SSW Library: An SIMD Smith-Waterman C/C++ Library for Use in Genomic Applications

Summary: The Smith Waterman (SW) algorithm, which produces the optimal pairwise alignment between two sequences, is frequently used as a key component of fast heuristic read mapping and variation detection tools, but current implementations are either designed as monolithic protein database searching tools or are embedded into other tools. To facilitate easy integration of the fast Single Instruction Multiple Data (SIMD) SW algorithm into third party software, we wrote a C/C++ library, which extends Farrars Striped SW (SSW) to return alignment information in addition to the optimal SW score. Availability: SSW is available both as a C/C++ software library, as well as a stand alone alignment tool wrapping the librarys functionality at https://github.com/mengyao/Complete- Striped-Smith-Waterman-Library Contact: [email protected]: 3 pages, 2 figure

One reference genome is not enough.

A recent study on human structural variation indicates insufficiencies and errors in the human reference genome, GRCh38, and argues for the construction of a human pan-genome

Solubility of red palm oil in supercritical carbon dioxide: measurement and modelling

The solubility of red palm oil (RPO) in supercritical carbon dioxide (scCO2) was determined using a dynamic method at 8.5–25 MPa and, 313.15–333.15 K and at a fixed scCO2 flow rate of 2.9 g·min− 1 using a full factorial design. The solubility was determined under low pressures and temperatures as a preliminary study for RPO particle formation using scCO2. The solubility of RPO was 0.5–11.3 mg·(g CO2)− 1 and was significantly affected by the pressure and temperature. RPO solubility increased with pressure and decreased with temperature. The Adachi–Lu model showed the best-fit for RPO solubility data with an average relative deviation of 14% with a high coefficient of determination, R2 of 0.9667, whereas the Peng–Robinson equation of state thermodynamic model recorded deviations of 17%–30%

Anti-malarial and anti-inflammatory effects of Gynura procumbens are mediated by kaempferol via inhibition of glycogen synthase kinase-3ß (GSK3ß)

Gynura procumbens is a medicinal plant, traditionally used to treat inflammation and fever. A yeast-based assay detected GSK3â-inhibitory activity in the aqueous extract of G. procumbens. GSK3â is now known to have a central role in the modulation of host inflammatory response during bacterial infections. In this study, we investigated the involvement of GSK3â in the anti-malarial and anti-inflammatory effects of an aqueous extract of G. procumbens. Our results showed that G. procumbens inhibited growth of P. falciparum 3D7. Consecutive four-day administration of 250 mg/kg body weight (b.w.) G. procumbens resulted in strong chemosuppression and improved survivability in P. berghei-infected mice. B. pseudomallei-infected mice treated with G. procumbens (50 mg/kg b.w.) showed increased survivability. TNF-á and IFN-ã levels in liver and serum of B. pseudomallei-infected mice were lowered by G. procumbens treatment. IL-10 level was higher in serum of G. procumbens-administered infected mice. G. procumbens treatment of P. berghei-and B. pseudomallei-infected animals each resulted in increased hepatic GSK3â (Ser9) phosphorylation. It is noteworthy that kaempferol (one of the compounds in G. procumbens) also inhibited the growth of P. falciparum 3D7; showed strong chemosuppression and improved survivability in P. berghei-infected mice at 5 mg/kg b.w. B. pseudomallei-infected mice treated with kaempferol (10 mg/kg b.w.) showed improved survivability. Concomitantly, the described effects due to kaempferol also involved enhanced GSK3â (Ser9) phosphorylation as observed with G. procumbens. In summary, the observed anti-malarial and anti-inflammatory effects of G. procumbens involved inhibition of GSK3â and kaempferol may in part be responsible for the pharmacological effects

The atypical Gaoligong orocline: Its geodynamic origin and evolution

Various orocline systems around the India–Eurasia collision zone have long been recognized and studied. Different portions of the India–Eurasia boundaries represent various scales and models of orocline-forming processes, such as the Baluchistan orocline formed by multiple deformation events and the Himalayan orocline formed by a mixture of complex structural mechanisms. The curvature from the eastern Himalayan syntaxis through east Burma to west Yunnan showed a unique convex curvature toward the mantle wedge. This is different from the concave Baluchistan orocline and the Himalayan orocline. The unique geometry of the Gaoligong orocline shows an N-S trend for the northern section and a NE-SW trend for the southern section. This curvature also marks the boundary between the Tengchong and Baoshan blocks along the Santaishan suture in western Yunnan, China. Our structural reconstruction identified five deformation events: 1) D1 is km-scale upright folding, which only affected the Neoproterozoic meta-sedimentary unit, 2) D2 recumbent folding, which only developed in the southern section of the Gaoligong orocline, 3) D3 large-scale gently westward-inclined thrust folding, 4) D4 right-lateral shear belt, and 5) the D5 normal faults. Since the D3 structure is the earliest event that shows penetrative foliation development along the orocline, we consider D1 and D2 as pre-orocline-forming events. The geometry of the Gaoligong orocline is controlled by the distribution of the Ordovician basement between the Tengchong and Baoshan blocks. Both north and south sections experienced the same structural evolution since D3 (a fault-propagation fold system occurred between 40 Ma and 28 Ma), D4 (steep right-lateral shear belt occurred between 28 Ma and 15 Ma), and D5 (normal faults after 15 Ma). The curvature first developed as a shovel-like top-to-the-NE thrust plane (S3) that formed under amphibolite-facies conditions between 40 Ma and 28 Ma. The following deformation events (D4 and D5) show orocline parallel foliation development under lower metamorphic conditions, indicating that the curvature of the Gaoligong orocline is not generated by additional rotation along multiple deformation events. However, due to the lack of orocline parallel foliation development for S3, and the lack of a proper position of the indenter, the Gaoligong orocline cannot be classified as a primary orocline nor a rotational orocline. The curved geometry is an interference pattern of topography relief to the shovel-like thrust plane that developed during D3. Our new reconstructed structural evolution concludes that the Gaoligong orocline is an “atypical” orocline

Apolipoprotein-induced conversion of phosphatidylcholine bilayer vesicles into nanodisks

AbstractApolipoprotein mediated formation of nanodisks was studied in detail using apolipophorin III (apoLp-III), thereby providing insight in apolipoprotein–lipid binding interactions. The spontaneous solubilization of 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) vesicles occured only in a very narrow temperature range at the gel–liquid–crystalline phase transition temperature, exhibiting a net exothermic interaction based on isothermal titration calorimetry analysis. The resulting nanodisks were protected from proteolysis by trypsin, endoproteinase Glu-C, chymotrypsin and elastase. DMPC solubilization and the simultaneous formation of nanodisks were promoted by increasing the vesicle diameter, protein to lipid ratio and concentration. Inclusion of cholesterol in DMPC dramatically enhanced the rate of nanodisk formation, presumably by stabilization of lattice defects which form the main insertion sites for apolipoprotein α-helices. The presence of fully saturated acyl chains with a length of 13 or 14 carbons in phosphatidylcholine allowed the spontaneous vesicle solubilization upon apolipoprotein addition. Nanodisks with C13:0-phosphatidylcholine were significantly smaller with a diameter of 11.7±3.1nm compared to 18.5±5.6nm for DMPC nanodisks determined by transmission electron microscopy. Nanodisk formation was not observed when the phosphatidylcholine vesicles contained acyl chains of 15 or 16 carbons. However, using very high concentrations of lipid and protein (>10mg/ml), 1,2,-dipalmitoyl-sn-glycero-3-phosphocholine nanodisks could be produced spontaneously although the efficiency remained low

Effects of Angelica dahurica

The main objective of wound treatments is to restore the functional skin properties and prevent infection. Traditional Chinese medicine provides alternative anti-inflammatory, antimicrobial, and wound healing therapies. Both Angelica dahurica extract (AE) and Rheum officinale extract (RE) possess antimicrobial activity. In this study, AE and RE were applied in wound treatment to investigate their healing effects. Thirty Sprague-Dawley rats with dorsal full-thickness skin excision were divided into normal saline (NS), AE, RE, AE plus RE (ARE), and Biomycin (BM) groups. The treatment and area measurement of wounds were applied daily for 21 days. Wound biopsies and blood samples were obtained for histology examinations and cytokine analysis. Results showed that wound contraction in ARE group was significantly higher than that in NS and BM groups (P 0.05), and plasma TGF-β1 levels were significantly lower than those in the NS group on days 3-4 (P < 0.05). In conclusion, ARE accelerates wound healing during inflammation and proliferation phases

Epidemic Pleurodynia Caused by Coxsackievirus B3 at a Medical Center in Northern Taiwan

Epidemic pleurodynia is seldom reported in Southeast Asia and there has been no report from Taiwan. We conducted a retrospective chart review of children = 18 years of age in the National Taiwan University Hospital from January 1 to December 31, 2005. Epidemic pleurodynia was defined as an acute illness characterized by sharp localized pain over the chest or upper abdomen. Patients with known heart diseases or pulmonary consolidations were excluded. In total, 28 patients met the case definition of epidemic pleurodynia. Coxsackievirus B3 (CB3) was isolated in 15 (60%) of the 25 throat swab specimens. Four (14%) of the 28 patients presented chest wall tenderness and only one (6%) of the 18 patients tested had an elevated creatinine kinase level. Twenty-one (75%) of the 28 patients described pleuritic chest pains and 10 (45%) of the 22 chest radiographies exhibited pulmonary infiltrates or pleural effusions. Six patients were observed with tonsillar exudates and one was confirmed to have a CB3 urinary tract infection. The clinical features and radiological findings suggest that CB3-associated epidemic pleurodynia might be a disease of the pleura and occasionally spreads to nearby tissues, resulting in chest wall myositis, pulmonary infiltrates and myopericarditis

Tangram: A comprehensive toolbox for mobile element insertion detection

© 2014 Wu et al.; licensee BioMed Central Ltd. Background: Mobile elements (MEs) constitute greater than 50% of the human genome as a result of repeated insertion events during human genome evolution. Although most of these elements are now fixed in the population, some MEs, including ALU, L1, SVA and HERV-K elements, are still actively duplicating. Mobile element insertions (MEIs) have been associated with human genetic disorders, including Crohn\u27s disease, hemophilia, and various types of cancer, motivating the need for accurate MEI detection methods. To comprehensively identify and accurately characterize these variants in whole genome next-generation sequencing (NGS) data, a computationally efficient detection and genotyping method is required. Current computational tools are unable to call MEI polymorphisms with sufficiently high sensitivity and specificity, or call individual genotypes with sufficiently high accuracy.Results: Here we report Tangram, a computationally efficient MEI detection program that integrates read-pair (RP) and split-read (SR) mapping signals to detect MEI events. By utilizing SR mapping in its primary detection module, a feature unique to this software, Tangram is able to pinpoint MEI breakpoints with single-nucleotide precision. To understand the role of MEI events in disease, it is essential to produce accurate individual genotypes in clinical samples. Tangram is able to determine sample genotypes with very high accuracy. Using simulations and experimental datasets, we demonstrate that Tangram has superior sensitivity, specificity, breakpoint resolution and genotyping accuracy, when compared to other, recently developed MEI detection methods.Conclusions: Tangram serves as the primary MEI detection tool in the 1000 Genomes Project, and is implemented as a highly portable, memory-efficient, easy-to-use C++ computer program, built under an open-source development model