Shotgun Phage Display - Selection for Bacterial Receptins or other Exported Proteins

Shotgun phage display cloning involves construction of libraries from randomly fragmented bacterial chromosomal DNA, cloned genes, or eukaryotic cDNAs, into a phagemid vector. The library obtained consists of phages expressing polypeptides corresponding to all genes encoded by the organism, or overlapping peptides derived from the cloned gene. From such a library, polypeptides with affinity for another molecule can be isolated by affinity selection, panning. The technique can be used to identify bacterial receptins and identification of their minimal binding domain, and but also to identify epitopes recognised by antibodies. In addition, after modification of the phagemid vector, the technique has also been used to identify bacterial extracytoplasmic proteins

Leaping and dancing with digitality : Exploring human-smartphone-entanglements in classrooms

This chapter explores digitality as part of young people’s everyday lives in the Arctic. It is based on two ethnographic studies situated in the political context of the “digital leap”, the governmental and curricular emphasis on digitality in education in Finland. With the more formal “digital leap”, informal engagements and attachments with digitality intertwine, in which students’ own smartphones play an increasingly significant role. The analyses use the notion of entanglement (Barad) to examine how primary school and upper secondary school students emerge in their situated and specific encounters with smartphones in school. The starting points of things, bodies, affect, time and space open up insights to connectivity between young people’s digital activities and global economic networks as well as to the multidirectionality between humans and technologies: while the students access their digital devices, the digitalities also access their users. We suggest that this wilder form of “digital leap” requires reconsidering materiality, affect, and instability of space and time.Peer reviewe

STAR: predicting recombination sites from amino acid sequence

BACKGROUND: Designing novel proteins with site-directed recombination has enormous prospects. By locating effective recombination sites for swapping sequence parts, the probability that hybrid sequences have the desired properties is increased dramatically. The prohibitive requirements for applying current tools led us to investigate machine learning to assist in finding useful recombination sites from amino acid sequence alone. RESULTS: We present STAR, Site Targeted Amino acid Recombination predictor, which produces a score indicating the structural disruption caused by recombination, for each position in an amino acid sequence. Example predictions contrasted with those of alternative tools, illustrate STAR'S utility to assist in determining useful recombination sites. Overall, the correlation coefficient between the output of the experimentally validated protein design algorithm SCHEMA and the prediction of STAR is very high (0.89). CONCLUSION: STAR allows the user to explore useful recombination sites in amino acid sequences with unknown structure and unknown evolutionary origin. The predictor service is available from

Metabolic signatures of healthy lifestyle patterns and colorectal cancer risk in a European cohort

Background & Aims Colorectal cancer risk can be lowered by adherence to the World Cancer Research Fund/American Institute for Cancer Research (WCRF/AICR) guidelines. We derived metabolic signatures of adherence to these guidelines and tested their associations with colorectal cancer risk in the European Prospective Investigation into Cancer cohort. Methods Scores reflecting adherence to the WCRF/AICR recommendations (scale, 1–5) were calculated from participant data on weight maintenance, physical activity, diet, and alcohol among a discovery set of 5738 cancer-free European Prospective Investigation into Cancer participants with metabolomics data. Partial least-squares regression was used to derive fatty acid and endogenous metabolite signatures of the WCRF/AICR score in this group. In an independent set of 1608 colorectal cancer cases and matched controls, odds ratios (ORs) and 95% CIs were calculated for colorectal cancer risk per unit increase in WCRF/AICR score and per the corresponding change in metabolic signatures using multivariable conditional logistic regression. Results Higher WCRF/AICR scores were characterized by metabolic signatures of increased odd-chain fatty acids, serine, glycine, and specific phosphatidylcholines. Signatures were inversely associated more strongly with colorectal cancer risk (fatty acids: OR, 0.51 per unit increase; 95% CI, 0.29–0.90; endogenous metabolites: OR, 0.62 per unit change; 95% CI, 0.50–0.78) than the WCRF/AICR score (OR, 0.93 per unit change; 95% CI, 0.86–1.00) overall. Signature associations were stronger in male compared with female participants. Conclusions Metabolite profiles reflecting adherence to WCRF/AICR guidelines and additional lifestyle or biological risk factors were associated with colorectal cancer. Measuring a specific panel of metabolites representative of a healthy or unhealthy lifestyle may identify strata of the population at higher risk of colorectal cancer

Dietary patterns related to biological mechanisms and survival after breast cancer diagnosis: results from a cohort study

BackgroundInflammatory, insulin and oestrogenic pathways have been linked to breast cancer (BC). We aimed to examine the relationship between pre-diagnostic dietary patterns related to these mechanisms and BC survival.MethodsThe diabetes risk reduction diet (DRRD), inflammatory score of diet (ISD) and oestrogen-related dietary pattern (ERDP) were calculated using dietary data from the European Prospective Investigation into Cancer and Nutrition (EPIC) study. Cox proportional hazards models were used to assess associations between dietary patterns and overall mortality and competing risk models for associations with BC-specific mortality.ResultsWe included 13,270 BC cases with a mean follow-up after diagnosis of 8.6 years, representing 2340 total deaths, including 1475 BC deaths. Higher adherence to the DRRD score was associated with lower overall mortality (HR1-SD 0.92; 95%CI 0.87-0.96). Greater adherence to pro-inflammatory diets was borderline associated with 6% higher mortality HR1-SD 1.06; 95%CI 1.00-1.12. No significant association with the oestrogen-related dietary pattern was observed. None of the dietary patterns were associated with BC-specific mortality.ConclusionsGreater adherence to an anti-diabetic and anti-inflammatory diet prior to diagnosis is associated with lower overall mortality among BC survivors. Long-term adherence to these dietary patterns could be a means to improve the prognosis of BC survivors

Child Studies Multiple - Collaborative play for thinking through theories and methods

This is the final version. Available on open access from Linköpings University Electronic Press via the DOI in this recordThis text is an exploration of collaborative thinking and writing through theories, methods, and experiences on the topic of the child, children, and childhood. It is a collaborative written text (with 32 authors) that sprang out of the experimental workshop Child Studies Multiple. The workshop and this text are about daring to stay with mess, “un-closure” , and uncertainty in order to investigate the (e)motions and complexities of being either a child or a researcher. The theoretical and methodological processes presented here offer an opportunity to shake the ground on which individual researchers stand by raising questions about scientific inspiration, theoretical and methodological productivity, and thinking through focusing on process, play, and collaboration. The effect of this is a questioning of the singular academic ‘I’ by exploring and showing what a plural ‘I’ can look like. It is about what the multiplicity of voice can offer research in a highly individualistic time. The article allows the reader to follow and watch the unconventional trial-and-error path of the ongoing-ness of exploring theories and methods together as a research community via methods of drama, palimpsest, and fictionary

Mental health of refugees following state-sponsored repatriation from Germany

von Lersner U, Elbert T, Neuner F. Mental health of refugees following state-sponsored repatriation from Germany. BMC Psychiatry. 2008;8(1): 88.BACKGROUND: In recent years, Voluntary Assisted Return Programmes (VARPs) have received increasing funding as a potential way of reducing the number of refugees in EU member states. A number of factors may affect the mental well-being of returnees. These include adjustment to the home country following return, difficult living conditions, and long-term effects resulting from the severe traumatic stress that had originally driven the affected out of their homes. Little is known about the extent to which these and other factors may promote or inhibit the willingness of refugees to return to their country of origin. The present pilot study investigated refugees who returned to their country of origin after having lived in exile in Germany for some 13 years. METHODS: Forty-seven VARP participants were interviewed concerning their present living conditions, their views of their native country, and their attitudes towards a potential return prior to actually returning. 33 participants were interviewed nine months after returning to their country of origin. Mental health and well-being were assessed using the questionnaires Posttraumatic Stress Diagnostic Scale (PDS) and EUROHIS and the structured Mini International Neuropsychiatric Interview (M.I.N.I.).Our objectives were to examine the mental health status of refugees returning to their home country following an extended period of exile. We also aimed to assess the circumstances under which people decided to return, the current living conditions in their home country, and retrospective returnee evaluations of their decision to accept assisted return. RESULTS: Prior to returning to their home country, participants showed a prevalence rate of 53% for psychiatric disorders. After returning, this rate increased to a sizeable 88%. Substantial correlations were found between the living situation in Germany, the disposition to return, and mental health. For two thirds of the participants, the decision to return was not voluntary. CONCLUSION: Psychological strain among study participants was of a considerable magnitude. As a result of traumatic stress experienced during war and refuge, victims were vulnerable and not well equipped to cope with either post-migration stressors in exile or with a return to their country of origin. It is noteworthy that the majority returned under pressure from immigration authorities. Living conditions after return (such as housing, work, and health care) were poor and unstable. Participants also had great difficulty readapting to the cultural environment after having lived abroad for an average of 13 years. Current VARPs do not take these factors into account and are therefore not able to assist in a humanitarian reintegration of voluntary returnees

Change in level of productivity in the treatment of schizophrenia with olanzapine or other antipsychotics

<p>Abstract</p> <p>Background</p> <p>When treating schizophrenia, improving patients' productivity level is a major goal considering schizophrenia is a leading cause of functional disability. Productivity level has been identified as the most preferred treatment outcome by patients with schizophrenia. However, little has been done to systematically investigate productivity levels in schizophrenia. We set out to better understand the change in productivity level among chronically ill patients with schizophrenia treated with olanzapine compared with other antipsychotic medications. We also assessed the links between productivity level and other clinical outcomes.</p> <p>Methods</p> <p>This post hoc analysis used data from 6 randomized, double-blind clinical trials of patients with schizophrenia or schizoaffective disorder, with each trial being of approximately 6 months duration. Change in productivity level was compared between olanzapine-treated patients (HGBG, n = 172; HGHJ, n = 277; HGJB, n = 171; HGLB, n = 281; HGGN, n = 159; HGDH, n = 131) and patients treated with other antipsychotic medications (separately vs. haloperidol [HGGN, n = 97; HGDH, n = 132], risperidone [HGBG, n = 167; HGGN, n = 158], quetiapine [HGJB, n = 175], ziprasidone [HGHJ, n = 271] and aripiprazole [HGLB, n = 285]). Productivity was defined as functional activities/work including working for pay, studying, housekeeping and volunteer work. Productivity level in the prior 3 months was assessed on a 5-point scale ranging from no useful functioning to functional activity/work 75% to 100% of the time.</p> <p>Results</p> <p>Chronically ill patients treated with olanzapine (OLZ) experienced significantly greater improvement in productivity when compared to patients treated with risperidone (RISP) (OLZ = 0.22 ± 1.19, RISP = -0.03 ± 1.17, p = 0.033) or ziprasidone (ZIP) (OLZ = 0.50 ± 1.38, ZIP = 0.25 ± 1.27, p = 0.026), but did not significantly differ from the quetiapine, aripiprazole or haloperidol treatment groups. Among first episode patients, OLZ therapy was associated with greater improvements in productivity levels compared to haloperidol (HAL), during the acute phase (OLZ = -0.31 ± 1.59, HAL = -0.69 ± 1.56, p = 0.011) and over the long-term (OLZ = 0.10 ± 1.50, HAL = -0.32 ± 1.91, p = 0.008). Significantly more chronically ill and first episode patients treated with olanzapine showed moderately high (>50%-75% of the time) and high levels of productivity (>75%-100% of the time) at endpoint, when compared to risperidone or haloperidol-treated patients (p < .05), respectively. Higher productivity level was associated with significantly higher study completion rates and better scores on the positive, negative, disorganized thoughts, hostility and depression subscales of the Positive and Negative Symptom Scale (PANSS).</p> <p>Conclusions</p> <p>Some antipsychotic medications significantly differed in beneficial impact on productivity level in the long-term treatment of patients with schizophrenia. Findings further highlight the link between clinical and functional outcomes, showing significant associations between higher productivity, lower symptom severity and better persistence on therapy.</p> <p>Trial Registration</p> <p>clinicaltrials.gov identifier <a href="http://www.clinicaltrials.gov/ct2/show/NCT00088049">NCT00088049</a>; <a href="http://www.clinicaltrials.gov/ct2/show/NCT00036088">NCT00036088</a></p

Possible import routes of proteins into the cyanobacterial endosymbionts/plastids of Paulinella chromatophora

The rhizarian amoeba Paulinella chromatophora harbors two photosynthetically active and deeply integrated cyanobacterial endosymbionts acquired ~60 million years ago. Recent genomic analyses of P. chromatophora have revealed the loss of many essential genes from the endosymbiont’s genome, and have identified more than 30 genes that have been transferred to the host cell’s nucleus through endosymbiotic gene transfer (EGT). This indicates that, similar to classical primary plastids, Paulinella endosymbionts have evolved a transport system to import their nuclear-encoded proteins. To deduce how these proteins are transported, we searched for potential targeting signals in genes for 10 EGT-derived proteins. Our analyses indicate that five proteins carry potential signal peptides, implying they are targeted via the host endomembrane system. One sequence encodes a mitochondrial-like transit peptide, which suggests an import pathway involving a channel protein residing in the outer membrane of the endosymbiont. No N-terminal targeting signals were identified in the four other genes, but their encoded proteins could utilize non-classical targeting signals contained internally or in C-terminal regions. Several amino acids more often found in the Paulinella EGT-derived proteins than in their ancestral set (proteins still encoded in the endosymbiont genome) could constitute such signals. Characteristic features of the EGT-derived proteins are low molecular weight and nearly neutral charge, which both could be adaptations to enhance passage through the peptidoglycan wall present in the intermembrane space of the endosymbiont’s envelope. Our results suggest that Paulinella endosymbionts/plastids have evolved several different import routes, as has been shown in classical primary plastids