Eco-label conveys reliable information on fish stock health to seafood consumers

Concerns over fishing impacts on marine populations and ecosystems have intensified the need to improve ocean management. One increasingly popular market-based instrument for ecological stewardship is the use of certification and eco-labeling programs to highlight sustainable fisheries with low environmental impacts. The Marine Stewardship Council (MSC) is the most prominent of these programs. Despite widespread discussions about the rigor of the MSC standards, no comprehensive analysis of the performance of MSC-certified fish stocks has yet been conducted. We compared status and abundance trends of 45 certified stocks with those of 179 uncertified stocks, finding that 74% of certified fisheries were above biomass levels that would produce maximum sustainable yield, compared with only 44% of uncertified fisheries. On average, the biomass of certified stocks increased by 46% over the past 10 years, whereas uncertified fisheries increased by just 9%. As part of the MSC process, fisheries initially go through a confidential pre-assessment process. When certified fisheries are compared with those that decline to pursue full certification after pre-assessment, certified stocks had much lower mean exploitation rates (67% of the rate producing maximum sustainable yield vs. 92% for those declining to pursue certification), allowing for more sustainable harvesting and in many cases biomass rebuilding. From a consumer's point of view this means that MSC-certified seafood is 3-5 times less likely to be subject to harmful fishing than uncertified seafood. Thus, MSC-certification accurately identifies healthy fish stocks and conveys reliable information on stock status to seafood consumers.     

Comparative proteomics profile of osteoblasts cultured on dissimilar hydroxyapatite biomaterials: an iTRAQ-coupled 2-D LC-MS/MS analysis

Hydroxyapatite (HA) and its derived bioceramic materials have been widely used for skeletal implants and/or bone repair scaffolds. It has been reported that carbon nanotube (CNT) is able to enhance the brittle ceramic matrix without detrimental to the bioactivity. However, interaction between osteoblasts and these bioceramics, as well as the underlying mechanism of osteoblast proliferation on these bioceramic surfaces remain to be determined. Using iTRAQ-coupled 2-D LC-MS/MS analysis, we report the first comparative proteomics profiling of human osteoblast cells cultured on plane HA and CNT reinforced HA, respectively. Cytoskeletal proteins, metabolic enzymes, signaling, and cell growth proteins previous associated with cell adhesion and proliferation were found to be differentially expressed on these two surfaces. The level of these proteins was generally higher in cells adhered to HA surface, indicating a higher level of cellular proliferation in these cells. The significance of these findings was further assessed by Western blot analysis. The differential protein profile in HA and CNT strengthened HA established in our study should be valuable for future design of biocompatible ceramics.     

Probing effects of pH change on dynamic response of Claudin-2 mediated adhesion using single molecule force spectroscopy

Claudins belong to a large family of transmembrane proteins that localize at tight junctions (TJs) where they play a central role in regulating paracellular transport of solutes and nutrients across epithelial monolayers. Their ability to regulate the paracellular pathway is highly influenced by changes in extracellular pH. However, the effect of changes in pH on the strength and kinetics of claudin mediated adhesion is poorly understood. Using atomic force microscopy, we characterized the kinetic properties of homophilic trans-interactions between full length recombinant GST tagged Claudin-2 (Cldn2) under different pH conditions. In measurements covering three orders of magnitude change in force loading rate of 10²–10⁴ pN/s, the Cldn2/Cldn2 force spectrum (i.e., unbinding force versus loading rate) revealed a fast and a slow loading regime that characterized a steep inner activation barrier and a wide outer activation barrier throughout pH range of 4.5–8. Comparing to the neutral condition (pH 6.9), differences in the inner energy barriers for the dissociation of Cldn2/Cldn2 mediated interactions at acidic and alkaline environments were found to be < 0.65 k_BT, which is much lower than the outer dissociation energy barrier (> 1.37 k_BT). The relatively stable interaction of Cldn2/Cldn2 in neutral environment suggests that electrostatic interactions may contribute to the overall adhesion strength of Cldn2 interactions. Our results provide an insight into the changes in the inter-molecular forces and adhesion kinetics of Cldn2 mediated interactions in acidic, neutral and alkaline environments.     

Genomic and proteomic perspectives in cell culture engineering.

In the last few years, the number of biologics produced by mammalian cells have been steadily increasing. The advances in cell culture engineering science have contributed significantly to this increase. A common path of product and process development has emerged in the last decade and the host cell lines frequently used have converged to only a few. Selection of cell clones, their adaptation to a desired growth environment, and improving their productivity has been key to developing a new process. However, the fundamental understanding of changes during the selection and adaptation process is still lacking. Some cells may undergo irreversible alteration at the genome level, some may exhibit changes in their gene expression pattern, while others may incur neither genetic reconstruction nor gene expression changes, but only modulation of various fluxes by changing nutrient/metabolite concentrations and enzyme activities. It is likely that the selection of cell clones and their adaptation to various culture conditions may involve alterations not only in cellular machinery directly related to the selected marker or adapted behavior, but also those which may or may not be essential for selection or adaptation. The genomic and proteomic research tools enable one to globally survey the alterations at mRNA and protein levels and to unveil their regulation. Undoubtedly, a better understanding of these cellular processes at the molecular level will lead to a better strategy for 'designing' producing cells. Herein the genomic and proteomic tools are briefly reviewed and their impact on cell culture engineering is discussed.     

Harmonizing Energy and Power Density toward 2.7 V Asymmetric Aqueous Supercapacitor

Tremendous research efforts are devoted to developing wide potential window aqueous supercapacitors to resolve their low energy density concern. While the operational potential window is dictated by the intrinsic electrochemical stability of water (1.23 V), such a bottleneck may be surpassed by leveraging the additional overpotential of the oxygen evolution reaction and the hydrogen evolution reaction (HER). Herein, by employing an electroreduction technique, Na⁺ is adsorbed onto the carbon negative electrode which effectively acts as a physical barrier to hinder intermediate HER product formation, thereby reducing HER activity. To complement the wide potential carbon electrode, Na_0.25MnO₂ is employed as the positive electrode to take advantage of the extra energy (i.e., increased overpotential) required for Na⁺ insertion process into the structure. The asymmetric supercapacitor exhibits high energy density of 61.1 W h kg^?1 at a power density of 982 W kg^?1, and even at an ultrahigh power density of 42.9 kW kg^?1, a respectable energy density of 16.3 W h kg^?1 is attained. In addition, 93.7% capacitance retention is recorded after cycling for 10 000 cycles which further demonstrates its suitability as supercapacitor. The present success in fabricating a 2.7 V asymmetric supercapacitor will open a promising research route toward achieving high energy density and high power density.     

Kinase gene fusions in defined subsets of melanoma

Genomic rearrangements resulting in activating kinase fusions have been increasingly described in a number of cancers including malignant melanoma, but their frequency in specific melanoma subtypes has not been reported. We used break‐apart fluorescence in situ hybridization (FISH) to identify genomic rearrangements in tissues from 59 patients with various types of malignant melanoma including acral lentiginous, mucosal, superficial spreading, and nodular. We identified four genomic rearrangements involving the genes BRAF, RET, and ROS1. Of these, three were confirmed by Immunohistochemistry (IHC) or sequencing and one was found to be an ARMC10‐BRAF fusion that has not been previously reported in melanoma. These fusions occurred in different subtypes of melanoma but all in tumors lacking known driver mutations. Our data suggest gene fusions are more common than previously thought and should be further explored particularly in melanomas lacking known driver mutations.     

Identification of Novel Serological Biomarkers for Inflammatory Bowel Disease Using Escherichia coli Proteome Chip

Specific antimicrobial antibodies present in the sera of patients with inflammatory bowel disease (IBD) have been proven to be valuable serological biomarkers for diagnosis/prognosis of the disease. Herein we describe the use of a whole Escherichia coli proteome microarray as a novel high throughput proteomics approach to screen and identify new serological biomarkers for IBD. Each protein array, which contains 4,256 E. coli K12 proteins, was screened using individual serum from healthy controls (n = 39) and clinically well characterized patients with IBD (66 Crohn disease (CD) and 29 ulcerative colitis (UC)). Proteins that could be recognized by serum antibodies were visualized and quantified using Cy3-labeled goat anti-human antibodies. Surprisingly significance analysis of microarrays identified a total of 417 E. coli proteins that were differentially recognized by serum antibodies between healthy controls and CD or UC. Among those, 169 proteins were identified as highly immunogenic in healthy controls, 186 proteins were identified as highly immunogenic in CD, and only 19 were identified as highly immunogenic in UC. Using a supervised learning algorithm (k-top scoring pairs), we identified two sets of serum antibodies that were novel biomarkers for specifically distinguishing CD from healthy controls (accuracy, 86 ± 4%; p < 0.01) and CD from UC (accuracy, 80 ± 2%; p < 0.01), respectively. The Set 1 antibodies recognized three pairs of E. coli proteins: Era versus YbaN, YhgN versus FocA, and GabT versus YcdG, and the Set 2 antibodies recognized YidX versus FrvX. The specificity and sensitivity of Set 1 antibodies were 81 ± 5 and 89 ± 3%, respectively, whereas those of Set 2 antibodies were 84 ± 1 and 70 ± 6%, respectively. Serum antibodies identified for distinguishing healthy controls versus UC were only marginal because their accuracy, specificity, and sensitivity were 66 ± 5, 69 ± 5, and 61 ± 7%, respectively (p < 0.04). Taken together, we identified novel sets of serological biomarkers for diagnosis of CD versus healthy control and CD versus UC.Crohn disease (CD)¹ and ulcerative colitis (UC) are chronic, idiopathic, and clinically heterogeneous intestinal disorders collectively known as inflammatory bowel disease (IBD) (1, 2). Although the distinction between UC and CD would seem clear based on the combination of clinical, endoscopic, and radiological criteria, indeterminate colitis is present in up to 10 and 20% of adult and pediatric patients with isolated colitis, respectively (3, 4).Serological testing is a non-invasive method for diagnosing IBD and differentiating UC from CD (5–7). Several serological IBD biomarkers have been identified in the past decade, and some have been used in IBD clinics (5–7) (see the list below). Many of these antibodies are produced on intestinal exposure to normal commensal bacteria in genetically susceptible individuals. Although it is not known whether these antibodies are pathogenic or not, they are specific to patients with either CD or UC and may reflect a dysregulated immune inflammatory response to intestinal bacterial antigens (2, 8–10). Several experimental animal models of IBD have led to the theory that the pathogenesis of IBD is the result of an aberrant immune response to normal commensal bacteria in genetically susceptible individuals (11, 12). In fact, most of the major serological biomarkers being used in IBD clinics are antibodies to microbial antigens, including yeast oligomannose (anti-Saccharomyces cerevisiae (ASCA)), bacterial outer membrane porin C (OmpC), Pseudomonas fluorescens bacterial sequence I2 (anti-I2), and most recently bacterial flagellin (CBir 1) (5–7, 13). All of these antimicrobial antibodies show a preponderance in patients with CD. However, ASCA has been identified in up to 5% of patients with UC (13, 14).In comparison, perinuclear anti-neutrophil cytoplasmic antibody (pANCA) with perinuclear highlighting was first described in 1990. Although generally considered an autoantibody, the specific antigenic stimulation for pANCA production remains unclear. This autoantibody is present in up to 70% of patients with UC and in up to 20% of patients with CD (6, 10). Recently a panel of five new anti-glycan antibodies have been identified, including anti-chitobioside IgA, anti-laminaribioside IgG, anti-mannobioside IgG, and antibodies against two major chemically synthesized (Σ) oligomannose epitopes, Man α-1,3 Man α-1,2 Man (ΣMan3) and Man α-1,3 Man α-1,2 Man α-1,2 Man (ΣMan4) (5, 13, 15). These new biomarkers serve as valuable complimentary tools to the available serological biomarkers mentioned above. Collectively these antibodies are not generally present in either children or adults with non-IBD disease and may represent serological markers of intestinal inflammation specific to UC or CD.Although encouraging, none of the current commercially available biomarker tests/assays, including all of those mentioned above, can be used as stand alone tools in clinics and therefore are only recommended as an adjunct to endoscopy in diagnosis and prognosis of the disease (5, 7, 16). Therefore, additional specific and sensitive IBD biomarkers are needed as are prospective studies to assess the utility of current and newly identified biomarkers (5, 13). Proteomics technologies such as two-dimensional gel electrophoresis, various variations of mass spectrometry, and protein chip (array) technology are now proving to be powerful tools in biomarker discovery and are beginning to be utilized in IBD biomarker discovery (5, 17). These technologies enable robust and/or large scale and high throughput identification and analysis of differential protein expression when comparing disease with control. Blood-based (serum- or plasma-based) proteomics holds particular promises for biomarker discovery of various human diseases such as neurodegenerative diseases and cancers (18–20). Antigen microarrays are also powerful tools that allow high throughput serum analysis of aberrant immune responses in autoimmune diseases (21–23) as well as efficient discovery of biomarkers for infectious pathogens (24). Herein we describe the use of an Escherichia coli proteome microarray to characterize the differential immune response (serum anti-E. coli antibodies) among patients clinically classified as CD, UC, and healthy controls. We hypothesized that novel IBD-specific antimicrobial antibodies, particularly anti-E. coli antibodies, are present in IBD patients and are likely to be identified by screening the sera with E. coli protein arrays.     

Stochasticity of bacterial attachment and its predictability by the extended derjaguin-landau-verwey-overbeek theory

Bacterial attachment onto materials has been suggested to be stochastic by some authors but nonstochastic and based on surface properties by others. We investigated this by attaching pairwise combinations of two Salmonella enterica serovar Sofia (S. Sofia) strains (with different physicochemical and attachment properties) with one strain each of S. enterica serovar Typhimurium, S. enterica serovar Infantis, or S. enterica serovar Virchow (all with similar physicochemical and attachment abilities) in ratios of 0.428, 1, and 2.333 onto glass, stainless steel, Teflon, and polysulfone. Attached bacterial cells were recovered and counted. If the ratio of attached cells of each Salmonella serovar pair recovered was the same as the initial inoculum ratio, the attachment process was deemed stochastic. Experimental outcomes from the study were compared to those predicted by the extended Derjaguin-Landau-Verwey-Overbeek (XDLVO) theory. Significant differences (P < 0.05) between the initial and the attached ratios for serovar pairs containing S. Sofia S1296a for all different ratios were apparent for all materials. For S. Sofia S1635-containing pairs, 7 out of 12 combinations of serovar pairs and materials had attachment ratios not significantly different (P > 0.05) from the initial ratio of 0.428. Five out of 12 and 10 out of 12 samples had attachment ratios not significantly different (P > 0.05) from the initial ratios of 1 and 2.333, respectively. These results demonstrate that bacterial attachment to different materials is likely to be nonstochastic only when the key physicochemical properties of the bacteria were significantly different (P < 0.05) from each other. XDLVO theory could successfully predict the attachment of some individual isolates to particular materials but could not be used to predict the likelihood of stochasticity in pairwise attachment experiments.     

Margination of red blood cells infected by Plasmodium falciparum in a microvessel

We investigated numerically the mechanism of margination of Plasmodium falciparum malaria-infected red blood cells (Pf-IRBCs) in micro-scale blood flow. Our model illustrates that continuous hydrodynamic interaction between a Pf-IRBC in the trophozoite stage (Pf-T-IRBC) and healthy red blood cells (HRBCs) results in the margination of the Pf-T-IRBC and, thus, a longer duration of contact with endothelial cells. The Pf-T-IRBC and HRBCs first form a "train". The volume fraction of RBCs is then locally increased, to approximately 40%, and this value is maintained for a long period of time due to the formation of a long train in high-hematocrit conditions. Even in low-hematocrit conditions, the local volume fraction is instantaneously elevated to 40% and the Pf-T-IRBC can migrate to the wall. However, the short train formed in low-hematocrit conditions does not provide continuous interaction, and the Pf-T-IRBC moves back to the center of the channel.