Multi-CSAR: a multiple reference-based contig scaffolder using algebraic rearrangements

Background

One of the important steps in the process of assembling a genome sequence from short reads is scaffolding, in which the contigs in a draft genome are ordered and oriented into scaffolds. Currently, several scaffolding tools based on a single reference genome have been developed. However, a single reference genome may not be sufficient alone for a scaffolder to generate correct scaffolds of a target draft genome, especially when the evolutionary relationship between the target and reference genomes is distant or some rearrangements occur between them. This motivates the need to develop scaffolding tools that can order and orient the contigs of the target genome using multiple reference genomes.

Results

In this work, we utilize a heuristic method to develop a new scaffolder called Multi-CSAR that is able to accurately scaffold a target draft genome based on multiple reference genomes, each of which does not need to be complete. Our experimental results on real datasets show that Multi-CSAR outperforms other two multiple reference-based scaffolding tools, Ragout and MeDuSa, in terms of many average metrics, such as sensitivity, precision, F-score, genome coverage, NGA50, scaffold number and running time.

Conclusions

Multi-CSAR is a multiple reference-based scaffolder that can efficiently produce more accurate scaffolds of a target draft genome by referring to multiple complete and/or incomplete genomes of related organisms. Its stand-alone program is available for download at https://github.com/ablab-nthu/Multi-CSAR.

     

Microneutralization Test for Determination of Rhinovirus and Coxsackievirus A Antibody in Human Diploid Cells

A method for determination of serum-neutralizing antibody titers to rhinovirus type 16 and coxsackievirus type A-4 in human diploid cells (WI-38) grown in Microtiter plates is described. A good correlation was observed when comparing neutralization tests in WI-38 and other cells. The WI-38 Microtiter method is relatively simple and economical. It is suitable for those laboratories which are required to conduct large-scale serological evaluation of antibodies for rhinoviruses and coxsackie A viruses. This system also can be used for cytomegalovirus and varicella-zoster virus, which grow relatively slowly.     

Metabolomic analysis and biochemical changes in the urine and serum of streptozotocin-induced normal- and obese-diabetic rats

Diabetes mellitus (DM) is a chronic disease that can affect metabolism of glucose and other metabolites. In this study, the normal- and obese-diabetic rats were compared to understand the diabetes disorders of type 1 and 2 diabetes mellitus. This was done by evaluating their urine metabolites using proton nuclear magnetic resonance (¹H NMR)-based metabolomics and comparing with controls at different time points, considering the induction periods of obesity and diabetes. The biochemical parameters of the serum were also investigated. The obese-diabetic model was developed by feeding the rats a high-fat diet and inducing diabetic conditions with a low dose of streptozotocin (STZ) (25 mg/kg bw). However, the normal rats were induced by a high dose of STZ (55 mg/kg bw). A partial least squares discriminant analysis (PLS-DA) model showed the biomarkers of both DM types compared to control. The synthesis and degradation of ketone bodies, tricarboxylic (TCA) cycles, and amino acid pathways were the ones most involved in the variation with the highest impact. The diabetic groups also exhibited a noticeable increase in the plasma glucose level and lipid profile disorders compared to the control. There was also an increase in the plasma cholesterol and low-density lipoprotein (LDL) levels and a decline in the high-density lipoprotein (HDL) of diabetic rats. The normal-diabetic rats exhibited the highest effect of all parameters compared to the obese-diabetic rats in the advancement of the DM period. This finding can build a platform to understand the metabolic and biochemical complications of both types of DM and can generate ideas for finding targeted drugs.     

Two new lathyrane-type diterpenoid glycosides with IL-6 production inhibitory activity from the roots of Euphorbia kansui

As part of our ongoing search for anti-inflammatory compounds from higher plants, we isolated and elucidated two new diterpenoid glycosides, kansuingol A (1) and kansuingol B (2), from the roots of Euphorbia kansui. These structures were elucidated by extensive spectroscopic methods such as NMR and MS. Compounds were assessed for their IL-6 production inhibitory activity in PMA?+?A23187-stimulated HMC-1 cells. As a result, compounds 1 and 2 exerted inhibitory activities in the production of IL-6 with IC₅₀ values of 2.96, and 1.94?μM, respectively. Further, kansuingol A (1) decreased mRNA expressions of TNF-α and IL-6.     

Paraquat toxicity is reduced by metal chelators in rice leaves

The possible mediatory role of transition metals in paraquat (PQ) toxicity in rice leaves was investigated. Metal chelators (2,2'-bipyridine, 8-hydroxylquinoline and 1,10-phenanthroline) reduced PQ toxicity in rice leaves. The reduction of PQ toxicity by 1,10-phenanthroline (PA) is closely associated with the decrease in lipid peroxidation and increase in activities of enzymes detoxifying active oxygen species. Our results support the notion that iron or copper plays a major role in PQ toxicity in detached rice leaves. Reduction of PQ toxicity by PA in detached rice leaves is most likely mediated through chelation of iron or copper and an increase in superoxide dismutase and glutathione reductase activities.     

Cloning and expression of a Bacillus sp. 79-23 cellulase gene

Summary A gene for encoding cellulase was cloned from Bacillus sp. 79-23 into Escherichia coli and the nucleotide sequence was determined. The cellulase gene, designated as celS, was composed of 1,497 base pairs and the nucleotide sequence of the celS gene was highly homologous to those of other B. subtilis cellulase genes. The enzyme encoded by celS was highly active on carboxymethylcellulose but also exhibited activity towards avicel and p-nitrophenyl--spd-cellobiopyranoside. When its native promoter was replaced with a strong B. subtilis promoter, the extracellular cellulase was produced up to 8.5 units per ml in B. subtilis DB104.     

Ligand-mediated metal-metal interactions in (ν:ν-fulvalene) bis (dicarbonylcobalt) and rhodium complexes

Gas phase photoelectron spectroscopy (PES) is used to investigate the bonding and electronic structure in (fv) [M(CO)₂]₂ (fv = fulvalene, η⁵:η⁵-C₁₀H₈²⁻; M = Co, Rh). The results for these bimetallic complexes are also compared to those for the analogous monometallic complexes CpM(CO)₂ (Cp = η⁵−C₅H₅⁻; M = Co, Rh) which have been reported previously. The low valence ionization patterns observed for CpCo(CO)₂ and (fv)[Co(CO)₂]₂ are very similar, indicating that there is little electronic interaction between the two metals of the dicobalt complex. The spectrum of (fv)[Rh(CO)₂]₂ also is very similar to the spectrum of CpRh(CO)₂, except that the first metal ionizations in the bimetallic rhodium compound show a significant splitting (0.45 eV). This splitting is due to electronic interaction between the two metal centers which occurs via communication through the fulvalene π system. The differences in electronic structure are compared to the differences in electrochemical behavior of the Co and Rh fulvalene complexes.     

Antiproliferative effect of nitric oxide on rat glomerular mesangial cells via inhibition of mitogen-activated protein kinase.

The effect of nitric oxide (NO) donors and lipopolysaccharide (LPS) on the proliferation of rat glomerular mesangial cells was characterized. Exogenous application of a NO donor inhibited serum-induced proliferation in a time- and dose-dependent manner. S-Nitrosoglutathione (GSNO) also increased cGMP generation and arachidonic acid release, but it did not cause any measurable increase in the cytosolic Ca2+ concentration. Chelation of cytosolic Ca2+ or inhibition of mitogen-activated protein kinase (MAPK) kinase had an inhibitory effect on proliferation, but neither enhanced the antiproliferative effect of GSNO. In contrast, inhibition of guanylate cyclase or phospholipase A2 had no effect on proliferation, but partially reversed GSNO-induced antiproliferation by approximately 98 and 65%, respectively. GSNO did not cause cell death. Incubation of cells with LPS induced endogenous NO generation and had an antiproliferative effect. LPS-induced antiproliferation was reversed completely by inhibition of nitric oxide synthase and partially by inhibition of guanylate cyclase or phospholipase A2. GSNO or LPS inhibited serum-induced MAPK activation, and both effects were partially reversed by inhibition of guanylate cyclase or phospholipase A2. Inclusion of 8-bromo-cGMP or arachidonic acid in the growth medium resulted in a similar antiproliferative effect. In conclusion, in rat glomerular mesangial cells, MAPK inhibition and an antiproliferative effect could be induced by either an increase in the cellular concentration of NO or exposure of the cells to LPS. Part of the effect of NO was attributable to the increased cellular cGMP generation and arachidonic acid release.     

Toxicity screening of materials from buildings with fungal indoor air quality problems (Stachybotrys chartarum)

Samples of building materials visibly contaminated with moisture-related fungi (drywall, fiberglass, wallpaper, wood) were tested with indirect (FFL) and direct (MTT) cytotoxicity screening tests that are particularly sensitive toStachybotrys chartarum toxins. In addition, microscopic, chemical, immunochemical (Roridin A enzyme immunoassay) and mycological culture analyses were performed. In all cases in which building occupants had reported verifiable skin, mucous membrane, respiratory, central nervous system or neuropsychological abnormalities, cytotoxicity was identified. Results of a cytotoxicity screening test of field samples, such as the direct MTT test method, will give investigators of health problems related to indoor air quality problems important toxicity information.     

Evolution of the WANCY region in amniote mitochondrial DNA

In most vertebrate mitochondrial genomes, the site for initiation of light-strand replication, OL, is found within a cluster of five transfer RNA (tRNA) genes (tRNA(Trp), tRNA(Ala), tRNA(Asn), tRNA(Cys), and tRNA(Tyr)). This region and part of the adjacent cytochrome c oxydase subunit I (COI) gene were sequenced for two crocodilian, two turtle, and one snake species and for Sphenodon punctatus; part of the adjacent nicotinamide adenine dinucleotide dehydrogenase subunit 2 (ND2) gene was also sequenced for the crocodilian and turtle species. All had the typical vertebrate gene order. The turtles and the snake have a lengthy noncoding sequence between the tRNA(Asn) and tRNA(Cys) genes that we assumed to be homologous to the mammalian OL. The crocodilians and Sphenodon lack such a sequence, a condition they share with birds. Most proposed phylogenies for the amniotes require that OL at this position was lost at least twice during their diversification or was evolved independently more than once. Within the five tRNA genes, frequencies of substitutions are much higher in loops than in stems. Many loops vary dramatically in size among the species; in the most extreme case, the D-arm of the Sphenodon tRNA(Cys) is a "D-arm replacement" loop of seven nucleotides. Frequency of transitions in stems is relatively uniform across tRNAs, but frequency of transversions varies greatly. Mismatches in stems are infrequent, and their relative frequency in a specific tRNA is unrelated to the frequency of substitution in the corresponding gene. Several features of mammalian mitochondrial tRNAs are conserved in WANCY tRNAs throughout amniotes. The inferred initiation codon for COI is GTG in crocodilians, turtles, and the snake, a condition they share with fishes, certain amphibians, and birds. TTG appears to be the initiation codon for COI in Sphenodon; if correct, this would be a novel initiation codon for vertebrate mitochondrial DNA. Phylogenetic analyses of the inferred amino acid sequences of ND2 and COI support the sister-group relationship of birds and crocodilians and suggest that mammals are an early derived lineage within the amniotes.