Dirk deBeer

Evolving perspectives of biofilm structure

The application of confocal scanning laser microscopy (CSLM) to biofilm research has provided detailed new information on the structural complexity of fully hydrated living biofilms. Biofilms studied by CSLM are widely reported to be heterogeneous and consist of micro‐colonies or cell clusters (aggregates of microbial cells in an extracellular polysaccharide matrix) separated by interstitial voids and channels. CSLM combined with molecular probing can identify the distribution of individual species within biofilms, while CSLM combined with microelectrodes and particle tracking has demonstrated the significance of structural heterogeneity on mass transfer in biofilms. In this review the contribution that CSLM has made towards the development of conceptual and mathematical biofilm models over the last decade is discussed. The significance of biofilm structural heterogeneity to understanding of mass transfer processes in biofilm systems and the fundamental significance of hydrodynamics in shaping biofilm str...

Real-time microsensor measurement of local metabolic activities in ex vivo dental biofilms exposed to sucrose and treated with chlorhexidine.

ABSTRACT Dental biofilms are characterized by structural and functional heterogeneity. Due to bacterial metabolism, gradients develop and diverse ecological microniches exist. The aims of this study were (i) to determine the metabolic activity of microorganisms in naturally grown dental biofilms ex vivo by measuring dissolved oxygen (DO) and pH profiles with microelectrodes with high spatial resolution and (ii) to analyze the impact of an antimicrobial chlorhexidine (CHX) treatment on microbial physiology during stimulation by sucrose in real time. Biofilms were cultivated on standardized human enamel surfaces in vivo. DO and pH profiles were measured in a flow cell system in sterile human saliva, after sucrose addition (10%), again after alternative treatment of the sucrose exposed biofilms with CHX (0.2%) for 1 or 10 min or after being killed with paraformaldehyde (4%). Biofilm structure was visualized by vitality staining with confocal microscopy. With saliva as the sole nutrient source oxygen consumption was high within the superficial biofilm layers rendering deeper layers (>220 μm) anoxic. Sucrose addition induced the thickness of the anaerobic zone to increase with a concurrent decrease in pH (7.1 to 4.4). CHX exposure reduced metabolic activity and microbial viability at the biofilm surface and drove metabolic activity deeper into the biofilm. CHX treatment led to a reduced viability at the biofilm surface with minor influence on overall biofilm physiology after 1 min; even after 10 min there was measurable respiration and fermentation inside the biofilm. However, the local microenvironment was more aerated, less acidogenic, and presumably less pathogenic.

Tonsillolith Not Just a Stone but a Living Biofilm

OBJECTIVE To study the morphology and activity of tonsilloliths, demonstrating oxygen respiration, denitrification, and acidification on exposure to sucrose. STUDY DESIGN Tonsilloliths were extracted in atraumatic conditions during tonsillectomy from 16 adults and sent to two different laboratories for histological, bacteriological, and biofilm studies under sterile conditions. SETTING Multicenter laboratory study. SUBJECTS AND METHODS Multiple tonsilloliths from two patients examined by confocal microscopy and microelectrodes were used to measure aerobic/anaerobic respiration and acid production (dissolved oxygen, nitrous oxide, pH) when exposed to saliva following addition of sucrose and fluoride. RESULTS Morphologically, tonsilloliths were similar to dental biofilms, containing corncob structures, filaments, and cocci. Microelectrodes showed that the microorganisms respired oxygen and nitrate. The oxygen concentration in the center of the tonsillolith was depleted to approximately one-tenth of that of the overlying fluid. The addition of sucrose resulted in acid production within the tonsillolith, dropping the pH from 7.3 to 5.8. The data showed stratification with oxygen respiration at the outer layer of tonsillolith, denitrification toward the middle, and acidification toward the bottom. The depletion of oxygen and acid production following addition of sucrose may allow the proliferation of anaerobic/acidophilic bacteria. Fluoride suppressed acid production in the presence of sucrose. CONCLUSIONS Tonsilloliths exhibit biofilm structure and the formation of chemical gradients through physiological activity. Although tonsillectomy is an option for treating cryptic infections, understanding the morphology and biofilm characteristics of tonsilloliths may stimulate scientists to use limited or targeted remedies in the future.OBJECTIVE: To study the morphology and activity of tonsilloliths, demonstrating oxygen respiration, denitrification, and acidification on exposure to sucrose. STUDY DESIGN: Tonsilloliths were extracted in atraumatic conditions during tonsillectomy from 16 adults and sent to two different laboratories for histological, bacteriological, and biofilm studies under sterile conditions. SETTING: Multicenter laboratory study. SUBJECTS AND METHODS: Multiple tonsilloliths from two patients examined by confocal microscopy and microelectrodes were used to measure aerobic/anaerobic respiration and acid production (dissolved oxygen, nitrous oxide, pH) when exposed to saliva following addition of sucrose and fluoride. RESULTS: Morphologically, tonsilloliths were similar to dental biofilms, containing corncob structures, filaments, and cocci. Microelectrodes showed that the microorganisms respired oxygen and nitrate. The oxygen concentration in the center of the tonsillolith was depleted to approximately one-tenth of that of the overlying fluid. The addition of sucrose resulted in acid production within the tonsillolith, dropping the pH from 7.3 to 5.8. The data showed stratification with oxygen respiration at the outer layer of tonsillolith, denitrification toward the middle, and acidification toward the bottom. The depletion of oxygen and acid production following addition of sucrose may allow the proliferation of anaerobic/acidophilic bacteria. Fluoride suppressed acid production in the presence of sucrose. CONCLUSIONS: Tonsilloliths exhibit biofilm structure and the formation of chemical gradients through physiological activity. Although tonsillectomy is an option for treating cryptic infections, understanding the morphology and biofilm characteristics of tonsilloliths may stimulate scientists to use limited or targeted remedies in the future.

Dust storms over the Arabian Gulf: a possible indicator of climate changes consequences

Dust storm frequencies and strengths were monitored during 2009 at various locations along the coast of the United Arab Emirates (UAE), as representative sites of the Arabian Gulf marine environment. The results have been compared with a pre-2009 five-year data set. Mineralogical components of dust samples collected during the 2009 study period were analyzed using both X-ray diffraction (XRD) and X-ray Fluorescence (XRF) techniques. The comparison of the 2009 and pre-2009 data revealed a shift in the characteristics of dust storms in the Arabian Gulf, which may constitute a sensitive indicator of climate change affecting the region. The range of mineral compositions of the collected dust samples is consistent with temporally and spatially variable dust sources, associated with changing wind patterns over the Arabian Gulf. From a positive perspective, the dust may deliver mineralogical nutrients enhancing microbial productivity in the marine ecosystem. Increasing productivity and liberation of iron from sediments will lead to an increase of Dimethyl Sulfide (DMS) in the atmosphere, which by oxidation will scatter solar radiation effectively with a consequent decrease in global temperature as a climate feedback.

Role of nitric oxide in Salmonella typhimurium-mediated cancer cell killing

BackgroundBacterial targeting of tumours is an important anti-cancer strategy. We previously showed that strain SL7838 of Salmonella typhimurium targets and kills cancer cells. Whether NO generation by the bacteria has a role in SL7838 lethality to cancer cells is explored. This bacterium has the mechanism for generating NO, but also for decomposing it.MethodsMechanism underlying Salmonella typhimurium tumour therapy was investigated through in vitro and in vivo studies. NO measurements were conducted either by chemical assays (in vitro) or using Biosensors (in vivo). Cancer cells cytotoxic assay were done by using MTS. Bacterial cell survival and tumour burden were determined using molecular imaging techniques.ResultsSL7838 generated nitric oxide (NO) in anaerobic cell suspensions, inside infected cancer cells in vitro and in implanted 4T1 tumours in live mice, the last, as measured using microsensors. Thus, under these conditions, the NO generating pathway is more active than the decomposition pathway. The latter was eliminated, in strain SL7842, by the deletion of hmp- and norV genes, making SL7842 more proficient at generating NO than SL7838. SL7842 killed cancer cells more effectively than SL7838 in vitro, and this was dependent on nitrate availability. This strain was also ca. 100% more effective in treating implanted 4T1 mouse tumours than SL7838.ConclusionsNO generation capability is important in the killing of cancer cells by Salmonella strains.

Dust Storms over the Arabian Gulf: An optimistic vision toward climate change consequences

The Earthquake of 2005 in Pakistan destroyed more than 600,000 houses in the area covering 30,000 square km, equal to the size of New Zealand. Most of the houses were located in the rural areas i.e. on the mountains or inside the deep mountainous valleys. However, the three major urban settlements in the area, the towns of Balakot, Muzafferabad and Bagh were badly affected. The ill-fated town of Balakot with estimated population of 37,000 was destroyed completely. 5000 people died and 95% of the infrastructure facilities were demolished. Later, the national and international consortium of specialists confirmed that the town is located on two major fault lines, running parallel all along the town. It was also confirmed that the epicenter of the 2005 Earthquake in Pakistan was 10 kmdeep beneath the town of Balakot. Interestingly, originating from central Asia region, the fault line enters Pakistan from the North West and pass through the towns of Balakot, Muzaffarabad and Bagh, then continues into Hindustan (India). To provide safe living environments for the affected towns, Urban Strategy was formulated by the Earthquake Reconstruction and Rehabilitation Authority. Transitional Housing Project and City Improvement Plan also became parts of the Urban Strategy to provide a reasonable, reliable and decent residential solution. In this paper, the interventions and strategies prepared and implemented to rehabilitate and reconstruct the town of Balakot and its peripheral areas after the devastating earthquake of 2005 is highlighted.Spirulina is a filamentous cyanobacteria with many applications in food and drug industries, as a food in human, aquaculture, vet and poultry industries… . Semi and mass culture of Spirulina carries out in different countries. This study was carried out in five phases in order to produce this microalga in Iran. The first phase, Spirulina pure stock was imported from Indonesia. After identification of species, it was cultured in laboratory until we took 20 liters of biomass. The semi-mass culture was carried out in green house. Cell concentration and size of Spirulina were recorded during culture daily and their growth rates were calculated. After two weeks, when the size of Spirulina was suitable, biomass of Spirulina was harvested then accumulated Spirulina weighted and dried in 24 hours in laboratory. In order to microbiological study, the samples of Spirulina (dry and fresh) were cultured on blood agar medium and coliforms were counted. The chemical composition of produced Spirulina was measured by standard methods. Fatty acid and amino acid profiles were acquired by GC and HPLC instruments, respectively. The amount of chlorophyll in Spirulina was determined by spectroscopy method. Also astaxanthin pigment as an important carotenoid was measured by HPLC in Spirulina and Penaeus semisulcatus larvae fed on Spirulina. At final phase of this project, larva fed on produced Spirulina (biomass and dry powder) was compared to Z plus, microencapsulated Spirulina (M.C.F) and Chaetoceros algae as control. This experiment was carried from zoa to early post larvae stage then survival and growth rate of larvae were recorded. The growth rate of larvae was evaluated with ANOVA test and survival rate of treatments was assessed by Log Rank (Mantel –Cox) test. Also during larvae stage, two parameters of water such as nitrate and nitrite were measured in zoa, mysis and post larvae stages. The results of this study were shown that colifom counts were 1.85×106 and 92.3×105 coliform per ml in fresh and dry spirulina, respectively. Protein percent of dry spirulina was 50.93 % (dry weight) and the amount of astaxanthin in spirulina and larvae fed on spirulina were 0.21 and 0.01 mg/kg, respectively. The most survival rate of larvae were observed in zoa III (88.8%) with Z plus supplement treatment, in mysis III (76.5%) combination of Z plus and dry spirulina in comparative between treatments. Larvae growth (4.5mm) of control in early post larvae was the best.Manuel Martinez-Garcia was graduated with full marks and honors in Biology from the University of Alicante (Spain) and received his PhD in Molecular Microbial Ecology in 2005. He conducted three short postdoctoral European stays in reputed research centres such as the Max Planck Institute for Marine Microbiology (Germany). During 2009-2011, he developed cutting-edge techniques on Single Cell Genomics combined with Metagenomics to study the metabolic capabilities of uncultured microbes at the Bigelow Laboratory for Ocean Sciences (Maine, USA). He has published several papers in high-impact journals based on single cell technologies. Currently, he is back to Spain as assistant professor in Microbiology and is serving as an editorial board member of the Oceanography-Open Access Journal. Time to move forward: Looking at microbes by the view of single cell technologiesYan Xiaodong is a Ecological Climatologist. He had completed his Ph.D. at the age of 29 years from the Chinese Academy and postdoctoral studies from Institute of Atmospheric Physics, CAS. He is a Professor of Ecological Climatology in Chinese Academy and Beijing Normal University. And he was a director of Chinese Academy Key Lab. of climate-environment for East Asia Region. He has published more than 100 papers in reputed journals and serving as an editorial board member of reputed journals. Climatic impacts on biological invasion severity in ChinaEngineers may need to design structures for loads imposed by natural occurrences such as earthquakes and meteorological events of various kinds. No matter what event is specified as a design base, something worse is always physically possible. Hence, engineering standards imply a risk of failure due to large but unlikely external natural events. This risk is accepted. Little account is taken of earthquakes, tsunamis, tornadoes and hurricanes in areas that are judged not prone to them but anything that is physically possible has a finite probability of occurring. Tsunamis are possible on any exposed coastline; earthquakes and storms can occur anywhere. The probabilities of such events vary enormously but are rarely zero. The acceptance of a risk by society depends more strongly on the nature of the risk than its size. This was clearly demonstrated by the disaster at Fukushima in March 2011. The earthquakes and tsunamis killed more than 15,000 people; radiation from the damaged Fukushima Daiichi nuclear power station killed no-one and is unlikely to have any public health effects; but fear of radiation has dominated public, media and political reactions to the disaster worldwide. In Japan, some risks to coastal communities from tsunamis are still accepted but the risk from nuclear power is considered by many to be unacceptable. Other nations, where tsunamis (the sole cause of damage to the nuclear plant) are not a matter of wide concern, have nevertheless turned away from the use of nuclear power. This means burning more fossil fuels, with greater industrial risks, environmental damage and harm to public health.S forest management has become the primary goal of forestry institutions worldwide, as it involves managing forests to achieve production of continuous flow of services without excessive reduction of their future productivity. In this paper a case study in semi arid forest (El Rawashda forest reserve, Gedaref State, Sudan) serves as a research. Multi-temporal Landsat ETM+ and Aster data acquired on early dry season dates in 2000 and 2006 have been used for classification and mapping land cover. Training data were selected in easily identifiable areas of the following four classes: Grassland, Close forest, Open forest and bare land. Following classification of imagery from the individual years, a postclassification, approach of subtracting the classification maps, 2000 and 2006, was applied. An advantage of the approach is that provides “from-to” change information. As part of our analysis we have compared area estimates from the Landsat classifications with aster classification. In our research, the potential to derive indicators of sustainable resource use from satellite remote sensing is discussed. Particular attention focuses on indicators related to land cover condition and type in semi-arid forest environments. This includes quantitative and qualitative assessment of forest cover change as well as the impacts of human and other biophysical factors on the forest. Each of these issues is discussed with emphasis placed on the potential to increase the level of information extraction beyond that derived with conventional approaches in order to more usefully inform sustainable development practices. Wafa Nori, J Marine Sci Res Dev 2013, 3:3 http://dx.doi.org/10.4172/2155-9910.S1.004T study aimed to determine the relationship between wellness and survival skills among the survivors of the devastating Typhoon Sendong in barangays Hinaplanon Proper, Upper Hinaplanon and Bayug, Iligan City, Philippines, last December 17, 2011. In addition, this study attempted to determine whether the moderating variables of age, gender, ponderal index, personal response and socioeconomic status affect the respondents survival skills. This research used a descriptive correlational method to answer the questions stated. Modified questionnaire and standardized test were used to generate the necessary data. The respondents of the study were the ninety (90) survivors who were willing to participate in the study. The study found out that most of the survivors were female, young adults, of medium weight, of average height, of very poor income, and of active personality. Most of the survivor’s house and belonging were totally devastated. Further, among the physical dimension, only taking of vitamins was significantly related with survival skills; among the mental dimension, enjoying creative and stimulating mental activities/games and good time management were significantly related with survival skills; among the emotional dimension, seeing challenges and change as opportunities for growth and being able to recognize and express feelings such as shouting for help during the devastating flood were significantly related with survival skills; among the social dimension, contributing time and/or money to social and community projects and being interested in others including those from different background have some degree of association with survival skills; among the spiritual dimension, prayer, meditation, and/or quiet personal reflection and consistently striving to grow spiritually and seeing it as a lifelong process also have high degree of association with survival skills. Among the moderating variables, however, only weight of survivors had some degree of association with survival skills. Corazon T. Biong, J Marine Sci Res Dev 2013, 3:3 http://dx.doi.org/10.4172/2155-9910.S1.004Teshome Tafesse is a lecturer at Addis Ababa University, where he obtained his MA in Journalism and Communication in 2006. He also received a professional certificate in International Cooperation from Wroclaw University, Poland in 2009. He has published a book entitled “News Coverage of Regions in Ethiopia: The Case of ETV Amharic Broadcast” He has also certain high school Oromo Language text books. He is currently doing his Ph.D. in Applied Linguistics and Communication at Addis Ababa University, Ethiopia. Environmental beliefs and values in borana oromo: A focus on narrativesA resistant strains of bacteria are on the rise in the United States. The reason for this trend is the over utilization of antibiotics in Western medicine. Antibiotic resistant strains are more virulent capable of causing prolonged and serious infections. A common practice in alternative medicine is the utilization of herbs or the use of herbs in conjunction with antibiotics for the treatment of bacterial infections. Herbs are effective agents capable of eradicating bacterial infections. Many herbs possess antimicrobial constituents with bacteriostatic and bactericidal activity for a broad spectrum of gram positive and gram negative bacteria. Although herbs are generally not as potent bacteriostatic or bactericidal agents as antibiotics, herbs may be an effective adjunct or monotherapy due to their ability to stimulate the immunes system enhancing the natural defenses of the body. Another consideration is the antioxidant activity of herbs. During an infection, macrophages and phagocytes denature bacteria using hydrogen peroxide in respiratory burst producing oxidative radicals. Oxidative radicals contribute to oxidative stress capable of increasing cortisol levels down-regulating immune function. Herbs attenuate these effects. The last beneficial aspect is that many herbs either do not disrupt or promote the growth of symbiotic bacteria in the gastrointestinal tract. Brett Martin, J Marine Sci Res Dev 2013, 3:3 http://dx.doi.org/10.4172/2155-9910.S1.004T Earth is warming rapidly due to the emission of greenhouse gases (GHGs), mainly from industrialization, deforestation and increased use of fossil fuels for transport. The GHGs from human activities are among the major causes for global warming and climate change which have contributed to the variations in rainfall patterns (high, low and intensive rainfall) and seasons. These have direct and indirect impacts on environment, water resources, agriculture, forests and biodiversity, health, infrastructure development, tourism and livelihoods. Glaciers are receding in the Himalayan region, Africa, South Pacific, Arctic, North America, South America, Europe and Antarctica. Glacial retreat is the most visually convincing evidence of climate change. The Problems: Scientific evidence, as cited by the Inter-governmental Panel on Climate Change (IPCC), clearly indicates the wide scale of climate change. Average global temperatures are expected to raise 1.4-5.8oC by the end of the 21st century. Warming in the Himalayan region has been higher than global average. Weather patterns are becoming more unpredictable and extreme dry seasons become dryer and wet seasons wetter. This phenomenon is causing threat in the water supply affecting lives and livelihoods of the people and food security. Conclusions: The issues of climate change can be addressed by formulating and implementing relevant policies and programmes. Policy makers must ease the transition to a carbon-free energy industry by passing legislation that creates favorable market conditions, shaping new frameworks for change and ensuring that the Kyoto Protocol enters into force. In addition, the effective implementation of the United Nations Framework Convention on Climate Change (UNFCCC) provisions can help to minimize the current effects. Meen B. Poudyal Chhetri, J Marine Sci Res Dev 2013, 3:3 http://dx.doi.org/10.4172/2155-9910.S1.004Kunshan Gao has completed his Ph.D. at the age of 31 years from Kyoto University and postdoctoral studies from University of Hawaii. He is the Chair professor of State key Laboratory of Marine Environmental Science (Xiamen University). He has published more than 170 papers in reputed journals and serving as editorial board members of Journal of applied Phycolology, Algae and American J. of Plant Sciences. Ocean acidification and solar radiation interacts to influence marine primary producersMarisa graduated in Natural Sciences at the University of Padua in 1983. Researcher at the University of Udine, Department of Food Sciences from 1990 to 2005, and Associate Professor of Molecular Biology Techniques from 2005 ongoing. Member of various Academic Comittee and Commissions. Author of a patent for the detection of Listeria monocytogenes in organic fluids by PCR (1996, C12Q). Coauthor/author of 111 papers; 8 book chapters; 62 papers/abstracts in proceedings, and 46 posters. Chairman and invited speaker at International workshops and conferences. Research fields: Development of DNA probes for pathogen detection using molecular methods methods (PCR, RT-PCR, DNA array) and biosensors. Evolution of molecular methods for microbial detection in seafoodT the world, climate change impact is the main concern for sustainability of water management and water use activities like agricultural production. Climate changes alter regional hydrologic conditions and results in a variety of impacts on water resource systems. Such hydrologic changes will affect almost every aspect of human well-being. The goal of this thesis is to assess the impact of climate change on the hydro climatology of Fincha Sub-basin located in upper Blue Nile Basin of Ethiopia. The GCM derived scenarios (HadCM3 A2a & B2a SRES emission scenarios) experiments were used for the climate projection. The statistical Downscaling Model (SDSM) was used to generate future possible local meteorological variables in the study area. The down-scaled data were then used as input to the Soil and Water Assessment Tool (SWAT) model to simulate the corresponding future stream flow in of Fincha Sub-basin located in upper Blue Nile Basin. A semi distributed hydrological model, SWAT was used to simulate future stream flow. Three benchmark periods simulated for this study were 2020s, 2050s and 2080s. The time series generated by GCM of HadCM3 A2a and B2a and Statistical Downscaling Model (SDSM) indicate a significant increasing trend in maximum and minimum temperature values and a slight decreasing trend in precipitation for both A2a and B2a emission scenarios in both Shambu and Neshe stations for all three bench mark periods. The hydrologic impact analysis made with the downscaled temperature and precipitation time series as input to the SWAT model suggested an overall decreasing trend in annual and monthly stream flow in the study area, in three benchmark periods in the future. This should be considered by policymakers of water resources planning and management. The hydrologic impact analysis made with the downscaled temperature and precipitation time series as input to the hydrological model SWAT suggested for both A2a and B2a emission scenarios. As a result, at the out let of the watershed the projected on average annual flow decrease by 5.59%,9.03%,11% and 2.16%,4.15 and 3.46% for the 2020s,2050s and 2080s for both A2a and B2a emissions scenarios. Potential evapotranspiration in the watershed also will increase annually on average 3 16% for the 2020s and 4-19% for the 2050s and 2080s for both A2a and B2a emissions scenarios. Mekonnen Daba, J Marine Sci Res Dev 2013, 3:3 http://dx.doi.org/10.4172/2155-9910.S1.004a b s t r a c t Vegetation dieback occurs frequently in various ecosystems and causes tremendous consequences. We here examined the impact of native reed (Phragmites australis) dieback on the salt marsh communities invaded by exotic Spartina alterniflora through monitoring dynamics of component species of Phragmites-Spartina mixture, and comparing their performances in monoculture, dieback mixture and healthy mixture in Dongtan wetland of Yangtze River estuary, China. Phragmites showed poorer performance in dieback mixture compared with other communities. Survival rate (30 ± 4.08%), ramet density (37 ± 9.15 plants/m 2 ), plant height (130.71 ± 20.39 cm) and aboveground biomass (222.64 ± 5.66 g/m 2 ) of Phragmites in dieback mixture were all significantly lower than those in healthy mixture (68 ± 4.79%; 99 ± 17.24 plants/m2; 185.06 ± 17.75 cm; 837.07 ± 205.13 g/m2, respectively) (for all P < 0.05). By contrast, Spartina resprouted well with survival rate of 100% over the course of the experiment. Both ramet density and plant height of Spartina tended to be higher in dieback mixture than in healthy mixture, and its aboveground biomass (1042.19 ± 156.46 g/m 2 ) was significantly higher than that in healthy mixture (618.76 ± 129.50 g/m2) (P < 0.05). Our results suggest that reduced dominance of native Phragmites due to