Biogenic methane in shale gas and coal bed methane : a review of current knowledge and gaps

Biogenic CH4 generation has been observed in many shallow, low temperature shale gas basins and coal seams. The depletion of conventional resources and the increasing demand of natural gas for human consumption have spurred the development of so-called unconventional gas resources such as shale gas (SG) and coal-bed methane (CBM). Such unconventional systems represent the opportunity for the stimulation of biogenic CH4 generation. Biogenic CH4 in shale and coal is produced by anaerobic biodegradation of organic matter (OM): methanogenic Archaea represent only the final step of biogenic CH4 generation. Several communities of microorganisms are involved in the initial breakdown of complex geopolymers and the production of intermediate compounds used by methanogens. There are several key knowledge gaps on biogenic CH4 production in unconventional gas systems, such as the exact fraction of bioavailable OM, the microbial communities involved and how they can be stimulated to enhance microbial methanogenesis. Progress on biodegradation studies, isotopic signatures, as well as DNA analyses and proteomics could help unravel interactions within the syntrophic community involved in the methanogenic biodegradation of OM. Questions also remain regarding the environmental impact of unconventional gas production, such as water quality and the mobility of toxic metals and radionuclides. The answers to these questions might have implications for both recovery practices and a sustainable development of unconventional resources. This review summarises the current knowledge regarding biogenic CH4 in SG and CBM: from the nature of the rocks to the producing microbial community and the indicators of biogenic CH4, illustrating how these two environments show remarkably similar opportunities for the stimulation of biogenic CH4 generation

Performance and bacterial community shifts during phosphogypsum biotransformation

Phosphogypsum (PG) is an industrial waste composed mainly by sulfate, turning it a suitable sulfate source for sulfate-reducing bacteria (SRB). In the present work, the capability of two SRB communities, one enriched from Portuguese PG (culture PG) and the other from sludge from a wastewater treatment plant (culture WWT-1), to use sulfate from PG was compared. In addition, the impact of this sulfate-rich waste in the microbial community was assessed. The highest efficiency in terms of sulfate reduction was observed with culture WWT-1. The bacterial composition of this culture was not significantly affected when sodium sulfate from the nutrient medium was replaced by PG as a sulfate source. Next generation sequencing (NGS) showed that this community was phylogenetically diverse, composed by bacteria affiliated to Clostridium, Arcobacter, and Sulfurospirillum genera and by SRB belonging to Desulfovibrio, Desulfomicrobium, and Desulfobulbus genera. In contrast, the bacterial structure of the community enriched from PG was modified when sodium sulfate was replaced by PG as the sulfate source. This culture, which showed the poorest performance in the use of sulfate from PG, was mainly composed by SRB related to Desulfosporosinus genus. The present work provides new information regarding the phylogenetic characterization of anaerobic bacterial communities with the ability to use PG as sulfate donor, thus, contributing to improve the knowledge of microorganisms suitable to be used in PG bioremediation. Additionally, this paper demonstrates that an alternative to lactate and low-cost carbon source (wine wastes) can be used efficiently for that purpose

Retargeted adenoviruses for radiation-guided gene delivery

The combination of radiation with radiosensitizing gene delivery or oncolytic viruses promises to provide an advantage that could improve the therapeutic results for glioblastoma. X-rays can induce significant molecular changes in cancer cells. We isolated the GIRLRG peptide that binds to radiation-inducible 78 kDa glucose-regulated protein (GRP78), which is overexpressed on the plasma membranes of irradiated cancer cells and tumor-associated microvascular endothelial cells. The goal of our study was to improve tumor-specific adenovirus-mediated gene delivery by selectively targeting the adenovirus binding to this radiation-inducible protein. We employed an adenoviral fiber replacement approach to conduct a study of the targeting utility of GRP78-binding peptide. We have developed fiber-modified adenoviruses encoding the GRP78-binding peptide inserted into the fiber-fibritin. We have evaluated the reporter gene expression of fiber-modified adenoviruses in vitro using a panel of glioma cells and a human D54MG tumor xenograft model. The obtained results demonstrated that employment of the GRP78-binding peptide resulted in increased gene expression in irradiated tumors following infection with fiber-modified adenoviruses, compared with untreated tumor cells. These studies demonstrate the feasibility of adenoviral retargeting using the GRP78-binding peptide that selectively recognizes tumor cells responding to radiation treatment

From Marx to Gramsci to us: Laboratory to prison, and back

Marx and Gramsci remain two of the most constant presences and inspirations for those on the left. Yet there is a persistent sense that we have still to get them right. Perhaps this indicates that sources like this are now fully classics, to be returned, and returned to. In the case of Marx and Gramsci, a series of major works published in the Brill Historical Materialism series breaks new ground as well as returning to older controversies, both resolved and unresolved. Apart from remaining arguments concerning the status of materials unpublished in their own lifetimes, the major tension that emerges here is that between the task of immanent, contextual philology and the challenge of reading ‘Marx for today’ or ‘Gramsci for today’. The tension between text and context, and the question of what travels, conceptually persists

Salinity Controls on Steel Biocorrosion relevant to the Disposal of High-level Radioactive Waste

In a geological disposal facility (GDF) for spent fuel and high-level radioactive waste, the canister serves as one of the main engineered barriers. The resistance of the canister to degradation processes such as microbially influenced corrosion (MIC) needs be characterised to support GDF environmental safety cases. Here the impacts of salinity on sulfate-reducing bacterial (SRB) activity and associated MIC were explored in 84-day batch incubations at 30 ◦C. A 5 % standard bentonite slurry (MX80) in a low-salinity (0.1 g l− 1 NaCl) artificial groundwater containing lactate added as an electron donor provided suitable conditions for the proliferation of SRB. Corrosion rates of carbon steel (080-A15) coupon surfaces in microcosms amended with lactate were > 2.5 times greater than those absent of lactate, and sterile controls. At an increased salinity of 12.4 g l− 1, adding lactate resulted in 2 times the corrosion depth of sterile conditions, but at 50 g l− 1 there was no detected microbial activity, and no pronounced increase in corrosion by adding lactate compared to sterile controls. Here, microbial activity and subsequent MIC was suppressed at high salinity (50 g l− 1) suggesting that groundwater composition played a controlling role in SRB biocorrosion. The relevance to geodisposal scenarios, where bentonite is used to protect and support the waste canister, is discussed

Creating the cultures of the future: cultural strategy, policy and institutions in Gramsci. Part one: Gramsci and cultural policy studies: some methodological reflections

Gramsci’s writings have rarely been discussed and used systematically by scholars in cultural policy studies, despite the fact that in cultural studies, from which the field emerged, Gramsci has been a major source of theoretical concepts. Cultural policy studies were, in fact, theorised as an anti-Gramscian project between the late 1980s and the early 1990s, when a group of scholars based in Australia advocated a major political and theoretical reorientation of cultural studies away from hegemony theory and radical politicisation, and towards reformist-technocratic engagement with the policy concerns of contemporary government and business. Their criticism of the ‘Gramscian tradition’ as inadequate for the study of cultural policy and institutions has remained largely unexamined in any detail for almost twenty years and seems to have had a significant role in the subsequent neglect of Gramsci’s contribution in this area of study. This essay, consisting of three parts, is an attempt to challenge such criticism and to provide an analysis of Gramsci’s writings, with the aim of proposing a more systematic contribution of his work to the theoretical development of cultural policy studies. In Part One, I question the use of the notion of ‘Gramscian tradition’ made by its critics and challenge the claim that it was inadequate for the study of cultural policy and institutions. In parts Two and Three, I consider Gramsci’s specific writings on questions of cultural strategy, policy and institutions, which have so far been overlooked by scholars, arguing that they provide further analytical insights to those offered by his more general concepts. More specifically, in Part Two, I consider Gramsci’s pre-prison writings and political practice in relation to questions of cultural strategy and institutions. I argue that the analysis of these early texts, which were written in the years in which Gramsci was active in party organisation and leadership, is fundamental not only for understanding the nature of Gramsci’s early and continued involvement with questions of cultural strategy and institutions, but also as a key for deciphering and interpreting cultural policy themes that he later developed in the prison notebooks, and which originated in earlier debates. Finally, in Part Three, I carry out a detailed analysis of Gramsci’s prison notes on questions of cultural strategy, policy and institutions, which enrich the theoretical underpinnings for critical frameworks of analysis as well as for radical practices of cultural strategy, cultural policy-making and cultural organisation. I then answer the question of whether Gramsci’s insights amount to a theory of cultural policy

Targeting NAD+ Metabolism to Enhance Radiation Therapy Responses

Nicotinamide adenine dinucleotide (NAD+) metabolism is integrally connected with the mechanisms of action of radiation therapy and is altered in many radiation-resistant tumors. This makes NAD+ metabolism an ideal target for therapies that increase radiation sensitivity and improve patient outcomes. This review provides an overview of NAD+ metabolism in the context of the cellular response to ionizing radiation, as well as current therapies that target NAD+ metabolism to enhance radiation therapy responses. Additionally, we summarize state-of-the-art methods for measuring, modeling, and manipulating NAD+ metabolism, which are being used to identify novel targets in the NAD+ metabolic network for therapeutic interventions in combination with radiation therapy

Extracting Gene Networks for Low-Dose Radiation Using Graph Theoretical Algorithms

Genes with common functions often exhibit correlated expression levels, which can be used to identify sets of interacting genes from microarray data. Microarrays typically measure expression across genomic space, creating a massive matrix of co-expression that must be mined to extract only the most relevant gene interactions. We describe a graph theoretical approach to extracting co-expressed sets of genes, based on the computation of cliques. Unlike the results of traditional clustering algorithms, cliques are not disjoint and allow genes to be assigned to multiple sets of interacting partners, consistent with biological reality. A graph is created by thresholding the correlation matrix to include only the correlations most likely to signify functional relationships. Cliques computed from the graph correspond to sets of genes for which significant edges are present between all members of the set, representing potential members of common or interacting pathways. Clique membership can be used to infer function about poorly annotated genes, based on the known functions of better-annotated genes with which they share clique membership (i.e., “guilt-by-association”). We illustrate our method by applying it to microarray data collected from the spleens of mice exposed to low-dose ionizing radiation. Differential analysis is used to identify sets of genes whose interactions are impacted by radiation exposure. The correlation graph is also queried independently of clique to extract edges that are impacted by radiation. We present several examples of multiple gene interactions that are altered by radiation exposure and thus represent potential molecular pathways that mediate the radiation response

Oncogene advance online publication

Inadvertent mammalian tissue exposures to low doses of ionizing radiation (IR) after radiation accidents, remediation of radioactive-contaminated areas, space travel or a dirty bomb represent an interesting trauma to an organism. Possible low-dose IR-induced bystander effects could impact our evaluation of human health effects, as cells within tissue are not equally damaged after doses of IR p10 cGy. To understand tissue responses after low IR doses, we generated a reporter system using the human clusterin promoter fused to firefly luciferase (hCLUp-Luc). Secretory clusterin (sCLU), an extracellular molecular chaperone, induced by low doses of cytotoxic agents, clears cell debris. Low-dose IR (X2 cGy) exposure induced hCLUp-Luc activity with peak levels at 96 h, consistent with endogenous sCLU levels. As doses increased (X1 Gy), sCLU induction amplitudes increased and time-to-peak response decreased. sCLU expression was stimulated by insulin-like growth factor-1, but suppressed by p53. Responses in transgenic hCLUp-Luc reporter mice after low IR doses showed that specific tissues (that is, colon, spleen, mammary, thymus and bone marrow) of female mice induced hCLUp-Luc activity more than male mice after whole body (X10 cGy) irradiation. Tissue-specific, non-linear dose-and time-responses of hCLUp-Luc and endogenous sCLU levels were noted. Colon maintained homeostatic balance after 10 cGy. Bone marrow responded with delayed, but prolonged and elevated expression. Intraperitoneal administration of a-transforming growth factor (TGF)b1 (1D11), but not control (13C4) antibodies, immediately following IR exposure abrogated CLU induction responses. Induction in vivo also correlated with Smad signaling by activated TGFb1 after IR. Mechanistically, media with elevated sCLU levels suppressed signaling, blocked apoptosis and increased survival of TGFb1-exposed tumor or normal cells. Thus, sCLU is a pro-survival bystander factor that abrogates TGFb1 signaling and most likely promotes wound healing

Geochemistry and microbiology of tropical serpentine soils in the Santa Elena Ophiolite, a landscape-biogeographical approach

This is the final version. Available on open access from BMC via the DOI in this recordAvailability of data and materials: The datasets supporting the conclusions of this article are available in https://doi.org/10.17632/w6cdt3sn99.4 with CC BY 4.0 license, in NCBI SRA (Sequence Read Archive; http://www.ncbi.nlm.nih.gov/sra/, under the project accession number: PRJNA606410) and within the article and its additional file.The Santa Elena Ophiolite is a well-studied ultramafic system in Costa Rica mainly comprised of peridotites. Here, tropical climatic conditions promote active laterite formation processes, but the biogeochemistry of the resulting serpentine soils is still poorly understood. The aim of this study was to characterize the soil geochemical composition and microbial community of contrasting landscapes in the area, as the foundation to start exploring the biogeochemistry of metals occurring there. The soils were confirmed as Ni-rich serpentine soils but differed depending on their geographical location within the ophiolite area, showing three serpentine soil types. Weathering processes resulted in mountain soils rich in trace metals such as cobalt, manganese and nickel. The lowlands showed geochemical variations despite sharing similar landscapes: the inner ophiolite lowland soils were more like the surrounding mountain soils rather than the north lowland soils at the border of the ophiolite area, and within the same riparian basin, concentrations of trace metals were higher downstream towards the mangrove area. Microbial community composition reflected the differences in geochemical composition of soils and revealed potential geomicrobiological inputs to local metal biogeochemistry: iron redox cycling bacteria were more abundant in the mountain soils, while more manganese-oxidizing bacteria were found in the lowlands, with the highest relative abundance in the mangrove areas. The fundamental ecological associations recorded in the serpentine soils of the Santa Elena Peninsula, and its potential as a serpentinization endemism hotspot, demonstrate that is a model site to study the biogeochemistry, geomicrobiology and ecology of tropical serpentine areas.Ministerio de Ciencia, Tecnología y Telecomunicaciones (MICITT), Government of Costa RicaUniversidad de Costa RicaMICITTNatural Environment Research Council (NERC