Genomic abundance is not predictive of tandem repeat localization in grass genomes.

Highly repetitive regions have historically posed a challenge when investigating sequence variation and content. High-throughput sequencing has enabled researchers to use whole-genome shotgun sequencing to estimate the abundance of repetitive sequence, and these methodologies have been recently applied to centromeres. Previous research has investigated variation in centromere repeats across eukaryotes, positing that the highest abundance tandem repeat in a genome is often the centromeric repeat. To test this assumption, we used shotgun sequencing and a bioinformatic pipeline to identify common tandem repeats across a number of grass species. We find that de novo assembly and subsequent abundance ranking of repeats can successfully identify tandem repeats with homology to known tandem repeats. Fluorescent in-situ hybridization shows that de novo assembly and ranking of repeats from non-model taxa identifies chromosome domains rich in tandem repeats both near pericentromeres and elsewhere in the genome

Aero Engine Fault Diagnosis Using an Optimized Extreme Learning Machine

A new extreme learning machine optimized by quantum-behaved particle swarm optimization (QPSO) is developed in this paper. It uses QPSO to select optimal network parameters including the number of hidden layer neurons according to both the root mean square error on validation data set and the norm of output weights. The proposed Q-ELM was applied to real-world classification applications and a gas turbine fan engine diagnostic problem and was compared with two other optimized ELM methods and original ELM, SVM, and BP method. Results show that the proposed Q-ELM is a more reliable and suitable method than conventional neural network and other ELM methods for the defect diagnosis of the gas turbine engine

Amplification and adaptation of centromeric repeats in polyploid switchgrass species.

Centromeres in most higher eukaryotes are composed of long arrays of satellite repeats from a single satellite repeat family. Why centromeres are dominated by a single satellite repeat and how the satellite repeats originate and evolve are among the most intriguing and long-standing questions in centromere biology. We identified eight satellite repeats in the centromeres of tetraploid switchgrass (Panicum virgatum). Seven repeats showed characteristics associated with classical centromeric repeats with monomeric lengths ranging from 166 to 187 bp. Interestingly, these repeats share an 80-bp DNA motif. We demonstrate that this 80-bp motif may dictate translational and rotational phasing of the centromeric repeats with the cenH3 nucleosomes. The sequence of the last centromeric repeat, Pv156, is identical to the 5S ribosomal RNA genes. We demonstrate that a 5S ribosomal RNA gene array was recruited to be the functional centromere for one of the switchgrass chromosomes. Our findings reveal that certain types of satellite repeats, which are associated with unique sequence features and are composed of monomers in mono-nucleosomal length, are favorable for centromeres. Centromeric repeats may undergo dynamic amplification and adaptation before the centromeres in the same species become dominated by the best adapted satellite repeat

Effects of Pure Oxygen on the Rate of Skin Browning and Energy Status in Longan Fruit

Postharvest pericarp browning is one of the main problems resulting in reduced shelf life of longan fruit. Experiments were conducted to examine the changes in concentrations of adenosine triphosphate (ATP), adenosine diphosphate (ADP) and adenosine monophosphate (AMP), energy charge levels and activities of polyphenol oxidase (PPO) and peroxidase (POD) in relation to pericarp browning of longan fruit. Fruit kept for 6 days in pure oxygen atmosphere at 28 C showed lower browning indices and higher ATP concentrations but lower AMP concentrations and higher respiratory rates, compared to those kept in air. While energy charge decreased during storage, the decrease was delayed markedly by exposure to pure oxygen. There was a lower energy charge in the browned fruit, which was associated with rapid increase in malondialdehyde concentration. Enhanced respiration of longan fruit exposed to pure oxygen can result in the production of ATP. However, fruit exposed to pure oxygen exhibited higher activities of PPO and POD, which was not associated with reduced skin browning inhibition. These results supported the hypothesis that skin browning of postharvest longan fruit may be a consequence of membrane injury caused by the lack of maintenance energy

Effects of Pure Oxygen on the Rate of Skin Browning and Energy Status in Longan Fruit

Postharvest pericarp browning is one of the main problems resulting in reduced shelf life of longan fruit. Experiments were conducted to examine the changes in concentrations of adenosine triphosphate (ATP), adenosine diphosphate (ADP) and adenosine monophosphate (AMP), energy charge levels and activities of polyphenol oxidase (PPO) and peroxidase (POD) in relation to pericarp browning of longan fruit. Fruit kept for 6 days in pure oxygen atmosphere at 28 C showed lower browning indices and higher ATP concentrations but lower AMP concentrations and higher respiratory rates, compared to those kept in air. While energy charge decreased during storage, the decrease was delayed markedly by exposure to pure oxygen. There was a lower energy charge in the browned fruit, which was associated with rapid increase in malondialdehyde concentration. Enhanced respiration of longan fruit exposed to pure oxygen can result in the production of ATP. However, fruit exposed to pure oxygen exhibited higher activities of PPO and POD, which was not associated with reduced skin browning inhibition. These results supported the hypothesis that skin browning of postharvest longan fruit may be a consequence of membrane injury caused by the lack of maintenance energy