LoFreq: a sequence-quality aware,ultra-sensitive variant caller for uncovering cell-population heterogeneity from high-throughput sequencing datasets

The study of cell-population heterogeneity in a range of biological systems, from viruses to bacterial isolates to tumor samples, has been transformed by recent advances in sequencing throughput. While the high-coverage afforded can be used, in principle, to identify very rare variants in a population, existing ad hoc approaches frequently fail to distinguish true variants from sequencing errors. We report a method (LoFreq) that models sequencing run-specific error rates to accurately call variants occurring in <0.05% of a population. Using simulated and real datasets (viral, bacterial and human), we show that LoFreq has near-perfect specificity, with significantly improved sensitivity compared with existing methods and can efficiently analyze deep Illumina sequencing datasets without resorting to approximations or heuristics. We also present experimental validation for LoFreq on two different platforms (Fluidigm and Sequenom) and its application to call rare somatic variants from exome sequencing datasets for gastric cancer. Source code and executables for LoFreq are freely available at http://sourceforge.net/projects/lofreq/.     

Targeting telomeres and telomerase

Telomeres and telomerase represent, at least in theory, an extremely attractive target for cancer therapy. The objective of this review is to present the latest view on the mechanism(s) of action of telomerase inhibitors, with an emphasis on a specific class of telomere ligands called G-quadruplex ligands, and to discuss their potential use in oncology.     

Sequence effects in single-base loops for quadruplexes

Intramolecular G-quadruplexes formed by a single DNA strand have attracted much interest due to the possibility that they may form in telomeres, oncogene promoter sequences and other biologically relevant regions of the genome. Therefore, it is important to understand the rules that govern the formation of these intramolecular structures and to determine their stabilities. We compared here 27 different sequences containing four tracts of three guanines with a medium (3) or relatively long (6-9 bases) central loop and two loops composed of a single nucleotide H (A, T or C) corresponding to the GGGHGGGN3-9GGGHGGG motif. These sequences are similar to sequence motifs that can be found in repeated and promoter sequences. Several conclusions were reached: (i) all sequences are prone to form very stable quadruplexes in potassium (Tm between 55 degrees C and 83 degrees C); (ii) these quadruplexes also form in sodium but with a strongly decreased Tm, with a 21 to 36 degrees C difference in melting temperature between Na+ and K+; (iii) a long (9 bases) central loop had a minimal deleterious impact on the stability of the quadruplex; (iv) pyrimidines are preferred over adenine in both single-base loops; (v) the folding topology is relatively robust in potassium: the CD spectra of all oligonucleotides matched the one of all-parallel stranded reference quadruplexes; (vi) conversely, in sodium the folding is diverse and sequence-dependent, as judged from CD and electrophoresis results.     

Multifunctional 0D–2D Ni2P Nanocrystals–Black Phosphorus Heterostructure

0D transition metal phosphides (TMPs) nanocrystals (NCs)–2D ultrathin black phosphorus (BP) heterostructure (Ni₂P@BP) have been synthesized via a facile sonication‐assisted exfoliation followed by a solvothermal process. Compared with the bare BP, the specially designed Ni₂P@BP architecture can enhance the electrical conductivity (from 2.12 × 10² to 6.25 × 10⁴ S m^–1), tune the charge carrier concentration (from 1.25 × 10¹⁷ to 1.37 × 10²⁰ cm^–3), and reduce the thermal conductivity (from 44.5 to 7.69 W m^–1 K^–1) at 300 K, which can be considered for multiple applications. As a result, the Ni₂P@BP exhibits excellent Li storage properties and high hydrogen evolution reaction electrocatalytic activities. The Ni₂P@BP shows improved Li diffusion kinetics (e.g., the Li ions diffusion coefficient increases from 1.14 × 10^–14 cm² s^–1 for pure BP nanosheets to 8.02 × 10^–13 cm² s^–1 for Ni₂P@BP). In addition, the Ni₂P@BP electrode sustains hydrogen production with almost unchanged activity over 3000 cycles, which indicates its good chemical stability when operating under strong reducing environment.     

Preparation of C-6 substituted chitin derivatives under homogeneous conditions

Tosylation of chitin under homogeneous conditions was achieved by the reaction of tosyl chloride with chitin in a DMAc/LiCl solvent system. The resultant tosyl-chitin was fully N-acetylated with acetic anhydride in methanol. The fully acetylated tosyl-chitin was subsequently reacted with the sodium salts of ethyl p-hydroxybenzoate, diethyl malonate, and diethyl phosphite in DMAc to give the corresponding chitin derivatives of 6-O-ethyl benzoate-chitin, 6-deoxy-diethyl malonate-chitin, and 6-(deoxydiethyl) phosphite-chitin, respectively. Subsequent hydrolysis of the chitin-ester derivatives with tert-butoxide in dimethyl sulfoxide (DMSO) generated 6-O-carboxyphenyl-chitin and 6-(deoxydicarboxy)methyl-chitin. The structures of the chitin derivatives were assessed by FT-IR, (13)C NMR, and (31)P NMR, while the degree of substitution of the S(N)2 reaction was estimated by elemental analysis. All the chitin derivatives were found to be soluble or swellable in water, DMAc, or DMSO.     

High frequency production of embryos from liquid flask cultures of oilseed rape

As part of the program to scale-up the production of artificial seeds of winter oilseed rape, Brassica napus ssp. oleifera, we established a liquid flask culture system that enables the high frequency production of freely suspended embryos. As many as 4000 embryos could be obtained from 1 mL packed-cell-volume of cells. For initiation of liquid flask cultures, four different types of callus tissues were used. Among them, the most embryogenic cell suspension cultures were obtained from spontaneous callus developed on the surface of secondary embryos precultured in medium supplemented with 2,4-dichlorophenoxyacetic acid (4.52 muM) and kinetin (0.46 muM) (type B callus). Growth curves of the cell suspension were determined and the cell suspension was able to grow in medium without plant growth regulators. Embryos were observed to developed directly from the cells without going through an obvious callus phase. When subcultured to agar medium containing 44.38 muM benzylaminopurine, about 43% of the embryos developed into plants. (c) 1997 John Wiley & Sons, Inc. Biotechnol Bioeng 54: 231-238, 1997.     

Changes in lipid profiles in the developing haustorium of oil palm seeds

Germinated oil palm seeds were placed in special trays in the field and at different intervals the haustoria were harvested. Changes in haustorial lipids were followed until the eighth week after germination. The moisture content decreased while the lipids increased. The haustorial fatty acid profile was similar to that of the palm kernel. Changes in fatty acid composition at different weeks after germination were observed. The major haustorial lipids were triacylglycerols; free fatty acids and diacylglycerols were also present     

An Air‐Stable Densely Packed Phosphorene–Graphene Composite Toward Advanced Lithium Storage Properties

Phosphorene, monolayer or few‐layer black phosphorus (BP), has recently triggered strong scientific interest for lithium/sodium ion batteries (LIBs/SIBs) applications. However, there are still challenges regarding large‐scale fabrication, poor air stability. Herein, we report the high‐yield synthesis of phosphorene with good crystallinity and tunable size distributions via liquid‐phase exfoliation of bulk BP in formamide. Afterwards, a densely packed phosphorene–graphene composite (PG‐SPS, a packing density of 0.6 g cm^?3) is prepared by a simple and easily up‐scalable spark plasma sintering (SPS) process. When working as anode materials of LIBs, PG‐SPS exhibit much improved first‐cycle Coloumbic efficiency (60.2%) compared to phosphorene (11.5%) and loosely stacked phosphorene–graphene composite (34.3%), high specific capacity (1306.7 mAh g^?1) and volumetric capacity (256.4 mAh cm^?3), good rate capabilities (e.g., 415.0 mAh g^?1 at 10 A g^?1) as well as outstanding long‐term cycling life (91.9% retention after 800 cycles at 10 A g^?1). Importantly, excellent air stability of PG‐SPS over the 60 days observation in maintaining its high Li storage properties can be achieved. On the contrary, 95.2% of BP in PG sample was oxidized after only 10 days exposure to ambience, leading to severe degradation of electrochemical properties.