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

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

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

Sampling of soil gas in surface geochemical surveys -- an attempt of depth optimization

W pracy przedstawiono wyniki badań nad optymalizacją głębokości poboru próbek gazu podglebowego przy powierzchniowych badaniach geochemicznych. Badania wykonano w dwóch obszarach: w niecce wałbrzyskiej i w rejonie Karlina na Pomorzu Zachodnim. Badania wykonane w niecce wałbrzyskiej nad zlikwidowanymi kopalniami węgla kamiennego wykazały, że najbardziej dogodny dla opróbowań geochemicznych jest interwał głębokościowy 1.0-1.8 m, który położony poniżej strefy aktywnej wymiany sięgającej do głębokości ok. 1 m charakteryzuje się wyrazistym sygnałem geochemicznym pochodzenia wgłębnego. Badania w rejonie Karlina na Pomorzu Zachodnim, wykonane nad akumulacjami naftowymi, polegały na ocenie uzyskanych wielkości stężeń węglowodorów gazowych szeregu metanowego na głębokościach 1.2 m i 1.8 m. Wykazały one, że głębokość 1.2 m jest optymalna dla powierzchniowych opróbowań geochemicznych, realizowanych metodą gazu wolnego w tym obszarze. Analogiczną głębokość opróbowania gazowego można przyjąć dla obszaru niecki wałbrzyskiej. W celu potwierdzenia uzyskanych wyników podobne badania powinny zostać przeprowadzone w innych perspektywicznych złożowo obszarach Polski.The paper presents the results of optimization of sampling depth for soil gas applied in the surface geochemical survey. The studies were carried out in two areas: the Wałbrzych Trough and the Karlino area (Western Pomerania). The studies in the Wałbrzych Trough was carried out over the closed and remediated coal mines. The results demonstrated that sampling depth interval 1.0-1.8 meters is an optimum for surface geochemical survey as it is located beneath the active exchange zone (i.e. beneath 1.0 meter) but provides distinct geochemical response from deep sources. The studies in the Karlino area (Western Pomerania) was carried out over oil and gas pools. It was found that 1.2 meter depth is an optimum for geochemical sampling with the "free" gas method in this area. The some sampling depth can be apply on in the Wałbrzych Trough. Such studies must be passed in other areas of Poland to confirm this depth of sampling

Methane emission measurements in selected areas of the Polish Outer Carpathians

W pracy przedstawiono wyniki pomiarów dynamiki stężeń metanu oraz jego emisji. Badania wykonano metodą komór statycznych na wybranych 16 stanowiskach położonych na obszarze polskich Karpat Zewnętrznych. Mierzono zmiany stężeń gazów węglowodorowych oraz dwutlenku węgla naturalnie uchodzących do atmosfery z powierzchni terenu, a także z głębokości 1 metra. Zmiany stężeń analizowano w różnych interwałach czasowych: od kilku minut do prawie 30 godzin. Stężenia metanu wahały się od ok. 1.6 ppm do prawie 8000 ppm. Dynamika zmian tych stężeń była najwyraźniejsza, kiedy metan wypływał z otworu o głębokości 1 m i zmieniała się w przedziale od -0.23 do 100.7 ppm x min-1. Obliczone wielkości emisji wahały się od -24.5 do 10 606.9 mg x m-2 x d-1, przy średniej 304.5 mg x m-2 x d-1 i medianie 0.21 mg x m-2 x d-1. Wyniki badań pozwoliły na zoptymalizowanie metodyki pomiarów terenowych, a także na szacunkową ocenę ilości metanu uwalnianego z jednostki powierzchni orogenu karpackiego w jednostce czasu.The paper presents measurement results of dynamics of methane concentrations and its emission. The investigations were carried out with application of the method of static chambers in 16 stations located in the Polish Outer Carpathians. The measurements included changes of concentrations of hydrocarbon gases and carbon dioxide, which naturally escape to the atmosphere from the land surface and flow from the depth of 1 m. The concentration changes were analyzed in various time intervals: from a few minutes up to almost 30 hours. Methane concentrations ranged from approximately 1.6 ppm up to nearly 8000 ppm. Dynamics of its concentrations was most distinct when it was flowing from the depth of 1 m and it was changing within the range of -0.23 to 100.7 ppm x min-1. The calculated emission quantities ranged from -24.5 to 10 606.9 mg x m-2 x d-1, with the mean value equal to 304.5 mg x m-2 x d-1 and median of 0.21 mg x m-2 x d-1. The results of the investigations enabled the authors to optimize the methodology of field measurements and to estimate the quantity of methane which escapes from an area unit of the Carpathian orogen during a time unit

Surface geochemical survey in selected areas of the Polish and Ukrainian Flysch Carpathians

W pracy przedstawiono wyniki rozpoznawczych powierzchniowych badań geochemicznych wykonanych w wybranych strefach polskich i ukraińskich Karpat fliszowych. Ich celem była ocena możliwości występowania wgłębnych akumulacji węglowodorów. Badania wykonano wzdłuż ośmiu profili o łącznej długości ok. 150 km, przebiegających generalnie z NE na SW. Polegały one na poborze próbek gazu glebowego, w których określano stężenia węglowodorów gazowych i helu. Ogółem pobrano 315 próbek z punktów rozmieszczonych w odstępach ok. 500-metrowych. Stężenia metanu wahały się od 0.9 ppm do prawie 50% obj., stężenia wyższych alkanów dochodziły do ok. 0.4% obj., a stężenia gazowych alkenów do ok. 132 ppm. Stwierdzono również obecność helu o stężeniu dochodzącym do 52 ppm. Zmiany stężeń składników węglowodorowych przedstawione graficznie na tle istniejącego modelu geologiczno-złożowego potwierdzają dotychczasowe rozpoznanie złożowe, a także wskazują na możliwość występowania innych, nieudokumentowanych dotąd, akumulacji wgłębnych.The paper presents results of reconnaissance surface geochemical survey carried out in selected zones of the Polish and Ukrainian Flysch Carpathians. It intended to assess the possibility of occurrence of subsurface hydrocarbon accumulations. The survey was conducted along 8 profiles with total length of approximately 150 km, in general running from NE to SW, and consisted in taking samples of soil gas, in which concentrations of hydrocarbons and helium were determined. In sum, 315 samples were taken at points with the 500 m spacing. Concentrations of methane ranged from 0.9 ppm to almost 50 vol. %, concentrations of higher alkanes amounted to approximately 0.4 vol. % and concentrations of gaseous alkenes came up to approximately 132 ppm. Also presence of helium was recorded, its concentration amounting to 52 ppm. Variations in concentration of hydrocarbon constituents, graphically presented against the background of the existing geological and reservoir model, confirm the previous recognition of oil and gas fields and are indicative of opportunity of occurrence other, still undocumented subsurface accumulations

Analysis of results of surface geochemical surveys in the transfrontier zone of the Polish and Ukrainian Carpathians

W pracy przedstawiono wyniki rozpoznawczych powierzchniowych badań geochemicznych wykonanych w latach 2007-2008 we wschodniej części polskich i zachodniej części ukraińskich Karpat Zewnętrznych, na północ od nasunięcia dukielskiego. Celem badań była ocena możliwości występowania wgłębnych akumulacji węglowodorów w obszarze cechującym się powszechnym występowaniem wycieków ropnych na wychodniach intensywnie sfałdowanych i głęboko rozciętych przez erozję warstw. Badania wykonano wzdłuż 11 profili przebiegających poprzecznie do rozciągłości fliszowych jednostek strukturalno-facjalnych. Ogółem pobrano 890 próbek gazu glebowego, w których określono stężenia węglowodorów gazowych i helu. Stężenia metanu, sumy wyższych alkanów, gazowych alkenów i helu dochodziły odpowiednio do 50% obj., 0.4% obj., 132 ppm i 52 ppm. Anomalne stężenia alkanów, przedstawione graficznie na tle głównych jednostek tektonicznych Karpat oraz udokumentowanych akumulacji złożowych, generalnie potwierdziły obecność tych ostatnich. Inne anomalie wskazują na możliwość występowania nieudokumentowanych dotąd, wgłębnych akumulacji węglowodorów.The paper presents results of reconnaissance surface geochemical surveys carried out in the years 2007 and 2008 in the eastern Polish Carpathians and western Ukrainian Carpathians between the Carpathian Foredeep and Dukla Overthrust. The surveys intended to assess the possibility of occurrence of subsurface hydrocarbon accumulations in the area characterized by common occurrence of oil seeps at outcrops of beds, which had been intensely folded and deeply dissected by erosion. The surveys were conducted along 11 profiles. The profiles were running transversally to the strike of flysch structural-facies units. The geochemical surveys consisted in taking 890 soil-gas samples, in which concentrations of gaseous hydrocarbons and helium were determined. Concentrations of methane, higher alkanes, gaseous alkenes and helium reached to nearly 50 vol.%, 0.4 vol.%, 132 ppm and 52 ppm, respectively. The anomalous alkanes concentrations, graphically presented against the background of major Carpathian tectonic units and documented hydrocarbon deposits, have confirmed, in general, the existence of the deposits, whereas some of the concentrations have indicated possible occurrence of other, still undocumented subsurface hydrocarbon accumulations

Surface geochemical survey at Starunia palaeontological site and vicinity (Carpathian region, Ukraine)

A surface geochemical survey was carried out in an abandoned ozokerite mine in Starunia, where remnants of a mammoth and three woolly rhinoceroses and one almost completely preserved rhinoceros carcass were found in 1907 and 1929. In total, 689 measurement sites were defined within the selected 300×350 m rectangle (ca. 10.5 ha). The analysed soil gases vary in their molecular and isotopic compositions. Several zones with anomalous methane concentrations over 10 vol% were identified in the study area. These anomalous concentrations correlate well with total C2-C5 alkane anomalies (over 1 vol%). The zones with carbon dioxide concentrations over 15 vol% are generally shifted SW of those, where the methane and the sum of C2-C5 alkanes anomalies were identified. High helium concentrations of crustal origin (over 0.001 vol%) are clustered near fault zones. In a majority of cases methane is of thermogenic origin, migrating to the near-surface zone from deep-seated accumulations. Microbial methane, or methane with a high microbial component, is genetically related to recent swamps. The high variability of concentrations of gaseous components together with the highly variable isotopic composition of individual gases in the soil, indicate their thermogenic and/or microbial origin, and point to the lithological diversity of Quaternary sediments in the study area. Several zones with thermogenic gaseous hydrocarbons and helium were delineated. It is likely that during the Pleistocene winters, under a thick ice and snow cover, the tundra lake and swamp zones around outflows of brines, oil, helium and thermogenic gases had a higher temperature, which resulted in melting and cracking of the ice cover. These sites would be more prospective for future search of well-preserved large vertebrates

Distribution and origin of gaseous hydrocarbons and carbon dioxide in the Quaternary sediments at Starunia palaeontological site and vicinity (Carpathian region, Ukraine)

Near-surface gases were investigated in Starunia, where remains of mammoth and woolly rhinoceroses were discovered at the beginning of the 20th century. Samples were collected at 30 measurement sites, from 0.8, 1.6, 2.4, 3.2 and 4.0 m depths and analysed for their molecular and isotopic compositions. Most of the methane and all higher gaseous hydrocarbons accumulated within the near-surface zone are of thermogenic origin. The distribution of thermogenic methane and higher gaseous hydrocarbons in Quaternary sediments is variable and, generally, increases with depth. Microbial methane or a mixture of microbial and thermogenic methane also occurs at the near-surface zone. The presence of hydrogen and alkenes in the near-surface gases also suggests a contribution from recent, microbial processes. Helium of crustal origin migrated through the Rinne Fault and other tectonic zones located in the study area, and was subsequently dispersed during migration through the lithologically diversified Pleistocene and Holocene sediments. The high variability of the carbon dioxide concentration and stable carbon isotope composition at various depths in the near-surface zone is caused by its polygenetic origin (thermogenic, microbial, and oxidation of hydrocarbons and Quaternary organic matter), and also by its dissolution in water and oil during migration through lithologically diversified Pleistocene and Holocene sediments. Zones of thermogenic methane occurrence within Pleistocene sediments, dominated by muds saturated with bitumen and brines, provide the most favourable environment for preservation of large extinct mammals. It is likely that during the Pleistocene winters, when thick ice and snow covered the tundra lake and swamp, zones of outflow of brines, oils, helium, and thermogenic gaseous hydrocarbons had a higher temperature, which could have resulted in melting and cracking of the ice cover and drowning of large mammals. The most favourable conditions for preservation of large, extinct mammals probably still exists in the vicinity of sampling probe sites Nos 21, 22, 23 and 36. Zones of dominance of microbial methane concentrations are less favourable sites for preservation of extinct mammals, because this methane was generated within recent swamps and also within recent descending meteoric waters which infiltrated into Pleistocene and Holocene sediments. Older Pleistocene microbial gases have already escaped to the atmosphere