Impact of selective genotyping in the training population on accuracy and bias of genomic selection

Estimating marker effects based on routinely generated phenotypic data of breeding programs is a cost-effective strategy to implement genomic selection. Truncation selection in breeding populations, however, could have a strong impact on the accuracy to predict genomic breeding values. The main objective of our study was to investigate the influence of phenotypic selection on the accuracy and bias of genomic selection. We used experimental data of 788 testcross progenies from an elite maize breeding program. The testcross progenies were evaluated in unreplicated field trials in ten environments and fingerprinted with 857 SNP markers. Random regression best linear unbiased prediction method was used in combination with fivefold cross-validation based on genotypic sampling. We observed a substantial loss in the accuracy to predict genomic breeding values in unidirectional selected populations. In contrast, estimating marker effects based on bidirectional selected populations led to only a marginal decrease in the prediction accuracy of genomic breeding values. We concluded that bidirectional selection is a valuable approach to efficiently implement genomic selection in applied plant breeding programs.     

Global transcriptional analysis of stress-response strategies in Acidithiobacillus ferrooxidans ATCC 23270 exposed to organic extractant—Lix984n

Acidithiobacillus ferrooxidans (A. ferrooxidans) ATCC 23270 is a model bacteria for bioleaching research. Because of the use of extractant in metal extraction industry, A. ferrooxidans needs to cope with the water-organic two-phase system. To get insight into the molecular response of A. ferrooxidans to organic solvent, global gene expression pattern was examined in A. ferrooxidans ATCC 23270 cells subjected to Lix984n (an organic extractant) using the method of whole-genome DNA microarray. The data suggested that the global response of A. ferrooxidans to Lix984n stress was characterized by the up-regulation of genes involved in pentose phosphate pathway, fatty acid and glutamate biosynthesis. In further study, compared to heterotrophic bacteria in dealing with short-time stress, A. ferrooxidans has a special strategy of continuously enhancing the expression of genes encoding proteins involved in electron transport, such as petI, petII, cyo and cyd. Besides, acrAB-tolC operon encoding organic solvent efflux pump and its positive regulator gene ostR were addressed.     

Glucagon-like peptide-1(1-37) can enhance blood glucose homeostasis in mice

Tyrosyl O-sulfation is a common posttranslational derivatization of proteins that may also modify regulatory peptides. Among these are members of the cholecystokinin (CCK)/gastrin family. While sulfation of gastrin peptides is without effect on the bioactivity, O-sulfation is crucial for the cholecystokinetic activity (i.e. gallbladder emptying) of CCK peptides. Accordingly, the purification of CCK as a sulfated peptide was originally monitored by its gallbladder emptying effect. Since then, the dogma has prevailed that CCK peptides are always sulfated. The dogma is correct in a semantic context since the gallbladder expresses only the CCK-A receptor that requires sulfation of the ligand. CCK peptides, however, are also ligands for the CCK-B receptors that do not require ligand sulfation. Consequently, unsulfated CCK peptides may act via CCK-B receptors. Since in vivo occurrence of unsulfated products of proCCK with an intact α-amidated C-terminal tetrapeptide sequence (-Trp-Met-Asp-PheNH(2)) has been reported, it is likely that unsulfated CCK peptides constitute a separate hormone system that acts via CCK-B receptors. This review discusses the occurrence, molecular forms, and possible physiological as well as pathophysiological significance of unsulfated CCK peptides.     

Activation of Notch-1 enhances epithelial-mesenchymal transition in gefitinib-acquired resistant lung cancer cells

Despite an initial response to EGFR tyrosine kinase inhibitors (EGFR-TKI) in EGFR mutant lung cancer, most patients eventually become resistant and result in treatment failure. Recent studies have shown that epithelial to mesenchymal transition (EMT) is associated with drug resistance and cancer cell metastasis. Strong multiple gene signature data indicate that EMT acts as a determinant of insensitivity to EGFR-TKI. However, the exact mechanism for the acquisition of the EMT phenotype in EGFR-TKI resistant lung cancer cells remains unclear. In the present study, we showed that the expression of Notch-1 was highly upregulated in gefitinib-resistant PC9/AB2 lung cancer cells. Notch-1 receptor intracellular domain (N1IC), the activated form of the Notch-1 receptor, promoted the EMT phenotype in PC9 cells. Silencing of Notch-1 using siRNA reversed the EMT phenotype and restored sensitivity to gefitinib in PC9/AB2 cells. Moreover, Notch-1 reduction was also involved in inhibition of anoikis as well as colony-formation activity of PC9/AB2 cells. Taken together, these results provide strong molecular evidence that gefitinib-acquired resistance in lung cancer cells undergoing EMT occurs through activation of Notch-1 signaling. Thus, inhibition of Notch-1 can be a novel strategy for the reversal of the EMT phenotype thereby potentially increasing therapeutic drug sensitivity to lung cancer cells.     

Conformation and structure of 2-amino-8-(β-d-ribofuranosyl)imidazo [1,2-a]-s-triazin-4-one (5-aza-7-deaza guanosine), a potent antiviral nucleoside

The crystal and molecular structure of one imidazo[1,2-a]-s-triazine nucleoside and its antiviral activity are described. The crystal structure of 2-amino-8-(β-d-ribofuranosyl)imidazo-[1,2-a]-s-triazin-4-one monohydrate (C₁₀H₁₃N₅O₅·H₂O) was solved by X-ray counter data. The compound crystallizes in the monoclinic space group P2₁ with cell dimensions a = 7.353 (1), b = 6.465 (1), c = 13.701 (1) Å, β = 104.64 (1)°. The structure was solved by direct methods and refined by full matrix least-squares technique to a final value of the conventional R-factor of 0.049 using 1998 observed intensities. The orientation of the base relative to the sugar ring defined in terms of rotation about the C(1′)-N(8) glycosyl bond is anti (47.8°). The ribose moiety exhibits C(2′)-endo, ²E conformation. The conformation around C(4′)-C(5′) is gauche^?. Molecular packing is dominated by hydrogen bonds. Base stacking occurs long the b axis. 5-Aza-7-deazaguanosine has shown a marked antiviral activity in vitro against herpes simplex virus despite the fact that N(3) is effective as the hydrogen acceptor only.     

Magnetic anisotropy of the radula of chiton Acanthochiton rubrolinestus LISCHKE

The magnetic anisotropy of the whole radula, the major lateral radula teeth, and magnetic material in the major lateral radula teeth of the chiton Acanthochiton rubrolinestus LISCHKE have been studied by a magnetic torque meter and superconducting quantum interference device (SQUID) magnetometer. The length and width axes of the teeth are the easily magnetized axes, while the thickness axis is difficult to magnetize. The width and thickness axes of the radula are the easily magnetized axes, and the length axis is difficult to magnetize. The measurement results of the whole radula and the major lateral radula teeth agree well with each other. The magnetic anisotropy of the magnetic material is given as well as a possible distribution of the magnetic material in the major lateral radula teeth.     

2D differential in-gel electrophoresis for the identification of esophageal scans cell cancer-specific protein markers

The reproducibility of conventional two-dimensional (2D) gel electrophoresis can be improved using differential in-gel electrophoresis (DIGE), a new emerging technology for proteomic analysis. In DIGE, two pools of proteins are labeled with 1-(5-carboxypentyl)-1'-propylindocarbocyanine halide (Cy3) N-hydroxy-succinimidyl ester and 1-(5-carboxypentyl)-1'-methylindodi-carbocyanine halide (Cy5) N-hydroxysuccinimidyl ester fluorescent dyes, respectively. The labeled proteins are mixed and separated in the same 2D gel. 2D DIGE was applied to quantify the differences in protein expression between laser capture microdissection-procured esophageal carcinoma cells and normal epithelial cells and to define cancer-specific and normal-specific protein markers. Analysis of the 2D images from protein lysates of approximately 250,000 cancer cells and normal cells identified 1038 protein spots in cancer cell lysates and 1088 protein spots in normal cell lysates. Of the detected proteins, 58 spots were up-regulated by >3-fold and 107 were down-regulated by >3-fold in cancer cells. In addition to previously identified down-regulated protein annexin I, tumor rejection antigen (gp96) was found up-regulated in esophageal squamous cell cancer. Global quantification of protein expression between laser capture-microdissected patient-matched cancer cells and normal cells using 2D DIGE in combination with mass spectrometry is a powerful tool for the molecular characterization of cancer progression and identification of cancer-specific protein markers.     

Polymorphic microsatellite DNA markers from the marine gastropod Littorina saxatilis

Seven polymorphic microsatellite loci are described in the marine intertidal gastropod Littorina saxatilis. Preliminary data on allelic variation of these loci in a White Sea population of L. saxatilis are presented in order to assess their potential utility as high‐resolution genetic markers for this model species.     

Effects of temperature on simultaneous nitrification and denitrification via nitrite in a sequencing batch biofilm reactor

A laboratory scale experiment was described in this paper to enhance biological nitrogen removal by simultaneous nitrification and denitrification (SND) via nitrite with a sequencing batch biofilm reactor (SBBR). Under conditions of total nitrogen (TN) about 30 mg/L and pH ranged 7.15–7.62, synthetic wastewater was cyclically operated within the reactor for 110 days. Optimal operation conditions were established to obtain consistently high TN removal rate and nitrite accumulation ratio, which included an optimal temperature of 31 °C and an aeration time of 5 h under the air flow of 50 L/h. Stable nitrite accumulation could be realized under different temperatures and the nitrite accumulation ratio increased with an increase of temperature from 15 to 35 °C. The highest TN removal rate (91.9%) was at 31 °C with DO ranged 3–4 mg/L. Process control could be achieved by observing changes in DO and pH to judge the end-point of oxidation of ammonia and SND.