Graduate School Experimental Plant Sciences

There is an urgent need to improve the infrastructure supporting the reuse of scholarly data. A diverse set of stakeholders-representing academia, industry, funding agencies, and scholarly publishers-have come together to design and jointly endorse a concise and measureable set of principles that we refer to as the FAIR Data Principles. The intent is that these may act as a guideline for those wishing to enhance the reusability of their data holdings. Distinct from peer initiatives that focus on the human scholar, the FAIR Principles put specific emphasis on enhancing the ability of machines to automatically find and use the data, in addition to supporting its reuse by individuals. This Comment is the first formal publication of the FAIR Principles, and includes the rationale behind them, and some exemplar implementations in the community.

Ecological data has several special properties: the presence or absence of species on a semi-quantitative abundance scale; non-linear relationships between species and environmental factors; and high inter-correlations among species and among environmental variables. The analysis of such data is important to the interpretation of relationships within plant and animal communities and with their environments. In this corrected version of Data Analysis in Community and Landscape Ecology, without using complex mathematics, the contributors demonstrate the methods that have proven most useful, with examples, exercises and case-studies. Chapters explain in an elementary way powerful data analysis techniques such as logic regression, canonical correspondence analysis, and kriging.

The development of the Dutch Eating Behaviour Questionnaire (DEBQ) with scales for restrained, emotional, and external eating is described. Factor analyses have shown that all items on restrained and external eating each have high loadings on one factor, but items on emotional eating have two dimensions, one dealing with eating in response to diffuse emotions, and the other with eating in response to clearly labelled emotions. The pattern of corrected item-total correlation coefficients and of the factors was very similar for various subsamples, which indicates a high degree of stability of dimensions on the eating behavior scales. The norms and Cronbach's alpha coefficients of the scales and also the Pearson's correlation coefficients to assess interrelationships between scales indicate that the scales have a high internal consistency and factorial validity. However, their external validity has yet to be investigated.

This paper reports the genome sequence of domesticated tomato, a major crop plant, and a draft sequence for its closest wild relative; comparative genomics reveal very little divergence between the two genomes but some important differences with the potato genome, another important food crop in the genus Solanum. Tomato (Solanum lycopersicum) is a major crop plant and a model system for fruit development. Solanum is one of the largest angiosperm genera1 and includes annual and perennial plants from diverse habitats. Here we present a high-quality genome sequence of domesticated tomato, a draft sequence of its closest wild relative, Solanum pimpinellifolium2, and compare them to each other and to the potato genome (Solanum tuberosum). The two tomato genomes show only 0.6% nucleotide divergence and signs of recent admixture, but show more than 8% divergence from potato, with nine large and several smaller inversions. In contrast to Arabidopsis, but similar to soybean, tomato and potato small RNAs map predominantly to gene-rich chromosomal regions, including gene promoters. The Solanum lineage has experienced two consecutive genome triplications: one that is ancient and shared with rosids, and a more recent one. These triplications set the stage for the neofunctionalization of genes controlling fruit characteristics, such as colour and fleshiness.

Here we present Primer3Plus, a new web interface to the popular Primer3 primer design program as an enhanced alternative for the CGI- scripts that come with Primer3. Primer3 consists of a command line program and a web interface. The web interface is one large form showing all of the possible options. This makes the interface powerful, but at the same time confusing for occasional users. Primer3Plus provides an intuitive user interface using present-day web technologies and has been developed in close collaboration with molecular biologists and technicians regularly designing primers. It focuses on the task at hand, and hides detailed settings from the user until these are needed. We also added functionality to automate specific tasks like designing primers for cloning or step-wise sequencing. Settings and designed primer sequences can be stored locally for later use. Primer3Plus supports a range of common sequence formats, such as FASTA. Finally, primers selected by Primer3Plus can be sent to an order form, allowing tight integration into laboratory ordering systems. Moreover, the open architecture of Primer3Plus allows easy expansion or integration of external software packages. The Primer3Plus Perl source code is available under GPL license from SourceForge. Primer3Plus is available at http://www.bioinformatics.nl/primer3plus.

Microbial transformations of cyclic hydrocarbons have received much attention during the past three decades. Interest in the degradation of environmental pollutants as well as in applications of microorganisms in the catalysis of chemical reactions has stimulated research in this area. The metabolic pathways of various aromatics, cycloalkanes, and terpenes in different microorganisms have been elucidated, and the genetics of several of these routes have been clarified. The toxicity of these compounds to microorganisms is very important in the microbial degradation of hydrocarbons, but not many researchers have studied the mechanism of this toxic action. In this review, we present general ideas derived from the various reports mentioning toxic effects. Most importantly, lipophilic hydrocarbons accumulate in the membrane lipid bilayer, affecting the structural and functional properties of these membranes. As a result of accumulated hydrocarbon molecules, the membrane loses its integrity, and an increase in permeability to protons and ions has been observed in several instances. Consequently, dissipation of the proton motive force and impairment of intracellular pH homeostasis occur. In addition to the effects of lipophilic compounds on the lipid part of the membrane, proteins embedded in the membrane are affected. The effects on the membrane-embedded proteins probably result to a large extent from changes in the lipid environment; however, direct effects of lipophilic compounds on membrane proteins have also been observed. Finally, the effectiveness of changes in membrane lipid composition, modification of outer membrane lipopolysaccharide, altered cell wall constituents, and active excretion systems in reducing the membrane concentrations of lipophilic compounds is discussed. Also, the adaptations (e.g., increase in lipid ordering, change in lipid/protein ratio) that compensate for the changes in membrane structure are treated.

Summary The aim of this review was to undertake a survey of researchers working with plant‐parasitic nematodes in order to determine a ‘top 10’ list of these pathogens based on scientific and economic importance. Any such list will not be definitive as economic importance will vary depending on the region of the world in which a researcher is based. However, care was taken to include researchers from as many parts of the world as possible when carrying out the survey. The top 10 list emerging from the survey is composed of: (1) root‐knot nematodes ( M eloidogyne spp.); (2) cyst nematodes ( H eterodera and G lobodera spp.); (3) root lesion nematodes ( P ratylenchus spp.); (4) the burrowing nematode R adopholus similis ; (5) D itylenchus dipsaci ; (6) the pine wilt nematode B ursaphelenchus xylophilus ; (7) the reniform nematode R otylenchulus reniformis ; (8) X iphinema index (the only virus vector nematode to make the list); (9) N acobbus aberrans ; and (10) A phelenchoides besseyi . The biology of each nematode (or nematode group) is reviewed briefly.

Crop loss due to soil salinization is an increasing threat to agriculture worldwide. This review provides an overview of cellular and physiological mechanisms in plant responses to salt. We place cellular responses in a time- and tissue-dependent context in order to link them to observed phases in growth rate that occur in response to stress. Recent advances in phenotyping can now functionally or genetically link cellular signaling responses, ion transport, water management, and gene expression to growth, development, and survival. Halophytes, which are naturally salt-tolerant plants, are highlighted as success stories to learn from. We emphasize that ( a ) filling the major knowledge gaps in salt-induced signaling pathways, ( b ) increasing the spatial and temporal resolution of our knowledge of salt stress responses, ( c ) discovering and considering crop-specific responses, and ( d ) including halophytes in our comparative studies are all essential in order to take our approaches to increasing crop yields in saline soils to the next level.

Potato (Solanum tuberosum L.) is the world’s most important non-grain food crop and is central to global food security. It is clonally propagated, highly heterozygous, autotetraploid, and suffers acute inbreeding depression. Here we use a homozygous doubled-monoploid potato clone to sequence and assemble 86% of the 844-megabase genome. We predict 39,031 protein-coding genes and present evidence for at least two genome duplication events indicative of a palaeopolyploid origin. As the first genome sequence of an asterid, the potato genome reveals 2,642 genes specific to this large angiosperm clade. We also sequenced a heterozygous diploid clone and show that gene presence/absence variants and other potentially deleterious mutations occur frequently and are a likely cause of inbreeding depression. Gene family expansion, tissue-specific expression and recruitment of genes to new pathways contributed to the evolution of tuber development. The potato genome sequence provides a platform for genetic improvement of this vital crop. The genome of the potato (Solanum tuberosum L.), a staple crop vital to food security, has been sequenced. The Potato Genome Sequencing Consortium sequenced a homozygous doubled-monoploid potato clone as well as a heterozygous diploid clone. Genome analysis reveals traces of at least two genome duplication events and genes specific to Asterids, a large clade of flowering plants of which the potato is the first to be sequenced. Gene presence/absence variants and other potentially deleterious mutations are frequent and may be the cause of inbreeding depression. The genome sequence will facilitate genetic improvements in the potato with a view to improving yield and to increasing disease and stress resistance of this crop, which is a now a significant component of worldwide food production and is becoming increasingly important in the developing world.

This chapter describes several laboratory methods of determining the hydraulic conductivity and hydraulic diffusivity. Water moves through soil in response to various forces acting upon it. The chemical species water may be transported due to bulk movement of the liquid phase or soil solution, or it may be transported by diffusion relative to the mean motion of the liquid phase. The chapter deals with bulk movement, under isothermal conditions, of the liquid phase in response to mechanical driving forces. However, the transport of water in the gas phase by vapor diffusion will be included in the measured hydraulic conductivity and diffusivity, especially at low water contents. The concept of parameter identification has been applied to the determination of the parameters in the hydraulic conductivity and water retention functions. The method involves the measurement of some aspect of the response of a soil water flow system to a set of applied boundary conditions.

Alterations in the human intestinal microbiota are linked to conditions including inflammatory bowel disease, irritable bowel syndrome, and obesity. The microbiota also undergoes substantial changes at the extremes of life, in infants and older people, the ramifications of which are still being explored. We applied pyrosequencing of over 40,000 16S rRNA gene V4 region amplicons per subject to characterize the fecal microbiota in 161 subjects aged 65 y and older and 9 younger control subjects. The microbiota of each individual subject constituted a unique profile that was separable from all others. In 68% of the individuals, the microbiota was dominated by phylum Bacteroides, with an average proportion of 57% across all 161 baseline samples. Phylum Firmicutes had an average proportion of 40%. The proportions of some phyla and genera associated with disease or health also varied dramatically, including Proteobacteria, Actinobacteria, and Faecalibacteria. The core microbiota of elderly subjects was distinct from that previously established for younger adults, with a greater proportion of Bacteroides spp. and distinct abundance patterns of Clostridium groups. Analyses of 26 fecal microbiota datasets from 3-month follow-up samples indicated that in 85% of the subjects, the microbiota composition was more like the corresponding time-0 sample than any other dataset. We conclude that the fecal microbiota of the elderly shows temporal stability over limited time in the majority of subjects but is characterized by unusual phylum proportions and extreme variability.

Building upon the scope of its predecessor, Dairy Science and Technology, Second Edition offers the latest information on the efficient transformation of milk into high-quality products. It focuses on the principles of physical, chemical, enzymatic, and microbial transformations. The authors, highly regarded educators and researchers, div

General rules for the optimization of different biocatalytic systems in various types of media containing organic solvents are derived by combining data from the literature, and the logarithm of the partition coefficient, log P, as a quantitative measure of solvent polarity. (1) Biocatalysis in organic solvents is low in polar solvents having a log P < 2, is moderate in solvents having a log P between 2 and 4, and is high in a polar solvents having a log P > 4. It was found that this correlation between polarity and activity parallels the ability of organic solvents to distort the essential water layer that stabilizes the biocatalysts. (2) Further optimization of biocatalysis in organic solvents is achieved when the polarity of the microenvironment of the biocatalyst (log P(i)) and the continuous organic phase (log P(cph)) is tuned to the polarities of both the substrate (log P(s)) and the product (log P(p)) according to the following rules: |log P(i) - log P(s)| and |log P(cph) - log P(p)| should be minimal and |log P(cph) - log P(s)| and |log P(i) - log P(p)| should be maximal, with the exception that in the case of substrate inhibition log P(i), should be optimized with respect to log P(s) In addition to these simple optimization rules, the future developments of biocatalysis in organic solvents are discussed.

This study tested the hypothesis that body mass index (BMI) is representative of body fatness independent of age, sex, and ethnicity. Between 1986 and 1992, the authors studied a total of 202 black and 504 white men and women who resided in or near New York City, were ages 20-94 years, and had BMIs of 18-35 kg/m2. Total body fat, expressed as a percentage of body weight (BF%), was assessed using a four-compartment body composition model that does not rely on assumptions known to be age, sex, or ethnicity dependent. Statistically significant age dependencies were observed in the BF%-BMI relations in all four sex and ethnic groups (p values < 0.05-0.001) with older persons showing a higher BF% compared with younger persons with comparable BMIs. Statistically significant sex effects were also observed in BF%-BMI relations within each ethnic group (p values < 0.001) after controlling first for age. For an equivalent BMI, women have significantly greater amounts of total body fat than do men throughout the entire adult life span. Ethnicity did not significantly influence the BF%-BMI relation after controlling first for age and sex even though both black women and men had longer appendicular bone lengths relative to stature (p values < 0.001 and 0.02, respectively) compared with white women and men. Body mass index alone accounted for 25% of between-individual differences in body fat percentage for the 706 total subjects; adding age and sex as independent variables to the regression model increased the variance (r2) to 67%. These results suggest that BMI is age and sex dependent when used as an indicator of body fatness, but that it is ethnicity independent in black and white adults.

Phenotypic plasticity is an environmentally based change in the phenotype. Understanding the evolution of adaptive phenotypic plasticity has been hampered by dissenting opinions on the merits of different methods of description, on the underlying genetic mechanisms, and on the way that plasticity is affected by natural selection in a heterogeneous environment. During much of this debate, the authors of this article have held opposing views. Here, we attempt to lay out current issues and summarize the areas of consensus and controversy surrounding the evolution of plasticity and the reaction norm (the set of phenotypes produced by a genotype over a range of environments).

BACKGROUND: Fatty acids that contain a trans double bond are consumed in large amounts as hydrogenated oils, but their effects on serum lipoprotein levels are unknown. METHODS: We placed 34 women (mean age, 26 years) and 25 men (mean age, 25 years) on three mixed natural diets of identical nutrient composition, except that 10 percent of the daily energy intake was provided as oleic acid (which contains one cis double bond), trans isomers of oleic acid, or saturated fatty acids. The three diets were consumed for three weeks each, in random order. RESULTS: On the oleic acid diet, the mean (+/- SD) serum values for the entire group for total, low-density lipoprotein (LDL), and high-density lipoprotein (HDL) cholesterol were 4.46 +/- 0.66. 2.67 +/- 0.54, and 1.42 +/- 0.32 mmol per liter (172 +/- 26, 103 +/- 21, and 55 +/- 12 mg per deciliter), respectively. On the trans-fatty-acid diet, the subjects' mean HDL cholesterol level was 0.17 mmol per liter (7 mg per deciliter) lower than the mean value on the diet high in oleic acid (P less than 0.0001; 95 percent confidence interval, 0.13 to 0.20 mmol per liter). The HDL cholesterol level on the saturated-fat diet was the same as on the oleic acid diet. The LDL cholesterol level was 0.37 mmol per liter (14 mg per deciliter) higher on the trans-fatty-acid diet than on the oleic acid diet (P less than 0.0001; 95 percent confidence interval, 0.28 to 0.45 mmol per liter) and 0.47 mmol per liter (18 mg per deciliter) higher on the saturated-fat diet (P less than 0.001; 95 percent confidence interval, 0.39 to 0.55 mmol per liter) than on the oleic acid diet. The effects on lipoprotein levels did not differ between women and men. CONCLUSIONS: The effect of trans fatty acids on the serum lipoprotein profile is at least as unfavorable as that of the cholesterol-raising saturated fatty acids, because they not only raise LDL cholesterol levels but also lower HDL cholesterol levels.

Summary A computerized procedure to construct integrated genetic maps is presented. The computer program (Join Map) can handle raw data from F 2 s, backcrosses and recombinant inbred lines, as well as listed pair‐wise recombination frequencies. The procedure is useful for combining linkage data that have been collected in different experiments; the result is a mathematical alignment of the distinct genetic maps. Data from single experiments can be dealt with as well. In view of the fast growing amount of linkage information for molecular markers, which is often being generated by different research groups, integrated maps provide useful information on the map position of genes and DNA markers. The procedure performs a sequential build‐up of the map and, at each step, a numerical search for the best fitting order of markers. Weighted least squares is used for the estimation of map distances.

In 1229 subjects, 521 males and 708 females, with a wide range in body mass index (BMI; 13.9-40.9 kg/m2), and an age range of 7-83 years, body composition was determined by densitometry and anthropometry. The relationship between densitometrically-determined body fat percentage (BF%) and BMI, taking age and sex (males = 1, females = 0) into account, was analysed. For children aged 15 years and younger, the relationship differed from that in adults, due to the height-related increase in BMI in children. In children the BF% could be predicted by the formula BF% = 1.51 x BMI-0.70 x age - 3.6 x sex + 1.4 (R2 0.38, SE of estimate (SEE) 4.4% BF%). In adults the prediction formula was: BF% = 1.20 x BMI + 0.23 x age - 10.8 x sex - 5.4 (R2 0.79, SEE = 4.1% BF%). Internal and external cross-validation of the prediction formulas showed that they gave valid estimates of body fat in males and females at all ages. In obese subjects however, the prediction formulas slightly overestimated the BF%. The prediction error is comparable to the prediction error obtained with other methods of estimating BF%, such as skinfold thickness measurements or bioelectrical impedance.

The filamentous fungus Aspergillus niger is widely exploited by the fermentation industry for the production of enzymes and organic acids, particularly citric acid. We sequenced the 33.9-megabase genome of A. niger CBS 513.88, the ancestor of currently used enzyme production strains. A high level of synteny was observed with other aspergilli sequenced. Strong function predictions were made for 6,506 of the 14,165 open reading frames identified. A detailed description of the components of the protein secretion pathway was made and striking differences in the hydrolytic enzyme spectra of aspergilli were observed. A reconstructed metabolic network comprising 1,069 unique reactions illustrates the versatile metabolism of A. niger. Noteworthy is the large number of major facilitator superfamily transporters and fungal zinc binuclear cluster transcription factors, and the presence of putative gene clusters for fumonisin and ochratoxin A synthesis.

Inference of evolutionary relationships between nematodes is severely hampered by their conserved morphology, the high frequency of homoplasy, and the scarcity of phylum-wide molecular data. To study the origin of nematode radiation and to unravel the phylogenetic relationships between distantly related species, 339 nearly full-length small-subunit rDNA sequences were analyzed from a diverse range of nematodes. Bayesian inference revealed a backbone comprising 12 consecutive dichotomies that subdivided the phylum Nematoda into 12 clades. The most basal clade is dominated by the subclass Enoplia, and members of the order Triplonchida occupy positions most close to the common ancestor of the nematodes. Crown Clades 8-12, a group formerly indicated as "Secernentea" that includes Caenorhabditis elegans and virtually all major plant and animal parasites, show significantly higher nucleotide substitution rates than the more basal Clades 1-7. Accelerated substitution rates are associated with parasitic lifestyles (Clades 8 and 12) or short generation times (Clades 9-11). The relatively high substitution rates in the distal clades resulted in numerous autapomorphies that allow in most cases DNA barcode-based species identification. Teratocephalus, a genus comprising terrestrial bacterivores, was shown to be most close to the starting point of Secernentean radiation. Notably, fungal feeding nematodes were exclusively found basal to or as sister taxon next to the 3 groups of plant parasitic nematodes, namely, Trichodoridae, Longidoridae, and Tylenchomorpha. The exclusive common presence of fungivorous and plant parasitic nematodes supports a long-standing hypothesis that states that plant parasitic nematodes arose from fungivorous ancestors.