Studies on bacteria-like particles sampled from the stratosphere

Bacteria-like particles recovered from the stratosphere and deposited on cellulose acetate membranes have been analysed to confirm their bacterial nature. One particle appeared to be attached to an inorganic particle apparently by mucoid material typically produced by bacteria. A filamentous structure, morphologically similar to a fungal hypha, was also observed. EDS analysis showed that the particles were all non-mineral and therefore could be biological in nature. However, the composition of several clumps of nanobacteria-sized particles were found, by SIMS analysis, to be inconsistent with that of bacteria. The results show that it is dangerous to assume that bacteria-like particles seen under scanning electron microscopy are necessarily bacteria.     

The effect of oligonucleotide microarray data pre-processing on the analysis of patient-cohort studies

Background  

Intensity values measured by Affymetrix microarrays have to be both normalized, to be able to compare different microarrays by removing non-biological variation, and summarized, generating the final probe set expression values. Various pre-processing techniques, such as dChip, GCRMA, RMA and MAS have been developed for this purpose. This study assesses the effect of applying different pre-processing methods on the results of analyses of large Affymetrix datasets. By focusing on practical applications of microarray-based research, this study provides insight into the relevance of pre-processing procedures to biology-oriented researchers.     

Transcriptomic response to differentiation induction

Background  

Microarrays used for gene expression studies yield large amounts of data. The processing of such data typically leads to lists of differentially-regulated genes. A common terminal data analysis step is to map pathways of potentially interrelated genes.     

Polyploid genome of <Emphasis Type=Italic>Camelina sativa</Emphasis>revealed by isolation of fatty acid synthesis genes

Background  

Camelina sativa, an oilseed crop in the Brassicaceae family, has inspired renewed interest due to its potential for biofuels applications. Little is understood of the nature of the C. sativa genome, however. A study was undertaken to characterize two genes in the fatty acid biosynthesis pathway, fatty acid desaturase (FAD) 2 and fatty acid elongase (FAE) 1, which revealed unexpected complexity in the C. sativa genome.     

Recycling cell surface glycoproteins undergo limited oligosaccharide reprocessing in LEC1 mutant Chinese hamster ovary cells

The ability of particular cell surface glycoproteins to recycle and become exposed to individual Golgi enzymes has been demonstrated. This study was designed to determine whether endocytic trafficking includes significant reentry into the overall oligosaccharide processing pathway. The Lec1 mutant of Chinese hamster ovary (CHO) cells lack N - acetylglucosaminyltransferase I (GlcNAc-TI) activity resulting in surface expression of incompletely processed Man5GlcNAc2 N -linked oligosaccharides. An oligosaccharide tracer was created by exoglycosylation of cell surface glycoproteins with purified porcine GlcNAc-TI and UDP-[3H]GlcNAc. Upon reculturing, all cell surface glycoproteins that acquired [3H]GlcNAc were acted upon by intracellular mannosidase II, the next enzyme in the Golgi processing pathway of complex N -linked oligosaccharides (t1/2= 3-4 h). That all radiolabeled cell surface glycoproteins were included in this endocytic pathway indicates a common intracellular compartment into which endocytosed cell surface glycoproteins return. Significantly, no evidence was found for continued oligosaccharide processing consistent with transit through the latter cisternae of the Golgi apparatus. These data indicate that, although recycling plasma membrane glycoproteins can be reexposed to individual Golgi-derived enzymes, significant reentry into the overall contiguous processing pathway is not evident.      

Spatial and temporal evolution of distal 10q deletion,a prognostically unfavorable event in diffuse low-grade gliomas

Background

The disease course of patients with diffuse low-grade glioma is notoriously unpredictable. Temporal and spatially distinct samples may provide insight into the evolution of clinically relevant copy number aberrations (CNAs). The purpose of this study is to identify CNAs that are indicative of aggressive tumor behavior and can thereby complement the prognostically favorable 1p/19q co-deletion.

Results

Genome-wide, 50 base pair single-end sequencing was performed to detect CNAs in a clinically well-characterized cohort of 98 formalin-fixed paraffin-embedded low-grade gliomas. CNAs are correlated with overall survival as an endpoint. Seventy-five additional samples from spatially distinct regions and paired recurrent tumors of the discovery cohort were analyzed to interrogate the intratumoral heterogeneity and spatial evolution. Loss of 10q25.2-qter is a frequent subclonal event and significantly correlates with an unfavorable prognosis. A significant correlation is furthermore observed in a validation set of 126 and confirmation set of 184 patients. Loss of 10q25.2-qter arises in a longitudinal manner in paired recurrent tumor specimens, whereas the prognostically favorable 1p/19q co-deletion is the only CNA that is stable across spatial regions and recurrent tumors.

Conclusions

CNAs in low-grade gliomas display extensive intratumoral heterogeneity. Distal loss of 10q is a late onset event and a marker for reduced overall survival in low-grade glioma patients. Intratumoral heterogeneity and higher frequencies of distal 10q loss in recurrences suggest this event is involved in outgrowth to the recurrent tumor.

Electronic supplementary material

The online version of this article (doi:10.1186/s13059-014-0471-6) contains supplementary material, which is available to authorized users.     

Women who wish breast reconstruction: characteristics,fears, and hopes

The aims of the present study were to identify the characteristics of a consecutive series of women with newly diagnosed breast cancer and to evaluate the perceived benefits and disadvantages of breast reconstruction. A consecutive series of 125 women completed the Breast Reconstruction Questionnaire, the Hospital Anxiety and Depression Scale, and the Eysenck Personality Questionnaire. The median age was 48 years (range, 28 to 75 years). A total of 49.6 percent (n = 62) indicated that, if it were possible, they would like breast reconstruction. Logistic regression (simultaneous entry) revealed that younger women (p = 0.0001) and more depressed women (p = 0.026) were more likely to wish reconstruction. Marital status, tumor size, extroversion, neuroticism, and tough-mindedness did not independently predict the desire for reconstruction. If given a choice of reconstruction at 3 months or 6 months after mastectomy, of the women who wished reconstruction, 74 percent would prefer it at 3 months. Of the women who wished reconstruction and expressed a preference, 63 percent were afraid reconstruction might mask recurrence, 39 percent were afraid that reconstruction might cause the cancer to return, and 89 percent thought they would be concerned with their appearance after the operation. Positively, 94 percent considered that reconstruction would be beneficial in terms of their self-esteem, 86 percent indicated that reconstruction would give greater freedom to wear any clothing, and 86 percent thought that the cosmetic appearance of breast reconstruction was better than that of a prosthesis. Concerns about recurrence were common. A better understanding of the concerns of women with regard to reconstruction would allow more informed preoperative discussion.     

Chronic exposure to sour gas emissions: meeting a community concern with epidemiologic evidence.

For 25 years residents of a rural area in southwestern Alberta have complained of health problems attributed to sour gas emissions from nearby natural gas refineries. We undertook a large epidemiologic study of the current health status and the selected morbidity rates among 2152 people in the exposed area. We established two comparison groups: one was a demographically similar unexposed population and the other a demographically different group also exposed to sour gas emissions in another region. The methods included a cross-sectional survey of current residents and separate historical cohort studies involving registry linkage to investigate cancer incidence and all-cause mortality. The cross-sectional survey involved a comprehensive health questionnaire, standardized clinical examinations by physicians blinded to the subjects'' symptoms and concerns, and several laboratory tests. We were able to contact just under 60% of the people who we knew had moved from each area since 1958 and found no evidence of selective migration for health reasons. Although the residents of the exposed area reported an excess number of symptoms and health problems there were no significant differences in the mortality rate, incidence of cancer, reproductive problems, major ailments, hair levels of arsenic and certain metals or respiratory function between the groups.