Formal Comment to Pettengill: The Time to Most Recent Common Ancestor Does Not (Usually) Approximate the Date of Divergence

In 2013 Zhou et al. concluded that Salmonella enterica serovar Agona represents a genetically monomorphic lineage of recent ancestry, whose most recent common ancestor existed in 1932, or earlier. The Abstract stated ‘Agona consists of three lineages with minimal mutational diversity: only 846 single nucleotide polymorphisms (SNPs) have accumulated in the non-repetitive, core genome since Agona evolved in 1932 and subsequently underwent a major population expansion in the 1960s.’ These conclusions have now been criticized by Pettengill, who claims that the evolutionary models used to date Agona may not have been appropriate, the dating estimates were inaccurate, and the age of emergence of Agona should have been qualified by an upper limit reflecting the date of its divergence from an outgroup, serovar Soerenga. We dispute these claims. Firstly, Pettengill’s analysis of Agona is not justifiable on technical grounds. Secondly, an upper limit for divergence from an outgroup would only be meaningful if the outgroup were closely related to Agona, but close relatives of Agona are yet to be identified. Thirdly, it is not possible to reliably date the time of divergence between Agona and Soerenga. We conclude that Pettengill’s criticism is comparable to a tempest in a teapot.     

The protective effect of cycloastragenol on aging mouse circadian rhythmic disorder induced by d-galactose

Aging process in mammals is associated with a decline in amplitude and a long period of circadian behaviors which are regulated by a central circadian regulator in the suprachiasmatic nucleus (SCN) and local oscillators in peripheral tissues. It is unclear whether enhancing clock function can retard aging. Using fibroblasts expressing per2::lucSV and senescent cells, we revealed cycloastragenol (CAG), a natural aglycone derivative from astragaloside IV, as a clock amplitude enhancing small molecule. CAG could activate telomerase to antiaging, but no reports focused on its effects on circadian rhythm disorders in aging mice. Here we analyze the potential effects of CAG on d -galactose-induced aging mice on the circadian behavior and expression of clock genes. For this purpose, CAG (20 mg/kg orally), was administered daily to d -galactose (150 mg/kg, subcutaneous) mice model of aging for 6 weeks. An actogram analysis of free-running activity of these mice showed that CAG significantly enhances the locomotor activity. We further found that CAG increase expressions of per2 and bmal1 genes in liver and kidney of aging mouse. Furthermore, CAG enhanced clock protein BMAL1 and PER2 levels in aging mouse liver and SCN. Our results indicated that the CAG could restore the behavior of circadian rhythm in aging mice induced by d -galactose. These data of present study suggested that CAG could be used as a novel therapeutic strategy for the treatment of age-related circadian rhythm disruption.     

Ant assemblage composition explains high predation pressure on artificial caterpillars during early night

1. Predator–prey interactions, especially those involving herbivorous insects, are of great importance in maintaining biodiversity. Predation pressure varies temporally in response to prey availability and activity. However, little is known about the patterns and drivers of fluctuations in predation pressure at fine temporal scales. 2. Artificial caterpillars (placed on plant leaves at breast height) were used to assess changes in predation pressure across four time intervals of the day in a monsoonal tropical rainforest in south-west China. The study examined how assemblage composition of arboreal ants, the dominant predators, changed across the same time intervals. The potential linkages between biotic (arboreal ants) and abiotic (temperature and light intensity) factors with predation rate were evaluated. 3. Predation rate on caterpillars during the early part of the night (19.00–01.00 hours) was significantly higher than in the morning, afternoon, or late night. Ant assemblage composition, rather than species richness or total abundance, best explained the variations in predation rate on artificial caterpillars. 4. The results help to strengthen understanding of trophic interactions by demonstrating that predation pressure fluctuates at finer timescales than previously tested, and that a particular set of ant species may play major roles in predation on caterpillars and possibly other organisms.     

Rock paper scissors: CRISPR/Cas9-mediated interference with geminiviruses in plants

<正>Geminiviruses are a group of circular single-stranded DNA viruses that constitute the largest family of plant viruses.Many diseases resulting from geminivirus infections, such as maize streak disease, cassava mosaic disease, tomato yellow leaf curl disease and cotton leaf curl diseases, cause significant problems in terms of economic losses, posing a serious threat to global crop productivity (Hanley-Bowdoin et al., 2013; Yang et al., 2019). As obligate intracellular     

Depression among Migrant and Left-Behind Children in China in Relation to the Quality of Parent-Child and Teacher-Child Relationships

The objective of this study was to examine rates of depression among migrant children (MC) and left-behind children (LBC) as compared to non-left-behind children (NLBC) and also to examine the relationship between depression among these children and the quality of their parent-child and teacher-child relationships. This study collected data from a large sample of 3,759 children aged from 8 to 17 years, including 824 who had been left behind by one parent (LBCO), 423 who had been left behind by both parents (LBCB), 568 MC and 1944 NLBC. Children’s Depression Inventory–Short Form was used to measure child depression. Parent-Child Relationship Scale (PCRS) and Teacher-Child Relationship Scale (TCRS) were used to measure the quality of parent-child and teacher-child relationships, respectively. The results showed that the prevalence of depression was 10.5% among NLBC, 13.1% among LBCO, 16.1% among LBCB, and 20.1% among MC. Depression was related to parent-child relationship quality and teacher-child relationship quality. Negative parent-child relationship was more relevant to depression than negative teacher-child relationship among LBCB, while negative teacher-child relationship was the most correlated with depression among MC.     

Indoor environmental study and post occupancy evaluation in an office environment

1. 1. The objective of this paper is to investigate the indoor environment from the viewpoint of interaction between physical environment and the human responses. The field survey has been conducted over 1 year.

2. 2. A continuous measurement has been carried out for 1 week and distribution of variables have been measured for 1 day.

3. 3. The attitude of workers was investigated by a questionnaire.

4. 4. As the result, average luminance represented more than 1000 lx in the new building, in contrast with less tha 300 lx in the existing building.

5. 5. There was a significant difference of the occupants' response to the light environment between the two buildings.

6. 6. Measured thermal conditions are on the edge of the ASHRAE comfort envelope in summer, and in the neighborhood of the lower dry limit of the envelope in spring.

7. 7. The occupants' evaluations were remarkably changed before and after the moving. The office environment is better than that of the factory.

Genome‐scale identification of miRNA–mRNA and miRNA–lncRNA interactions in domestic animals

Domestic animals show considerable genetic diversity. Previous studies suggested that animal phenotypes were affected by miRNA–mRNA interplay, but these studies focused mainly on the analysis of one or several miRNA–mRNA interactions. However, in this study, we investigated miRNA–mRNA and miRNA–lncRNA interactions on a genomic scale using miranda and targetscan algorithms. There has been strong directional artificial selection practiced during the domestication of animals. Thus, we investigated SNPs that were located in miRNAs and miRNA binding sites and found that several SNPs located in 3′‐UTRs of mRNAs had the potential to affect miRNA–mRNA interactions. In addition, a database, named miRBond, was developed to provide visualization, analysis and downloading of the resulting datasets. Our results open the way to further experimental verification of miRNA–mRNA and miRNA–lncRNA interactions as well as the influence of SNPs upon such interplay.     

Identification of chalcone synthase genes and their expression patterns reveal pollen abortion in cotton

Chalcone synthase (CHS) is a key enzyme and producing flavonoid derivatives as well play a vital roles in sustaining plant growth and development. However, the systematic and comprehensive analysis of CHS genes in island cotton (G. barbadense) has not been reported yet especially response to cytoplasmic male sterility (CMS). To fill this knowledge gap, a genome-wide investigation of CHS genes were studied in island cotton. A total of 20 GbCHS genes were identified and grouped into five GbCHSs. The gene structure analysis revealed that most of GbCHS genes consisted of two exons and one intron, and 20 motifs were identified. Twenty five pairs duplicated events (12 GbCHS genes) were identified including 23 segmental duplication pairs and two tandem duplication events, representing that GbCHS gene family amplification mainly owned to segmental duplication events and evolving slowly. Gene expression analysis exhibited that the GbCHS family genes presented a diversity expression patterns in various organs of cotton. Coupled with functional predictions and gene expression, the abnormal expression of GbCHS06, 10, 16 and 19 might be associated with pollen abortion of CMS line in island cotton. Conclusively, GbCHS genes exhibited diversity and conservation in many aspects, which will help to better understand functional studies and a reference for CHS research in island cotton and other plants.     

Effects of SOX2 on Proliferation,Migration and Adhesion of Human Dental Pulp Stem Cells

As a key factor for cell pluripotent and self-renewing phenotypes, SOX2 has attracted scientists’ attention gradually in recent years. However, its exact effects in dental pulp stem cells (DPSCs) are still unclear. In this study, we mainly investigated whether SOX2 could affect some biological functions of DPSCs. DPSCs were isolated from the dental pulp of human impacted third molar. SOX2 overexpressing DPSCs (DPSCs-SOX2) were established through retroviral infection. The effect of SOX2 on cell proliferation, migration and adhesion ability was evaluated with CCK-8, trans-well system and fibronectin-induced cell attachment experiment respectively. Whole genome expression of DPSCs-SOX2 was analyzed with RNA microarray. Furthermore, a rescue experiment was performed with SOX2-siRNA in DPSC-SOX2 to confirm the effect of SOX2 overexpression in DPSCs. We found that SOX2 overexpression could result in the enhancement of cell proliferation, migration, and adhesion in DPSCs obviously. RNA microarray analysis indicated that some key genes in the signal pathways associated with cell cycle, migration and adhesion were upregulated in different degree, and the results were further confirmed with qPCR and western-blot. Finally, DPSC-SOX2 transfected with SOX2-siRNA showed a decrease of cell proliferation, migration and adhesion ability, which further confirmed the biological effect of SOX2 in human DPSCs. This study indicated that SOX2 could improve the cell proliferation, migration and adhesion ability of DPSCs through regulating gene expression about cell cycle, migration and adhesion, and provided a novel strategy to develop seed cells with strong proliferation, migration and adhesion ability for tissue engineering.