Gases in the near-surface zone of the reclaimed Barycz municipal waste landfill – a case study from southern Poland

The formation of biogas at municipal landfills and the significant emission of greenhouse gases from these facilities into the environment were the main reasons for analyzing the molecular composition of soil gas in the near-surface zone at the reclaimed part of the Barycz municipal waste landfill. The relations between the studied components (methane, carbon dioxide, light hydrocarbons and non-hydrocarbon components) and impact of the magnitude of recorded concentrations of methane and carbon dioxide on their emission to the atmosphere were evaluated. Two profiles were determined, along which 41 soil and landfill gas samples were taken at 20-meter intervals. At the same time, emissions were measured at each sampling point using a static chamber with a portable fluxometer. Chromatographic analysis showed that the concentrations of methane and carbon dioxide fluctuated in the ranges: 2.1 ppm – 76 vol% and 0.04 ppm – 11 vol%, respectively. Relatively high concentrations of these gases were determined at many of the measurement points, and this was particularly evident at the A-A’ profile, indicating stronger biochemical processes in this part of the landfill, or lateral migration of methane from the neighbouring stage II of the landfill, where biogas extraction is currently taking place. In addition, significant correlations between methane, carbon dioxide, and oxygen were demonstrated, indicating ongoing methane fermentation processes. Based on the study, it can be concluded that the southern part of the A-A’ profile is an optimal place to locate a degassing well from which biogas production could be used. However, the research is only preliminary and, it will be necessary to extend the soil gas tests before the final decision on the location of the well is made. Moreover, it has been shown that the concentrations of methane and carbon dioxide measured at points located outside the landfill were low. This means that generated biogas probably does not migrate beyond the boundaries of reclaimed waste landfill, but this will need to be confirmed by performing additional soil gas tests inside and outside the landfill area. The preliminary assessment of the effectiveness of the reclamation carried out was confirmed by the negligible values of the measured methane and carbon dioxide emissions on the surface

Fluctuations in methane and carbon dioxide concentrations in the nearsurface zone and their genetic characterization in abandoned and active coal mines in the SW part of the Upper Silesian Coal Basin, Poland

The objective of this paper is to determine the origin and variability of methane and carbon dioxide concentrations in the near-surface zone and of coalbed methane in the SW part of the Chwałowice Trough and adjacent areas of the Main Syncline of the Upper Silesian Coal Basin (USCB). For this purpose soil-gas samples were taken at 202 measuring points, arranged along 5 profiles located in the mining area of the abandoned 1 Maja mine and directly adjacent areas as well as in the vicinity of four abandoned and remediated mining shafts. The maximum methane and carbon dioxide concentrations in the gas samples measured exceeds 22 and 9 vol%, respectively. The carbon isotope composition of methane and carbon dioxide was determined in samples in which elevated concentrations of these gases were found. Moreover, seven coalbed gas samples and bituminous coals were collected from coal seams exclusively from virgin parts of the Anna, Marcel, Jastrzębie, and Zofiówka mines. These data were supplemented with results of archival research for genetic interpretation of coalbed gases. Research reveals that typical humic low- and medium-volatile bituminous coals occur in Mississippian and Pennsylvanian coal-bearing strata in the study area. Fluctuations in methane and carbon dioxide concentration in the near-surface zone are related to the lithostratigraphy and tectonics of the area as well as to complicated methane depth distribution. Faults may play an important role in the microseepage of gases from deep to the near-surface zone. The connection of near-surface gases with subsurface gases was confirmed by similar stable carbon isotope composition in the methane recorded in the soil-gas samples and in the gas samples from the coal seams and sandstones of the Carboniferous formations. Distribution of anomalous methane concentrations recorded in soil-gas samples taken from profiles may indicate natural gas accumulations in the top zone of the Pennsylvanian coal-bearing formations. One example of this kind of accumulation is the Marklowice natural gas field, located within the mining area of the Marcel coal mine. Relatively high methane concentrations measured in soil gas in the vicinity of shafts I and III indicate that the degassing systems of closed and remediated mining shafts are not fully effective. Increases in carbon dioxide concentrations in the surface zone and frequent associated decreases in methane concentration were most often the result of microbial methane oxidation

Investigation of the Genes Involved in Antigenic Switching at the vlsE Locus in Borrelia burgdorferi: An Essential Role for the RuvAB Branch Migrase

Persistent infection by pathogenic organisms requires effective strategies for the defense of these organisms against the host immune response. A common strategy employed by many pathogens to escape immune recognition and clearance is to continually vary surface epitopes through recombinational shuffling of genetic information. Borrelia burgdorferi, a causative agent of Lyme borreliosis, encodes a surface-bound lipoprotein, VlsE. This protein is encoded by the vlsE locus carried at the right end of the linear plasmid lp28-1. Adjacent to the expression locus are 15 silent cassettes carrying information that is moved into the vlsE locus through segmental gene conversion events. The protein players and molecular mechanism of recombinational switching at vlsE have not been characterized. In this study, we analyzed the effect of the independent disruption of 17 genes that encode factors involved in DNA recombination, repair or replication on recombinational switching at the vlsE locus during murine infection. In Neisseria gonorrhoeae, 10 such genes have been implicated in recombinational switching at the pilE locus. Eight of these genes, including recA, are either absent from B. burgdorferi, or do not show an obvious requirement for switching at vlsE. The only genes that are required in both organisms are ruvA and ruvB, which encode subunits of a Holliday junction branch migrase. Disruption of these genes results in a dramatic decrease in vlsE recombination with a phenotype similar to that observed for lp28-1 or vls-minus spirochetes: productive infection at week 1 with clearance by day 21. In SCID mice, the persistence defect observed with ruvA and ruvB mutants was fully rescued as previously observed for vlsE-deficient B. burgdorferi. We report the requirement of the RuvAB branch migrase in recombinational switching at vlsE, the first essential factor to be identified in this process. These findings are supported by the independent work of Lin et al. in the accompanying article, who also found a requirement for the RuvAB branch migrase. Our results also indicate that the mechanism of switching at vlsE in B. burgdorferi is distinct from switching at pilE in N. gonorrhoeae, which is the only other organism analyzed genetically in detail. Finally, our findings suggest a unique mechanism for switching at vlsE and a role for currently unidentified B. burgdorferi proteins in this process

Analysis of Thyroid Response Element Activity during Retinal Development

Thyroid hormone (TH) signaling components are expressed during retinal development in dynamic spatial and temporal patterns. To probe the competence of retinal cells to mount a transcriptional response to TH, reporters that included thyroid response elements (TREs) were introduced into developing retinal tissue. The TREs were placed upstream of a minimal TATA-box and two reporter genes, green fluorescent protein (GFP) and human placental alkaline phosphatase (PLAP). Six of the seven tested TREs were first tested in vitro where they were shown to drive TH-dependent expression. However, when introduced into the developing retina, the TREs reported in different cell types in both a TH-dependent and TH-independent manner, as well as revealed specific spatial patterns in their expression. The role of the known thyroid receptors (TR), TRα and TRβ, was probed using shRNAs, which were co-electroporated into the retina with the TREs. Some TREs were positively activated by TR+TH in the developing outer nuclear layer (ONL), where photoreceptors reside, as well as in the outer neuroblastic layer (ONBL) where cycling progenitor cells are located. Other TREs were actively repressed by TR+TH in cells of the ONBL. These data demonstrate that non-TRs can activate some TREs in a spatially regulated manner, whereas other TREs respond only to the known TRs, which also read out activity in a spatially regulated manner. The transcriptional response to even simple TREs provides a starting point for understanding the regulation of genes by TH, and highlights the complexity of transcriptional regulation within developing tissue

Central Role of the Holliday Junction Helicase RuvAB in vlsE Recombination and Infectivity of Borrelia burgdorferi

Antigenic variation plays a vital role in the pathogenesis of many infectious bacteria and protozoa including Borrelia burgdorferi, the causative agent of Lyme disease. VlsE, a 35 kDa surface-exposed lipoprotein, undergoes antigenic variation during B. burgdorferi infection of mammalian hosts, and is believed to be a critical mechanism by which the spirochetes evade immune clearance. Random, segmental recombination between the expressed vlsE gene and adjacent vls silent cassettes generates a large number of different VlsE variants within the infected host. Although the occurrence and importance of vlsE sequence variation is well established, little is known about the biological mechanism of vlsE recombination. To identify factors important in antigenic variation and vlsE recombination, we screened transposon mutants of genes known to be involved in DNA recombination and repair for their effects on infectivity and vlsE recombination. Several mutants, including those in BB0023 (ruvA), BB0022 (ruvB), BB0797 (mutS), and BB0098 (mutS-II), showed reduced infectivity in immunocompetent C3H/HeN mice. Mutants in ruvA and ruvB exhibited greatly reduced rates of vlsE recombination in C3H/HeN mice, as determined by restriction fragment polymorphism (RFLP) screening and DNA sequence analysis. In severe combined immunodeficiency (C3H/scid) mice, the ruvA mutant retained full infectivity; however, all recovered clones retained the ‘parental’ vlsE sequence, consistent with low rates of vlsE recombination. These results suggest that the reduced infectivity of ruvA and ruvB mutants is the result of ineffective vlsE recombination and underscores the important role that vlsE recombination plays in immune evasion. Based on functional studies in other organisms, the RuvAB complex of B. burgdorferi may promote branch migration of Holliday junctions during vlsE recombination. Our findings are consistent with those in the accompanying article by Dresser et al., and together these studies provide the first examples of trans-acting factors involved in vlsE recombination

Emission Measurements of Geogenic Greenhouse Gases in the Area of “Pusty Las” Abandoned Oilfield (Polish Outer Carpathians)

The Carpathians may play a significant role as a supplier of greenhouse gases to the atmosphere. Unfortunately, most of the discovered oil and gas deposits are recently only historical objects. An example is the Sękowa-Ropica Górna-Siary oil deposit located in the marginal part of the Magura Nappe where oil had been extracted in dug wells until the mid XX century. One of such extraction sites is the “Pusty Las” oilfield. In that area, 10 methane and carbon dioxide emission measurement sites were located, among which 4 in dried dug wells and 6 in dig wells still filled with oil and/or water. Dynamics of methane and carbon dioxide concentration changes were measured with the modified static chambers method. Gas samples were collected immediately after the installation of the chamber and again, after 5 and 10 minutes. In the case of reclaimed or dry dug wells, static chamber was installed directly at the ground surface. In wells still filled with oil and/or water the chamber was equipped with an “apron” mounted on special sticks. The dynamics of concentrations changes varied from -0.871 to 119.924 ppm∙min-1 for methane and from -0.005 to 0.053% obj∙min-1 for carbon dioxide. Average methane emission was 1.9 g∙m-2∙d-1 and that of carbon dioxide was 26.95 g∙-2∙d-1. The measurements revealed that an abandoned oil field supplies significant amounts of greenhouse gases to the atmosphere although the emission of methane is lower than that measured e.g. in mud volcanoes located in various parts of the world