Dealing with virtual aggregation – a new index for analysing heterogeneous point patterns

Point pattern analyses such as the estimation of Ripley's K‐function or the pair‐correlation function g are commonly used in ecology to characterise ecological patterns in space. However, a major disadvantage of these methods is their missing ability to deal with spatial heterogeneity. A heterogeneous intensity of points causes a systematic bias in estimates of the K‐ and g‐functions, a phenomenon termed “virtual aggregation” in the recent literature. To address this problem, we derive a new index, called K2‐index, as an extension of existing point pattern characteristics. The K2‐index has a heuristic interpretation as an approximation to the first derivative of the g‐function. We estimate the K‐, g‐ and K2‐functions for six different types of simulated point patterns and show that the K2‐index may provide important information on point patterns that the other methods fail to detect. The results indicate that particularly the small‐scale distributions of points are better represented by the K2‐index. This might be important for testing hypotheses on ecological processes, because most of these processes, such as direct neighbour interactions, occur very locally. When applied to empirical patterns of molehill distribution, the results of the K2‐analysis show regularity up to distances between 0.1 and 0.4 m in most of the study areas, and aggregation of molehills up to distances between 0.2 and 1.1 m. The type and scale of these deviations from randomness agree with a priori expectations on the hill‐building behaviour of moles. In contrast, the estimated g‐functions merely indicate aggregation at the full range from 0 to 7 m (or even above). Considering the advantages and disadvantages of the different methods, we suggest that the K2‐index should be used as a complement to existing approaches, particularly for point patterns generated by processes that act on more than one scale.     

Ultra performance liquid chromatography-mass spectrometric determination of the site specificity of modification of β-casein by glucose and methylglyoxal

Modification of protein by carbonyl compounds under in vitro physiological conditions is site-directed. There are few reports of the site specificity of glycation of proteins using heating conditions of relevance to food processing. The aim of this study was to determine the site specificity of modification of β-casein (βCN) by glucose and methylglyoxal (MGO). βCN (1.33 M, 3.2%) was heated with either glucose (1.345 M, 4.6%) or MGO (1 mM) at 95°C for up to 4 h. Tryptic digests were prepared and analysed by ultra performance liquid chromatography electrospray ionisation mass spectrometry (UPLC-ES/MS). The sites of formation of the Amadori product, N ^ε -(fructosyl)lysine (FL), and the advanced glycation end-products, N ^ε -(carboxymethyl)lysine (CML), MGO-derived dihydroxyimidazolidine (MG-DH) and MGO-derived hydroimidazolone (MG-HI), were located. FL and CML were detected at K107 and K176 residues in βCN/glucose incubations. Indigenous N ^ε -(lactulosyl)lysine was detected at K107 only. MG-DH and MG-HI were detected at R202 and possibly R183 residues in both βCN/glucose and βCN/MGO incubations. Glycation of βCN by glucose and MGO resulted in similar site specificity for MG-DH and MG-HI formation.     

Enzymic saccharification of sugar beet pulp

Culture filtrates of Talaromyces emersonii UCG 208 grown on beet pulp can convert the polysaccharide components of this agricultural waste to soluble sugars. The saccharification process is facilitated if the pulp is milled or incubated with alkali or peracetic acid before addition of enzyme. However, treatment of unmilled pulp with commercial pectinase prior to incubation with Talaromyces filtrate is also very effective; under suitable conditions, complete hydrolysis of total polysaccharides has been achieved.     

Membrane topology and sequence requirements for oil body targeting of oleosin

Oleosin protein is targeted to oil bodies via the endoplasmic reticulum (ER) and consists of a lipid-submerged hydrophobic (H) domain that is flanked by cytosolic hydrophilic domains. We investigated the relationship between oleosin ER topology and its subsequent ability to target to oil bodies. Oleosin variants were created to yield differing ER membrane topologies and tagged with a reporter enzyme. Localisation was assessed by fractionation after transient expression in embryonic cells. Membrane-straddled topologies with N-terminal sequence in the ER lumen and C-terminal sequence in the cytosol were unable to target to oil bodies efficiently. Similarly, a translocated topology with only ER membrane and lumenal sequence was unable to target to oil bodies efficiently. Both topology variants accumulated proportionately higher in ER microsomal fractions, demonstrating a block in transferring from ER to oil bodies. The residual oil body accumulation for the inverted topology was shown to be because of partial adoption of native ER membrane topology, using a reporter variant, which becomes inactivated by ER-mediated glycosylation. In addition, the importance of H domain sequence for oil body targeting was assessed using variants that maintain native ER topology. The central proline knot motif (PKM) has previously been shown to be critical for oil body targeting, but here the arms of the H domain flanking this motif were shown to be interchangeable with only a moderate reduction in oil body targeting. We conclude that oil body targeting of oleosin depends on a specific ER membrane topology but does not require a specific sequence in the H domain flanking arms.     

Exposure to Hypertensive Disorders of Pregnancy Increases the Risk of Autism Spectrum Disorder in Affected Offspring

There is growing awareness that prenatal adversity may increase the risk of autism spectrum disorder (ASD). Here, we examined the association between hypertensive disorders of pregnancy (HDP) and ASD risk at 7 years of age using the Millennium Cohort Study (MCS), a representative cohort of 13,192 children born in the UK from 2000 to 2001. We also sought to examine cytokine expression in the serum of women with pre-eclampsia, which is the most common HDP, and whether exposure of foetal neurons to this serum could change patterns of neuronal growth. HDP were reported by mothers 9 months post-delivery. ASD was parent reported at age seven, based on a doctor or health care professional’s diagnosis. Weighted logistic regression was used for data analysis, adjusting for several potential confounders including maternal alcohol consumption, education, depression, age, and poverty status. Sensitivity analyses were performed excluding pre-term births, small for gestational age (SGA), and pre-pregnancy hypertension and depression. There was a significant association between HDP and a twofold increased risk of ASD (AOR = 2.10 [95% CI 1.20–3.70]). Excluding preterm births, SGA births, and offspring of women who had pre-pregnancy hypertension or over the age of 40 did not change the results materially. At the cellular level, exposure of foetal cortical neurons to 3% serum isolated from women with an established HDP increased neuronal growth and branching in vitro. These findings indicate that HDP exposure may increase the risk of ASD in the offspring.     

Sampling and analysis of gut contents in relation to environmental variability and diel vertical migration by herbivorous zooplankton

The accuracy of standard sampling and analysis procedures forestimating ingestion by herbivorous zooplankton was assessedusing models. Artificial environments were created in a computermodel, allowing for depth-dependent variability in temperature,chlorophyll and primary production. Model zooplankton were simulatedwithin these artificial environments using individual-basedmodels. The model zooplankton feed and defaecate at rates determinedby temperature and food concentrations, and also exhibit dielvertical migration (DVM) according to a variety of migrationmodels. The computer model was run for different combinationsof these nine environmental and five DVM models. Data were ‘sampled’from the model output, similar to field sampling of mesozooplanktongrazing. Daily ingestion was calculated from the gut ‘samples’using standard procedures for analysing gut fluorescence. Thesample results were compared with the actual ingestion valuesin the model, and some causes of discrepancies were noted. (i)If incorrect temperatures were assumed when calculating thegut evacuation rate (K), then estimates of ingestion were wrongby up to 40%. (ii) Non-uniform food environments gave errorsof up to 30% because of the large variability of measured gutcontents among individuals. (iii) Sampling from only part ofthe total depth range (e.g. at the chlorophyll maximum) resultedin estimates of ingestion being only 5% of the real value. Thissampling practice should be discouraged, because the sampleis not random. (iv) If sampling is not frequent enough, errorscan be as large as 45%, but more usually were 10% for realisticsampling frequencies. We describe an analysis procedure thatuses Monte Carlo-type simulations in a computer spreadsheetto estimate population consumption. These calculations takeinto account natural variability due to populations, samplesand assumptions. We urge that results should be presented asranges of possible values, rather than as single ‘mean’values, to allow for easier recognition of meaningful differencesamong samples and systems.     

Auxin requirements of sycamore cells in suspension culture

Sycamore (Acer pseudoplatanus L.) cell suspension cultures (strain OS) require 2,4-dichlorophenoxyacetic acid (2,4-D) in their culture medium for normal growth. If the 2,4-D is omitted, rates of cell division are dramatically reduced and cell lysis may occur. Despite this `auxin requirement,' it has been shown by gas chromatography-mass spectrometry that the cells synthesize indol-3yl-acetic acid (IAA). Changes in free 2,4-D and IAA in the cells during a culture passage have been monitored.

There is a rapid uptake of 2,4-D by the cells during the lag phase leading to a maximum concentration per cell (125 nanograms per 10⁶ cells) on day 2 followed by a decline to 45 nanograms per 10⁶ cells by day 9 (middle of linear phase). The initial concentration of IAA (0.08 nanograms per 10⁶ cells) rises slowly to a peak of 1.4 nanograms per 10⁶ cells by day 9 then decreases rapidly to 0.2 nanograms per 10⁶ cells by day 15 (early declining phase) and 0.08 nanograms per 10⁶ cells by day 23 (early stationary phase).