Comparative proteogenomics: combining mass spectrometry and comparative genomics to analyze multiple genomes

Recent proliferation of low-cost DNA sequencing techniques will soon lead to an explosive growth in the number of sequenced genomes and will turn manual annotations into a luxury. Mass spectrometry recently emerged as a valuable technique for proteogenomic annotations that improves on the state-of-the-art in predicting genes and other features. However, previous proteogenomic approaches were limited to a single genome and did not take advantage of analyzing mass spectrometry data from multiple genomes at once. We show that such a comparative proteogenomics approach (like comparative genomics) allows one to address the problems that remained beyond the reach of the traditional "single proteome" approach in mass spectrometry. In particular, we show how comparative proteogenomics addresses the notoriously difficult problem of "one-hit-wonders" in proteomics, improves on the existing gene prediction tools in genomics, and allows identification of rare post-translational modifications. We therefore argue that complementing DNA sequencing projects by comparative proteogenomics projects can be a viable approach to improve both genomic and proteomic annotations.     

Heterophils isolated from chickens resistant to extra-intestinal Salmonella enteritidis infection express higher levels of pro-inflammatory cytokine mRNA following infection than heterophils from susceptible chickens

Previous studies showed differences in in vitro heterophil function between parental (A > B) broilers and F1 reciprocal crosses (D > C). Our objectives were to (1) determine if in vitro variations translate to differences in resistance to Salmonella enteritidis (SE) and (2) quantitate cytokine mRNA in heterophils from SE-infected chicks. One-day-old chicks were challenged and organs were cultured for SE. Chicks with efficient heterophils (A and D) were less susceptible to SE compared to chicks with inefficient heterophils (B and C). Heterophils were isolated from SE-infected chicks and cytokine mRNA expression was evaluated using quantitative real-time RT-PCR. Pro-inflammatory cytokine mRNA was up-regulated in heterophils from SE-resistant chicks compared to susceptible chicks. This is the first report to quantitate cytokine mRNA in heterophils from SE-infected chicks. These data show a relationship between in vitro heterophil function, increased pro-inflammatory cytokine mRNA expression, and increased resistance to SE in 1-day-old chicks.     

Bidi cigarette use among young adults in 15 states

BACKGROUND: There is a paucity of research on bidi use in the US and the few studies conducted have focused solely on adolescents. This article describes patterns and explores factors associated with bidi use among young adults, aged 18-24. METHODS: Data from 63,728 adults, including 5,324 young adults, aged 18-24, were derived from an optional tobacco module on the 2001 Behavioral Risk Factor Surveillance System, administered by 15 states. Logistic regression was utilized to examine factors associated with ever and current bidi use among young adults. RESULTS: Nearly two thirds of adults who reported current bidi use were under the age of 25; 16.5% of young adults reported ever use and 1.4% reported current bidi use. Among young adults, higher rates of ever and current bidi use were noted for males, blacks, and current cigarette smokers. CONCLUSIONS: The rates of ever bidi use among young adults may reflect experimentation with bidis during adolescence and raises questions about whether bidis may act as a gateway product to regular cigarette use. The disparities among certain subgroups are noteworthy and deserve further exploration. Tobacco prevention and control programs should address all forms of tobacco use and be cognizant of emerging products.     

Content of acid proteins in neuron and glial cell nuclei of the rat hypothalamus during cold adaptation

The content of acid proteins in nuclei of neurons and glial satellite cells in the medial preoptic region and supraoptic nucleus of the rat hypothalamus was studied by two-wave cytospectrophotometry on the 1st, 3rd, 7th, and 15th days of adaptation of the animal to cold (temperature 2–4°C). Cooling led to an initial decrease in the content of nuclear proteins in the whole neuronal-neuroglial system of the medial preoptic region, followed by gradual restoration to normal by the 15th day of cooling. In the glial cells of this region, before the return to normal there was a temporary increase in the content of acid proteins above the control level. In the neuronal-neuroglial system of the supraoptic nucleus a gradual accumulation of acid proteins was followed by a return to the control level. By the 15th day of the rats' stay in the cold, the content of neuronal and glial acid proteins of this nucleus fell somewhat below the control level.Department of Biochemistry, Rostov-on-Don University. Laboratory of Functional Neurochemistry, I. P. Pavlov Institute of Physiology, Academy of Sciences of the USSR, Leningrad. (Presented by Academician V. N. Chernigovskii.) Translated from Byulleten' Éksperimental'noi Biologii i Meditsiny, Vol. 86, No. 8, pp. 187–190, August, 1978.     

Hemoglobin M equon beta 41 (C7) phenylalanine leads to tyrosine

A severe hemolytic crisis was observed in a 34-yr-old female of English- Irish extraction following a viral illness treated with acetaminophen. Heinz bodies and heat instability were present only during a transient hemolytic event. A challenge dose of acetaminophen caused no detectable hematologic abnormality. Structural studies of the hemoglobin during hemolysis and again after complete recovery localized the abnormality to tryptic peptide beta Tp-5, and automated sequencing of I 125-labeled beta chains indicated a replacement of phenylalanine (C7) beta 41 by tyrosine. Substitution of the next residue, phenylalanine (CD1) beta 42 by serine (Hb Hammersmith), has resulted in chronic severe Heinz body hemolytic anemia. The lack of chronic anemia in the present disorder may reflect the different relationships of beta41 and beta 42 and/or the similarities in volume and hydrophobicity of tyrosine and phenylalanine. It is suggested that substitution of tyrosine for phenylalanine in Hb Mequon may disturb the critical environment around the heme group and render it susceptible to oxidative denaturation in the presence of infections and/or drugs.     

Sarcomas in the groin and inguinal canal �C often missed and difficult to manage

INTRODUCTION

This is a 7-year retrospective review summarising the North of England Bone and Soft Tissue Tumour Service''s experience of managing 13 cases of groin sarcoma requiring soft tissue flap reconstruction. This study was performed to try to identify where national referral guidelines in sarcoma management had been followed and reasons for any delays. The study also includes outcome data relating to these patients.

PATIENTS AND METHODS

A retrospective, case-note review was undertaken using the local sarcoma database to identify approriate patients.

RESULTS

In nine patients, national referral guidelines were not followed. This resulted in a mean delay of presentation to the multidisciplinary team of 4.4 months. Ten patients had unplanned excision or exploration of tumours before referral. There were no lower limb amputations. All patients with narrow margins or high grade tumours were referred for radiotherapy. Four patients died; three as a result of distant metastases and one as a result of local recurrence.

CONCLUSIONS

Despite delays in referral, treatment by wide excision and plastic surgical reconstruction allowed for local control of these tumours with functional limb salvage. Implementation of National Institute for Health and Clinical Excellence (NICE) guidelines and local strategies could improve the expedient management of these patients.     

Long-term outcome of decompressive surgery for Lumbar spinal stenosis in octogenarians

The purpose of our prospective study is to evaluate the surgical outcome among patients aged 80 years and above, who underwent surgery for lumbar spinal stenosis. We assessed patients’ clinical and demographic data, procedures, perioperative complications, preoperative and postoperative pain intensity, basic activities of daily living (BADL), patients’ satisfaction, the need for repeated surgery, and overall mortality. Thirty-nine patients more than 80 years of age were operated in our institution in the last decade. Twenty-five of them were followed-up with a mean 36.8 months after the operation. The Barthel index was used to evaluate pre and postsurgery ADL, and the visual analogue scale (VAS) was used to evaluate pain. The satisfaction rate of the patients before and after the operation and the complication rate were also evaluated. A significant reduction in VAS (P < 0.001) and a significant increase in the Barthel index (P < 0.001) were recorded. Seventy-six percent of the patients were very satisfied or somewhat satisfied with the operative results. Fifty-two percent of the patients had complications (0.9 complications per patients), however, about half of them were minor. No operative or perioperative mortality was noticed and the overall hospital stay for these elderly patients was 3.6 days on average. Surgery in very old elderly patients is safe and effective in the treatment of spinal stenosis, who did not respond well to the conservative treatment. The surgery did not increase the associated morbidity and mortality and most of the patients benefited from the surgery in terms of reduction in pain, increase in ADL and walking ability and overall increase in the satisfaction rate. An erratum to this article can be found at