Index hopping on the Illumina HiseqX platform and its consequences for ancient DNA studies

The high‐throughput capacities of the Illumina sequencing platforms and the possibility to label samples individually have encouraged wide use of sample multiplexing. However, this practice results in read misassignment (usually <1%) across samples sequenced on the same lane. Alarmingly high rates of read misassignment of up to 10% were reported for lllumina sequencing machines with exclusion amplification chemistry. This may make use of these platforms prohibitive, particularly in studies that rely on low‐quantity and low‐quality samples, such as historical and archaeological specimens. Here, we use barcodes, short sequences that are ligated to both ends of the DNA insert, to directly quantify the rate of index hopping in 100‐year old museum‐preserved gorilla (Gorilla beringei) samples. Correcting for multiple sources of noise, we identify on average 0.470% of reads containing a hopped index. We show that sample‐specific quantity of misassigned reads depends on the number of reads that any given sample contributes to the total sequencing pool, so that samples with few sequenced reads receive the greatest proportion of misassigned reads. This particularly affects ancient DNA samples, as these frequently differ in their DNA quantity and endogenous content. Through simulations we show that even low rates of index hopping, as reported here, can lead to biases in ancient DNA studies when multiplexing samples with vastly different quantities of endogenous material.     

Effect of liquid pulses with 6-benzyladenine on the induction of somatic embryogenesis from coffee (Coffea arabica L.) callus cultures

We investigated the effect of the physical state of the nutrient medium on the induction of somatic embryogenesis on cell cultures derived from coffee (Coffea arabica L.). Non-embryogenic callus tissues were pulsed initially with 50 μM 6-benzyladenine (BA) for 6, 24 or 48 h in half-strength liquid Murashige and Skoog (MS) medium. After pretreatment, calli were transferred to agar-solidified half-strength MS medium supplemented with 50 μM BA (‘standard induction medium’). Control callus tissues were incubated directly on the solid standard induction medium. Callus growth was promoted by longer pretreatment periods. Formation of globular somatic embryos was observed on callus tissues pretreated with BA for 24 or 48 h, which developed fully to cotyledonary-stage within only 2 weeks after transfer to agar-solidified medium supplemented with BA. No embryo formation occurred in control cultures. Pretreatment with BA in liquid medium was associated with changes in the redox status of cultured cells, such as alterations of the ascorbate–glutathione redox systems and the accumulation of free radicals and oxidized lipids, as well as the possible reduction of cytochrome c-mediated apoptotic pathways. In particular, the induction of somatic embryogenesis was highly positively correlated (r ² = 0.822) with the accumulation of protein carbonyls. The physiological role of BA as an inducer of both embryonic differentiation and cellular death is discussed.     

Predictors of new atherosclerotic carotid plaque development in patients with rheumatoid arthritis: a longitudinal study

Introduction

Rheumatoid arthritis (RA) is associated with increased cardiovascular morbidity and mortality attributed to both classical risk factors and chronic inflammation. We assessed longitudinally the factors associated with new carotid plaques in nondiabetic RA patients and apparently healthy individuals.

Methods

In our present prospective observational study, carotid plaques were identified by ultrasonography at baseline and follow-up end, separated by an average of 3.6 ± 0.2 years, in 64 patients (mean age 59.2 ± 12.0 and disease duration at baseline 7.8 ± 6.2 years, 83% women, clinical and laboratory evaluation every 3 to 6 months). In a substudy, 35 of the patients were matched 1:1 for traditional cardiovascular risk factors with 'healthy' controls and were studied in parallel.

Results

New atherosclerotic plaques formed in 30% of patients (first plaque in 9%) who were significantly older than the remaining patients. Tobacco use, blood pressure, body mass index, average cumulative low-density lipoprotein, high-sensitivity C-reactive protein, erythrocyte sedimentation rate level, RA stage, functional class, disease duration and treatment modalities during follow-up did not differ significantly between subgroups after application of the Bonferroni correction. RA was in clinical remission, on average, for approximately 70% of the follow-up time and was not different between subgroups. Multivariate analysis including all the above parameters revealed that age (P = 0.006), smoking (P = 0.009) and duration of low-dose corticosteroid use (P = 0.016) associated independently with new plaque formation. RA patients displayed similar numbers of newly formed carotid plaques to the tightly matched for traditional cardiovascular risk factors 'healthy' controls, although more patients than controls had carotid plaques at baseline.

Conclusions

Formation of new atherosclerotic plaques in this small cohort of patients with well-controlled RA depended mainly on traditional cardiovascular risk factors and corticosteroid use, whereas an adverse effect of residual systemic inflammation was not readily detectable.     

Characterization of PTPRG in Knockdown and Phosphatase-Inactive Mutant Mice and Substrate Trapping Analysis of PTPRG in Mammalian Cells

Receptor tyrosine phosphatase gamma (PTPRG, or RPTPγ) is a mammalian receptor-like tyrosine phosphatase which is highly expressed in the nervous system as well as other tissues. Its function and biochemical characteristics remain largely unknown. We created a knockdown (KD) line of this gene in mouse by retroviral insertion that led to 98–99% reduction of RPTPγ gene expression. The knockdown mice displayed antidepressive-like behaviors in the tail-suspension test, confirming observations by Lamprianou et al. 2006. We investigated this phenotype in detail using multiple behavioral assays. To see if the antidepressive-like phenotype was due to the loss of phosphatase activity, we made a knock-in (KI) mouse in which a mutant, RPTPγ C1060S, replaced the wild type. We showed that human wild type RPTPγ protein, expressed and purified, demonstrated tyrosine phosphatase activity, and that the RPTPγ C1060S mutant was completely inactive. Phenotypic analysis showed that the KI mice also displayed some antidepressive-like phenotype. These results lead to a hypothesis that an RPTPγ inhibitor could be a potential treatment for human depressive disorders. In an effort to identify a natural substrate of RPTPγ for use in an assay for identifying inhibitors, “substrate trapping” mutants (C1060S, or D1028A) were studied in binding assays. Expressed in HEK293 cells, these mutant RPTPγs retained a phosphorylated tyrosine residue, whereas similarly expressed wild type RPTPγ did not. This suggested that wild type RPTPγ might auto-dephosphorylate which was confirmed by an in vitro dephosphorylation experiment. Using truncation and mutagenesis studies, we mapped the auto-dephosphorylation to the Y1307 residue in the D2 domain. This novel discovery provides a potential natural substrate peptide for drug screening assays, and also reveals a potential functional regulatory site for RPTPγ. Additional investigation of RPTPγ activity and regulation may lead to a better understanding of the biochemical underpinnings of human depression.     

Some Aspects of PCB Metabolism by Horseradish Cells

Transformation of polychlorinated biphenyls was studied using different strains of in vitro cultured cells of horseradish (Armoracia rusticana L.). Time and concentration dependence of this process and production of intracellular and extracellular peroxidases were measured with differentiated shooty teratoma culture K54. The yield of PCB transformation and the viability of the cells were highly dependent on PCB concentration. 100 ppm PCB totally inhibited growth of the cells, and reduced their metabolism of xenobiotics. Experiments with a peroxidase (POX) inhibitor, propylgallate, and a cytochrome P450 inhibitor, aminobenztriazole, indicated the involvement of both enzymatic systems in PCB metabolism.     

Nutrition in the life cycle assessment of foods—function or impact?

Purpose

This work provides an unambiguous conceptual framework for inclusion of nutrition in Life Cycle Assessments (LCAs) of food that enables the distinction between two different roles of nutrition, namely serving as the basis of food comparisons via the functional unit and as an impact pathway that links food ingestion with human health effects.

Methods

We compare how nutritional aspects have been considered in the functional unit of published LCAs of food with the procedural requirements for ensuring comparability of the functional units. We consider the relevance of nutrient profiling models for assessing food- and diet-related health damages and benefits in the context of LCAs of food. We finally recommend a method that will enable a systematic, comparative, and holistic assessment of the marginal health effect of food products on human health.

Results and discussion

Satiety is proposed as a central attribute for comparisons of food products, while weighted measures of nutrient content are suggested to be largely misplaced as part of the functional unit. In contrast, nutritional measures have a large role to play in assessing the human health impacts of the marginal ingestion of specific food products. Such measures should enable a direct quantification of human health effect and benefits and should take advantage of robust epidemiological evidence.

Conclusions

Nutritional measures enter into both the functional unit in the form of satiety measures and into the calculation of impacts in the form of the marginal influence of the specific food item on the human health impact of the overall diet. To enhance the differentiation of health impacts at the level of individual food items, it is recommended to combine the nutrient balance indicator with the DALY Nutritional Index (DANI) in each specific dietary context.

     

Positional behavior of Siberian chipmunks (Tamias sibiricus) in captivity

Arboreal and semi-arboreal mammals have remarkably diverse positional behavior and associated morpho-functional adaptations related to the three-dimensional nature of their arboreal habitat. In this context, we investigated the positional behavior of captive Siberian chipmunks (Tamias sibiricus), small bodied semi-arboreal sciurids, in an aviary-type wire-mesh cage containing both terrestrial and arboreal supports. We sampled four adult individuals during a five-month period using focal animal sampling every 30 s. Results showed that animals preferred 8–10 cm horizontal supports and always avoided vertical supports. Locomotion occurred on both terrestrial and 8–10 cm arboreal supports whereas postural behavior occurred primarily on 8–10 cm arboreal supports. Quadrupedal walk dominated during locomotion, and occurred primarily on terrestrial horizontal supports, as is observed for other squirrels. The predominance of quadrupedal locomotion is consistent with the postcranial morphology of chipmunks. In contrast, clawed locomotion occurred on wire mesh and on >13 cm arboreal vertical supports. Finally, pronograde and orthograde sitting, both on 8–10 cm arboreal supports and on terrestrial supports, were the predominant postures, implying general predisposition to selection of stable postures on stable supports for food item manipulation and ingestion.