Petrographical and geochemical evidences for paragenetic sequence interpretation of diagenesis in mixed siliciclastic–carbonate sediments: Mozduran Formation (Upper Jurassic), south of Agh-Darband, NE Iran

The Upper Jurassic Mozduran Formation with a thickness of 420 m at the type locality is the most important gas-bearing reservoir in NE Iran. It is mainly composed of limestone, dolostone with shale and gypsum interbeds that grade into coarser siliciclastics in the easternmost part of the basin. Eight stratigraphic sections were studied in detail in south of the Agh-Darband area. These analyses suggest that four carbonate facies associations and three siliciclastic lithofacies were deposited in shallow marine to shoreline environments, respectively. Cementation, compaction, dissolution, micritization, neomorphism, hematitization, dolomitization and fracturing are diagenetic processes that affected these sediments.Stable isotope variations of δ18O and δ13C in carbonate rocks show two different trends. High depletion of δ18O and low variation of δ13C probably reflect increasing temperatures during burial diagenesis, while the higher depletion in carbon isotope values with low variations in oxygen isotopes are related to fresh water flushing during meteoric diagenesis. Negative values of carbon isotopes may have also resulted from organic matter alteration during penetration of meteoric water. Fe and Mn enrichment with depletion of δ18O also supports the contention that alteration associated with higher depletion in carbon isotope values with low variations in oxygen isotopes took place during meteoric diagenesis. The presence of bright luminescence indicates redox conditions during precipitation of calcite cement

ADAM8 signaling drives neutrophil migration and ARDS severity

Acute respiratory distress syndrome (ARDS) results in catastrophic lung failure and has an urgent, unmet need for improved early recognition and therapeutic development. Neutrophil influx is a hallmark of ARDS and is associated with the release of tissue-destructive immune effectors, such as matrix metalloproteinases (MMPs) and membrane-anchored metalloproteinase disintegrins (ADAMs). Here, we observed using intravital microscopy that Adam8–/– mice had impaired neutrophil transmigration. In mouse pneumonia models, both genetic deletion and pharmacologic inhibition of ADAM8 attenuated neutrophil infiltration and lung injury while improving bacterial containment. Unexpectedly, the alterations of neutrophil function were not attributable to impaired proteolysis but resulted from reduced intracellular interactions of ADAM8 with the actin-based motor molecule Myosin1f that suppressed neutrophil motility. In 2 ARDS cohorts, we analyzed lung fluid proteolytic signatures and identified that ADAM8 activity was positively correlated with disease severity. We propose that in acute inflammatory lung diseases such as pneumonia and ARDS, ADAM8 inhibition might allow fine-tuning of neutrophil responses for therapeutic gain

Broken replication forks trigger heritable DNA breaks in the terminus of a circular chromosome

<p><u>(A) Circular map of the <i>E</i>. <i>coli</i> chromosome</u>: <i>oriC</i>, <i>dif</i> and <i>terD</i> to <i>terB</i> sites are indicated. Numbers refer to the chromosome coordinates (in kb) of MG1655. (<u>B) Linear map of the terminus region:</u> chromosome coordinates are shown increasing from left to right, as in the marker frequency panels (see Figure 1C for example), therefore in the opposite direction to the circular map. In addition to <i>dif</i> and <i>ter</i> sites, the positions of the <i>parS</i>_pMT1 sites used for microscopy experiments are indicated. (<u>C) MFA analysis of terminus DNA loss in the <i>recB</i> mutant</u>: sequence read frequencies of exponential phase cells normalized to the total number of reads were calculated for each strain. Ratios of normalized reads in isogenic wild-type and <i>recB</i> mutant are plotted against chromosomal coordinates (in kb). The profile ratio of the terminus region is enlarged and the profile of the corresponding entire chromosomes is shown in inset. Original normalized profiles used to calculate ratios are shown in <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1007256#pgen.1007256.s005" target="_blank">S1 Fig</a>. The position of <i>dif</i> is indicated by a red arrow. The <i>ter</i> sites that arrest clockwise forks (<i>terC</i>, <i>terB</i>, green arrow) and counter-clockwise forks (<i>terA</i>, <i>terD</i>, blue arrow) are shown. <u>(D) Schematic representation of focus loss in the <i>recB</i> mutant:</u> Time-lapse microscopy experiments showed that loss of a focus in the <i>recB</i> mutant occurs concomitantly with cell division in one of two daughter cells, and that the cell that keeps the focus then generates a focus-less cell at each generation. The percentage of initial events was calculated as the percentage of cell divisions that generate a focus-less cell, not counting the following generations. In this schematic representation, two initial events occurred (generations #2 and #7) out of 9 generations, and focus loss at generation #2 is heritable. Panels shown in this figure were previously published in [<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1007256#pgen.1007256.ref019" target="_blank">19</a>] and are reproduced here to introduce the phenomenon.</p

A Bioinformatics Filtering Strategy for Identifying Radiation Response Biomarker Candidates

The number of biomarker candidates is often much larger than the number of clinical patient data points available, which motivates the use of a rational candidate variable filtering methodology. The goal of this paper is to apply such a bioinformatics filtering process to isolate a modest number (<10) of key interacting genes and their associated single nucleotide polymorphisms involved in radiation response, and to ultimately serve as a basis for using clinical datasets to identify new biomarkers. In step 1, we surveyed the literature on genetic and protein correlates to radiation response, in vivo or in vitro, across cellular, animal, and human studies. In step 2, we analyzed two publicly available microarray datasets and identified genes in which mRNA expression changed in response to radiation. Combining results from Step 1 and Step 2, we identified 20 genes that were common to all three sources. As a final step, a curated database of protein interactions was used to generate the most statistically reliable protein interaction network among any subset of the 20 genes resulting from Steps 1 and 2, resulting in identification of a small, tightly interacting network with 7 out of 20 input genes. We further ranked the genes in terms of likely importance, based on their location within the network using a graph-based scoring function. The resulting core interacting network provides an attractive set of genes likely to be important to radiation response

The relation between glauconitization and calcite cementation with the relative sea level changes in the mixed silisiclastic- carbonate sediments of Aitamir Formation (Mid-Cretaceous), Kopet-Dagh basin

Two diagenetic processes of glauconitization and calcite cementation and relation those to sea level changes in the siliciclastic-carbonate sediments of the Aitamir Formation (Albian-Cenomanian) in Kopet-Dagh basin have studied. The lower sandstone unit consists of mainly sandstone intercalated with shale and limestone and the upper shale units are two major sediments of this formation. The sandstone of the lower unit based on composition and their relations with sea level change subdivided into two transgressive and regressive facies and in this relation, show different pathways of the diagenesis. In the transgressive facies display by high content of the shell remains, with development in diagenesis shows extensive cementation and a little compaction during burial stage. In the regressive sandstone, characterized by little skeletal elements, display little calcite cements and high burial compaction. The glauconitic grains and calcite cementation in the Aitamir Formation concentrated in the transgressive facies and especially in the maximum flooding surface and transgresive surface. Whereas, in the regressive facies the glauconitic grains and calcite cementation is principally low. Moreover, the transgressive system tract and maximum flooding surface is characterized by mature and high mature glauconitic grains

Using electrofacies cluster analysis to evaluate shale-gas potential: Carynginia Formation, Perth Basin, Western Australia

Unconventional hydrocarbon resources are becoming increasingly important to keep pace with the global rising energy demands. Identification of reservoir electrofacies plays an important role in petro physical evaluation of hydrocarbon bearing intervals. In order to provide criteria to highlight the sweet spots for shale-gas in the Perth Basin, electrofacies analysis was done for Carynginia Formation, using cluster analysis techniques. This analysis was carried out by identifying electrofacies from wireline well log responses and from the available core data, focused in six selected wells. Three types of situations have been defined, regarding shale-gas potential and characteristic electrofacies identification – Type I, Gas-window wells with shale-gas; Type II, oil-window wells with shale-gas; Type III, non-mature wells with no shale-gas. From the 30 identified electrofacies, three appear as more promising in terms of shale-gas bearing layers of the Carynginia formation. This method may be used to help detecting shale-gas targets based on electrofacies analysis

The Evaluation of Reservoir Quality of Sarvak Formation in One of Oil Fields of the Persian Gulf

Sarvak formation, with the middle cretaceous (Cenomanian) age, is one of the stratigraphic units of the Bangestan group in the southern Iran. The carbonate rocks of this formation form the reservoir rock in the study field. Generally, Sarvak formation is subdivided into three members including Mishrif, Khatiyah, and Maddud in the Persian Gulf, and the average thickness of the reservoir unit (i.e. Mishrif) in the field varies from 55 to 73 meters. The purpose of this study is to investigate the petrophysical properties of Sarvak formation in terms of rock type and hydraulic flow unit analysis. In this context, at the first step, the geological characteristics (i.e. sedimentary texture and diagenetic features) of the reservoir rocks were studied in this field. Then, the core porosity and permeability data obtained from different facies plots of the petrophysical diagram of Lucia in which different facies distribute on the three petrophysical classes of diagram based on sedimentary and diagenetic characteristics resulted in the differentiation of eight rock types. Also, using the concept of reservoir quality index (RQI) and flow zone index (FZI), eight hydraulic flow units were recognized and named as A, B, C, D, E, F, G, and H in an ascending reservoir quality order. The results show a good relation between different identified rock types and HFUs in the reservoir, which can be interpreted based on geological attributes

Provenance of the Oligo-Miocene Zivah Formation, NW Iran, assessed using heavy mineral assemblage, detrital clinopyroxene and detrital apatite geochemistry

Heavy mineral analysis and geochemical analysis of detrital clinopyroxene and apatite have been used to determine provenance and tectonic setting of the Oligocene-Miocene Zivah Formation, in three outcrop sections from the Moghan area in northwest Iran. The composition of assemblages from the Zivah sandstones have a majority of clinopyroxene, apatite, biotite and opaque minerals with minor amounts of hornblende, zircon, garnet and epidote. The abundance of a mafic heavy-mineral suite such as clinopyroxene relative to metamorphic and felsic heavy mineral suites such as epidote, garnet and zircon indicates a convergent tectonic setting. Geochemistry of detrital clinopyroxenes from the Zivah Formation also indicates that these detrital grains probably crystallized from calk-alkaline magmas. They also show orogenic tectonic setting at the time of Zivah deposition. This is consistent with the derivation of these sediments from areas with calc-alkaline volcanic rocks like Talysh and Lesser Caucasus as a result of Caucasus orogeny. Compositions of detrital apatites of the Zivah Formation are also consistent with the widespread distribution of unfractionated (mafic / intermediate) volcanic rocks of both alkaline and calc-alkaline composition in the Lesser Caucasus and Talysh