intersections. Even in the absence of a more definitive demonstration of beneficial effects, destination lighting is perceived by officials in most of the counties having such installations as yielding desirable effects and is recognized as helpful to motorists in performing the guidance function in driving. Given this benefit and a relatively low cost (an average of $74 per year for one luminaire), and given that the subjective criteria that have been used in the past to justify the installation of destination lighting have led to a high degree of public acceptance and satisfaction, it is recommended that the same subjective criteria continue to be used in lieu of definitive warrants.

A Sufficiency Rating System for Secondary Roads in Iowa, HR-264, Volume II, 1985

The goal of this study is to develop a usable sufficiency rating system for secondary roads. There are several assumptions that have been made at the outset. These are: 1. County engineers currently use at least a limited set of decision criteria to make decisions regarding project priorities. 2. Some degree of consensus exists among the county engineers in terms of which are the most important criteria and that there is some agreement on their relative importance. Accordingly, a questionnaire was developed which could be used as a survey tool. The results of the survey were used to develop a final list of weighted rating elements which were used as part of the proposed sufficiency rating system. State and local jurisdictions from other states were also surveyed to determine the status of the use of sufficiency rating systems for secondary roads outside of Iowa and to gather some applicable data.

Snow Removal on Iowa's Secondary Roads, HR-267, 1984

Snow removal on the 90,000 mile Iowa secondary road system is a major concern of county engineers. Rural residents rely almost entirely on motor vehicles for travel. They have come to expect passable roads during all types of weather and as most county engineers know, the public is less tolerant of problems in snow removal than in any other highway department function. To avoid snow removal problems, maintenance personnel begin preparation before the winter maintenance season. The slide tape presentation, "Snow Removal on Iowa's Secondary Roads", was developed to assist in training and retraining maintenance personnel each year prior to winter. The program covers preparation for winter, snow and ice removal, and after storm care of equipment.