Molecular genetic analyses of extracellular signaling pathways during murine retinal development

Extracellular signaling pathways initiated by secreted proteins are important in the co-ordination of tissue interactions in multi-cellular organisms, particularly during embryonic development. These signaling cascades direct diverse cellular events, including proliferation, differentiation and migration, in both autocrine and paracrine modes. In adult animals, abnormal function of these proteins often results in degenerative and tumourigenic syndromes. In this study, I have focused on elucidating the role of Bone Morphogenetic Protein (Bmp) signal transduction during neuronal specification and differentiation in the vertebrate embryo, using the mouse retina as a model. Using tissue-specific conditional knock-out approaches, the consequences of genetic loss-of-function of this signaling pathway on retinal physiology were examined. Mutant mice lacking Bmp type I receptor function displayed a range of retinal phenotypes, each of which appeared to be regulated at a different threshold of Bmp receptor activity. Novel essential functions for Bmp signaling were uncovered for retinal neurogenesis, cell survival, and axonal pathfinding at the optic disc. Further, BmprIa and BmprIa exhibited genetic interactions suggestive of functional redundancy. To further characterize the underlying molecular bases for the pleiotropic effects of Bmp receptors, retina-specific loss-of-function mutants of the obligate Bmp-activated transcriptional mediator Smad4 were generated. A comparison of the retina-specific Smad4 mutant phenotypes with those of the Bmp receptor mutant retina revealed that only a subset of retinal phenotypes, namely optic disc axon pathfinding and axial patterning were common for both classes of mutant animals. Thus, these results suggest that, contrary to the classic scheme of Bmp signal transduction, Smad4-independent pathways may be operative downstream of the type I receptors. Indeed, such alternative intracellular signaling cascades may constitute a molecular basis for the multiple cellular responses elicited by Bmp signaling. Finally, I tested whether the potential Bmp pathway targets, the extracellular ligands Fgf9 and Fgf15, mediate essential cellular processes in the retina. The analyses of Fgf9 −/−; Fgf15−/− mutant mice posit a novel shared role for these genes in intra-retinal axon pathfinding. Collectively, these studies have elucidated part of the molecular machinery directing mammalian neuro-retinal development, and provided useful in vivo models to study visual function. ^

Correlation of tuberculosis and human immunodeficiency virus in Harris County, Texas from 2009 through 2010 using Geographic Information Systems

A population based ecological study was conducted to identify areas with a high number of TB and HIV new diagnoses in Harris County, Texas from 2009 through 2010 by applying Geographic Information Systems to determine whether distinguished spatial patterns exist at the census tract level through the use of exploratory mapping. As of 2010, Texas has the fourth highest occurrence of new diagnoses of HIV/AIDS and TB.[31] The Texas Department of State Health Services (DSHS) has identified HIV infected persons as a high risk population for TB in Harris County.[29] In order to explore this relationship further, GIS was utilized to identify spatial trends. ^ The specific aims were to map TB and HIV new diagnoses rates and spatially identify hotspots and high value clusters at the census tract level. The potential association between HIV and TB was analyzed using spatial autocorrelation and linear regression analysis. The spatial statistics used were ArcGIS 9.3 Hotspot Analysis and Cluster and Outlier Analysis. Spatial autocorrelation was determined through Global Moran's I and linear regression analysis. ^ Hotspots and clusters of TB and HIV are located within the same spatial areas of Harris County. The areas with high value clusters and hotspots for each infection are located within the central downtown area of the city of Houston. There is an additional hotspot area of TB located directly north of I-10 and a hotspot area of HIV northeast of Interstate 610. ^ The Moran's I Index of 0.17 (Z score = 3.6 standard deviations, p-value = 0.01) suggests that TB is statistically clustered with a less than 1% chance that this pattern is due to random chance. However, there were a high number of features with no neighbors which may invalidate the statistical properties of the test. Linear regression analysis indicated that HIV new diagnoses rates (β=−0.006, SE=0.147, p=0.970) and census tracts (β=0.000, SE=0.000, p=0.866) were not significant predictors of TB new diagnoses rates. ^ Mapping products indicate that census tracts with overlapping hotspots and high value clusters of TB and HIV should be a targeted focus for prevention efforts, most particularly within central Harris County. While the statistical association was not confirmed, evidence suggests that there is a relationship between HIV and TB within this two year period.^

(Table 1) Nd and Sr isotopic analyses of ODP Leg 127 basalts

Sr and Nd isotopic compositions are reported for basaltic rocks collected during ODP Leg 127 from the Yamato Basin, a rifted backarc basin in the Japan Sea. The basalts are classified into two groups in terms of Nd isotopic composition: the upper sills at Site 797 are characterized by higher 143Nd/144Nd ratios (0.513083-0.513158, epsilon-Nd = 8.68-10.14) and the basalts from Site 794 and the lower sills at Site 797 have lower 143Nd/144Nd ratios (0.512684-0.512862, epsilon-Nd = 0.90-4.37). All of the basalts show higher Sr isotopic compositions than those of the mantle array, which is attributed to seawater alteration. The basalts with lower Nd isotopic values ranging in age from 20.6 to 17.3 Ma have tapped an enriched subcontinental upper mantle (SCUM) with the minor involvement of a depleted asthenospheric mantle (AM). Subsequent change in composition through the physical replacement of SCUM by AM yielded the basalts of the upper sills of higher Nd isotopic compositions. This event within the upper mantle was associated with the breakup of the overlying lithosphere during the rifting of the Japan Sea backarc basin.

Sediment geochemistry of ODP Leg 127 sites

The relative effects of paleoceanographic and paleogeographic variations, sediment lithology, and diagenetic processes on the final preserved chemistry of Japan Sea sediments are evaluated by investigating the rare earth element (REE), major element, and trace element concentrations in 59 squeeze-cake whole-round and 27 physical-property sample residues from Sites 794, 795, and 797, cored during ODP Leg 127. The most important variation in sedimentary chemical composition is the increase in SiO2 concentration through the Pliocene diatomaceous sequences, which dilutes most other major and trace element components by various degrees. This biogenic input is largest at Site 794 (Yamato Basin), moderately developed at Site 797 (Yamato Basin), and of only minor importance at Site 795 (Japan Basin), potentially reflecting basinal contrasts in productivity with the Yamato Basin recording greater biogenic input than the Japan Basin and with the easternmost sequence of Site 794 lying beneath the most productive waters. There are few systematic changes in solid-phase chemistry resulting from the opal-A/opal-CT or opal-CT/quartz silica phase transformations. Most major and trace element concentrations are controlled by the aluminosilicate fraction of the sediment, although the effects of diagenetic silica phases and manganese carbonates are of localized importance. REE total abundances (Sum REE) in the Japan Sea are strongly dependent upon the paleoceanographic position of a given site with respect to terrigenous and biogenic sources. REE concentrations at Site 794 overall correspond well to aluminosilicate chemical indices and are strongly diluted by SiO2 within the upper Miocene-Pliocene diatomaceous sequence. Eu/Eu* values at Site 794 reach a maximum through the diatomaceous interval as well, most likely suggesting an association of Eu/Eu* with the siliceous component, or reflecting slight incorporation of a detrital feldspar phase. SumREE at Site 795 also is affiliated strongly with aluminosilicate phases and yet is diluted only slightly by siliceous input. At Site 797, SumREE is not as clearly associated with the aluminosilicate fraction, is correlated moderately to siliceous input, and may be sporadically influenced by detrital heavy minerals originating from the nearby rifted continental fragment composing the Yamato Rise. Ce/Ce* profiles at all three sites increase essentially monotonically with depth and record progressive diagenetic LREE fractionation. The observed Ce/Ce* increases are not responding to changes in the paleoceanographic oxygenation state of the overlying water, as there is no independent evidence to suggest the proper oceanographic conditions. Ce/Ce* correlates slightly better with depth than with age at the two Yamato Basin sites. The downhole increase in Ce/Ce* at Sites 794 and 797 is a passive response to the diagenetic transfer of LREE (except Ce) from sediment to interstitial water. At Site 795, the overall lack of correlation between Ce/Ce* and Lan/Ybn suggests that other processes mask the diagenetic behavior of all LREEs. First-order calculations of the Ce budget in Japan Sea waters and sediment indicate that ~20% of the excess Ce adsorbed by settling particles is recycled within the water column and that an additional ~38% is recycled at or near the seafloor. Thus, because the remaining excess Ce is only ~10% of the total Ce, there is not a large source of Ce to the deeply buried sediment, further suggesting that the downhole increase in Ce/Ce* is a passive response to diagenetic behavior of the other LREEs. The REE chemistry of Japan Sea sediment therefore predicts successive downhole addition of LREEs to deeply buried interstitial waters.

(Table S1) Molecular analyses and morphological comparisons of deep-sea clams

Large vesicomyid clams are common inhabitants of sulphidic deep-sea habitats such as hydrothermal vents, hydrocarbon seeps and whale-falls. Yet, the species- and genus-level taxonomy of these diverse clams has been unstable due to insufficiencies in sampling and absence of detailed taxonomic studies that would consistently compare molecular and morphological characters. To clarify uncertainties about species-level assignments, we examined DNA sequences from mitochondrial cytochrome-c-oxidase subunit I (COI) in conjunction with morphological characters. New and published COI sequences were used to create a molecular database for 44 unique evolutionary lineages corresponding to species. Overall, the congruence between molecular and morphological characters was good. Several discrepancies due to synonymous species designations were recognized, and acceptable species names were rectified with published COI sequences in cases where morphological specimens were available. We identified seven species with trans-Pacific distributions, and two species with Indo-Pacific distributions. Presently, 27 species have only been documented from one region, which might reflect limited ranges, or insufficient geographical sampling. Vesicomyids exhibit the greatest species diversity along the northwest Pacific ridge systems and in the eastern Pacific, along the western America margin, where depth zonation typically results in segregation of closely related species. The broad distributions of several vesicomyid species suggest that their required chemosynthetic habitats might be more common than previously recognized and occur along most continental margins.

Pedogeomorphology, geochronology and paleobotany of soil profiles obtained in the Kyichu River catchment, sourthern Tibet

Results of pedogeomorphological, geochronological and paleobotanical investigations are presented covering the last ca. 4,000 years. The study sites are located in the heavily degraded Kyichu River catchment around Lhasa at 3,600-4,600 m a.s.l. Repeatedly, colluvial sediments have been recorded overlying paleosols. These deposits can be divided into i) coarse-grained sediments with a high proportion of stones and boulders originating from alluvial fans and debris flows, ii) matrix supported sediments with some stones and boulders originating from mudflows or combined colluvial processes such as hillwash plus rock fall, and iii) fine-grained sediments originating from hill wash. The IRSL multi-level dating of profile QUG 1 points to a short-time colluvial sedimentation between 1.0 ± 0.1 and 0.8 ± 0.1 ka. In contrast, dated paleosols of profile GAR 1 (7,908 ± 99 and 3,668 ± 57 BP) encompass a first colluvial episode. Here, the upper colluvial sedimentation took place during several periods between 2.6 ± 0.3 and 0.4 ± 0.1 ka. For the first time in Tibet, a systematic extraction, determination and dating of charcoals from buried paleosols was conducted. The charcoals confirm the Late Holocene presence of juniper forests or woodlands in a now treeless, barren environment. A pollen diagram from Lhasa shows a distinct decline of pollen of the Jumperus-type around 4,140 ± 50 BP, which is interpreted as indicating a clearing of forests on the adjacent slopes. It is assumed that the environmental changes from forests to desertic rangelands since ca. 4,000 BP have been at least reinforced by humans.

Calcareous nannofossil biostratigraphy of ODP Leg 127 sites

Calcareous nannofossils were studied by light microscopy in Neogene sedimentary rocks recovered at four sites of the Ocean Drilling Program Leg 127 in the Japan Sea. Nannofossils occur sporadically at all sites, and allow recognition of seven zones and two subzones; four zones in the Holocene to the uppermost Pliocene, and three zones and two subzones in the middle to lower Miocene. Forty-eight nannofossil species are recognized in 95 of the 808 irregularly-spaced samples taken from all the sites. The nannofossil assemblages in the Miocene are more diverse than those in the Holocene to Pliocene sedimentary interval. The greater diversity and the presence of warm-water taxa, such as Sphenolithus and discoasters in the upper lower Miocene to lower middle Miocene, suggest a relatively warm and stable surface-water condition, attributed to an increased supply of warm water from the subtropical western Pacific Ocean. Site 797 in the southern part of the Yamato Basin contains the most complete and the oldest nannofossil record so far reported from the Japan Sea. The lowermost nannofossil zone at this site, the Helicosphaera ampliaperta Zone (15.7-18.4 Ma) gives a minimum age for the Yamato Basin. This age range predates rotation of southwest Japan, an event previously believed to be caused by the opening of the Japan Sea.

Main components and isotopic composition of gases from mineral waters of the Taman Peninsula and Caucasus

Helium isotope composition as an indicator of the mantle-derived component was studied in gases from mineral springs, stratal waters, and mud volcanoes developed west of the Teberda River valley (10 objects) and two springs in the central segment of the Greater Caucasus orogen between the active El'brus and Kazbek volcanoes. In the western segment of the orogen ratios of 3He/4He = R_corr vary from 46x10**-8 to 114x10**-8 (from 0.33 to 0.81 R_atm, where R_atm = 1.4x10**-6 is the atmospheric ratio). They are substantially lower relative to ratios in the vicinity of El'brus and Kazbek and close to those in samples from the central segment (from 70x10**-8 to 134x10**-8 (from 0.50 to 0.96 R_atm), as well as to ratios previously recorded in the Caucasian Mineral Waters (CMW) area. Moreover, concentration of 3He in them is notably higher than its crustal radiogenic level characteristic of mud volcanoes in the Taman Peninsula, where 3He/4He varies from 1.4x10**-8 to 2.8x10**-8 (from 0.01 to 0.02 R_atm). Nitrogen-methane gas from northern piedmonts of the western Caucasus also contains nonatmogenic components including radiogenic 40Ar (40Ar/36Ar = 900), excessive nitrogen (~87% of total N2 concentration in sample) and mantle He. These data specify distribution of mantle derivates along the orogen strike and age of intrusive magmatic activity in its different segments.

Age models and sea-surface paleotemperature reconstruction of sediment cores from the eastern equatorial Atlantic

Based on the faunal record of planktonic foraminifers in three long gravity sediment cores from the eastern equatorial Atlantic, the sea-surface temperature history ove the last 750,000 years was studied at a resolution of 3,000 to 10,000 years. Detailed oxygen-isotope and paleomagnetic stratigraphy helped to identify the following major faunal events: Globorotaloides hexagonus and Globorotalia tumida flexuosa became extinct in the eastern tropical Atlantic at the isotope stage 4/5 boundary, now dated at 68,000 years B.P. The persistent occurrence of the pink variety of Globigerinoides ruber started during the late stage 12 at 410,000 years B.P. CARTUNE-age. This datum may provide an easily detectible faunal stratigraphic marker for the mid-Brunhes Chron. The updated scheme of the Ericson zones helped the recognition of a hiatus at the northwestern slope of the Sierra Leone Basin covering oxygen-isotope stages 10 to 12. Classifying the planktonic foraminifer counts into six faunal assemblages, according to the factor analysis derived model of Pflaumann (1985), the tropical and the tropical-upwelling communities account for 57 % at Site 16415, and 86 % at Site 13519, respectively of the variance of the faunal record. A largely continuous paleotemperature record for both winter and summer seasons was obtained from the top of the Sierra Leone Rise with the winter temperatures ranging between 20 and 25 °C, and the summer ones between 24 and 30 °C. The record of cores from greater water depths is frequently interrupted by samples with no-analogue faunal communities and/or poor preservation. Based on the seasonality signal, during cold periods the termal equator shifted to a geographically mnore asymmetrical northern position. Dissolution altering the faunal communities becomes stronger with greater water depth, the estimated mean minimum loss of specimens increases from 70 % to 80 % between 2,860 and 3,850 water depth although some species will be more susceptible than others. Enhanced dissolution occured during stage 4 but also during cold phases in the warm stage 7 and 9. Correlations between the Foraminiferal Dissolution Index and the estimated sea-surface temperatures are significant. Foraminiferal flux rates, negatively correlated to the flux rates of organic carbon and of diatoms, may be a result of enhanced dissolution during cold stages, destroying still more of the faunal signal than indicated by the calculated minimum loss. The fluctuations of the oxygen-isotope curves and the hibernal sea-surfave temperatures are fairly coherent. During warm oxygen-isotope stages the temperature maxima lag often by 5 to 15 ka behind the respective sotope minima. During cold stages, sea-surface temperature changes are partly out of phase and contain additional fluctuations.

(Table 2) Correlation of Mi zones with hiatuses in ODP Site 181-1124

Results from Ocean Drilling Program sites 1121-1124 show the Eastern New Zealand Oceanic Sedimentary System (ENZOSS) evolved in response to: (1) the inception of the circum-Antarctic circulation, (2) orbital and nonorbital regulation of the global thermohaline flow, and (3) development of the New Zealand plate boundary. ENZOSS began in the early Oligocene following opening of the Tasmanian gateway and inception of the ancestral Antarctic Circumpolar Current (ACC) and SW Pacific Deep Western Boundary Current (DWBC). Widespread erosion, marked by the Marshall Paraconformity, was followed by extensive drift formation in the late Oligocene- early Miocene. Alternating nannofossil chalk and nannofossil-rich mud deposited in response to 41-kyr orbital regulation of the abyssal circulation, with the mudstones representing times of increased inflow of corrosive southernsource waters. Drift deposition at the deepest sites was interrupted by bouts of erosion coincident with Mi 1-5 isotopic events signifying expansions of the East Antarctic Ice Sheet and enhanced bottom water formation. By late Miocene times, the basic ENZOSS was established. South of Bounty Trough, the energetic ACC instigated an erosional/low depositional regime. To the north, where the DWBC prevailed, orbitally regulated drift deposition continued. Increased convergence at the New Zealand plate boundary enhanced the terrigenous supply, but little of this sediment reached the deep ENZOSS as the three main sediment conduits - Solander, Bounty and Hikurangi channels - had not fully developed. The Plio-Pleistocene heralded a change from a carbonate- to terrigenous-dominant supply caused by interception of the DWBC by the three channels (~1.6 Ma for Bounty and Hikurangi, time of Solander interception unknown). The Solander and Bounty fans, and Hikurangi Fan-drift systems formed, and drifts downstream of those systems, received terrigenous detritus. Supply increased with accelerating uplift along the plate boundary, but delivery to the DWBC was regulated by eustatic fluctuations of sea level. Times of maximum supply to all three channels was during glacial lowstands whereas the supply either ceased (Bounty, Solander), or reduced (Hikurangi) in highstands. In glacial times, sediment was entrained by a DWBC invigorated by an increased input of Antarctic bottom water. The ACC also accelerated under strengthened glacial winds. Thus, glacials were times of optimum sediment supply to ENZOSS depocentres where depositional rates were 2-3 times more than interglacial rates.

Integrated Paleocene calcareous plankton magnetobiochronology of DSDP Hole 43-384 in the Northwest Atlantic Ocean

At Deep Sea Drilling Site 384 (J-Anomaly Ridge, Grand Banks Continental Rise, NW Atlantic Ocean) Paleocene nannofossil chalks and oozes (~70 m thick) are unconformably/disconformably underlain (~168 m; upper Maastrichtian) and overlain (~98.7 m; upper lower Eocene) by sediments of comparable lithologies. The chalks are more indurated in stratigraphically higher levels of the Paleocene reflecting increasing amounts of biosiliceous (radiolarians and diatoms) components. This site serves as an excellent location for an integrated calcareous and siliceous microfossil zonal stratigraphy and stable isotope stratigraphy. We report the results of a magnetostratigraphic study which, when incorporated with published magnetostratigraphic results, reveals an essentially complete magnetostratigraphic record spanning the interval from Magnetochron C31n (late Maastrichtian) to C25n (partim) (late Paleocene, Thanetian). Integrated magnetobiochronology and stable isotope stratigraphy support the interpretation of, and constrain the estimated duration of, a short hiatus (~0.9 my) within the younger part of Chron C29r (including the K/P boundary) and an ~6 my hiatus separating upper Paleocene (Magnetozone C25n) and upper lower Eocene (Magnetozone C22r) sediments. Some 30 planktonic foraminiferal datum levels [including the criteria used to denote the Paleocene planktonic foraminiferal (sub)tropical zonal scheme of Berggren and Miller, Micropaleontology 34 (4) (1988) 362-380 and Berggren et al., SEPM Spec. Publ. 54 (1995) 129-212, Geol. Soc. Am. Bull. 107 (11) (1995) 1272-1287], and nearly two dozen calcareous nannoplankton datum levels have been recognized and calibrated to the magnetochronology. Planktonic foraminiferal Subzones P4a and P4b of (upper Paleocene) Zone P4 are emended/redefined based on the discovery of a longer stratigraphic extension of Acarinina subsphaerica (into at last Magnetozone C25n). Stable isotope stratigraphies from benthic foraminifera and fine fraction (<38 µm) carbonate have been calibrated to the biochronology and magnetostratigraphy. A minimum in benthic foraminifer delta13C was reached near the Danian/Selandian boundary (within Chron C26r, planktonic foraminiferal Zone P3a and calcareous nannoplankton Zone NP4) and is followed by the rise to maximum delta13C values in the late Thanetian (near the base of C25n, in Zone P4c and NP9a, respectively) that can be used for global correlation in the Paleocene.

Benthic foraminifera and sea level analyses from IODP Hole 310-M0005D

The course of sea-level fluctuations during Termination II (TII; the penultimate deglaciation), which is critical for understanding ice-sheet dynamics and suborbital climate variability, has yet to be established. This is partly because most shallow-water sequences encompassing TII were eroded during sea-level lowstands of the last glacial period or were deposited below the present sea level. Here we report a new sequence recording sea-level changes during TII in the Pleistocene sequence at Hole M0005D (water depth: 59.63 m below sea level [mbsl]) off Tahiti, French Polynesia, which was drilled during Integrated Ocean Drilling Program Expedition 310. Lithofacies variations and stratigraphic changes in the taxonomic composition, preservation states, and intraspecific test morphology of large benthic foraminifers indicate a deepening-upward sequence in the interval from Core 310-M0005D-26R (core depth: 134 mbsl) through -16R (core depth: 106 mbsl). Reconstruction of relative sea levels, based on paleodepth estimations using large benthic foraminifers, indicated a rise in sea level of about 90 m during this interval, suggesting its correlation with one of the terminations. Assuming that this rise in sea level corresponds to that during TII, after correcting for subsidence since the time of deposition, a highstand sea-level position would be 2 ± 15 m above present sea level (masl), which is generally consistent with highstand sea-level positions in MIS 5e (4 ± 2 masl). If this rise in sea level corresponds to that during older terminations, the subsidence-corrected highstand sea-level positions (30 ± 15 masl for Termination III and 54 ± 15 masl for Termination IV) are not consistent with reported ranges of interglacial sea-level highstands (-18 to 15 masl). Therefore, the studied interval likely records the rise in sea level and associated environmental changes during TII. In particular, the intervening cored materials between the two episodes of sea-level rise found in the studied interval might record the sea-level reversal event during TII. This conclusion is consistent with U/Th ages of around 133 ka, which were obtained from slightly diagenetically altered (i.e., < 1% calcite) in situ corals in the studied interval (Core 310-M0005D-20R [core depth: 118 mbsl]). This study also suggests that our inverse approach to correlate a stratigraphic interval with an approximate time frame could be useful as an independent check on the accuracy of uranium-series dating, which has been applied extensively to fossil corals in late Quaternary sea-level studies.