Molecular phylogeny and habitat diversification of the genus Farfugium (Asteraceae) based on nuclear rDNA and plastid DNA

Background and Aims

Farfugium (Asteraceae) is a small genus that contains the two species F. japonicum and F. hiberniflorum and is distributed along a long archipelago in east Asia. The common taxon, F. japonicum, includes three varieties associated with a wide range of habitats, including forest understorey (sciophytes), coastal crag (heliophytes) and riverbed (rheophytes). Leaf shape is an important taxonomic character within this genus and is associated with the habitat.

Methods

Twenty populations that included all Farfugium taxa were collected throughout its range. Leaf morphology was measured to determine differences amongst the taxa. Phylogenetic analyses based on sequences of the internal transcribed spacer of nuclear rDNA and four plastid DNA regions (matK, trnL-trnF, trnH-psbA and rpl20-rps12) were conducted separately.

Key Results

Leaf morphology was significantly different amongst taxa, but morphological variations were partly explained by adaptation to certain environmental conditions that each population inhabited. Molecular phylogenies for the nDNA internal transcribed spacer and cpDNA were consistent in classifying F. hiberniflorum and the Taiwanese var. formosanum, whilst suggesting polyphyletic origins for the rheophyte, sciophyte and heliophyte taxa. All samples from the southern Ryukyus (Japan) and Taiwan clustered into a monophyletic group, which corroborates the land configuration theory involving Quaternary land-bridge formation and subsequent fragmentation into islands. The incongruence between the two DNA datasets may imply traces of introgressive hybridization and/or incomplete lineage sorting.

Conclusions

The occurrence of rheophyte, sciophyte and heliophyte plants within Farfugium may be attributable to their isolation on islands and subsequent adaptation to the riparian, coastal crag and forest understorey environments, following their migration over the Quaternary land-bridge formation along their distribution range. Nearly identical DNA sequences coupled with highly divergent morphologies amongst these taxa suggest that diversification was rapid.     

Regulation of tillering in sorghum: genotypic effects

MethodsFive sorghum hybrids, derived from inbred lines with a common genetic background and with similar phenology and plant height but contrasting tillering, were grown in five experiments. The experiments covered a wide range in radiation and temperature conditions, so that number of tillers produced varied significantly. Data on leaf area, tiller number, and biomass accumulation and partitioning were collected at regular intervals. To quantify internal plant competition for carbohydrates, a carbohydrate supply–demand index (S/D_index) was developed and related to variation in tillering.ConclusionsThe results support the hypothesis that genotypic differences in tillering were associated with differences in plant carbon S/D balance, associated with differences in leaf size and in the threshold at which tillers grow out. The results provide avenues for phenotyping of mapping populations to identify genomic regions regulating tillering. Incorporating the results in crop growth simulation models could provide insight into the complex genotype-by-management-by-environment interactions associated with drought adaptation.     

Ozone exposure during growth affects the feeding value of rice shoots

Rising tropospheric ozone concentrations have been observed in many Asian countries in recent years. Ozone pollution reduces the yield of agricultural crops but may also affect crop quality. This study aimed at estimating the effect of ozone exposure on feeding quality of rice shoots for ruminant herbivores. Rice plants from two genotypes differing in ozone tolerance were exposed to ozone at a concentration of 120 nl/l for 18 days, and feeding value was determined by chemical analyses and in vitro incubation in rumen fluid. Rice biomass was reduced by an average of 24% in the ozone treatment as compared to the control. Moreover, ozone exposure affected various feed quality parameters. Crude protein content was lower in ozone treated plants (P<0.05). Potential gas production during the in vitro incubation for 96 h also dropped (P<0.01) due to ozone treatment, indicating reduced digestibility of the plant materials. This was explained with an increase in the antinutritive components lignin (P<0.05) and phenolics (P<0.001) due to ozone exposure. An ozone tolerant genotype exhibited a more pronounced increase in phenolics, suggesting that this may constitute a stress defense mechanism. Our results suggest that ozone may affect the feeding value of cereal straws and calls for further research in this direction.     

The evolutionary-developmental analysis of plant microRNAs

MicroRNAs (miRNAs) control many important aspects of plant development, suggesting these molecules may also have played key roles in the evolution of developmental processes in plants. However, evolutionary-developmental (evo-devo) studies of miRNAs have been held back by technical difficulties in gene identification. To help solve this problem, we have developed a two-step procedure for the efficient identification of miRNA genes in any plant species. As a test case, we have studied the evolution of the MIR164 family in the angiosperms. We have identified novel MIR164 genes in three species occupying key phylogenetic positions and used these, together with published sequence data, to partially reconstruct the evolution of the MIR164 family since the last common ancestor of the extant flowering plants. We use our evolutionary reconstruction to discuss potential roles for MIR164 genes in the evolution of leaf shape and carpel closure in the angiosperms. The techniques we describe may be applied to any miRNA family and should thus enable plant evo-devo to begin to investigate the contributions miRNAs have made to the evolution of plant development.     

引种保护植物对西双版纳极端冷年的春季物候响应

气温被普遍认为是春季物候期最主要的控制因子之一,然而低温对植物物候的影响效应一直都存在不同的观点。西双版纳由于地处热带地区的北缘,其气温相对于赤道附近的热带地区较低。自1959年以来,西双版纳热带植物园引入了来自世界各个热带地区的4万余种植物进行保护,之前的研究证明西双版纳的低温对这些引种植物的生长有很大影响。因此,1974年西双版纳出现的极端低温势必对引种植物造成极大威胁,同时也是对这些植物低温适应能力的一个考验。通过对比43种引种植物物候期（生长抽梢期与开花期）在1974年与常年的差异情况,分析不同来源（热带亚洲、热带美洲与热带非洲）引种植物对西双版纳低温的适应性。结果表明,经历西双版纳1974年初的极端低温之后,使81%的引种植物生长抽梢期提前,同时也造成35%的引种植物在该年没有开花;而植物生长抽梢提前的主要原因则是极端低温以及低温过后气温迅速回升。引种植物均能顺利度过1974年的最冷时期,并出现生长抽梢物候,这意味着引种植物在经历极端低温之后都能够进行正常的生长活动,但极端低温对引种植物繁殖活动的不利影响大于其对生长活动的影响;引种植物对西双版纳极端低温的适应能力由大到小顺序依次为：亚洲来源植物〉美洲来源植物〉非洲来源植物。因此在迁地保护植物的选择过程中,应多选择亚洲热带植物,其次为美洲热带植物,而对非洲热带植物的引入则需谨慎考察。     

rimJ基因缺失不影响大肠杆菌BL21(DE3)生长的温度敏感性

目的:研究rimJ基因对大肠杆菌BL21(DE3)菌株生长的温度敏感性的影响。方法:利用SceⅠ-Red同源重组技术将大肠杆菌BL21(DE3)基因组中的rimJ基因缺失,得到rimJ缺失突变菌;比较缺失突变株和原始菌株在不同温度(25℃、37℃、42℃)下的最大比生长速率,利用统计学方法分析rimJ基因的缺失对BL21(DE3)菌株生长的温度敏感性是否有影响。结果:rimJ基因被成功敲除;统计分析结果表明缺失突变株和原始菌株的最大比生长速率没有明显区别。结论:rimJ基因缺失对大肠杆菌BL21(DE3)生长的温度敏感性无影响。     

Critical oxygen tension increases during digestion in the perch Perca fluviatilis

Oxygen uptake () and critical oxygen tension (P_crit) were measured in resting perch Perca fluviatilis that were either fasting or digesting. Digestion caused to double (from 61 to 117 mg O₂ kg^?1h^?1) and was associated with a rise in P_crit (from 3·4 to 4·9 kPa), showing that the animal's digestive state must be considered when assessing the effect of hypoxia in natural conditions, and when defining optimal oxygen conditions in aquaculture.     

Alkali‐based AFEX pretreatment for the conversion of sugarcane bagasse and cane leaf residues to ethanol

Sugarcane is one of the major agricultural crops cultivated in tropical climate regions of the world. Each tonne of raw cane production is associated with the generation of 130 kg dry weight of bagasse after juice extraction and 250 kg dry weight of cane leaf residue postharvest. The annual world production of sugarcane is ～1.6 billion tones, generating 279 MMT tones of biomass residues (bagasse and cane leaf matter) that would be available for cellulosic ethanol production. Here, we investigated the production of cellulosic ethanol from sugar cane bagasse and sugar cane leaf residue using an alkaline pretreatment: ammonia fiber expansion (AFEX). The AFEX pretreatment improved the accessibility of cellulose and hemicelluloses to enzymes during hydrolysis by breaking down the ester linkages and other lignin carbohydrate complex (LCC) bonds and the sugar produced by this process is found to be highly fermentable. The maximum glucan conversion of AFEX pretreated bagasse and cane leaf residue by cellulases was ～85%. Supplementation with hemicellulases during enzymatic hydrolysis improved the xylan conversion up to 95–98%. Xylanase supplementation also contributed to a marginal improvement in the glucan conversion. AFEX‐treated cane leaf residue was found to have a greater enzymatic digestibility compared to AFEX‐treated bagasse. Co‐fermentation of glucose and xylose, produced from high solid loading (6% glucan) hydrolysis of AFEX‐treated bagasse and cane leaf residue, using the recombinant Saccharomyces cerevisiae (424A LNH‐ST) produced 34–36 g/L of ethanol with 92% theoretical yield. These results demonstrate that AFEX pretreatment is a viable process for conversion of bagasse and cane leaf residue into cellulosic ethanol. Biotechnol. Bioeng. 2010;107: 441–450. © 2010 Wiley Periodicals, Inc.     

Quantification of non‐specific binding of magnetic micro‐ and nanoparticles using cell tracking velocimetry: Implication for magnetic cell separation and detection

The maturation of magnetic cell separation technology places increasing demands on magnetic cell separation performance. While a number of factors can cause sub‐optimal performance, one of the major challenges can be non‐specific binding of magnetic nano‐ or microparticles to non‐targeted cells. Depending on the type of separation, this non‐specific binding can have a negative effect on the final purity, the recovery of the targeted cells, or both. In this work, we quantitatively demonstrate that non‐specific binding of magnetic nanoparticles can impart a magnetization to cells such that these cells can be retained in a separation column and thus negatively impact the purity of the final product and the recovery of the desired cells. Through experimental data and theoretical arguments, we demonstrate that the number of MACS magnetic particles needed to impart a magnetization that is sufficient to cause non‐targeted cells to be retained in the column to be on the order of 500–1,000 nanoparticles. This number of non‐specifically bound particles was demonstrated experimentally with an instrument, cell tracking velocimeter, CTV, and it is demonstrated that the sensitivity of the CTV instrument for Fe atoms contained in magnetic nanoparticles on the order of 1 × 10^?15 g/mL of Fe. Biotechnol. Bioeng. 2010;105: 1078–1093. © 2009 Wiley Periodicals, Inc.     

Characterization of cryobiological responses in TF-1 cells using interrupted freezing procedures

Cryopreservation currently is the only method for long-term preservation of cellular viability and function for uses in cellular therapies. Characterizing the cryobiological response of a cell type is essential in the approach to designing and optimizing cryopreservation protocols. For cells used in therapies, there is significant interest in designing cryopreservation protocols that do not rely on dimethyl sulfoxide (Me₂SO) as a cryoprotectant, since this cryoprotectant has been shown to have adverse effects on hematopoietic stem cell (HSC) transplant patients. This study characterized the cryobiological responses of the human erythroleukemic stem cell line TF-1, as a model for HSC. We measured the osmotic parameters of TF-1 cells, including the osmotically-inactive fraction, temperature-dependent membrane hydraulic conductivity and the membrane permeability to 1 M Me₂SO. A two-step freezing procedure (interrupted rapid cooling with hold time) and a graded freezing procedure (interrupted slow cooling without hold time) were used to characterize TF-1 cell recovery during various phases of the cooling process. One outcome of these experiments was high recovery of TF-1 cells cryopreserved in the absence of traditional cryoprotectants. The results of this study of the cryobiology of TF-1 cells will be critical for future understanding of the cryobiology of HSC, and to the design of cryopreservation protocols with specific design criteria for applications in cellular therapies.