Detecting the signature of natural selection with microsatellites

Natural selection is one of the major factors in the evolution of all organisms. Detecting the signature of natural selection has been a central theme in evolutionary genetics. With the availability of microsatellite data, it is of interest to study how natural selection can be detected with microsatellites. ^ The overall aim of this research is to detect signatures of natural selection with data on genetic variation at microsatellite loci. The null hypothesis to be tested is the neutral mutation theory of molecular evolution, which states that different alleles at a locus have equivalent effects on fitness. Currently used tests of this hypothesis based on data on genetic polymorphism in natural populations presume that mutations at the loci follow the infinite allele/site models (IAM, ISM), in the sense that at each site at most only one mutation event is recorded, and each mutation leads to an allele not seen before in the population. Microsatellite loci, which are abundant in the genome, do not obey these mutation models, since the new alleles at such loci can be created either by contraction or expansion of tandem repeat sizes of core motifs. Since the current genome map is mainly composed of microsatellite loci and this class of loci is still most commonly studied in the context of human genome diversity, this research explores how the current test procedures for testing the neutral mutation hypothesis should be modified to take into account a generalized model of forward-backward stepwise mutations. In addition, recent literature also suggested that past demographic history of populations, presence of population substructure, and varying rates of mutations across loci all have confounding effects for detecting signatures of natural selection. ^ The effects of the stepwise mutation model and other confounding factors on detecting signature of natural selection are the main results of the research. ^

Natural history of placebo treatment in adults acquiring travelers' diarrhea in Mexico

The natural history of placebo treated travelers' diarrhea and the prognostic factors of recovery from diarrhea were evaluated using 9 groups of placebo treated subjects from 9 clinical trial studies conducted since 1975, for use as a historical control in the future clinical trial of antidiarrheal agents. All of these studies were done by the same group of investigators in one site (Guadalajara, Mexico). The studies are similar in terms of population, measured parameters, microbiologic identification of enteropathogens and definitions of parameters. The studies had two different durations of followup. In some studies, subjects were followed for two days, and in some they were followed for five days.^ Using definitions established by the Infectious Diseases society of America and the Food and Drug Administration, the following efficacy parameters were evaluated: Time to last unformed stool (TLUS), number of unformed stools post-initiation of placebo treatment for five consecutive days of followup, microbiologic cure, and improvement of diarrhea. Among the groups that were followed for five days, the mean TLUS ranged from 59.1 to 83.5 hours. Fifty percent to 78% had diarrhea lasting more than 48 hours and 25% had diarrhea more than five days. The mean number of unformed stools passed on the first day post-initiation of therapy ranged from 3.6 to 5.8 and, for the fifth day ranged from 0.5 to 1.5. By the end of followup, diarrhea improved in 82.6% to 90% of the subjects. Subjects with enterotoxigenic E. coli had 21.6% to 90.0% microbiologic cure; and subjects with shigella species experienced 14.3% to 60.0% microbiologic cure.^ In evaluating the prognostic factors of recovery from diarrhea (primary efficacy parameter in evaluating the efficacy of antidiarrheal agents against travelers' diarrhea). The subjects from five studies were pooled and the Cox proportional hazard model was used to evaluate the predictors of prolonged diarrhea. After adjusting for design characteristics of each trial, fever with a rate ratio (RR) of 0.40, presence of invasive pathogens with a RR of 0.41, presence of severe abdominal pain and cramps with a RR of 0.50, number of watery stools more than five with a RR of 0.60, and presence of non-invasive pathogens with a RR of 0.84 predicted a longer duration of diarrhea. Severe vomiting with a RR of 2.53 predicted a shorter duration of diarrhea. The number of soft stools, presence of fecal leukocytes, presence of nausea, and duration of diarrhea before enrollment were not associated with duration of diarrhea. ^

Revised depth scale, splice tie points and chron boundaries of ODP Hole 151-907A and Site 162-907

The magnetic polarity stratigraphy at Site 907 obtained from the shipboard pass-through magnetometer and from discrete samples is readily interpretable back to the onset of the Gilbert Chron (5.89 Ma). From this level to the base of the section at ~14 Ma, the interpretation is corroborated by silicoflagellate datums with predictable correlation to polarity chrons. The resulting magnetostratigraphic interpretation differs from those proposed in the Leg 151 (Hole 907A) and 162 (Holes 907B and 907C) Initial Reports volumes. An important hiatus in the 7-10 Ma interval at Site 907 caused sedimentation to slow or cease for ~2.7 m.y. We have revised the shipboard correlation among the three holes at Site 907, resulting in a new composite section splice and recalculation of composite depths. For Site 985, magnetostratigraphic interpretation is possible down to ~150 meters below seafloor (mbsf) (C3An/C3Ar) at ~6 Ma. There are no useful biostratigraphic datums from Site 985 to support this interpretation; however, the interpretation is supported by the correlation of Sites 985 and 907 using natural gamma data from the shipboard multisensor track. Below ~150 mbsf at Site 985, drilling-related deformation at the onset of extended core barrel drilling precluded magnetostratigraphic interpretation.

Foraminiferal isotope ratios from IODP Site U1313

Large-amplitude millennial-scale climate oscillations have been identified in late Pleistocene climate archives from around the world. These oscillations appear to be of larger amplitude during times of enlarged ice sheets. This observation suggests the existence of a relationship between large-amplitude millennial variations in climate and extreme glacial conditions and therefore that the emergence of millennial-scale climate variability may be linked to the Pliocene intensification of northern hemisphere glaciation (iNHG). Here we test this hypothesis using new late Pliocene high-resolution (ab. 400 year) records of ice-rafted debris deposition and stable isotopes in planktic foraminiferal calcite (Globigerinoides ruber) generated from Integrated Ocean Drilling Program Site U1313 in the subpolar North Atlantic (a reoccupation of the classic Deep Sea Drilling Project Site 607). Our records span marine oxygen isotope stages (MIS) 103-95 (ab. 2600 to 2400 ka), the first interval during iNHG (ab. 3.5 to 2.5 Ma) in which large-amplitude glacial-interglacial cycles and inferred sea level changes occur. Our records reveal small-amplitude variability at periodicities of ab. 1.8 to 6.2 kyr that prevails regardless of (inter)glacial state with no significant amplification during the glacials MIS 100, 98, and 96. These findings imply that the threshold for the amplification of such variability to the proportions seen in the marine archive of the last glacial was not crossed during the late Pliocene and, in view of all available data, likely not until the Mid-Pleistocene Transition.

Site characteristics, and major and trace element composition of sediment cores sampled around the Windmill Islands in 1998

To establish a natural background and its temporal and spatial variability for the area around Casey Station in the Windmill Islands, East Antarctica, the authors studied major and trace element concentrations and the distribution of organic matter in marine and lacustrine sediments. A wide range of natural variability in trace metal concentrations was identified between sites and within a time scale of 9 ka (e.g., Ni 5-37 mg/kg, Cu 20-190 mg/kg, Zn 50-300 mg/kg, Pb 4.5- 34 mg/kg). TOC concentrations are as high as 3 wt.% at the marine sites and 20 wt.% at the lacustrine sites, and indicate highly productive ecosystems. These data provide a background upon which the extent of human impact can be established, and existing data indicate negligible levels of disturbance. Geochemical and lithological data for a lacustrine sediment core from Beall Lake confirm earlier interpretation of recent climatic changes based on diatom distribution, and the onset of deglaciation in the northern part of the Windmill Islands between 8.6 and 8.0 ka BP. The results demonstrate that geochemical and lithological data can not only be used to define natural background values, but also to assess long-term climatic changes of a specific environment. Other sites, however, preserve a completely different sedimentary record. Therefore, inferred climatic record, and differences between sites, can be ascribed to differences in elevation, distance from the shore, water depth, and local catchment features. The extreme level of spatial variability seems to be a feature of Antarctic coastal areas, and demonstrates that results obtained from a specific site cannot be easily generalized to a larger area.

Reefs shift from net accretion to net erosion along a natural environmental gradient

Coral reefs persist in an accretion-erosion balance and ocean acidification resulting from anthropogenic CO2 emissions threatens to shift this balance in favor of net reef erosion. Corals and calcifying algae, largely responsible for reef accretion, are vulnerable to environmental changes associated with ocean acidification, but the direct effects of lower pH on reef erosion has received less attention, particularly in the context of known drivers of bioerosion and natural variability. This study examines the balance between reef accretion and erosion along a well-characterized natural environmental gradient in Kane'ohe Bay, Hawai'i using experimental blocks of coral skeleton. Comparing before and after micro-computed tomography (µCT) scans to quantify net accretion and erosion, we show that, at the small spatial scale of this study (tens of meters), pH was a better predictor of the accretion-erosion balance than environmental drivers suggested by prior studies, including resource availability, temperature, distance from shore, or depth. In addition, this study highlights the fine-scale variation of pH in coastal systems and the importance of microhabitat variation for reef accretion and erosion processes. We demonstrate significant changes in both the mean and variance of pH on the order of meters, providing a local perspective on global increases in pCO2. Our findings suggest that increases in reef erosion, combined with expected decreases in calcification, will accelerate the shift of coral reefs to an erosion-dominated system in a high-CO2 world. This shift will make reefs increasingly susceptible to storm damage and sea-level rise, threatening the maintenance of the ecosystem services that coral reefs provide.

Consolidation properties and strength characteristics of ODP Site 204-1244 sediments

Eight whole-core samples from Ocean Drilling Program Site 1244, Hydrate Ridge, Cascadia continental margin, were provided to Massachusetts Institute of Technology (Cambridge, Massachusetts, USA) for geotechnical characterization. The samples were collected from depths ranging from 5 to 136 meters below seafloor (mbsf). Seven of the eight whole-core samples were located within the gas hydrate stability zone, whereas the eighth sample was located in the free gas zone. Atterberg limits testing showed that the average liquid limit of the soil is 81% and the average plastic limit is 38%, giving an average plasticity index of 43%. The liquid limit is sensitive to oven drying, shown by a drop in liquid limit to 64% when tests were performed on an oven-dried sample. Loss on ignition averages 5.45 wt%. Constant rate of strain consolidation (CRSC) tests were performed to obtain the compression characteristics of the soil, as well as to determine the stress history of the site. CRSC tests also provided hydraulic conductivity and coefficient of consolidation characteristics for these sediments. The compression ratio (Cc) ranges from 0.340 to 0.704 (average = 0.568). Cc is fairly constant to a depth of 79 mbsf, after which Cc decreases downhole. The recompression ratio (Cr) ranges from 0.035 to 0.064 (average = 0.052). Cr is constant throughout the depth range. In situ hydraulic conductivity varies between 1.5 x 10**-7 and 3 x 10**-8 cm/s and shows no trend with depth. Ko-consolidated undrained compression/extension (CKoUC/E) tests were also performed to determine the peak undrained shear strength, stress-strain curve, and friction angle. The normalized undrained strength ranges from 0.29 to 0.35. The friction angle ranges from 27 to 37. Because of the limited amount of soil, CRSC and CKoUC/E tests were also conducted on resedimented specimens.

Magnetic properties, grain sizes and minerals at DSDP Site 83-504B

Twenty-seven samples from the Leg 83 section of Hole 504B have been investigated using magnetic, optical, and electron optical methods. The primary magnetic mineral to crystallize was titanomagnetite of approximate composition Fe2.4Ti0.6O4 (TM60), but none survives, nor is there evidence of titanomaghemite produced by oxidation of TM60. The average measured magnetic properties can be interpreted in terms of magnetite, Fe3O4, having average grain size of <1 µm and present in average volume concentration of - 0.5%. The intensity of the natural remanent magnetization (NRM) of the rocks could also be accounted for as being a thermoremanence carried by this mineral. Although the heterogeneity of the titanomagnetite grains could be detected optically, the texture of the intergrown phases is poorly developed. In some samples from the massive units of the lower part of the section, trellis patterns were visible. The Fe3O4 present in the intergrowths is too intimately mixed with the other intergrown phases to be revealed by electron microprobe analysis that simply returns the bulk composition of the intergrowth (oxidized TM60). The path by which the mineral assemblage evolved from TM60 to an Fe304-containing intergrowth, under the temperature and pressure conditions obtaining in the Leg 83 section, makes interesting speculation. Deuteric oxidation, maghemitization/inversion, or some hypothetical low-temperature/high-pressure oxidation by a leaching-of-iron process may all play roles.

Sedimentation at Manop Site H in the eastern equatorial Pacific

Gravity cores recovered from Manganese Nodule Project site H (6°33'N, 92°49'W) show marked downcore variations in the abundance of calcium carbonate, organic carbon, opal, manganese, and other components deposited over the past 400,000 years. Variations in the downcore abundance of organic carbon, which ranges from 0.2 to 1.0%, can be used to hindcast redox conditions in the surface sediments over this time. The results indicate that the depth to the manganese redox boundary varied from about 5 to 25 cm below the seafloor during four major cycles. Downcore variations in solid phase Mn, Ni, and Cu can be produced by such changes in redox conditions. A model which predicts that solid phase Mn can be trapped and buried when the Mn redox boundary migrates rapidly upward is consistent with the observed organic carbon and Mn records and supports the reconstructed redox variations. The history of redox variations at site H can be explained by changes with time in surface water productivity. Major productivity variations at the site occur over 100-kyr cycles, with relatively higher productivity occurring during glacial stages. Thus Quaternary climate changes influence surface water productivity, redox conditions in sediments, and the cycling of transition metals.

Communication and enhancement of Italian cultural heritage by Google

Tras liderar la investigación e indización de la información por cerca de una década, el motor de búsqueda Google se ha convertido en un sistema económico que influye nuestro mundo contemporáneo, contribuyendo grandemente a la transformación de nuestro mundo en un único globo virtual. En años recientes, Google ha comenzado a ofrecer a los usuarios globales aplicaciones o software que son usados para nuestra herencia cultural. Este software se resalta aquí en su potencial, desde un punto de vista económico, cultural y turístico. Tratamos de describir lo más importante del software de Google (como Google Maps, Google Street View, Google Earth, Google SketchUp, Google Books y Google Art Project), con el mayor y más evidente impacto en los sectores culturales y turísticos. Este ensayo muestra la digitalización y promoción de la herencia cultural italiana en Google, a través de sus programas informáticos (por ejemplo, Google Street View que ha llevado al uso de vistas tridimensionales remotas de algunos de los más importantes monumentos y sitios arqueológicos de Italia; el uso de Google SketchUp ha llevado al diseño de reconstrucción tridimensional del histórico centro de la ciudad de L'Aquila, devastada luego del terremoto de abril de 2009 y nunca reconstruida), y a través de diversos programas asociados específicos con el Ministerio Italiano de Cultura