Cerulean: A hybrid assembly using high throughput short and long reads

Genome assembly using high throughput data with short reads, arguably, remains an unresolvable task in repetitive genomes, since when the length of a repeat exceeds the read length, it becomes difficult to unambiguously connect the flanking regions. The emergence of third generation sequencing (Pacific Biosciences) with long reads enables the opportunity to resolve complicated repeats that could not be resolved by the short read data. However, these long reads have high error rate and it is an uphill task to assemble the genome without using additional high quality short reads. Recently, Koren et al. 2012 proposed an approach to use high quality short reads data to correct these long reads and, thus, make the assembly from long reads possible. However, due to the large size of both dataset (short and long reads), error-correction of these long reads requires excessively high computational resources, even on small bacterial genomes. In this work, instead of error correction of long reads, we first assemble the short reads and later map these long reads on the assembly graph to resolve repeats. Contribution: We present a hybrid assembly approach that is both computationally effective and produces high quality assemblies. Our algorithm first operates with a simplified version of the assembly graph consisting only of long contigs and gradually improves the assembly by adding smaller contigs in each iteration. In contrast to the state-of-the-art long reads error correction technique, which requires high computational resources and long running time on a supercomputer even for bacterial genome datasets, our software can produce comparable assembly using only a standard desktop in a short running time.Comment: Peer-reviewed and presented as part of the 13th Workshop on Algorithms in Bioinformatics (WABI2013

PI3K/AKT/mTOR pathway activation in actinic cheilitis and lip squamous cell carcinomas

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/156448/2/jdv16420_am.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/156448/1/jdv16420.pd

Cyanobacterial allelochemicals but not cyanobacterial cells markedly reduce microbial community diversity

The freshwater cyanobacterium Phormidium sp. LEGE 05292 produces allelochemicals, including the cyclic depsipeptides portoamides, that influence the growth of heterotrophic bacteria, cyanobacteria, and eukaryotic algae. Using 16S rRNA gene amplicon metagenomics, we show here that, under laboratory conditions, the mixture of metabolites exuded by Phormidium sp. LEGE 05292 markedly reduces the diversity of a natural planktonic microbial community. Exposure of the same community to the portoamides alone resulted in a similar outcome. In both cases, after 16 days, alpha-diversity estimates for the allelochemical-exposed communities were less than half of those for the control communities. Photosynthetic organisms, but also different heterotrophic-bacteria taxa were found to be negatively impacted by the allelochemicals. Intriguingly, when Phormidium sp. LEGE 05292 was co-cultured with the microbial community, the latter remained stable and closer to non-exposed than to allelochemical-exposed communities. Overall, our observations indicate that although under optimal growth conditions Phormidium sp. LEGE 05292 is able to synthesize potent allelochemicals that severely impact different microorganisms, its allelopathic effect is not pronounced when in contact with a complex microbial community. Therefore, under ecologically relevant conditions, the allelopathic behavior of this cyanobacterium may be regulated by nutrient availability or by interactions with the surrounding microbiota. Copyright © 2017 Dias, Antunes, Ribeiro, Azevedo, Vasconcelos and Leão.Funding We acknowledge support from Fundação para a Ciência e a Tecnologia (FCT) through grant IF/01358/2014 to PL and through the project UID/Multi/04423/2013. This work was also supported by the Structured Program of R&D&I INNOVMAR (reference NORTE-01-0145-FEDER-000035, Research Line NOVELMAR), funded by the Northern Regional Operational Program (NORTE2020) through the European Regional Development Fund (ERDF)

Copolymerisation as a way to enhance the electrochromic properties of an alkylthiophene oligomer and a pyrrole derivative: copolymer of 3,3'" dihexyl-2,2':5',2":5",2'"-quaterthiophene with (R)-(-)-3-(1-pyrrolyl)propyl-N-(3,5-dinitrobenzoyl)-α-phenylglycinate

The copolymerisation of 3,3'" Dihexyl-2,2':5',2":5",2'"-quaterthiophene (DHQT) and (R)-(-)-3-(1-pyrrolyl)propyl-N-(3,5-dinitrobenzoyl)-α-phenylglycinate (DNBP) was successfully performed electrochemically in acetonitrile (CH3CN) containing tetrabutylammonium tetrafluoroborate ((C4H9)4NBF4) by direct oxidation of monomer mixtures in different feed ratios. Copolymerisation improved the properties of the films of both polymers PDHQT and PDNBP, in respect to the adhesion of PDHQT onto ITO/glass surface and the chromatic contrast of these electrochromic materials. PDHQT, PDNBP and P(DHQT-co-DNBP) films were characterised by FTIR spectroscopy, fluorescence spectroscopy, Scanning Electron Microscopy (SEM) and spectroelectrochemical techniques. Solutions of PDHQT and its copolymers with DNBP (independently of the feed ratio) in N-methylpyrrolidone are fluorescent with emission bands at 555 and 585 nm when excited at 375 nm. Reversible changes in the hue and saturation occur in all the copolymer films from yellow or orange in the reduced state to green or blue in the oxidised state, but were dependent on the proportion of the comonomers used to prepare the copolymers. These changes are more significant for P(DHQT-co-DNBP) films deposited onto ITO/glass with 1:5 feed ratio, as shown by the track of the CIE 1931 xy chromaticity coordinates and by the electrochromic parameters in which this film (thickness 0.8±0.2 μm) presented chromatic contrast (Δ%T) at 660 nm of 62%, coloration efficiency (η) of 266 cm2 C-1 and stability to redox cycling (Δ%T=17% at the 1000th cycle). Therefore, these copolymers are potentially applicable in displays and optoelectronic devices as electrochromic and fluorescent materials

Metal-insulator transition in two-dimensional disordered systems with power-law transfer terms

We investigate a disordered two-dimensional lattice model for noninteracting electrons with long-range power-law transfer terms and apply the method of level statistics for the calculation of the critical properties. The eigenvalues used are obtained numerically by direct diagonalization. We find a metal-insulator transition for a system with orthogonal symmetry. The exponent governing the divergence of the correlation length at the transition is extracted from a finite size scaling analysis and found to be $\nu=2.6\pm 0.15$. The critical eigenstates are also analyzed and the distribution of the generalized multifractal dimensions is extrapolated.Comment: 4 pages with 4 figures, printed version: PRB, Rapid Communication

Distinct Microbial Signatures between Periodontal Profile Classes

Precise classification of periodontal disease has been the objective of concerted efforts and has led to the introduction of new consensus-based and data-driven classifications. The purpose of this study was to characterize the microbiological signatures of a latent class analysis (LCA)–derived periodontal stratification system, the Periodontal Profile Class (PPC) taxonomy. We used demographic, microbial (subgingival biofilm composition), and immunological data (serum IgG antibody levels, obtained with checkerboard immunoblotting technique) for 1,450 adult participants of the Dental Atherosclerosis Risk in Communities (ARIC) study, with already generated PPC classifications. Analyses relied on t tests and generalized linear models with Bonferroni correction. Men and African Americans had higher systemic antibody levels against most microorganisms compared to women and Caucasians (P < 0.05). Healthy individuals (PPC-I) had low levels of biofilm bacteria and serum IgG levels against most periodontal pathogens (P < 0.05). Subjects with mild to moderate disease (PPC-II to PPC-III) showed mild/moderate colonization of multiple biofilm pathogens. Individuals with severe disease (PPC-IV) had moderate/high levels of biofilm pathogens and antibody levels for orange/red complexes. High gingival index individuals (PPC-V) showed moderate/high levels of biofilm Campylobacter rectus and Aggregatibacter actinomycetemcomitans. Biofilm composition in individuals with reduced periodontium (PPC-VI) was similar to health but showed moderate to high antibody responses. Those with severe tooth loss (PPC-VII) had significantly high levels of multiple biofilm pathogens, while the systemic antibody response to these microorganisms was comparable to health. The results support a biologic basis for elevated risk for periodontal disease in men and African Americans. Periodontally healthy individuals showed a low biofilm pathogen and low systemic antibody burden. In the presence of PPC disease, a microbial-host imbalance characterized by higher microbial biofilm colonization and/or systemic IgG responses was identified. These results support the notion that subgroups identified by the PPC system present distinct microbial profiles and may be useful in designing future precise biological treatment interventions

Cytotoxic drugs for patients with breast cancer in the era of targeted treatment: Back to the future?

Background: Despite current trend of targeted therapy development, cytotoxic agents are a mainstay of treatment of patients with breast cancer. We reviewed recent advances in cytotoxic therapy for patients with metastatic breast cancer (MBC). Materials and methods: Medline searches were conducted for English language studies using the term =MBC= and 'cytotoxic drugs'. The data search was restricted to the period 2000-2011. Results: Several novel cytotoxic compounds, all microtubule inhibitors, have been approved for clinical use in MBC: (i) nab-paclitaxel, reported to improve tumour response and decrease hypersensitivity reactions in comparison with other taxanes; (ii) ixabepilone, shown to have clinical benefit in taxane- and anthracycline-resistant disease and (iii) eribulin, shown to improve overall survival in heavily pre-treated patients, when compared with best available standard treatment. Agents, such as larotaxel, vinflunine, trabectidin and formulations, including cationic liposomal paclitaxel or paclitaxel poliglumex, are currently under evaluation in phase II/III trials. Conclusion: Toxicity and chemotherapy resistance are still major limitations in the treatment of patients with MBC. Further research into new cytotoxic compounds is needed in order to maximise benefit, whilst minimising toxicity