Novel high-resolution characterization of ancient DNA reveals C > U-type base modification events as the sole cause of post mortem miscoding lesions

Ancient DNA (aDNA) research has long depended on the power of PCR to amplify trace amounts of surviving genetic material from preserved specimens. While PCR permits specific loci to be targeted and amplified, in many ways it can be intrinsically unsuited to damaged and degraded aDNA templates. PCR amplification of aDNA can produce highly-skewed distributions with significant contributions from miscoding lesion damage and non-authentic sequence artefacts. As traditional PCR-based approaches have been unable to fully resolve the molecular nature of aDNA damage over many years, we have developed a novel single primer extension (SPEX)-based approach to generate more accurate sequence information. SPEX targets selected template strands at defined loci and can generate a quantifiable redundancy of coverage; providing new insights into the molecular nature of aDNA damage and fragmentation. SPEX sequence data reveals inherent limitations in both traditional and metagenomic PCR-based approaches to aDNA, which can make current damage analyses and correct genotyping of ancient specimens problematic. In contrast to previous aDNA studies, SPEX provides strong quantitative evidence that C U-type base modifications are the sole cause of authentic endogenous damage-derived miscoding lesions. This new approach could allow ancient specimens to be genotyped with unprecedented accuracy.

Identification of a novel mammalian post-translational modification, phosphocholine, on placental secretory polypeptides

Placental neurokinin B appears to be post-translationally modified by phosphocholine (PC) attached to the aspartyl side chain at residue 4 of the mature peptide. Corticotrophin releasing factor (CRF) was found to be expressed by the rat placenta with the main secreted forms being phosphocholinated proCRF+/- one or two polysaccharide moieties. A combination of high-pressure liquid chromatography (HPLC) and two-site immunometric analysis suggested that PC was also attached to the placental precursors of adrenocorticotrophin, hemokinin, activin and follistatin. However, the fully processed forms of rat placental activin and CRF were free of PC. Formerly, the parasitic filarial nematodes have used PC as a post-translational modification, attached via the polysaccharicle moiety of certain secretory glycoproteins to attenuate the host immune system allowing parasite survival, but it is the PC group itself which endows the carrier with the biological activity. The fact that treatment of proCRF peptides with phospholipase C but not endoglycosidase destroyed PC immunoreactivity suggested a simpler mode of attachment of PC to placental peptides than that used by nematodes. Thus, it is possible that by analogy the placenta uses its secreted phosphocholinated hormones to modulate the mother's immune system and help protect the placenta from rejection.

Use of essential and molecular dynamics to study gamma B-crystallin unfolding after non-enzymic post-translational modifications

Essential and Molecular Dynamics (ED/MD) have been used to model the conformational changes of a protein implicated in a conformational disease-cataract, the largest cause of blindness in the world-after non-enzymic post-translational modification. Cyanate modification did not significantly alter flexibility, while the Schiff's base adduct produced a more flexible N-terminal domain, and intra-secondary structure regions, than either the cyanate adduct or the native structure. Glycation also increased linker flexibility and disrupted the charge network. A number of post-translational adducts showed structural disruption around Cys15 and increased linker flexibility; this may be important in subsequent protein aggregation. Our modelling results are in accord with experimental evidence, and show that ED/MD is a useful tool in modelling conformational changes in proteins implicated in disease processes. (C) 2003 Published by Elsevier Ltd.

Modification of cell wall properties in lettuce improves shelf life

It is proposed that post-harvest longevity and appearance of salad crops is closely linked to pre-harvest leaf morphology (cell and leaf size) and biophysical structure (leaf strength). Transgenic lettuce plants (Lactuca sativa cv. Valeria) were produced in which the production of the cell wall-modifying enzyme xyloglucan endotransglucosylase/hydrolase (XTH) was down-regulated by antisense inhibition. Independently transformed lines were shown to have multiple members of the LsXTH gene family down-regulated in mature leaves of 6-week-old plants and during the course of shelf life. Consequently, xyloglucan endotransglucosylase (XET) enzyme activity and action were down-regulated in the cell walls of these leaves and it was established that leaf area and fresh weight were decreased while leaf strength was increased in the transgenic lines. Membrane permeability was reduced towards the end of shelf life in the transgenic lines relative to the controls and bacteria were evident inside the leaves of control plants only. Most importantly, an extended shelf-life of transgenic lines was observed relative to the non-transgenic control plants. These data illustrate the potential for engineering cell wall traits for improving quality and longevity of salad crops using either genetic modification directly, or by using markers associated with XTH genes to inform a commercial breeding programme.

Enhanced effects of combined cognitive bias modification and computerised cognitive behaviour therapy on social anxiety

This study examines whether combined cognitive bias modification for interpretative biases (CBM-I) and computerised cognitive behaviour therapy (C-CBT) can produce enhanced positive effects on interpretation biases and social anxiety. Forty socially anxious students were randomly assigned into two conditions, an intervention group (positive CBM-I + C-CBT) or an active control (neutral CBM-I + C-CBT). At pre-test, participants completed measures of social anxiety, interpretative bias, cognitive distortions, and social and work adjustment. They were exposed to 6 × 30 min sessions of web-based interventions including three sessions of either positive or neutral CBM-I and three sessions of C-CBT, one session per day. At post-test and two-week follow-up, participants completed the baseline measures. A combined positive CBM-I + C-CBT produced less negative interpretations of ambiguous situations than neutral CBM-I + C-CBT. The results also showed that both positive CBM-I + C-CBT and neutral CBM-I + C-CBT reduced social anxiety and cognitive distortions as well as improving work and social adjustment. However, greater effect sizes were observed in the positive CBM-I + C-CBT condition than the control. This indicates that adding positive CBM-I to C-CBT enhanced the training effects on social anxiety, cognitive distortions, and social and work adjustment compared to the neutral CBM-I + C-CBT condition.

Is cognitive bias modification training truly beneficial for adolescents?

Background Cognitive Bias Modification (CBM) has been shown to change interpretation biases commonly associated with anxiety and depression and may help ameliorate symptoms of these disorders. However, its evidence base for adolescents is scarce. Previous results have been hard to interpret because of methodological issues. In particular, many studies have used negative bias training as the control condition. This would tend to inflate any apparent benefits of CBM compared to a neutral control. Most studies also only examined the effects of a single training session and lacked follow-up assessment or ecologically valid outcome measures. Method Seventy-four adolescents, aged 16–18 years, were randomised to two sessions of CBM training or neutral control. Interpretation bias and mood were assessed three times: at baseline, immediately post-training and 1 week post-training. A controlled experimental stressor was also used, and responses to everyday stressors were recorded for 1 week after training to assess responses to psychological challenges. Feedback for the training programme was collected. Results The CBM group reported a greater reduction in negative affect than control participants. However, other hypothesised advantages of CBM were not demonstrated. Regardless of training group, participants reported increased positive interpretations, decreased negative interpretations, reduced depressive symptoms and no change in trait anxiety. The two groups did not differ in their stress reactivity. After controlling for group differences in training performance, all the mood effects disappeared. Conclusions When tested under stringent experimental conditions the effects of CBM in healthy adolescents appear to be minimal. Future studies should concentrate on participants with elevated cognitive biases and/or mood symptoms who may be more sensitive to CBM.

Effects of a multi-session Cognitive Bias Modification program on interpretative biases and social anxiety symptoms in a sample of Iranian socially-anxious students

This study examines the effects of a multi-session Cognitive Bias Modification (CBM) program on interpretative biases and social anxiety in an Iranian sample. Thirty-six volunteers with a high score on social anxiety measures were recruited from a student population and randomly allocated into the experimental and control groups. In the experimental group, participants received 4 sessions of positive CBM for interpretative biases (CBM-I) over 2 weeks in the laboratory. Participants in the control condition completed a neutral task matched the active CBM-I intervention in format and duration but did not encourage positive disambiguation of socially ambiguous scenarios. The results indicated that after training the positive CBM-I group exhibited more positive (and less negative) interpretations of ambiguous scenarios and less social anxiety symptoms relative to the control condition at both 1 week post-test and 7 weeks follow-up. It is suggested that clinical trials are required to establish the clinical efficacy of this intervention for social anxiety.