Oncolytic measles viruses produced at different scales under serum‐free conditions

Measles virus (MV) with attenuated pathogenicity has potential as oncolytic agent. However, the clinical translation of this therapy concept has one major hurdle: the production of sufficient amounts of infectious oncolytic MV particles. The current study describes oncolytic MV production in Vero cells grown on microcarrier using serum‐free medium. The impact of the number of harvests, cell concentration at infection (CCI), multiplicity of infection (MOI), and temperature on MV production was determined in different production scales/systems (static T‐flasks, dynamic spinner, and bioreactor system) and modes (batch, repeated‐batch, and perfusion). Cell growth, metabolic, and production kinetics were analyzed. It was found that the number of harvests had the strongest positive impact on MV yield in each production scale, and that high temperatures affected MV yield adversely. Moderate MV titers were produced in T‐ and spinner flasks at 37°C (～10⁷ TCID₅₀ mL^?1, where TCID₅₀ is tissue culture infective doses 50%), but stirred tank reactor (STR) MV production at 37°C yielded up to 10 000‐fold lower MV titers. In contrast, at lower temperatures (32°C, 27°C), 1.4 × 10⁷ TCID₅₀ mL^?1 were achieved in the STR. Variations in MOI and CCI had almost no influence on MV production yield. The current study improves oncolytic MV production process understanding and identifies process bottlenecks for large‐scale production.     

pH effects on growth and lipid accumulation of the biofuel microalgae Nannochloropsis salina and invading organisms

Biofuels derived from non-crop sources, such as microalgae, offer their own advantages and limitations. Despite high growth rates and lipid accumulation, microalgae cultivation still requires more energy than it produces. Furthermore, invading organisms can lower efficiency of algae production. Simple environmental changes might be able to increase algae productivity while minimizing undesired organisms like competitive algae or predatory algae grazers. Microalgae are susceptible to pH changes. In many production systems, pH is kept below 8 by CO₂ addition. Here, we uncouple the effects of pH and CO₂ input, by using chemical pH buffers and investigate how pH influences Nannochloropsis salina growth and lipid accumulation as well as invading organisms. We used a wide range of pH levels (5, 6, 7, 8, 9, and 10). N. salina showed highest growth rates at pH 8 and 9 (0.19?±?0.008 and 0.19?±?0.011, respectively; mean ± SD). Maximum cell densities in these treatments were reached around 21 days into the experiment (95.6?×?10⁶?±?9?×?10⁶ cells mL^?1 for pH 8 and 92.8?×?10⁶?±?24?×?10⁶ cells mL^?1 for pH 9). Lipid accumulation of unbuffered controls were 21.8?±?5.8 % fatty acid methyl esters content by mass, and we were unable to trigger additional significant lipid accumulation by manipulating pH levels at the beginning of stationary phase. Ciliates (grazing predators) occurred in significant higher densities at pH 6 (56.9?±?39.6?×?10⁴ organisms mL^?1) than higher pH treatments (0.1–6.8?×?10⁴ organisms mL^?1). Furthermore, the addition of buffers themselves seemed to negatively impact diatoms (algal competitors). They were more abundant in an unbuffered control (12.7?±?5.1?×?10⁴ organisms mL^?1) than any of the pH treatments (3.6–4.7?×?10⁴ organisms mL^?1). In general, pH values of 8 to 9 might be most conducive to increasing algae production and minimizing invading organisms. CO₂ addition seems more valuable to algae as an inorganic carbon source and not as an essential mechanism to reduce pH.     

Production and scale‐up of a monoclonal antibody against 17‐hydroxyprogesterone

The hybridoma 192 was used to produce a monoclonal antibody (MAb) against 17‐hydroxyprogesterone (17‐OHP), for possible use in screening for congenital adrenal hyperplasia (CAH). The factors influencing the MAb production were screened and optimized in a 2 L stirred bioreactor. The production was then scaled up to a 20 L bioreactor. All of the screened factors (aeration rate, stirring speed, dissolved oxygen concentration, pH, and temperature) were found to significantly affect production. Optimization using the response surface methodology identified the following optimal production conditions: 36.8°C, pH 7.4, stirring speed of 100 rpm, 30% dissolved oxygen concentration, and an aeration rate of 0.09 vvm. Under these conditions, the maximum viable cell density achieved was 1.34 ± 0.21 × 10⁶ cells mL^?1 and the specific growth rate was 0.036 ± 0.004 h^?1. The maximum MAb titer was 11.94 ± 4.81 μg mL^?1 with an average specific MAb production rate of 0.273 ± 0.135 pg cell^?1 h^?1. A constant impeller tip speed criterion was used for the scale‐up. The specific growth rate (0.040 h^?1) and the maximum viable cell density (1.89 × 10⁶ cells mL^?1) at the larger scale were better than the values achieved at the small scale, but the MAb titer in the 20 L bioreactor was 18% lower than in the smaller bioreactor. A change in the culture environment from the static conditions of a T‐flask to the stirred bioreactor culture did not affect the specificity of the MAb toward its antigen (17‐OHP) and did not compromise the structural integrity of the MAb. © 2012 American Institute of Chemical Engineers Biotechnol. Prog., 2013     

Scalable Manufacturing of Human Mesenchymal Stromal Cells in the Vertical‐Wheel Bioreactor System: An Experimental and Economic Approach

Mesenchymal stromal cells (MSC) hold great promise for tissue engineering applications and cell‐based therapies. Large cell doses (>1 × 10⁶ cells kg^?1) and Good Manufacturing Practices (GMP)‐compliant processes are however required for clinical purposes. Here, a serum‐ and xenogeneic‐free (S/XF) microcarrier‐based culture system is established for the expansion of human umbilical cord matrix (UCM)‐ and adipose tissue (AT)‐derived MSC using the Vertical‐Wheel system (PBS‐0.1 MAG; PBS Biotech). UCM and AT MSC are expanded to maximum cell densities of 5.3 ± 0.4 × 10⁵ cell mL^?1 (n = 3) and 3.6 ± 0.7 × 10⁵ cell mL^?1 (n = 3), respectively, after 7 days of culture, while maintaining their identity, according to standard criteria. An economic evaluation of the process transfer from T‐flasks to PBS‐0.1 MAG shows a reduction in the costs associated with the production of a dose for an average 70 kg adult patient (i.e., 70 million cells). Costs decrease from $17.0 K to $11.1 K for UCM MSC and from $21.5 K to $11.1 K for AT MSC, proving that the transition to Vertical‐Wheel reactors provides a cost‐effective alternative for MSC expansion. The present work reports the establishment of a scalable and cost‐effective culture platform for the manufacturing of UCM and AT MSC in a S/XF microcarrier‐based system.     

Quantum‐dots‐based fluoroimmunoassay for the rapid and sensitive detection of avian influenza virus subtype H5N1

The continuous spread of highly pathogenic avian influenza virus (AIV) subtype H5N1 is threatening the poultry industry and human health worldwide. Rapid and sensitive diagnostic methods are required for the H5N1 surveillance. In this study, the fluorescent (FL) probe of CdTe quantum dots (QDs) was designed using covalently linked rabbit anti‐AIV H5N1 antibody. Based on these QD–antibody conjugates, a novel sandwich FL‐linked immunosorbent assay (sFLISA) was developed for H5N1 viral antigen detection. The sFLISA allowed for H5N1 viral antigen determination in a linear range of 8.0 × 10^?3 to 5.1 × 10^?1 μg mL^?1 with the limit of detection (LOD) of 1.5 × 10^?4 μg mL^?1. In comparison with virus isolation for 103 clinic samples, the sensitivity and specificity of sFLISA were found to be 93.6 and 91.1% respectively. The sFLISA supplied a novel approach to rapid and sensitive detection of AIV subtype H5N1 and showed great potential for biological applications in immunoassays. Copyright © 2009 John Wiley & Sons, Ltd.     

Resonance light scattering technique for determination of polychlorinated biphenyls with silver nanoparticles

In this paper, a simple and novel method for the determination of polychlorinated biphenyls (PCBs), using silver nanoparticles (AgNPs) as a resonance light scattering (RLS) probe, is proposed. Under optimized conditions, there existed linear relationships between the enhancing RLS intensity of the system and the concentrations of PCBs in the range 8.0 × 10^?8?1.0 × 10^?6 g mL^?1 for 2,4,4′‐trichlorbiphenyl (PCB28), 9.0 × 10^?8?1.0 × 10^?6 g mL^?1 for 2,2′,5,5′‐tetrachlorbiphenyl (PCB52) and 4.0 × 10^?8?1.0 × 10^?6 g mL^?1 for 3,3′,4,4′‐tetrachlorobiphenyl (PCB77). The corresponding detection limits (S/N = 3) were 2.6 × 10^?8 g mL^?1 for PCB28, 3.3 × 10^?8 g mL^?1 for PCB52 and 6.3 × 10^?9 g mL^?1 for PCB77, respectively. Finally, the mechanism of RLS enhancement was also studied. The results indicated that PCBs were adsorbed on the surface of AgNPs to form larger AgNP–PCB aggregates, resulting in the RLS enhancement of the system. Copyright © 2011 John Wiley & Sons, Ltd.     

Recombinant exochitinase of the thermophilic mould Myceliopthora thermophila BJA: Characteristics and utility in generating N‐acetyl glucosamine and in biocontrol of phytopathogenic fungi

Chitinase from the thermophilic mould Myceliopthora thermophila BJA (MtChit) is an acid tolerant, thermostable and organic solvent stable biocatalyst which does not require any metal ions for its activity. To produce high enzyme titres, reduce fermentation time and overcome the need for induction, this enzyme has been heterologously expressed under GAP promoter in the GRAS yeast, Pichia pastoris. The production medium supplemented with the permeabilizing agent Tween‐20 supported two‐fold higher rMtChit production (5.5 × 10³ U L^?1). The consensus sequences S(132)xG(133)G(134) and D(168)xxD(171)xD(173)xE(175) in the enzyme have been found to represent the substrate binding and catalytic sites, respectively. The rMtChit, purified to homogeneity by a two‐step purification strategy, is a monomeric glycoprotein of ～48 kDa, which is optimally active at 55°C and pH 5.0. The enzyme is thermostable with t_1/2 values of 113 and 48 min at 65 and 75°C, respectively. Kinetic parameters K_m, V_max, k_cat, and k_cat/K_m of the enzyme are 4.655 mg mL^?1, 34.246 nmol mg^?1 s^?1, 3.425 × 10⁶ min^?1, and 1.36 × 10^?6 mg mL^?1 min^?1, respectively. rMtChit is an unique exochitinase, since its action on chitin liberates N‐acetylglucosamine NAG. The enzyme inhibits the growth of phytopathogenic fungi like Fusarium oxysporum and Curvularia lunata, therefore, this finds application as biofungicide at high temperatures during summer in tropics. © 2016 American Institute of Chemical Engineers Biotechnol. Prog., 33:70–80, 2017     

Capillary electrophoresis analysis of isoniazid using luminol-periodate potassium chemiluminescence system

A rapid and simple capillary electrophoresis method coupled with chemiluminescent (CL) detection was proposed for analysis of isoniazid (ISO) based on the enhancement effect of ISO to CL emission of luminol‐periodate potassium reaction. Under the optimal conditions, ISO can be assayed in the range of 7.0 × 10^?7 to 3.0 × 10^?5 g mL^?1 (R² = 0.9990) with a limit of detection of 3.0 × 10^?7 g mL^?1 (signal‐to‐noise ratio of 3). The whole analysis process can be completed within 2.5 min with a theoretical plate number of 6258. The relative standard deviations of the signal intensity and the migration time were 3.1 and 1.4% for a standard sample at 1.0 × 10^?5 g mL^?1 (n = 5), respectively. The presented novel strategy was successfully applied to the determination of ISO in commercial pharmaceutical preparations and spiked human serum samples. Copyright © 2010 John Wiley & Sons, Ltd.     

Control of chitin nanofiber production by the lipid‐producing diatom Cyclotella Sp. through fed‐batch addition of dissolved silicon and nitrate in a bubble‐column photobioreactor

Diatoms are single‐celled algae that make cell walls of nanopatterned biogenic silica called frustules through metabolic uptake of dissolved silicon and its templated condensation into biosilica. The centric marine diatom Cyclotella sp. also produces intracellular lipids and the valued coproduct chitin, an N‐acetyl glucosamine biopolymer that is extruded from selected frustule pores as pure nanofibers. The goal of this study was to develop a nutrient feeding strategy to control the production of chitin nanofibers from Cyclotella with the coproduction of biofuel lipids. A two‐stage phototrophic cultivation process was developed where Stage I set the cell suspension to a silicon‐starved state under batch operation, and Stage II continuously added silicon and nitrate to the silicon‐starved cells to enable one more cell doubling to 4 × 10⁶ cells mL^?1. The silicon delivery rate was set to enable a silicon‐limited cell division rate under cumulative delivery of 0.8 mM Si and 1.2 mM nitrate (1.5:1 mol N/mol Si) over a 4‐ to 14‐day addition period. In Stage II, both cell number and chitin production were linear with time. Cell number and the specific chitin production rate increased linearly with increasing silicon delivery rate to achieve cumulative product yields of 13 ± 1 mg chitin/10⁹ cells and 33 ± 3 mg lipid/10⁹ cells. Therefore, chitin production is controlled through cell division, which is externally controlled through silicon delivery. Lipid production was not linearly correlated to silicon delivery and occurred primarily during Stage I, just after the complete co‐consumption of both dissolved silicon and nitrate. © 2017 American Institute of Chemical Engineers Biotechnol. Prog., 33:407–415, 2017     

Impact of nutritional conditions on yields,germination rate and shelf-life of Plectosporium alismatis conidia and chlamydospores as potential candidates for the development of a mycoherbicide of weeds in rice crops

The effect of nutritional conditions on spore qualities was investigated in order to select which propagules, conidia or chlamydospores, would be most suitable for mycoherbicide development. Plectosporium alismatis was grown in a liquid basal medium supplemented with glucose and a mineral nitrogen source (sodium nitrate) or an organic nitrogen source (casamino acids). Conidial and chlamydospore yields, germination rate and shelf-life were compared. Two growth models were developed: on one hand, sodium nitrate added as the sole nitrogen source was partially utilised (8%), resulting in poor growth (1.77±0.02 mg mL^?1; 6±1.7×10⁵ conidia mL^?1). Under these conditions, P. alismatis produced dense, melanised-like aggregates that contained chlamydospores (12.4±0.7×10⁴ chlamydospores mL^?1). Germination rates of chlamydospores and conidia produced under these conditions was high (80%). Twenty percent of chlamydospores were able to germinate after 4 months storage at 25°C, while survival of conidia declined rapidly (<2%). When casamino acids were added to the liquid medium as the sole nitrogen source, P. alismatis produced sparser pellets resulting in high dry weights (5.37±0.09 mg mL^?1 and high conidia numbers (9.6±1.5×10⁶ conidia mL^?1), while no chlamydospore were observed. The germination rate of conidia produced in casamino acids was low (33±13%) after 8 h incubation and microcycle conidiation occurred. Five percent of these conidia germinated after 4 months storage. These data indicate that chlamydospores may be suitable for mycoherbicide development, provided further optimisation of yields is achieved.     

Assessment of adenovirus,hepatitis A virus and rotavirus presence in environmental samples in Florianopolis,South Brazil

Aims: To assess the presence of human adenovirus (HAdV), hepatitis A (HAV) virus and rotavirus A (RV‐A) in environmental samples from the Southern region of Brazil and to provide viral contamination data for further epidemiological studies and governmental actions. Methods and Results: Water samples from various sources (seawater, lagoon brackish water, urban wastewater, drinking water sources‐with and without chlorination and water derived from a polluted creek) and oysters of two growing areas were analysed by enzymatic amplification (nested PCR and RT‐PCR), quantification of HAdV genome (qPCR) and viral viability assay by integrated cell culture‐PCR (ICC‐PCR). From June 2007 to May 2008 in a total of 84 water samples, 54 (64·2%) were positive for HAdV, 16 (19%) for RV‐A and 7 (8·3%) for HAV. Viability assays showed nonpositive samples for HAV; though, infectious viruses were confirmed for RV‐A (12·5%) and HAdV (88·8%). Oyster samples by PCR were positive for HAdV (87·5%) and RV‐A (8·3%), but none for HAV. Quantitative PCR in oysters showed means loads in genomic copies (gc) of 9·1 × 10⁴ gc g^?1 (oyster farm south) and 1·5 × 10⁵ gc g^?1 (oyster farm north) and in waters ranging from 2·16 × 10⁶ (lagoon water) to 1·33 × 10⁷ gc l^?1 (untreated drinking water). Conclusions: This study has shown a widespread distribution of the analysed viruses in this particular region with high loads of HAdV in the environment which suggests the relevance of evaluating these viruses as positive indicators of viral contamination of water. Significance and Impact of the Study: The environmental approach in this study provides data concerning the prevalence, viability and quantification of enteric viruses in environmental waters and oysters in the South region of Brazil and has indicated that their presence might pose a risk to population in contact with the environmental samples searched.     

Postprocessing microflora of commercial attieke (a fermented cassava product) produced in the south of Côte d'Ivoire

The distribution and presence of hygiene indicator and pathogenic micro‐organisms in 375 samples of attieke marketed in Côte d'Ivoire, and their roles in the food poisoning were evaluated. Microbiological analyses were carried out, which included the total viable bacteria, coliforms, Escherichia coli, Staphylococcus aureus, Salmonella, Bacillus spores, fungi and Clostridium perfringens. The results revealed that the viable bacteria counts ranged from 2·2 ± 1·2 × 10⁵ to 3·4 ± 1·4 × 10⁶ CFU g^?1, while the yeasts and the moulds counts ranged, respectively, from 2·4 ± 0·12 × 10⁴ to 9·8 ± 0·4 × 10⁵ CFU g^?1 and 1·3 ± 0·7 × 10¹ to 1·7 ± 0·7 × 10² CFU g^?1. Bacillus subtilis, Bacillus cereus, Staphylococcus aureus, Citrobacter freundi, Enterobacter amnigenus, Citrobacter youngae, Enterobacter aerogenes, Klebsiella pneumoniae, Serratia marcescens, Enterobacter agglomerans and Klebsiella oxytoca were the bacteria isolated, and Rhizopus spp., Mucor spp., Thamnidium spp., Fusarium spp., Moniliella spp. the fungi. Escherichia coli, Clostridium perfringens and Salmonella spp. were not found. The occurrence of some bacteria and fungi illustrate that attieke collected in Côte d'Ivoire markets may act as a reservoir of pathogenic micro‐organisms for human.

Significance and Impact of Study

This study demonstrates the great need to carry out microbiological tests frequently on attieke and even more the need to apply correct HACCP system during the production. Attieke is especially a well‐known product in West Africa; hence, it is extremely important to ensure an adequate microbiological quality to guarantee consumers health. Overall, the study highlighted the need for effective communication on microbiological food risks, proper instruction and supervision in food‐handling procedures, greater education on food safety risks.     

Long‐range quantitative PCR for determining inactivation of adenovirus 2 by ultraviolet light

Aims

An extra‐long‐range quantitative PCR (LR‐qPCR) method was developed for estimating genome damage to adenovirus 2 caused by UV irradiation. The objective was to use LR‐qPCR as a rapid method to determine adenovirus UV inactivation.

Methods

The LR‐qPCR consisted of two steps: a long‐range PCR (up to 10 kb fragment) and a real‐time, quantitative (q) PCR for quantifying the products of the first PCR. We evaluated LR‐qPCR with adenovirus irradiated with medium‐pressure (MP, polychromatic emission) and low‐pressure (LP, 254 nm) mercury vapour lamps and compared results with cell culture infectivity.

Results

Using LR‐qPCR, a fragment of 6 kb estimated DNA damage in a linear relationship to doses between 0 and 20 mJ cm^?2, and a 1‐kb fragment related linearly to doses between 20 and 100 mJ cm^?2. The LR‐qPCR results for the 6‐kb fragment were similar to infectivity assays results for adenovirus exposed to MP UV. For adenovirus irradiated with LP lamps, LR‐qPCR results for the shorter fragment size (1 kb) were similar to reduction in viral infectivity. No difference was observed between 10 and 6 kb LR‐qPCR results.

Conclusion

The LR‐qPCR can be used as a tool for estimating DNA damage caused by UV in adenovirus. The LR‐qPCR results were related to reduction in viral infectivity.

Significance and Impact of the Study

The use of LR‐qPCR to determine DNA damage and estimate inactivation of adenovirus 2 from UV disinfection allows for same‐day results compared with >7 days required for cell culture. This accelerates adenovirus inactivation results for the water industry where adenovirus is used as a representative virus for crediting UV systems. This PCR approach provides a framework that can be used for other viral viability assays using the inhibition of amplification of viral nucleic acid after pretreatments, such as propidium monoazide, and for cellular biology studies of DNA damage.     

Development of an experimental laboratory fertilization protocol for the South African abalone,Haliotis midae (Linnaeus 1758)

In this study, effective gamete concentrations, egg viability, and fertilization volumes were evaluated for Haliotis midae (L.). Sperm concentrations between 5?×?10³ and 5?×?10⁴?mL^?1 (p?>?0.05) consistently resulted in high hatch-out rates (96?±?1%). At concentrations higher than 5?×?10⁵?mL^?1, hatch-out rates decreased to 69?±?7% (p??1 resulted in high fertilization rates, with 50?eggs?mL^?1 being the ideal concentration for fertilization in H. midae. Egg viability was consistently high up to 100?min post-spawning, with a decrease in hatch-out success, when eggs were fertilized 120?min post-spawning. Fertilization volumes did not affect successful hatch-out. The results from this study can be implemented by South African abalone farms to increase hatch-out rates and subsequent culture. It can also be used as basis for the development of fertilization protocols in other marine invertebrate species.     

NaCS‐PDMDAAC immobilized cultivation of recombinant Dictyostelium discoideum for soluble human Fas ligand production

Dictyostelium discoideum is a promising eukaryotic host for the expression of heterologous proteins requiring post‐translational modifications. However, the dilute nature of D. discoideum cell culture limits applications for high value proteins production. D. discoideum cells, entrapped in sodium cellulose sulfate/poly‐dimethyl‐diallyl‐ammonium chloride (NaCS‐PDMDAAC) capsules were used for biosynthesis of the heterologous protein, soluble human Fas ligand (hFasL). Semi‐continuous cultivations with capsules recycling were carried out in shake flasks. Also, a scaled‐up cultivation of immobilized D. discoideum for hFasL production in a customized vitreous airlift bioreactor was conducted. The results show that NaCS‐PDMDAAC capsules have desirable biophysical properties including biocompatibility with the D. discoideum cells and good mechanical stability throughout the duration of cultivation. A maximum cell density of 2.02 × 10⁷ cells mL^?1 (equivalent to a maximum cell density of 2.22 × 10⁸ cells mL^?1 in capsules) and a hFasL concentration of 130.40 μg L^?1 (equivalent to a hFasL concentration of 1434.40 μg L^?1 in capsules) were obtained in shake flask cultivation with capsules recycling. Also, a maximum cell density of 1.72 × 10⁷cells mL^?1 (equivalent to a maximum cell density of 1.89 × 10⁸ cells mL^?1 in capsules) and a hFasL concentration of 106.10 μg L^?1 (equivalent to a hFasL concentration of 1167.10 μg L^?1 in capsules) were obtained after ～170 h cultivation in the airlift bioreactor (with a working volume of 200 mL in a 315 mL bioreactor). As the article presents a premier work in the application of NaCS‐PDMDAAC immobilized D. discoideum cells for the production of hFasL, more work is required to further optimize the system to generate higher cell densities and hFasL titers for large‐scale applications. © 2014 American Institute of Chemical Engineers Biotechnol. Prog., 31:424–430, 2015     

Absolute configuration and biological profile of pyrazoline enantiomers as MAO inhibitory activity

A new racemic pyrazoline derivative was synthesized and resolved to its enantiomers using analytic and semipreparative high‐pressure liquid chromatography. The absolute configuration of both fractions was established using vibrational circular dichroism. The in vitro monoamine oxidase (MAO) inhibitory profiles were evaluated for the racemate and both enantiomers separately for the two isoforms of the enzyme. The racemic compound and both enantiomers were found to inhibit hMAO‐A selectively and competitively. In particular, the R enantiomer was detected as an exceptionally potent and a selective MAO‐A inhibitor (K_i = 0.85 × 10^?3 ± 0.05 × 10^?3 μM and SI: 2.35 × 10^?5), whereas S was determined as poorer compound than R in terms of K_i and SI (0.184 ± 0.007 and 0.001). The selectivity of the enantiomers was explained by molecular modeling docking studies based on the PDB enzymatic models of MAO isoforms.     

Variations in Abundance,Genome Size,Morphology, and Functional Role of the Virioplankton in Lakes Annecy and Bourget over a 1-Year Period

We sampled the surface waters (2–50 m) of two deep peri-alpine lakes over a 1-year period in order to examine (1) the abundance, vertical distribution, genome size, and morphology structures of the virioplankton; (2) the virus-mediated bacterial mortality; and (3) the specific genome size range of double-stranded DNA (dsDNA) phytoplankton viruses. Virus-like particle (VLP) concentrations varied between 4.16?×?10⁷ (January) and 2.08?×?10⁸ part mL^?1 (May) in Lake Bourget and between 2.7?×?10⁷ (June) and 8.39?×?10⁷ part mL^?1 (November) in Lake Annecy. Our flow cytometry analysis revealed at least three viral groups (referred to as virus-like particles 1, 2, and 3) that exhibited distinctive dynamics suggestive of different host types. Phage-induced bacterial mortality varied between 6.1 % (June) and 33.2 % (October) in Lake Bourget and between 7.4 % (June) and 52.6 % (November) in Lake Annecy, suggesting that viral lysis may be a key cause of mortality of the bacterioplankton. Virioplankton genome size ranged from 27 to 486 kb in Lake Bourget, while it reached 620 kb in Lake Annecy for which larger genome sizes were recorded. Our analysis of pulsed field gel electrophoresis bands using different PCR primers targeting both cyanophages and algal viruses showed that (1) dsDNA viruses infecting phytoplankton may range from 65 to 486 kb, and (2) both cyanophage and algal “diversity” were higher in Lake Annecy. Lakes Annecy and Bourget also differed regarding the proportions of both viral families (with the dominance of myoviruses vs. podoviruses) and infected bacterial morphotypes (short rods vs. elongated rods), in each of these lakes, respectively. Overall, our results reveal that (1) viruses displayed distinct temporal and vertical distribution, dynamics, community structure in terms of genome size and morphology, and viral activity in the two lakes; (2) the Myoviridae seemed to be the main cause of bacterial mortality in both lakes and this group seemed to be related to VLP2; and (3) phytoplankton viruses may have a broader range of genome size than previously thought. This study adds to growing evidence that viruses are diverse and play a significant role in freshwater microbial dynamics and more globally lake functioning. It highlights the importance of further considering this biological compartment for a better understanding of plankton ecology in peri-alpine lakes.     

CpG‐related SNPs in the MS4A region have a dose‐dependent effect on risk of late–onset Alzheimer disease

CpG‐related single nucleotide polymorphisms (CGS) have the potential to perturb DNA methylation; however, their effects on Alzheimer disease (AD) risk have not been evaluated systematically. We conducted a genome‐wide association study using a sliding‐window approach to measure the combined effects of CGSes on AD risk in a discovery sample of 24 European ancestry cohorts (12,181 cases, 12,601 controls) from the Alzheimer's Disease Genetics Consortium (ADGC) and replication sample of seven European ancestry cohorts (7,554 cases, 27,382 controls) from the International Genomics of Alzheimer's Project (IGAP). The potential functional relevance of significant associations was evaluated by analysis of methylation and expression levels in brain tissue of the Religious Orders Study and the Rush Memory and Aging Project (ROSMAP), and in whole blood of Framingham Heart Study participants (FHS). Genome‐wide significant (p < 5 × 10^?8) associations were identified with 171 1.0 kb‐length windows spanning 932 kb in the APOE region (top p < 2.2 × 10^?308), five windows at BIN1 (top p = 1.3 × 10^?13), two windows at MS4A6A (top p = 2.7 × 10^?10), two windows near MS4A4A (top p = 6.4 × 10^?10), and one window at PICALM (p = 6.3 × 10^‐9). The total number of CGS‐derived CpG dinucleotides in the window near MS4A4A was associated with AD risk (p = 2.67 × 10^?10), brain DNA methylation (p = 2.15 × 10^?10), and gene expression in brain (p = 0.03) and blood (p = 2.53 × 10^?4). Pathway analysis of the genes responsive to changes in the methylation quantitative trait locus signal at MS4A4A (cg14750746) showed an enrichment of methyltransferase functions. We confirm the importance of CGS in AD and the potential for creating a functional CpG dosage‐derived genetic score to predict AD risk.     

Virus dynamics in a large epishelf lake (Beaver Lake,Antarctica)

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Virus and microbial loop dynamics over an annual cycle in three contrasting Antarctic lakes

1. Viral and microbial loop dynamics were investigated over an annual cycle in three contrasting saline Antarctic lakes – Highway Lake (salinity 4‰), Pendant Lake (salinity 19‰) and Ace Lake, a meromictic system (with a mixolimnion salinity of 18‰) in order to assess the importance of viruses in extreme, microbially dominated systems. 2. Virus like particles (VLP) showed no clear seasonal pattern, with high concentrations occurring in both winter and summer (range 0.89 × 10⁷ ± 0.038 to 12.017 × 10⁷ ± 1.28 mL^?1). VLP abundances reflected lake productivity based on chlorophyll a concentrations. Bacterial abundances and biomass did not correlate with VLP numbers except in Pendant Lake, the most productive of the three lakes studied. 3. Pendant Lake supported the highest bacterial biomass (range Highway: 18.44 ± 1.35 to 59.43 ± 2.80 ng C mL^?1; Ace: 14.42 ± 2.69 to 68.39 ± 2.95 ng C mL^?1; Pendant: 31.36 ± 3.94 to 115.95 ± 4.49 ng C mL^?1) so that virus to bacteria ratios (VBR) (range 30.48 ± 7.96 to 96.67 ± 8.21) were higher in Ace Lake (range 30.58 ± 3.98 to 80.037 ± 1.60) and Highway Lake (range 18.63 ± 3.12 to 126.74 ± 6.50). 4. Negative correlations occurred between VLP and cryptophytes (dominant phototrophic nanoflagellates), suggesting that they were not hosts to lytic viruses. Among the other protists only the heterotrophic nanoflagellates of Highway Lake (dominated by the marine choanoflagellate Diaphanoeca grandis) showed a positive correlation with VLP. 5. The VLP was negatively correlated with photosynthetically active radiation (PAR) and temperature, both of which increased with ice thinning and breakout, increasing viral decay. In winter VLP probably persisted in cold, dark water. 6. High VLP concentrations and high VBR (values at the upper end of those reported for marine and lacustrine systems) indicated that viruses, most of which were probably bacteriophage, are a major element within the microbial communities in extreme, saline lakes.