Seawater carbonate chemistry and diatom Phaeodactylum tricornutum (CCMA 106) biological processes during experiments, 2010

CO2/pH perturbation experiments were carried out under two different pCO2 levels (39.3 and 101.3 Pa) to evaluate effects of CO2-induced ocean acidification on the marine diatom Phaeodactylum tricornutum. After acclimation (>20 generations) to ambient and elevated CO2 conditions (with corresponding pH values of 8.15 and 7.80, respectively), growth and photosynthetic carbon fixation rates of high CO2 grown cells were enhanced by 5% and 12%, respectively, and dark respiration stimulated by 34% compared to cells grown at ambient CO2. The half saturation constant (Km) for carbon fixation (dissolved inorganic carbon, DIC) increased by 20% under the low pH and high CO2 condition, reflecting a decreased affinity for HCO3- or/and CO2 and down-regulated carbon concentrating mechanism (CCM). In the high CO2 grown cells, the electron transport rate from photosystem II (PSII) was photoinhibited to a greater extent at high levels of photosynthetically active radiation, while non-photochemical quenching was reduced compared to low CO2 grown cells. This was probably due to the down-regulation of CCM, which serves as a sink for excessive energy. The balance between these positive and negative effects on diatom productivity will be a key factor in determining the net effect of rising atmospheric CO2 on ocean primary production.

Data compilation on the biological response to ocean acidification: environmental and experimental context of data sets and related literature

The exponential growth of studies on the biological response to ocean acidification over the last few decades has generated a large amount of data. To facilitate data comparison, a data compilation hosted at the data publisher PANGAEA was initiated in 2008 and is updated on a regular basis (doi:10.1594/PANGAEA.149999). By January 2015, a total of 581 data sets (over 4 000 000 data points) from 539 papers had been archived. Here we present the developments of this data compilation five years since its first description by Nisumaa et al. (2010). Most of study sites from which data archived are still in the Northern Hemisphere and the number of archived data from studies from the Southern Hemisphere and polar oceans are still relatively low. Data from 60 studies that investigated the response of a mix of organisms or natural communities were all added after 2010, indicating a welcomed shift from the study of individual organisms to communities and ecosystems. The initial imbalance of considerably more data archived on calcification and primary production than on other processes has improved. There is also a clear tendency towards more data archived from multifactorial studies after 2010. For easier and more effective access to ocean acidification data, the ocean acidification community is strongly encouraged to contribute to the data archiving effort, and help develop standard vocabularies describing the variables and define best practices for archiving ocean acidification data.

Biological impacts of enhanced alkalinity in Carcinus maenas

Further steps are needed to establish feasible alleviation strategies that are able to reduce the impacts of ocean acidification, whilst ensuring minimal biological side-effects in the process. Whilst there is a growing body of literature on the biological impacts of many other carbon dioxide reduction techniques, seemingly little is known about enhanced alkalinity. For this reason, we investigated the potential physiological impacts of using chemical sequestration as an alleviation strategy. In a controlled experiment, Carcinus maenas were acutely exposed to concentrations of Ca(OH)2 that would be required to reverse the decline in ocean surface pH and return it to pre-industrial levels. Acute exposure significantly affected all individuals' acid-base balance resulting in slight respiratory alkalosis and hyperkalemia, which was strongest in mature females. Although the trigger for both of these responses is currently unclear, this study has shown that alkalinity addition does alter acid-base balance in this comparatively robust crustacean species.

Effect of enhanced pCO2 levels on the production of dissolved organic carbon and transparent exopolymer particles in short-term bioassay experiments

It has been proposed that increasing levels of pCO2 in the surface ocean will lead to more partitioning of the organic carbon fixed by marine primary production into the dissolved rather than the particulate fraction. This process may result in enhanced accumulation of dissolved organic carbon (DOC) in the surface ocean and/or concurrent accumulation of transparent exopolymer particles (TEPs), with important implications for the functioning of the marine carbon cycle. We investigated this in shipboard bioassay experiments that considered the effect of four different pCO2 scenarios (ambient, 550, 750 and 1000 µatm) on unamended natural phytoplankton communities from a range of locations in the northwest European shelf seas. The environmental settings, in terms of nutrient availability, phytoplankton community structure and growth conditions, varied considerably between locations. We did not observe any strong or consistent effect of pCO2 on DOC production. There was a significant but highly variable effect of pCO2 on the production of TEPs. In three of the five experiments, variation of TEP production between pCO2 treatments was caused by the effect of pCO2 on phytoplankton growth rather than a direct effect on TEP production. In one of the five experiments, there was evidence of enhanced TEP production at high pCO2 (twice as much production over the 96 h incubation period in the 750 ?atm treatment compared with the ambient treatment) independent of indirect effects, as hypothesised by previous studies. Our results suggest that the environmental setting of experiments (community structure, nutrient availability and occurrence of phytoplankton growth) is a key factor determining the TEP response to pCO2 perturbations.

Comparing gold nano-particle enhanced radiotherapy with protons, megavoltage photons and kilovoltage photons: a Monte Carlo simulation

Gold nanoparticles (GNPs) have shown potential to be used as a radiosensitizer for radiation therapy. Despite extensive research activity to study GNP radiosensitization using photon beams, only a few studies have been carried out using proton beams. In this work Monte Carlo simulations were used to assess the dose enhancement of GNPs for proton therapy. The enhancement effect was compared between a clinical proton spectrum, a clinical 6 MV photon spectrum, and a kilovoltage photon source similar to those used in many radiobiology lab settings. We showed that the mechanism by which GNPs can lead to dose enhancements in radiation therapy differs when comparing photon and proton radiation. The GNP dose enhancement using protons can be up to 14 and is independent of proton energy, while the dose enhancement is highly dependent on the photon energy used. For the same amount of energy absorbed in the GNP, interactions with protons, kVp photons and MV photons produce similar doses within several nanometers of the GNP surface, and differences are below 15% for the first 10 nm. However, secondary electrons produced by kilovoltage photons have the longest range in water as compared to protons and MV photons, e.g. they cause a dose enhancement 20 times higher than the one caused by protons 10 μm away from the GNP surface. We conclude that GNPs have the potential to enhance radiation therapy depending on the type of radiation source. Proton therapy can be enhanced significantly only if the GNPs are in close proximity to the biological target.

The effect of Ligula intestinalis on blood sex steroid hormones, gonadal tissue and some other biological parameters changes of Chalcalburnus mossulensis in Vahdat dam of Kordestan-Iran

Chalcalburnus mossulensis from the cyprinidae family is one of the indigenous fish in Gheshlag Lake of Kordestan-Iran. Ligula intestinalis is one of the infective parasites of this fish. In this study, the effect of this parasite on some biological aspects of this fish like weight, length, PI, CF, GSR, blood sex steroid hormones and gonadal tissue, was investigated. During one year, by seasonal sampling, 144 fish sample from mentioned species were collected using trap net. By considering the scale sample, the fish with the same age were separated and tested as the point of infection with the parasite. By biochemical and histopathological investigation of fish blood and gonad tissue, it was clear that increase in infection rate of fish, caused decrease in biological parameters. There was a significant difference (p<0.05) between the means of sex steroid hormones (17-B Estradiol and Testostreone) of infected and non-infected fish and this parameter was significantly lower in infected ones. This significant difference also was seen between the means of male and female gonads maturation steps of infected and non-infected samples. The reason for lack of maturation of gonads tissue is infection by Ligula intestinalis. Also in gonads of infected fish, abnormal degenerative changes like MMC (Melano-Macrophage Center), hemorrhage and necrosis were seen that were not reported by other researchers. So the spread of this parasite in different water sources should be consider as the point of the maintenance of native species and cultivated fish.

Effect of temperature on genomic and some biological indices during embryonic and larval development of Caspian trout Salmo trutta caspius Kessler, 1877

Since 1966 especially recent decade, Caspian trout (Salmo trutta caspius Kessler, 1877) considered as a strategic endemic species for Caspian Sea fisheries resources also coldwater aquaculture in Iran. Nowadays habitat condition effects on this subspecies during life stages, artificial breeding and incubation period noticed by research and execution sessions of fisheries in Iran. Incubation duration of Caspian trout from artificial fertilization followed by green egg and eyed egg, hatching and yolk sac absorption identified as most sensitive stages for fish and any pollution, stress and deviation by natural life conditions of embryo up to larvae could provide possible mortalities and observable or hidden alterations. Among all vital factors for Caspian trout welfare even in conservation plans and stocks rehabilitation programs or recent attempts for domestication of this fish for introduction to cold water aquaculture industry, water temperature as the most important physical factor which might conserve or induce stress to rearing environment condition is not considered yet. In hatcheries activities, the temperature for incubation and rearing Caspian trout eggs is determining by available water temperature and wide range of temperatures in governmental or private farms is using depend on the water resources availability. Also global climate change consideration and increase temperature trend accompany with group of physical and chemical factors provided by fish farm discharges and other source points entered to the migration pathway of Caspian trout in spawning season were not investigated before. Natural spawning migration pathway is upstream of Caspian tout south and south west rivers especially in Cheshmehkileh upstream in Tonekabon, Iran directed this research focus on the mentioned location. For simulation of natural spawning bed for Caspian trout, water supplied from the upstream of Daryasar branch as headwater of Cheshmehkileh River which provided REDD water condition for in vitro incubation. Green eggs treatments of wild and F1 cultured brooders both 3+ were incubated. Incubation implemented in dark, constant temperature (4, 8, 12 degree centigrade) and DO–pH–temperature digital monitoring in 3 recycling incubators ended to yolk sac absorption and entering larval stage. Hatching success, possible genome alterations by HSP70 gene expression and comet assay implemented as diagnostic tools in 3 life stages of eyed egg– Alevin and Larvae. Numbers and diameters of larvae white fiber muscles measured by histology experiment and Hematoxylin–eosine staining. Results stated significant effect of incubation temperature on hatching success, genome and white fiber muscles of wild and F1 samples. Hatching success measured as 31% and 38% for cultured and wild cold treatments, 79% and 91% for normal and 64% and 73% for warm cultured and wild treatments respectively. Considerable mortality occurred for cold treatment and 8 degree centigrade stated the best thermal condition in normal incubator according to hatching success in wild Caspian trout samples.

Radioprotective effect and other biological benefits associated with flavonoids

Ionizing radiation has the potential to cause extensive damage to living organisms. It can directly act on DNA, proteins and lipids, resulting in ionizing excitation and chemical bond cleavage, which can lead to molecular and cellular damage. Ionizing radiation can hydrolyze water molecules in the body, resulting in increased numbers of free radicals with strong oxidation ability. This process indirectly leads to tissue degeneration and necrosis, which can possibly result in cancer. In this paper, the intervention mechanism of flavonoids on ionizing radiation was analyzed. It has been revealed that the intervention mechanism associated with flavonoids may offer protective properties for DNA, prevent scavenging free radicals, and protect against auto-immune damage. In addition, this invention mechanism can protect the hematopoietic system and reduce inflammation.

The effect of sample and sample matrix on DNA processing: Mechanisms for the detection and management of inhibition in forensic samples

The presence of inhibitory substances in biological forensic samples has, and continues to affect the quality of the data generated following DNA typing processes. Although the chemistries used during the procedures have been enhanced to mitigate the effects of these deleterious compounds, some challenges remain. Inhibitors can be components of the samples, the substrate where samples were deposited or chemical(s) associated to the DNA purification step. Therefore, a thorough understanding of the extraction processes and their ability to handle the various types of inhibitory substances can help define the best analytical processing for any given sample. A series of experiments were conducted to establish the inhibition tolerance of quantification and amplification kits using common inhibitory substances in order to determine if current laboratory practices are optimal for identifying potential problems associated with inhibition. DART mass spectrometry was used to determine the amount of inhibitor carryover after sample purification, its correlation to the initial inhibitor input in the sample and the overall effect in the results. Finally, a novel alternative at gathering investigative leads from samples that would otherwise be ineffective for DNA typing due to the large amounts of inhibitory substances and/or environmental degradation was tested. This included generating data associated with microbial peak signatures to identify locations of clandestine human graves. Results demonstrate that the current methods for assessing inhibition are not necessarily accurate, as samples that appear inhibited in the quantification process can yield full DNA profiles, while those that do not indicate inhibition may suffer from lowered amplification efficiency or PCR artifacts. The extraction methods tested were able to remove >90% of the inhibitors from all samples with the exception of phenol, which was present in variable amounts whenever the organic extraction approach was utilized. Although the results attained suggested that most inhibitors produce minimal effect on downstream applications, analysts should practice caution when selecting the best extraction method for particular samples, as casework DNA samples are often present in small quantities and can contain an overwhelming amount of inhibitory substances.^

Impeding good governance implementation in Indonesian regional government : the effect of a bureaucratic generation gap

The implementation of ‘good governance’ in Indonesia’s regional government sector became a central tenet in governance research following the introduction of the national code for governance in 2006. The code was originally drafted in 1999 as a response to the Asian financial crises and many cases of unearthed corruption, collusion, and nepotism. It was reviewed in 2001 and again in 2006 to incorporate relevant political, economical, and social developments. Even though the national code exists along with many regional government decrees on good governance, the extent of implementation of the tenets of good governance in Indonesia’s regional government is still questioned. Previous research on good governance implementation in Indonesian regional government (Mardiasmo, Barnes and Sakurai, 2008) identified differences in the nature and depth of implementation between various Indonesian regional governments. This paper analyses and extends this recent work and explores key factors that may impede the implementation and sustained application of governance practices across regional settings. The bureaucratic culture of Indonesian regional government is one that has been shaped for over approximately 30 years, in particular during that of the Soeharto regime. Previous research on this regime suggests a bureaucratic culture with a mix of positive and negative aspects. On one hand Soeharto’s regime resulted in strong development growth and strong economic fundamentals, resulting in Indonesia being recognised as one of the Asian economic tigers prior to the 1997 Asian financial crises. The financial crises however revealed a bureaucratic culture that was rife with corruption, collusion, and nepotism. Although subsequent Indonesian governments have been committed to eradicating entrenched practices it seems apparent that the culture is ingrained within the bureaucracy and eradication of it will take time. Informants from regional government agree with this observation, as they identify good governance as an innovative mechanism and to implement it will mean a deviation from the “old ways.” Thus there is a need for a “changed” mind set in order to implement sustained governance practices. Such an exercise has proven to be challenging so far, as there is “hidden” resistance from within the bureaucracy to change its ways. The inertia of such bureaucratic cultures forms a tension against the opportunity for the implementation of good governance. From this context an emergent finding is the existence of a ‘bureaucratic generation gap’ as an impeding variable to enhanced and more efficient implementation of governance systems. It was found that after the Asian financial crises the Indonesian government (both at national and regional level) drew upon a wider human resources pool to fill government positions – including entrants from academia, the private sector, international institutions, foreign nationals and new graduates. It suggested that this change in human capital within government is at the core of this ‘inter-generational divide.’ This divergence is exemplified, at one extreme, by [older] bureaucrats who have been in-position for long periods of time serving during the extended Soeharto regime. The “new” bureaucrats have only sat in their positions since the end of Asian financial crisis and did not serve during Soeharto’s regime. It is argued that the existence of this generation gap and associated aspects of organisational culture have significantly impeded modernising governance practices across regional Indonesia. This paper examines the experiences of government employees in five Indonesian regions: Solok, Padang, Gorontalo, Bali, and Jakarta. Each regional government is examined using a mixed methodology comprising of on-site observation, document analysis, and iterative semi-structured interviewing. Drawing from the experiences of five regional governments in implementing good governance this paper seeks to better understand the causal contexts of variable implementation governance practices and to suggest enhancements to the development of policies for sustainable inter-generational change in governance practice across regional government settings.

Effect of inaccuracies in anthropometric data and linked-segment inverse dynamic modeling on kinetics of gait in persons with partial foot amputation

The accuracy of data derived from linked-segment models depends on how well the system has been represented. Previous investigations describing the gait of persons with partial foot amputation did not account for the unique anthropometry of the residuum or the inclusion of a prosthesis and footwear in the model and, as such, are likely to have underestimated the magnitude of the peak joint moments and powers. This investigation determined the effect of inaccuracies in the anthropometric input data on the kinetics of gait. Toward this end, a geometric model was developed and validated to estimate body segment parameters of various intact and partial feet. These data were then incorporated into customized linked-segment models, and the kinetic data were compared with that obtained from conventional models. Results indicate that accurate modeling increased the magnitude of the peak hip and knee joint moments and powers during terminal swing. Conventional inverse dynamic models are sufficiently accurate for research questions relating to stance phase. More accurate models that account for the anthropometry of the residuum, prosthesis, and footwear better reflect the work of the hip extensors and knee flexors to decelerate the limb during terminal swing phase.

Seeing pedestrians at night : visual clutter does not mask biological motion

Although placing reflective markers on pedestrians’ major joints can make pedestrians more conspicuous to drivers at night, it has been suggested that this “biological motion” effect may be reduced when visual clutter is present. We tested whether extraneous points of light affected the ability of 12 younger and 12 older drivers to see pedestrians as they drove on a closed road at night. Pedestrians wore black clothing alone or with retroreflective markings in four different configurations. One pedestrian walked in place and was surrounded by clutter on half of the trials. Another was always surrounded by visual clutter but either walked in place or stood still. Clothing configuration, pedestrian motion, and driver age influenced conspicuity but clutter did not. The results confirm that even in the presence of visual clutter pedestrians wearing biological motion configurations are recognized more often and at greater distances than when they wear a reflective vest.

The effect of unlocking RGD-motifs in collagen I on pre-osteoblast adhesion and differentiation

Denaturation of extracellular matrix proteins exposes cryptic binding sites. It is hypothesized that binding of cell adhesion receptors to these cryptic binding sites regulates cellular behaviour during tissue repair and regeneration. To test this hypothesis, we quantify the adhesion of pre-osteoblastic cells to native (Col) and partially-denatured (pdCol) collagen I using single-cell force spectroscopy. During early stages of cell attachment (≤180 s) pre-osteoblasts (MC3T3-E1) adhered significantly stronger to pdCol compared to Col. RGD (Arg-Gly-Asp)-containing peptides suppressed this elevated cell adhesion. We show that the RGD-binding α5β1- and αv-integrins mediated pre-osteoblast adhesion to pdCol, but not to Col. On pdCol pre-osteoblasts had a higher focal adhesion kinase tyrosine-phosphorylation level that correlated with enhanced spreading and motility. Moreover, pre-osteoblasts cultured on pdCol showed a pronounced matrix mineralization activity. Our data suggest that partially-denatured collagen exposes RGD-motifs that trigger binding of α5β1- and αv-integrins. These integrins initiate cellular processes that stimulate osteoblast adhesion, spreading, motility and differentiation. Taken together, these quantitative insights reveal an approach for the development of alternative collagen I- based surfaces for tissue engineering applications.