Exploring the Schistosoma mansoni adult male transcriptome using RNA-seq

Schistosoma mansoni is one of the agents of schistosomiasis, a chronic and debilitating disease. Here we, present a transcriptome-wide characterization of adult S. mansoni males by high-throughput RNA-sequencing. We obtained 1,620,432 high-quality ESTs from a directional strand-specific cDNA library, resulting in a 26% higher coverage of genome bases than that of the public ESTs available at NCBI. With a 15 x-deep coverage of transcribed genomic regions, our data were able to (i) confirm for the first time 990 predictions without previous evidence of transcription; (ii) correct gene predictions; (iii) discover 989 and 1196 RNA-seq contigs that map to intergenic and intronic genomic regions, respectively, where no gene had been predicted before. These contigs could represent new protein-coding genes or non-coding RNAs (ncRNAs). Interestingly, we identified 11 novel Micro-exon genes (MEGs). These data reveal new features of the S. mansoni transcriptional landscape and significantly advance our understanding of the parasite transcriptome. (c) 2011 Elsevier Inc. All rights reserved.

The etiology of liver damage imparts cytokines transforming growth factor beta1 or interleukin-13 as driving forces in fibrogenesis

It is unknown whether transforming growth factor beta1 (TGF-beta1) signaling uniformly participates in fibrogenic chronic liver diseases, irrespective of the underlying origin, or if other cytokines such as interleukin (IL)-13 share in fibrogenesis (e.g., due to regulatory effects on type I pro-collagen expression). TGF-beta1 signaling events were scored in 396 liver tissue samples from patients with diverse chronic liver diseases, including hepatitis B virus (HBV), hepatitis C virus (HCV), Schistosoma japonicum infection, and steatosis/steatohepatitis. Phospho-Smad2 staining correlated significantly with fibrotic stage in patients with HBV infection (n = 112, P < 0.001) and steatosis/steatohepatitis (n = 120, P < 0.01), but not in patients with HCV infection (n = 77, P > 0.05). In tissue with HBx protein expression, phospho-Smad2 was detectable, suggesting a functional link between viral protein expression and TGF-beta1 signaling. For IL-13, immunostaining correlated with fibrotic stage in patients with HCV infection and steatosis/steatohepatitis. IL-13 protein was more abundant in liver tissue lysates from three HCV patients compared with controls, as were IL-13 serum levels in 68 patients with chronic HCV infection compared with 20 healthy volunteers (72.87 +/- 26.38 versus 45.41 +/- 3.73, P < 0.001). Immunohistochemistry results suggest that IL-13-mediated liver fibrogenesis may take place in the absence of phospho-signal transducer and activator of transcription protein 6 signaling. In a subgroup of patients with advanced liver fibrosis (stage > or =3), neither TGF-beta nor IL-13 signaling was detectable. Conclusion: Depending on the cause of liver damage, a predominance of TGF-beta or IL-13 signaling is found. TGF-beta1 predominance is detected in HBV-related liver fibrogenesis and IL-13 predominance in chronic HCV infection. In some instances, the underlying fibrogenic mediator remains enigmatic.

Breakdown of chlorophyll: A nonenzymatic reaction accounts for the formation of the colorless "nonfluorescent" chlorophyll catabolites

Senescent higher plants degrade their chlorophylls (Chls) to polar colorless tetrapyrrolic Chl catabolites, which accumulate in the vacuoles. In extracts from degreened leaves of the tree Cercidiphyllum japonicum an unpolar catabolite of this type was discovered. This tetrapyrrole was named Cj-NCC-2 and was found to be identical with the product of a stereoselective nonenzymatic isomerization of a “fluorescent” Chl catabolite. This (bio-mimetic) formation of the “nonfluorescent” catabolite Cj-NCC-2 took place readily at ambient temperature and at pH 4.9 in aqueous solution. The indicated nonenzymatic process is able to account for a crucial step during Chl breakdown in senescent higher plants. Once delivered to the acidic vacuoles, the fluorescent Chl catabolites are due to undergo a rapid, stereoselective isomerization to the ubiquitous nonfluorescent catabolites. The degradation of the Chl macrocycle is thus indicated to rely on just two known enzymes, one of which is senescence specific and cuts open the chlorin macroring. The two enzymes supply the fluorescent Chl catabolites, which are “programmed” to isomerize further rapidly in an acidic medium, as shown here. Indeed, only small amounts of the latter are temporarily observable during senescence in higher plants.

DIAGNOSTIC ANTIGENS FOR SCHISTOSOMIASIS MANSONI: PRODUCTION, CHARACTERIZATION AND PURIFICATION OF MONOCLONAL ANTIBODIES, AND AFFINITY PURIFICATION OF ANTIGENS

Attempts have been made in this dissertation to develop a purified antigen with high sensitivity and specificity for diagnosis of Schistosoma mansoni (Sm) infection by using the hybridoma technique.^ Spleen cells, obtained from mice immunized by infection with Sm and boosted by cercarial antigens, or by injection of circulating antigen (CA) in serum from infected mice, were fused with Sp2/0 myeloma cells. The active infection resulted a higher number of hybridomas (100%) than by CA (20%), and higher levels of antibody reactivity as measured by ELISA.^ The IgM and IgG monoclonal antibodies (MCAbs) were purified respectively by gel filtration, DE 52 ion exchange column and proteinase A affinity column. The cercarial and egg antigens were purified by affinity chromatography through MCAb/affi-gel column. The reactivity of the purified antigens were then monitored by ELISA, SDS-PAGE silver stain and EITB.^ The respective MCAbs recognized varying antigenic determinants (AD) present in adult, cercaria and egg stages. By EITB the MCAbs IgM and IgG, when reacted with nine antigens from the various stages, revealed identical bands, suggesting that the two MCAb classes originated from identical AD. By ELISA and COPT, the MCAbs from thirteen cell lines gave same results. But by CHR, two MCAbs showed negative results while eleven other MCAbs showed strong positive. It is assumed that the AD in the immunogen that ilicited the MCAbs were immunochemically closely related.^ One egg purified by immunoaffinity indicated that the epitopes recognized by MCAb were present on four antigenic components with molecular weights (Mr) of approximately 19, 25, 60 and >224 kd, respectively. By EITB the Mr 19 doublet appeared to be species specific; the Mr 25 kd genus specific. They reacted with mouse serum from 13-16 weeks after infection. In monkey serum Mr 19 doublet appeared 8-10 weeks after infection and disappeared at 8-12 weeks after Droncit treatment, paralleled to the disappearance of fecal egg. The Mr 60 and >224 kd bands were also demonstrated with S. japonicum, S. haematobium and Trichinella spiralis infection sera and may be the cause of cross-reaction in conventional serological test. ^

Benthic foraminifers from the Japan Sea

Five holes were drilled at two sites in the Sea of Japan during Ocean Drilling Program (ODP) Leg 128. Site 798 is located on Oki Ridge at a depth of about 900 m. Sediment age at Site 798 ranges from Pliocene to Holocene. Site 799 is located in the Kita-Yamato Trough at depth of 2000 m and below the present calcite compensation depth (CCD); the sediment ranges from Miocene to Holocene in age. Samples from all holes contain benthic foraminifers. Faunal evidence of downslope displacement is frequent in Holes 799A and 799B. The vertical frequency distribution of some dominant species shows that significant faunal changes occur in Holes 798A-C on Oki Ridge. Based on the faunal change and the thickness of sediments, it appears that the Oki Ridge was uplifted more than 1,000 m during last 4 m.y. Benthic foraminifers also demonstrate that the water depth of Site 799 rapidly changed from upper bathyal to lower bathyal during middle Miocene time. The appearance of benthic foraminifer species common to anaerobic environments suggests that the dysaerobic to anaerobic bottom conditions existed during the evolution of the Sea of Japan. Faunal distributions also suggest that the 'Tertiary-type' species recognized in the Neogene strata of the Japan Sea coastal regions disappeared sequentially from the Sea of Japan during Pliocene to late Pleistocene.

Biostratigraphy of sediment core CRP-3 from the Ross Sea, Antarctica

Early Oligocene siliceous microfossils were recovered in the upper c. 193 m of the CRP-3 drillcore. Although abundance and preservation are highly variable through this section, approximately 130 siliceous microfossil taxa were identified, including diatoms, silicoflagellates, ebridians, chrysophycean cysts, and endoskeletal dinoflagellates. Well-preserved and abundant assemblages characterize samples in the upper c. 70 m and indicate deposition in a coastal setting with water depths between 50 and 200 m. Abundance fluctuations over narrow intervals in the upper c. 70 mbsf are interpreted to reflect environmental changes that were either conducive or deleterious to growth and preservation of siliceous microfossils. Only poorly-preserved (dissolved, replaced, and/or fragmented) siliceous microfossils are present from c. 70 to 193 mbsf. Diatom biostratigraphy indicates that the CRP-3 section down to c. 193 mbsf is early Oligocene in age. The lack of significant changes in composition of the siliceous microfossil assemblage suggests that no major hiatuses are present in this interval. The first occurrence (FO) of Cavitatus jouseanus at 48.44 mbsf marks the base of the Cavitatus jouseanus Zone. This datum is inferred to be near the base of Subchron C12n at c. 30.9 Ma. The FO of Rhizosolenia antarctica at 68.60 mbsf marks the base of the Rhizosolenia antarctica Zone. The FO of this taxon is correlated in deep-sea sections to Chron C13 (33.1 to 33.6 Ma). However, the lower range of R. antarctica is interpreted as incomplete in the CRP-3 drillcore, as it is truncated at an underlying interval of poor preservation: therefore, an age of c. 33.1 to 30.9 Ma is inferred for interval between c. 70 and 50 mbsf. The absence of Hemiaulus caracteristicus from diatom-bearing interval of CRP-3 further indicates an age younger than c. 33 Ma (Subchron C13n) for strata above c. 193 mbsf. Siliceous microfossil assemblages in CRP-3 are significantly different from the late Eocene assemblages reported CIROS-1 drillcore. The absence of H. caracteristicus, Stephanopyxis splendidus, and Pterotheca danica, and the ebridians Ebriopsis crenulata, Parebriopsis fallax, and Pseudoammodochium dictyoides in CRP-3 indicates that the upper 200 m of the CRP-3 drillcore is equivalent to part of the stratigraphic interval missing within the unconformity at c. 366 mbsf in CIROS-1.

Dinoflagellate cysts abundance and events of ODP Hole 189-1168A sediments

Palynomorphs were studied in samples from Ocean Drilling Program (ODP) Leg 189, Hole 1168A (slope of the western margin of Tasmania; 2463 m water depth). Besides organic-walled dinoflagellate cysts (dinocysts), broad categories of other palynomorphs were quantified in terms of relative abundance. In this contribution, we provide an overview of the early late Eocene-Quaternary dinocyst distribution and illustrate main trends in palynomorph distribution. Dinocyst species throughout Hole 1168A are largely cosmopolitan with important contributions of typical low-latitude taxa and virtual absence of endemic Antarctic taxa. Dinocyst stratigraphic distribution broadly matches that known from the Northern Hemisphere and equatorial regions, although significant differences are noted. Selected potentially biochronostratigraphically useful events are summarized. The distribution of dinocysts in the middle-upper Miocene interval is rather patchy, probably due to prolonged exposure to oxygen. An important general aspect in the dinocyst assemblages is the near absence of Antarctic endemic species and the apparent influence of relatively warm waters throughout the succession at Site 1168. General palynomorph distribution indicates continued deepening from an initial shallow, even restricted, marine setting from late Eocene-Quaternary times. A curious massive influx of small skolochorate acritarchs is recorded throughout the late early-early middle Miocene; the significance of this signal is not yet understood. A general long-term oligotrophic nature of the surface waters influencing Site 1168 is suggested from the low abundance of (proto) peridinioid, presumably heterotrophic, species. The overall dinocyst distribution pattern corresponds to the long-term existence of a Leeuwin-like current influencing the region, including Site 1168, confirming results of earlier studies on other microfossil groups. The occasional influence of colder surface water conditions is, however, also apparent, notably during the late Pliocene-Quaternary, indicating the potential of high-resolution dinocyst analysis for future paleoceanographic studies.

Upper Cenozoic dinoflagellate cysts from the continental slope and rise off New Jersey

This report contains the occurrence data for dinoflagellate cysts recorded from 163 samples taken from Sites 902 through 906, during Ocean Drilling Program (ODP) Leg 150. The dinoflagellate cyst (dinocyst) stratigraphy has been presented in Mountain, Miller, Blum, et al. (1994, doi:10.2973/odp.proc.ir.150.1994), and was based on these data. This report provides the full dinocyst data set supporting the dinocyst stratigraphic interpretations made in Mountain, Miller, Blum, et al. (1994). For Miocene shipboard dinocyst stratigraphy, I delineated 10 informal zones: pre-A, and A through I, in ascending stratigraphic order. These zones are defined in Shipboard Scientific Party (1994a, doi:10.2973/odp.proc.ir.150.103.1994), and are based on my studies of Miocene dinocyst stratigraphy in the Maryland and Virginia coastal plain (de Verteuil and Norris, 1991, 1992; de Verteuil, 1995). This zonation has been slightly revised (de Verteuil and Norris, 1996), and the new formal zone definitions are repeated below. Each new zone has an alpha-numeric abbreviation starting with "DN" (for Dinoflagellate Neogene). The equivalence between the informal zones reported in Mountain, Miller, Blum, et al. (1994), and the new DN zones is illustrated in Figure 1. For clarity, I delineated both zonations in the range charts that accompany this report (Tables 1-6). De Verteuil and Norris (1996a), using these and other data, correlated the DN zonation with the geological time scale of Berggren et al. (1995). Figure 2 summarizes these correlations and can be used to check the chronostratigraphic position of samples in this report, as determined by dinocyst stratigraphy. A thorough discussion of the basis for, and levels of uncertainty associated with, these correlations to the Cenozoic time scale can be found in de Verteuil and Norris (1996a). The Appendix lists all the dinocyst taxa recorded during shipboard analyses of Leg 150 samples. Open nomenclature is used for undescribed taxa. The range charts and Appendix also include reference to several new taxa that de Verteuil and Norris (1996b) described from Miocene coastal plain strata in Maryland and Virginia. Names of these taxa in Tables 1 through 6 and in the Appendix of this report are not intended for effective publication as defined in the International Code of Botanical Nomenclature (ICBN, Greuter et al., 1994). Therefore, taxonomic nomenclature contained in this report is not to be treated as meeting the conditions of effective and valid publication (ICBN; Article 29).

Late Quateranry dinoflagellate cysts of ODP Site 202-1233

The late Quaternary organic-walled dinoflagellate cyst record of Site 1233 (41°S, offshore Chile) was studied with a ?200 year resolution spanning the last 25,000 years. The study provides the first continuous record of sub-recent and recent dinoflagellate cysts in the Southeast (SE) Pacific. Major changes in the composition of the cyst association, cyst concentration and morphology of Operculodinium centrocarpum reflect changes in sea surface temperature (SST), sea surface salinity (SSS), palaeoproductivity and upwelling intensity. These changes can be associated with latitudinal shifts of the circumpolar frontal systems. The high cyst concentration, high Brigantedinium spp. abundances, low species diversity and the occurrence of certain cold water species are supportive for a 7-10° equatorward shift of the Antarctic Circumpolar Current (ACC) during the coldest phase of the Last Glacial Maximum (LGM) between 25 and 21.1 cal ka BP. Deglacial warming initiated at ~18.6 cal ka BP. Termination I (18.6-11.1 cal ka BP) is interrupted by an unstable period of extreme seasonality, rather than a cooling event, between 14.4 and 13.2 cal ka BP, synchronous with the Antarctic Cold Reversal (ACR). The Holocene Maximum is observed between 11.6 and 9.8 cal ka BP and is typified by the most southward position of the northern margin of the ACC. A cooling phase occurred during the early Holocene (until ~7 cal ka BP) and during the last ~0.8 ka. Our data indicates that the SE Pacific (41°S) climate has been influenced over the whole record by changes in the Southern Hemisphere (SH) high-latitudes, while during the mid to late Holocene, also a tropical forcing mechanism was involved, including the El Niño Southern Oscillation and the variable Hadley cell intensity. Furthermore, this study showed a relationship between the variable morphology of the spines/processes of O. centrocarpum and the combined variation of sea surface salinity and temperature (SSS/SST-ratio).

Dinoflagellates of ODP Leg 104 holes

Dinoflagellate cysts, pollen, and spores were studied from 78 samples of the Eocene to Miocene section of ODP Site 643 at the outer Wring Plateau. Dinoflagellate cysts ranging from less than 1,000 to rarely over 30,000 per gram of sediment in the Paleogene, and generally between 50,000 and 100,000 in the Miocene were present. The shift to conspicuously higher cyst frequencies takes place in the lowermost Miocene section and appears to reflect increased cyst recruitment rather than a change in sedimentation rate. Of the 179 dinoflagellate cyst forms whose ranges were recorded, 129 are known species. Fifteen assemblage zones have been recognized, although the upper Eocene is missing and no substantial lower Eocene was recorded at Site 643. Norwegian Sea and Rockall Plateau zonations were compared with this study. Detailed correlation with existing onshore section zonations was difficult because key zonal species are inadequately represented; however, the middle to upper Miocene zonation established for Denmark is applicable. Pollen and spores occur with relatively low frequencies, and palynodebris is generally absent, in contrast to the observations from DSDP Leg 38. Thirty-nine samples from Eocene to Miocene sediments at Site 642 were studied and correlated with Site 643. A lower Eocene cyst assemblage present in Hole 642D is older than the questionably lower Eocene assemblage from Site 643. Site 642 has a lower Eocene to lower Miocene hiatus.

Neogene diatoms of the Japan Sea

A series of excellent upper Miocene through Quaternary diatomaceous sequences recovered at four sites during Leg 127 was examined for diatoms. The diagenetic transition from opal-A to opal-CT is a diachronic horizon from the uppermost part of the Denticulopsis katayamae Zone (8.5 Ma) at Hole 797B to the uppermost part of the Neodenticula kamtschatica Zone (5.73 Ma) at Hole 795A. The diatom zonation of Koizumi (1985) best divides the upper Miocene to Quaternary sequences above the opal-A/opal-CT boundary and also is useful to date carbonate concretions including diatoms below the boundary. Forty diatom datum levels were evaluated biostratigraphically based on the sediment accumulation rate curve, and several isochronous datum levels are newly proposed for the Japan Sea area. A warm-water current did not penetrated into the Japan Sea through the Tsushima strait during the late Miocene and Pliocene time, because subtropical warm-water diatoms are essentially not present in such sediment samples. The occurrences of diatom are cyclic throughout the Quaternary sediments and are affected by eustatic sea level changes.

Sea surface temperature reconstruction based on dinoflagellates from the North Atlantic

The application of quantitative and semiquantitative methods to assemblage data from dinoflagellate cysts shows potential for interpreting past environments, both in terms of paleotemperature estimates and in recognizing water masses and circulation patterns. Estimates of winter sea-surface temperature (WSST) were produced by using the Impagidinium Index (II) method, and by applying a winter-temperature transfer function (TFw). Estimates of summer sea-surface temperature (SSST) were produced by using a summer-temperature transfer function (TFs), two methods based on a temperature-distribution chart (ACT and ACTpo), and a method based on the ratio of gonyaulacoid:protoperidinioid specimens (G:P). WSST estimates from the II and TFw methods are in close agreement except where Impagidinium species are sparse. SSST estimates from TFs are more variable. The value of the G:P ratio for the Pliocene data in this paper is limited by the apparent sparsity of protoperidinioids, which results in monotonous SSST estimates of 14-26°C. The ACT methods show two biases for the Pliocene data set: taxonomic substitution may force 'matches' yielding incorrect temperature estimates, and the method is highly sensitive to the end-points of species distributions. Dinocyst assemblage data were applied to reconstruct Pliocene sea-surface temperatures between 3.5-2.5 Ma from DSDP Hole 552A, and ODP Holes 646B and 642B, which are presently located beneath cold and cool-temperate waters north of 56°N. Our initial results suggest that at 3.0 Ma, WSSTs were a few degrees C warmer than the present and that there was a somewhat reduced north-south temperature gradient. For all three sites, it is likely that SSSTs were also warmer, but by an unknown, perhaps large, amount. Past oceanic circulation in the North Atlantic was probably different from the present.

Palynology and dinoflagellate counts of surface sediments, and sea surface conditions, of sites in the North Pacific

Palynological analyses were performed on 53 surface sediment samples from the North Pacific Ocean, including the Bering and Okhotsk Seas (37-64°N, 144°E-148°W), in order to document the relationships between the dinocyst distribution and sea-surface conditions (temperatures, salinities, primary productivity and sea-ice cover). Samples are characterized by concentrations ranging from 18 to 143816 cysts/cm**3 and the occurrence of 32 species. A canonical correspondence analysis (CCA) was carried out to determine the relationship between environmental variables and the distribution of dinocyst taxa. The first and second axes represent, respectively, 47% and 17.8% of the canonical variance. Axis 1 is positively correlated with all parameters except to the sea-ice and primary productivity in August, which are on the negative side. Results indicate that the composition of dinocyst assemblages is mostly controlled by temperature and that all environmental variables are correlated together. The CCA distinguishes 3 groups of dinocysts: the heterotrophic taxa, the genera Impagidinium and Spiniferites as well as the cyst of Pentapharsodinium dalei and Operculodinium centrocarpum. Five assemblage zones can be distinguished: 1) the Okhotsk Sea zone, which is associated to temperate and eutrophic conditions, seasonal upwellings and Amur River discharges. It is characterized by the dominance of O. centrocarpum, Brigantedinium spp. and Islandinium minutum; 2) the Western Subarctic Gyre zone with subpolar and mesotrophic conditions due to the Kamchatka Current and Alaska Stream inflows. Assemblages are dominated by Nematosphaeropsis labyrinthus, Pyxidinopsis reticulata and Brigantedinium spp.; 3) the Bering Sea zone, depicting a subpolar environment, influenced by seasonal upwellings and inputs from the Anadyr and Yukon Rivers. It is characterized by the dominance of I. minutum and Brigantedinium spp.; 4) the Alaska Gyre zone with temperate conditions and nutrient-enriched surface waters, which is dominated by N. labyrinthus and Brigantedinium spp. and 5) the Kuroshio Extension-North Pacific-Subarctic Current zone characterized by a subtropical and oligotrophic environment, which is dominated by O. centrocarpum, N. labyrinthus and warm taxa of the genus Impagidinium. Transfer functions were tested using the modern analog technique (MAT) on the North Pacific Ocean (= 359 sites) and the entire Northern Hemisphere databases ( = 1419 sites). Results confirm that the updated Northern Hemisphere database is suitable for further paleoenvironmental reconstructions, and the best results are obtained for temperatures with an accuracy of +/-1.7 °C.

Dinoflagellate abundance and events of ODP Site 189-1172 sediments

Palynomorphs were studied in samples from Ocean Drilling Program (ODP) Leg 189, Holes 1172A and 1172D (East Tasman Plateau; 2620 m water depth). Besides organic walled dinoflagellate cysts (dinocysts), broad categories of other palynomorphs were quantified in terms of relative abundance. In this contribution, we provide an overview of the dinocyst distribution from the Maastrichtian to lowermost Oligocene and Quaternary intervals and illustrate main trends in palynomorph distribution. The uppermost Cretaceous-lowermost Oligocene succession of Site 1172 has a confident biomagnetostratigraphy, enabling us to tie early Paleogene Southern Hemisphere dinocyst events to the geomagnetic polarity timescale for the first time. Dinocyst species from the Maastrichtian to earliest Oligocene at Site 1172 are largely endemic ("Transantarctic Flora") or bipolar; cosmopolitan taxa are present in the background as well. The Maastrichtian-early late Eocene dinocyst assemblages are indicative of shallow-marine to restricted marine, pro-deltaic conditions, closely tied to a massive siliciclastic sequence. By middle late Eocene times (~35.5 Ma), the siliciclastic sequence gave way to a thin glauconitic unit, considered to reflect the deepening of the Tasmanian Gateway. This transition coincides with the most prominent change in dinocyst associations of the Paleogene. The turnover is inferred to reflect a change from marginal marine to more offshore conditions, with increased winnowing and oxidation. Overlying pelagic carbonate ooze of middle early Oligocene and younger age is virtually barren of organic microfossils, although Quaternary assemblages have been recovered. This aspect is taken to reflect average low sedimentation rates and well-oxygenated water masses during most of the Oligocene and Neogene. The few palynologically productive samples from the Oligocene-Quaternary interval have a stronger cosmopolitan to subtropical signature, with warm-water species being common to abundant.