Diversity of active root-associated methanotrophs of three emergent plants in a eutrophic wetland in northern China

Abstract Root-associated aerobic methanotrophs play an important role in regulating methane emissions from the wetlands. However, the influences of the vegetation type on root-associated methanotrophic structures, especially on active flora, remain poorly understood. Transcription of the pmo A gene, encoding particulate methane monooxygenase in methanotrophs, was analyzed by reverse transcription PCR (RT-PCR) of mRNA isolated from root samples of three emergent macrophytes, including Phragmites australis , Typha angustifolia , and Scirpus triqueter from a eutrophic wetland. High-throughput sequencing of pmo A based on DNA and cDNA was used to analyze the methanotrophic community . Sequencing of cDNA pmo A amplicons confirmed that the structure of active methanotrophic was not always consistent with DNA. A type I methanotroph, M ethylomonas , was the most active group in P. australis , whereas Methylocystis, a type II methanotroph, was the dominant group in S. triqueter . In T. angustifolia , these two types of methanotroph existed in similar proportions. However, at the DNA level, Methylomonas was predominant in the roots of all three plants. In addition, vegetation type could have a profound impact on root-associated methanotrophic community at both DNA and cDNA levels. These results indicate that members of the genera Methylomonas (type I) and Methylocystis (type II) can significantly contribute to aerobic methane oxidation in a eutrophic wetland.

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Molecular characterization and analysis of a gene encoding the acidic repeat protein (Arp) of Treponema pallidum

Journal of Medical Microbiology ◽

10.1099/jmm.0.46943-0 ◽

2007 ◽

Vol 56 (6) ◽

pp. 715-721 ◽

Cited By ~ 20

Author(s):

Hsi Liu ◽

Berta Rodes ◽

Robert George ◽

Bret Steiner

Keyword(s):

Synthetic Peptides ◽

Treponema Pallidum ◽

Signal Peptidase ◽

Type I ◽

Type Ii ◽

Gene Encoding ◽

Western Blot Assay ◽

Repeat Protein ◽

Signal Peptidase I ◽

Cdc 2

The acidic repeat protein (arp) genes from three subspecies of the treponeme Treponema pallidum (T. pallidum subsp. pallidum, Nichols strain; T. pallidum subsp. pertenue, CDC-1 and CDC-2 strains; and T. pallidum subsp. endemicum, Bosnia A strain) were cloned and sequenced. The predicted protein sequence contained a high percentage of glutamic acid, hence the name acidic repeat protein, or Arp. The protein had a potential membrane-spanning domain and a signal peptidase I site. The gene from the Nichols strain of T. pallidum subsp. pallidum contained a set of 14 nearly identical repeats of a 60 bp sequence, which occupied ∼51 % of the length of the gene. Analyses of arp from laboratory strains showed that the 5′ and 3′ ends of the genes were conserved, but there was considerable heterogeneity in the number of repeats of this 60 bp sequence. Based on amino acid variations, the 14 sequence repeats could be classified into three types, which were named type I, type II and type III repeats. The type II repeat was the most common in the strains examined. The arp gene of the Nichols strain was subsequently cloned into the expression vector pBAD/TOPO ThioFusion. The expressed protein was detected in a Western blot assay using rabbit immune sera produced against T. pallidum, or synthetic peptides derived from the repeat sequences. Using an ELISA, rapid plasma reagin (RPR) test-positive sera reacted with synthetic peptides derived from the repeat region but not with peptides derived from N and C termini of the Arp protein. These results show that the Arp protein is immunogenic and could prove to be a useful target for serological diagnosis of T. pallidum infection.

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Sequence and expression of a type II keratin, K5, in human epidermal cells

Molecular and Cellular Biology ◽

10.1128/mcb.8.1.486-493.1988 ◽

1988 ◽

Vol 8 (1) ◽

pp. 486-493

Author(s):

R Lersch ◽

E Fuchs

Keyword(s):

Human Gene ◽

Basal Layer ◽

Epidermal Cells ◽

Amino Acid Sequences ◽

Type I ◽

Type Ii ◽

Gene Encoding ◽

Human Epidermal Cells ◽

Rna Blot Analysis

We report here the cDNA and amino acid sequences of a human 58-kilodalton type II keratin, K5, which is coexpressed with a 50-kilodalton type I keratin partner, K14, in stratified squamous epithelia. Using a probe specific for the 3'-noncoding portion of this K5 cDNA, we demonstrated the existence of a single human gene encoding this sequence. Using Northern (RNA) blot analysis and in situ hybridization with cRNA probes for both K5 and K14, we examined the expression of these mRNAs in the epidermis and in cultured epidermal cells. Our results indicate that the mRNAs for K5 and K14 are coordinately expressed and abundant in the basal layer of the epidermis. As cells undergo a commitment to terminally differentiate, the expression of both mRNAs seems to be downregulated.

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Sequence and expression of a type II keratin, K5, in human epidermal cells.

Molecular and Cellular Biology ◽

10.1128/mcb.8.1.486 ◽

1988 ◽

Vol 8 (1) ◽

pp. 486-493 ◽

Cited By ~ 49

Author(s):

R Lersch ◽

E Fuchs

Keyword(s):

Human Gene ◽

Basal Layer ◽

Epidermal Cells ◽

Amino Acid Sequences ◽

Type I ◽

Type Ii ◽

Gene Encoding ◽

Human Epidermal Cells ◽

Rna Blot Analysis

We report here the cDNA and amino acid sequences of a human 58-kilodalton type II keratin, K5, which is coexpressed with a 50-kilodalton type I keratin partner, K14, in stratified squamous epithelia. Using a probe specific for the 3'-noncoding portion of this K5 cDNA, we demonstrated the existence of a single human gene encoding this sequence. Using Northern (RNA) blot analysis and in situ hybridization with cRNA probes for both K5 and K14, we examined the expression of these mRNAs in the epidermis and in cultured epidermal cells. Our results indicate that the mRNAs for K5 and K14 are coordinately expressed and abundant in the basal layer of the epidermis. As cells undergo a commitment to terminally differentiate, the expression of both mRNAs seems to be downregulated.

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Wide Distribution of a Novel pmoA-Like Gene Copy among Type II Methanotrophs, and Its Expression in Methylocystis Strain SC2

Applied and Environmental Microbiology ◽

10.1128/aem.69.9.5593-5602.2003 ◽

2003 ◽

Vol 69 (9) ◽

pp. 5593-5602 ◽

Cited By ~ 71

Author(s):

Merlin Tchawa Yimga ◽

Peter F. Dunfield ◽

Peter Ricke ◽

Jürgen Heyer ◽

Werner Liesack

Keyword(s):

Purifying Selection ◽

Wide Distribution ◽

Gene Copy ◽

Northern Hybridization ◽

Rrna Gene ◽

Type I ◽

Type Ii ◽

Methylococcus Capsulatus ◽

Reverse Transcription Pcr ◽

Wide Range

ABSTRACT Experiments were conducted to determine if a novel pmoA-like gene (pmoA2) recently discovered in the methane-oxidizing bacterium Methylocystis strain SC2 (P. F. Dunfield, M. Tchawa Yimga, S. D. Dedysh, U. Berger, W. Liesack, and J. Heyer, FEMS Microbiol. Ecol. 41:17-26, 2002) is present in other methane-oxidizing bacteria (MOB), and if it is expressed. A newly developed primer combination (pmoA206f-pmoA703b) allowed a differential detection of pmoA1 and pmoA2. By using this primer combination, we identified pmoA2 in a wide range of type II MOB of the Methylosinus-Methylocystis group. However, screening by PCR and by Southern hybridization using a newly developed pmoA2-specific oligonucleotide probe also showed that closely related type II MOB, exhibiting 16S rRNA gene sequence identities of higher than 97%, may or may not harbor pmoA2. No pmoA2 was detected in five type I MOB tested: Methylococcus capsulatus strain Bath, Methylocaldum strain E10A, Methylobacter luteus, Methylomicrobium album, and Methylomonas strain D1a. In comparative sequence analyses, all pmoA2-like sequences formed a coherent cluster clearly distinct from pmoA1 sequences of type I and type II MOB, and from amoA sequences of the Nitrosomonas-Nitrosospira group. Phylogenetic analysis using the paml model suggested that pmoA2 is subject to strong purifying selection and therefore has an important cellular function. We probed total RNA extracts of Methylocystis strain SC2 for gene expression of pmoA. A strong signal was observed for pmoA1 in Northern hybridization, while the results obtained for pmoA2 were ambiguous. However, reverse transcription-PCR confirmed that pmoA2 was expressed, albeit at lower level than pmoA1. This provided experimental evidence that the gene product of pmoA2 may be a functionally active enzyme.

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Cloning and characterization of a transmembrane serine kinase that acts as an activin type I receptor

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.90.23.11242 ◽

1993 ◽

Vol 90 (23) ◽

pp. 11242-11246 ◽

Cited By ~ 70

Author(s):

K Tsuchida ◽

L S Mathews ◽

W W Vale

Keyword(s):

Transforming Growth Factor Beta ◽

Transforming Growth Factor ◽

Transmembrane Protein ◽

Biological Effects ◽

Kinase Domain ◽

Type I ◽

Type Ii ◽

Serine Kinase ◽

Reverse Transcription Pcr ◽

Serine Kinases

Activin type II receptors are transmembrane protein-serine/threonine kinases. By using a reverse-transcription PCR assay to screen for protein kinase sequences, we isolated a cDNA clone, activin X1 receptor, from rat brain that encodes a 55-kDa transmembrane protein-serine kinase which is structurally related to other receptors in this kinase subfamily. The predicted protein consists of 509 amino acids, and the kinase domain shows 40% and 37% identity to the activin and transforming growth factor beta type II receptors, respectively. No activin-binding was observed when activin X1 receptor was expressed alone in COS-M6 cells; however, coexpression with type II activin receptors gave rise to a 68-kDa affinity-labeled complex in addition to the 85-kDa type II receptor complex. The size of this cross-linked band is consistent with the size of the type I activin receptor; furthermore, activin X1 receptor associated with type II receptors, as judged by coimmunoprecipitation with type II receptor antibodies. These data suggest that activin X1 receptor can serve as an activin type I receptor and that the diverse biological effects of activins may be mediated by a complex formed by the interaction of two transmembrane protein-serine kinases.

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Mechanisms of vegetation uprooting by flow in alluvial non-cohesive sediment

Hydrology and Earth System Sciences Discussions ◽

10.5194/hessd-8-1365-2011 ◽

2011 ◽

Vol 8 (1) ◽

pp. 1365-1398 ◽

Cited By ~ 7

Author(s):

K. Edmaier ◽

P. Burlando ◽

P. Perona

Keyword(s):

Root System ◽

Time Scales ◽

River Restoration ◽

Vegetation Type ◽

Vegetative Reproduction ◽

Cohesive Sediment ◽

Type I ◽

Type Ii ◽

Mechanical Anchoring ◽

Preliminary Experimental Data

Abstract. The establishment of riparian pioneer vegetation is of crucial importance within river restoration projects. After germination or vegetative reproduction on river bars juvenile plants are often exposed to mortality by uprooting caused by floods. At later stages of root development vegetation uprooting by flow is seen to occur as a consequence of a marked erosion gradually exposing the root system and accordingly reducing the mechanical anchoring. How time scales of flow-induced uprooting do depend on vegetation stages growing in alluvial non-cohesive sediment is currently an open question that we conceptually address in this work. After reviewing vegetation root issues in relation to morphodynamic processes, we then propose two modelling mechanisms (Type I and Type II), respectively concerning the uprooting time scales of early germinated and of mature vegetation. Type I is a purely flow-induced drag mechanism, which causes alone a nearly instantaneous uprooting when exceeding root resistance. Type II arises as a combination of substantial sediment erosion exposing the root system and resulting in a decreased anchoring resistance, eventually degenerating into a Type I mechanism. We support our conceptual models with some preliminary experimental data and discuss the importance of better understanding such mechanisms in order to formulate sounding mathematical models that are suitable to plan and to manage river restoration projects.

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Mechanisms of vegetation uprooting by flow in alluvial non-cohesive sediment

Hydrology and Earth System Sciences ◽

10.5194/hess-15-1615-2011 ◽

2011 ◽

Vol 15 (5) ◽

pp. 1615-1627 ◽

Cited By ~ 58

Author(s):

K. Edmaier ◽

P. Burlando ◽

P. Perona

Keyword(s):

Root System ◽

Time Scales ◽

River Restoration ◽

Vegetation Type ◽

Vegetative Reproduction ◽

Cohesive Sediment ◽

Type I ◽

Type Ii ◽

Mechanical Anchoring ◽

Preliminary Experimental Data

Abstract. The establishment of riparian pioneer vegetation is of crucial importance within river restoration projects. After germination or vegetative reproduction on river bars juvenile plants are often exposed to mortality by uprooting caused by floods. At later stages of root development vegetation uprooting by flow is seen to occur as a consequence of a marked erosion gradually exposing the root system and accordingly reducing the mechanical anchoring. How time scales of flow-induced uprooting do depend on vegetation stages growing in alluvial non-cohesive sediment is currently an open question that we conceptually address in this work. After reviewing vegetation root issues in relation to morphodynamic processes, we then propose two modelling mechanisms (Type I and Type II), respectively concerning the uprooting time scales of early germinated and of mature vegetation. Type I is a purely flow-induced drag mechanism, which causes alone a nearly instantaneous uprooting when exceeding root resistance. Type II arises as a combination of substantial sediment erosion exposing the root system and resulting in a decreased anchoring resistance, eventually degenerating into a Type I mechanism. We support our conceptual models with some preliminary experimental data and discuss the importance of better understanding such mechanisms in order to formulate sounding mathematical models that are suitable to plan and to manage river restoration projects.

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Coli-aerogenes bacteria in soils

Epidemiology and Infection ◽

10.1017/s0022172400044053 ◽

1951 ◽

Vol 49 (2-3) ◽

pp. 162-168 ◽

Cited By ~ 12

Author(s):

C. B. Taylor

Keyword(s):

Vegetation Type ◽

Natural Habitat ◽

Large Population ◽

Coliform Bacteria ◽

Type I ◽

Type Ii ◽

Arable Soils ◽

The United Kingdom ◽

Different Types ◽

Annual Application

The prevalence of the different types of coli–aerogenes bacteria has been determined in various soils collected from widely separated locations in the United Kingdom and in Denmark. Of the soils examined, 27% contained no coli–aerogenes organisms in 15 g. of soil tested. The number of these organisms in the positive soils was very low; only 11% had confirmed counts greater than 100 organisms/g. and 33% less than 1 organism/g.The most prevalent organism isolated was Bacterium coli type I, whatever the location or vegetation type of the soil; intermediate type I, Bact. aerogenes type I and Bact. coli type II were the only other organisms of numerical importance. The annual application of large amounts of either farmyard or inorganic manures produces no permanently large population of coli-aerogenes organisms in soils.Presumptive tests in MacConkey broth were unreliable, since only 6 % of the positive tubes from hill and moorland soils and 28 % from arable soils were confirmed as containing coli-aerogenes bacteria. Such discrepancies are considered to be partly due to coliform bacteria with weak lactose-fermenting properties.It is considered that there is now sufficient experimental evidence to discredit statements that soil is the natural habitat of Bact. aerogenes or intermediate types of coli-aerogenes organism.

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Biomass and carbon stocks of the natural forests at Me Linh biodiversity station, Vinh Phuc province, Vietnam

Journal of Vietnamese Environment ◽

10.13141/jve.vol6.no3.pp281-287 ◽

2014 ◽

Vol 6 (3) ◽

pp. 281-287

Author(s):

Thi Thu Huong Dang ◽

Huu Thu Do

Keyword(s):

Shifting Cultivation ◽

Carbon Stock ◽

Vegetation Type ◽

Carbon Stocks ◽

Forest Vegetation ◽

Viet Nam ◽

Type I ◽

Type Ii ◽

Natural Forests ◽

Clear Cutting

Biomass and carbon stock of the natural forests in Vietnam are still not clear due to limitation of knowledge and financial. In this paper, the results of estimating biomass and carbon stocks of the natural forests at Me Linh Biodiversity Station are shown. There are two forest types in this study: the forest vegetation restored after shifting cultivation (vegetation type I) and the forest vegetation restored after clear cutting exploitation (vegetation type II). As the results, the estimated biomass of the forest vegetation restored after shifting cultivation is 86.80 ton.ha-1 and the estimated biomass of the forest vegetation restored after clear cutting exploitation is higher, about 131.59 ton.ha-1. The carbon stock in plants was about 43.40 ton.ha-1 of vegetation type I and 65.79 ton.ha-1 of vegetation type II. The carbon storage in soil of vegetation type I is 79.01 ton.ha-1 and vegetation type II is 99.65 ton.ha-1. Hence, the total of carbon stock in forest vegetation I and II are accounted by 122.41ton.ha-1 and 165.44 ton.ha-1, respectively. In general, it can be pointed out that the naturally recovering secondary forest at Me Linh Station is the secondary young forest with the low economic value due to shortly restored process (about 10-20 years), the flora is not rich and abundant, and there are only commonly pioneer and light demanding tree species. Sinh khối và trữ lượng các bon của rừng tự nhiên ở Việt Nam vẫn ít được quan tâm của do hạn chế về kiến thức và tài chính. Trong bài báo này, chúng tôi đưa ra kết quả của việc ước lượng sinh khối và tổng hợp các bon của các thảm thực vật rừng thứ sinh phục hồi tự nhiên tại Trạm Đa dạng Sinh học Mê Linh, tỉnh Vĩnh Phúc - Việt Nam, nơi có loại hình thảm thực vật chính, đó là thảm thực vật phục hồi sau nương rẫy (kiểu thảm thục vật I) và thảm thực vật phục hồi sau khai thác kiệt (kiểu thảm thực vật II) nhằm mục đích đánh giá tiềm năng của rừng thứ sinh tại khu vực nghiên cứu. Sinh khối của thảm thực vật phục hồi sau nương rẫy là 86,80 tấn/ha. Sinh khối của thảm thực vật phục hồi sau khai thác cao hơn, đạt 131.59 tấn/ha. Lượng các bon hấp thu trong đất của thảm thực vật I là 79,01 tấn/ha và thảm thực vật II là 99,65 tấn/ha. Như vậy, tổng lượng các bon được hấp thu trong mỗi loại hình thảm thực vật trên là: 122,41 tấn/ha (thảm thực vật I) và 165,14 tấn/ha. Nhìn chung, rừng thứ sinh phục hồi tự nhiên tại Trạm Đa dạng Mê Linh chủ yếu là rừng non thứ sinh, ít có giá trị kinh tế do quá trình phục hồi diễn ra ngắn (khoảng 10-20 năm) nên thành phần thực vật nghèo nàn, không phong phú, thành phần chính chủ yếu là các cây gỗ tiên phong, ưa sáng.

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