Synonymous Codon Usage Bias in Plant Mitochondrial Genes Is Associated with Intron Number and Mirrors Species Evolution

Synonymous codon usage bias (SCUB) is a common event that a non-uniform usage of codons often occurs in nearly all organisms. We previously found that SCUB is correlated with both intron number and exon position in the plant nuclear genome but not in the plastid genome; SCUB in both nuclear and plastid genome can mirror the evolutionary specialization. However, how about the rules in the mitochondrial genome has not been addressed. Here, we present an analysis of SCUB in the mitochondrial genome, based on 24 plant species ranging from algae to land plants. The frequencies of NNA and NNT (A- and T-ending codons) are higher than those of NNG and NNC, with the strongest preference in bryophytes and the weakest in land plants, suggesting an association between SCUB and plant evolution. The preference for NNA and NNT is more evident in genes harboring a greater number of introns in land plants, but the bias to NNA and NNT exhibits even among exons. The pattern of SCUB in the mitochondrial genome differs in some respects to that present in both the nuclear and plastid genomes.     

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.     

模拟穿透雨减少对锐齿栎(Quercus aliena var. acuteserrata)树干液流密度的影响

降水格局变化是全球气候变化的重要特征之一,未来气候变化下,较为频繁和严峻的干旱将威胁地球中纬度部分地区的森林,但森林植被如何响应季节性干旱胁迫及其机制尚不清楚。北亚热带-暖温带过渡区分布着以锐齿栎(Quercus aliena var.acuteserrata)为优势树种的落叶阔叶林,研究其水分蒸腾代谢过程对干旱的响应是评估气候变化对过渡区天然落叶阔叶林生态系统水碳影响的关键科学问题。在典型的锐齿栎天然林中通过开展模拟穿透雨减少大型野外实验,采用Granier热扩散式探针技术监测锐齿栎树干液流密度的动态变化,研究了不同径级锐齿栎树干液流密度对模拟干旱的响应规律。结果表明:(1)穿透雨减少对树干液流密度的影响呈现季节变异。在7月份,林内穿透雨减少显著降低了锐齿栎的树干液流密度,但生长季后期的10月份林内穿透雨减少反而使锐齿栎树干液流密度显著升高。(2)不同径级的锐齿栎树干液流密度在生长季内对干旱有不同的响应,特别是小径级的树干液流密度与其他径级有较多的不同。小径级的锐齿栎树干液流密度在5、7月份表现为减雨样地显著小于对照样地,在9、10月份则表现为减雨样地显著大于对照样地。中径级的锐齿栎树干液流密度在5、10月份表现为减雨样地显著大于对照样地,在7月份则表现为减雨样地极显著小于对照样地。大径级的锐齿栎树干液流密度在6、7月份表现为减雨样地显著小于对照样地,在10月份则表现为减雨样地显著大于对照样地。     

Phylogenetics of Tribe Collabieae (Orchidaceae,Epidendroideae) Based on Four Chloroplast Genes with Morphological Appraisal

Collabieae (Orchidaceae) is a long neglected tribe with confusing tribal and generic delimitation and little-understood phylogenetic relationships. Using plastid matK, psaB, rbcL, and trnH-psbA DNA sequences and morphological evidence, the phylogenetic relationships within the tribe Collabieae were assessed as a basis for revising their tribal and generic delimitation. Collabieae (including the previously misplaced mycoheterotrophic Risleya) is supported as monophyletic and nested within a superclade that also includes Epidendreae, Podochileae, Cymbidieae and Vandeae. Risleya is nested in Collabiinae and sister to Chrysoglossum, a relationship which, despite their great vegetative differences, is supported by floral characters. Ania is a distinct genus supported by both morphological and molecular evidence, while redefined Tainia includes Nephelaphyllum and Mischobulbum. Calanthe is paraphyletic and consists four clades; the genera Gastrorchis, Phaius and Cephalantheropsis should be subsumed within Calanthe. Calanthe sect. Ghiesbreghtia is nested within sect. Calanthe, to which the disputed Calanthe delavayi belongs as well. Our results indicate that, in Collabieae, habit evolved from being epiphytic to terrestrial.     

A simplified diphenylamine colorimetric method for growth quantification

Cell growth needs to be monitored in biological studies and bioprocess optimization. In special circumstances, such as microbial fermentations in media containing insoluble particles, accurate cell growth quantification is a challenge with current methods. Only the Burton method is applicable in such circumstances. The original Burton method was previously simplified by adopting a two-step sample pretreatment in perchloric acid procedure to eliminate the need for DNA extraction. Here, we further simplified the Burton method by replacing the previous two-step perchloric acid pretreatment with a new and one-step diphenylamine reagent pretreatment. The reliability and accuracy of this simplified method were assessed by measuring the biomass of four model microorganisms: Escherichia coli, Streptomyces clavuligerus, Saccharomyces cerevisiae, and Trichoderma reesei grown in normal media or those containing solid particles. The results demonstrate that this new simplified method performs comparably to the conventional methods, such as OD₆₀₀ or the previously modified Burton method, and is much more sensitive than the dry weight method. Overall, the new method is simple, reliable, easy to perform, and generally applicable in most circumstances, and it reduces the operation time from more than 12 h (for the previously simplified Burton method) to about 2 h.     

Differential expression of microRNAs in mouse liver under aberrant energy metabolic status

Despite years of effort, exact pathogenesis of nonalcoholic fatty liver disease (NAFLD) remains obscure. To gain an insight into the regulatory roles of microRNAs (miRNAs) in aberrant energy metabolic status and pathogenesis of NAFLD, we analyzed the expression of miRNAs in livers of ob/ob mice, streptozotocin (STZ)-induced type 1 diabetic mice, and normal C57BL/6 mice by miRNA microarray. Compared with normal C57BL/6 mice, ob/ob mice showed upregulation of eight miRNAs and downregulation of four miRNAs in fatty livers. Upregulation of miR-34a and downregulation of miR-122 was found in livers of STZ-induced diabetic mice. These results demonstrate that distinct miRNAs are strongly dysregulated in NAFLD and hyperglycemia. Comparison between miRNA expressions in livers of ob/ob mice and STZ-administered mice further revealed upregulation of four miRNAs and downregulation of two miRNAs in livers of ob/ob mice, indicating that these miRNAs may represent a molecular signature of NAFLD. A distinctive miRNA expression pattern was identified in ob/ob mouse liver, and hierarchical clustering of this pattern could clearly discriminate ob/ob mice from either normal C57BL/6 mice or STZ-administered mice. These findings suggest an important role of miRNAs in hepatic energy metabolism and implicate the participation of miRNAs in the pathophysiological processes of NAFLD.