Alla Lapidus - Academia.edu (original) (raw)

Papers by Alla Lapidus

Research paper thumbnail of Genome sequence of the button mushroom Agaricus bisporus reveals mechanisms governing adaptation to a humic-rich ecological niche

Proceedings of the National Academy of Sciences, 2012

ABSTRACT Agaricus bisporus is the model fungus for the adaptation, persistence, and growth in the... more ABSTRACT Agaricus bisporus is the model fungus for the adaptation, persistence, and growth in the humic-rich leaf-litter environment. Aside from its ecological role, A. bisporus has been an important component of the human diet for over 200 y and worldwide cultivation of the "button mushroom" forms a multibillion dollar industry. We present two A. bisporus genomes, their gene repertoires and transcript profiles on compost and during mushroom formation. The genomes encode a full repertoire of polysaccharide-degrading enzymes similar to that of wood-decayers. Comparative transcriptomics of mycelium grown on defined medium, casing-soil, and compost revealed genes encoding enzymes involved in xylan, cellulose, pectin, and protein degradation are more highly expressed in compost. The striking expansion of heme-thiolate peroxidases and β-etherases is distinctive from Agaricomycotina wood-decayers and suggests a broad attack on decaying lignin and related metabolites found in humic acid-rich environment. Similarly, up-regulation of these genes together with a lignolytic manganese peroxidase, multiple copper radical oxidases, and cytochrome P450s is consistent with challenges posed by complex humic-rich substrates. The gene repertoire and expression of hydrolytic enzymes in A. bisporus is substantially different from the taxonomically related ectomycorrhizal symbiont Laccaria bicolor. A common promoter motif was also identified in genes very highly expressed in humic-rich substrates. These observations reveal genetic and enzymatic mechanisms governing adaptation to the humic-rich ecological niche formed during plant degradation, further defining the critical role such fungi contribute to soil structure and carbon sequestration in terrestrial ecosystems. Genome sequence will expedite mushroom breeding for improved agronomic characteristics.

Research paper thumbnail of Appendix: ExSPAnder: a Universal Repeat Resolver for DNA Fragment Assembly

Research paper thumbnail of Comparative genomics of biotechnologically important yeasts

Proceedings of the National Academy of Sciences of the United States of America, Jan 17, 2016

Ascomycete yeasts are metabolically diverse, with great potential for biotechnology. Here, we rep... more Ascomycete yeasts are metabolically diverse, with great potential for biotechnology. Here, we report the comparative genome analysis of 29 taxonomically and biotechnologically important yeasts, including 16 newly sequenced. We identify a genetic code change, CUG-Ala, in Pachysolen tannophilus in the clade sister to the known CUG-Ser clade. Our well-resolved yeast phylogeny shows that some traits, such as methylotrophy, are restricted to single clades, whereas others, such as l-rhamnose utilization, have patchy phylogenetic distributions. Gene clusters, with variable organization and distribution, encode many pathways of interest. Genomics can predict some biochemical traits precisely, but the genomic basis of others, such as xylose utilization, remains unresolved. Our data also provide insight into early evolution of ascomycetes. We document the loss of H3K9me2/3 heterochromatin, the origin of ascomycete mating-type switching, and panascomycete synteny at the MAT locus. These data a...

Research paper thumbnail of 113.Wu.GEBA.Supplement

Research paper thumbnail of Catalytic hydrocondensation of carbon monoxide with olefins and their hydropolymerization under the effect of carbon monoxide and oxygen. Communication 58. Hydropolymerization of ethylene in the presence of Co-Carbonyl catalysts

Research paper thumbnail of De Wit et al PLoS Pathogens

Research paper thumbnail of Comparing polysaccharide decomposition between the type strains Gramella echinicola KMM 6050(T) (DSM 19838(T)) and Gramella portivictoriae UST040801-001(T) (DSM 23547(T)), and emended description of Gramella echinicola Nedashkovskaya et al. 2005 emend. Shahina et al. 2014 and Gramella portivictor...

Standards in genomic sciences, 2016

Strains of the genus Gramella (family Flavobacteriacae, phylum Bacteroidetes) were isolated from ... more Strains of the genus Gramella (family Flavobacteriacae, phylum Bacteroidetes) were isolated from marine habitats such as tidal flat sediments, coastal surface seawater and sea urchins. Flavobacteriaceae have been shown to be involved in the decomposition of plant and algal polysaccharides. However, the potential to decompose polysaccharides may differ tremendously even between species of the same genus. Gramella echinicola KMM 6050(T) (DSM 19838(T)) and Gramella portivictoriae UST040801-001(T) (DSM 23547(T)) have genomes of similar lengths, similar numbers of protein coding genes and RNA genes. Both genomes encode for a greater number of peptidases compared to 'G. forsetii'. In contrast to the genome of 'G. forsetii', both genomes comprised a smaller set of CAZymes. Seven polysaccharide utilization loci were identified in the genomes of DSM 19838(T) and DSM 23547(T). Both Gramella strains hydrolyzed starch, galactomannan, arabinoxylan and hydroxyethyl-cellulose, but ...

Research paper thumbnail of Complete genome sequence of the haloalkaliphilic, obligately chemolithoautotrophic thiosulfate and sulfide-oxidizing γ-proteobacterium Thioalkalimicrobium cyclicum type strain ALM 1 (DSM 14477(T))

Standards in genomic sciences, 2016

Thioalkalimicrobium cyclicum Sorokin et al. 2002 is a member of the family Piscirickettsiaceae in... more Thioalkalimicrobium cyclicum Sorokin et al. 2002 is a member of the family Piscirickettsiaceae in the order Thiotrichales. The γ-proteobacterium belongs to the colourless sulfur-oxidizing bacteria isolated from saline soda lakes with stable alkaline pH, such as Lake Mono (California) and Soap Lake (Washington State). Strain ALM 1(T) is characterized by its adaptation to life in the oxic/anoxic interface towards the less saline aerobic waters (mixolimnion) of the stable stratified alkaline salt lakes. Strain ALM 1(T) is the first representative of the genus Thioalkalimicrobium whose genome sequence has been deciphered and the fourth genome sequence of a type strain of the Piscirickettsiaceae to be published. The 1,932,455 bp long chromosome with its 1,684 protein-coding and 50 RNA genes was sequenced as part of the DOE Joint Genome Institute Community Sequencing Program (CSP) 2008.

Research paper thumbnail of Transposable Elements versus the Fungal Genome: Impact on Whole-Genome Architecture and Transcriptional Profiles

PLoS genetics, Jun 1, 2016

Transposable elements (TEs) are exceptional contributors to eukaryotic genome diversity. Their ub... more Transposable elements (TEs) are exceptional contributors to eukaryotic genome diversity. Their ubiquitous presence impacts the genomes of nearly all species and mediates genome evolution by causing mutations and chromosomal rearrangements and by modulating gene expression. We performed an exhaustive analysis of the TE content in 18 fungal genomes, including strains of the same species and species of the same genera. Our results depicted a scenario of exceptional variability, with species having 0.02 to 29.8% of their genome consisting of transposable elements. A detailed analysis performed on two strains of Pleurotus ostreatus uncovered a genome that is populated mainly by Class I elements, especially LTR-retrotransposons amplified in recent bursts from 0 to 2 million years (My) ago. The preferential accumulation of TEs in clusters led to the presence of genomic regions that lacked intra- and inter-specific conservation. In addition, we investigated the effect of TE insertions on th...

Research paper thumbnail of A New Monte-Carlo Simulation Model for the Temporal Development of Cloud Droplet Spectra

J Atmos Sci, 1972

A new Monte-Carlo simulation model for computing the temporal development of cloud droplet spectr... more A new Monte-Carlo simulation model for computing the temporal development of cloud droplet spectra is presented. Since the simulation is carried out in probability space, the new model does not need to follow the growth history and position of each and every drop. Additional physical processes, such as turbulence, electrical effects, glaciation, etc., can be added to the primary growth

Research paper thumbnail of Influence of Preparation Method on Activity of Cobalt Catalysts for Hydrocarbon Synthesis from Co and H2

Russ Chem Bull, 1984

ABSTRACT 1. The method used for the preparation of cobalt catalysts has a considerable influence ... more ABSTRACT 1. The method used for the preparation of cobalt catalysts has a considerable influence on their activity in the synthesis of hydrocarbons from CO and H2. 2. In the selection of a method for preparing cobalt catalysts for the Fischer-Tropsch synthesis, the mean pore radius of the support that is used is a decisive factor. 3. The chemisorption of carbon monoxide on cobalt catalysts depends on the method of their preparation.

Research paper thumbnail of Expression of a Stress- and Starvation-Induced dps/pexB- Homologous Gene Is Controlled by the Alternative Sigma Factor sB in Bacillus subtilis

B -dependent general stress proteins (Gsps) of Bacillus subtilis are essential for the developmen... more B -dependent general stress proteins (Gsps) of Bacillus subtilis are essential for the development of glucosestarvation-induced cross-resistance to oxidative challenge. However, the proteins directly involved in this nonspecific resistance to oxidative stress have to be identified. We found that one prominent Gsp displayed strong sequence similarity to the previously characterized oxidative-stress-inducible MrgA protein of B. subtilis and to the starvation-induced Dps/PexB protein of Escherichia coli. We therefore designated this prominent Gsp Dps. While MrgA belongs to the peroxide-stress-inducible proteins needed for the H 2 O 2 -inducible adaptive response to oxidative stress, Dps belongs to the proteins induced by heat, salt, or ethanol stress and after starvation for glucose but not by a sublethal oxidative challenge. Primer extension experiments identified two overlapping promoters upstream of the coding region of dps, one being B dependent (P B ) and the other being B independent (P 1 ). Both promoters contribute to the basal level of dps during growth. After stress or during entry into the stationary phase, transcription from P B strongly increased whereas transcription from P 1 decreased. Mutant strains lacking Dps completely failed to develop glucose-starvation-induced resistance to oxidative stress. These results confirm our suggestion that B -dependent general stress proteins of B. subtilis are absolutely required for the development of nonspecific resistance to oxidative stress.

Research paper thumbnail of The genome of Methylobacillus flagellatus, the molecular basis for obligate methylotrophy, and the polyphyletic origin of methylotrophy

Lawrence Berkeley National Laboratory, Apr 28, 2008

Along with methane, methanol and methylated amines represent important biogenic atmospheric const... more Along with methane, methanol and methylated amines represent important biogenic atmospheric constituents; thus, not only methanotrophs but also nonmethanotrophic methylotrophs play a significant role in global carbon cycling. The complete genome of a model obligate methanol and methylamine utilizer, Methylobacillus flagellatus (strain KT) was sequenced. The genome is represented by a single circular chromosome of approximately 3 Mbp, potentially encoding a total of 2,766 proteins. Based on genome analysis as well as the results from previous genetic and mutational analyses, methylotrophy is enabled by methanol and methylamine dehydrogenases and their specific electron transport chain components, the tetrahydromethanopterin-linked formaldehyde oxidation pathway and the assimilatory and dissimilatory ribulose monophosphate cycles, and by a formate dehydrogenase. Some of the methylotrophy genes are present in more than one (identical or nonidentical) copy. The obligate dependence on single-carbon compounds appears to be due to the incomplete tricarboxylic acid cycle, as no genes potentially encoding alpha-ketoglutarate, malate, or succinate dehydrogenases are identifiable. The genome of M. flagellatus was compared in terms of methylotrophy functions to the previously sequenced genomes of three methylotrophs, Methylobacterium extorquens (an alphaproteobacterium, 7 Mbp), Methylibium petroleiphilum (a betaproteobacterium, 4 Mbp), and Methylococcus capsulatus (a gammaproteobacterium, 3.3 Mbp). Strikingly, metabolically and/or phylogenetically, the methylotrophy functions in M. flagellatus were more similar to those in M. capsulatus and M. extorquens than to the ones in the more closely related M. petroleiphilum species, providing the first genomic evidence for the polyphyletic origin of methylotrophy in Betaproteobacteria.

Research paper thumbnail of Complete genome sequence of Pyrolobus fumarii type strain (1AT)

Standards in Genomic Sciences, 2011

Pyrolobus fumarii Blöchl et al. 1997 is the type species of the genus Pyrolobus, which belongs to... more Pyrolobus fumarii Blöchl et al. 1997 is the type species of the genus Pyrolobus, which belongs to the crenarchaeal family Pyrodictiaceae. The species is a facultatively microaerophilic non-motile crenarchaeon. It is of interest because of its isolated phylogenetic location in ...

Research paper thumbnail of Complete genome sequence of Halanaerobium praevalens type strain (GSLT)

Standards in Genomic Sciences, 2011

Halanaerobium praevalens Zeikus et al. 1984 is the type species of the genus Halanaerobium, which... more Halanaerobium praevalens Zeikus et al. 1984 is the type species of the genus Halanaerobium, which in turn is the type genus of the family Halanaerobiaceae. The species is of interest because it is able to reduce a variety of nitro-substituted aromatic ...

Research paper thumbnail of Genome sequence of the thermophilic sulfate-reducing ocean bacterium Thermodesulfatator indicus type strain (CIR29812T)

Standards in Genomic Sciences, 2012

Abstract Thermodesulfatator indicus Moussard et al. 2004 is a member of the genomically so far po... more Abstract Thermodesulfatator indicus Moussard et al. 2004 is a member of the genomically so far poorly characterized family Thermodesulfobacteriaceae in the phylum Thermodesulfobacteria. Members of this phylum are of interest because they represent a ...

Research paper thumbnail of Expression of a stress- and starvation-induced dps/pexB-homologous gene is controlled by the alternative sigma factor sigmaB in Bacillus subtilis

Journal of Bacteriology, Dec 1, 1997

B -dependent general stress proteins (Gsps) of Bacillus subtilis are essential for the developmen... more B -dependent general stress proteins (Gsps) of Bacillus subtilis are essential for the development of glucosestarvation-induced cross-resistance to oxidative challenge. However, the proteins directly involved in this nonspecific resistance to oxidative stress have to be identified. We found that one prominent Gsp displayed strong sequence similarity to the previously characterized oxidative-stress-inducible MrgA protein of B. subtilis and to the starvation-induced Dps/PexB protein of Escherichia coli. We therefore designated this prominent Gsp Dps. While MrgA belongs to the peroxide-stress-inducible proteins needed for the H 2 O 2 -inducible adaptive response to oxidative stress, Dps belongs to the proteins induced by heat, salt, or ethanol stress and after starvation for glucose but not by a sublethal oxidative challenge. Primer extension experiments identified two overlapping promoters upstream of the coding region of dps, one being B dependent (P B ) and the other being B independent (P 1 ). Both promoters contribute to the basal level of dps during growth. After stress or during entry into the stationary phase, transcription from P B strongly increased whereas transcription from P 1 decreased. Mutant strains lacking Dps completely failed to develop glucose-starvation-induced resistance to oxidative stress. These results confirm our suggestion that B -dependent general stress proteins of B. subtilis are absolutely required for the development of nonspecific resistance to oxidative stress.

Research paper thumbnail of Fungi Contribute Critical but Spatially Varying Roles in Nitrogen and Carbon Cycling in Acid Mine Drainage

Frontiers in Microbiology, 2016

The ecosystem roles of fungi have been extensively studied by targeting one organism and/or biolo... more The ecosystem roles of fungi have been extensively studied by targeting one organism and/or biological process at a time, but the full metabolic potential of fungi has rarely been captured in an environmental context. We hypothesized that fungal genome sequences could be assembled directly from the environment using metagenomics and that transcriptomics and proteomics could simultaneously reveal metabolic differentiation across habitats. We reconstructed the near-complete 27 Mbp genome of a filamentous fungus, Acidomyces richmondensis, and evaluated transcript and protein expression in floating and streamer biofilms from an acid mine drainage (AMD) system. A. richmondensis transcripts involved in denitrification and in the degradation of complex carbon sources (including cellulose) were up-regulated in floating biofilms, whereas central carbon metabolism and stress-related transcripts were significantly up-regulated in streamer biofilms. These findings suggest that the biofilm niches are distinguished by distinct carbon and nitrogen resource utilization, oxygen availability, and environmental challenges. An isolated A. richmondensis strain from this environment was used to validate the metagenomics-derived genome and confirm nitrous oxide production at pH 1. Overall, our analyses defined mechanisms of fungal adaptation and identified a functional shift related to different roles in carbon and nitrogen turnover for the same species of fungi growing in closely located but distinct biofilm niches.

Research paper thumbnail of Permanent draft genome sequence of Desulfurococcus mobilis type strain DSM 2161, a thermoacidophilic sulfur-reducing crenarchaeon isolated from acidic hot springs of Hveravellir, Iceland

Standards in genomic sciences, 2016

This report presents the permanent draft genome sequence of Desulfurococcus mobilis type strain D... more This report presents the permanent draft genome sequence of Desulfurococcus mobilis type strain DSM 2161, an obligate anaerobic hyperthermophilic crenarchaeon that was isolated from acidic hot springs in Hveravellir, Iceland. D. mobilis utilizes peptides as carbon and energy sources and reduces elemental sulfur to H2S. A metabolic construction derived from the draft genome identified putative pathways for peptide degradation and sulfur respiration in this archaeon. Existence of several hydrogenase genes in the genome supported previous findings that H2 is produced during the growth of D. mobilis in the absence of sulfur. Interestingly, genes encoding glucose transport and utilization systems also exist in the D. mobilis genome though this archaeon does not utilize carbohydrate for growth. The draft genome of D. mobilis provides an additional mean for comparative genomic analysis of desulfurococci. In addition, our analysis on the Average Nucleotide Identity between D. mobilis and De...

Research paper thumbnail of The US Department of Energy Joint Genome Institute Microbial Genome Program

Lawrence Berkeley National Laboratory, Feb 11, 2005

Research paper thumbnail of Genome sequence of the button mushroom Agaricus bisporus reveals mechanisms governing adaptation to a humic-rich ecological niche

Proceedings of the National Academy of Sciences, 2012

ABSTRACT Agaricus bisporus is the model fungus for the adaptation, persistence, and growth in the... more ABSTRACT Agaricus bisporus is the model fungus for the adaptation, persistence, and growth in the humic-rich leaf-litter environment. Aside from its ecological role, A. bisporus has been an important component of the human diet for over 200 y and worldwide cultivation of the "button mushroom" forms a multibillion dollar industry. We present two A. bisporus genomes, their gene repertoires and transcript profiles on compost and during mushroom formation. The genomes encode a full repertoire of polysaccharide-degrading enzymes similar to that of wood-decayers. Comparative transcriptomics of mycelium grown on defined medium, casing-soil, and compost revealed genes encoding enzymes involved in xylan, cellulose, pectin, and protein degradation are more highly expressed in compost. The striking expansion of heme-thiolate peroxidases and β-etherases is distinctive from Agaricomycotina wood-decayers and suggests a broad attack on decaying lignin and related metabolites found in humic acid-rich environment. Similarly, up-regulation of these genes together with a lignolytic manganese peroxidase, multiple copper radical oxidases, and cytochrome P450s is consistent with challenges posed by complex humic-rich substrates. The gene repertoire and expression of hydrolytic enzymes in A. bisporus is substantially different from the taxonomically related ectomycorrhizal symbiont Laccaria bicolor. A common promoter motif was also identified in genes very highly expressed in humic-rich substrates. These observations reveal genetic and enzymatic mechanisms governing adaptation to the humic-rich ecological niche formed during plant degradation, further defining the critical role such fungi contribute to soil structure and carbon sequestration in terrestrial ecosystems. Genome sequence will expedite mushroom breeding for improved agronomic characteristics.

Research paper thumbnail of Appendix: ExSPAnder: a Universal Repeat Resolver for DNA Fragment Assembly

Research paper thumbnail of Comparative genomics of biotechnologically important yeasts

Proceedings of the National Academy of Sciences of the United States of America, Jan 17, 2016

Ascomycete yeasts are metabolically diverse, with great potential for biotechnology. Here, we rep... more Ascomycete yeasts are metabolically diverse, with great potential for biotechnology. Here, we report the comparative genome analysis of 29 taxonomically and biotechnologically important yeasts, including 16 newly sequenced. We identify a genetic code change, CUG-Ala, in Pachysolen tannophilus in the clade sister to the known CUG-Ser clade. Our well-resolved yeast phylogeny shows that some traits, such as methylotrophy, are restricted to single clades, whereas others, such as l-rhamnose utilization, have patchy phylogenetic distributions. Gene clusters, with variable organization and distribution, encode many pathways of interest. Genomics can predict some biochemical traits precisely, but the genomic basis of others, such as xylose utilization, remains unresolved. Our data also provide insight into early evolution of ascomycetes. We document the loss of H3K9me2/3 heterochromatin, the origin of ascomycete mating-type switching, and panascomycete synteny at the MAT locus. These data a...

Research paper thumbnail of 113.Wu.GEBA.Supplement

Research paper thumbnail of Catalytic hydrocondensation of carbon monoxide with olefins and their hydropolymerization under the effect of carbon monoxide and oxygen. Communication 58. Hydropolymerization of ethylene in the presence of Co-Carbonyl catalysts

Research paper thumbnail of De Wit et al PLoS Pathogens

Research paper thumbnail of Comparing polysaccharide decomposition between the type strains Gramella echinicola KMM 6050(T) (DSM 19838(T)) and Gramella portivictoriae UST040801-001(T) (DSM 23547(T)), and emended description of Gramella echinicola Nedashkovskaya et al. 2005 emend. Shahina et al. 2014 and Gramella portivictor...

Standards in genomic sciences, 2016

Strains of the genus Gramella (family Flavobacteriacae, phylum Bacteroidetes) were isolated from ... more Strains of the genus Gramella (family Flavobacteriacae, phylum Bacteroidetes) were isolated from marine habitats such as tidal flat sediments, coastal surface seawater and sea urchins. Flavobacteriaceae have been shown to be involved in the decomposition of plant and algal polysaccharides. However, the potential to decompose polysaccharides may differ tremendously even between species of the same genus. Gramella echinicola KMM 6050(T) (DSM 19838(T)) and Gramella portivictoriae UST040801-001(T) (DSM 23547(T)) have genomes of similar lengths, similar numbers of protein coding genes and RNA genes. Both genomes encode for a greater number of peptidases compared to 'G. forsetii'. In contrast to the genome of 'G. forsetii', both genomes comprised a smaller set of CAZymes. Seven polysaccharide utilization loci were identified in the genomes of DSM 19838(T) and DSM 23547(T). Both Gramella strains hydrolyzed starch, galactomannan, arabinoxylan and hydroxyethyl-cellulose, but ...

Research paper thumbnail of Complete genome sequence of the haloalkaliphilic, obligately chemolithoautotrophic thiosulfate and sulfide-oxidizing γ-proteobacterium Thioalkalimicrobium cyclicum type strain ALM 1 (DSM 14477(T))

Standards in genomic sciences, 2016

Thioalkalimicrobium cyclicum Sorokin et al. 2002 is a member of the family Piscirickettsiaceae in... more Thioalkalimicrobium cyclicum Sorokin et al. 2002 is a member of the family Piscirickettsiaceae in the order Thiotrichales. The γ-proteobacterium belongs to the colourless sulfur-oxidizing bacteria isolated from saline soda lakes with stable alkaline pH, such as Lake Mono (California) and Soap Lake (Washington State). Strain ALM 1(T) is characterized by its adaptation to life in the oxic/anoxic interface towards the less saline aerobic waters (mixolimnion) of the stable stratified alkaline salt lakes. Strain ALM 1(T) is the first representative of the genus Thioalkalimicrobium whose genome sequence has been deciphered and the fourth genome sequence of a type strain of the Piscirickettsiaceae to be published. The 1,932,455 bp long chromosome with its 1,684 protein-coding and 50 RNA genes was sequenced as part of the DOE Joint Genome Institute Community Sequencing Program (CSP) 2008.

Research paper thumbnail of Transposable Elements versus the Fungal Genome: Impact on Whole-Genome Architecture and Transcriptional Profiles

PLoS genetics, Jun 1, 2016

Transposable elements (TEs) are exceptional contributors to eukaryotic genome diversity. Their ub... more Transposable elements (TEs) are exceptional contributors to eukaryotic genome diversity. Their ubiquitous presence impacts the genomes of nearly all species and mediates genome evolution by causing mutations and chromosomal rearrangements and by modulating gene expression. We performed an exhaustive analysis of the TE content in 18 fungal genomes, including strains of the same species and species of the same genera. Our results depicted a scenario of exceptional variability, with species having 0.02 to 29.8% of their genome consisting of transposable elements. A detailed analysis performed on two strains of Pleurotus ostreatus uncovered a genome that is populated mainly by Class I elements, especially LTR-retrotransposons amplified in recent bursts from 0 to 2 million years (My) ago. The preferential accumulation of TEs in clusters led to the presence of genomic regions that lacked intra- and inter-specific conservation. In addition, we investigated the effect of TE insertions on th...

Research paper thumbnail of A New Monte-Carlo Simulation Model for the Temporal Development of Cloud Droplet Spectra

J Atmos Sci, 1972

A new Monte-Carlo simulation model for computing the temporal development of cloud droplet spectr... more A new Monte-Carlo simulation model for computing the temporal development of cloud droplet spectra is presented. Since the simulation is carried out in probability space, the new model does not need to follow the growth history and position of each and every drop. Additional physical processes, such as turbulence, electrical effects, glaciation, etc., can be added to the primary growth

Research paper thumbnail of Influence of Preparation Method on Activity of Cobalt Catalysts for Hydrocarbon Synthesis from Co and H2

Russ Chem Bull, 1984

ABSTRACT 1. The method used for the preparation of cobalt catalysts has a considerable influence ... more ABSTRACT 1. The method used for the preparation of cobalt catalysts has a considerable influence on their activity in the synthesis of hydrocarbons from CO and H2. 2. In the selection of a method for preparing cobalt catalysts for the Fischer-Tropsch synthesis, the mean pore radius of the support that is used is a decisive factor. 3. The chemisorption of carbon monoxide on cobalt catalysts depends on the method of their preparation.

Research paper thumbnail of Expression of a Stress- and Starvation-Induced dps/pexB- Homologous Gene Is Controlled by the Alternative Sigma Factor sB in Bacillus subtilis

B -dependent general stress proteins (Gsps) of Bacillus subtilis are essential for the developmen... more B -dependent general stress proteins (Gsps) of Bacillus subtilis are essential for the development of glucosestarvation-induced cross-resistance to oxidative challenge. However, the proteins directly involved in this nonspecific resistance to oxidative stress have to be identified. We found that one prominent Gsp displayed strong sequence similarity to the previously characterized oxidative-stress-inducible MrgA protein of B. subtilis and to the starvation-induced Dps/PexB protein of Escherichia coli. We therefore designated this prominent Gsp Dps. While MrgA belongs to the peroxide-stress-inducible proteins needed for the H 2 O 2 -inducible adaptive response to oxidative stress, Dps belongs to the proteins induced by heat, salt, or ethanol stress and after starvation for glucose but not by a sublethal oxidative challenge. Primer extension experiments identified two overlapping promoters upstream of the coding region of dps, one being B dependent (P B ) and the other being B independent (P 1 ). Both promoters contribute to the basal level of dps during growth. After stress or during entry into the stationary phase, transcription from P B strongly increased whereas transcription from P 1 decreased. Mutant strains lacking Dps completely failed to develop glucose-starvation-induced resistance to oxidative stress. These results confirm our suggestion that B -dependent general stress proteins of B. subtilis are absolutely required for the development of nonspecific resistance to oxidative stress.

Research paper thumbnail of The genome of Methylobacillus flagellatus, the molecular basis for obligate methylotrophy, and the polyphyletic origin of methylotrophy

Lawrence Berkeley National Laboratory, Apr 28, 2008

Along with methane, methanol and methylated amines represent important biogenic atmospheric const... more Along with methane, methanol and methylated amines represent important biogenic atmospheric constituents; thus, not only methanotrophs but also nonmethanotrophic methylotrophs play a significant role in global carbon cycling. The complete genome of a model obligate methanol and methylamine utilizer, Methylobacillus flagellatus (strain KT) was sequenced. The genome is represented by a single circular chromosome of approximately 3 Mbp, potentially encoding a total of 2,766 proteins. Based on genome analysis as well as the results from previous genetic and mutational analyses, methylotrophy is enabled by methanol and methylamine dehydrogenases and their specific electron transport chain components, the tetrahydromethanopterin-linked formaldehyde oxidation pathway and the assimilatory and dissimilatory ribulose monophosphate cycles, and by a formate dehydrogenase. Some of the methylotrophy genes are present in more than one (identical or nonidentical) copy. The obligate dependence on single-carbon compounds appears to be due to the incomplete tricarboxylic acid cycle, as no genes potentially encoding alpha-ketoglutarate, malate, or succinate dehydrogenases are identifiable. The genome of M. flagellatus was compared in terms of methylotrophy functions to the previously sequenced genomes of three methylotrophs, Methylobacterium extorquens (an alphaproteobacterium, 7 Mbp), Methylibium petroleiphilum (a betaproteobacterium, 4 Mbp), and Methylococcus capsulatus (a gammaproteobacterium, 3.3 Mbp). Strikingly, metabolically and/or phylogenetically, the methylotrophy functions in M. flagellatus were more similar to those in M. capsulatus and M. extorquens than to the ones in the more closely related M. petroleiphilum species, providing the first genomic evidence for the polyphyletic origin of methylotrophy in Betaproteobacteria.

Research paper thumbnail of Complete genome sequence of Pyrolobus fumarii type strain (1AT)

Standards in Genomic Sciences, 2011

Pyrolobus fumarii Blöchl et al. 1997 is the type species of the genus Pyrolobus, which belongs to... more Pyrolobus fumarii Blöchl et al. 1997 is the type species of the genus Pyrolobus, which belongs to the crenarchaeal family Pyrodictiaceae. The species is a facultatively microaerophilic non-motile crenarchaeon. It is of interest because of its isolated phylogenetic location in ...

Research paper thumbnail of Complete genome sequence of Halanaerobium praevalens type strain (GSLT)

Standards in Genomic Sciences, 2011

Halanaerobium praevalens Zeikus et al. 1984 is the type species of the genus Halanaerobium, which... more Halanaerobium praevalens Zeikus et al. 1984 is the type species of the genus Halanaerobium, which in turn is the type genus of the family Halanaerobiaceae. The species is of interest because it is able to reduce a variety of nitro-substituted aromatic ...

Research paper thumbnail of Genome sequence of the thermophilic sulfate-reducing ocean bacterium Thermodesulfatator indicus type strain (CIR29812T)

Standards in Genomic Sciences, 2012

Abstract Thermodesulfatator indicus Moussard et al. 2004 is a member of the genomically so far po... more Abstract Thermodesulfatator indicus Moussard et al. 2004 is a member of the genomically so far poorly characterized family Thermodesulfobacteriaceae in the phylum Thermodesulfobacteria. Members of this phylum are of interest because they represent a ...

Research paper thumbnail of Expression of a stress- and starvation-induced dps/pexB-homologous gene is controlled by the alternative sigma factor sigmaB in Bacillus subtilis

Journal of Bacteriology, Dec 1, 1997

B -dependent general stress proteins (Gsps) of Bacillus subtilis are essential for the developmen... more B -dependent general stress proteins (Gsps) of Bacillus subtilis are essential for the development of glucosestarvation-induced cross-resistance to oxidative challenge. However, the proteins directly involved in this nonspecific resistance to oxidative stress have to be identified. We found that one prominent Gsp displayed strong sequence similarity to the previously characterized oxidative-stress-inducible MrgA protein of B. subtilis and to the starvation-induced Dps/PexB protein of Escherichia coli. We therefore designated this prominent Gsp Dps. While MrgA belongs to the peroxide-stress-inducible proteins needed for the H 2 O 2 -inducible adaptive response to oxidative stress, Dps belongs to the proteins induced by heat, salt, or ethanol stress and after starvation for glucose but not by a sublethal oxidative challenge. Primer extension experiments identified two overlapping promoters upstream of the coding region of dps, one being B dependent (P B ) and the other being B independent (P 1 ). Both promoters contribute to the basal level of dps during growth. After stress or during entry into the stationary phase, transcription from P B strongly increased whereas transcription from P 1 decreased. Mutant strains lacking Dps completely failed to develop glucose-starvation-induced resistance to oxidative stress. These results confirm our suggestion that B -dependent general stress proteins of B. subtilis are absolutely required for the development of nonspecific resistance to oxidative stress.

Research paper thumbnail of Fungi Contribute Critical but Spatially Varying Roles in Nitrogen and Carbon Cycling in Acid Mine Drainage

Frontiers in Microbiology, 2016

The ecosystem roles of fungi have been extensively studied by targeting one organism and/or biolo... more The ecosystem roles of fungi have been extensively studied by targeting one organism and/or biological process at a time, but the full metabolic potential of fungi has rarely been captured in an environmental context. We hypothesized that fungal genome sequences could be assembled directly from the environment using metagenomics and that transcriptomics and proteomics could simultaneously reveal metabolic differentiation across habitats. We reconstructed the near-complete 27 Mbp genome of a filamentous fungus, Acidomyces richmondensis, and evaluated transcript and protein expression in floating and streamer biofilms from an acid mine drainage (AMD) system. A. richmondensis transcripts involved in denitrification and in the degradation of complex carbon sources (including cellulose) were up-regulated in floating biofilms, whereas central carbon metabolism and stress-related transcripts were significantly up-regulated in streamer biofilms. These findings suggest that the biofilm niches are distinguished by distinct carbon and nitrogen resource utilization, oxygen availability, and environmental challenges. An isolated A. richmondensis strain from this environment was used to validate the metagenomics-derived genome and confirm nitrous oxide production at pH 1. Overall, our analyses defined mechanisms of fungal adaptation and identified a functional shift related to different roles in carbon and nitrogen turnover for the same species of fungi growing in closely located but distinct biofilm niches.

Research paper thumbnail of Permanent draft genome sequence of Desulfurococcus mobilis type strain DSM 2161, a thermoacidophilic sulfur-reducing crenarchaeon isolated from acidic hot springs of Hveravellir, Iceland

Standards in genomic sciences, 2016

This report presents the permanent draft genome sequence of Desulfurococcus mobilis type strain D... more This report presents the permanent draft genome sequence of Desulfurococcus mobilis type strain DSM 2161, an obligate anaerobic hyperthermophilic crenarchaeon that was isolated from acidic hot springs in Hveravellir, Iceland. D. mobilis utilizes peptides as carbon and energy sources and reduces elemental sulfur to H2S. A metabolic construction derived from the draft genome identified putative pathways for peptide degradation and sulfur respiration in this archaeon. Existence of several hydrogenase genes in the genome supported previous findings that H2 is produced during the growth of D. mobilis in the absence of sulfur. Interestingly, genes encoding glucose transport and utilization systems also exist in the D. mobilis genome though this archaeon does not utilize carbohydrate for growth. The draft genome of D. mobilis provides an additional mean for comparative genomic analysis of desulfurococci. In addition, our analysis on the Average Nucleotide Identity between D. mobilis and De...

Research paper thumbnail of The US Department of Energy Joint Genome Institute Microbial Genome Program

Lawrence Berkeley National Laboratory, Feb 11, 2005