Is 'big biology' a commercial enterprise?

Big projects in biology - such as the human genome project and a number of related and ensuing enterprises - require big funding. A new tradition is growing in which some types of basic research take place within commercial organizations. This article reviews some of the reasons for this and some of the key players, in the USA, Europe and Japan, and highlights some issues to be considered when deciding whether particular research belongs in a company rather than an academic setting.     

Film forming microbial biopolymers for commercial applications—A review

Abstract

Microorganisms synthesize intracellular, structural and extracellular polymers also referred to as biopolymers for their function and survival. These biopolymers play specific roles as energy reserve materials, protective agents, aid in cell functioning, the establishment of symbiosis, osmotic adaptation and support the microbial genera to function, adapt, multiply and survive efficiently under changing environmental conditions. Viscosifying, gelling and film forming properties of these have been exploited for specific significant applications in food and allied industries. Intensive research activities and recent achievements in relevant and important research fields of global interest regarding film forming microbial biopolymers is the subject of this review. Microbial polymers such as pullulan, kefiran, bacterial cellulose (BC), gellan and levan are placed under the category of exopolysaccharides (EPS) and have several other functional properties including film formation, which can be used for various applications in food and allied industries. In addition to EPS, innumerable bacterial genera are found to synthesis carbon energy reserves in their cells known as polyhydroxyalkanoates (PHAs), microbial polyesters, which can be extruded into films with excellent moisture and oxygen barrier properties. Blow moldable biopolymers like PHA along with polylactic acid (PLA) synthesized chemically in vitro using lactic acid (LA), which is produced by LA bacteria through fermentation, are projected as biodegradable polymers of the future for packaging applications. Designing and creating of new property based on requirements through controlled synthesis can lead to improvement in properties of existing polysaccharides and create novel biopolymers of great commercial interest and value for wider applications. Incorporation of antimicrobials such as bacteriocins or silver and copper nanoparticles can enhance the functionality of polymer films especially in food packaging applications either in the form of coatings or wrappings. Use of EPS in combinations to obtain desired properties can be evaluated to increase the application range. Controlled release of active compounds, bioactive protection and resistance to water can be investigated while developing new technologies to improve the film properties of active packaging and coatings. An holistic approach may be adopted in developing an economical and biodegradable packaging material with acceptable properties. An interdisciplinary approach with new innovations can lead to the development of new composites of these biopolymers to enhance the application range. This current review focuses on linking and consolidation of recent research activities on the production and applications of film forming microbial polymers like EPS, PHA and PLA for commercial applications.     

An overview of commercial fishers’ attitudes towards marine protected areas

Marine protected areas (MPAs) are attracting widespread attention worldwide as a tool for fishery management and marine ecosystem conservation. The establishment of MPAs has increased greatly in recent years mostly due to international commitments to the establishment of a global network of MPAs by 2012. MPAs have the potential to strongly affect the fishing industry, and their success depends, at least partly, on fishers’ attitudes towards this management measure. However, research on MPAs tends to focus on the ecological and conservation aspects of this management approach and not on its human dimensions. Studies in attitudes, perceptions, beliefs and preferences related to MPA issues have been identified as priority social science topics in need of research. We present a ‘rapid review’, conducted systematically, of the literature published up to September 2009 and aimed at identifying the most investigated topics related to commercial fishers’ attitudes towards MPAs, describing the main findings from these studies, and analysing the implications for management. Most published work focuses on fishers’ attitudes towards issues of governance, conservation of biodiversity and the environment, and the impact of MPAs on fishing activity. Despite the recent increase in the literature on the human dimensions of MPAs, the present review reveals that little of this literature originates from empirical studies. Hence, given the forthcoming increase in the implementation of MPAs in the near future, research on fishers’ attitudes towards these management measures is critically needed.     

Bioreactors in tissue engineering—principles,applications and commercial constraints

Bioreactor technology is vital for tissue engineering. Usually, bioreactors are used to provide a tissue-specific physiological in vitro environment during tissue maturation. In addition to this most obvious application, bioreactors have the potential to improve the efficiency of the overall tissue-engineering concept. To date, a variety of bioreactor systems for tissue-specific applications have been developed. Of these, some systems are already commercially available. With bioreactor technology, various functional tissues of different types were generated and cultured in vitro. Nevertheless, these efforts and achievements alone have not yet led to many clinically successful tissue-engineered implants. We review possible applications for bioreactor systems within a tissue-engineering process and present basic principles and requirements for bioreactor development. Moreover, the use of bioreactor systems for the expansion of clinically relevant cell types is addressed. In contrast to cell expansion, for the generation of functional three-dimensional tissue equivalents, additional physical cues must be provided. Therefore, bioreactors for musculoskeletal tissue engineering are discussed. Finally, bioreactor technology is reviewed in the context of commercial constraints.     

Persistence of extended-spectrum β-lactamase plasmids among Enterobacteriaceae in commercial broiler farms

To clarify the persistence of extended-spectrum β-lactamase (ESBL) producers, 13 plasmids from two broiler farms were analyzed. On the farm not using antimicrobials, one plasmid from Klebsiella pneumoniae isolated from a day-old chick was similar to that from Escherichia coli isolated a year later, with the deletion of two transposons. On the farm using antimicrobials, most circulating plasmids (eight out of nine) in a flock of 40-days-old chicks were identical, although one from K. pneumoniae had a deletion of a transposon carrying a class 1 integron containing aadA2 and dfrA12. Thus, ESBL plasmids persisted in the farms with or without antimicrobial agent use.     

Effects of midas® on nematodes in commercial floriculture production in Florida

Cut flower producers currently have limited options for nematode control. Four field trials were conducted in 2006 and 2007 to evaluate Midas® (iodomethane:chloropicrin 50:50) for control of root-knot nematodes (Meloidogyne arenaria) on Celosia argentea var. cristata in a commercial floriculture production field in southeastern Florida. Midas (224 kg/ha) was compared to methyl bromide:chloropicrin (98:2, 224 kg/ha), and an untreated control. Treatments were evaluated for effects on Meloidogyne arenaria J2 and free-living nematodes in soil through each season, and roots at the end of each season. Plant growth and root disease were also assessed. Population levels of nematodes isolated from soil were highly variable in all trials early in the season, and generally rebounded by harvest, sometimes to higher levels in fumigant treatments than in the untreated control. Although population levels of nematodes in soil were not significantly reduced during the growing season, nematodes in roots and galling at the end of the season were consistently reduced with both methyl bromide and Midas compared to the untreated control. Symptoms of phytotoxicity were observed in Midas treatments during the first year and were attributed to Fe toxicity. Fertilization was adjusted during the second year to investigate potential fumigant/fertilizer interactions. Interactions occurred at the end of the fourth trial between methyl bromide and fertilizers with respect to root-knot nematode J2 isolated from roots and galling. Fewer J2 were isolated from roots treated with a higher level of Fe (3.05%) in the form of Fe sucrate, and galling was reduced in methyl bromide treated plots treated with this fertilizer compared to Fe EDTA. Reduced galling was also seen with Midas in Fe sucrate fertilized plots compared to Fe EDTA. This research demonstrates the difficulty of reducing high root-knot nematode population levels in soil in subtropical conditions in production fields that have been repeatedly fumigated. Although soil population density may remain stable, root population density and disease can be reduced.     

Dolly for dinner? Assessing commercial and regulatory trends in cloned livestock

As cloning technologies become more widely established, will products enter the food chain sooner than regulatory agencies and the public might be prepared for?     

Genetic barcoding of commercial Bêche-de-mer species (Echinodermata: Holothuroidea)

There are more than 47 species of holothurians used for bêche-de-mer production, many of which are locally overfished. With three exceptions, all bêche-de-mer species are Aspidochirotida and species identification of many of these is difficult. We analysed available genetic information and newly generated sequences to determine if genetic barcoding with the mitochondrial COI gene can be used to identify bêche-de-mer species. Although genetic data were available for ～50% of bêche-de-mer species, sufficient information and within-species replication were only available for six species. We generated 96 new COI sequences extending the existing database to cover most common species. COI unambiguously identified most bêche-de-mer species providing a genetic barcode for the identification of known species. In addition, conspecific (1.3%) variation and congeneric (16.9%) divergence were well separated ('barcoding-gap') albeit with a small overlap, which may lead to some error if genetic sampling alone was applied for species discovery. In addition to identification of adults, COI sequences were useful to identify juveniles that are often morphologically different. Sequence data showed that large (deep) and small (shallow) morphotypes of Holothuria atra are the same species, but suggested potential cryptic species within this taxon. For bêche-de-mer, the COI barcode proved useful in species clarification and discovery, but further genetic and taxonomic work is essential for several species. Some bêche-de-mer clades were problematic with morphologically disparate specimens sharing the same barcode. Our study indicated the presence of undescribed species (Bohadschia sp.) and species that constitute separate species in the Indian and Pacific Ocean (e.g. Holothuria fuscogilva).     

Deoxynivalenol in commercial beer — screening for the toxin with an indirect competitive ELISA

Antibodies specific for deoxynivalenol (DON) were prepared by immunizing rabbits with a deoxynivalenol-hemiglutaryl-HSA conjugate. The antibody showed cross-reactivity with DON, 15a-acetyl-DON (15-Ac DON), and 3a-acotyl-DON (3-Ac DON) of 100%, 216%, and 260%, respectively. No cross-reactivity was observed against 20 further trichothecenes of the A-, B-, and C-type. An indirect competitive ELISA procedure was set up for the detection of DON in liquid matrices occurring in the brewing process, Including beer. ELISA was sensitive down to 3.8 ng/mL. Detection limit for DON in tenfold diluted beer was 50 ppb. Recovery of the toxin in spiked beer was 45%, 77%, and 83% at toxin levels of 50; 500; and 1,000 ppb, respectively. ELISA results corresponded quite well with HPLC data. 196 commercial beers from several German breweries, including 36 gushing-positive samples, were assayed for DON. Screening revealed toxin levels from not detectable to 569 ppb. 69% of the gushing beers had marked levels of DON. 37% of the gushing-negative beer samples contained DON in detectable amounts with a maximum content of 172 ppb. Wheat beers had significantly higher DON-contents than beers derived from barley. Concentration of the toxin was significantly higher in gushing beers than in nongushing beers from both cereal sources.     

Characterization of commercial and biological growth curves in the Segureña sheep breed

Non-linear models were analysed to describe both the biological and commercial growth curves of the Segureña sheep, one of the most important Spanish breeds. We evaluated Brody, von Bertalanffy, Verhulst, logistic and Gompertz models, using historical data from the National Association of Segureña Sheep Breeders (ANCOS). These records were collected between 2000 and 2013, from a total of 129 610 weight observations ranging from birth to adulthood. The aim of this research was to establish the mathematical behaviour of body development throughout this breed’s commercial life (birth to slaughter) and biological life (birth to adulthood); comparison between both slopes gives important information regarding the best time for slaughter, informs dietary advice according to animals’ needs, permits economical predictions of productions and, by using the curve parameters as selection criteria, enables improvements in growth characteristics of the breed. Models were fitted according to the non-linear regression procedure of statistical package SPSS version19. Model parameters were estimated using the Levenberg–Marquardt algorithm. Candidate models were compared using the determinative coefficient, mean square error, number of iterations, Akaike information coefficient and biological coherence of the estimated parameters. The von Bertalanffy and logistic models were found to be best suited to the biological and commercial growth curves, respectively, for both sexes. The Brody equation was found to be unsuitable for studying the commercial growth curve. Differences between the parameters in both sexes indicate a strong impact of sexual dimorphism on growth. This can emphasize the value of the highest growth rate for females, indicating that they reach maturity earlier.     

Molecular identification of 16S rII phytoplasma group in commercial pistachio cultivars in Iran

Evaluation of phytoplasmas infection was conducted in the pistachio-growing areas of Iran (Rafsanjan in Kerman province) in early autumn of 2011. A total of 30 pistachio trees collected from a pistachio orchard in Rafsanjan showing Psylla damage symptoms and 10 samples with different abnormal symptoms from miscellaneous orchards were tested for the presence of phytoplasma. By using nested PCR with primer pairs P1/P7 and internal primer sets R16F2N/R16R2 and fU3-rU5, amplified fragment of expected size was observed in some trees with deformation and yellowing symptoms. On the basis of nucleotide sequence analysis of 16S?rDNA amplified by PCR, this phytoplasma was classified in group 16S?rII. In addition, we observed false positive reaction in three trees of Ahmadaghaei cultivar by using primer sets R16F2N/R16R2 and sequence analysis of ~1250bp PCR product indicated that amplified fragment was related to Schinus terebinthifolius; a species of flowering plant in the Anacardiaceae family.     

Toxicological implications of a commercial formulation of deltamethrin (Decis®) in developing chick embryo

A deltamethrin containing insecticide formulation (Decis®) was evaluated for its toxic potential in developing chick embryos. For the present study, three water emulsified concentrations of Decis® (12.5 mg L^?1, 25 mg L^?1, and 50 mg L^?1) were used. Fertilized eggs of Gallus domesticus were immersed in these three concentrations of the insecticide for 60 min at 37°C on day 0 of incubation and kept for incubation till embryonic day 7. Recovered embryos were evaluated for teratogenic and biochemical changes. The results revealed that administration of Decis® at its lower concentrations (12.5 mg L^?1 and 25 mg L^?1) did not show any significant teratological changes but the significant number of abnormal survivors was observed at 50 mg L^?1 of dose concentration when compared with vehicle-treated control. Among biochemical changes, total glycogen and RNA contents of embryos was significantly decreased at 25 mg L^?1 and 50 mg L^?1 of Decis® concentrations. Similarly, significant alteration (p ≤ .05) was observed in alanine transaminase activity at 50 mg L^?1 concentration of Decis®. Thus, the present study concluded that the no-effect-level for developmental toxicity for Decis® is below the concentration of 25 mg L^?1 under standard laboratory conditions.     

Detection of metallo-β-lactamase genes in clinical specimens by a commercial multiplex PCR system

hyplex®-MBL ID Multiplex PCR-ELISA, a novel method for identifying metallo-β-lactamase genes directly in clinical specimens, was evaluated using a consecutive collection of 326 samples from three hospitals in Greece characterized by high prevalence of VIM producers. The method exhibited high sensitivity (98.0%) and specificity (98.6%) and was proven reliable in detecting bla_VIM genes in blood, urine, pus, and sputum samples that, as confirmed by conventional methods, contained various VIM-producing species. Future multicenter studies should be considered for the thorough evaluation of this method and its potential diagnostic utility.     

Purification and characterization of glycyrrhizin-β-d-glucuronidase and baicalin-β-d-glucuronidase from a commercial enzyme preparation

Abstract

Five commercial enzyme preparations were screened for hydrolysis of the glucuronic acid units of glycyrrhizin (GL) and baicalin. Two preparations hydrolyzing GL to glycyrrhetic acid (GA) and four enzyme preparations hydrolyzing baicalin to baicalein were obtained. One enzyme preparation with the ability to hydrolyze both GL and baicalin, namely Rapidase Pineapple, was purified by anion exchange, cation exchange and molecular sieve chromatography. The results of purification indicated that the enzymes containing the glycyrrhizin-β-d-glucuronidase (GBDG) and baicalin-β-d-glucuronidase (BBDG) activities were distinct, with different substrate specificities, molecular weights and enzymatic characteristics. GBDB hydrolyzed GL to GA, but had no detectable activity on baicalin, and BBDG hydrolyzed baicalin to baicalein, but could not hydrolyze GL. However, both GBDG and BBDG could hydrolyze the artificial substrate p-nitrophenyl- β-d-glucuronide (pNPGA).     

Do commercial serologic tests for Trypanosoma cruzi infection detect Mexican strains in women and newborns?

We sought to determine the serological test that could be used for Trypanosoma cruzi seroprevalence studies in Mexico, where lineage I predominates. In a previous study among pregnant women and their newborns in the states of Yucatan and Guanajuato, we reported a 0.8-0.9% of prevalence for T. cruzi -specific antibodies by Stat-Pak and Wiener ELISA. We have expanded this study here by performing an additional non-commercial ELISA and confirming the seropositives with Western blot, using whole antigens of a local parasite strain. We found a seroprevalence of 0.6% (3/500) in Merida and 0.4% in Guanajuato (2/488). The 5 seropositive umbilical cord samples reacted to both non-commercial ELISA and Western blot tests, and only 1 of the maternal samples was not reactive to non-commercial ELISA. A follow-up of the newborns at 10 mo was performed in Yucatan to determine the presence of T. cruzi antibodies in children as evidence of congenital infection. None of the children was seropositive. One newborn from an infected mother died at 2 wk of age of cardiac arrest, but T. cruzi infection was not confirmed. The T. cruzi seroprevalence data obtained with both commercial tests (Stat-Pak and ELISA Wiener) are similar to those from non-commercial tests using a local Mexican strain of T. cruzi.     

Cory’s shearwater by-catch in the Mediterranean Spanish commercial longline fishery: implications for management

Cory’s shearwater Calonectris diomedea is the main seabird species by-caught by the Spanish longline fleet operating in the western Mediterranean Sea. Identification of the principal factors that determine this by-catch and understanding how they could be controlled is fundamental for improving the management of fisheries and so carry out a better conservation of Cory’s shearwater populations in the Mediterranean. The aim of this paper was to model the longline by-catch of Mediterranean Cory’s shearwater in the Spanish Mediterranean longline fishery as a function of time of the year, technical characteristics of the fishing operation, and geographical location. We used data recorded by an onboard observer program monitoring commercial longline fisheries. During the 10 years covered in this study, 80 birds were captured in 30 fishing operations out of a total of 2,587 observed fishing sets. We used favourability functions and Random Forest analyses to relate the presence of Cory’s shearwater in the by-catch with the explanatory factors. The most explanatory factor in relation to incidence of by-catch was the geographical location (longitude and fishing over the continental shelf) and then the technical characteristics of the fishing operation (number of hooks and fishing during non-working days). Our conclusion is clear, because seabirds are more likely to approach longline vessels when trawlers are not allowed to operate (i.e. non-working days), activity of longliners should be limited to working days, and closing longliners activity during the month of October could reduce greatly reducing seabird bycatch.     

The care and feeding of a commercial liposomal product: liposomal amphotericin B (AmBisome®)

Abstract

AmBisome (liposomal amphotericin B) is among the earliest approved liposomal therapeutics, and has been in commercial use since the early 1990s. This review provides examples of non-clinical, regulatory, clinical label expansion, adverse event management, and supply chain control reflecting the real world challenges of a commercial liposomal therapeutic. We review examples of post-approval clinical development in severe lung infections, development of US and European guidance documents around liposomal therapeutics, the creation of a suitable placebo for blinded clinical trials, response to findings of a possible new category of adverse event (what turned out to be pseudohyperphosphatemia), challenges in handling the finished product in a setting with high risk of exposure of the product to temperatures outside of the established label storage conditions, and elements of continuingly increased aseptic processing requirements for manufacturing.