Linked‐read sequencing enables haplotype‐resolved resequencing at population scale

The feasibility to sequence entire genomes of virtually any organism provides unprecedented insights into the evolutionary history of populations and species. Nevertheless, many population genomic inferences – including the quantification and dating of admixture, introgression and demographic events, and inference of selective sweeps – are still limited by the lack of high‐quality haplotype information. The newest generation of sequencing technology now promises significant progress. To establish the feasibility of haplotype‐resolved genome resequencing at population scale, we investigated properties of linked‐read sequencing data of songbirds of the genus Oenanthe across a range of sequencing depths. Our results based on the comparison of downsampled (25×, 20×, 15×, 10×, 7×, and 5×) with high‐coverage data (46–68×) of seven bird genomes mapped to a reference suggest that phasing contiguities and accuracies adequate for most population genomic analyses can be reached already with moderate sequencing effort. At 15× coverage, phased haplotypes span about 90% of the genome assembly, with 50% and 90% of phased sequences located in phase blocks longer than 1.25–4.6 Mb (N50) and 0.27–0.72 Mb (N90). Phasing accuracy reaches beyond 99% starting from 15× coverage. Higher coverages yielded higher contiguities (up to about 7 Mb/1 Mb [N50/N90] at 25× coverage), but only marginally improved phasing accuracy. Phase block contiguity improved with input DNA molecule length; thus, higher‐quality DNA may help keeping sequencing costs at bay. In conclusion, even for organisms with gigabase‐sized genomes like birds, linked‐read sequencing at moderate depth opens an affordable avenue towards haplotype‐resolved genome resequencing at population scale.     

On-line glucose monitoring by near infrared spectroscopy during the scale up steps of mammalian cell cultivation process development

NIR spectroscopy is a non-destructive tool for in-situ, on-line bioprocess monitoring. One of its most frequent applications is the determination of metabolites during cultivation, especially glucose. Previous studies have usually investigated the applicability of Near Infrared (NIR) spectroscopy at one bioreactor scale but the effect of scale up was not explored. In this study, the complete scale up from shake flask (1 L) through 20 L, 100 L and 1000 L up to 5000 L bioreactor volume level was monitored with on-line NIR spectroscopy. The differences between runs and scales were examined using principal component analysis. The bioreactor runs were relatively similar regardless of scales but the shake flasks differed strongly from bioreactor runs. The glucose concentration throughout five 5000 L scale bioreactor runs were predicted by partial least squares regression models that were based on pre-processed spectra of bioreactor runs and combinations of them. The model that produced the lowest error of prediction (4.18 mM on a 29 mM concentration range) for all five runs in the prediction set was based on the combination of 20 L and 100 L data. This result demonstrated the capabilities and the limitations of an NIR system for glucose monitoring in mammalian cell cultivations.

     

Adaptation of the toxic freshwater cyanobacterium Microcystis aeruginosa to salinity is achieved by the selection of spontaneous mutants

The cyanobacterium Microcystis aeruginosa causes most of the harmful toxic blooms in freshwater ecosystems. Some strains of M. aeruginosa tolerate low‐medium levels of salinity, and because salinization of freshwater aquatic systems is increasing worldwide it is relevant to know what adaptive mechanisms allow tolerance to salinity. The mechanisms involved in the adaptation of M. aeruginosa to salinity (acclimation vs. genetic adaptation) were tested by a fluctuation analysis design, and then the maximum capacity of adaptation to salinity was studied by a ratchet protocol experiment. Whereas a dose of 10 g NaCl L^?1 completely inhibited the growth of M. aeruginosa, salinity‐resistant genetic variants, capable of tolerating up to 14 g NaCl L^?1, were isolated in the fluctuation analysis experiment. The salinity‐resistant cells arose by spontaneous mutations at a rate of 7.3 × 10^?7 mutants per cell division. We observed with the ratchet protocol that three independent culture populations of M. aeruginosa were able to adapt to up to 15.1 g L^?1 of NaCl, suggesting that successive mutation‐selection processes can enhance the highest salinity level to which M. aeruginosa cells can initially adapt. We propose that increasing salinity in water reservoirs could lead to the selection of salinity‐resistant mutants of M. aeruginosa.     

Diversity of endophytic fungi in <Emphasis Type="Italic">Eucalyptus microcorys</Emphasis> assessed by complementary isolation methods

Brazil is the world’s largest producer country of eucalyptus. Although widely applied in the charcoal industry, no studies have focused on the microorganisms associated with Eucalyptus microcorys. Here, we evaluated the composition and structure of endophytic fungal communities in leaves of E. microcorys through two isolation techniques. A total of 120 fresh leaves were collected in a year-long survey at an eucalyptus plantation in the State of São Paulo (Brazil). Endophytic fungi were isolated by particle filtration (PF) and direct leaf fragment plating (LP) in two media: modified dicloran and synthetic nutrient agar, both supplemented with rose bengal and chloramphenicol. The isolates were grouped into morphospecies and identified by morphology and DNA sequencing. We recovered a total of 709 isolates, representing 59 taxa. All taxa found are reported as endophytic for the first time for E. microcorys. Castanediella eucalypticola and Neophaeomoniella eucalypti are new occurrences reported for Brazil. The LP technique recovered a higher number of taxa and isolates than the PF. However, the PF technique retrieved a higher species/isolate ratio than the LP method, 0.12 and 0.09, respectively. Fungal diversity assessed by diversity metrics did not significantly differ between isolation methods. Both techniques recovered a high number of unique taxa, demonstrating that neither method would individually represent the species richness from E. microcorys. The use of LP and PF provided a greater number of observed taxa and consequently new occurrence of species for Brazil.     

Zopiclone versus placebo for short-term treatment of insomnia in patients with advanced cancer: study protocol for a double-blind,randomized, placebo-controlled,clinical multicenter trial

Background

Despite the high prevalence of insomnia in patients with advanced cancer, there are no randomized controlled trials on pharmacological interventions for insomnia in this group of patients. A variety of pharmacological agents is recommended to manage sleep disturbance for insomnia in the general population, but their efficacy and safety in adults with advanced cancer are not established. Thus, there is a need to evaluate the effectiveness of medications for insomnia in order to improve the evidence in patients with advanced cancer. One of the most used sleep medications at present in patients with cancer is zopiclone.

Methods

This is a randomized, double-blind, placebo-controlled, parallel-group, multicenter trial. A total of 100 patients with metastatic cancer who report insomnia will be randomly allocated to zopiclone or placebo. The treatment duration with zopiclone/placebo is 6 consecutive nights. The primary endpoint is patient-reported sleep quality during the final study night (night 6) assessed on a numerical rating scale of 0–10, where 0?=?Best sleep and 10?=?Worst possible sleep. Secondary endpoints include the mean patient-reported total sleep time and sleep onset latency during the final study night (night 6).

Discussion

Results from this study on treatment of insomnia in advanced cancer will contribute to clinical decision-making and improve the treatment of sleep disturbance in this patient cohort.

Trial registration

ClinicalTrials.gov, NCT02807922. Registered on 21 June 2016.

     

Mismatches between habitat preferences and risk avoidance for birds in intensive Mediterranean farmland

Land use intensification may create habitats that organisms perceive as suitable, but where reproduction or survival is insufficient to maintain self-sustaining populations. Such conditions may qualify as ecological traps, but their existence is often hard to prove. Here, we provide a practical framework to evaluate a potential ecological trap resulting from mismatch between habitat preferences and predation risk, focusing on ground-nesting farmland birds of conservation concern. The framework is based on species-specific associations with safe or unsafe habitat types (i.e. field and landscape types with high or low nest survival), and the occurrence of risk avoidance (i.e. negative responses to predator abundances or to nest failure rates after controlling for habitat effects). Bird densities were far more influenced by field characteristics than landscape context. Corn bunting and fan-tailed warbler were associated with tall swards (safe habitats), and did not show risk avoidance. Tawny pipit and and Galerida larks were associated with short swards (unsafe habitats), with the former avoiding fields with high nest predation rates, and the later avoiding high mongoose abundances. Short-toed lark was associated with fields with short swards and low nest trampling rates. Results suggest that short-toed lark may be the most vulnerable to ecological trapping, because it nests on unsafe habitats and did not show predation risk avoidance. Our approach provides a practical first step to infer vulnerability to a potential ecological trap, though further research is needed to confirm this effect. Management actions increasing nest survival in short sward fields will likely favour grassland bird conservation in intensive Mediterranean farmland.     

Palmar flexion creases in schizophrenia

Palmar flexion creases have been studied in schizophrenics with a family history of schizophrenia or other psychiatric disorders and without such a background, and compared to a control population. Palmar flexion creases have been analyzed according to the method suggested byBali & Chaube (1971). When compared to controls, differences in the DRBC and TRBC frequencies are significant in the subgroup with no family history, supporting the existence of biological heterogeneity in schizophrenia, and of congenital factors when there is no known genetic background.     

Transformation of distinct mycobacterial species by shuttle vectors derived from theMycobacterium fortuitum pAL5000 plasmid

Mycobacterium tuberculosis H37Ra,M. smegmatisATCC 607,M. smegmatis MC²155,M. aurum A +,M. aurum A11, and one representative strain ofM. flavescens were transformed by electroporation with plasmid pMY10 and cosmid pDC100. Plasmid pMY 10 contained the origin of replication of pAL5000, the origin of replication of pBR322, a kanamycin resistance gene, and the origin of transfer of the Inc plasmid RK2; the cosmid pDC100 contained the pHC79 SS cosmid, the origin of replication of pAL5000, and a kanamycin resistance gene. The efficiency of transformation varied with the recipient cells used and was in decreasing order: 7×10⁵ forM. smegmatis MC²155, 6×10³ forM. tuberculosis H37Ra, 10³ forM. aurum, 50 forM. smegmatis ATCC 607, and 5 forM. flavescens. A rapid protocol for plasmid extraction from mycobacteria was developed.The satisfactory transformation of the nonvirulentM. tuberculosis strain H37Ra was of interest for future studies on cloning of virulence genes, while the satisfactory transformation ofM. aurum was of interest for future studies on the genetics of drug resistance because these bacteria are sensitive to drugs specifically used in the treatment of tuberculosis and leprosy. However, neither vector was stably maintained inM. smegmatis, indicating that further investigations are still necessary to resolve this difficulty.