Which function describes the species–area relationship best? A review and empirical evaluation

Aim The aims of this study are to resolve terminological confusion around different types of species–area relationships (SARs) and their delimitation from species sampling relationships (SSRs), to provide a comprehensive overview of models and analytical methods for SARs, to evaluate these theoretically and empirically, and to suggest a more consistent approach for the treatment of species–area data. Location Curonian Spit in north‐west Russia and archipelagos world‐wide. Methods First, I review various typologies for SARs and SSRs as well as mathematical models, fitting procedures and goodness‐of‐fit measures applied to SARs. This results in a list of 23 function types, which are applicable both for untransformed (S) and for log‐transformed (log S) species richness. Then, example data sets for nested plots in continuous vegetation (n = 14) and islands (n = 6) are fitted to a selection of 12 function types (linear, power, logarithmic, saturation, sigmoid) both for S and for log S. The suitability of these models is assessed with Akaike’s information criterion for S and log S, and with a newly proposed metric that addresses extrapolation capability. Results SARs, which provide species numbers for different areas and have no upper asymptote, must be distinguished from SSRs, which approach the species richness of one single area asymptotically. Among SARs, nested plots in continuous ecosystems, non‐nested plots in continuous ecosystems, and isolates can be distinguished. For the SARs of the empirical data sets, the normal and quadratic power functions as well as two of the sigmoid functions (Lomolino, cumulative beta‐P) generally performed well. The normal power function (fitted for S) was particularly suitable for predicting richness values over ten‐fold increases in area. Linear, logarithmic, convex saturation and logistic functions generally were inappropriate. However, the two sigmoid models produced unstable results with arbitrary parameter estimates, and the quadratic power function resulted in decreasing richness values for large areas. Main conclusions Based on theoretical considerations and empirical results, I suggest that the power law should be used to describe and compare any type of SAR while at the same time testing whether the exponent z changes with spatial scale. In addition, one should be aware that power‐law parameters are significantly influenced by methodology.     

Modification of cell proliferation patterns alters leaf vein architecture in <Emphasis Type="Italic">Arabidopsis thaliana</Emphasis>

Formation of leaf vascular pattern requires regulation of a number of cellular processes, including cell proliferation. To assess the role of cell proliferation during vein order formation, leaf development in genetic lines exhibiting aberrant cell proliferation patterns due to altered expression patterns of ANT and ICK1 genes was analyzed. Modification of cell proliferation patterns alters the number of higher order veins and the number of minor tertiary veins remodeled as intersecondary veins in Arabidopsis rosette leaves. Minor vein complexity, as indicated by branch point and freely ending veinlet number, is highly correlated with a decrease or increase in cell proliferation. Observations of procambial strand formation in modified cell proliferation pattern lines showed that vein pattern is specified early in leaf development and that formation of freely ending veinlets is temporally correlated with the expansion of ground meristem when cell proliferation is terminated prematurely. Taken together, our observations indicate that: (1) genes that modulate cell proliferation play a key role in regulating the meristematic competence of ground meristem cells to form procambium and vein pattern during leaf development, and (2) ANT is a crucial part of this regulation.     

Mutation in the C-Di-AMP Cyclase dacA Affects Fitness and Resistance of Methicillin Resistant Staphylococcus aureus

Faster growing and more virulent strains of methicillin resistant Staphylococcus aureus (MRSA) are increasingly displacing highly resistant MRSA. Elevated fitness in these MRSA is often accompanied by decreased and heterogeneous levels of methicillin resistance; however, the mechanisms for this phenomenon are not yet fully understood. Whole genome sequencing was used to investigate the genetic basis of this apparent correlation, in an isogenic MRSA strain pair that differed in methicillin resistance levels and fitness, with respect to growth rate. Sequencing revealed only one single nucleotide polymorphism (SNP) in the diadenylate cyclase gene dacA in the faster growing but less resistant strain. Diadenylate cyclases were recently discovered to synthesize the new second messenger cyclic diadenosine monophosphate (c-di-AMP). Introduction of this mutation into the highly resistant but slower growing strain reduced resistance and increased its growth rate, suggesting a direct connection between the dacA mutation and the phenotypic differences of these strains. Quantification of cellular c-di-AMP revealed that the dacA mutation decreased c-di-AMP levels resulting in reduced autolysis, increased salt tolerance and a reduction in the basal expression of the cell wall stress stimulon. These results indicate that c-di-AMP affects cell envelope-related signalling in S. aureus. The influence of c-di-AMP on growth rate and methicillin resistance in MRSA indicate that altering c-di-AMP levels could be a mechanism by which MRSA strains can increase their fitness levels by reducing their methicillin resistance levels.     

The whole and its parts: why and how to disentangle plant communities and synusiae in vegetation classification

Most plant communities consist of different structural and ecological subsets, ranging from cryptogams to different tree layers. The completeness and approach with which these subsets are sampled have implications for vegetation classification. Non‐vascular plants are often omitted or sometimes treated separately, referring to their assemblages as “synusiae” (e.g. epiphytes on bark, saxicolous species on rocks). The distinction of complete plant communities (phytocoenoses or holocoenoses) from their parts (synusiae or merocoenoses) is crucial to avoid logical problems and inconsistencies in the resulting classification systems. We here describe theoretical differences between the phytocoenosis as a whole and its parts, and outline consequences of this distinction for practice and terminology in vegetation classification. To implement a clearer separation, we call for modifications of the International Code of Phytosociological Nomenclature and the EuroVegChecklist. We believe that these steps will make vegetation classification systems better applicable and raise recognition of the importance of non‐vascular plants in the vegetation as well as their interplay with vascular plants.     

Structure of the serine-containing capsular poly-saccharide K40 antigen from Escherichia coli O8:K40:H9

The structure of the K40 antigenic capsular polysaccharide (K40 antigen) of E. coli O8:K40:H9 was elucidated by determination of the composition, ¹H- and ¹³C-n.m.r. spectroscopy, periodate oxidation and Smith degradation, and methylation analysis. The K40 polysaccharide consists of [(O-β- -glucopyranosyluronic acid)-(1→4)-O-(2-acetamido-2-deoxy-- -glucopyranosyl)-(1→6)-O-(2-acetamido-2-deoxy-- -glucopyranosyl)-(1→4)] repeating units. All of the glucuronic acid residues are substituted amidically with -serine.     

Phosphoenolpyruvate carboxylase from the cyanobacterium Synechocystis sp. PCC 6803 is under global metabolic control by PII signaling

Phosphoenolpyruvate carboxylase (PEPC) is the second major carbon-fixing enzyme in photoautotrophic organisms. PEPC is required for the synthesis of amino acids of the glutamate and aspartate family by replenishing the TCA cycle. Furthermore, in cyanobacteria, PEPC, together with malate dehydrogenase and malic enzyme, forms a metabolic shunt for the synthesis of pyruvate from PEP. During this process, CO₂ is first fixed and later released again. Due to its central metabolic position, it is crucial to fully understand the regulation of PEPC. Here, we identify PEPC from the cyanobacterium Synechocystis sp. PCC 6803 (PEPC) as a novel interaction partner for the global signal transduction protein P_II. In addition to an extensive characterization of PEPC, we demonstrate specific P_II–PEPC complex formation and its enzymatic consequences. PEPC activity is tuned by the metabolite-sensing properties of P_II: Whereas in the absence of P_II, PEPC is subjected to ATP inhibition, it is activated beyond its basal activity in the presence of P_II. Furthermore, P_II–PEPC complex formation is inhibited by ADP and PEPC activation by P_II-ATP is mitigated in the presence of 2-OG, linking PEPC regulation to the cell's global carbon/nitrogen status. Finally, physiological relevance of the in vitro measurements was proven by metabolomic analyses of Synechocystis wild-type and P_II-deficient cells.     

HISTONES AND ALKALINE FAST GREEN STAINING OF ONION ROOTS

Onion root tips were freeze killed or fixed in 12 different chemical fixatives to determine the possible effects of such treatments on subsequent staining with alkaline Fast green (pH 8.0-8.1) to reveal the presence of histones. Ethanol, methanol, neutral formalin, and a mixture of methanolchloroform-acetic acid produced nearly comparable results. Subsequent to fixation or freeze drying the sections were treated with hot 5% trichloroacetic acid (TCA) to remove nucleic acids prior to Fast green staining. Staining of histones does not occur in chemically fixed material if TCA hydrolysis is omitted. Nuclei, chromosomes during mitosis, and cytoplasm (to varying degrees) were stainable after TCA treatment. Positive staining occurs in nuclei, nucleoli, and cytoplasm in freeze-dried material with or without prior TCA treatment. Comparisons are made with chemical fixations. The use of ribonuclease instead of TCA permits staining of the cytoplasm and of chromosomes during mitosis. Discussions are included on the stainability of nucleoli and the possibility that native histone is associated with ribonucleic acid (RNA).