Comparative analysis of marine ecosystems: international production modelling workshop

Understanding the drivers that dictate the productivity of marine ecosystems continues to be a globally important issue. A vast literature identifies three main processes that regulate the production dynamics of such ecosystems: biophysical, exploitative and trophodynamic. Exploring the prominence among this ‘triad’ of drivers, through a synthetic analysis, is critical for understanding how marine ecosystems function and subsequently produce fisheries resources of interest to humans. To explore this topic further, an international workshop was held on 10–14 May 2010, at the National Academy of Science''s Jonsson Center in Woods Hole, MA, USA. The workshop compiled the data required to develop production models at different hierarchical levels (e.g. species, guild, ecosystem) for many of the major Northern Hemisphere marine ecosystems that have supported notable fisheries. Analyses focused on comparable total system biomass production, functionally equivalent species production, or simulation studies for 11 different marine fishery ecosystems. Workshop activities also led to new analytical tools. Preliminary results suggested common patterns driving overall fisheries production in these ecosystems, but also highlighted variation in the relative importance of each among ecosystems.     

Cassava: an appraisal of its phytochemistry and its biotechnological prospects

The present state of knowledge of the phytochemistry of small molecules isolated from the roots and leaves of cassava, Manihot esculenta Crantz (Euphorbiaceae), is reviewed. Cassava roots are an important source of dietary and industrial carbohydrates, mainly eaten as a source of starch, forming the staple food to over 500 million; additionally, the roots have value as a raw material for industrial starch production and for animal feed giving the crop high economic value, but it suffers markedly from post-harvest physiological deterioration (PPD). The hydroxycoumarins scopoletin and its glucoside scopolin as well as trace quantities of esculetin and its glucoside esculin are identified from cassava roots during PPD. The biotechnological prospects for cassava are also reviewed including a critical appraisal of transgenic approaches for crop improvement, together with its use for bioethanol production, due to cassava's efficient ability to fix carbon dioxide into carbohydrate.     

Rootstock genotype succession influences apple replant disease and root-zone microbial community composition in an orchard soil

Apple replant disease (ARD) is a soil-borne disease complex that affects young apple trees in replanted orchards, resulting in stunted growth and reduced yields. Newly developed rootstock genotypes with tolerance to ARD may help to control this disease. We determined the effects of rootstock genotype rotations during orchard renovation, by investigating root-zone soil microbial consortia and the relative severity of ARD on seven rootstock genotypes (M.9, M.26, G.30, G.41, G.65, G.935, and CG.6210) planted in soil where trees on four of those same rootstocks (M.9, M.26, G.30 and CG.6210) had grown for the previous 15 years. Rootstock genotyping indicated that genetic distances among rootstocks were loosely correlated with their differential responses to ARD. Root-zone fungal and bacterial community composition, assessed by DNA fingerprinting (T-RFLP), differed between M.26 and CG.6210. Soil bacterial communities were influenced most by which rootstock had grown in the soil previously, while fungal communities were influenced more by the current replanted rootstock. In a clone library of bacteria from M.26 and CG.6210 root-zone soil, β-Proteobacteria was the most abundant phylum (25% of sequences). Sequences representing the Burkholderia cepacia complex were obtained only from CG.6210 soil. Rootstock genotypes that were grown in the orchard soil previously affected subsequent ARD severity, but replanting with the same or closely related rootstocks did not necessarily exacerbate this disease problem. Our results suggest that genotype-specific interactions with soil microbial consortia are linked with apple rootstock tolerance or susceptibility to ARD.     

Nicotiana attenuata SIPK,WIPK, NPR1, and Fatty Acid-Amino Acid Conjugates Participate in the Induction of Jasmonic Acid Biosynthesis by Affecting Early Enzymatic Steps in the Pathway

Wounding and herbivore attack elicit the rapid (within minutes) accumulation of jasmonic acid (JA) that results from the activation of previously synthesized biosynthetic enzymes. Recently, several regulatory factors that affect JA production have been identified; however, how these regulators affect JA biosynthesis remains at present unknown. Here we demonstrate that Nicotiana attenuata salicylate-induced protein kinase (SIPK), wound-induced protein kinase (WIPK), nonexpressor of PR-1 (NPR1), and the insect elicitor N-linolenoyl-glucose (18:3-Glu) participate in mechanisms affecting early enzymatic steps of the JA biosynthesis pathway. Plants silenced in the expression of SIPK and NPR1 were affected in the initial accumulation of 13-hydroperoxy-linolenic acid (13-OOH-18:3) after wounding and 18:3-Glu elicitation by mechanisms independent of changes in 13-lipoxygenase activity. Moreover, 18:3-Glu elicited an enhanced and rapid accumulation of 13-OOH-18:3 that depended partially on SIPK and NPR1 but was independent of increased 13-lipoxygenase activity. Together, the results suggested that substrate supply for JA production was altered by 18:3-Glu elicitation and SIPK- and NPR1-mediated mechanisms. Consistent with a regulation at the level of substrate supply, we demonstrated by virus-induced gene silencing that a wound-repressed plastidial glycerolipase (NaGLA1) plays an essential role in the induction of de novo JA biosynthesis. In contrast to SIPK and NPR1, mechanisms mediated by WIPK did not affect the production of 13-OOH-18:3 but were critical to control the conversion of this precursor into 12-oxo-phytodienoic acid. These differences could be partially accounted for by reduced allene oxide synthase activity in WIPK-silenced plants.Jasmonic acid (JA) and some of its precursors and derivatives are signal molecules that function as essential mediators of the plant''s wound, antiherbivore, and antipathogen responses, as well as in growth and development (Farmer, 1994; Creelman and Mullet, 1997; Turner et al., 2002). In unelicited mature leaves, JA is maintained at very low levels, however, upon specific stimulations, its biosynthesis is induced within a few minutes (Glauser et al., 2008). This rapid biosynthetic response must result from the activation of constitutively expressed JA biosynthesis enzymes in unelicited tissue by substrate availability and/or posttranslational modifications. At present, little is known about the molecular mechanisms that activate JA biosynthetic enzymes.According to the canonical mechanism for JA biosynthesis (Vick and Zimmerman, 1983), free α-linolenic acid (18:3^Δ9,12,15, 18:3) forms 13(S)-hydroperoxyoctadecatrienoic acid [13S-(OOH)-18:3] by the action of 13-lipoxygenase (13-LOX) in plastids. 13S-(OOH)-18:3 is converted by allene oxide synthase (AOS) into a highly unstable allene oxide intermediate that is processed by allene oxide cyclase (AOC) to yield (9S,13S)-12-oxo-phytodienoic acid (OPDA). OPDA is transported from the plastid into the peroxisome where it is reduced by the action of OPDA reductase 3 (OPR3) and after three cycles of β-oxidation, (3R,7S)-JA is formed. Due to the large number of enzymes and different cellular compartments involved in JA biosynthesis, it is expected that the pathway is regulated at multiple steps. Resolution of the structures of the tomato (Solanum lycopersicum) OPR3 and Arabidopsis (Arabidopsis thaliana) AOC2 and ACX1 has provided insights into potential regulatory mechanisms for these enzymes (e.g. oligomerization and phosphorylation; Pedersen and Henriksen, 2005; Breithaupt et al., 2006; Hofmann et al., 2006).The identification of two Arabidopsis plastidial glycerolipases, DAD1 and DGL (Ishiguro et al., 2001; Hyun et al., 2008), has provided genetic evidence for the importance of the release of trienoic fatty acids (FAs) from plastidial lipids in the activation of JA biosynthesis. Recently, some oxylipins have been found esterified to galactolipids in Arabidopsis leaves and hence it is possible that in this species preformed precursors could also supply the JA biosynthesis pathway after their release from lipids (Stelmach et al., 2001; Hisamatsu et al., 2003; Buseman et al., 2006). However, lipid-bound oxylipins are not formed in the leaves of all plant families (Böttcher and Weiler, 2007).In Nicotiana attenuata, wound-induced JA production is amplified by the application of lepidopteran larvae (e.g. Manduca sexta) oral secretions (OS) to mechanical wounds. Major elicitors of the OS-mediated response are FA-amino acid conjugates (FACs) that are sufficient to enhance JA production in leaves of this plant species (Halitschke et al., 2001). Recently, several regulatory factors with a potential function upstream of JA biosynthesis have been identified (Ludwig et al., 2005; Takabatake et al., 2006; Schweighofer et al., 2007; Takahashi et al., 2007); however, how these regulators affect JA biosynthesis is at present unknown. For example, wounding and herbivory in Nicotina spp. and tomato activate the mitogen-activated protein kinases salicylate-induced protein kinase (SIPK) and wound-induced protein kinase (WIPK; Seo et al., 1999; Kandoth et al., 2007; Wu et al., 2007). When SIPK and WIPK expression is silenced in tobacco (Nicotiana tabacum), the plants accumulate 60% to 70% less JA than wild type after wounding or OS elicitation (Seo et al., 2007; Wu et al., 2007). Another regulatory component that affects JA production in N. attenuata is Nonexpressor of PR-1 (NPR1), an essential component of the salicylic acid (SA) signal transduction pathway first identified in Arabidopsis (Cao et al., 1994). N. attenuata NPR1-silenced plants accumulate 60% to 70% lower JA levels after elicitation than wild type (Rayapuram and Baldwin, 2007). NPR1 interacts with the JA and ethylene signaling cascades, and a cytosolic role for this factor in the regulation of JA-dependent responses/biosynthesis has been proposed (Spoel et al., 2003).In contrast to the mechanisms acting upstream of JA biosynthesis, the mechanisms mediating downstream JA responses are better characterized (Kazan and Manners, 2008; Browse, 2009). Among the best-characterized regulators of these responses is CORONATIVE INSENSITIVE1 (COI1), a gene that participates in jasmonate perception (Xie et al., 1998) and regulates gene expression through its interaction with the JASMONATE ZIM-DOMAIN repressors (Chini et al., 2007; Thines et al., 2007).To understand the early processes regulating the activation of JA biosynthesis by wounding and FAC elicitation in N. attenuata leaves, we quantified the initial rates of accumulation of plastid-derived JA precursors after these stimuli in wild type and four JA-deficient genotypes previously described: ir-sipk, ir-wipk, ir-npr1, and ir-coi1 (Rayapuram and Baldwin, 2007; Paschold et al., 2008; Meldau et al., 2009). We show that SIPK, WIPK, NPR1, and FACs contribute to the activation of de novo JA biosynthesis by affecting diverse early enzymatic steps in this pathway. The identification of a plastidial glycerolipase A₁ type I family protein (GLA1) essential for JA biosynthesis pointed to this enzyme as one potential target of some of these activating mechanisms.     

Effects of open-top chambers on physical properties of air and soil at post-disturbance sites in northwestern Quebec

Ecosystem responses to current global climate change can be predicted through experimental climate simulations. One such simulation method is the open-top chamber (OTC). The effects of OTCs on environmental factors are potentially complex, and recognizing the numerous interactions among these factors is crucial for the proper use of chambers. We studied the effects of OTCs on microclimatic factors including ambient temperature, relative humidity, soil temperature, and soil moisture. Plant abundance responses were also assessed. Our study involved the construction of 20 OTCs (1 m in diameter and 0.75 m in height; made of clear acrylic plastic) and 20 control plots on substrates with and without Sphagnum moss, at post-fire and logging sites of the transitional mixedwood-boreal forest in the southern part of James Bay region, Quebec. Experimental trials were also conducted to test the effects of OTCs on snowmelt in the Montreal region. Our results suggest that OTC treatment is most evident in terms of increased daytime maximum temperatures (2°C to 3°C), and cooler (up to ～2.4°C), drier (up to 10% volumetric moisture content) soils. Advanced thawing of the insulating snow cover and exposure of soil in the OTCs to low spring temperatures appeared to prolong soil freeze and result in cooler soils. Earlier snowmelt probably also led to earlier onset and overall increased evaporation of meltwater in the OTCs, leading to drier soils. Plant abundance responses to OTC treatment differed depending on plant species. Overall, open-top chambers provide an effective and simple method of climate change simulation, but it is highly advisable that the complex interactive effects, both desired and undesired, are well understood and appreciated before using OTCs for experimental climate simulation.     

Plant genotypic diversity does not beget root-fungal species diversity

The number of genetically distinct individuals within a community is a key component of biodiversity and yet its impact at different trophic levels, especially upon the diversity of functionally important soil microorganisms is poorly understood. Here, we test the hypothesis that plant communities that are genetically impoverished will support fewer species of root-associated fungi. We used established grassland mesocosms comprising non-sterile natural soil supporting defined communities of 11 clonally-propagated plant species. Half of the mesocosms contained one genotype per species and half 16 genotypes per species. After 8 years growth, we sampled roots from the mesocosms and measured root-associated fungal richness and diversity using terminal restriction fragment length polymorphism (T-RFLP). Contrary to our hypothesis, we found that the roots of genetically impoverished communities contained more species of fungi and had greater diversity compared to genetically rich communities. Analysis of the plant species composition of the mesocosm communities indicated that genotypic diversity affects root-fungal diversity indirectly through its influence upon plant species diversity. Our findings highlight the need to include feedbacks with plant intraspecific diversity into existing models describing the maintenance of soil biodiversity.     

Follow-on Biologics: A New Play for Big Pharma: Healthcare 2010

The U.S. pharmaceutical industry plays a vital role in shaping the face of American healthcare. As an industry rooted in innovation, its continued evolution is inherent. With major patent expirations looming and thin product pipelines, the industry now must consider new directions to maintain growth and stability. Follow-on biologics, derived from living organisms and marketed after the patent expiration of similar therapies, represent a growing opportunity for big pharmaceutical firms, as discussed during Yale’s Healthcare 2010 conference in April. Key characteristics of follow-on biologics make them a worthwhile investment for big pharma companies: They command high prices, will likely have fewer entrants than generics due to high barriers to entry, and play to the existing strengths of big pharma firms. With the recent healthcare legislation providing the way for consistent Food and Drug Administration (FDA) regulation, the timing seems right to continue the push into this new and growing market.At a time when healthcare issues are on the mind of every American, it would serve us well to consider the future of one of the most influential players in the sector: pharmaceutical companies. National health expenditures for pharmaceutical products are hovering around 10 percent, meaning that one out of every 10 dollars that we, as a nation, spend on healthcare goes toward drugs. These drugs regulate our cholesterol levels, promote the growth of white blood cells in cancer patients, manage our restless leg syndrome, help us sleep better at night, and provide myriad other benefits to our health and well-being. Yet, for all the benefits that the pharmaceutical industry provides, it is also criticized by many for the expense of its products and the high profit margins that these products command. The growing popularity of biologics — treatments derived from living organisms, such as antibodies and interleukins — has particularly increased the price of drugs in the United States. The current price of the average biologic is more than 20 times that of a traditional, chemically synthesized small-molecule drug. There is a trade-off between high prices and innovative new therapies. Moreover, pharmaceutical companies themselves argue justifiably that prices account not only for the price of production, but also for the research and development (R&D) for that therapy as well as numerous others that did not make it all the way through the regulatory process and to the clinic.In recent years, we have witnessed the breakdown of the well-oiled innovation machinery of the traditional big pharma company. While R&D departments spent more and more (well over $1B per drug), they did not see promising results in the form of late-stage drug candidates [1]. Over time, this led to a strategic shift in portfolio management within big pharma companies toward an acquisition-heavy plan to build up their pipeline of drugs. In-house R&D projects were cut, and layoffs of scientific staff were rampant. This phenomenon continues, with 2009 bearing witness to the most mergers and acquisitions in the pharmaceutical industry to date. Industry-wide consolidation aimed to find complementary development projects and synergies in manufacturing and emerging markets. What has been the effect of all of this? The answer is not as hopeful as the pharmaceutical industry would have liked. A giant “patent cliff” still persists, referring to a number of blockbuster drugs that will go off patent over the next two years and cause a dramatic decrease in sales for big pharma firms. Without a strong pipeline to fill in the valley with new product sales, big pharma companies have begun scrambling to find new ways to generate revenue.Meanwhile, the biotech industry’s foray into therapeutics has been a wild success story. From the 1980s to the present, biologics have reshaped the face of medicine in many disease areas. The spawn of highly innovative, nimble biotech firms, biologic drugs are large, complex molecules grown in living cells rather than synthesized chemically like small molecules. For example, Enbrel is a fusion protein that acts as a tumor necrosis factor (TNF) inhibitor to stop inflammation. This drug is being widely prescribed for rheumatoid arthritis as well as psoriasis, among other indications, with sales last year reaching $5.9 billion, up 9.3 percent from 2008 [2]. Enbrel was first developed by Immunex and released in 1998. Immunex was acquired by a rival biotech firm, Amgen, in 2001 [3], and subsequent marketing of the drug in the United States was jointly undertaken by Amgen and Wyeth (now taken over by Pfizer in the mega-merger of 2009). Enbrel’s is the classic story of the modern biologic: a novel therapy developed at a small biotech firm and acquired or licensed up the food chain to feed bigger firms’ appetites for late-stage assets.Enbrel is by no means unique; there are many blockbuster biologics on the market. Like Enbrel, many of them will reach the end of their patent life soon. Enbrel’s patent expiration is set for 2012, at which time it will be exposed to potential competition from generic versions. Therefore, though there are many novel biologics therapies that can provide new ways of treating patients, there is also a huge opportunity for generic versions of biologics that did not exist even one decade ago. This opportunity is hard to quantify, but one recent estimate shows that biologics responsible for $20B in annual sales will go off patent by 2015 [4]. Unsurprisingly, small-molecule generics firms are flocking to this space. Teva, the world’s largest generics manufacturer, has partnered with the Lonza Group to make and sell so-called follow-on biologics. These treatments are similar, but not identical, to preceding biologics whose patents expired. Meanwhile, Novartis’s generics arm, Sandoz, has increased capacity in biomanufacturing to ramp up its efforts. Big pharma itself has made motions of interest in the business of follow-on biologics, as witnessed by the dedicated division of Merck, BioVentures, established in late 2008 for the development of follow-on biologics. Interestingly, even Pfizer is testing a follow-on version of Enbrel, now in phase 2 clinical trials [5]. With a big market opportunity and a number of firms interested, follow-on biologics will surely play an important role in shaping the future of the pharma industry.For large pharmaceutical firms, what is needed is a way to diversify and mitigate risk, a way to supplement their rollercoaster sales figures year after year. Follow-on biologics may be a smart play for big pharma companies. Like their generic cousins, biologics manufacturing has strong economies of scale that big pharma firms can leverage. But unlike generics, there are higher barriers to entry because of the technical challenges of manufacturing biologics and the necessary clinical proofs of equivalency. Pharmaceutical companies already are practiced at navigating the global clinical-trials arena and should be able to exercise a significant competitive advantage in this area, especially over the existing generics manufacturers attempting a play in the follow-on biologics market. It has been estimated that the investment necessary to bring a follow-on biologic to market is eight to 10 years and will cost $100-$200M [6]. This investment of time and capital is substantial and tends to favor larger firms with significant R&D budgets. However, to put the investment into perspective, this is only one-tenth of the cost of developing a full-scale innovative pharmaceutical product and has less associated risk of failure — a proposition that the big pharma industry should find appealing. Additionally, the trend for current follow-on biologics on the market in the European Union (EU) and United States has been to use traditional detailing and marketing practices to compete with branded products. This, too, puts big pharma at a competitive advantage over other players lacking an army of detailing pharmaceutical reps, who can use their established relationships with doctors and medical personnel to promote new follow-on biologics.One counter-argument to the case for a move into follow-on biologics is that the new healthcare reform, the Patient Protection and Affordable Care Act (PPACA), passed in March of this year will harm any would-be generic biologics makers with its 12-year exclusivity for branded biologics. However, while this length of time is significantly longer than the proposed five years that generics proponents pushed for, the surety of a secure path forward through the FDA for follow-on biologics outweighs the downside of lengthy biologics exclusivity. It is reasonable to hope that within two to three years, the FDA will have functional guidelines for the regulation of this nascent market. Now more than at any other time in the past, the ambiguity associated with government regulation is manageable. And if big pharma becomes more intentional about entering the follow-on biologics market, its powerful lobby, PhRMA, could influence the way that the details of the FDA regulations are written.If the pharma industry does find the follow-on biologics market appealing and makes a bet on it for supplementary revenue, what can we expect from the patient perspective? It could mean greater access at cheaper prices, but the dynamics are much more nuanced. The economics of the small-molecule generics market likely will not be transferrable to the follow-on biologics market. High barriers to entry, high fixed costs of manufacturing, and marketing expenses will more likely manifest themselves in a market that has a small number of firms with relatively small price drops upon introduction of follow-on therapies. In small-molecule generics, the price typically decreases by about 80 percent from the original branded drug price after one year of generic competition. However, in current follow-on markets in the EU, this has not been the case. Since its introduction of biosimilars regulation in 2004, the EU has successfully introduced numerous follow-on biologics for three classes of branded drugs. The results hint at what might be expected for U.S. firms: By 2008 in Germany, biosimilars had captured an estimated 14 percent to 30 percent market share and discounted prices by 25 percent [7]. The U.S. story of follow-on biologics will likely mirror that of EU biosimilars rather than that of small-molecule generics.With healthcare legislation passed and the inevitable refocusing on bending the cost curve in healthcare expenditures, big pharma firms may be able to boost their reputation with the public as well as their bottom line with a continued push into follow-on biologics. The decreased risk of approval and steady returns will help diversify pharmaceutical companies’ volatile revenue streams, while concurrently winning favorable public opinion by promoting price reductions for some of the most expensive drugs available. The cost savings to consumers will increase access for patients as FDA regulation is finalized and more and more follow-on biologics enter the market. This could be a win-win scenario for big pharma and for patients.     

Mutational analysis of an archaeal minichromosome maintenance protein exterior hairpin reveals critical residues for helicase activity and DNA binding

Background

The mini-chromosome maintenance protein (MCM) complex is an essential replicative helicase for DNA replication in Archaea and Eukaryotes. While the eukaryotic complex consists of six homologous proteins (MCM2-7), the archaeon Sulfolobus solfataricus has only one MCM protein (ssoMCM), six subunits of which form a homohexamer. We have recently reported a 4.35Å crystal structure of the near full-length ssoMCM. The structure reveals a total of four β-hairpins per subunit, three of which are located within the main channel or side channels of the ssoMCM hexamer model generated based on the symmetry of the N-terminal Methanothermobacter thermautotrophicus (mtMCM) structure. The fourth β-hairpin, however, is located on the exterior of the hexamer, near the exit of the putative side channels and next to the ATP binding pocket.

Results

In order to better understand this hairpin's role in DNA binding and helicase activity, we performed a detailed mutational and biochemical analysis of nine residues on this exterior β-hairpin (EXT-hp). We examined the activities of the mutants related to their helicase function, including hexamerization, ATPase, DNA binding and helicase activities. The assays showed that some of the residues on this EXT-hp play a role for DNA binding as well as for helicase activity.

Conclusions

These results implicate several current theories regarding helicase activity by this critical hexameric enzyme. As the data suggest that EXT-hp is involved in DNA binding, the results reported here imply that the EXT-hp located near the exterior exit of the side channels may play a role in contacting DNA substrate in a manner that affects DNA unwinding.

     

Peak and averaged bicoherence for different EEG patterns during general anaesthesia

Background  

Changes in nonlinear neuronal mechanisms of EEG generation in the course of general anaesthesia have been extensively investigated in research literature. A number of EEG signal properties capable of tracking these changes have been reported and employed in anaesthetic depth monitors. The degree of phase coupling between different spectral components is a marker of nonlinear EEG generators and is claimed to be an important aspect of BIS. While bicoherence is the most direct measure of phase coupling, according to published research it is not directly used in the calculation of BIS, and only limited studies of its association with anaesthetic depth and level of consciousness have been published. This paper investigates bicoherence parameters across equal band and unequal band bifrequency regions, during different states of anaesthetic depth relating to routine clinical anaesthesia, as determined by visual inspection of EEG.