cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.1378770.v1
title: Metagenomic and Metatranscriptomic Analyses of Bacterial Communities Derived From a Calcifying Karst Water Creek Biofilm and Tufa

description: Calcification of freshwater streams and the involvement of microorganisms in this process are still not fully understood. Here, we report on the metagenomic and metatranscriptomic analyses of bacterial community structures derived from an actively calcifying karst water creek biofilm and underlying tufa by employing next-generation sequencing technologies.The persistent and metabolically active bacterial communities were assessed by DNA-based and RNA-based 16S rRNA gene sequence analysis, respectively. We identified filamentous <i>Cyanobacteria</i> belonging to the <i>Oscillatoriales</i> as the predominant bacterial microorganisms in the biofilm. <i>Cyanobacteria</i> were accompanied by a high diversity of mainly aerobic members affiliated to different bacterial phyla. The second most abundant phylum was <i>Proteobacteria,</i> represented by the classes <i>Alphaproteobacteria</i>, <i>Betaproteobacteria</i>, <i>Gammaproteobacteria</i>, and <i>Deltaproteobacteria</i>. In addition, <i>Chloroflexi</i>, <i>Planctomycetes</i>, <i>Actinobacteria</i>, <i>Acidobacteria</i>, <i>Bacteroidetes</i>, <i>Spirochaetes</i>, and <i>Verrucomicrobia</i> were present in higher abundances (&gt;0.5%). Several of these phyla included potentially novel subgroups. The tufa stromatolite carbonate one centimeter below the surface exhibited a similar prokaryotic community as the superficial biofilm but showed a lower abundance of <i>Cyanobacteria</i> and a more diverse microbial community. We obtained insights into the <i>in situ</i> microbial metabolism by employing directed sequencing of enriched mRNA (cDNA) and subsequent taxonomic and functional analysis of biofilm-derived reads. High activities in photosynthesis, carbon and protein metabolism were indicated.
DOI: 10.6084/m9.figshare.1378766
title: An Imaging Mass Spectrometry Study on the Formation of Conditioning Films and Biofilms in the Subsurface (Äspö Hard Rock Laboratory, SE Sweden)

description: Conditioning films and biofilms forming on surfaces of solid materials exposed to aqueous media play a key role in in the interaction between the geo- and biospheres. In this study, time-of-flight secondary ion mass spectrometry and scanning electron microscopy were used to investigate the time scale, mode of formation, and chemistry of conditioning films and biofilms that formed on Si substrates exposed to aquifer water in the subsurface Äspö Hard Rock Laboratory, SE-Sweden. The detection of fragment ions of amino acids, carbohydrates, and carboxylic acids revealed that different types of organic compounds had adhered to the Si surface already after 10 min of exposure to the aquifer fluids, whereas the attachment of microbial cells was first observed after 1000 min. The organic compounds first formed isolated μm-sized accumulations and subsequently started to distribute on the wafer surface more homogenously. Simultaneously further microorganisms attached to the surface and formed biofilm-like cell accumulations after 3 months of exposure to aquifer water.
DOI: 10.6084/m9.figshare.1378768.v2
title: Diversity of Microscopic Green Algae (Chlorophyta) in Calcifying Biofilms of Two Karstic Streams in Germany

description: For the first time the diversity of microscopic green algae (Chlorophyta) from calcified biofilms of karstic streams was analyzed using a combined approach based on pure cultures, i.e., 18S rRNA gene sequencing and microscopic analyses. Our study focused on two creeks in Germany. A considerable diversity of 34 species of green microalgae comprising three classes, the Trebouxiophyceae, Chlorophyceae and Ulvophyceae, was recovered. The biofilms of both streams were rather different in their species compositions which may reflect that they are exposed to differed hydrochemical conditions. The shallow Westerhöfer creek harbored predominantly Trebouxiophyceae and exhibited higher Mg<sup>2+</sup> and SO<sub>4</sub><sup>2−</sup> concentrations. In contrast, the deeper, longer and spatially more heterogeneous Deinschwanger creek harbored numerous species of Chlorophyceae. A lower number of species from the Ulvophyceae were spread on both studied streams. The closest relatives of the identified species were from other freshwater habitats, but mostly from phytoplankton. However, also several species we recovered from freshwater for the first time; so far they have been known from terrestrial habitats only. Less than half of the recovered species could be identified with names at the species level based on high sequence identities with available sequences from named reference strains. Most recovered species could not be identified with names to species level, i.e., they may represent species for which no 18S rRNA gene sequence have become available yet or which have been retrieved for the first time. The genus <i>Gongrosira</i> Kützing, often reported from freshwater tufa-stromatolites, was found to represent most likely a collective morphotype formed by several genera nested within the Ulvophyceae.
DOI: 10.6084/m9.figshare.1378768.v1
title: Diversity of Microscopic Green Algae (Chlorophyta) in Calcifying Biofilms of Two Karstic Streams in Germany

description: For the first time the diversity of microscopic green algae (Chlorophyta) from calcified biofilms of karstic streams was analyzed using a combined approach based on pure cultures, i.e., 18S rRNA gene sequencing and microscopic analyses. Our study focused on two creeks in Germany. A considerable diversity of 34 species of green microalgae comprising three classes, the Trebouxiophyceae, Chlorophyceae and Ulvophyceae, was recovered. The biofilms of both streams were rather different in their species compositions which may reflect that they are exposed to differed hydrochemical conditions. The shallow Westerhöfer creek harbored predominantly Trebouxiophyceae and exhibited higher Mg<sup>2+</sup> and SO<sub>4</sub><sup>2−</sup> concentrations. In contrast, the deeper, longer and spatially more heterogeneous Deinschwanger creek harbored numerous species of Chlorophyceae. A lower number of species from the Ulvophyceae were spread on both studied streams. The closest relatives of the identified species were from other freshwater habitats, but mostly from phytoplankton. However, also several species we recovered from freshwater for the first time; so far they have been known from terrestrial habitats only. Less than half of the recovered species could be identified with names at the species level based on high sequence identities with available sequences from named reference strains. Most recovered species could not be identified with names to species level, i.e., they may represent species for which no 18S rRNA gene sequence have become available yet or which have been retrieved for the first time. The genus <i>Gongrosira</i> Kützing, often reported from freshwater tufa-stromatolites, was found to represent most likely a collective morphotype formed by several genera nested within the Ulvophyceae.
DOI: 10.6084/m9.figshare.1378766.v2
title: An Imaging Mass Spectrometry Study on the Formation of Conditioning Films and Biofilms in the Subsurface (Äspö Hard Rock Laboratory, SE Sweden)

description: Conditioning films and biofilms forming on surfaces of solid materials exposed to aqueous media play a key role in in the interaction between the geo- and biospheres. In this study, time-of-flight secondary ion mass spectrometry and scanning electron microscopy were used to investigate the time scale, mode of formation, and chemistry of conditioning films and biofilms that formed on Si substrates exposed to aquifer water in the subsurface Äspö Hard Rock Laboratory, SE-Sweden. The detection of fragment ions of amino acids, carbohydrates, and carboxylic acids revealed that different types of organic compounds had adhered to the Si surface already after 10 min of exposure to the aquifer fluids, whereas the attachment of microbial cells was first observed after 1000 min. The organic compounds first formed isolated μm-sized accumulations and subsequently started to distribute on the wafer surface more homogenously. Simultaneously further microorganisms attached to the surface and formed biofilm-like cell accumulations after 3 months of exposure to aquifer water.
DOI: 10.6084/m9.figshare.1378766.v1
title: An Imaging Mass Spectrometry Study on the Formation of Conditioning Films and Biofilms in the Subsurface (Äspö Hard Rock Laboratory, SE Sweden)

description: Conditioning films and biofilms forming on surfaces of solid materials exposed to aqueous media play a key role in in the interaction between the geo- and biospheres. In this study, time-of-flight secondary ion mass spectrometry and scanning electron microscopy were used to investigate the time scale, mode of formation, and chemistry of conditioning films and biofilms that formed on Si substrates exposed to aquifer water in the subsurface Äspö Hard Rock Laboratory, SE-Sweden. The detection of fragment ions of amino acids, carbohydrates, and carboxylic acids revealed that different types of organic compounds had adhered to the Si surface already after 10 min of exposure to the aquifer fluids, whereas the attachment of microbial cells was first observed after 1000 min. The organic compounds first formed isolated μm-sized accumulations and subsequently started to distribute on the wafer surface more homogenously. Simultaneously further microorganisms attached to the surface and formed biofilm-like cell accumulations after 3 months of exposure to aquifer water.
DOI: 10.6084/m9.figshare.1378763
title: Self-Assembly of 2D Lanthanide-Metal Coordination Polymers Based on 5-Nitroisophthalic Acid Linker: Synthesis, Structures, and Luminescence

description: Three 2D novel lanthanide-based metallic coordination frameworks involving the 5-nitroisophthalic acid ligand were characterized by elemental analysis, infrared spectroscopy, thermogravimetric analysis, and single-crystal X-ray diffraction, namely, [Er(NIPH)<sub>2</sub>(H<sub>2</sub>O)<sub>2</sub>](H<sub>2</sub>O)<sub>2</sub><b>(1)</b>, [Eu<sub>4</sub>(NIPH)<sub>6</sub>(H<sub>2</sub>O)<sub>8</sub>](H<sub>2</sub>O)<sub>5</sub><b>(2),</b> and [Eu<sub>4</sub>(NIPH)<sub>6</sub>(H<sub>2</sub>O)<sub>6</sub>](H<sub>2</sub>O)<sub>4</sub><b>(3)</b>, synthesized under hydrothermal conditions, self-assemble through Ln<sub>2</sub>[NIPH]<sub>2</sub> building blocks to give a 2D coordination layer structure. The adjacent layers stack to form a 3D supramolecular framework through weak interactions, such as hydrogen bonding, π–π interactions, and lone pair-π interactions. However, in <b>1</b> and <b>2</b> formed 2D 4-connected (4,4) topological network. In addition, in this work the photoluminescent property of the compound <b>3</b> has been studied.
DOI: 10.6084/m9.figshare.1378763.v1
title: Self-Assembly of 2D Lanthanide-Metal Coordination Polymers Based on 5-Nitroisophthalic Acid Linker: Synthesis, Structures, and Luminescence

description: Three 2D novel lanthanide-based metallic coordination frameworks involving the 5-nitroisophthalic acid ligand were characterized by elemental analysis, infrared spectroscopy, thermogravimetric analysis, and single-crystal X-ray diffraction, namely, [Er(NIPH)<sub>2</sub>(H<sub>2</sub>O)<sub>2</sub>](H<sub>2</sub>O)<sub>2</sub><b>(1)</b>, [Eu<sub>4</sub>(NIPH)<sub>6</sub>(H<sub>2</sub>O)<sub>8</sub>](H<sub>2</sub>O)<sub>5</sub><b>(2),</b> and [Eu<sub>4</sub>(NIPH)<sub>6</sub>(H<sub>2</sub>O)<sub>6</sub>](H<sub>2</sub>O)<sub>4</sub><b>(3)</b>, synthesized under hydrothermal conditions, self-assemble through Ln<sub>2</sub>[NIPH]<sub>2</sub> building blocks to give a 2D coordination layer structure. The adjacent layers stack to form a 3D supramolecular framework through weak interactions, such as hydrogen bonding, π–π interactions, and lone pair-π interactions. However, in <b>1</b> and <b>2</b> formed 2D 4-connected (4,4) topological network. In addition, in this work the photoluminescent property of the compound <b>3</b> has been studied.
DOI: 10.6084/m9.figshare.1378749
title: RBM4-MEF2C network constitutes a feed-forward circuit that facilitates the differentiation of brown adipocytes

description: Myocyte enhancer factor 2c (MEF2C) is the MADS-box type transcription factor involved in the differentiation of cardiac and skeletal muscle and synaptic formation. Alternatively spliced transcripts of the <i>MEF2C</i> gene were proven to encode isoforms which exert distinct functions in transcriptional regulation. During the differentiation of brown adipocytes, upregulated RBM4 enhanced skipping of the <i>MEF2C</i>γ region which functions as a transcriptional repressor. The presence of an overexpressed MEF2Cγ- isoform in turn induced transcriptional activity of the <i>RBM4</i> promoter, constituting a positive feedback circuit in differentiating brown adipocytes. The RBM4-MEF2Cγ- network induced the expression of "myogenic" miR-1 to a greater extent than did <i>PRDM17, BMP7 C/EBP</i>β, or <i>UCP1</i> transcripts in C3H10T1/2 cells. Overexpression of miR-1 independently exerted the same activity as RBM4 and the MEF2Cγ- isoform of upregulating brown adipocyte-specific factors in C3H10T1/2 cells, which suggests a potential effect of miR-1 on brown adipocytes. These results indicated that the RBM4-MEF2C-miR-1 network constitutes a novel mechanism which programs the gene expression profile toward the development of brown adipocytes.
DOI: 10.6084/m9.figshare.1378748
title: Design criteria for synthetic riboswitches acting on transcription

description: Riboswitches are RNA-based regulators of gene expression composed of a ligand-sensing aptamer domain followed by an overlapping expression platform. The regulation occurs at either the level of transcription (by formation of terminator or antiterminator structures) or translation (by presentation or sequestering of the ribosomal binding site). Due to a modular composition, these elements can be manipulated by combining different aptamers and expression platforms and therefore represent useful tools to regulate gene expression in synthetic biology. Using computationally designed theophylline-dependent riboswitches we show that 2 parameters, terminator hairpin stability and folding traps, have a major impact on the functionality of the designed constructs. These have to be considered very carefully during design phase. Furthermore, a combination of several copies of individual riboswitches leads to a much improved activation ratio between induced and uninduced gene activity and to a linear dose-dependent increase in reporter gene expression. Such serial arrangements of synthetic riboswitches closely resemble their natural counterparts and may form the basis for simple quantitative read out systems for the detection of specific target molecules in the cell.
DOI: 10.6084/m9.figshare.1378749.v1
title: RBM4-MEF2C network constitutes a feed-forward circuit that facilitates the differentiation of brown adipocytes

description: Myocyte enhancer factor 2c (MEF2C) is the MADS-box type transcription factor involved in the differentiation of cardiac and skeletal muscle and synaptic formation. Alternatively spliced transcripts of the <i>MEF2C</i> gene were proven to encode isoforms which exert distinct functions in transcriptional regulation. During the differentiation of brown adipocytes, upregulated RBM4 enhanced skipping of the <i>MEF2C</i>γ region which functions as a transcriptional repressor. The presence of an overexpressed MEF2Cγ- isoform in turn induced transcriptional activity of the <i>RBM4</i> promoter, constituting a positive feedback circuit in differentiating brown adipocytes. The RBM4-MEF2Cγ- network induced the expression of "myogenic" miR-1 to a greater extent than did <i>PRDM17, BMP7 C/EBP</i>β, or <i>UCP1</i> transcripts in C3H10T1/2 cells. Overexpression of miR-1 independently exerted the same activity as RBM4 and the MEF2Cγ- isoform of upregulating brown adipocyte-specific factors in C3H10T1/2 cells, which suggests a potential effect of miR-1 on brown adipocytes. These results indicated that the RBM4-MEF2C-miR-1 network constitutes a novel mechanism which programs the gene expression profile toward the development of brown adipocytes.
DOI: 10.6084/m9.figshare.1378746
title: Transcriptional profiling of <i>Bordetella pertussis</i> reveals requirement of RNA chaperone Hfq for Type III secretion system functionality

description: <i>Bordetella pertussis</i>, the causative agent of human whooping cough (pertussis) produces a complex array of virulence factors in order to establish efficient infection in the host. The RNA chaperone Hfq and small regulatory RNAs are key players in posttranscriptional regulation in bacteria and have been shown to play an essential role in virulence of a broad spectrum of bacterial pathogens. This study represents the first attempt to characterize the Hfq regulon of the human pathogen <i>B. pertussis</i> under laboratory conditions as well as upon passage in the host and indicates that loss of Hfq has a profound effect on gene expression in <i>B. pertussis</i>. Comparative transcriptional profiling revealed that Hfq is required for expression of several virulence factors in <i>B. pertussis</i> cells including the Type III secretion system (T3SS). In striking contrast to the wt strain, T3SS did not become operational in the <i>hfq</i> mutant passaged either through mice or macrophages thereby proving that Hfq is required for the functionality of the <i>B. pertussis</i> T3SS. Likewise, expression of virulence factors <i>vag8</i> and <i>tcfA</i> encoding autotransporter and tracheal colonization factor, respectively, was strongly reduced in the <i>hfq</i> mutant. Importantly, for the first time we demonstrate that <i>B. pertussis</i> T3SS can be activated upon contact with macrophage cells <i>in vitro</i>.
DOI: 10.6084/m9.figshare.1378748.v1
title: Design criteria for synthetic riboswitches acting on transcription

description: Riboswitches are RNA-based regulators of gene expression composed of a ligand-sensing aptamer domain followed by an overlapping expression platform. The regulation occurs at either the level of transcription (by formation of terminator or antiterminator structures) or translation (by presentation or sequestering of the ribosomal binding site). Due to a modular composition, these elements can be manipulated by combining different aptamers and expression platforms and therefore represent useful tools to regulate gene expression in synthetic biology. Using computationally designed theophylline-dependent riboswitches we show that 2 parameters, terminator hairpin stability and folding traps, have a major impact on the functionality of the designed constructs. These have to be considered very carefully during design phase. Furthermore, a combination of several copies of individual riboswitches leads to a much improved activation ratio between induced and uninduced gene activity and to a linear dose-dependent increase in reporter gene expression. Such serial arrangements of synthetic riboswitches closely resemble their natural counterparts and may form the basis for simple quantitative read out systems for the detection of specific target molecules in the cell.
DOI: 10.6084/m9.figshare.1378749.v2
title: RBM4-MEF2C network constitutes a feed-forward circuit that facilitates the differentiation of brown adipocytes

description: Myocyte enhancer factor 2c (MEF2C) is the MADS-box type transcription factor involved in the differentiation of cardiac and skeletal muscle and synaptic formation. Alternatively spliced transcripts of the <i>MEF2C</i> gene were proven to encode isoforms which exert distinct functions in transcriptional regulation. During the differentiation of brown adipocytes, upregulated RBM4 enhanced skipping of the <i>MEF2C</i>γ region which functions as a transcriptional repressor. The presence of an overexpressed MEF2Cγ- isoform in turn induced transcriptional activity of the <i>RBM4</i> promoter, constituting a positive feedback circuit in differentiating brown adipocytes. The RBM4-MEF2Cγ- network induced the expression of "myogenic" miR-1 to a greater extent than did <i>PRDM17, BMP7 C/EBP</i>β, or <i>UCP1</i> transcripts in C3H10T1/2 cells. Overexpression of miR-1 independently exerted the same activity as RBM4 and the MEF2Cγ- isoform of upregulating brown adipocyte-specific factors in C3H10T1/2 cells, which suggests a potential effect of miR-1 on brown adipocytes. These results indicated that the RBM4-MEF2C-miR-1 network constitutes a novel mechanism which programs the gene expression profile toward the development of brown adipocytes.
DOI: 10.6084/m9.figshare.1378749.v4
title: RBM4-MEF2C network constitutes a feed-forward circuit that facilitates the differentiation of brown adipocytes

description: Myocyte enhancer factor 2c (MEF2C) is the MADS-box type transcription factor involved in the differentiation of cardiac and skeletal muscle and synaptic formation. Alternatively spliced transcripts of the <i>MEF2C</i> gene were proven to encode isoforms which exert distinct functions in transcriptional regulation. During the differentiation of brown adipocytes, upregulated RBM4 enhanced skipping of the <i>MEF2C</i>γ region which functions as a transcriptional repressor. The presence of an overexpressed MEF2Cγ- isoform in turn induced transcriptional activity of the <i>RBM4</i> promoter, constituting a positive feedback circuit in differentiating brown adipocytes. The RBM4-MEF2Cγ- network induced the expression of "myogenic" miR-1 to a greater extent than did <i>PRDM17, BMP7 C/EBP</i>β, or <i>UCP1</i> transcripts in C3H10T1/2 cells. Overexpression of miR-1 independently exerted the same activity as RBM4 and the MEF2Cγ- isoform of upregulating brown adipocyte-specific factors in C3H10T1/2 cells, which suggests a potential effect of miR-1 on brown adipocytes. These results indicated that the RBM4-MEF2C-miR-1 network constitutes a novel mechanism which programs the gene expression profile toward the development of brown adipocytes.
DOI: 10.6084/m9.figshare.1378745
title: The VrrA sRNA controls a stationary phase survival factor Vrp of <i>Vibrio cholerae</i>

description: Small non-coding RNAs (sRNAs) are emerging regulatory elements in bacteria. The <i>Vibrio cholerae</i> sRNA VrrA has previously been shown to down-regulate outer membrane proteins (OmpA and OmpT) and biofilm matrix protein (RbmC) by base-pairing with the 5′ region of the corresponding mRNAs. In this study, we present an additional target of VrrA in <i>V. cholerae</i>, the mRNA coding for the ribosome binding protein Vrp. Vrp is homologous to ribosome-associated inhibitor A (RaiA) of <i>Escherichia coli</i> which facilitates stationary phase survival through ribosome hibernation. We show that VrrA down-regulates Vrp protein synthesis by base-pairing to the 5′ region of <i>vrp</i> mRNA and that the regulation requires the RNA chaperone protein, Hfq. We further demonstrate that Vrp is highly expressed during stationary phase growth and associates with the ribosome of <i>V. cholerae</i>. The effect of the Vrp protein in starvation survival is synergistic with that of the VC2530 protein, a homolog of the <i>E. coli</i> hibernation promoting factor HPF, suggesting a combined role for these proteins in ribosome hibernation in <i>V. cholerae</i>. Vrp and VC2530 are important for <i>V. cholerae</i> starvation survival under nutrient deficient conditions. While VC2530 is down-regulated in cells lacking <i>vrrA</i>, mutation of <i>vrp</i> results in VC2530 activation. This is the first report indicating a regulatory role for an sRNA, modulating stationary factors involved in bacterial ribosome hibernation.