An evaluation of the state of spatial point pattern analysis in ecology

Over the last two decades spatial point pattern analysis (SPPA) has become increasingly popular in ecological research. To direct future work in this area we review studies using SPPA techniques in ecology and related disciplines. We first summarize the key elements of SPPA in ecology (i.e. data types, summary statistics and their estimation, null models, comparison of data and models, and consideration of heterogeneity); second, we review how ecologists have used these key elements; and finally, we identify practical difficulties that are still commonly encountered and point to new methods that allow current key questions in ecology to be effectively addressed. Our review of 308 articles published over the period 1992–2012 reveals that a standard canon of SPPA techniques in ecology has been largely identified and that most of the earlier technical issues that occupied ecologists, such as edge correction, have been solved. However, the majority of studies underused the methodological potential offered by modern SPPA. More advanced techniques of SPPA offer the potential to address a variety of highly relevant ecological questions. For example, inhomogeneous summary statistics can quantify the impact of heterogeneous environments, mark correlation functions can include trait and phylogenetic information in the analysis of multivariate spatial patterns, and more refined point process models can be used to realistically characterize the structure of a wide range of patterns. Additionally, recent advances in fitting spatially‐explicit simulation models of community dynamics to point pattern summary statistics hold the promise for solving the longstanding problem of linking pattern to process. All these newer developments allow ecologists to keep up with the increasing availability of spatial data sets provided by newer technologies, which allow point patterns and environmental variables to be mapped over large spatial extents at increasingly higher image resolutions.     

Photoaffinity labelling of isopenicillin N synthetase by laser-flash photolysis.

Isopenicillin N synthetase (IPNS) from Acremonium chrysogenum was photolabelled by laser-flash photolysis in the presence of a diazirinyl-containing substrate, 2-[3-(3-trifluoromethyl-3H-diazirin-3-yl)-phenoxy]acetyl-S- methyloxycarbonylsulphenyl-L-cysteinyl-D-valine (DCV). Labelling of IPNS by DCV is partially inhibited in the presence of an excess of L-alpha-aminoadipoyl-L-cysteinyl-D-valine (ACV), the natural substrate. In the absence of light, DCV is converted into the corresponding penicillin with comparable Km but significantly depressed Vmax relative to ACV. Selective incorporation of [14C]DCV into IPNS has been demonstrated by fluorography of IPNS analysed by SDS/polyacrylamide-gel electrophoresis. Scintillation counting of labelled IPNS purified on an ion-exchange f.p.l.c. column confirms this result. This methodology may be applicable for studies aimed at investigating the binding of substrates to IPNS.     

Radiation dose and second cancer risk in patients treated for cancer of the cervix

The risk of cancer associated with a broad range of organ doses was estimated in an international study of women with cervical cancer. Among 150,000 patients reported to one of 19 population-based cancer registries or treated in any of 20 oncology clinics, 4188 women with second cancers and 6880 matched controls were selected for detailed study. Radiation doses for selected organs were reconstructed for each patient on the basis of her original radiotherapy records. Very high doses, on the order of several hundred gray, were found to increase the risk of cancers of the bladder [relative risk (RR) = 4.0], rectum (RR = 1.8), vagina (RR = 2.7), and possibly bone (RR = 1.3), uterine corpus (RR = 1.3), cecum (RR = 1.5), and non-Hodgkin's lymphoma (RR = 2.5). For all female genital cancers taken together, a sharp dose-response gradient was observed, reaching fivefold for doses more than 150 Gy. Several gray increased the risk of stomach cancer (RR = 2.1) and leukemia (RR = 2.0). Although cancer of the pancreas was elevated, there was no evidence of a dose-dependent risk. Cancer of the kidney was significantly increased among 15-year survivors. A nonsignificant twofold risk of radiogenic thyroid cancer was observed following an average dose of only 0.11 Gy. Breast cancer was not increased overall, despite an average dose of 0.31 Gy and 953 cases available for evaluation (RR = 0.9); there was, however, a weak suggestion of a dose response among women whose ovaries had been surgically removed. Doses greater than 6 Gy to the ovaries reduced breast cancer risk by 44%. A significant deficit of ovarian cancer was observed within 5 years of radiotherapy; in contrast, a dose response was suggested among 10-year survivors. Radiation was not found to increase the overall risk of cancers of the small intestine, colon, ovary, vulva, connective tissue, breast, Hodgkin's disease, multiple myeloma, or chronic lymphocytic leukemia. For most cancers associated with radiation, risks were highest among long-term survivors and appeared concentrated among women irradiated at relatively younger ages.     

The synergism of natural compounds in the pursuit of safe and healthier food

Food producers apply modern processing techniques and use a variety of preservative additives to guarantee safe food and a longer shelflife. Regrettably many of these impact the sensory characteristics of the foodstuffs, such as colour, texture, and flavour, which can result in low consumer acceptance. Additionally, strategies used to reduce growth of spoilage and pathogenic bacteria are not selective enough and may inactivate also desired microbiota. Food is usually overdosed with antimicrobials that are supplemented ‘just in case.’ Consequently, food producers are searching for natural preservation methods that are not harmful to humans. Nature offers a wide spectrum of biologically active (phyto) chemicals that can be used as potential natural preservatives. Compounds with bacterial growth-limiting properties are detected in all parts of plants, including their leaves, flowers, fruits, roots, etc. These are mostly acids, alcohols, medium and long-chain organic acids, terpenic compounds, and their derivatives. This study focused on the effectiveness of plant extracts, i.e., synergism between terpenoids and medium chain fatty acids in cured cooked meat. Bacterial strains that were tested include typical members of the spoilage microflora in vacuum (Lactobacillus curvatus) and MA-packed meats (Brochothrix thermosphacta). These were isolated and identified in a separate study. L. curvatus was observed to be very resistant against either terpenoids or fatty acids when used separately, whereas its growth was strongly inhibited when both chemicals were combined. Growth of B. thermosphacta was significantly inhibited when antimicrobial compounds were solely applied, whereas a blend of terpenoids and fatty acids showed an almost bactericidal effect.     

Simulated long-term vegetation response to alternative stocking strategies in savanna rangelands

Increasing cover by woody vegetation, prevalent in semiarid savanna rangelands throughout the world, is a degrading process attributed to the grazing impact as a major causal factor. We studied grazing effects on savanna vegetation dynamics under alternative stocking strategies with a spatially explicit grid-based simulation model grounded in Kalahari (southern Africa) ecology. Plant life histories were modeled for the three major life forms: perennial grasses, shrubs, annuals. We conducted simulation experiments over a range of livestock utilization intensities for three alternative scenarios of small scale grazing heterogeneity, and two alternative strategies: fixed stocking versus adaptive stocking tracking herbage production. Additionally, the impact of the duration of the management planning horizon was studied, by comparing community response and mean stocking rates after 20 and 50 years. Results confirmed a threshold behavior of shrub cover increase: at low, subcritical utilization intensity little change occurred; when utilization intensity exceeded a threshold, shrub cover increased drastically. For both stocking strategies, thresholds were highly sensitive to grazing heterogeneity. At a given critical utilization intensity, the long term effect of grazing depended on the level of grazing heterogeneity: whereas under low heterogeneity, shrub cover remained unchanged, a large increase occurred under highly heterogeneous grazing. Hence, information on spatial grazing heterogeneity is crucial for correct assessment of the impact of livestock grazing on vegetation dynamics, and thus for the assessment of management strategies. Except for the least heterogeneous grazing scenario, adaptive stocking allowed a more intensive utilization of the range without inflating the risk of shrub cover increase. A destabilizing feedback between rainfall and herbage utilization was identified as the major cause for the worse performance of fixed compared to adaptive stocking, which lacks this feedback. Given the usually high grazing heterogeneity in semiarid rangelands, adaptive stocking provides a management option for increasing herbage utilization and thus returns of livestock produce without increasing degradation risks.     

Production of a Brassica napus Low-Molecular Mass Acyl-Coenzyme A-Binding Protein in Arabidopsis Alters the Acyl-Coenzyme A Pool and Acyl Composition of Oil in Seeds

Low-molecular mass (10 kD) cytosolic acyl-coenzyme A-binding protein (ACBP) has a substantial influence over fatty acid (FA) composition in oilseeds, possibly via an effect on the partitioning of acyl groups between elongation and desaturation pathways. Previously, we demonstrated that the expression of a Brassica napus ACBP (BnACBP) complementary DNA in the developing seeds of Arabidopsis (Arabidopsis thaliana) resulted in increased levels of polyunsaturated FAs at the expense of eicosenoic acid (20:1^cisΔ11) and saturated FAs in seed oil. In this study, we investigated whether alterations in the FA composition of seed oil at maturity were correlated with changes in the acyl-coenzyme A (CoA) pool in developing seeds of transgenic Arabidopsis expressing BnACBP. Our results indicated that both the acyl-CoA pool and seed oil of transgenic Arabidopsis lines expressing cytosolic BnACBP exhibited relative increases in linoleic acid (18:2^cisΔ9,12; 17.9%–44.4% and 7%–13.2%, respectively) and decreases in 20:1^cisΔ11 (38.7%–60.7% and 13.8%–16.3%, respectively). However, alterations in the FA composition of the acyl-CoA pool did not always correlate with those seen in the seed oil. In addition, we found that targeting of BnACBP to the endoplasmic reticulum resulted in FA compositional changes that were similar to those seen in lines expressing cytosolic BnACBP, with the most prominent exception being a relative reduction in α-linolenic acid (18:3^cisΔ9,12,15) in both the acyl-CoA pool and seed oil of the former (48.4%–48.9% and 5.3%–10.4%, respectively). Overall, these data support the role of ACBP in acyl trafficking in developing seeds and validate its use as a biotechnological tool for modifying the FA composition of seed oil.Cytosolic low-molecular mass (approximately 10 kD) acyl-coenzyme A-binding protein (ACBP) consists of a four-α-helix domain capable of binding acyl-CoAs with high affinity in a wide range of eukaryotic organisms (Faergeman et al., 2007). It is believed to serve a housekeeping function of maintaining free acyl-CoA concentrations at low nanomolar levels and, thus, prevents micelle formation and the partitioning of acyl-CoA into membranes (Knudsen et al., 1999). This protein is also considered to contribute to another facet of acyl-CoA pool maintenance via its role in the intracellular transport of acyl-CoAs in the aqueous environment of the cytosol (Rasmussen et al., 1994). Moreover, it has also been shown to exhibit more specialized functions in metabolic processes in which acyl-CoA is actively involved, depending on the tissue and physiological state (Guerrero et al., 2006; Xiao and Chye 2011; Yurchenko and Weselake, 2011).In the developing seeds of oleaginous plants, fatty acids (FAs) are synthesized de novo in plastids and are activated to acyl-CoAs upon their transfer to the cytosol, after which time they can undergo additional modifications (e.g. elongation and desaturation) on the membranes of the endoplasmic reticulum (ER; for review, see Rawsthorne, 2002). While FA elongation is performed on the acyl-CoA substrate, the introduction of the second and third double bonds requires the acyl group to be esterified to phosphatidylcholine (PC; Jaworski, 1987). The composition of the acyl-CoA pool, therefore, is highly dynamic and represents a net result of both de novo synthesis and acyl-editing processes (Bates et al., 2009).The acyl-CoA pool provides substrate for acyltransferases involved in the biosynthesis of triacylglycerol (TAG), which is a major component of seed oil (Weselake et al., 2009). More specifically, TAG synthesis typically occurs via a series of acyl-CoA-dependent acylations of a glycerol backbone derived from sn-glycerol-3-phosphate in a pathway known as the sn-glycerol-3-phosphate or Kennedy pathway (for review, see Snyder et al., 2009; Weselake et al., 2009), although acyl-CoA-independent reactions can also be involved in the production of TAG (Stobart et al., 1997; Banaś et al., 2000; Dahlqvist et al., 2000) and thus contribute to its final composition. Low-molecular mass ACBPs have been demonstrated to modulate the activities of Kennedy pathway acyltransferases in a manner dependent upon the ratio of ACBP to acyl-CoA, stimulating TAG biosynthesis under conditions of acyl-CoA excess and inhibiting acyltransferase activities when relative amounts of acyl-CoA are low compared with ACBP, thus regulating the size of the acyl-CoA pool (for review, see Yurchenko and Weselake, 2011).The acyl-CoA pool in seeds is also influenced through a distinct route involving lysophosphatidylcholine acyltransferase (LPCAT), which catalyzes the acyl-CoA-dependent acylation of lysophosphatidylcholine at the sn-2 position to form PC (Ichihara et al., 1995). Acyl groups esterified to PC become substrates for FA desaturation and other modifications (Miquel and Browse, 1992; Broun et al., 1998) and can then be returned back to the acyl-CoA pool or channeled into TAG through acyl-CoA-independent mechanisms (Stymne and Stobart, 1984; Weselake, 2005; Lager et al., 2013). The efficiency of this acyl group channeling to and from PC is an important determinant of the overall composition of FAs in the acyl-CoA pool and, subsequently, in seed oil.Previously, we demonstrated that the expression of the Brassica napus low-molecular mass ACBP (hereafter referred to as BnACBP) in the presence of Arabidopsis (Arabidopsis thaliana) LPCAT isoforms in an in vitro system enhanced the incorporation of oleic acid (18:1^cisΔ9; hereafter referred to as 18:1) into PC and the release of linoleic acid (18:2^cisΔ9,12; hereafter referred to as 18:2) from PC into acyl-CoA (Yurchenko et al., 2009). In line with these results, the expression of BnACBP complementary DNA (cDNA) in Arabidopsis developing seeds was also shown to result in elevated levels of the polyunsaturated fatty acids (PUFAs) 18:2 and α-linolenic acid (18:3^cisΔ9,12,15; hereafter referred to as 18:3) in seed oil, mainly at the expense of eicosenoic acid (20:1^cisΔ11; hereafter referred to as 20:1) and saturated fatty acids (SFAs; Yurchenko et al., 2009). Based on these findings, BnACBP was proposed to be involved in acyl exchange between acyl-CoA and PC pools, which may affect the rate of FA modifications and, ultimately, the FA composition of seed oil (Yurchenko et al., 2009).In this study, we endeavored to provide further evidence that low-molecular mass ACBP functions in acyl trafficking by investigating whether changes in the FA composition of TAG in Arabidopsis seeds expressing BnACBP were correlated with modifications in the composition of the acyl-CoA pool. In addition, since FA modifications such as elongation and desaturation as well as TAG synthesis occur on ER membranes, we also examined the effect of changing the subcellular localization of BnACBP (from the cytosol to the ER) on the acyl composition of TAG and the acyl-CoA pool in transgenic Arabidopsis. Consequently, we generated localized pools of acyl-CoAs that could be readily accessed by acyltransferases involved in seed oil biosynthesis. Taken together, our findings provide insight into the role of low-molecular mass ACBP in seed oil metabolism and suggest that ACBP (either in its native cytosolic form or as an ER-targeted fusion protein) may serve as a useful tool in biotechnological modifications of FA composition in oil crops.