Determining the quality and complexity of next-generation sequencing data without a reference genome

We describe an open-source kPAL package that facilitates an alignment-free assessment of the quality and comparability of sequencing datasets by analyzing k-mer frequencies. We show that kPAL can detect technical artefacts such as high duplication rates, library chimeras, contamination and differences in library preparation protocols. kPAL also successfully captures the complexity and diversity of microbiomes and provides a powerful means to study changes in microbial communities. Together, these features make kPAL an attractive and broadly applicable tool to determine the quality and comparability of sequence libraries even in the absence of a reference sequence. kPAL is freely available at https://github.com/LUMC/kPAL.

Electronic supplementary material

The online version of this article (doi:10.1186/s13059-014-0555-3) contains supplementary material, which is available to authorized users.     

Changes in the adrenal steroidogenic responsiveness of the mallard duck (Anas platyrhynchos) during early post-natal development

1. Plasma concentrations of corticosterone (B), aldosterone (Aldo) and deoxycorticosterone (DOC) were measured in mallard ducklings immediately before and after exposure to acute immobilization stress. 2. Except for transient declines in B and DOC between the 4th and 14th days after hatching, the resting concentration of each hormone did not change significantly during post-natal development. 3. The stress-induced in Aldo was maximal at hatching while maximal increases in B and DOC did not occur until one day later. 4. Thereafter the magnitude of the stress-induced increases in the concentrations of all of the hormones decreased steadily and on the 21st and 28th days after hatching only B increased significantly in response to stress.     

Conversion of furfural into furfuryl alcohol by saccharomyces cervisiae 354

The influence of aeration, stirring conditions, and the addition of furfural on the yield and productivity of furfural – furfuryl alcohol bioconversion by the yeast strain Saccharomyces cerevisiae 354 was investigated. The formation of furfuryl alcohol increases up to 32 hours of incubation corresponding to the addition of furfural, while the cell growth essentially ceased at 20 hours. The conversion of furfural into furfuryl alcohol under anaerobic and low aeration conditions was 70% and the productivity 0.5g · 1^?1 · h^?1, when the final concentrationof of furfural amounted to 35 g · 1^?1.     

Analysis and quantification of mental stress and fatigue using Maxwell relations from thermodynamics

Several experimental and theoretical techniques have been developed to analyze both physical and psychological stresses. These techniques have relied mainly on certain parameters based on physiological, behavioral, and performance related data. This study is based on a thought experiment which describes the technique to quantify mental stress based on physiological responses using the entropy concept. It relates different physiological parameters using the Maxwell relations of thermodynamics with a systems approach. Data for testing this analytical approach were obtained from an experimental study which was conducted to determine the effects of a mentally stressful situation (final examination) on the common physiological responses (blood pressure, pulse rate, and oral body temperature) of students. The results indicated that the imposed mental stress causes significant changes in physiological responses. The Maxwell relations of thermodynamics were used to quantify the level of stress under different conditions. The results obtained from these relations validated the principles of thermodynamics as applied to the human system.     

The role of protein kinase C in T lymphocyte proliferation. Existence of protein kinase C-dependent and -independent pathways

The mouse cytotoxic T cell clone (CTLL-2) was able to grow in the presence of culture medium supplemented only with transferrin, 2-mercaptoethanol, and recombinant interleukin 2 (IL-2). This lymphokine stimulated the synthesis of DNA in these cells. Similarly, phorbol esters, which activate protein kinase C, induced DNA synthesis in this clone. Furthermore, this later proliferation was not blocked by anti-IL-2 receptor antibodies, which inhibited IL-2-induced proliferation, suggesting that it was not indirectly due to the secretion of IL-2 by the cells. CTLL-2 cells pretreated with high doses of phorbol esters for 48 h down regulated protein kinase C and were depleted of this enzyme. This was shown by: 1) purification and in vitro assay of protein kinase C; 2) the lack of effect of phorbol esters in the stimulation of the Na+/H+ anti-porter which has been directly linked to the activation of protein kinase C. As expected, those protein kinase C-depleted cells no longer synthesized DNA and proliferated in response to phorbol esters. However, they proliferated identically to control cells in response to IL-2. Therefore, our results suggest two different pathways for T cell proliferation, one which involves protein kinase C and the other which does not.     

Treatment with 5-fluoro-2-oxindole Increases the Antinociceptive Effects of Morphine and Inhibits Neuropathic Pain

Cellular and Molecular Neurobiology - The efficacy of µ-opioid receptors (MOR) in neuropathic pain is low and with numerous side effects that limited their use. Chronic neuropathic pain is...     

Structural and functional characteristics of primary cell cultures derived from the adrenal gland tissue of neonatal mallard ducklings (Anas platyrhynchos)

Summary Primary cell cultures were prepared from the adrenal glands of one-day-old mallard ducklings (Anas platyrhynchos). The cells attached equally well to uncoated plastic and glass surfaces and on surfaces that had been coated with collagen. The phase of logarithmic growth occurred between the second and the fourth day, and the cells became confluent between the fifth and the sixth day. Staining with Sudan black B and toluidine blue and viewing fixed preparations by transmission electron microscopy indicated that the cultures consisted mostly of steroidogenic cells. A smaller population of chromaffin cells was also present. Scanning electron microscopy showed that most of the cells had long filopodia, and some cells had numerous surface blebs that were interpreted as exocytotic vesicles. When incubated in Krebs-Henseleit buffer containing 1–24 ACTH the cultured cells released three corticosteroids, namely, corticosterone, aldosterone and deoxycorticosterone. These responses occurred within 15 min of exposure to medium containing 1–24 ACTH and continued throughout a 60-min period of continuous stimulation. The minimally effective concentration of 1–24 ACTH was 0.078 ng per ml (0.0234 nM) and, as the concentration was increased up to 10 ng per ml (2.99 nM), the total output of each hormone during the 60-min incubation period increased significantly according to the following semi-logarithmic relationship: Y=a+b log X, where Y=the total output of hormone, X=the concentration of 1–24 ACTH in the medium, and a=the total output of hormone when the medium contained 1.0 ng of 1–24 ACTH per ml. The total outputs of each hormone in the presence of a maximally effective concentration of 1–24 ACTH, however, were low compared to the responses of similarly stimulated tissue slices taken from the neonatal duckling. It is concluded that most of the cells comprising the confluent cultures were derived from steroidogenic cells in the neonatal adrenal. These cells appeared to retain corticotropin receptors during the course of developing into confluent monolayers, but their diminished steroidogenic capacity to respond when stimulated maximally suggests that some generational changes may have occurred.This work was supported by grants to James Cronshaw and W.N. Holmes from the University of California Committee on Research and the National Science Foundation (DIR-8820923), Washington, DC, USA