Molecular
dynamics (MD) simulations were performed to provide molecular
insight into the aggregation process of graphene oxide (GO) in water.
The aggregation was found to be a point–line–plane
process. Five forces were involved during the process: van der Waals
attraction, electrostatic interaction, hydrogen-bond interaction,
π–π stacking, and the collision of water molecules.
The dominant forces were different in the three stages. The connection
“line” was important to the aggregation process and
the final overlapping area of the GO aggregate. To study the effect
of oxygen content and functional group on the aggregation of GO, four
different GOs were used: C10O1(OH)1(COOH)0.5, C30O1(OH)1(COOH)0.5, C10O1(COOH)0.5, and C10O1(OH)1 (termed OGO, RGO,
GO-COOH, and GO-OH, respectively). RGO aggregated faster than OGO,
and GO-OH aggregated faster than GO-COOH. A quantitative analysis
showed the difference in aggregation rate of these four GOs should
be attributed to the hydrogen bonds. Additionally, the closer GOs
were to each other initially, the faster they aggregated. This study
reveals the aggregation process of GO and will be helpful in understanding
its behavior in water.
MicroRNAs (miRNAs) are endogenous non-coding genes that participate in post-transcription regulation by either degrading mRNA or blocking its translation. It is considered to be very important in regulating insect development and metamorphosis. We conducted a large-scale screening for miRNA genes in the silkworm Bombyx mori using sequence-by-synthesis (SBS) deep sequencing of mixed RNAs from egg, larval, pupal, and adult stages. Of 2,227,930 SBS tags, 1,144,485 ranged from 17 to 25 nt, corresponding to 256,604 unique tags. Among these non-redundant tags, 95,184 were matched to the silkworm genome. We identified 3,750 miRNA candidate genes using a computational pipeline combining RNAfold and TripletSVM algorithms. We confirmed 354 miRNA genes using miRNA microarrays and then performed expression profile analysis on these miRNAs for all developmental stages. While 106 miRNAs were expressed in all stages, 248 miRNAs were egg- and pupa-specific, suggesting that insect miRNAs play a significant role in embryogenesis and metamorphosis. We selected eight miRNAs for quantitative RT-PCR analysis; six of these were consistent with our microarray results. In addition, we searched for orthologous miRNA genes in mammals, a nematode, and other insects and found that most silkworm miRNAs are conserved in insects, whereas only a small number of silkworm miRNAs has orthologs in mammals and the nematode. These results suggest that there are many miRNAs unique to insects.
Current evidences do not support prophylactic antibiotics as a routine treatment for SAP, but the potentially benefited sub-population requires further investigations.
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