The Use of Discontinuities and Functional Groups to Assess Relative Resilience in Complex Systems

It is evident when the resilience of a system has been exceeded and the system qualitatively changed. However, it is not clear how to measure resilience in a system prior to the demonstration that the capacity for resilient response has been exceeded. We argue that self-organizing human and natural systems are structured by a relatively small set of processes operating across scales in time and space. These structuring processes should generate a discontinuous distribution of structures and frequencies, where discontinuities mark the transition from one scale to another. Resilience is not driven by the identity of elements of a system, but rather by the functions those elements provide, and their distribution within and across scales. A self-organizing system that is resilient should maintain patterns of function within and across scales despite the turnover of specific elements (for example, species, cities). However, the loss of functions, or a decrease in functional representation at certain scales will decrease system resilience. It follows that some distributions of function should be more resilient than others. We propose that the determination of discontinuities, and the quantification of function both within and across scales, produce relative measures of resilience in ecological and other systems. We describe a set of methods to assess the relative resilience of a system based upon the determination of discontinuities and the quantification of the distribution of functions in relation to those discontinuities.     

Reproductive Biology and Ecology of Shortspine Thornyhead Rockfish, Sebastolobus alascanus, and longspine thornyhead rockfish, S. altivelis, from the northeastern Pacific Ocean

We examined the reproductive biology and estimated life history parameters for female shortspine thornyhead, Sebastolobus alascanus, and longspine thornyhead, S. altivelis, from histological samples prepared from specimens collected from both Alaska and the West Coast of the United States. Both species spawn pelagic gelatinous egg masses, although timing differs between taxa and locations. Shortspines spawn between April and July in Alaska and between December and May along the West Coast. Longspines spawn between January and April along the West Coast. Length at 50% maturity differed between species and areas, with shortspines at 21.48cm in Alaska and 18.19cm on the West Coast, and longspines at 17.83cm on the West Coast. We used the gonadosomatic index to estimate instantaneous rates of natural mortality (M). Values of M differed little between species and areas despite substantial differences in temperature and dissolved oxygen concentrations. Estimates for shortspines from both Alaska and the West Coast ranged between 0.013 and 0.017, while longspines from the West Coast showed an M value of 0.015. Such low estimates of M suggest Sebastolobus are extremely long-lived.     

Leaf dynamics of a deciduous forest canopy: no response to elevated CO<Subscript>2</Subscript>

Leaf area index (LAI) and its seasonal dynamics are key determinants of terrestrial productivity and, therefore, of the response of ecosystems to a rising atmospheric CO₂ concentration. Despite the central importance of LAI, there is very little evidence from which to assess how forest LAI will respond to increasing [CO₂]. We assessed LAI and related leaf indices of a closed-canopy deciduous forest for 4 years in 25-m-diameter plots that were exposed to ambient or elevated CO₂ (542 ppm) in a free-air CO₂ enrichment (FACE) experiment. LAI of this Liquidambar styraciflua (sweetgum) stand was about 6 and was relatively constant year-to-year, including the 2 years prior to the onset of CO₂ treatment. LAI throughout the 1999–2002 growing seasons was assessed through a combination of data on photosynthetically active radiation (PAR) transmittance, mass of litter collected in traps, and leaf mass per unit area (LMA). There was no effect of [CO₂] on any expression of leaf area, including peak LAI, average LAI, or leaf area duration. Canopy mass and LMA, however, were significantly increased by CO₂ enrichment. The hypothesized connection between light compensation point (LCP) and LAI was rejected because LCP was reduced by [CO₂] enrichment only in leaves under full sun, but not in shaded leaves. Data on PAR interception also permitted calculation of absorbed PAR (APAR) and light use efficiency (LUE), which are key parameters connecting satellite assessments of terrestrial productivity with ecosystem models of future productivity. There was no effect of [CO₂] on APAR, and the observed increase in net primary productivity in elevated [CO₂] was ascribed to an increase in LUE, which ranged from 1.4 to 2.4 g MJ^–1. The current evidence seems convincing that LAI of non-expanding forest stands will not be different in a future CO₂-enriched atmosphere and that increases in LUE and productivity in elevated [CO₂] are driven primarily by functional responses rather than by structural changes. Ecosystem or regional models that incorporate feedbacks on resource use through LAI should not assume that LAI will increase with CO₂ enrichment of the atmosphere.     

Multiple strains of the parasitic dinoflagellate Amoebophrya exist in Chesapeake Bay

Small subunit rRNA sequences were amplified from Amoebophrya strains infecting Karlodinium micrum, Gymnodinium instriatum and an unidentified Scrippsiella species in Chesapeake Bay. The alignable parts of the sequences differed from each other and from the previously reported rRNA sequence of the Amoebophrya strain infecting Akashiwo sanguinea in Chesapeake Bay by 4 to 10%. This is a greater degree of difference than sometimes found between sequences from separate genera of free-living dinoflagellates. These sequence differences indicate that the Amoebophrya strains parasitizing dinoflagellates in Chesapeake Bay do not all belong to the same species. In spite of their relative dissimilarity, the sequences do group together into a single clade with high bootstrap support in phylogenetic trees constructed from the sequences.     

Phase I and II liver enzyme activities in juvenile alligators (Alligator mississippiensis) collected from three sites in the Kissimmee-Everglades drainage, Florida (USA)

We examined CYP1A (measured using hepatic EROD and MROD activities) and glutathione-S-transferase (GST) activities in juvenile alligators (Alligator mississippiensis) collected from three sites with varying contamination in the Kissimmee-Everglades drainage in south Florida. We hypothesized that contaminants present in areas with intermediate or higher contaminant concentrations would alter hepatic enzyme activities in juvenile alligators from those sites when compared to hepatic enzyme activity in animals from the area with the least contamination. EROD activity was found to be higher in animals from the site with lower reported levels of contamination relative to those from the site with the highest reported contamination suggesting an inhibition of CYP1A expression or activity. No differences among animals from the three sites were observed for hepatic MROD and GST activities. A significant negative relationship between EROD, MROD, and GST activities and body size was exhibited in alligators from the site with the lowest contamination. No relationship between body size and hepatic enzyme activity was found in animals from the sites with intermediate and higher contamination, suggesting that contaminants present at these sites act to alter this relationship. No correlation was observed in this study between plasma steroid concentrations (estradiol-17 beta or testosterone) and hepatic EROD, MROD, or GST activities.     

The NMR structure of the 38 kDa U1A protein - PIE RNA complex reveals the basis of cooperativity in regulation of polyadenylation by human U1A protein

The status of the poly(A) tail at the 3'-end of mRNAs controls the expression of numerous genes in response to developmental and extracellular signals. Poly(A) tail regulation requires cooperative binding of two human U1A proteins to an RNA regulatory region called the polyadenylation inhibition element (PIE). When bound to PIE RNA, U1A proteins also bind to the enzyme responsible for formation of the mature 3'-end of most eukaryotic mRNAs, poly(A) polymerase (PAP). The NMR structure of the 38 kDa complex formed between two U1A molecules and PIE RNA shows that binding cooperativity depends on helix C located at the end of the RNA-binding domain and just adjacent to the PAP-interacting domain of U1A. Since helix C undergoes a conformational change upon RNA binding, the structure shows that binding cooperativity and interactions with PAP occur only when U1A is bound to its cognate RNA. This mechanism ensures that the activity of PAP enzyme, which is essential to the cell, is only down regulated when U1A is bound to the U1A mRNA.     

Age, growth, maturity, and mortality of the Alaska skate, Bathyraja parmifera, in the eastern Bering Sea

The Alaska skate, Bathyraja parmifera, is the most abundant species of skate on the eastern Bering Sea shelf, accounting for over 90% of total skate biomass. However, little is known regarding the life history of this species despite its common occurrence as bycatch in several Bering Sea fisheries. This is the first study to focus on the age and growth of B. parmifera. From 2003 to 2005, more than one thousand specimens were collected by fisheries observers and on scientific groundfish surveys. Annual banding patterns in more than 500 thin sections of vertebral centra were examined for age determination. Caudal thorns were tested as a potentially non-lethal ageing structure. Annual band pair deposition was verified through edge and marginal increment analyses. A three-parameter von Bertalanffy growth function and a Gompertz growth function were fit to observed length-at-age data. Both models provided significant fits, although the Gompertz function best described the overall pattern of growth in both males and females, based upon statistical criteria and parameter estimates. Age and size at 50% maturity were 9 years and 92 cm TL for males and 10 years and 93 cm TL for females. The maximum observed ages for males and females were 15 years and 17 years, respectively. Estimates of natural mortality (M) ranged from 0.14 to 0.28, and were based on published relationships between M and longevity, age at maturity, and the von Bertalanffy growth coefficient. Due to these life history characteristics and a lack of long-term species-specific stock data, a conservative management approach would be appropriate for B. parmifera.     

Evaluating the evidence for targeting FOXO3a in breast cancer: a systematic review

Background

Tumour cells show greater dependency on glycolysis so providing a sufficient and rapid energy supply for fast growth. In many breast cancers, estrogen, progesterone and epidermal growth factor receptor-positive cells proliferate in response to growth factors and growth factor antagonists are a mainstay of treatment. However, triple negative breast cancer (TNBC) cells lack receptor expression, are frequently more aggressive and are resistant to growth factor inhibition. Downstream of growth factor receptors, signal transduction proceeds via phosphatidylinositol 3-kinase (PI3k), Akt and FOXO3a inhibition, the latter being partly responsible for coordinated increases in glycolysis and apoptosis resistance. FOXO3a may be an attractive therapeutic target for TNBC. Therefore we have undertaken a systematic review of FOXO3a as a target for breast cancer therapeutics.

Methods

Articles from NCBI were retrieved systematically when reporting primary data about FOXO3a expression in breast cancer cells after cytotoxic drug treatment.

Results

Increased FOXO3a expression is common following cytotoxic drug treatment and is associated with apoptosis and cell cycle arrest. There is some evidence that metabolic enzyme expression is also altered and that this effect is also elicited in TNBC cells. FOXO3a expression serves as a positive prognostic marker, especially in estrogen (ER) receptor positive cells.

Discussion

FOXO3a is upregulated by a number of receptor-dependent and -independent anti-cancer drugs and associates with apoptosis. The identification of microRNA that regulate FOXO3a directly suggest that it offers a tangible therapeutic target that merits wider evaluation.     

Indel arrays: an affordable alternative for genotyping

Natural variation and induced mutations are important resources for gene discovery and the elucidation of genetic circuits. Mapping such polymorphisms requires rapid and cost-efficient methods for genome-wide genotyping. Here we report the development of a microarray-based method that assesses 240 unique markers in a single hybridization experiment at a cost of less than US$50 in materials per line. Our genotyping array is built with 70-mer oligonucleotide elements representing insertion/deletion (indel) polymorphisms between the Arabidopsis thaliana accessions Columbia-0 (Col) and Landsberg erecta (Ler). These indel polymorphisms are recognized with great precision by comparative genomic hybridization, eliminating the need for array replicates and complex statistical analysis. Markers are present genome-wide, with an average spacing of approximately 500 kb. PCR primer information is provided for all array indels, allowing rapid single-locus inquiries. Multi-well chips allow groups of 16 lines to be genotyped in a single experiment. We demonstrate the utility of the array for accurately mapping recessive mutations, RIL populations and mixed genetic backgrounds from accessions other than Col and Ler. Given the ease of use of shotgun sequencing to generate partial genomic sequences of unsequenced species, this approach is readily transferable to non-model organisms.     

Psychrophilic and Mesophilic Fungi in Frozen Food Products

The mold flora of certain frozen pastries and chicken pies was investigated. Molds were determined qualitatively or quantitatively, or both, by preparing pour plates of the blended product and incubating the plates at various temperatures. The mesophilic fungal flora developed on plates incubated at 10 and 20 C, whereas psychrophilic fungi were obtained on plates incubated at 0 and 5 C. About 2,000 cultures of fungi, representing about 100 different species, were isolated from various products. Four different brands of blueberry, two brands of cherry pastries, two brands of apple, and one brand of raspberry pastries were examined. In addition, two brands of chicken pies were studied. Blueberry pastries had a much higher total fungal population than the other products, although different brands of blueberry pastries varied considerably. Blueberry pastries had from 347 to 1,586 psychrophilic fungi per g. Cherry pastries had about 70 to 110 psychrophiles per g, and apple pastries had 19 to 92 psychrophiles per g. Chicken pies contained very few psychrophilic fungi, about 15 per g. Aureobasidium pullulans was recovered most frequently. About 90% of the psychrophilic fungi found in blueberry products was A. pullulans. Depending upon the brand of cherry pastry, either Phoma spp. or A. pullulans was the most common fungus present. Apple pastries also displayed brand variation, but were unique in having many mesophilic aspergilli. This genus was generally absent from other products. The Penicillium content of apple pastries was also rather high; 50% of the psychrophilic flora was represented by this genus. The psychrophilic fungal flora of chicken pies was composed primarily of penicillia (50%) and Chrysosporium pannorum (46%).