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.     

Hemoglobin adducts in 1,3-butadiene exposed Czech workers: Female–male comparisons

We previously reported results of a molecular epidemiological study of female and male 1,3-butadiene (BD) exposed Czech workers showing that females appeared to absorb or metabolize less BD per unit exposure concentration than did males, based on metabolite concentrations in urine (Chem. Biol. Interact. 166 (2007) 63–77). However, that unexpected observation could not be verified at the time because the only additional BD metabolite measurement attempted was for 1,2,3,4-diepoxybutane (DEB) as reflected in specific N,N[2,3-dihydroxy-1,4-butyl]valine (pyr-Val) hemoglobin adduct concentrations, which were not quantifiable in any subject with the method then employed. Neither somatic gene mutations nor chromosome aberrations were associated with BD exposure levels in that study, consistent with findings in an earlier Czech study of males only. We have since measured production and accumulation of the 1,2-dihydroxy-3,4-epoxybutane (EBD) metabolite as reflected in N-[2,3,4-trihydroxy-butyl]valine (THB-Val) hemoglobin adduct concentrations. The mean THB-Val concentration was significantly higher in exposed males than in control males (922.3 pmol/g and 275.5 pmol/g, respectively), but exposed and control females did not differ significantly (224.5 pmol/g and 181.1 pmol/g, respectively). In both the control and exposed groups mean THB-Val concentrations were significantly higher for males than females. THB-Val concentrations were significantly correlated with mean 8-h TWA exposures for both males and females, but the rate of increase with increasing BD exposure was significantly lower for females. THB-Val concentrations also increased with increasing urine M2 metabolite [isomeric mixture of 1-hydroxy-2-{N-actylcysteinyl}-3-butene and 2-hydroxy-1-{N-acetylcysteinyl}-3-butene] concentrations in both sexes but the rate of increase was also lower in females than in males. There were no significant correlations between THB-Val concentrations and either somatic gene mutations or chromosome aberrations in either males or females. These results using another biomarker to measure a second metabolite of BD support the original conclusion that females absorb or metabolize less BD than males per unit exposure and indicate that the size of the difference increases with exposure. This observation in humans differs from findings in rodents where at prolonged exposures to high BD levels the females form higher amounts of hemoglobin adducts than do males, a difference that disappears at shorter duration lower exposure levels, while female susceptibility to BD induced mutations and tumorgenesis in rodents appears to persist at all BD exposure levels.     

Viral infection and the evolution of caspase 8-regulated apoptotic and necrotic death pathways

Pathogens specifically target both the caspase 8-dependent apoptotic cell death pathway and the necrotic cell death pathway that is dependent on receptor-interacting protein 1 (RIP1; also known as RIPK1) and RIP3 (also known as RIPK3). The fundamental co-regulation of these two cell death pathways emerged when the midgestational death of mice deficient in FAS-associated death domain protein (FADD) or caspase 8 was reversed by elimination of RIP1 or RIP3, indicating a far more entwined relationship than previously appreciated. Thus, mammals require caspase 8 activity during embryogenesis to suppress the kinases RIP1 and RIP3 as part of the dialogue between two distinct cell death processes that together fulfil reinforcing roles in the host defence against intracellular pathogens such as herpesviruses.     

The Effect of Badger Culling on Breakdown Prolongation and Recurrence of Bovine Tuberculosis in Cattle Herds in Great Britain

Bovine tuberculosis is endemic in cattle herds in Great Britain, with a substantial economic impact. A reservoir of Mycobacterium bovis within the Eurasian badger (Meles meles) population is thought to have hindered disease control. Cattle herd incidents, termed breakdowns, that are either ‘prolonged’ (lasting ≥240 days) or ‘recurrent’ (with another breakdown within a specified time period) may be important foci for onward spread of infection. They drain veterinary resources and can be demoralising for farmers. Randomised Badger Culling Trial (RBCT) data were re-analysed to examine the effects of two culling strategies on breakdown prolongation and recurrence, during and after culling, using a Bayesian hierarchical model. Separate effect estimates were obtained for the ‘core’ trial areas (where culling occurred) and the ‘buffer’ zones (up to 2 km outside of the core areas). For breakdowns that started during the culling period, ‘reactive’ (localised) culling was associated with marginally increased odds of prolongation, with an odds ratio (OR) of 1.7 (95% credible interval [CI] 1.1–2.4) within the core areas. This effect was not present after the culling ceased. There was no notable effect of ‘proactive’ culling on prolongation. In contrast, reactive culling had no effect on breakdown recurrence, though there was evidence of a reduced risk of recurrence in proactive core areas during the culling period (ORs and 95% CIs: 0.82 (0.64–1.0) and 0.69 (0.54–0.86) for 24- and 36-month recurrence respectively). Again these effects were not present after the culling ceased. There seemed to be no effect of culling on breakdown prolongation or recurrence in the buffer zones. These results suggest that the RBCT badger culling strategies are unlikely to reduce either the prolongation or recurrence of breakdowns in the long term, and that reactive strategies (such as employed during the RBCT) are, if anything, likely to impact detrimentally on breakdown persistence.     

IRE1α induces thioredoxin-interacting protein to activate the NLRP3 inflammasome and promote programmed cell death under irremediable ER stress

When unfolded proteins accumulate to irremediably high levels within the endoplasmic reticulum (ER), intracellular signaling pathways called the unfolded protein response (UPR) become hyperactivated to?cause programmed cell death. We discovered that?thioredoxin-interacting protein (TXNIP) is?a critical node in this "terminal UPR." TXNIP becomes rapidly induced by IRE1α, an ER bifunctional kinase/endoribonuclease (RNase). Hyperactivated IRE1α increases TXNIP mRNA stability by reducing levels of a TXNIP destabilizing microRNA, miR-17. In turn, elevated TXNIP protein activates the NLRP3 inflammasome, causing procaspase-1 cleavage and interleukin 1β (IL-1β) secretion. Txnip gene deletion reduces pancreatic β cell death during ER stress and suppresses diabetes caused by proinsulin misfolding in the Akita mouse. Finally, small molecule?IRE1α RNase inhibitors suppress TXNIP production to block IL-1β secretion. In summary, the IRE1α-TXNIP pathway is used in the terminal UPR to promote sterile inflammation and programmed cell death and may be targeted to develop effective treatments for cell degenerative diseases.