Immature Samples Research Articles

Source rock kinetics and petroleum generation history of the Upper Ordovician calcareous shales of the Hudson Bay Basin and surrounding areas

The current understanding of the Paleozoic petroleum system in Hudson Bay Basin remains far from complete due in no small part to the uncertainty in locally-calibrated generation and migration models underpinned with reliable source rock kinetic data. To improve the petroleum systems model, four representative immature organic-rich calcareous shales of Late Ordovician age from onshore outcrops surrounding the Hudson Bay were analysed to characterize their source rock generation kinetics. To constrain uncertainty due to laboratory measurement errors in kinetic parameter estimation, six heating rates were used in the pyrolysis experiments for each sample, resulting in 24 kinetic datasets that reduce uncertainty from both source rock heterogeneity and inherited laboratory measurement errors. Under the assumed geological time and geothermal framework, application of the kinetic models resulted in internally consistent generation histories, suggesting that the source rock started to generate oil when temperature reached 100 °C. It is likely where the maximum burial depth excessed 3000 m, the source rocks were in oil generation window with kerogen transformation ratio varying in a range between 52 and 78%. The modeled source rock maturity range from the immature outcrop samples is supported by bulk rock geochemistry data from cuttings of the source rock interval in offshore wells with high S1 peaks, large humps on the left shoulder on S2 curves, typical feature of FID pyrograms in the oil window. Comparison of the kinetic behavior of the samples in this study with those of typical marine Type I, Type II and Type IIS source rocks under laboratory condition and the assumed geological time/temperature framework suggests that kerogen converts to oil in a lower temperature range than those typical normal marine Type II source rock. We attribute the moderate sulfur content (likely high sulfoxide/thiophene ratio) and presence of kerogen component groups that are more prone to cleavage at low temperature as the cause for low temperature onset of hydrocarbon generation.

The thermal maturity of sedimentary basins as revealed by magnetic mineralogy

AbstractThe thermal evolution of sedimentary basins is usually constrained by maturity data, which is interpreted from Rock‐Eval pyrolysis and vitrinite reflectance analytical results on field or boreholes samples. However, some thermal evolution models may be inaccurate due to the use of elevated maturities measured in samples collected within an undetected metamorphic contact aureole surrounding a magmatic intrusion. In this context, we investigate the maturity and magnetic mineralogy of 16 claystone samples from Disko‐Svartenhuk Basin, part of the SE Baffin Bay volcanic margin. Samples were collected within thermal contact metamorphic aureoles near magma intrusions, as well as equivalent reference samples not affected by intrusions. Rock‐Eval pyrolysis (Tmax), and vitrinite reflectance (Ro) analysis were performed to assess the thermal maturity, which lies in the oil window when 435°C ≤ Tmax ≤ 470°C and 0.6%–0.7% ≤ Ro ≤ 1.3%. In addition, we performed low‐ (<300K) and high‐temperature (>300K) investigations of isothermal remanent magnetization to assess the magnetic mineralogy of the selected samples. The maturity results (0.37% ≤ Ro ≤ 2%, 22°C ≤ Tmax ≤ 604°C) show a predominance of immature to early mature Type III organic matter, but do not reliably identify the contact aureole when compared to the reference samples. The magnetic assemblage of the immature samples consists of iron sulphide (greigite), goethite and oxidized or non‐stoichiometric magnetite. The magnetic assemblage of the early mature to mature samples consists of stoichiometric magnetite and fine‐grained pyrrhotite (<1 μm). These results document the disappearance of the iron sulphide (greigite) and increase in content of magnetite during normal burial. On the other hand, magnetite is interpreted to be the dominant magnetic mineral inside the contact aureole surrounding dyke/sill intrusions where palaeotemperatures indicate mature to over‐mature state. Interestingly, the iron sulphide (greigite) is still detected in the contact aureole where palaeotemperatures exceeded 130°C. Therefore, the magnetic mineralogy is a sensitive method that can characterize normal burial history, as well as identify hidden metamorphic contact aureoles where the iron sulphide greigite is present at temperatures beyond its stability field.

Body-size spectra of biofilm-dwelling ciliates at different layers in water column of coastal ecosystems

It is increasingly recognized that the body-size spectrum of biofilm-dwelling ciliates is an informative bioindicator of environmental change in marine ecosystems. In order to reveal the effects of water depth on the body-size spectrum of biofilm-dwelling ciliates during the colonization process, a 1-month baseline survey was carried out in coastal waters of the Yellow Sea, northern China. Using glass slides as artificial substrates, a total of 240 microscopy slides were collected from four depths, i.e., 1, 2, 3.5 and 5 m, after colonization periods of 3, 7, 10, 14, 21 and 28 days. A total of 92 ciliate species were collected. Based on its equivalent spherical diameter (ESD), each species was allocated to one of eight body-size ranks (S1–S8): S1 (13–17μm), S2 (20–26μm), S3 (30–34μm), S4 (35–49μm), S5 (54–63μm), S6 (66–93μm), S7 (120–161μm) and S8 (162–247μm). The body-size spectrum showed a clear temporal variability in both frequency of occurrence and probability density during the colonization process at the four depths: S1 was dominant in immature samples whereas mature samples were dominated by S3. Multidimensional scaling ordinations (MDS) and bootstrap average analyses revealed a clear shift in body-size spectra from surface to deeper water layers during the colonization process. Ellipse tests demonstrated that the samples showed different patterns of departure from the expected body-size spectrum at each depth during the colonization period. These findings suggest that water depth may significantly shape the body-size spectra of biofilm-dwelling ciliates, and that there may be an optimal water depth when using this feature for monitoring marine ecosystems.

Pattern recognition-based Raman spectroscopy for non-destructive detection of pomegranates during maturity.

In this study, the feasibility of utilizing Fourier transform Raman spectroscopy, combined with supervised and unsupervised pattern recognition methods was considered, to distinguish the maturity stage of pomegranate "Ashraf variety" during four distinct maturity stages between 88 and 143days after full bloom. Principal component analysis (PCA) as an unsupervised pattern recognition method was performed to verify the possibility of clustering of the pomegranate samples into four groups. Two supervised pattern recognition techniques namely, partial least squares Discriminant Analysis (PLS-DA) and Soft Independent Modeling of Class Analogy (SIMCA) were also used as powerful supervised pattern recognition methods to classify the samples. The results showed that in all groups of samples, the Raman spectra of the samples were correctly clustered using PCA. The accuracy of the SIMCA classification for differentiation of four pomegranate groups was 82%. Also, the overall discriminant power of PLS-DA classes was about 96%, and 95% for calibration and validation sample sets, respectively. Due to the misclassification among different classes of immature pomegranates, that was lower than the expected, it was not possible to discriminate all the immature samples in individual classes. However, when considering only the two main categories of "immature" and "mature", a reasonable separation between the classes were obtained using supervised pattern recognition methods of SIMCA and PLS-DA. The SIMCA based on PCA modeling could correctly categorize the samples in two classes of immature and mature with classification accuracy of 100%.

Reservoir Temperature Calculation of Immature Geothermal Water from Hot Spring Around the Slamet Volcano

The temperature of some geothermal reservoirs around Slamet Volcano can be estimated from hot spring water geochemistry around it. Calculation of reservoir temperature from immature hot water samples has the potential to cause uncertainty. This is due to a mixture of geothermal water and meteoric water. The manifestation of the geothermal water appears in several different places, including on the southern slope of Slamet Volcano which consists of Pancuran-7 and Pancuran-3 Hot Springs. On the northwest slope of Slamet Volcano, several manifestations also appear, namely Pancuran-13 and Pengasihan in the Guci Area and Sigedong Hot springs in Sigedong Area. This study uses geochemical methods of geothermal water and hot springs water sample data from previous studies for analysis of geoindicators and geothermometers. Reservoir temperature calculation is based on the content of silica and enthalpy of immature geothermal water and meteoric water in the study area. Based on the Cl- Li-B geoindicator analysis, it was interpreted that there were 3 geothermal systems with different reservoirs around Slamet Volcano, namely the Baturaden, Guci and Sigedong Systems. Based on the Na-K-Mg plot for the geothermometer, the five hot springs around Slamet Volcano are included in the immature water group. Based on the enthalpy vs. silica analyses, the geothermal reservoir temperatures for Baturaden, Guci, and Sigedong are 204°C-210°C, 187°C-196°C and 181°C.

Biomarkers of Oligocene lacustrine source rocks, Beibuwan-Song Hong basin junction, offshore northern Vietnam

Abstract Highly oil prone source rocks containing sapropelic Type I and mixed Types I and III kerogen are found in 233 m of the 500 m deep, fully cored ENRECA-3 well drilled on Bach Long Vi Island, located at the junction between the Beibuwan and the Song Hong basins offshore northern Vietnam. The cored succession is made up entirely by Oligocene, deep lacustrine deposits. The origin of the organic matter (OM) in 62 samples is evaluated on the basis of gas chromatography-mass spectrometry (GC-MS and GC-MS/MS). OM in 55 samples is sourced primarily from lacustrine organisms and contains abundant 4-methylsteranes, tetracyclic polyprenoids (TPP) and lycopane, and no markers for marine organic matter. The proportion of triterpanes derived from angiosperms is low in most saturated fractions and only traces of gymnosperm diterpanes are detected. In contrast, all aromatic fractions have a high proportion of compounds having an origin from both gymnosperms and angiosperms. Very high concentrations of hopanoids in both fractions suggest significant bacterial alteration of the original OM. Most samples have a high concentration of rare C31 diaromatic 8,14-secohopanes with a fluorene moiety. Low pristane/phytane (Pr/Ph) ratios indicate that anoxic/suboxic bottom water conditions existed during OM accumulation. The presence of β-carotane, gammacerane and traces of arylisoprenoids could indicate a stratified water column. OM in a few samples with lower than average hydrogen index (HI) is mainly of terrestrial origin with a higher proportion of C29 steranes, diterpanes and oleanoids and lower concentrations of both saturated and aromatic hopanes. Higher Pr/Ph, a higher C34 isohopane ratio (IHR34) and a lower homohopane index (HHI) indicate that this low-HI OM was originally deposited under more oxic conditions and subsequently transported to deeper water. Low sterane and hopane isomerization ratios show that no samples have reached the oil-window. Some novel maturity parameters for immature lacustrine samples are proposed.

Iron isotopic composition of very low-titanium basalt deduced from the iron isotopic signature in Luna 16, 20, and 24 soils

Isotopic analysis of Fe has proved to be a productive tool for the study of the formation and evolution of planetary bodies. The Fe isotopic studies on the Moon revealed that low-Ti and high-Ti basalts are positively correlated with TiO2 contents, indicating the occurrence of Fe isotopic fractionation during lunar magma ocean differentiation (Weyer et al., 2005; Liu et al., 2010; Wang et al., 2015; Sossi and Moynier, 2017). If true, very low-Ti basalts may be more representative of the lunar mantle than high-Ti and low-Ti basalts. Thus, an Fe isotopic study of very low-Ti basalts is required to investigate the Fe isotopic evolution scenario during lunar magma ocean differentiation.In this study, we measured Fe isotopic ratios of soil samples from the Soviet Luna missions, Luna 16, 20, and 24, using MC-ICP-MS. Bulk soil samples without isolation of components and separated monomineralic grains (olivine, pyroxene, and agglutinate) were dedicated for the Fe isotopic study. Among our samples, Luna 24 soil is recognized as very low-Ti basalt. Evidence of non-mass-dependent Fe isotopic fractionation was not found in bulk soils and separated monomineralic olivine, pyroxene, and agglutinate grains. Lunar regolith samples are weathered by meteorite impacts on the Moon’s surface. A mature regolith sample, L1613, showed clearly distinguished Fe isotopic compositions between the fine-grained fraction (δ57Fe = 0.54 ± 0.06‰) and the coarse-grained fraction (δ57Fe = 0.20 ± 0.06‰). Such Fe isotopic differences among different size fractions were smaller in the submature sample (L2001) and the immature sample (L24130.3). The Fe isotopic ratios of separated grains show that agglutinates have higher δ57Fe values than bulk and monomineralic grains, indicating abundant nanophase Fe in agglutinates and partial evaporation of Fe during its melting.The δ57Fe value for the coarsest-grained fraction of L24130.3 was found to be 0.08 ± 0.04‰, which is the first Fe isotopic composition reported for lunar samples with very low-Ti mare basalt composition. This value is clearly lower than previously reported δ57Fe values for high-Ti and low-Ti basalts and is nearly identical to those of Mg-suite rocks. This observation is consistent with the Fe isotopic evolution model during lunar magma ocean differentiation (Sossi and Moynier, 2017). Our results related to very low-Ti basalt showed that the bulk silicate Moon has lower Fe isotopic composition than the value estimated from averaged low-Ti or high-Ti basalts.Given the data known to date, including our results, we conclude that it is most likely that Earth and the Moon have the same Fe isotopic composition. We believe that isotopically heavy Fe of silicate Earth is balanced by isotopically light Fe of Earth’s core, as suggested by Galimov’s (2011) model for the formation of the Earth-Moon system.

Comparative study of aromatic hydrocarbons in bitumens and expelled oils generated by hydrous pyrolysis of coal

An immature humic coal sample from the Yaojie Formation of the Muli coal field is pyrolysed in a hydrous closed system. The differences in aromatic hydrocarbon compositon between bitumens and expelled oils are investigated with the simulation temperature ranging from 250 to 500 °C. The absolute concentrations of the main aromatic classes in bitumens and expelled oils initially increase and thereafter decrease with increasing maturity. The absolute concentrations of naphthalene are always higher in expelled oils than in the corresponding bitumens; however, the absolute concentrations of alkyl-naphthalenes, phenanthrene, and alkyl-phenanthrenes are higher in bitumens than in expelled oils at the lower-maturity stage, and reversals occur with continuous increase in RO. Most of the common parameters—MNR, MPI1, MPR, F1, and F2—exhibit regular differences in bitumen–expelled oil pairs. The ratios of different alkylation degrees of naphthalenes and phenanthrenes (such as N/C1–5-N, C1-N/C1–5-N, C1-N/C5-N, P/C1–3-P, and C1-P/C3-P) and the ratios of aromatic components (such as naphthalene/phenanthrene, phenanthrene/fluoranthene, and phenanthrene/pyrene) that have different numbers of aromatic rings exhibit regular differences in bitumen–expelled oil pairs. These ratios of expelled oils are always higher than those of corresponding bitumens; reversals may occur at a high maturity stage. The systematic differences between the compositions of the main aromatic hydrocarbons in bitumens and expelled oils could be predominantly controlled by the fractionation effect at a lower-temperature stage and differentiated decomposition at a higher-temperature stage during the hydrous pyrolysis of coal.

Evaluation of DNA Extraction Methods on Individual Helminth Egg and Larval Stages for Whole-Genome Sequencing.

Whole-genome sequencing is being rapidly applied to the study of helminth genomes, including de novo genome assembly, population genetics, and diagnostic applications. Although late-stage juvenile and adult parasites typically produce sufficient DNA for molecular analyses, these parasitic stages are almost always inaccessible in the live host; immature life stages found in the environment for which samples can be collected non-invasively offer a potential alternative; however, these samples typically yield very low quantities of DNA, can be environmentally resistant, and are susceptible to contamination, often from bacterial or host DNA. Here, we have tested five low-input DNA extraction protocols together with a low-input sequencing library protocol to assess the feasibility of whole-genome sequencing of individual immature helminth samples. These approaches do not use whole-genome amplification, a common but costly approach to increase the yield of low-input samples. We first tested individual parasites from two species spotted onto FTA cards—egg and L1 stages of Haemonchus contortus and miracidia of Schistosoma mansoni—before further testing on an additional five species—Ancylostoma caninum, Ascaridia dissimilis, Dirofilaria immitis, Strongyloides stercoralis, and Trichuris muris—with an optimal protocol. A sixth species—Dracunculus medinensis—was included for comparison. Whole-genome sequencing followed by analyses to determine the proportion of on- and off-target mapping revealed successful sample preparations for six of the eight species tested with variation both between species and between different life stages from some species described. These results demonstrate the feasibility of whole-genome sequencing of individual parasites, and highlight a new avenue toward generating sensitive, specific, and information-rich data for the diagnosis and surveillance of helminths.

Hydrocarbon retention in lacustrine shales during thermal maturation: Insights from semi-open system pyrolysis

Evaporative loss of light hydrocarbons during shale core collection and sample preparation makes it challenging to characterize hydrocarbon retention and accurately evaluate petroleum resources in a shale layer with high thermal maturity. Here, semi-open system pyrolysis experiment was applied to investigate the evolution of hydrocarbon in shales during thermal maturation, using an immature lacustrine shale with total organic carbon (TOC) of 2.13 wt% from the Es3 Member in Dongpu Depression, Bohai Bay Basin, China. Moreover, Ro measurement, solvent extraction, kinetic study, open-system pyrolysis, thermovaporization-gas chromatography (Tvap-GC) and pyrolysis-gas chromatography (Py-GC) were also conducted on the products from semi-open system pyrolysis experiments.Retained oil in shales consists of free oil (pyrolysis S1) and sorbed oil (involved in pyrolysis S2). A preponderance of sorbed oil retained in the studied lacustrine shale is observed, with its content reaching to more than 4 times larger than that of free oil at a given thermal maturity. As thermal maturity increases, molecular weights of n-alkanes in free oil show a more obvious reduction than sorbed oil. In addition, compared to sorbed oil, free oil is more likely to be retained at higher thermal maturity. Despite of the larger oil generation potential than gas of the immature shale sample, residual hydrocarbon generation potential of heated lacustrine shales is dominated by gaseous hydrocarbon, and consists of >90% of the potential losses before entering into gas window. Change of TOC in lacustrine shales, which roughly characterizes hydrocarbon generation process, is attributed to both the loss of hydrocarbon generation potential and the formation of pyrobitumen. Although hydrocarbon retention in shales is affected by many complex processes and is controlled by various factors, it can be virtually considered as a status when hydrocarbon generation, expulsion and retention during thermal maturation come to a balance. A “retention ratio (RR)” index is thus suggested in this study, based on experimental results from semi-open system and open-system pyrolysis. Application of RR in resource evaluation in a shale play is reasonable especially in high-mature shales, because evaporative loss of light hydrocarbon is considered in this method.

Leaf harvesting severity affects total phenolic and tannin content of fresh and dry leaves of Moringa oleifera Lam. trees growing in Gauteng, South Africa

The most important chemicals common in Moringa oleifera Lam. leaves are polyphenols and tannins. They are synthesised during development and the amount and composition are primarily dependent on environmental conditions and factors such as leaf harvesting. Trials were conducted in the Gauteng Province at the University of Pretoria Experimental Farm on Hillcrest Campus (250 45′ 08.6″S, 280 15′ 30.S" E), with an altitude of 1372 m above sea level and an average annual rainfall of 640 mm. Five year old M. oleifera tree orchard were used for this study and treatments were laid in a randomised complete block design, where 12 plants were used in each plot within a row, with a plant spacing of 2 × 2 m2. Partial harvesting was done at 25% leaf removal, while severe leaf harvesting was done at 75% leaf removal. The control trees were not harvested, but only leaf (mature and immature) samples were harvested for analyses. Leaf samples from all plots were harvested in September, November, February and May in years 1 and 2. Leaf samples (equal quantities of immature and mature leaves) from partially, severely harvested and control plots were harvested and separated into batches, one to be analysed as fresh material and the other as dry material. The dry material was placed in paper bags and allowed to immediately air dry under normal room conditions of 26 °C. Partially harvested M. oleifera leaves produced an increased accumulation of total phenolic content (TPC) 35–44 g/kg dry weight, from spring to summer season, in comparison to severe harvesting 26–35 g/kg dry weight. With severe leaf harvesting (75%), because of probable lower photosynthetic capacity, phenols across September to May of years 1 and 2 decreased. The onset of low temperatures in May resulted mostly higher TPC and tannin build up, which means that cold stress may improve more bio-active compounds in the leaves. Dark and fully developed mature leaves mainly contained the highest amount of TPC. Moringa oleifera leaves collected and dried at each harvesting interval, instead of freshly milled, do show the same quantity of TPC and tannins across the season illustrating that air drying can be used as a post-harvest handling technique, extending shelf life without losses of vital phenols. With harvesting severity as a concern in Moringa, this study confirms that the TPC and tannins in mature and immature leaves did not rise to toxic levels for human consumption.

Space Weathering and Lunar OH/H2O—Insights from Ab Initio Mie Modeling of Submicroscopic Iron

Abstract Lunar OH/H2O has been confirmed and mapped by analyzing the 3 μm absorption band in spectra acquired by the Moon Mineralogy Mapper (M3) instrument. Space weathering leads to accumulation of submicroscopic iron particles in the uppermost layer of the regolith which gradually changes the spectral signature of airless planetary bodies and thus may affect the detection of lunar OH/H2O. The contribution of this paper is twofold. (1) Our new technique combines Hapke reflectance modeling and ab initio Mie scattering calculations to model the scattering behavior of submicroscopic iron which governs the optical effects due to space weathering. (2) Thermally corrected M3 spectra of mature and immature sample points in mare and highland regions are used to assess the performance of the simulation framework and are analyzed to understand maturity-related changes of the OH/H2O band depth. We find that the simulation method can convincingly reproduce the spectral changes of maturing lunar soil. It becomes clear that there is only a minor effect on the 3 μm absorption feature. This finding makes the analysis of the lunar OH/H2O mapping largely invariant with respect to space weathering. In general, the absorption features around 1 and 2 μm are more strongly obstructed than the feature around 3 μm. Further, we discuss agglutination as the main cause for slight deviations found around the 2 μm band and layering/clustering as a likely reason to explain predicted iron particle sizes that are larger than observed.

Effect of bitumen and migrated oil on hydrocarbon generation kinetic parameters derived from Rock-Eval pyrolysis

Thermally immature whole rock and related bitumen-extracted samples were pyrolyzed. Investigating the influence of high molecular weight hydrocarbons and degradation products of non-hydrocarbon constituents of bitumen and associated migrated oil (i.e. resins and asphaltenes) on petroleum generation kinetic parameters derived from Rock-Eval pyrolysis is the main aim of this study. Based on the optimized kinetic parameters, frequency factor values of the bitumen-free samples show an obvious increase compared to whole rocks, while the range of activation energies for them is narrower. On the other hand, the predicted geological temperatures of the onset (TR 10%) and the peak hydrocarbon generation (geological Tmax) from the whole rocks are generally lower than the corresponding extracted samples. In other words, the whole rock samples underestimate the petroleum formation temperatures. Thus, the results of this study suggest the extraction of bitumen prior to Rock-Eval pyrolysis in order to obtain precise kinetic parameters for the source rocks bearing a large amounts of heavy bitumen or migrated oil.

Evolution of water content in organic-rich shales with increasing maturity and its controlling factors: Implications from a pyrolysis experiment on a water-saturated shale core sample

Abstract In the present study, a pyrolysis experiment was performed on an immature water-saturated shale core sample, and a set of artificially matured subsamples (maturity with equivalent vitrinite reflectance values of 0.67–3.20%, i.e., EqVRo values) with initial water phases was obtained. The water content of these shale samples and its influencing factors were investigated. The results show that the water content significantly varies with maturity and is closely related to the hydrocarbon generation and expulsion, clay mineral transformation, and pore structure evolution of shales. According to the changes of water content with maturity and the main influencing factors, the evolution of the water content in shales is approximately divided into three stages. At the low maturity stage (0.67% 1.36%), with increasing maturity, the water content remarkably decreases at the wet gas window (1.36% 1.90%), which is mainly controlled by the displacement drainage of gaseous hydrocarbons. In addition, the pore structure evolution of shale, which changes its water-storage capacity, also has an influence on the water content evolution.

A model for porosity evolution in shale reservoirs: An example from the Upper Devonian Duvernay Formation, Western Canada Sedimentary Basin

The influence of thermal maturity on porosity in shale samples from the Upper Devonian Duvernay Formation is examined. The samples span a maturity range from immature to the wet gas window. Porosity decreases from immature to the oil window, primarily because of compaction. Relatively high porosity of wet gas window samples is ascribed to formation of secondary organic pores, feldspar dissolution pores, and primary pore preservation by the quartz framework. The final decline in the porosity of the dry gas window samples is explained by greater compaction, the disappearance of secondary organic pores, and feldspar dissolution pores. Porosity correlates positively to quartz content and negatively to carbonate content; no relationship was evident between porosity and clay or total organic carbon content. No obvious correlations exist between rock composition and permeability except that SiO2 content shows a weakly positive correlation to permeability. Permeability is highest in immature samples, which have the greatest pore and pore-throat sizes. Nitrogen adsorption and mercury injection analysis show that pore and pore-throat sizes decrease with increasing maturity. Visible pores, imaged by scanning electron microscopy and helium ion microscopy, exist as organic pores, including bubblelike pores developed within organic matter (OM) and fissure-type pores, intraparticle pores mainly developed within carbonate grains, and interparticle pores either within a clay-rich matrix or between rigid mineral grains. In immature samples, the primary pores are interparticle pores between clay minerals and other mineral grains. The OM fissures are ubiquitous in oil window samples, and secondary bubblelike OM–hosted pores are well developed within gas window samples.

Identification of piRNAs and piRNA clusters in the testes of the Mongolian horse

P-element induced wimpy testis-interacting RNAs (piRNAs) are essential for testicular development and spermatogenesis in mammals. Comparative analyses of the molecular mechanisms of spermatogenesis among different organisms are therefore dependent on accurate characterizations of piRNAs. At present, little is known of piRNAs in non-model organisms. Here, we characterize piRNAs in the Mongolian horse, a hardy breed that reproduces under extreme circumstances. A thorough understanding of spermatogenesis and reproduction in this breed may provide insights for the improvement of fecundity and reproductive success in other breeds. We identified 4,936,717 piRNAs and 7,890 piRNA clusters across both testicular developmental stages. Of these, 2,236,377 putative piRNAs were expressed in the mature samples only, and 2,391,271 putative piRNAs were expressed in the immature samples only. Approximately 3,016 piRNA clusters were upregulated in the mature testes as compared to the immature testes, and 4,874 piRNA clusters were downregulated. Functional and pathway analyses indicated that the candidate generating genes of the predicted piRNAs were likely involved in testicular development and spermatogenesis. Our results thus provide information about differential expression patterns in genes associated with testicular development and spermatogenesis in a non-model animal.

Cancer-Associated Fibroblasts and Desmoplastic Reactions Related to Cancer Invasiveness in Patients With Colorectal Cancer.

Purpose We evaluated the relationship of cancer-associated fibroblasts (CAFs) and desmoplastic reactions with cancer invasiveness and long-term outcomes in patients with colorectal cancer (CRC).Methods Histologic evaluation of mature CAFs and desmoplasia was performed by observing the collagen fiber structure and fibroblast cytomorphology in the intratumoral stroma and invasive front of CRC tissues. Cancer-cell invasiveness was evaluated using lymphatic invasion, vascular invasion, perineural invasion, tumor budding, and tumor growth patterns. Overall survival and systemic recurrence were analyzed. A network analysis was performed between CAF maturation, desmoplastic reaction, and cancer invasiveness.Results The proportions of mature CAFs in the intratumoral stroma and the invasive front were 57.6% and 60.3%, respectively. Epidermal growth factor receptor (EGFR) overexpression was significantly higher in the mature CAFs in the invasive front as compared to immature CAFs. Lymphatic invasion increased as the number of mature fibroblasts in the intratumoral stroma increased. Tumor budding was observed in almost half of both mature and immature stroma samples and occurred more frequently in infiltrating tumors. On network analysis, well-connected islands were identified that was associated with EGFR overexpression, CAF maturation, and infiltrating tumor growth patterns leading to tumor budding.Conclusion The maturity of CAFs and desmoplastic reactions were associated with cancer invasion. However, the cytomorphologic characteristics of CAFs were insufficient as an independent prognostic factor for patients with CRC.

Leukoencephalomalacia in horses associated with immature corn consumption

ABSTRACT: Horse leukoencephalomalacia (ELEM) is a disease caused by the ingestion of mycotoxins (fumonisins) produced by fungi of the genus Fusarium that infect corn and/or its byproducts. This disease has been described by ingestion of mature corn with humidity above 15% at temperatures below 20°C. The aim of this paper was to report an outbreak of leukoencephalomalacia in horses fed with immature corn. Two horses out of three showed neurological signs approximately seven days after eating immature corn in its reproductive phase (R2, milky grains). Corn was harvested and administered directly to the animals, with no storage. Deaths occurred approximately 24 hours after the onset of clinical signs. Grossly, there were multifocal dark red to brown areas in the white matter of the telencephalon and hyppocampus and thalamus. Histologically, there was edema and hemorrhage in several areas of the telencephalon white matter, which corresponded to dark red to brown areas observed in the macroscopy. There was also foci of malacia with presence of reactive astrocytes with abundant eosinophilic cytoplasm and inflammatory cells. Diffuse capillary wall degeneration and endothelial cell swelling were also observed. Two ppm of fumonisin were detected by immunoaffinity column method (VICAM) in the immature corn sample. The water activity in this cereal, when the grain is still milky, is 0.98 and can predispose it to growth of mycotoxin-producing fungi. In the present case, fumonisin was found in milky grains in the beginning of the reproductive phase (R2), which suggested that even immature corn may be infected by Fusarium spp. and should not be administered to horses.

Prognostic Impact of Notch Signaling in Acute Myeloid Leukemia (AML)

Background: Notch signaling is a developmental pathway involved in normal and malignant hematopoiesis. Mutations in Notch genes lead to T-ALL and are associated with poor prognosis in B-CLL. However its role in AML is still under investigation, with controversial results. In addition, although the pathway consists of 4 receptors and 5 ligands, many studies are mostly based on single receptor or ligand.Aims: This study was conducted to determine if the expression level of each Notch receptor and ligand are associated with known prognostic factors and patient's survival.Methods: AML primary cells were collected from 79 AML patients after informed consent. The follow-up was for 36 months. Flow cytometry analysis was used to study the expression of each Notch receptor and ligand. Prognostics or risk factors considered were sex, white blood counts, FAB and cytogenetics. The Mann-Whitney test was used for analyzing differences in expression levels between two groups. Spearman test was used for correlation between Notch expression levels and prognostics factors. Differences in overall (OS) and progression free (PFS) survival were established through Gehan-Breslow-Wilcoxon test.Results: Consistently with previous findings, we found expression of Notch1, Notch2, Notch3, Notch4, Jagged1, Jagged2 and DLL3 in AML samples. There were no differences in expression levels between male and female. For each receptor or ligand, higher expression levels were found in more immature samples (M0, M1, and M2). Notch3, Notch4 and Jagged2 were enriched in adverse cytogenenetics risk groups compared to favorable cytogenetics risk patients. Then, for each receptor or ligand, patients were divided into two groups; patients with higher expression levels and patients with lower expression levels. Analyzing OS and PFS, we found that patients with lower expression levels of Notch4, Jagged2 and DLL3 displayed a longer survival compared to patients with higher expression levels.Conclusion: Given its oncogenic role in T-ALL and other malignancies Notch1 has been the more studied receptors in hematological malignancies. However, we have previously demonstrated that Notch4, DLL3 and Jagged2 are all involved in survival of AML and B-ALL cells. Studying the prognostic value of all Notch receptors and ligands, the current research clearly shows that higher levels of Notch4 and Jagged2 are found in poor cytogenetics risk groups and are associated with a shorter patient's survival. These demonstrations suggest that expression levels of Notch receptors and ligands in AML patient's samples at diagnostic could stand as prognostic marker for clinical care. DisclosuresNo relevant conflicts of interest to declare.

An integrated diagnostic setup for the morphological and molecular identification of the Ceratitis FAR complex (C. anonae, C. fasciventris, C. rosa, C. quilicii, Diptera, Tephritidae).

The Ceratitis FAR complex (Diptera, Tephritidae) includes four economically important frugivorous flies (Ceratitis anonae, Ceratitis fasciventris, Ceratitis quilicii, Ceratitis rosa) whose immature stages and adult females cannot be properly resolved through morphological identification. In order to develop a simplified molecular tool for the identification of two of these species (C. rosa, C. quilicii), we selected a subset of six microsatellite markers out of a panel of 16 loci that were previously developed for the molecular differentiation of the taxa within the complex. These six markers were first tested in silico and then used for the actual genotyping of C. quilicii and C. rosa, resulting in the correct identification of all male reference specimens. Here, we propose an integrated morphological and molecular setup for the identification of the four species of the FAR complex. The decision map relies on preliminary DNA barcoding or morphological identification (when possible) to exclude species not belonging to the complex followed by (a) morphological identification of all adult male specimens and female C. anonae, (b) molecular identification via a panel of 16 microsatellite markers for immature stages, damaged vouchers and samples potentially including adult female C. fasciventris/C. quilicii/C. rosa and (c) molecular identification via a reduced panel of six microsatellite markers for samples including only C. quilicii and C. rosa. This simplified diagnostic setup was profitably implemented in the framework of the ERAfrica fruit fly project and will help correctly identify species within the FAR complex for their early detection and monitoring.