The application of reduced-size short tandem repeat primer sets in the analysis of human DNA from degraded and compromised samples

The purpose of this research was to demonstrate the applicability of reduced-size STR (Miniplex) primer sets to challenging samples and to provide the forensic community with new information regarding the analysis of degraded and inhibited DNA. The Miniplex primer sets were validated in accordance with guidelines set forth by the Scientific Working Group on DNA Analysis Methods (SWGDAM) in order to demonstrate the scientific validity of the kits. The Miniplex sets were also used in the analysis of DNA extracted from human skeletal remains and telogen hair. In addition, a method for evaluating the mechanism of PCR inhibition was developed using qPCR. The Miniplexes were demonstrated to be a robust and sensitive tool for the analysis of DNA with as low as 100 pg of template DNA. They also proved to be better than commercial kits in the analysis of DNA from human skeletal remains, with 64% of samples tested producing full profiles, compared to 16% for a commercial kit. The Miniplexes also produced amplification of nuclear DNA from human telogen hairs, with partial profiles obtained from as low as 60 pg of template DNA. These data suggest smaller PCR amplicons may provide a useful alternative to mitochondrial DNA for forensic analysis of degraded DNA from human skeletal remains, telogen hairs, and other challenging samples. In the evaluation of inhibition by qPCR, the effect of amplicon length and primer melting temperature was evaluated in order to determine the binding mechanisms of different PCR inhibitors. Several mechanisms were indicated by the inhibitors tested, including binding of the polymerase, binding to the DNA, and effects on the processivity of the polymerase during primer extension. The data obtained from qPCR illustrated a method by which the type of inhibitor could be inferred in forensic samples, and some methods of reducing inhibition for specific inhibitors were demonstrated. An understanding of the mechanism of the inhibitors found in forensic samples will allow analysts to select the proper methods for inhibition removal or the type of analysis that can be performed, and will increase the information that can be obtained from inhibited samples.

Diversity in Education: Profiles of Students at FIU's School of Hospitality Management

The authors are conducting a study of career patterns for students enrolled in the Florida International University School of Hospitality Management. A preliminary ethnographic phase of the study was to profile a variety of student participants in order to identify potential factors which might affect career patterns. The result is a fascinating and diverse mosaic of ambitious young people and a wealth of insight for corporate recruiting.

Tourism Management Profiles: Implications for Tourism Education

Studies of state tourism directors and convention and visitor bureau directors show that there is a need for organized tourism management educations. The author discusses these studies and how they can be used in the development of tourism management education.

An Analytical Workflow for Metagenomic Data and its Application to the Study of Chronic Obstructive Pulmonary Disease (COPD)

Metagenomics is the culture-independent study of genetic material obtained directly from environmental samples. It has become a realistic approach to understanding microbial communities thanks to advances in high-throughput DNA sequencing technologies over the past decade. Current research has shown that different sites of the human body house varied bacterial communities. There is a strong correlation between an individual’s microbial community profile at a given site and disease. Metagenomics is being applied more often as a means of comparing microbial profiles in biomedical studies. The analysis of the data collected using metagenomics can be quite challenging and there exist a plethora of tools for interpreting the results. An automatic analytical workflow for metagenomic analyses has been implemented and tested using synthetic datasets of varying quality. It is able to accurately classify bacteria by taxa and correctly estimate the richness and diversity of each set. The workflow was then applied to the study of the airways microbiome in Chronic Obstructive Pulmonary Disease (COPD). COPD is a progressive lung disease resulting in narrowing of the airways and restricted airflow. Despite being the third leading cause of death in the United States, little is known about the differences in the lung microbial community profiles of healthy individuals and COPD patients. Bronchoalveolar lavage (BAL) samples were collected from COPD patients, active or ex-smokers, and never smokers and sequenced by 454 pyrosequencing. A total of 56 individuals were recruited for the study. Substantial colonization of the lungs was found in all subjects and differentially abundant genera in each group were identified. These discoveries are promising and may further our understanding of how the structure of the lung microbiome is modified as COPD progresses. It is also anticipated that the results will eventually lead to improved treatments for COPD.

A model of the hydrothermal system at Casa Diablo in Long Valley, California, based on resistivity profiles and soil mercury analyses

A description and model of the near-surface hydrothermal system at Casa Diablo, with its implications for the larger-scale hydrothermal system of Long Valley, California, is presented. The data include resistivity profiles with penetrations to three different depth ranges, and analyses of inorganic mercury concentrations in 144 soil samples taken over a 1.3 by 1.7 km area. Analyses of the data together with the mapping of active surface hydrothermal features (fumaroles, mudpots, etc.), has revealed that the relationship between the hydrothermal system, surface hydrothermal activity, and mercury anomalies is strongly controlled by faults and topography. There are, however, more subtle factors responsible for the location of many active and anomalous zones such as fractures, zones of high permeability, and interactions between hydrothermal and cooler groundwater. In addition, the near-surface location of the upwelling from the deep hydrothermal reservoir, which supplies the geothermal power plants at Casa Diablo and the numerous hot pools in the caldera with hydrothermal water, has been detected. The data indicate that after upwelling the hydrothermal water flows eastward at shallow depth for at least 2 km and probably continues another 10 km to the east, all the way to Lake Crowley.

Age determinations and stable isotope records of four sediment profiles off Nova Scotia

Continental margin sediments off Nova Scotia accumulate at high rates (up to 360 cm/kyr) and contain a history of millennial-scale environmental changes which are dominated by the proximity of the Laurentide ice sheet during the latest Quaternary. Using stable isotope ratios of oxygen, accelerator mass spectrometer radiocarbon dating, micropaleontology, and sedimentology, we document these changes in six piston cores ranging in water depth from ab. 450 to ab. 4300 m. We find that maximum d18O in N. pachyderma occurred about 15 ka and preceded the maximum abundance of this species in these cores by ab. 1000 years. Between 13 and 14 ka we find a second peak in abundance of N. pachyderma, minimum d18O, and two pulses of ice rafting. The sediment lithology supports terrestrial studies which indicate that there was a general withdrawal of ice beyond the upper Paleozoic and Mesozoic red beds by 14 ka in southeastern Canada, so the ice rafting events between 13 and 14 ka probably reflect ice stream activity in the St. Lawrence valley. The Younger Dryas event is recognized as a peak in abundance of N. pachyderma and ice rafting (dated as ab. 11.3 ka), but meltwater discharge to the Gulf of St. Lawrence was either too small or occurred over too long a time to leave a distinct d18O minimum off Nova Scotia. At 7.1 ka, in the middle of Holocene warming, we find a third peak in abundance of N. pachyderma and another d18O minimum but no ice rafting. We interpret these data as evidence of a late-occurring meltwater event which, if correct, could have originated in the Great Lakes, in the Labrador-Ungava region, or in both. The final millennial-scale phenomenon off Nova Scotia is the onset of "Neoglaciation," marked by increased ice rafting and increased % N. pachyderma beginning about 5 kyr ago.

Seafloor images along 14 ROV profiles during METEOR cruise M114/2

Complete Data set of ROV postition data, onboard CTD data, underwater photos and underwater videos that were produced with ROV MARUM-Quest during Meteor Expedition M114/2. Data set organized as a single folder for each dive.

Results of analysis and model simulation of the bed profiles

Bedforms such as dunes and ripples are ubiquitous in rivers and coastal seas, and commonly described as triangular shapes from which height and length are calculated to estimate hydrodynamic and sediment dynamic parameters. Natural bedforms, however, present a far more complicated morphology; the difference between natural bedform shape and the often assumed triangular shape is usually neglected, and how this may affect the flow is unknown. This study investigates the shapes of natural bedforms and how they influence flow and shear stress, based on four datasets extracted from earlier studies on two rivers (the Rio Paraná in Argentina, and the Lower Rhine in The Netherlands). The most commonly occurring morphological elements are a sinusoidal stoss side made of one segment and a lee side made of two segments, a gently sloping upper lee side and a relatively steep (6 to 21°) slip face. A non-hydrostatic numerical model, set up using Delft3D, served to simulate the flow over fixed bedforms with various morphologies derived from the identified morphological elements. Both shear stress and turbulence increase with increasing slip face angle and are only marginally affected by the dimensions and positions of the upper and lower lee side. The average slip face angle determined from the bed profiles is 14°, over which there is no permanent flow separation. Shear stress and turbulence above natural bedforms are higher than above a flat bed but much lower than over the often assumed 30° lee side angle.

426 ozonesonde profiles from Georg-Forster-Station

On 22 May 1985 the first balloon-borne ozonesonde was successfully launched by the staff of Georg-Forster-Station (70°46' S, 11°41' E). The following weekly ozone soundings mark the beginning of the continuous investigation of Germany to study the vertical ozone distribution in the southern hemisphere. In 1985 these ozone soundings have been the only record showing the change of vertical ozone distribution in the southern polar stratosphere in September and October. The regular ozone soundings from 1985 until 1992 are a valuable reference data set since the chemical ozone loss became a significant feature in the southern polar stratosphere. The balloon-borne soundings were performed at the upper air sounding facility of the neighbouring station Novolazarevskaya, just 2 km apart from Georg-Forster-Station. Till 1992, ozone soundings were taken without interruption. Afterwards, the ozone sounding program was moved to Neumayer-Station (70°39' S, 8°15' W) 750 km further west.

(Supplementary Material 2) Landmark coordinates of the analyzed specimens with associated metadata

The use of planktonic foraminifera in paleoceanographic studies relies on the assumption that morphospecies represent biological species with ecological preferences that are stable through time and space. However, genetic surveys unveiled a considerable level of diversity in most morphospecies of planktonic foraminifera. This diversity is significant for paleoceanographic applications because cryptic species were shown to display distinct ecological preferences that could potentially help refine paleoceanographic proxies. Subtle morphological differences between cryptic species of planktonic foraminifera have been reported, but so far their applicability within paleoceanographic studies remains largely unexplored. Here we show how information on genetic diversity can be transferred to paleoceanography using Globorotalia inflata as a case study. The two cryptic species of G. inflata are separated by the Brazil-Malvinas Confluence (BMC), a major oceanographic feature in the South Atlantic. Based on this observation, we developed a morphological model of cryptic species detection in core top material. The application of the cryptic species detection model to Holocene samples implies latitudinal oscillations in the position of the confluence that are largely consistent with reconstructions obtained from stable isotope data. We show that the occurrence of cryptic species in G. inflata, can be detected in the fossil record and used to trace the migration of the BMC. Since a similar degree of morphological separation as in G. inflata has been reported from other species of planktonic foraminifera, the approach presented in this study can potentially yield a wealth of new paleoceanographical proxies.

Radionuclides measured on 27 water bottle profiles during POLARSTERN cruise ANT-XXIV/3

As part of the GEOTRACES Polarstern expedition ANT XXIV/3 (ZERO and DRAKE) we have measured the vertical distribution of 234Th on sections through the Antarctic Circumpolar Current along the zero meridian and in Drake Passage and on an EW section through the Weddell Sea. Steady state export fluxes of 234Th from the upper 100m, derived from the depletion of 234Th with respect to its parent 238U, ranged from 621±105 dpm/m**2/d to 1773±90 dpm/m**2/d. This 234Th flux was converted into an export flux of organic carbon ranging from 3.1-13.2 mmolC/m**2/d (2.1-9.0 mmolC/m**2/d) using POC/234Th ratio of bulk (respectively >50 µm) suspended particles at the export depth (100 m). Non-steady state fluxes assuming zero flux under ice cover were up to 23% higher. In addition, particulate and dissolved 234Th were measured underway in high resolution in the surface water with a semi-automated procedure. Particulate 234Th in surface waters is inversely correlated with light transmission and pCO2 and positively with fluorescence and optical backscatter and is interpreted as a proxy for algal biomass. High resolution underway mapping of particulate and dissolved 234Th in surface water shows clearly where trace elements are absorbed by plankton and where they are exported to depth. Quantitative determination of the export flux requires the full 234Th profile since surface depletion and export flux become decoupled through changes in wind mixed layer depth and in contribution to export from subsurface layers. In a zone of very low algal abundance (54-58 °S at the zero meridian), confirmed by satellite Chl-a data, the lowest carbon export of the ACC was observed, allowing Fe and Mn to maintain their highest surface concentrations (Klunder et al., this issue, Middag et al., this issue). An ice-edge bloom that had developed in Dec/Jan in the zone 60-65 °S as studied during the previous leg (Strass et al., in prep) had caused a high export flux at 64.5 °S when we visited the area two months later (Feb/March). The ice-edge bloom had then shifted south to 65-69 °S evident from uptake of CO2 and dissolved Fe, Mn and 234Th, without causing export yet. In this way, the parallel analysis of 234Th can help to explain the scavenging behaviour of other trace elements.

Radionuclides measured on 21 water bottle profiles during POLARSTERN cruise ANT-XXIV/3

Drake Passage is a major route for many water masses from the strong Antarctic Circumpolar Current. During the ANTXXIV-3 expedition (in 2008) the vertical distributions of dissolved and size-fractionated particulate 231Pa and thorium isotopes (230Th, 232Th and 234Th) were investigated in order to better define the scavenging regimes and the effects of the oceanic circulation on the fate of particulate material and on the Pa-Th distributions in the water column. The reversible scavenging-model applied to both 230Th and 234Th, in the upper 1500 m depth, gives estimates of the particle dynamics (settling velocities S~ 500-1300 m/y, adsorption and desorption rate constants of 0.1-0.4 1/y and 1-6 1/y respectively). Particulate 234Th/230Th activity ratio shows a depth dependence, with decreasing ratio with increasing depth in agreement with previous studies, but no relationship with particle size was found. 231Pa and thorium isotope fractionation and partition coefficients were investigated with particle size vs depth and latitude and appear to vary horizontally following a North-South gradient. This suggests that both radionuclides are mostly bound to the fine suspended particles. At Drake Passage, the 230Thxs distribution is controlled by a southward upwelling of deep water (clearly visible on the vertical section of total 230Thxs, defined as dissolved + particulate concentrations) and reversible-scavenging processes (linear increase of 230Thxs with increasing depth) with North of the Southern ACC Front, higher settling velocities and less adsorption/desorption cycles, than South of it. Distributions of dissolved and total 231Paxs also reflect the influence of the North-South upwelling but somehow this effect appears to be limited to the upper 1500 m depth of the water column. Below this depth, 231Paxs vertical profiles exhibit contrasted concentrations, with some high dissolved activities in the deep water of the stations in the northern part of the ACC and not South of the ACC. These N-S differences in dissolved 231Paxs were attributed to the different origins and scavenging history of the deep Pacific waters flowing across Drake Passage. Here at North, radionuclides-rich deep water originates from the Central Pacific, while at South, deep water derives from the Southern Pacific in which the observed low radionuclides concentrations are attributed to high opal abundance. South of the Drake Passage, high dissolved and particulate activities of 230Th and 232Th confirmed the intrusion of 230Th-rich Weddell Sea Deep Water (WSDW) close to the Antarctic Peninsula.

Seabed photographs taken along OFOS profiles during POLARSTERN cruise PS96 (ANT-XXXI/2 FROSN)

Within the context of the overall ecological working programme Dynamics of Antarctic Marine Shelf Ecosystems (DynAMo) of the PS96 (ANT-XXXI/2) cruise of RV "Polarstern" to the Weddell Sea (Dec 2015 to Feb 2016), seabed imaging surveys were carried out along drift profiles by means of the Ocean Floor Observation System (OFOS) of the Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research (AWI) Bremerhaven. The setup and mode of deployment of the OFOS was similar to that described by Bergmann and Klages (2012, doi:10.1016/j.marpolbul.2012.09.018). OFOS is a surface-powered gear equipped with two downward-looking cameras installed side-by-side: one high-resolution, wide-angle still camera (CANON® EOS 5D Mark III; lens: Canon EF 24 f/1.4L II, f stop: 13, exposure time: 1/125 sec; in-air view angles: 74° (horizontal), 53° (vertical), 84° (diagonal); image size: 5760 x 3840 px = 21 MPix; front of pressure resistant camera housing consisting of plexiglass dome port) and one high-definition color video camera (SONY® FCB-H11). The system was vertically lowered over the stern of the ship with a broadband fibre-optic cable, until it hovers approximately 1.5 m above the seabed. It was then towed after the slowly sailing ship at a speed of approximately 0.5 kn (0.25 m/s). The ship's Global Acoustic Positioning System (GAPS), combining Ultra Short Base Line (USBL), Inertial Navigation System (INS) and satellite-based Global Positioning System (GPS) technologies, was used to gain highly precise underwater position data of the OFOS. During the profile, OFOS was kept hanging at the preferred height above the seafloor by means of the live video feed and occasional minor cable-length adjustments with the winch to compensate small-scale bathymetric variations in seabed morphology. Information on water depth and height above the seafloor were continuously recorded by means of OFOS-mounted sensors (GAPS transponder, Tritech altimeter). Three lasers, which are placed beside the still camera, emit parallel beams and project red light points, arranged as an equilateral triangle with a side length of 50 cm, in each photo, thus providing a scale that can be used to calculate the seabed area depicted in each image and/or measure the size of organisms or seabed features visible in the image. In addition, the seabed area depicted was estimated using altimeter-derived height above seafloor and optical characteristics of the OFOS still camera. In automatic mode, a seabed photo, depicting an area of approximately 3.45 m**2 (= 2.3 m x 1.5 m; with variations depending on the actual height above ground), was taken every 30 seconds to obtain series of "TIMER" stills distributed at regular distances along the profiles that vary in length depending on duration of the cast. At a ship speed of 0.5 kn, the average distance between seabed images was approximately 5 m. Additional "HOTKEY" photos were taken from interesting objects (organisms, seabed features, such as putative iceberg scours) when they appeared in the live video feed (which was also recorded, in addition to the stills, for documentation and possible later analysis). If any image from this collection is used, please cite the reference as given above.

Physical properties and sedimentology of 4 profiles fom the South Atlantic

Ultrasonic P wavc transmission seismograms recorded on sediment cores have been analyzed to study the acoustic and estimate the clastic properties of marine sediments from different provinces dominated by terrigenous, calcareous, amI diatomaceous sedimentation. Instantaneous frequencies computed from the transmission seismograms are displayed as gray-shaded images to give an acoustic overview of the lithology of each core. Ccntirneter-scale variations in the ultrasonic waveforms associated with lithological changes are illustrated by wiggle traces in detail. Cross-correlation, multiple-filter, and spectral ratio techniques are applied to derive P wave velocities and attenuation coefficients. S wave velocities and attenuation coefficients, elastic moduli, and permeabilities are calculated by an inversion scheme based on the Biot-Stoll viscoelastic model. Together wilh porosity measurements, P and S wave scatter diagrams are constructed to characterize different sediment types by their velocity- and attenuation-porosity relationships. They demonstrate that terrigenous, calcareous, and diatomaceous sediments cover different velocity- and attenuation-porosity ranges. In terrigcnous sediments, P wave vclocities and attenuation coefficients decrease rapidly with increasing porosity, whereas S wave velocities and shear moduli are very low. Calcareous sediments behave similarly at relatively higher porosities. Foraminifera skeletons in compositions of terrigenous mud and calcareous ooze cause a stiffening of the frame accompanied by higher shear moduli, P wave velocities, and attenuation coefficients. In diatomaceous ooze the contribution of the shear modulus becomes increasingly important and is controlled by the opal content, whereas attenuation is very low. This leads to the opportunity to predict the opal content from nondestructive P wave velocity measurements at centimeter-scale resolution.

Sea-bed photographs (benthos) from the Weddell Sea along two ROV profiles during Polarstern cruise ANT-XIII/3

Young specimens of cf. Pagothenia borchgrevinki were observed for the first time to cling to the subsurface of the marginal ice shelf in Drescher Inlet, southeastern Weddell Sea. Along an approximately 40-m-long videotransect at 80 m water depth, the abundance was roughly estimated to be 7 individuals per 10 m**2. This behaviour is interpreted to represent the most advanced adaptation to ice as a microhabitat for Antarctic fish.