Real-time detection of DNA interactions with long-period fiber-grating-based biosensor

Using an optical biosensor based on a dual-peak long-period fiber grating, we have demonstrated the detection of interactions between biomolecules in real time. Silanization of the grating surface was successfully realized for the covalent immobilization of probe DNA, which was subsequently hybridized with the complementary target DNA sequence. It is interesting to note that the DNA biosensor was reusable after being stripped off the hybridized target DNA from the grating surface, demonstrating a function of multiple usability. © 2007 Optical Society of America.

Water temperature reconstructions based on paired Uk'37 and Tex86 records, and paired surface and subsurface Mg/Ca records

This dataset contains the collection of available published paired Uk'37 and Tex86 records spanning multi-millennial to multi-million year time scales, as well as a collection of Mg/Ca-derived temperatures measured in parallel on surface and subsurface dwelling foraminifera, both used in the analyses of Ho and Laepple, Nature Geoscience 2016. As the signal-to-noise ratios of proxy-derived Holocene temperatures are relatively low, we selected records that contain at least the last deglaciation (oldest sample >18kyr BP).

Documentation and sedimentology of core PS1021-1 from the Antarctic continental margin off Kap Norvegia

Sedimentological analyses concerning ice rafted debris, grain size distribution, biogenous components, and clay mineral composition of four sediment cores from the Antarctic continental margin off Kapp Norvegia reveal a cyclical pattern of three different sediment facies. These are classified into warm and cold types representing warm and cold climatic periods and a short transition period from cold to warm events. The sedimentological parameters reflect the variations within the cryosphere and the hydrosphere, which are directly influenced by the climatic fluctuations. The unusually high content of carbonaceous planktonic and benthonic foraminifera in these polar sediments, as well as the interfingering of terrigeneous and biogeneous-rich sediments with increasing distance from the continent, might reflect the influence of the Weddell Sea Polynya and the oscillations of polynya, pack-ice and ice shelf extent during the late Pleistocene.

Planktonic foraminiferal d18O and d13C values, derived sea-surface temperatures from d18O and selected planktonic foraminiferal species for core P69 of Hawke Bay off eastern North Island

Recent evidence suggests that the Subtropical Convergence (STC) zone east of New Zealand shifted little from its modern position along Chatham Rise during the last glaciation, and that offshore surface waters north of the STC zone cooled only slightly. However, at nearshore core site P69 (2195 m depth), 115 km off the east coast of North Island and ca 300 km north of the modern STC zone, planktonic foraminiferal species, transfer function data and stable oxygen and carbon isotope records suggest that surface waters were colder by up to 6°C during the late last glacial period compared to the Holocene, and included a strong upwelling signature. Presently site P69 is bathed by south-flowing subtropical waters in the East Cape Current. The nearshore western end of Chatham Rise supports a major bathymetric depression, the Mernoo Saddle, through which some exchange between northern subtropical and southern subantarctic water presently occurs. It is proposed that as a result of much intensified current flows south of the Rise during the last glaciation, a consequence of more compressed subantarctic water masses, lowered sea level, and an expanded and stronger Westerly Wind system, there was accelerated leakage northwards of both Australasian Subantarctic Water and upwelled Antarctic Intermediate Water over Mernoo Saddle in a modified and intensified Southland Current. The expanded cold water masses displaced the south-flowing warm East Cape Current off southeastern North Island, and offshore divergence was accompanied by wind-assisted upwelling of nutrient-rich waters in the vicinity of P69. A comparable kind of inshore cold water jetting possibly characterised most glacial periods since the latest Miocene, and may account for the occasional occurrence of subantarctic marine fossils in onland late Cenozoic deposits north of the STC zone, rather than invoking wholesale major oscillations of the oceanic STC itself.

Sedimentology on cores off Filchner Shelf Ice, Weddell Sea, Antarctica

The sediments of 14 box cores and 7 gravity cores, mainly taken directly in front of the Filchner(-Ronne) ice shelf northwest of Berkner Island (Weddell Sea), allowed to distinguish six sediment types. On the one hand,the retreat of the at first grounded and then floated ice from the last glacial maximum is documented. On the other hand,the sediments give an insight into extensive Holocene sediment deposition and remobilization northwest of Berkner Island. The ortho till was deposited directly by the grounded ice sheet and is lacking any marine influence. After floating of the ice shelf, partly very weIl stratified, partly unstratified, non-bioturbated paratill is deposited beneath the ice shelf. Lack of IRD-content in the paratill immediately above the orthotill indicates freezing at the bottom of the ice, at least for a short period after the ice became afloat. The orthotill and paratill contain small amounts of fragmented Tertiary diatoms, which allow the conclusion, that glacial-marine sediments in the accumulation area of the Ronne ice shelf will be eroded and later deposited by ice in the investigation area. Starting of bioturbation and therefore change in sedimentation from paratill to bioturbated paratill,is caused by the retreat of the ice shelf to its actual position. Isostatic uplift of the sea-bed after the Ice Age causes minor water depths with higher current velocities. The fine-fraction is eroding and mean particle-size will increase. Maybe, also isostatic uplift is responsible for repeated great advances of the floated ice shelf as shown in an erosional horizon in some cores containing bioturbated paratill. Postglacial sediment-thicknesses exceed 3 m. Assuming floating of the ice 15.000 YBP, accumulation rates reach nearly 20cm/lOOO years. Following the theories about sediment input in front of wide ice shelves, this was not expected. In the shallower water depths of Berkner Bank, the oscillations of the ice shelf are recorded in the sediments. Sorting and redistribution by high current velocities from beneath the ice up to the calving line, lead to the deposition of the weIl to very weIl sorted sandy till. In front of the calving line the finer fraction will settle down. Remobilization is possible by bioturbation and increasing current-velocity. According to the intensity of mixing of the sandy till with the fine fraction, modified till or muddy till results.

Results of wave modelling for Moreton Bay, Southeast Queensland, and a reef lagoon off Lizard Island, Great Barrier Reef, Australia

The distribution, abundance, behaviour, and morphology of marine species is affected by spatial variability in the wave environment. Maps of wave metrics (e.g. significant wave height Hs, peak energy wave period Tp, and benthic wave orbital velocity URMS) are therefore useful for predictive ecological models of marine species and ecosystems. A number of techniques are available to generate maps of wave metrics, with varying levels of complexity in terms of input data requirements, operator knowledge, and computation time. Relatively simple "fetch-based" models are generated using geographic information system (GIS) layers of bathymetry and dominant wind speed and direction. More complex, but computationally expensive, "process-based" models are generated using numerical models such as the Simulating Waves Nearshore (SWAN) model. We generated maps of wave metrics based on both fetch-based and process-based models and asked whether predictive performance in models of benthic marine habitats differed. Predictive models of seagrass distribution for Moreton Bay, Southeast Queensland, and Lizard Island, Great Barrier Reef, Australia, were generated using maps based on each type of wave model. For Lizard Island, performance of the process-based wave maps was significantly better for describing the presence of seagrass, based on Hs, Tp, and URMS. Conversely, for the predictive model of seagrass in Moreton Bay, based on benthic light availability and Hs, there was no difference in performance using the maps of the different wave metrics. For predictive models where wave metrics are the dominant factor determining ecological processes it is recommended that process-based models be used. Our results suggest that for models where wave metrics provide secondarily useful information, either fetch- or process-based models may be equally useful.

Ratio of Diene/Triene of sediment core MD03-2601

Micropaleontological and biomarker data from two high-accumulation marine sites from the Coastal and Continental Shelf Zone (CCSZ) off East Antarctica (Adélie Land at w140°E and eastern Prydz Bay at w77°E) are used to reconstruct Holocene changes in sea ice and wind stress at the basin-wide scale. These data demonstrate congruent increase in sea-ice concentration/persistence and wind stress-related sea-surface turbulence in the two regions since 7 cal ka BP, with a particularly strong signal since 4.5 - 3.5 cal ka BP. Comparison of these high latitude records with sea ice and turbulence records from the southern mid-latitudes highlights distinctive climatic evolutions according to the different latitudinal bands. Sea-ice persistence and turbulence increase in East Antarctica CCSZ are opposite to sea-surface warming and sea-ice retreat recorded after 4.5 - 3.5 cal ka BP in the East Atlantic and Indian sector between 55 and 45°S. At the same period, paleodata suggest SST cooling in all major coastal upwelling systems of the southern hemisphere, caused by the northward transport of subpolar surface waters as a response to southern Westerlies reinforcement. We therefore propose, as suggested for the northern hemisphere, that Holocene changes in the latitudinal insolation gradient, primarily forced by obliquity and precession and amplified by sea-ice and glacial-ice expansions in the Antarctic realm, are responsible for the observed contrasted latitudinal patterns of southern latitudes.

Sea surface temperature reconstruction based on planktonic foraminifera of surface sediments and sediment cores off Iberia

Quantitative and qualitative analyses of planktonic foraminiferal assemblages from 134 core-top sediment samples collected along the western Iberian margin were used to assess the latitudinal and longitudinal changes in surface water conditions and to calibrate a Sea Surface Temperature (SST) transfer function for this seasonal coastal upwelling region. Q-mode factor analysis performed on relative abundances yielded three factors that explain 96% of the total variance: factor 1 (50%) is exclusively defined by Globigerina bulloides, the most abundant and widespread species, and reflects the modern seasonal (May to September) coastal upwelling areas; factor 2 (32%) is dominated by Neogloboquadrina pachyderma (dextral) and Globorotalia inflata and seems to be associated with the Portugal Current, the descending branch of the North Atlantic Drift; factor 3 (14%) is defined by the tropical-sub-tropical species Globigerinoides ruber (white), Globigerinoides trilobus trilobus, and G. inflata and mirrors the influence of the winter-time eastern branch of the Azores Current. In conjunction with satellite-derived SST for summer and winter seasons integrated over an 18 year period the regional foraminiferal data set is used to calibrate a SST transfer function using Imbrie & Kipp, MAT and SIMMAX(ndw) techniques. Similar predicted errors (RMSEP), correlation coefficients, and residuals' deviation from SST estimated for both techniques were observed for both seasons. All techniques appear to underestimate SST off the southern Iberia margin, an area mainly occupied by warm waters where upwelling occurs only occasionally, and overestimate SST on the northern part of the west coast of the Iberia margin, where cold waters are present nearly all year round. The comparison of these regional calibrations with former Atlantic and North Atlantic calibrations for two cores, one of which is influenced by upwelling, reveals that the regional one attests more robust paleo-SSTs than for the other approaches.

Planktonic foraminiferal flux and shell geochemistry data in the sediment trap time series JAM 1-3 off south Java

Results from sediment trap experiments conducted in the seasonal upwelling area off south Java from November 2000 until July 2003 revealed significant monsoon-, El Niño-Southern Oscillation-, and Indian Ocean Dipole-induced seasonal and interannual variations in flux and shell geochemistry of planktonic foraminifera. Surface net primary production rates together with total and species-specific planktonic foraminiferal flux rates were highest during the SE monsoon-induced coastal upwelling period from July to October, with three species Globigerina bulloides, Neogloboquadrina pachyderma dex., and Globigerinita glutinata contributing to 40% of the total foraminiferal flux. Shell stable oxygen isotopes (d18O) and Mg/Ca data of Globigerinoides ruber sensu stricto (s.s.), G. ruber sensu lato (s.l.), Neogloboquadrina dutertrei, Pulleniatina obliquiloculata, and Globorotalia menardii in the sediment trap time series recorded surface and subsurface conditions. We infer habitats of 0-30 m for G. ruber at the mixed layer depth, 60-80 m (60-90 m) for P. obliquiloculata (N. dutertrei) at the upper thermocline depth, and 90-110 m (100-150 m) for G. menardii in the 355-500 mm (>500 µm) size fraction corresponding to the (lower) thermocline depth in the study area. Shell Mg/Ca ratio of G. ruber (s.l. and s.s.) reveals an exponential relationship with temperature that agrees with published relationships particularly with the Anand et al. (2003) equations. Flux-weighted foraminiferal data in sediment trap are consistent with average values in surface sediment samples off SW Indonesia. This consistency confirms the excellent potential of these proxies for reconstructing past environmental conditions in this part of the ocean realm.

Stable carbon isotope ratios and accumulation rates of organic carbon and nutrients of DSDP Hole 79-545 (Appendix A)

Future warming is predicted to shift the Earth system into a mode with progressive increase and vigour of extreme climate events possibly stimulating other mechanisms that invigorate global warming. This study provides new data and modelling investigating climatic consequences and biogeochemical feedbacks that happened in a warmer world ~112 Myr ago. Our study focuses on the Cretaceous Oceanic Anoxic Event (OAE) 1b and explores how the Earth system responded to a moderate ~25,000 yr lasting climate perturbation that is modelled to be less than 1 °C in global average temperature. Using a new chronological model for OAE 1b we present high-resolution elemental and bulk carbon isotope records from DSDP Site 545 from Mazagan Plateau off NW Africa and combine this information with a coupled atmosphere-land-ocean model. The simulations suggest that a perturbation at the onset of OAE 1b caused almost instantaneous warming of the atmosphere on the order of 0.3 °C followed by a longer (~45,000 yr) period of ~0.8 °C cooling. The marine records from DSDP Site 545 support that these moderate swings in global climate had immediate consequences for African continental supply of mineral matter and nutrients (phosphorous), subsequent oxygen availability, and organic carbon burial in the eastern subtropical Atlantic, however, without turning the ocean anoxic. The match between modelling results and stratigraphic isotopic data support previous studies [summarized in Jenkyns 2003, doi:10.1098/rsta.2003.1240] in that methane emission from marine hydrates, albeit moderate in dimension, may have been the trigger for OAE 1b, though we can not finally rule out alternative mechanisms. Following the hydrate mechanism a total of 1.15 * 10**18 g methane carbon (delta13C=-60 ?), equivalent to about 10% to the total modern gas hydrate inventory, generated the delta13Ccarb profile recorded in the section. Modelling suggests a combination of moderate-scale methane pulses supplemented by continuous methane emission at elevated levels over ~25,000 yr. The proposed mechanism, though difficult to finally confirm in the geological past, is arguably more likely to occur in a warmer world and apparently perturbs global climate and ocean chemistry almost instantaneously. This study shows that, once set-off, this mechanism can maintain Earth's climate in a perturbed mode over geological time leading to pronounced changes in regional climate.

Effect of cooling rate on properties of plasma nitrided AISI 1010 steel

In this work, AISI 1010 steel samples were plasma nitrided into 20% N 2 100 Pa and 400 Pa for N 2 and H 2 , respectively), temperatures of 500 and 580 °C, during 2 h. Three different procedures for cooling were accomplished after nitriding. In the first procedure the cooling occurred naturally, that is, the sample was kept on substrate holder. In the second one the sample was pulled off and cooling in a cold surface. Finally, in the third cooling process the sample was pulled off the substrate holder down into special reservoir filled with oil held at ambient temperature. The properties of the AISI 1010 steel samples were characterized by optical and electron microscopy, X-ray diffraction, Mössbauer spectroscopy and microhardness tests. Thermal gradient inside the sample kept on substrate holder during cooling process was measured by three inserted thermocouples at different depths. When samples were cooled rapidly the transformation of ϵ-Fe 2 − 3 N to γ′-Fe 4 N was inhibited. Such effect is indicated by the high concentration of ϵ-Fe compound zone. To get solid state solution of nitrogen in the diffusion zone, instead of precipitates of nitride phases, the cooling rate should be higher than a critical value of about 0.95 °C/s. When this value is reached at any depth of the diffusion zone, two distinct diffusion zones will appear. Temperature gradients were measured inside the samples as a consequence of the plasma treatment. It's suggested the need for standardization of the term “treatment temperature” for plasma treatment because different nitrided layer properties could be reported for the same “treatment temperature”.

The pre-reproductive period in a tropical bird: parental care, dispersal, survival, and avian life histories

The period between offspring birth and recruitment into the breeding population is considered one of the least understood components of animal life histories. Yet, examining this period is essential for studies of parental care, dispersal, demography, and life histories. Studies of the pre-reproductive period are particularly few in tropical regions, where the organization of life histories are predicted to differ compared to northern hemisphere species. For my dissertation I used radio-telemetry, mark-resighting, and field observations to study the pre-reproductive period in a Neotropical bird, the western slaty-antshrike (Thamnophilus atrinucha), in Panama. First, I found that parental care after offspring left the nest (the post-fledging period) was greater than care during the nestling period. Prolonged care resulted in a clear trade-off for parents as they did not nest again until fledglings from the first brood were independent. Parents fed offspring for a prolonged duration during the post-fledging period and higher post-fledging survival was observed compared to many northern hemisphere species. Second, I observed that offspring that remained with parents for longer periods on the natal territory had higher survival both while on the natal territory and after dispersal compared to those dispersing earlier. Parental aggression towards offspring increased with offspring age and offspring dispersed earlier when parents renested. Contrary to other family living species, only a small proportion of antshrike offspring remained on the natal territory until the following year and all dispersed to float. Floating is when juveniles wander within other breeding pairs’ territories. These results suggest that the benefits of delayed dispersal declined with offspring age and with renesting by parents. Third, I observed that survival during the dependent period and first year was greater in slaty antshrikes compared to that of northern hemisphere species. Pre-reproductive survival relative to adult survival was equal or greater than that observed in northern hemisphere species. The date offspring left the nest, mass, and age at dispersal influenced offspring survival, whereas offspring sex and year did not. Relatively high survival during the pre-reproductive period coupled with comparatively low annual productivity clarifies how many tropical species achieve replacement. High juvenile survival appears to obtain from extended post-fledging parental care, delayed dispersal, low costs of dispersal, and a less seasonal environment. Lastly, I experimentally manipulated begging at the nest to examine changes in parental behavior. Under elevated begging, parents increased provisioning rates and reduced the time between arrival to the nest and feeding of nestlings, potentially to reduce begging sounds. Furthermore, parents switched to preferentially feed the closest offspring during the begging treatment. This suggests parents either allowed sibling competition to influence feeding decisions, or feeding the closer nestling increased the efficiency of provisioning. In summary, I found that slaty antshrikes have delayed age at reproduction, higher post-fledging and first year survival, extended post-fledging parental care, equal or greater pre-reproductive survival relative to adult survival, and delayed dispersal compared to many northern hemisphere passerines. These results suggest that this tropical species has a strategy of high investment into few offspring. Furthermore, reproductive effort is equal or greater at least in slaty antshrikes compared to northern hemisphere species, suggesting that the latitudinal gradient in clutch size is not explained by a gradient in reproductive effort.

Experimental and analytical investigation of refrigerant and lubricant migration

The off-cycle refrigerant mass migration has a direct influence on the on-cycle performance since compressor energy is necessary to redistribute the refrigerant mass. No studies, as of today, are available in the open literature which experimentally measured the lubricant migration within a refrigeration system during cycling or stop/start transients. Therefore, experimental procedures measuring the refrigerant and lubricant migration through the major components of a refrigeration system during stop/start transients were developed and implemented. Results identifying the underlying physics are presented. The refrigerant and lubricant migration of an R134a automotive A/C system-utilizing a fixed orifice tube, minichannel condenser, plate and fin evaporator, U-tube type accumulator and fixed displacement compressor-was measured across five sections divided by ball valves. Using the Quick-Closing Valve Technique (QCVT) combined with the Remove and Weigh Technique (RWT) using liquid nitrogen as the condensing agent resulted in a measurement uncertainty of 0.4 percent regarding the total refrigerant mass in the system. The determination of the lubricant mass distribution was achieved by employing three different techniques-Remove and Weigh, Mix and Sample, and Flushing. To employ the Mix and Sample Technique a device-called the Mix and Sample Device-was built. A method to separate the refrigerant and lubricant was developed with an accuracy-after separation-of 0.04 grams of refrigerant left in the lubricant. When applying the three techniques, the total amount of lubricant mass in the system was determined to within two percent. The combination of measurement results-infrared photography and high speed and real time videography-provide unprecedented insight into the mechanisms of refrigerant and lubricant migration during stop-start operation. During the compressor stop period, the primary refrigerant mass migration is caused by, and follows, the diminishing pressure difference across the expansion device. The secondary refrigerant migration is caused by a pressure gradient as a result of thermal nonequilibrium within the system and causes only vapor phase refrigerant migration. Lubricant migration is proportional to the refrigerant mass during the primary refrigerant mass migration. During the secondary refrigerant mass migration lubricant is not migrating. The start-up refrigerant mass migration is caused by an imbalance of the refrigerant mass flow rates across the compressor and expansion device. The higher compressor refrigerant mass flow rate was a result of the entrainment of foam into the U-tube of the accumulator. The lubricant mass migration during the start-up was not proportional to the refrigerant mass migration. The presence of water condensate on the evaporator affected the refrigerant mass migration during the compressor stop period. Caused by an evaporative cooling effect the evaporator held 56 percent of the total refrigerant mass in the system after three minutes of compressor stop time-compared to 25 percent when no water condensate was present on the evaporator coil. Foam entrainment led to a faster lubricant and refrigerant mass migration out of the accumulator than liquid entrainment through the hole at the bottom of the U-tube. The latter was observed for when water condensate was present on the evaporator coil because-as a result of the higher amount of refrigerant mass in the evaporator before start-up-the entrainment of foam into the U-tube of the accumulator ceased before the steady state refrigerant mass distribution was reached.

Effect of cooling rate on properties of plasma nitrided AISI 1010 steel

In this work, AISI 1010 steel samples were plasma nitrided into 20% N 2 100 Pa and 400 Pa for N 2 and H 2 , respectively), temperatures of 500 and 580 °C, during 2 h. Three different procedures for cooling were accomplished after nitriding. In the first procedure the cooling occurred naturally, that is, the sample was kept on substrate holder. In the second one the sample was pulled off and cooling in a cold surface. Finally, in the third cooling process the sample was pulled off the substrate holder down into special reservoir filled with oil held at ambient temperature. The properties of the AISI 1010 steel samples were characterized by optical and electron microscopy, X-ray diffraction, Mössbauer spectroscopy and microhardness tests. Thermal gradient inside the sample kept on substrate holder during cooling process was measured by three inserted thermocouples at different depths. When samples were cooled rapidly the transformation of ϵ-Fe 2 − 3 N to γ′-Fe 4 N was inhibited. Such effect is indicated by the high concentration of ϵ-Fe compound zone. To get solid state solution of nitrogen in the diffusion zone, instead of precipitates of nitride phases, the cooling rate should be higher than a critical value of about 0.95 °C/s. When this value is reached at any depth of the diffusion zone, two distinct diffusion zones will appear. Temperature gradients were measured inside the samples as a consequence of the plasma treatment. It's suggested the need for standardization of the term “treatment temperature” for plasma treatment because different nitrided layer properties could be reported for the same “treatment temperature”.

Early life history of larvae and early juvenile atlantic horse mackerel trachurus trachurus off the portuguese west coast

Early life history traits (ELHTs) are key to understand recruitment patterns in marine animals. However, for reef fishes, studies on ELHTs are mainly focused on tropical systems and little is known for temperate reefs. In this study we used SMURFs (Standard Monitoring Units for the Recruitment of Reef Fishes) to collect fish in a temperate rocky reef system (Arrábida Marine Park, Portugal) on a weekly basis for three months during the recruitment period. Six sub-surface SMURFs sampled 2490 Atlantic horse mackerel (Trachurus trachurus) postlarvae and juveniles. Sagittal and lapilli otoliths were extracted from a subsample of 296 fish and ELHTs, such as size and age at settlement, growth rate and age at first secondary growth formation were examined. Additionally, we tested three growth curves and selected the best suited to back-calculate the hatching pattern based on the lengths of all sampled fish. Standard length ranged from 6.13 mm to 48.56 mm and subsampled fish were aged between 19 days to 44 days. Age and size at settlement were estimated between 19 days and 36 days for individuals of 6.13 mm and 24.95 mm, respectively. Otolith shape changed clearly with increasing age and, on average, secondary growth started to form on day 33 (±3 days). Age/length relationship was well described by a Gompertz growth model which was used to back-calculate hatching dates. Four distinct hatching cohorts were identified with fish of the earliest cohort showing a faster body and otolith growth. This study indicates that the nearshore environment might have an important role in the early growth, development and hence recruitment of Atlantic horse mackerel. Information on the early life history of Atlantic horse mackerel is key to understand recruitment processes for this economically and biologically important species.