Abundance and biomass of mesozooplankton in the Levantine Basin during the Bilim 2 cruise in April 2008

The Sesame dataset contains mesozooplankton data collected during April 2008 in the Levantine Basin (between 33.20 and 36.50 N latitude and between 30.99 and 31.008 E longitude). Mesozooplankton samples were collected by using a WP-2 closing net with 200 µm mesh size during day hours (07:00-18:00). Samples were taken from 0-50, 50-100, 100-200 m layers at 5 stations in Levantine Basin The dataset includes samples analyzed for mesozooplankton species composition, abundance and total mesozooplankton biomass. Sampling volume was estimated by multiplying the mouth area with the wire length. Sampling biomass was measured by weighing filters and then determined by sampling volume. The samples were sieved sequentially through meshes of 500 and 200 micron to separate the mesozooplankton into size fractions. The entire sample (1/2) or an aliquot of the taxon-specific mesozooplankton abundance and the total abundance of the mesozooplankton were was analyzed under the binocular microscope. Minimum 500 individuals of mesozooplankton were identified and numerated at higher taxonomic level. Taxonomic identification was done at the METU- Institute of Marine Sciences by Alexandra Gubanova,Tuba Terbiyik using the relevant taxonomic literatures. Mesozooplankton abundance and biomass were estimated by Zahit Uysal and Yesim Ak.

Chlorophyll-a in gut from Microsetella norvegica and Oncaea collected during James Cook cruise JC087

Gut chlorophyll of Microsetella norvegica and Oncaea spp. was measured daily at the PAP site from 8th to 14th of June, 2013. Copepods were collected using a WP2 -type net with a mesh size of 50 µm. Immediately after, 40-70 adults and late copepodites of each species (with 2-3 replicate samples) were washed in filtered sea water, placed on CF/F filters and extracted in acetone. Chlorophyll-a on filters was analysed using standard methods.

Development of bacterial and archaeal communities in erupted subsurface muds at the Håkon Mosby mud volcano

The microbial oxidation of methane controls the emission of the greenhouse gas methane from the ocean floor. However, some seabed structures such as mud volcanoes have leaky microbial methane filters and can be important sources of methane. We investigated the disturbance and recovery of a methanotrophic mud volcano microbiome (Håkon Mosby mud volcano, 1250 m water depth), to assess time scales of community succession and function in the natural deep-sea environment. We analyzed 10 surface and 5 subsurface sediment samples across HMMV mud flows from most recently discharged subsurface muds towards old consolidated muds as well as one reference site (REF) located approximately 0.5 km outside of the HMMV. Surface samples were obtained in 2003, 2009 and 2010. The surface of the new mud flows at the geographical center was sampled in 2009 and 2010. Around 100 m south of the center, we sampled more consolidated aged muds in 2003 and 2010. Old mud flows were sampled around 300 m southeast and 100 m north of the geographical center in 2003, 2009 and 2010. Surface sediment samples (0-20 cm) were recovered either by TV-guided Multicorer or by push cores using the remotely operated vehicle Quest (Marum, University Bremen). Subsurface sediments of all zones (>2 m below sea floor) were obtained in 2003 by gravity corer. After recovery, sediments were immediately subsampled in a refrigerated container (0°C) and further processed for biogeochemical analyses or preserved at -20°C for later DNA analyses. Our study show that freshly erupted muds hosted heterotrophic deep subsurface communities, which were replaced by surface communities within a few years of exposure. Aerobic methanotrophy was established at the top surface layer within less than a year, followed by anaerobic methanotrophy, sulfate reduction and finally thiotrophy. Our data indicate that it takes decades in cold environments before efficient methanotrophic communities establish to control methane emission. The observed succession provides insights to the response time of complex deep-sea communities to seafloor disturbances.

Assessing the physiological responses of the gastropod Crepidula fornicata to predicted ocean acidification and warming

Organisms inhabiting coastal waters naturally experience diel and seasonal physico-chemical variations. According to various assumptions, coastal species are either considered to be highly tolerant to environmental changes or, conversely, living at the thresholds of their physiological performance. Therefore, these species are either more resistant or more sensitive, respectively, to ocean acidification and warming. Here, we focused on Crepidula fornicata, an invasive gastropod that colonized bays and estuaries on northwestern European coasts during the 20th century. Small (<3 cm in length) and large (>4.5 cm in length), sexually mature individuals of C. fornicata were raised for 6 months in three different pCO2 conditions (390 µatm, 750 µatm, and 1400 µatm) at four successive temperature levels (10°C, 13°C, 16°C, and 19°C). At each temperature level and in each pCO2 condition, we assessed the physiological rates of respiration, ammonia excretion, filtration and calcification on small and large individuals. Results show that, in general, temperature positively influenced respiration, excretion and filtration rates in both small and large individuals. Conversely, increasing pCO2 negatively affected calcification rates, leading to net dissolution in the most drastic pCO2 condition (1400 µatm) but did not affect the other physiological rates. Overall, our results indicate that C. fornicata can tolerate ocean acidification, particularly in the intermediate pCO2 scenario. Moreover, in this eurythermal species, moderate warming may play a buffering role in the future responses of organisms to ocean acidification.

Multiple Frequency Solidly Mounted BAW Filters

This paper reports the simultaneous fabrication of Receive and Transmit Bulk Acoustic Wave filters for the WCDMA standard on the same die. Both filters are based on Solidly Mounted Resonators using a common Bragg mirror, but with each having a specific piezoelectric film thickness. Electrical measurements reveal that the process steps required to provide the two different piezoelectric film thicknesses on the same die does not impact the electrical performances of resonators and filters and that this approach could thus be generalised to more than two filters.

Fractal analysis of laplacian pyramidal filters applied to segmentation of soil images

The laplacian pyramid is a well-known technique for image processing in which local operators of many scales, but identical shape, serve as the basis functions. The required properties to the pyramidal filter produce a family of filters, which is unipara metrical in the case of the classical problem, when the length of the filter is 5. We pay attention to gaussian and fractal behaviour of these basis functions (or filters), and we determine the gaussian and fractal ranges in the case of single parameter ?. These fractal filters loose less energy in every step of the laplacian pyramid, and we apply this property to get threshold values for segmenting soil images, and then evaluate their porosity. Also, we evaluate our results by comparing them with the Otsu algorithm threshold values, and conclude that our algorithm produce reliable test results.

Tratamientos avanzados de agua potable para eliminación de materia orgánica disuelta : aplicación del BAC

Los procesos de biofiltración por carbón activo biológico se han utilizado desde hace décadas, primeramente en Europa y después en Norte América, sin embargo no hay parámetros de diseño y operación específicos que se puedan utilizar de guía para la biofiltración. Además, el factor coste a la hora de elegir el carbón activo como medio de filtración impacta en el presupuesto, debido al elevado coste de inversión y de regeneración. A la hora de diseñar y operar filtros de carbón activo los requisitos que comúnmente se buscan son eliminar materia orgánica, olor, y sabor de agua. Dentro de la eliminación de materia orgánica se precisa la eliminación necesaria para evitar subproductos en la desinfección no deseados, y reducir los niveles de carbono orgánico disuelto biodegradable y asimilable a valores que consigan la bioestabilidad del agua producto, a fin de evitar recrecimiento de biofilm en las redes de distribución. El ozono se ha utilizado durante años como un oxidante previo a la biofiltración para reducir el olor, sabor, y color del agua, oxidando la materia orgánica convirtiendo los compuestos no biodegradables y lentamente biodegradables en biodegradables, consiguiendo que puedan ser posteriormente eliminados biológicamente en los filtros de carbón activo. Sin embargo la inestabilidad del ozono en el agua hace que se produzcan ácidos carboxilos, alcoholes y aldehídos, conocidos como subproductos de la desinfección. Con esta tesis se pretende dar respuesta principalmente a los siguientes objetivos: análisis de parámetros requeridos para el diseño de los filtros de carbón activo biológicos, necesidades de ozonización previa a la filtración, y comportamiento de la biofiltración en un sistema compuesto de coagulación sobre un filtro de carbón activo biológico. Los resultados obtenidos muestran que la biofiltración es un proceso que encaja perfectamente con los parámetros de diseño de plantas con filtración convencional. Aunque la capacidad de eliminación de materia orgánica se reduce a medida que el filtro se satura y entra en la fase biológica, la biodegradación en esta fase se mantienen estable y perdura a lo lago de los meses sin preocupaciones por la regeneración del carbón. Los valores de carbono orgánico disuelto biodegradable se mantienen por debajo de los marcados en la literatura existente para agua bioestable, lo que hace innecesaria la dosificación de ozono previa a la biofiltración. La adición de la coagulación con la corrección de pH sobre el carbón activo consigue una mejora en la reducción de la materia orgánica, sin afectar a la biodegradación del carbón activo, cumpliendo también con los requerimientos de turbidez a la salida de filtración. Lo que plantea importantes ventajas para el proceso. Granular activated carbon filters have been used for many years to treat and produce drinking water using the adsorption capacity of carbon, replacing it once the carbon lost its adsorption capacity and became saturated. On the other hand, biological activated carbon filters have been studied for decades, firstly in Europe and subsequently in North America, nevertheless are no generally accepted design and operational parameters documented to be used as design guidance for biofiltration. Perhaps this is because of the cost factor; to choose activated carbon as a filtration media requires a significant investment due to the high capital and regeneration costs. When activated carbon filters are typically required it is for the reduction of an organic load, removal of colour, taste and / or odour. In terms of organic matter reduction, the primary aim is to achieve as much removal as possible to reduce or avoid the introduction of disinfection by products, the required removal in biodegradable dissolved organic carbon and assimilable organic carbon to produce a biologically stable potable water which prohibits the regrowth of biofilm in the distribution systems. The ozone has historically been used as an oxidant to reduce colour, taste and odour by oxidizing the organic matter and increasing the biodegradability of the organic matter, enhancing the effectiveness of organic removal in downstream biological activated carbon filters. Unfortunately, ozone is unstable in water and reacts with organic matter producing carboxylic acids, alcohols, and aldehydes, known as disinfection by products. This thesis has the following objectives: determination of the required parameters for the design of the biological activated filters, the requirement of ozonization as a pre-treatment for the biological activated filters, and a performance assessment of biofiltration when coagulation is applied as a pretreatment for biological activated carbon filters. The results show that the process design parameters of biofiltration are compatible with those of conventional filtration. The organic matter removal reduces its effectiveness as soon as the filter is saturated and the biological stage starts, but the biodegradation continues steadily and lasts for a long period of time without the need of carbon regeneration. The removal of the biodegradable dissolved organic carbon is enough to produce a biostable water according to the values shown on the existing literature; therefore ozone is not required prior to the filtration. Furthermore, the addition of coagulant and pH control before the biological activated carbon filter achieves a additional removal of organic matter, without affecting the biodegradation that occurs in the activated carbon whilst also complying with the required turbidity removal.

Reduction of tobacco smoke components yield in commercial cigarette brands by addition of HUSY, NaY and Al-MCM-41 to the cigarette rod

The effect of two zeolites, HUSY, NaY and a mesoporous synthesized Al-MCM-41 material on the smoke composition of ten commercial cigarettes brands has been studied. Cigarettes were prepared by mixing the tobacco with the three powdered materials, and the smoke obtained under the ISO conditions was analyzed. Up to 32 compounds were identified and quantified in the gas fraction and 80 in the total particulate matter (TPM) condensed in the cigarettes filters and in the traps located after the mouth end of the cigarettes. Al-MCM-41 is by far the best additive, providing the highest reductions of the yield for most compounds and brands analyzed. A positive correlation was observed among the TPM and nicotine yields with the reduction obtained in nicotine, CO, and most compounds with the three additives. The amount of ashes in additive free basis increases due to the coke deposited on the solids, especially with Al-MCM-41. Nicotine is reduced with Al-MCM-41 by an average of 34.4% for the brands studied (49.5% for the brand where the major reduction was obtained and 18.5 for the brand behaving the worst). CO is reduced by an average of 18.6% (ranging from 10.3 to 35.2% in the different brands).

Seawater carbonate chemistry and photosynthetic response of Emiliania huxleyi (CS-369) to UV radiation and elevated temperature duirng experiments, 2011

Changes in calcification of coccolithophores may affect their photosynthetic responses to both, ultraviolet radiation (UVR, 280-400 nm) and temperature. We operated semi-continuous cultures of Emiliania huxleyi (strain CS-369) at reduced (0.1 mM, LCa) and ambient (10 mM, HCa) Ca2+ concentrations and, after 148 generations, we exposed cells to six radiation treatments (>280, >295, >305, >320, >350 and >395 nm by using Schott filters) and two temperatures (20 and 25 °C) to examine photosynthesis and calcification responses. Overall, our study demonstrated that: (1) decreased calcification resulted in a down regulation of photoprotective mechanisms (i.e., as estimated via non-photochemical quenching, NPQ), pigments contents and photosynthetic carbon fixation; (2) calcification (C) and photosynthesis (P) (as well as their ratio) have different responses related to UVR with cells grown under the high Ca2+ concentration being more resistant to UVR than those grown under the low Ca2+ level; (3) elevated temperature increased photosynthesis and calcification of E. huxleyi grown at high Ca2+concentrations whereas decreased both processes in low Ca2+ grown cells. Therefore, a decrease in calcification rates in E. huxleyi is expected to decrease photosynthesis rates, resulting in a negative feedback that further reduces calcification.

Isolation and characterization of integron-containing bacteria without antibiotic selection

The emergence of antibiotic resistance among pathogenic and commensal bacteria has become a serious problem worldwide. The use and overuse of antibiotics in a number of settings are contributing to the development of antibiotic-resistant microorganisms. The class 1 and 2 integrase genes (intI1 and intI2, respectively) were identified in mixed bacterial cultures enriched from bovine feces by growth in buffered peptone water (BPW) followed by integrase-specific PCR. Integrase-positive bacterial colonies from the enrichment cultures were then isolated by using hydrophobic grid membrane filters and integrase-specific gene probes. Bacterial clones isolated by this technique were then confirmed to carry integrons by further testing by PCR and DNA sequencing. Integron-associated antibiotic resistance genes were detected in bacteria such as Escherichia coli, Aeromonas spp., Proteus spp., Morganella morganii, Shewanella spp., and urea-positive Providencia stuartii isolates from bovine fecal samples without the use of selective enrichment media containing antibiotics. Streptomycin and trimethoprim resistance were commonly associated with integrons. The advantages conferred by this methodology are that a wide variety of integron-containing bacteria may be simultaneously cultured in BPW enrichments and culture biases due to antibiotic selection can be avoided. Rapid and efficient identification, isolation, and characterization of antibiotic resistance-associated integrons are possible by this protocol. These methods will facilitate greater understanding of the factors that contribute to the presence and transfer of integron-associated antibiotic resistance genes in bacterial isolates from red meat production animals.

Advanced fibre gratings and their applications

This thesis describes a detailed study of advanced fibre grating devices using Bragg (FBG) and long-period (LPG) structures and their applications in optical communications and sensing. The major contributions presented in this thesis are summarised below. One of the most important contributions from the research work presented in this thesis is a systematic theoretical study of many distinguishing structures of fibre gratings. Starting from the Maxwell equations, the coupled-mode equations for both FBG and LPG were derived and the mode-overlap factor was analytically discussed. Computing simulation programmes utilising matrix transform method based on the models built upon the coupled-mode equations were developed, enabling simulations of spectral response in terms of reflectivity, bandwidth, sidelobes and dispersion of gratings of different structures including uniform and chirped, phase-shifted, Moiré, sampled Bragg gratings, phase-shifted and cascaded long-period gratings. Although the majority of these structures were modelled numerically, analytical expressions for some complex structures were developed with a clear physical picture. Several apodisation functions were proposed to improve sidelobe suppression, which guided effective production of practical devices for demanding applications. Fibre grating fabrication is the other major part involved in the Ph.D. programme. Both the holographic and scan-phase-mask methods were employed to fabricate Bragg and long-period gratings of standard and novel structures. Significant improvements were particularly made in the scan-phase-mask method to enable the arbitrarily tailoring of the spectral response of grating devices. Two specific techniques - slow-shifting and fast-dithering the phase-mask implemented by a computer controlled piezo - were developed to write high quality phase-shifted, sampled and apodised gratings. A large number of LabVIEW programmes were constructed to implement standard and novel fabrication techniques. In addition, some fundamental studies of grating growth in relating to the UV exposure and hydrogenation induced index were carried out. In particular, Type IIa gratings in non-hydrogenated B/Ge co-doped fibres and a re-generated grating in hydrogenated B/Ge fibre were investigated, showing a significant observation of thermal coefficient reduction. Optical sensing applications utilising fibre grating devices form the third major part of the research work presented in this thesis. Several experiments of novel sensing and sensing-demodulating were implemented. For the first time, an intensity and wavelength dual-coding interrogation technique was demonstrated showing significantly enhanced capacity of grating sensor multiplexing. Based on the mode-splitting measurement, instead of using conventional wavelength-shifting detection technique, successful demonstrations were also made for optical load and bend sensing of ultra-high sensitivity employing LPG structures. In addition, edge-filters and low-loss high-rejection bandpass filters of 50nm stop-band were fabricated for application in optical sensing and high-speed telecommunication systems

Characterisation of a harvesting step for monoclonal antibodies from mammalian cell culture

The focus of this research was defined by a poorly characterised filtration train employed to clarify culture broth containing monoclonal antibodies secreted by GS-NSO cells: the filtration train blinded unpredictably and the ability of the positively charged filters to adsorb DNA from process material was unknown. To direct the development of an assay to quantify the ability of depth filters to adsorb DNA, the molecular weight of DNA from a large-scale, fed-batch, mammalian cell culture vessel was evaluated as process material passed through the initial stages of the purification scheme. High molecular weight DNA was substantially cleared from the broth after passage through a disc stack centrifuge and the remaining low molecular weight DNA was largely unaffected by passage through a series of depth filters and a sterilising grade membrane. Removal of high molecular weight DNA was shown to be coupled with clarification of the process stream. The DNA from cell culture supernatant showed a pattern of internucleosomal cleavage of chromatin when fractionated by electrophoresis but the presence of both necrotic and apoptotic cells throughout the fermentation meant that the origin of the fragmented DNA could not be unequivocally determined. An intercalating fluorochrome, PicoGreen, was elected for development of a suitable DNA assay because of its ability to respond to low molecular weight DNA. It was assessed for its ability to determine the concentration of DNA in clarified mammalian cell culture broths containing pertinent monoclonal antibodies. Fluorescent signal suppression was ameliorated by sample dilution or by performing the assay above the pI of secreted IgG. The source of fluorescence in clarified culture broth was validated by incubation with RNase A and DNase I. At least 89.0 % of fluorescence was attributable to nucleic acid and pre-digestion with RNase A was shown to be a requirement for successful quantification of DNA in such samples. Application of the fluorescence based assay resulted in characterisation of the physical parameters governing adsorption of DNA by various positively charged depth filters and membranes in test solutions and the DNA adsorption profile of the manufacturing scale filtration train. Buffers that reduced or neutralised the depth filter or membrane charge, and those that impeded hydrophobic interactions were shown to affect their operational capacity, demonstrating that DNA was adsorbed by a combination of electrostatic and hydrophobic interactions. Production-scale centrifugation of harvest broth containing therapeutic protein resulted in the reduction of total DNA in the process stream from 79.8 μg m1-1 to 9.3 μg m1-1 whereas the concentration of DNA in the supernatant of pre-and post-filtration samples had only marginally reduced DNA content: from 6.3 to 6.0 μg m1-1 respectively. Hence the filtration train was shown to ineffective in DNA removal. Historically, blinding of the depth filters had been unpredictable with data such as numbers of viable cells, non-viable cells, product titre, or process shape (batch, fed-batch, or draw and fill) failing to inform on the durability of depth filters in the harvest step. To investigate this, key fouling contaminants were identified by challenging depth filters with the same mass of one of the following: viable healthy cells, cells that had died by the process of apoptosis, and cells that had died through the process of necrosis. The pressure increase across a Cuno Zeta Plus 10SP depth filter was 2.8 and 16.5 times more sensitive to debris from apoptotic and necrotic cells respectively, when compared to viable cells. The condition of DNA released into the culture broth was assessed. Necrotic cells released predominantly high molecular weight DNA in contrast to apoptotic cells which released chiefly low molecular weight DNA. The blinding of the filters was found to be largely unaffected by variations in the particle size distribution of material in, and viscosity of, solutions with which they were challenged. The exceptional response of the depth filters to necrotic cells may suggest the cause of previously noted unpredictable filter blinding whereby a number of necrotic cells have a more significant impact on the life of a depth filter than a similar number of viable or apoptotic cells. In a final set of experiments the pressure drop caused by non-viable necrotic culture broths which had been treated with DNase I or benzonase was found to be smaller when compared to untreated broths: the abilities of the enzyme treated cultures to foul the depth filter were reduced by 70.4% and 75.4% respectively indicating the importance of DNA in the blinding of the depth filter studied.

Ecological studies on river pollution control

This collection of papers records a series of studies, carried out over a period of some 50 years, on two aspects of river pollution control - the prevention of pollution by sewage biological filtration and the monitoring of river pollution by biological surveillance. The earlier studies were carried out to develop methods of controlling flies which bred in the filters and caused serious nuisance and possible public health hazard, when they dispersed to surrounding villages. Although the application of insecticides proved effective as an alleviate measure, because it resulted in only a temporary disturbance of the ecological balance, it was considered ecologically unsound as a long-term solution. Subsequent investigations showed that the fly populations in filters were largely determined by the amount of food available to the grazing larval stage in the form of filter film. It was also established that the winter deterioration in filter performance was due to the excessive accumulation of film. Subsequent investigations were therefore carried out to determine the factors responsible for the accumulation of film in different types of filter. Methods of filtration which were considered to control film accumulation by increasing the flushing action of the sewage, were found to control fungal film by creating nutrient limiting conditions. In some filters increasing the hydraulic flushing reduced the grazing fauna population in the surface layers and resulted in an increase in film. The results of these investigations were successfully applied in modifying filters and in the design of a Double Filtration process. These studies on biological filters lead to the conclusion that they should be designed and operated as ecological systems and not merely as hydraulic ones. Studies on the effects of sewage effluents on Birmingham streams confirmed the findings of earlier workers justifying their claim for using biological methods for detecting and assessing river pollution. Further ecological studies showed the sensitivity of benthic riffle communities to organic pollution. Using experimental channels and laboratory studies the different environmental conditions associated with organic pollution were investigated. The degree and duration of the oxygen depletion during the dark hours were found to be a critical factor. The relative tolerance of different taxa to other pollutants, such as ammonia, differed. Although colonisation samplers proved of value in sampling difficult sites, the invertebrate data generated were not suitable for processing as any of the commonly used biotic indexes. Several of the papers, which were written by request for presentation at conferences etc., presented the biological viewpoint on river pollution and water quality issues at the time and advocated the use of biological methods. The information and experiences gained in these investigations was used as the "domain expert" in the development of artificial intelligence systems for use in the biological surveillance of river water quality.

All-optical passive 2R regeneration for N×40 Gbit/s WDM transmission using NOLM and novel filtering technique

We propose an all-optical passive 2R regeneration method for WDM (N×40 Gbit/s) dispersion-managed RZ transmission based on specially designed WDM guiding filters and in-line nonlinear optical loop mirrors. By system optimisation, the feasibility of 150 GHz-spaced × l6 channel transmission over 25,000 km of standard fibre is numerically demonstrated.

All-optical passive 2R regeneration for N × 40 Gbit/s WDM transmission using NOLM and novel filtering technique

We propose a passive all-optical 2R regeneration method for WDM (N×40 Gbit/s) dispersion-managed RZ transmission based on specially designed WDM guiding filters and in-line nonlinear optical loop mirrors. By system optimisation, the feasibility of 150 GHz-spaced × 16 channel 25000 km transmission over standard fibre is numerically demonstrated.