HUMAN ENDOGENOUS RETROVIRUS K AS A NOVEL TUMOR-ASSOCIATED ANTIGEN FOR DEVELOPMENT OF AN OVARIAN CANCER VACCINE

HUMAN ENDOGENOUS RETROVIRUS K AS A NOVEL TUMOR-ASSOCIATED ANTIGEN FOR DEVELOPMENT OF AN OVARIAN CANCER VACCINE Publication No.________Kiera Rycaj, B.S.Supervisory Professor: Feng Wang-Johanning, Ph.D., M.D. Ovarian cancer (OC) is the fourth most common cancer in women, and the most lethal gynecologic malignancy in the United States. Adequate screening methodologies are currently lacking and most women first present with either stage III or IV disease. To date, there has been no substantial decrease in death rates and the majorities of patients relapse and die from their disease despite response to first-line therapy. Several proteins, such as CA-125, are elevated in OC, but none has proven specific and sensitive enough to serve as a screening tool or for tumor cell recognition and lysis. It has been proposed that human endogenous retrovirus sequences (HERVs) may play a role in the etiology of certain cancers. In a previous study, we showed that HERV-K envelope (env) proteins are widely expressed in human invasive breast cancer (BC) and ductal carcinoma in situ (DCIS), and elicit both serologic and cell-mediated immune responses in BC patients. We also reported the expression of multiple HERV genes and proteins in OC cell lines and tissues. In this study, we strengthened our previous data by determining that HERV-K env mRNAs are expressed in 69% of primary OC tissues (n=29), but in only 24% of benign tissues (N=17). Immmunohistochemistry (IHC) staining revealed HERV-Kpositivecancer cells detected in endometrioid adenocarcinoma and serous adenocarcinoma but not in benign cyst or normal epithelium biopsies. Immunofluorescence staining (IFS) showed greater cell surface expression of HERV-K in OC samples compared to adjacent uninvolved samples. Enzyme-linked immunosorbent assay (ELISA) data confirmed that a humoral immune response is elicited against HERV-K in OC patients. T-cell responses against HERV-K in lymphocytes from OC patients stimulated with autologous HERV-K pulsed dendritic cells included induction of T-cell proliferation and IFN-γ production. HERV-K–specific cytolytic T cells induced greater specific lysis of OC target cells compared to benign and adjacent uninvolved target cells. Finally, upon T regulatory cell (T-reg) depletion, 64% of OC patients displayed an increase in the specific lysis of target cells expressing HERV-K env protein. These findings suggest that HERV-K env protein is a tumor-associated antigen capable of activating both T-cell and B-cell responses in OC patients, and has great potential in the development of immunotherapy regimens against OC.

A Comparison of Soybean Seed Treatments

Seed treatment options are available to manage various fungi, insects, and nematodes that can damage soybeans before, during, and after emergence. These treatments are potentially beneficial for stand establishment and for protection against soybean cyst nematode (SCN). However, these seed treatments represent an additional cost to the producer.

Geochemical and palynological results of IODP Hole 302-M0004A from Lomonosov Ridge, Arctic Ocean

Several episodes of abrupt and transient warming, each lasting between 50,000 and 200,000 years, punctuated the long-term warming during the Late Palaeocene and Early Eocene (58 to 51 Myr ago) epochs**1,2. These hyperthermal events, such as the Eocene Thermal Maximum 2 (ETM2) that took place about 53.5 Myr ago**2, are associated with rapid increases in atmospheric CO2 content. However, the impacts of most events are documented only locally**3,4. Here we show, on the basis of estimates from the TEX86' proxy, that sea surface temperatures rose by 3-5 °C in the Arctic Ocean during the ETM2. Dinoflagellate fossils demonstrate a concomitant freshening and eutrophication of surface waters, which resulted in euxinia in the photic zone. The presence of palm pollen implies**5 that coldest month mean temperatures over the Arctic land masses were no less than 8 °C, in contradiction of model simulations that suggest hyperthermal winter temperatures were below freezing**6. In light of our reconstructed temperature and hydrologic trends, we conclude that the temperature and hydrographic responses to abruptly increased atmospheric CO2 concentrations were similar for the ETM2 and the better-described Palaeocene-Eocene Thermal Maximum**7,8, 55.5 Myr ago.

Mid-Pliocene palynomorph record of the North Atlantic

The mid-Pliocene was an episode of prolonged global warmth and strong North Atlantic thermohaline circulation, interrupted briefly at circa 3.30 Ma by a global cooling event corresponding to marine isotope stage (MIS) M2. Paleoceanographic changes in the eastern North Atlantic have been reconstructed between circa 3.35 and 3.24 Ma at Deep Sea Drilling Project Site 610 and Integrated Ocean Drilling Program Site 1308. Mg/Ca ratios and d18O from Globigerina bulloides are used to reconstruct the temperature and relative salinity of surface waters, and dinoflagellate cyst assemblages are used to assess variability in the North Atlantic Current (NAC). Our sea surface temperature data indicate warm waters at both sites before and after MIS M2 but a cooling of ~2-3°C during MIS M2. A dinoflagellate cyst assemblage overturn marked by a decline in Operculodinium centrocarpum reflects a southward shift or slowdown of the NAC between circa 3.330 and 3.283 Ma, reducing northward heat transport 23-35 ka before the global ice volume maximum of MIS M2. This will have established conditions that ultimately allowed the Greenland ice sheet to expand, leading to the global cooling event at MIS M2. Comparison with an ice-rafted debris record excludes fresh water input via icebergs in the northeast Atlantic as a cause of NAC decline. The mechanism causing the temporary disruption of the NAC may be related to a brief reopening of the Panamanian Gateway at about this time.

Late Pliocene and Early Pleistocene dinoflagellate cysts and sea surface temperture reconstruction for several IODP and DSDP sites in the North Atlantic

In an attempt to document the palaeoecological affinities of individual extant and extinct dinoflagellate cysts, Late Pliocene and Early Pleistocene dinoflagellate cyst assemblages have been compared with geochemical data from the same samples. Mg/Ca ratios of Globigerina bulloides were measured to estimate the spring-summer sea-surface temperatures from four North Atlantic IODP/DSDP sites. Currently, our Pliocene-Pleistocene database contains 204 dinoflagellate cyst samples calibrated to geochemical data. This palaeo-database is compared with modern North Atlantic and global datasets. The focus lies in the quantitative relationship between Mg/Ca-based (i.e. spring-summer) sea-surface temperature (SSTMg/Ca) and dinoflagellate cyst distributions. In general, extant species are shown to have comparable spring-summer SST ranges in the past and today, demonstrating that our new approach is valid for inferring spring-summer SST ranges for extinct species. For example, Habibacysta tectata represents SSTMg/Ca values between 10° and 15°C when it exceeds 30% of the assemblage, and Invertocysta lacrymosa exceeds 15% when SSTMg/Ca values are between 18.6° and 23.5°C. However, comparing Pliocene and Pleistocene SSTMg/Ca values with present day summer values for the extant Impagidinium pallidum suggests a greater tolerance of higher temperatures in the past. This species occupies more than 5% of the assemblage at SSTMg/Ca values of 11.6-17.9°C in the Pliocene and Pleistocene, whereas present day summer SSTs are around -1.7 to 6.9°C. This observation questions the value of Impagidinium pallidum as reliable indicator of cold waters in older deposits, and may explain its bipolar distribution.

New Pliocene and Pleistocene acritarchs from the North Atlantic, Arctic Ocean and Bering Sea

Acritarchs have received limited attention in palynological studies of the Cenozoic, although they have much potential both for refining Neogene and Quaternary stratigraphy, especially in mid- and high northern latitudes, and developing palaeoceanographical reconstructions. Here we formally describe and document the stratigraphical and palaeotemperature ranges (from foraminiferal Mg/Ca) of four new acritarch species: Cymatiosphaera? aegirii sp. nov., Cymatiosphaera? fensomei sp. nov., Cymatiosphaera? icenorum sp. nov. and Lavradosphaera canalis sp. nov. In reviewing the stratigraphical distributions of all species of the genus Lavradosphaera De Schepper & Head, 2008, we demonstrate their correlation potential between the North Atlantic and Bering Sea in the Pliocene. Additionally, Lavradosphaera lucifer De Schepper & Head, 2008 and Lavradosphaera canalis sp. nov., while not themselves overlapping stratigraphically, have morphological intermediates that do partially overlap and may represent an evolutionary trend consequent upon climate cooling in the Late Pliocene. Finally, we show that the highest abundances of the acritarchs presented here were living in the eastern North Atlantic, in surface-water temperatures not very different from today.

Calcareous dinoflagellate cycst in the mid-Cenomanian Boreal realm

A transect from the bathyal to proximal shelf facies of the Boreal Realm was investigated to compare spatial and temporal distribution changes of calcareous dinoflagellate cysts (c-dinocysts) throughout the mid-Cenomanian in order to gain information on the ecology of these organisms. Pithonelloideae dominated the cyst assemblages to more than 95% on the shelf, a prevalence that can be observed throughout most of the Upper Cretaceous. The affinity of this group with the dinoflagellates, which is still controversially discussed, can be confirmed, based on evidence from morphological features and distribution patterns. The consistent prevalence of Pithonella sphaerica and P. ovalis in c-dinocyst assemblages throughout the Upper Cretaceous indicates that they were produced more frequently than cysts of the other species and might, therefore, represent a vegetative dinoflagellate life stage. P. sphaerica and P. ovalis are interpreted as eutrophic species. P. sphaerica is the main species in a marginal-shelf upwelling area, offshore Fennoscandia. Here, sedimentary cyclicity appears to have been reduced to the strongest light/dark changes, while in the outer shelf sediments, light/dark cycles are well-developed and show pronounced temporal assemblage changes. Cyclic fluctuations in the P. sphaerica / P. ovalis ratio reflect shifts of the preferred facies zones and indicate changes in surface mixing patterns. During periods of enhanced surface mixing most parts of the shelf were well-ventilated, and nutrient-enriched surface waters led to high productivity and dominance of the Pithonelloideae. These conditions on the shelf contrasted with those in the open ocean, where more oligotrophic and probably stratified waters prevailed, and an assemblage with very few Pithonelloideae and dominance of Cubodinellum renei and Orthopithonella ? gustafsonii was characteristic. While orbitally-forced light/dark sedimentary cyclicity of the shelf sections was mainly related to surface-water carbonate productivity changes, no cyclic modulation of productivity was observed in the oceanic profile. Therefore, dark layer formation in the open ocean was predominantly controlled by the cyclic establishment of anoxic bottom water conditions. Orbitally-forced interruptions in mixing on the shelf resulted in cyclic periods of stratification and oligotrophy in the surface waters, an expansion of oceanic species to the outer shelf, and a shelfward shift of pithonelloid-facies zones, which were probably related to shelfward directed oceanic ingressions.

The Cenomanian/Turronian Boundary Event at ODP Hole 103-641A

Drilling at ODP Site 641 (on the western margin of Galicia Bank, off northwestern Spain) revealed a thin, but pronounced, interval of black shale and gray-green claystone. Our high-resolution study combines the sedimentology, micropaleontology (palynomorphs and others), organic and inorganic geochemistry, and isotopic values of this layer to demonstrate the distinct nature of the sediment and prove that the sequence represents the local sedimentary expression of the global Cenomanian/Turonian Oceanic Anoxic Event (OAE) of Schlanger and Jenkyns (1976), Arthur and Schlanger (1979), and Jenkyns (1980), also called the Cenomanian/Turonian Boundary Event (CTBE). The most striking evidence is that the strong positive d13C excursion characterizing the CTBE sequences in shallow areas can be traced into a pronounced deep-sea expression, thus providing a good stratigraphic marker for the CTBE in various paleosettings. The isotopic excursion at Site 641 coincides with an extremely enriched trace metal content, with values that were previously unknown for the Cretaceous Atlantic. Similar to other CTBE occurrences, the organic carbon content is high (up to 11%) and the organic matter is of dominantly marine origin (kerogen type II). The bulk mineralogy of the CTBE sediments does not differ significantly from the general trend of Cretaceous North Atlantic sediments (dominance of smectite and zeolite with minor amounts of illite and scattered palygorskite, kaolinite, and chlorite); thus, no evidence for either increased volcanic activity nor a drastic climatic change in the borderlands was found. Results from Site 641 are compared with the CTBE section found at Site 398, DSDP Leg 47B (Vigo Seamount at the southern end of the Galicia Bank).

Distribution of dinoflagellate cycst at ODP Site 123-765 (Table 1)

Site 765 contains a sequence of tropical, middle Miocene to Holocene dinoflagellate cysts. These diverse assemblages are characterized by abundant Polysphaeridium zoharyi and Spiniferites bulloideus. Abundances of Impagidinium spp. and Nematosphaeridium spp. reflect the shelf-to-slope origin of the assemblages. One new genus, Blysmatodinium, and two new species, Nematosphaeridium (?) wrennii sp. nov. and Blysmatodinium argoi, are described.

(Data S1) Palynological analysis of IODP and ODP sediment cores around the Antarctic margin

The circum-Antarctic Southern Ocean is an important region for global marine food webs and carbon cycling because of sea-ice formation and its unique plankton ecosystem. However, the mechanisms underlying the installation of this distinct ecosystem and the geological timing of its development remain unknown. Here, we show, on the basis of fossil marine dinoflagellate cyst records, that a major restructuring of the Southern Ocean plankton ecosystem occurred abruptly and concomitant with the first major Antarctic glaciation in the earliest Oligocene (~33.6 million years ago). This turnover marks a regime shift in zooplankton-phytoplankton interactions and community structure, which indicates the appearance of eutrophic and seasonally productive environments on the Antarctic margin. We conclude that earliest Oligocene cooling, ice-sheet expansion, and subsequent sea-ice formation were important drivers of biotic evolution in the Southern Ocean.

(Appendix A) Organic facies at DSDP Hole 93-603B

The Palynology of two sections recovered during Leg 93 drilling by the Deep Sea Drilling Project in the continental rise along the western margin of the North Atlantic is reported. In Hole 603B at Site 603, the dinoflagellate stratigraphy indicates that the interval from Cores 603B-82 to 603B-26 ranges in age from late Berriasian to Santonian. The BlakeBahama Formation ranges from late Berriasian to Aptian. The Hatteras Formation ranges from Aptian to Cenomanian, although the uppermost part may be Turonian. Dinoflagellate evidence from the middle part of the Plantagenet Formation indicates an age from late Coniacian or early Santonian to Santonian within the interval of Cores 603B-28 to 603B-26. Magnetic polarity evidence of the stratigraphy of the Early Cretaceous for the western North Atlantic indicates a reliable correlation with the dinoflagellate zonation. The stratigraphic sequence of palynologically defined organic facies in carbonaceous claystone lithologies in Hole 603B shows that organic stratigraphic units consisting predominantly of fecal-pellet-derived, pelagic organic matter (xenomorphic facies) alternate with units consisting predominantly of terrigenous organic matter (tracheal and exinitic facies), corresponding to that described from other sites in the North Atlantic. A terrigenous organic facies is identified for the first time from the Plantagenet Formation. The claystone organic facies and major lithofacies are closely correlated. The tracheal and exinitic facies occur in carbonaceous terrigenous claystones and claystone turbidites associated with sandstone/siltstone terrigenous turbidites. The xenomorphic facies occurs in claystones within pelagic limestones lacking any turbidites, and in blackish, noncalcareous claystones which correlate in age with the marine-carbon-rich sapropels which are widespread in the North Atlantic Cenomanian. This facies also occurs with an admixture of terrigenous organic particles in the Blake-Bahama Formation, but the mixture is consistent with the submarine fan setting of this interval. The concentration of refractory organic matter (carbonized particles) in the micrinitic and carbonized tracheal facies is considered to be the result, at least in part, of the oxidation of sediment buried below a surface slowly accumulating pelagic clays below the carbonate compensation depth. The progressive increase in number of dinoflagellate species per stage through the Early Cretaceous (except for the late Barremian-Aptian) may have resulted indirectly from the generally progressive rise in global sea level during this time. At Site 605, the dinoflagellate stratigraphy across the Cretaceous/Tertiary boundary is remarkably close to that published from the Maestrichtian and Danian of Denmark. The Maestrichtian/Danian boundary is placed precisely within Section 605-66-1 by dinoflagellate evidence, agreeing with that predicted by other microfossils. The new dinoflagellate-cyst-based genus, Pierceites and its new species P. schizocystis, and the new combination P. ( = Trithyrodinium) pentagonum (May) are proposed. Diacanthum hollisteri Habib, type species of Diacanthum, is emended to accommodat e cysts with the archeopyle formulas P3'', 2P2''-3'', 2P3''-4'', and 3P2''-3''-4''.

Carbon and oxygen isotope data for carbonates and benthic foraminifers from ODP Hole 113-689B

At Ocean Drilling Program Site 689 (Maud Rise, Southern Ocean), d18O records of fine-fraction bulk carbonate and benthic foraminifers indicate that accelerated climate cooling took place following at least two closely spaced early late Eocene extraterrestrial impact events. A simultaneous surface-water productivity increase, as interpreted from d13C data, is explained by enhanced water-column mixing due to increased latitudinal temperature gradients. These isotope data appear to be in concert with organic-walled dinoflagellate-cyst records across the same microkrystite-bearing impact-ejecta layer in the mid-latitude Massignano section (central Italy). In particular, the strong abundance increase of Thalassiphora pelagica is interpreted to indicate cooling or increased productivity at Massignano. Because impact-induced cooling processes are active on time scales of a few years at most, the estimated 100 k.y. duration of the cooling event appears to be too long to be explained by impact scenarios alone. This implies that a feedback mechanism, such as a global albedo increase due to extended snow and ice cover, may have sustained impact-induced cooling for a longer time after the impacts.

Pollen profiles from 8 sediment cores from the Degersee, Southern Germany

The discovery of a neolithic pile field in the shallow water near the eastern shore of the Degersee confirmed earlier palynological and sedimentological studies stating that early man was active in the region since more than 6000 years. The already available off-site data were freshly assessed, completed by additional data from old and new cores and the interpretations revised. A common time scale for the off-site data and the on-site data was obtained by AMS dating of terrestrial macro remains of the neolithic section of off-site core De_I+De_H. The ages can thus be parallelled with AMS ages of construction timber on-site. Pollen analyses from all cores provide a further time scale. The continuously and densely sampled pollen profile of the profundal zone embracing the entire Late glacial and Holocene serves as a reference. From the Boreal onwards the relative ages are transformed by AMS ages and varve counts into calibrated and absolute. A transect cored close to the neolithic pile field across the lake marl-platform demonstrates its geological architecture in the shallow water since the Lateglacial. Studies of the microfabric of thin sections of drilled cores and of box cores from the excavations demonstrate that neolithic settlements now at 2-3,5 m water depth had been erected on lake marl freshly fallen dry, thus indicating earlier lake levels dropped by 1.5-2 m. The neolithic section of the highly resolved off-site profile in the lake=s profundal zone has laminated and calcareous zones alternating with massive ones. Assemblages of diatoms and concentrations of trace elements changing simultaneously characterise the calcareous sections as deposits of low lake levels that lasted between some 40 and more than 300 years. The ages of discovered lake shore dwellings fall into calcareous segments with low lake levels. From the end of the Upper Atlantic period (F VII) appear Secondary Forest Cycles in the beech forest, a man-made sequence of repeated vegetational development with an identical pattern: With a decrease of beech pollen appear pollen of grasses, herbs and cultural indicators. These are suppressed by the light demanding hazel and birch, those again by ash, and finally by the shade demanding beech forming a new pollen peak. Seven main Forest Cycles are identified In the upper Neolithic period each comprising some 250, 450 or 800 years. They are subdivided into subcycles that can be broken down by very dense sampling in even shorter cycles of decadal length. Farming settlers have caused minor patchy clearances of the beech-mixed-forest with the use of fire. The phases of clearance coincide with peaks of charcoal and low stands of the lake levels. The Secondary Forest Cycles and the continuous occurrence of charcoal prove a continued occupation of the region. Together with the repeated restoration of the beech climax forest they point to pulsating occupation probably associated with dynamic demography. The synchronism of the many palynological, sedimentological and archaeological data point to an external forcing as the climate that affects comprehensively all these proxies. The fluctuations of the activity of the sun as manifested in the residual d14C go largely along with the proxies. The initial clearances at the begin of the forest cycles are linked to low lake levels and negative values of d14C that point to dry and warm phases of a more continental climate type. The subcycles exist independent from climatic changes, indicating that early man acted largely independent from external forces.