Chemically defined medium and <Emphasis Type="Italic">Caenorhabditis elegans</Emphasis>

Background  

C. elegans has been established as a powerful genetic system. Use of a chemically defined medium (C. elegans Maintenance Medium (CeMM)) now allows standardization and systematic manipulation of the nutrients that animals receive. Liquid cultivation allows automated culturing and experimentation and should be of use in large-scale growth and screening of animals.     

Predicting impacts of Arctic climate change: Past lessons and future challenges

General circulation models predict increases in temperature and precipitation in the Arctic as the result of increases in atmospheric carbon dioxide concentrations. Arctic ecosystems are strongly constrained by temperature, and may be expected to be markedly influenced by climate change. Perturbation experiments have been used to predict how Arctic ecosystems will respond to global climatic change, but these have often simulated individual perturbations (e.g. temperature alone) and have largely been confined to the short Arctic summer. The importance of interactions between global change variables (e.g. CO₂, temperature, precipitation) has rarely been examined, and much experimentation has been short-term. Similarly, very little experimentation has occurred in the winter when General circulation models predict the largest changes in climate will take place. Recent studies have clearly demonstrated that Arctic ecosystems are not dormant during the winter and thus much greater emphasis on experimentation during this period is essential to improve our understanding of how these ecosystems will respond to global change. This, combined with more long-term experimentation, direct observation of natural vegetation change (e.g. at the tundra/taiga boundary) and improvements in model predictions is necessary if we are to understand the future nature and extent of Arctic ecosystems in a changing climate.     

基于优化MaxEnt模型的中国紫堇属植物生境适宜性研究

气候变化正深刻地影响着植物的地理分布格局,预测紫堇属植物的潜在适生区有利于认识气候变化对紫堇属植物分布的影响,对制定紫堇属植物的保护策略具有重要意义。以紫堇属植物作为研究对象,基于优化的MaxEnt模型,对1910个紫堇属植物分布点和22个环境因子进行潜在适生区预测,探讨影响紫堇属植物分布的主要环境因子,并预测其在末次盛冰期（last glacial maximum,LGM）、当代（Current）、未来2021-2040年（2040s）、2041-2060年（2060s）、2061-2080年（2080s）和2081-2100年（2100s）2种温室气体排放浓度场景（SSP126和SSP585）下的潜在适生区的空间分布格局及其质心迁移趋势,最后对其保护现状进行了分析。结果表明：（1）最优化模型参数组合为RM=1.4,FC=LQPT,此时MaxEnt模型的复杂度和过拟合都最低,模型预测精度较高,AUC=0.793;（2）由刀切法贡献率、置换贡献率和单因子响应曲线可知影响紫堇属植物地理分布的主要环境因子为气温年较差（bio7）、气温季节性变动系数（bio4）、年降水量（bio12）、平均气温日较差（bio2）,其中温度是影响紫堇属植物分布的最重要环境因子;（3）当前气候条件下紫堇属植物分布的范围几乎涵盖整个中国,在气候分区上看,从北亚热带、南亚热带、中温带、南温带及高原气候区均有分布。然而,各个时期间紫堇属植物的潜在适生区变化较大,其潜在适生区总体呈现向高原气候区及中温带地区扩张的趋势,且面积不断扩大;随着温室气体浓度的增加,适生区的破碎化逐渐严重。质心迁移结果也表明紫堇属植物在未来的潜在适生区总体呈现向西北移动的趋势;（4）我国东喜马拉雅地区及横断山区为紫堇属植物保护的关键地区,然而该地区自然保护区面积较小且破碎化严重,亟待对该地区的紫堇属植物进行保护,同时也应继续加强西北地区自然保护区的建设。     

Survival Tests for r Groups

In this paper we give the generalization of the score tests covering the case of ties and we give examples where the expressions in matrix form are completely specified for the weighted tests and the score tests for the case of r groups. It is worth mentioning that although the score tests are not generally included in the commercial software, these tests should be used if it can be assumed that the censoring mechanism is equal in the r groups or if there is no censoring (Lawless , 1982). We establish the equivalence between “numerators” of these families of tests. As result of this equivalence we define four new tests that complete the classification of score and weighted tests. The Kruskal‐Wallis test (1952) appears as a particular case of the score tests for the case of non‐censoring. A simulation study has been done in order to compare the performance of the tests described in this paper. An example is included to make the understanding of the paper easier.     

Species delineation using Bayesian model-based assignment tests: a case study using Chinese toad-headed agamas (genus <Emphasis Type="Italic">Phrynocephalus</Emphasis>)

Background  

Species are fundamental units in biology, yet much debate exists surrounding how we should delineate species in nature. Species discovery now requires the use of separate, corroborating datasets to quantify independently evolving lineages and test species criteria. However, the complexity of the speciation process has ushered in a need to infuse studies with new tools capable of aiding in species delineation. We suggest that model-based assignment tests are one such tool. This method circumvents constraints with traditional population genetic analyses and provides a novel means of describing cryptic and complex diversity in natural systems. Using toad-headed agamas of the Phrynocephalus vlangalii complex as a case study, we apply model-based assignment tests to microsatellite DNA data to test whether P. putjatia, a controversial species that closely resembles P. vlangalii morphologically, represents a valid species. Mitochondrial DNA and geographic data are also included to corroborate the assignment test results.     

Climate change and cereal aphids: the relative effects of increasing CO2 and temperature on aphid population dynamics

Experimental evidence regarding the responses of cereal aphids to rising atmospheric CO₂ has been ambiguous. Some studies suggest increased population sizes under future CO₂ levels, others suggest decreased population sizes, and still others suggest little or no difference. Recently, Newman et al. (2003) constructed a general mathematical model of the aphid–grass interaction to investigate whether or not we should, in fact, expect a general aphid response to rising CO₂. They concluded that aphid populations are likely to be larger under future CO₂ concentrations if soil N levels are high, the aphid species' nitrogen requirement is low and the aphid species' density‐dependent response in winged morph production is weak. In that model, and in field experiments, CO₂ concentration influences aphid population dynamics through the effect it has on plant quality. However, future CO₂ concentrations are also likely to be accompanied by higher ambient temperatures, a combination that has received little focus to date. In the present paper, the Newman et al. model is used to consider the combined effects of increased CO₂ concentrations and temperature on aphid population sizes. It is concluded that, when both factors are elevated, aphid population dynamics will be more similar to current ambient conditions than expected from the results of experiments studying either factor alone. This result has important implications for future experimentation.     

Phylogenetics and Ecology: As Many Characters as Possible Should Be Included in the Cladistic Analysis1

As many data as possible must be included in any scientific analysis, provided that they follow the logical principles on which this analysis is based. Phylogenetic analysis is based on the basic principle of evolution, i.e., descent with modification. Consequently, ecological characters or any other nontraditional characters must be included in phylogenetic analyses, provided that they can plausibly be postulated heritable. The claim of Zrzavý (1997, Oikos 80, 186–192) or Luckow and Bruneau (1997, Cladistics 13, 145–151) that any character of interest should be included in the analysis is thus inaccurate. Many characters, broadly defined or extrinsic (such as distribution areas), cannot be considered as actually heritable. It is argued that we should better care for the precise definition and properties of characters of interest than decide a priori to include them in any case in the analysis. The symmetrical claim of de Queiroz (1996, Am. Nat. 148, 700–708) that some characters of interest should better be excluded from analyses to reconstruct their history is similarly inaccurate. If they match the logical principles of phylogenetic analysis, there is no acceptable reason to exclude them. The different statistical testing strategies of Zrzavý (1997) and de Queiroz (1996) aimed at justifying inclusion versus exclusion of characters are ill‐conceived, leading respectively to Type II and Type I errors. It is argued that phylogenetic analyses should not be constrained by testing strategies that are downstream of the logical principles of phylogenetics. Excluding characters and mapping them on an independent phylogeny produces a particular and suboptimal kind of secondary homology, the use of which can be justified only for preliminary studies dealing with broadly defined characters.     

The in vivo response of corn mitochondria to Bipolaris (Helminthosporium) maydis (race T) toxin

The addition of 2-deoxyglucose to tissue elicits an in vivo mitochondrial conformation response (contraction) that can be viewed ultrastructurally and is indicative of the phosphorylative capability of mitochondria. Utilizing this technique toxin from Bipolaris (Helminthosporium) maydis race T was found to penetrate leaf and root tissue of Texas male-sterile cytoplasm corn (Zea mays L. W64A) only slowly, but once in cells the toxin had a rapid deleterious effect on mitochondrial function. It is concluded that B. maydis (race T) toxin has effects on in vivo mitochondria similar to those reported after in vitro experimentation and that mitochondria are a primary site of toxin action. These observations are followed by the suggestion that susceptibility or resistance to B. maydis (race T) is conferred in corn by a cytoplasmically inheritable character associated with mitochondria.     

Protecting wildlife from predation by owned domestic cats: Application of a precautionary approach to the acceptability of proposed cat regulations

Abstract While it is undeniable that owned domestic cats Felis catus (Mammalia: Felidae) kill large numbers of wildlife, it is contentious if this has significant impacts on wildlife populations. Under the precautionary principle such uncertainty does not preclude measures to reduce putative risk, but action should follow consultation with stakeholders. To initiate such consultation for the City of Armadale, Western Australia, we surveyed urban and rural residents to determine their opinions regarding putative impacts of owned cats on wildlife and the acceptability of proposed regulations. Key statements accepted by 70% or more of respondents, irrespective of their residence, gender or cat ownership status, included: (i) there is a need to regulate owned domestic cats; (ii) the presence of cats in nature reserves is harmful to wildlife; (iii) cats not owned by licensed breeders should be desexed; and (iv) local councils should be empowered to restrict the maximum number of cats per household. Seventy per cent or more of owners agreed to keep their cats on their property from sunset to sunrise and to register them if these measures became compulsory. All groups except urban men also indicated 70% or greater willingness to keep their cats on their property constantly if required. However, fewer than 40% of owners supported empowering local councils to enforce cat‐free zones. In this community, cat regulation excluding cat‐free zones should enjoy support. Similar approaches should be effective wherever the environmental impacts of owned domestic cats are debated, because compliance with such regulations should be high.     

Integrating farmers’ knowledge on toxic plants and grassland management: a case study on Colchicum autumnale in Austria

High densities of Colchicum autumnale may endanger grassland management in Austria. As the toxic components persist in hay and silage, the continuation of the management of these grasslands, which are often characterised by a high biodiversity, is uncertain. Farmers possess valuable and context-specific know-how on toxic plants and grassland management. This study aims at assessing the contribution of farmers’ knowledge to nature conservation research on toxic plants in grasslands. In total, we conducted 170 face-to-face interviews with farmers managing grasslands with C. autumnale in four areas of Lower Austria. In addition, the farmers were invited to regional workshops to discuss C. autumnale, control measures and related problems. We also encouraged farmers to carry out on-farm experiments. To provide triangulation of the participatory with academic research results, C. autumnale was mapped in three municipalities, covering in total 686 ha. The majority of all grassland plots were extensively managed meadows. More than half of them were not fertilised and were subject to nature conservation regulations. Farmers reported an increase of C. autumnale on 44% of all grassland plots. Of these, grassland management has been extensified in 64%. About 27% of all farmers regarded C. autumnale as a problem. Among farmers who sold hay, 48% considered it as problematic. The field survey showed that C. autumnale covers up to 73% of grasslands. Farmers’ knowledge is an important contribution to nature conservation research and should be included in the design and implementation of agri-environmental schemes so that long-term extensive grassland management can be assured.     

Phylogeny of wall-less green flagellates inferred from 18SrDNA sequence data

To elucidate the phylogeny of the Dunaliellales sensu Ettl. the taxon often thought to be intermediate between primitive green flagellates such as the prasinophytes and the advanced chlorophycean algae, the sequences of the nuclear-encoded small subunit ribosomal RNA gene (18SrDNA) were determined and analyzed for five green algae, including three dunaliellalean algae. Phylogenetic trees based on 18SrDNA suggest that Oltmannsiellopsis viridis (Margraves et Steele) Chihara et Inouye represents an early divergence in the Ulvophyceae/Trebouxio-phyceae/Chlorophyceae clade and has no close relationship to any other green algae, as also suggested from ultrastructural characters. We propose Oltmannsiellopsidates ord. nov. for this genus. Hafniomonas and Polytomella are included in the clade which is characterized by clockwise basal bodies (CW group). The 18SrDNA trees suggest that multiple losses of the cell wall of the flagellate cell occurred in the CW group, and that the Dunaliellales sensu Ettl has a polyphyletic nature. This study also suggests that Planophita terrestns Groover et Hof-stetter (Chaetopeltidales) and Chaetophora incras-sata (Hudson) Hazen (Chaetophorales) are distinct lineages in the Chlorophyceae.     

A review of recent advances in the study of early angiosperms from northeastern China

The last 10 years (1998–2007) were very productive and important in the study of early angiosperms in northeastern China. The new discoveries of the earliest well-documented records of angiosperms such as Archaefructus, as well as Hyrcantha decussata (= Sinocarpus decussatus), provided fresh knowledge for better understanding the primitive characters of the ancient angiosperms and also their aquatic (or wet) habitat and their herbaceous nature. Some new approaches such as the combination of molecular and morphological characters joined together to place Archaefructus in the angiosperm phylogenetic framework. These fossils demonstrate that we should expect more ancient angiosperms to be found in the pre-Cretaceous which will continue to add important new understanding to the nature of the origin and evolution of the angiosperms.     

A toolbox approach for the rapid evaluation of multi-step enzymatic syntheses comprising a ‘mix and match’ E. coli expression system with microscale experimentation

Abstract

This work describes an experimental ‘toolbox’ for the rapid evaluation and optimisation of multi-step enzymatic syntheses comprising a ‘mix and match’ E. coli-based expression system and automated microwell scale experimentation. The approach is illustrated with a de novo designed pathway for the synthesis of optically pure amino alcohols using the enzymes transketolase (TK) and transaminase (TAm) to catalyze asymmetric carbon-carbon bond formation and selective chiral amine group addition respectively. The E. coli expression system, based on two compatible plasmids, enables pairs of enzymes from previously engineered and cloned TK and TAm libraries to be evaluated for the sequential conversion of different initial substrates. This is complemented by the microwell experimentation which enables efficient investigation of different biocatalyst forms, use of different amine donors and substrate feeding strategies. Using this experimental ‘toolbox’, one-pot syntheses of the diastereoisomers (2S,3S)-2-aminopentane-1,3-diol (APD) and (2S,3R)-2-amino-1,3,4-butanetriol (ABT) were designed and performed, which gave final product yields of 90% mol/mol for APD and 87% mol/mol for ABT (relative to the initial TK substrates) within 25 hours. For the synthesis of APD, the E coli TK mutant D469E was paired with the TAm from Chromobacterium violaceum 2025 while for ABT synthesis the wild-type E. coli TK exhibited the highest specific activity and ee( enantiomeric excess) of >95%. For both reactions, whole-cell forms of the TK-TAm biocatalyst performed better than cell lysates while isopropylamine (IPA) was a preferable amine donor than methylbenzylamine (MBA) since side reactions with the initial TK substrates were avoided. The available libraries of TK and TAm enzymes and scalable nature of the microwell data suggest this ‘toolbox’ provides an efficient approach to early stage bioconversion process design in the chemical and pharmaceutical sectors.     

Next‐generation QTL mapping: crowdsourcing SNPs,without pedigrees

For many molecular ecologists, the mantra and mission of the field of ecological genomics could be encapsulated by the phrase ‘to find the genes that matter’ (Mitchell‐Olds 2001 ; Rockman 2012 ). This phrase of course refers to the early hope and current increasing success in the search for genes whose variation underlies phenotypic variation and fitness in natural populations. In the years since the modern incarnation of the field of ecological genomics, many would agree that the low‐hanging fruit has, at least in principle, been plucked: we now have several elegant examples of genes whose variation influences key adaptive traits in natural populations, and these examples have revealed important insights into the architecture of adaptive variation (Hoekstra et al. 2006 ; Shapiro et al. 2009 ; Chan et al. 2010 ). But how well will these early examples, often involving single genes of large effect on discrete or near‐discrete phenotypes, represent the dynamics of adaptive change for the totality of phenotypes in nature? Will traits exhibiting continuous rather than discrete variation in natural populations have as simple a genetic basis as these early examples suggest (Prasad et al. 2012 ; Rockman 2012 )? Two papers in this issue (Robinson et al. 2013 ; Santure et al. 2013 ) not only suggest answers to these questions but also provide useful extensions of statistical approaches for ecological geneticists to study the genetics of continuous variation in nature. Together these papers, by the same research groups studying evolution in a natural population of Great Tits (Parus major), provide a glimpse of what we should expect as the field begins to dissect the genetic basis of what is arguably the most common type of variation in nature, and how genome‐wide surveys of variation can be applied to natural populations without pedigrees.     

Systematics of the Saguinus oedipus group of the bare-face tamarins: Evidence from facial morphology

The systematics of the Saguinus oedipus group within the bare-face tamarins remains open to question. Hershkovitz (Living New World Monkeys (Platyrrhini), Vol. 1. Chicago: University of Chicago Press, 1977) places the cotton-top and rufus-naped tamarins as subspecies of Saguinus oedipus (S. o. oedipus and S. o. geoffroyi, respectively). In contrast, several other authors have argued that these two taxa should be considered separate species (S. oedipus and S. geoffroyi). Phylogenetic relationships within the group are also disputed. Resolving these different interpretations has been difficult in part because no study of this group has included an objective measure of expected levels of specific vs. subspecific variation. We used facial measurements from 179 adult crania to address the systematics of this group and included a related species that is known to include multiple subspecies. Our sample included three taxa from the S. oedipus group of the bare-face tamarins (S. oedipus, S. geoffroyi, and S. leucopus) and six subspecies from the related hairy-face tamarin species S. fuscicollis. Comparisons to S. leucopus provided a relative measure of species-level differences. Analyses that included S. fuscicollis provided a measure of subspecific variation. There was no evidence of facial sexual dimorphism in any of these taxa. A variety of multivariate statistical analyses including discriminant function and cluster analysis suggest that S. oedipus and S. geoffroyi differ morphologically at a level consistent with species-level distinctions. The extent of differences between these taxa is large. The differences in their facial morphology was on the order of differences between S. oedipus or S. geoffroyi and S. leucopus rather than the extent of variation among S. fuscicollis subspecies. Furthermore, a comparison of collecting localities revealed that the variation we observed among S. oedipus and S. geoffroyi was not clinal but presented a large morphological discontinuity at the boundary between taxa. Our analyses also suggested that S. leucopus is more similar to S. oedipus than is either to S. geoffroyi. Finally, it may be that there are some distinct species within the S. fuscicollis group. However, this hypothesis, along with other phylogenetic relationships suggested by this study, will require more data and further study. © 1992 Wiley-Liss, Inc.     

Molecular Characterization of an Aux/IAA of Catharanthus roseus

In Catharanthus roseus cells, auxins are known to negatively regulate the biosynthesis of monoterpenoid indole alkaloids (MIA), a class of valuable secondary metabolites. Despite extensive studies of this regulation, no protein of the auxin signaling pathway has been isolated to date in this plant. We therefore decided to clone and characterize a C. roseus Aux/IAA protein that belongs to a family of gene expression repressors mediating auxin effects. Using PCR, a cDNA encoding the first C. roseus Aux/IAA was cloned and named CrIAA1. The deduced amino acid sequence has four highly conserved domains that are typical of the Aux/IAA protein family and has high homology to the Aux/IAA isoforms of Arabidopsis (>67%). The CrIAA1 gene expression, monitored by real-time PCR, was found to be dramatically induced by auxin treatment in C. roseus cells. Using GFP imagery and a bimolecular fluorescence complementation assay, we found that CrIAA1 can form oligomers in the nucleus. We also found that CrIAA1 is quickly degraded following auxin treatments, suggesting that auxin regulates CrIAA1 availability via a feedback mechanism. These results should help to elucidate the molecular nature of the processes responsible for the auxin-mediated regulation of MIA biosynthesis in C. roseus.     

Alteration of bacterial surface electrostatic potential and pH upon adhesion to a solid surface and impacts to cellular bioenergetics

In our previous study [Hong Y, Brown DG (2009) Appl Environ Microbiol 75(8):2346–2353], the adenosine triphosphate (ATP) level of adhered bacteria was observed to be 2–5 times higher than that of planktonic bacteria. Consequently, the proton motive force (Δp) of adhered bacteria was approximately 15% greater than that of planktonic bacteria. It was hypothesized that the cell surface pH changes upon adhesion due to the charge‐regulated nature of the bacterial cell surface and that this change in surface pH can propagate to the cytoplasmic membrane and alter Δp. In the current study, we developed and applied a charge regulation model to bacterial adhesion and demonstrated that the charge nature of the adhering surface can have a significant effect on the cell surface pH and ultimately the affect the ATP levels of adhered bacteria. The results indicated that the negatively charged glass surface can result in a two‐unit drop in cell surface pH, whereas adhesion to a positively charged amine surface can result in a two‐unit rise in pH. The working hypothesis indicates that the negatively charged surface should enhance Δp and increase cellular ATP, while the positively charged surface should decrease Δp and decrease ATP, and these results of the hypothesis are directly supported by prior experimental results with both negatively and positively charged surfaces. Overall, these results suggest that the nature of charge on the solid surface can have an impact on the proton motive force and cellular ATP levels. Biotechnol. Bioeng. 2010;105: 965–972. © 2009 Wiley Periodicals, Inc.