Genome sequence of the oleaginous yeast Rhodotorula toruloides strain CGMCC 2.1609

This is the final version of the article. Available from the publisher via the DOI in this record.Most eukaryotic oleaginous species are yeasts and among them the basidiomycete red yeast, Rhodotorula (Rhodosporidium) toruloides (Pucciniomycotina) is known to produce high quantities of lipids when grown in nitrogen-limiting media, and has potential for biodiesel production. The genome of the CGMCC 2.1609 strain of this oleaginous red yeast was sequenced using a hybrid of Roche 454 and Illumina technology generating 13 × coverage. The de novo assembly was carried out using MIRA and scaffolded using MAQ and BAMBUS. The sequencing and assembly resulted in 365 scaffolds with total genome size of 33.4 Mb. The complete genome sequence of this strain was deposited in GenBank and the accession number is LKER00000000. The annotation is available on Figshare (doi:10.6084/m9.figshare.4754251).This research was funded by grants from Shell Global Solutions (UK). We gratefully acknowledge Liverpool Advanced Genomics Facility and Exeter Sequencing Service and computational core facilities at the University of Exeter supported by Wellcome Trust Institutional Strategic Support Fund (WT097835MF) and Wellcome Trust Multi User Equipment Award (WT101650MA)

Compactness in Banach space theory - selected problems

We list a number of problems in several topics related to compactness in nonseparable Banach spaces. Namely, about the Hilbertian ball in its weak topology, spaces of continuous functions on Eberlein compacta, WCG Banach spaces, Valdivia compacta and Radon-Nikod\'{y}m compacta

Local Treatment of Hand-Foot Syndrome with Uridine/Thymidine: In Vitro Appraisal on a Human Keratinocyte Cell Line HaCaT

5-fluorouracil (5-FU) is one of the most commonly used antineoplastic drugs in the anticancer therapy. The hand-foot (HF) syndrome (palmar-plantar erythrodysesthesia) is an adverse effect frequently related to long-term i.v. administration of 5-FU or its orally applicable prodrug capecitabine. Its severity can even lead to interruption of the otherwise effective anticancer therapy. Tentative practice in some clinics has shown that topical application of 10% uridine ointment is beneficial for calming down the HF syndrome. This study is focused on verifying the alleged protective activity of uridine in the in vitro model of cultured human keratinocyte cell line HaCaT. We also tested the protective effects of thymidine alone or uridine-thymidine combination. The cellular viability time progression was measured in order to evaluate the effect of protective agents by three different types of cytopathogenicity tests—NTCA test (non-destructive test of cellular activity), modified MTT test and RTCA (real-time cell analyser, Roche). All three methods proved the ability of uridine and uridine-thymidine combination to protect keratinocytes against 5-FU damage in vitro. While thymidine alone did not show any remarkable effect, the thymidine-uridine combination demonstrated enhanced protective activity compared to uridine alone. Our findings provided the supporting rationale for using uridine or uridine-thymidine ointments in the HF syndrome local therapy

Evolution of moth sex pheromone composition by a single amino acid substitution in a fatty acid desaturase

For sexual communication, moths primarily use blends of fatty acid derivatives containing one or more double bonds in various positions and configurations, called sex pheromones (SPs). To study the molecular basis of novel SP component (SPC) acquisition, we used the tobacco hornworm (Manduca sexta), which uses a blend of mono-, di-, and uncommon triunsaturated fatty acid (3UFA) derivatives as SP. We identified pheromone-biosynthetic fatty acid desaturases (FADs) MsexD3, MsexD5, and MsexD6 abundantly expressed in the M. sexta female pheromone gland. Their functional characterization and in vivo application of FAD substrates indicated that MsexD3 and MsexD5 biosynthesize 3UFAs via E/Z14 desaturation from diunsaturated fatty acids produced by previously characterized Z11-desaturase/conjugase MsexD2. Site-directed mutagenesis of sequentially highly similar MsexD3 and MsexD2 demonstrated that swapping of a single amino acid in the fatty acyl substrate binding tunnel introduces E/Z14-desaturase specificity to mutated MsexD2. Reconstruction of FAD gene phylogeny indicates that MsexD3 was recruited for biosynthesis of 3UFA SPCs in M. sexta lineage via gene duplication and neofunctionalization, whereas MsexD5 representing an alternative 3UFA-producing FAD has been acquired via activation of a presumably inactive ancestral MsexD5. Our results demonstrate that a change as small as a single amino acid substitution in a FAD enzyme might result in the acquisition of new SP compounds

Thermal, Cardiac and Adrenergic Responses to Repeated Local Cooling

Summary The aim of this study was to ascertain whether repeated local cooling induces the same or different adaptational responses as repeated whole body cooling. Repeated cooling of the legs (immersion into 12 °C water up to the knees for 30 min, 20 times during 4 weeks = local cold adaptation -LCA) attenuated the initial increase in heart rate and blood pressure currently observed in control subjects immersed in cold water up to the knees. After LCA the initial skin temperature decrease tended to be lower, indicating reduced vasoconstriction. Heart rate and systolic blood pressure appeared to be generally lower during rest and during the time course of cooling in LCA humans, when compared to controls. All these changes seem to indicate attenuation of the sympathetic tone. In contrast, the sustained skin temperature in different areas of the body (finger, palm, forearm, thigh, chest) appeared to be generally lower in LCA subjects than in controls (except for temperatures on the forehead). Plasma levels of catecholamines (measured 20 and 40 min after the onset of cooling) were also not influenced by local cold adaptation. Locally cold adapted subjects, when exposed to whole body cold water immersion test, showed no change in the threshold temperature for induction of cold thermogenesis. This indicates that the hypothermic type of cold adaptation, typically occurring after systemic cold adaptation, does not appear after local cold adaptation of the intensity used. It is concluded that in humans the cold adaptation due to repeated local cooling of legs induces different physiological changes than systemic cold adaptation

Impact of the Nucleosome Histone Core on the Structure and Dynamics of DNA-Containing Pyrimidine–Pyrimidone (6–4) Photoproduct

International audienceThe pyrimidine-pyrimidone (6-4) photoproduct (64-PP) is an important photoinduced DNA lesion, which constitutes a mutational signature for melanoma. The structural impact of 64-PP on DNA complexed with compaction proteins, and notably histones, affects the mechanism of its mutagenicity and repair but remains poorly understood. Here we investigate the conformational dynamics of DNA containing 64-PP lesions within the nucleosome core particle by atomic-resolution molecular dynamics simulations at the multi-microsecond time scale. We demonstrate that the histone core exerts important mechanical restraints that largely decrease global DNA structural fluctuations. However, we also show that local DNA flexibility at the damaged site is enhanced, due to imperfect structural adaptation to restraints imposed by the histone core. In particular, if 64-PP faces the histone core and is therefore not directly accessible by the repair protein, the complementary strand facing the solvent exhibits higher flexibility than the corresponding strand in a naked, undamaged DNA. This may serve as an initial recognition signal for repair. Our simulations also pinpoint the structural role of proximal residues from the truncated histone tails

Original Article Why We Are Not Able to Find the Coronary Heart Disease Gene -apoE As an Example (apoprotein E / cardiovascular risk /gene polymorphism / myocardial infarction)

Abstract. The apoprotein E gene ranks among the most discussed candidate genes for cardiovascular disease. We studied whether the association between apoprotein E gene polymorphism and manifestation of acute coronary syndrome is modulated by the presence/absence of traditional cardiovascular risk factors. The population under study were 1066 patients (men under 65 years) admitted between 2006-2009 to five coronary care units in Prague (GENetic DEtermination of Myocardial Infarction in Prague) and the control population (1066 age-matched men selected from the Czech population sample). The frequency of disadvantage genotype E4 + was significantly higher (P < 0.01) in acute coronary syndrome patients (22.38 %) than in controls (16.76 %). When the acute coronary syndrome group was step by step limited to non-smokers, non-diabetics and normotensive individuals, the odds ratio displayed a gradual increase from 1.35 (for the entire group) through 1.48 (non-smokers), 1.53 (non-smokers+non-diabetics) to 1.71 (non-smokers+non-diabetics+normoten-sives). The effect of the apoprotein E gene on the individual risk of acute coronary syndrome is nonhomogenous within the patient groups. This association of apoprotein E gene with acute coronary syndrome is strongly modified by the presence/absence of traditional cardiovascular factors of atherosclerosis in a high-risk Czech population