Terrestrial-type nitrogen-fixing symbiosis between seagrass and a marine bacterium.

Symbiotic N2-fixing microorganisms have a crucial role in the assimilation of nitrogen by eukaryotes in nitrogen-limited environments1-3. Particularly among land plants, N2-fixing symbionts occur in a variety of distantly related plant lineages and often involve an intimate association between host and symbiont2,4. Descriptions of such intimate symbioses are lacking for seagrasses, which evolved around 100 million years ago from terrestrial flowering plants that migrated back to the sea5. Here we describe an N2-fixing symbiont, 'Candidatus Celerinatantimonas neptuna', that lives inside seagrass root tissue, where it provides ammonia and amino acids to its host in exchange for sugars. As such, this symbiosis is reminiscent of terrestrial N2-fixing plant symbioses. The symbiosis between Ca. C. neptuna and its host Posidonia oceanica enables highly productive seagrass meadows to thrive in the nitrogen-limited Mediterranean Sea. Relatives of Ca. C. neptuna occur worldwide in coastal ecosystems, in which they may form similar symbioses with other seagrasses and saltmarsh plants. Just like N2-fixing microorganisms might have aided the colonization of nitrogen-poor soils by early land plants6, the ancestors of Ca. C. neptuna and its relatives probably enabled flowering plants to invade nitrogen-poor marine habitats, where they formed extremely efficient blue carbon ecosystems7.

UnCoVar: a reproducible and scalable workflow for transparent and robust virus variant calling and lineage assignment using SARS-CoV-2 as an example.

BACKGROUND: At a global scale, the SARS-CoV-2 virus did not remain in its initial genotype for a long period of time, with the first global reports of variants of concern (VOCs) in late 2020. Subsequently, genome sequencing has become an indispensable tool for characterizing the ongoing pandemic, particularly for typing SARS-CoV-2 samples obtained from patients or environmental surveillance. For such SARS-CoV-2 typing, various in vitro and in silico workflows exist, yet to date, no systematic cross-platform validation has been reported. RESULTS: In this work, we present the first comprehensive cross-platform evaluation and validation of in silico SARS-CoV-2 typing workflows. The evaluation relies on a dataset of 54 patient-derived samples sequenced with several different in vitro approaches on all relevant state-of-the-art sequencing platforms. Moreover, we present UnCoVar, a robust, production-grade reproducible SARS-CoV-2 typing workflow that outperforms all other tested approaches in terms of precision and recall. CONCLUSIONS: In many ways, the SARS-CoV-2 pandemic has accelerated the development of techniques and analytical approaches. We believe that this can serve as a blueprint for dealing with future pandemics. Accordingly, UnCoVar is easily generalizable towards other viral pathogens and future pandemics. The fully automated workflow assembles virus genomes from patient samples, identifies existing lineages, and provides high-resolution insights into individual mutations. UnCoVar includes extensive quality control and automatically generates interactive visual reports. UnCoVar is implemented as a Snakemake workflow. The open-source code is available under a BSD 2-clause license at github.com/IKIM-Essen/uncovar.

Proposal to reclassify the proteobacterial classes Deltaproteobacteria and Oligoflexia, and the phylum Thermodesulfobacteria into four phyla reflecting major functional capabilities.

The class Deltaproteobacteria comprises an ecologically and metabolically diverse group of bacteria best known for dissimilatory sulphate reduction and predatory behaviour. Although this lineage is the fourth described class of the phylum Proteobacteria, it rarely affiliates with other proteobacterial classes and is frequently not recovered as a monophyletic unit in phylogenetic analyses. Indeed, one branch of the class Deltaproteobacteria encompassing Bdellovibrio-like predators was recently reclassified into a separate proteobacterial class, the Oligoflexia. Here we systematically explore the phylogeny of taxa currently assigned to these classes using 120 conserved single-copy marker genes as well as rRNA genes. The overwhelming majority of markers reject the inclusion of the classes Deltaproteobacteria and Oligoflexia in the phylum Proteobacteria. Instead, the great majority of currently recognized members of the class Deltaproteobacteria are better classified into four novel phylum-level lineages. We propose the names Desulfobacterota phyl. nov. and Myxococcota phyl. nov. for two of these phyla, based on the oldest validly published names in each lineage, and retain the placeholder name SAR324 for the third phylum pending formal description of type material. Members of the class Oligoflexia represent a separate phylum for which we propose the name Bdellovibrionota phyl. nov. based on priority in the literature and general recognition of the genus Bdellovibrio. Desulfobacterota phyl. nov. includes the taxa previously classified in the phylum Thermodesulfobacteria, and these reclassifications imply that the ability of sulphate reduction was vertically inherited in the Thermodesulfobacteria rather than laterally acquired as previously inferred. Our analysis also indicates the independent acquisition of predatory behaviour in the phyla Myxococcota and Bdellovibrionota, which is consistent with their distinct modes of action. This work represents a stable reclassification of one of the most taxonomically challenging areas of the bacterial tree and provides a robust framework for future ecological and systematic studies.

Refining the taxonomic structure of the phylum Acidobacteria.

The phylum Acidobacteria was created in 1997 in order to accommodate a large number of 16S rRNA gene sequences retrieved from various environments in cultivation-independent studies. At present, 26 major sequence clades or subdivisions (SDs) are recognized within this phylum, but only seven of them (SDs 1, 3, 4, 6, 8, 10 and 23) are commonly addressed as containing taxonomically described representatives. Here, we examined the currently explored diversity within the Acidobacteria using the candidate taxonomic unit circumscription system. Based on this analysis, 26 subdivisions were assigned to 15 class-level units, five of which contain described members. These include three earlier established classes Acidobacteriia, Blastocatellia and Holophagae, as well as two as-yet-undescribed groups defined by SDs 6 and 23, which we propose to name Vicinamibacteria classis nov. and Thermoanaerobaculia classis nov., respectively. The former assignment of Thermotomaculum hydrothermale to SD10 was found to be incorrect. This bacterium, therefore, was placed in the family Thermotomaculaceae fam. nov., order Thermotomaculales ord. nov. within the class Holophagae. We also propose establishing a number of high-level taxa to accommodate described representatives of SDs 3, 4, 6 and 23. The family Bryobacteraceae of SD3 Acidobacteria is placed in the order Bryobacterales ord. nov. within the taxonomic range of the class Acidobacteriia. The order Vicinamibacteriales ord. nov. is proposed to accommodate the family Vicinamibacteriaceae of SD6 Acidobacteria. Finally, the family Thermoanaerobaculaceae fam. nov., the order Thermoanaerobaculales ord. nov. are proposed to accommodate the only described representative of SD23, Thermoanaerobaculum aquaticum.

Phylogeny-aware identification and correction of taxonomically mislabeled sequences.

Molecular sequences in public databases are mostly annotated by the submitting authors without further validation. This procedure can generate erroneous taxonomic sequence labels. Mislabeled sequences are hard to identify, and they can induce downstream errors because new sequences are typically annotated using existing ones. Furthermore, taxonomic mislabelings in reference sequence databases can bias metagenetic studies which rely on the taxonomy. Despite significant efforts to improve the quality of taxonomic annotations, the curation rate is low because of the labor-intensive manual curation process. Here, we present SATIVA, a phylogeny-aware method to automatically identify taxonomically mislabeled sequences ('mislabels') using statistical models of evolution. We use the Evolutionary Placement Algorithm (EPA) to detect and score sequences whose taxonomic annotation is not supported by the underlying phylogenetic signal, and automatically propose a corrected taxonomic classification for those. Using simulated data, we show that our method attains high accuracy for identification (96.9% sensitivity/91.7% precision) as well as correction (94.9% sensitivity/89.9% precision) of mislabels. Furthermore, an analysis of four widely used microbial 16S reference databases (Greengenes, LTP, RDP and SILVA) indicates that they currently contain between 0.2% and 2.5% mislabels. Finally, we use SATIVA to perform an in-depth evaluation of alternative taxonomies for Cyanobacteria. SATIVA is freely available at https://github.com/amkozlov/sativa.

SILVA tree viewer: interactive web browsing of the SILVA phylogenetic guide trees.

BACKGROUND: Phylogenetic trees are an important tool to study the evolutionary relationships among organisms. The huge amount of available taxa poses difficulties in their interactive visualization. This hampers the interaction with the users to provide feedback for the further improvement of the taxonomic framework. RESULTS: The SILVA Tree Viewer is a web application designed for visualizing large phylogenetic trees without requiring the download of any software tool or data files. The SILVA Tree Viewer is based on Web Geographic Information Systems (Web-GIS) technology with a PostgreSQL backend. It enables zoom and pan functionalities similar to Google Maps. The SILVA Tree Viewer enables access to two phylogenetic (guide) trees provided by the SILVA database: the SSU Ref NR99 inferred from high-quality, full-length small subunit sequences, clustered at 99% sequence identity and the LSU Ref inferred from high-quality, full-length large subunit sequences. CONCLUSIONS: The Tree Viewer provides tree navigation, search and browse tools as well as an interactive feedback system to collect any kinds of requests ranging from taxonomy to data curation and improving the tool itself.

UniEuk: Time to Speak a Common Language in Protistology!

Universal taxonomic frameworks have been critical tools to structure the fields of botany, zoology, mycology, and bacteriology as well as their large research communities. Animals, plants, and fungi have relatively solid, stable morpho-taxonomies built over the last three centuries, while bacteria have been classified for the last three decades under a coherent molecular taxonomic framework. By contrast, no such common language exists for microbial eukaryotes, even though environmental '-omics' surveys suggest that protists make up most of the organismal and genetic complexity of our planet's ecosystems! With the current deluge of eukaryotic meta-omics data, we urgently need to build up a universal eukaryotic taxonomy bridging the protist -omics age to the fragile, centuries-old body of classical knowledge that has effectively linked protist taxa to morphological, physiological, and ecological information. UniEuk is an open, inclusive, community-based and expert-driven international initiative to build a flexible, adaptive universal taxonomic framework for eukaryotes. It unites three complementary modules, EukRef, EukBank, and EukMap, which use phylogenetic markers, environmental metabarcoding surveys, and expert knowledge to inform the taxonomic framework. The UniEuk taxonomy is directly implemented in the European Nucleotide Archive at EMBL-EBI, ensuring its broad use and long-term preservation as a reference taxonomy for eukaryotes.

The SILVA and "All-species Living Tree Project (LTP)" taxonomic frameworks.

SILVA (from Latin silva, forest, http://www.arb-silva.de) is a comprehensive resource for up-to-date quality-controlled databases of aligned ribosomal RNA (rRNA) gene sequences from the Bacteria, Archaea and Eukaryota domains and supplementary online services. SILVA provides a manually curated taxonomy for all three domains of life, based on representative phylogenetic trees for the small- and large-subunit rRNA genes. This article describes the improvements the SILVA taxonomy has undergone in the last 3 years. Specifically we are focusing on the curation process, the various resources used for curation and the comparison of the SILVA taxonomy with Greengenes and RDP-II taxonomies. Our comparisons not only revealed a reasonable overlap between the taxa names, but also points to significant differences in both names and numbers of taxa between the three resources.

Hydrogen sulfide can inhibit and enhance oxygenic photosynthesis in a cyanobacterium from sulfidic springs.

We used microsensors to investigate the combinatory effect of hydrogen sulfide (H2 S) and light on oxygenic photosynthesis in biofilms formed by a cyanobacterium from sulfidic springs. We found that photosynthesis was both positively and negatively affected by H2 S: (i) H2 S accelerated the recovery of photosynthesis after prolonged exposure to darkness and anoxia. We suggest that this is possibly due to regulatory effects of H2 S on photosystem I components and/or on the Calvin cycle. (ii) H2 S concentrations of up to 210 µM temporarily enhanced the photosynthetic rates at low irradiance. Modelling showed that this enhancement is plausibly based on changes in the light-harvesting efficiency. (iii) Above a certain light-dependent concentration threshold H2 S also acted as an inhibitor. Intriguingly, this inhibition was not instant but occurred only after a specific time interval that decreased with increasing light intensity. That photosynthesis is most sensitive to inhibition at high light intensities suggests that H2 S inactivates an intermediate of the oxygen evolving complex that accumulates with increasing light intensity. We discuss the implications of these three effects of H2 S in the context of cyanobacterial photosynthesis under conditions with diurnally fluctuating light and H2 S concentrations, such as those occurring in microbial mats and biofilms.

Anoxygenic photosynthesis controls oxygenic photosynthesis in a cyanobacterium from a sulfidic spring.

Before the Earth's complete oxygenation (0.58 to 0.55 billion years [Ga] ago), the photic zone of the Proterozoic oceans was probably redox stratified, with a slightly aerobic, nutrient-limited upper layer above a light-limited layer that tended toward euxinia. In such oceans, cyanobacteria capable of both oxygenic and sulfide-driven anoxygenic photosynthesis played a fundamental role in the global carbon, oxygen, and sulfur cycle. We have isolated a cyanobacterium, Pseudanabaena strain FS39, in which this versatility is still conserved, and we show that the transition between the two photosynthetic modes follows a surprisingly simple kinetic regulation controlled by this organism's affinity for H2S. Specifically, oxygenic photosynthesis is performed in addition to anoxygenic photosynthesis only when H2S becomes limiting and its concentration decreases below a threshold that increases predictably with the available ambient light. The carbon-based growth rates during oxygenic and anoxygenic photosynthesis were similar. However, Pseudanabaena FS39 additionally assimilated NO3 (-) during anoxygenic photosynthesis. Thus, the transition between anoxygenic and oxygenic photosynthesis was accompanied by a shift of the C/N ratio of the total bulk biomass. These mechanisms offer new insights into the way in which, despite nutrient limitation in the oxic photic zone in the mid-Proterozoic oceans, versatile cyanobacteria might have promoted oxygenic photosynthesis and total primary productivity, a key step that enabled the complete oxygenation of our planet and the subsequent diversification of life.

The magnitude of gonadotoxicity of chemotherapy drugs on ovarian follicles and granulosa cells varies depending upon the category of the drugs and the type of granulosa cells.

STUDY QUESTION: Do different chemotherapy drugs exert the same magnitude of cytotoxicity on dormant primordial follicles and the growing follicle fraction in the ovary in vivo and on mitotic non-luteinized and non-mitotic luteinized granulosa cells in vitro? SUMMARY ANSWER: Cyclophosphamide (alkylating agent) and cisplatin (alkylating like) impacted both primordial and pre-antral/antral follicles and both mitotic and non-mitotic granulosa cells, whereas the anti-metabolite cancer drug gemcitabine was detrimental only to pre-antral/antral follicles and mitotic non-luteinized granulosa cells. WHAT IS KNOWN ALREADY: It is already known that anti-metabolite cancer drugs are less detrimental to the ovary than alkylating and alkylating like agents, such as cyclophosphamide and cisplatin. This assumption is largely based on the results of clinical reports showing lower rates of amenorrhea in women receiving anti-metabolite agent-based regimens compared with those treated with the protocols containing an alkylating drug or a platinum compound. But a quantitative comparison of gonadotoxicity with a histomorphometric proof of evidence has not been available for many chemotherapy drugs. Therefore, we combined in this study in vivo and in vitro models of human and rat origin that allows a comparative analysis of the impact of different chemotherapy agents on the ovary and granulosa cells using real-time quantitative cell indices, histomorphometry, steroidogenesis assays, and DNA damage and cell death/viability markers. We also aimed to investigate if there is a difference between mitotic and non-mitotic granulosa cells in terms of their sensitivity to the cytotoxic actions of chemotherapy drugs with different mechanisms of action. This issue has not been addressed previously. STUDY DESIGN, SIZE, DURATION: This translational research study involved in vivo analyses of ovaries in rats and in vitro analyses of granulosa cells of human and rat origin. PARTICIPANTS/MATERIALS, SETTING, METHODS: For the in vivo assays, 54 4- to 6-week old Sprague-Dawley young female rats were randomly allocated into four groups of 13 to receive a single IP injection of: saline (control), gemcitabine (200 mg/kg), cisplatin (50 mg/kg) or cyclophosphamide (200 mg/kg). The animals were euthanized 72 h later. Follicle counts and serum AMH levels were compared between the groups. In vitro cytotoxicity studies were performed using mitotic non-luteinized rat (SIGC) and human (COV434, HGrC1) granulosa cells, and non-mitotic luteinized human (HLGC) granulosa cells. The cells were plated at a density of 5000 cells/well using DMEM-F12 culture media supplemented with 10% FBS. Chemotherapy agents were used at their therapeutic blood concentrations. The growth of mitotic granulosa cells was monitored real-time using xCelligence system. Live/dead cell and apoptosis assays were also carried out using intravital Yo-Pro-1 staining and cleaved caspase-3 expression, respectively. Estradiol (E2), progesterone (P) and anti-Mullerian hormone (AMH) levels were assayed with ELISA. MAIN RESULTS AND THE ROLE OF CHANCE: Cyclophosphamide and cisplatin caused massive atresia of both primordials and growing follicles in the rat ovary whereas gemcitabine impacted pre-antral/antral follicles only. Cyclophosphamide and cisplatin induced apoptosis of both mitotic non-luteinized and non-mitotic luteinized granulosa cells in vitro. By contrast, cytotoxicity of gemcitabine was confined to mitotic non-luteinized granulosa cells. LIMITATIONS, REASONS FOR CAUTION: This study tested only three chemotherapeutic agents. The experimental methodology described here could be applied to other drugs for detailed analysis of their ovarian cytotoxicity. WIDER IMPLICATIONS OF THE FINDINGS: These findings indicate that in vivo and in vitro cytotoxic actions of chemotherapy drugs on the ovarian follicles and granulosa cells vary depending upon the their mechanism of action and the nature of the granulosa cells.

The SILVA ribosomal RNA gene database project: improved data processing and web-based tools.

SILVA (from Latin silva, forest, http://www.arb-silva.de) is a comprehensive web resource for up to date, quality-controlled databases of aligned ribosomal RNA (rRNA) gene sequences from the Bacteria, Archaea and Eukaryota domains and supplementary online services. The referred database release 111 (July 2012) contains 3 194 778 small subunit and 288 717 large subunit rRNA gene sequences. Since the initial description of the project, substantial new features have been introduced, including advanced quality control procedures, an improved rRNA gene aligner, online tools for probe and primer evaluation and optimized browsing, searching and downloading on the website. Furthermore, the extensively curated SILVA taxonomy and the new non-redundant SILVA datasets provide an ideal reference for high-throughput classification of data from next-generation sequencing approaches.

Simultaneous determination of seven phthalic acid esters in beverages using ultrasound and vortex-assisted dispersive liquid-liquid microextraction followed by high-performance liquid chromatography.

A sensitive, rapid, and simple high-performance liquid chromatography with UV detection method was developed for the simultaneous determination of seven phthalic acid esters (dimethyl phthalate, dipropyl phthalate, di-n-butyl phthalate, benzyl butyl phthalate, dicyclohexyl phthalate, di-(2-ethylhexyl) phthalate, and di-n-octyl phthalate) in several kinds of beverage samples. Ultrasound and vortex-assisted dispersive liquid-liquid microextraction method was used. The separation was performed using an Intersil ODS-3 column (C18 , 250 × 4.6 mm, 5.0 µm) and a gradient elution with a mobile phase consisting of MeOH/ACN (50:50) and 0.2 M KH2 PO4 buffer. Analytes were detected by a UV detector at 230 nm. The developed method was validated in terms of linearity, limit of detection, limit of quantification, repeatability, accuracy, and recovery. Calibration equations and correlation coefficients (> 0.99) were calculated by least squares method with weighting factor. The limit of detection and quantification were in the range of 0.019-0.208 and 0.072-0.483 µg/L. The repeatability and intermediate precision were determined in terms of relative standard deviation to be within 0.03-3.93 and 0.02-4.74%, respectively. The accuracy was found to be in the range of -14.55 to 15.57% in terms of relative error. Seventeen different beverage samples in plastic bottles were successfully analyzed, and ten of them were found to be contaminated by different phthalic acid esters.

Chemical constituents and biological activities of Cirsium leucopsis, C. sipyleum, and C. eriophorum.

Two endemic Cirsium species, C. leucopsis DC. and C. sipyleum O. Schwarz, and C. eriophorum (L.) Scop. growing in Turkey were investigated to establish their secondary metabolites, fatty acid compositions, and antioxidant and anticholinesterase potentials. Spectroscopic methods were used to elucidate the structures of thirteen known compounds (p-hydroxy-benzoic acid, vanillic acid, cis-epoxyconiferyl alcohol, syringin, balanophonin, 1'-O-methyl-balanophonin, apigenin, kaempferol-3- O-ß-D-glucopyranoside, kaempferol-3-O-α-L-rhamnopyranoside, taraxasterol, taraxasterol acetate, ß-sitosterol, ß-sitosterol-3-O-ß-D-glucopyranoside). cis-Epoxyconiferyl alcohol and 1'-O-methyl- balanophonin were isolated for the first time from Cirsium species. Palmitic acid (47.1%) was found to be the main fatty acid of C. leucopsis, linoleic acid in both C. sipyleum (42.1%) and C. eriophorum (37.8 %). Assays of ß-carotene bleaching, scavenging of 1,1-diphenyl-2-picrylhydrazyl (DPPH) free radicals, 2,2-azinobis (3-ethylbenzothiazoline-6-sulfonic acid) diammonium (ABTS) cation radicals, and superoxide anion radicals, as well as cupric reducing antioxidant capacity (CUPRAC) were used to determine the antioxidant activities of the extracts and isolated compounds. Vanillic acid, balanohonin, and kaempferol-3-O-aαL-rhamnopyranoside exhibited strong antioxidant activity. Taraxa-terol was a potent inhibitor of acetyl- and butyrylcholinesterase activity, respectively.

Ultrasound- and Vortex-Assisted Dispersive Liquid-Liquid Microextraction of Parabens from Personal Care Products and Urine, Followed by High-Performance Liquid Chromatography.

Objectives: Parabens, which are p-hydroxybenzoic acid esters, are used as preservatives in personal care products, pharmaceuticals, and food because of their antimicrobial activity. However, they are also classified as suspected endocrine disruptors and carcinogens. In the present study, we aimed to optimize an ultrasound and vortex-assisted dispersive liquid-liquid microextraction (DLLME) procedure for the simultaneous extraction of methyl, ethyl, isopropyl, propyl, isobutyl, and butyl parabens from personal care products and urine. Materials and Methods: The extraction solvent type, extraction solvent volume, disperser solvent volume, sodium chloride concentration, ultrasonication time, and vortex application time were evaluated to obtain optimum recoveries by ultrasound and vortex-assisted DLLME. Parabens were detected using a validated high performanc-liquid chromatography (HPLC) method with fluorescence detection. Method validation was performed by examining linearity, the limit of detection, limit of quantification, accuracy, and precision. Results: The limits of detection and quantification of the HPLC method were between 0.09-0.18 µg/mL and 0.28-0.54 µg/mL, respectively. Precision was examined as the relative standard deviation, which was 0.22-1.81% and 1.12-2.03% for intra- and interday studies. Recovery percentages were higher than 96.00%. Samples of two paraben-free personal care products and synthetic urine were spiked with the analyses at 0.02 µg/mL and were successfully analyzed using the developed procedure with recovery values higher than 82.00%. Conclusion: The proposed procedure provided quantification of selected parabens at 20 ng/mL in analyzed personal care products and urine matrices with good precision and accuracy.

Development and Validation of a SPE-HPLC Method for Quantification of Rhein, Emodin, Chrysophanol and Physcion in Rhamnus petiolaris Boiss. & Balansa.

Anthraquinones exhibit a significant group of natural and synthetic quinone derivatives because of their biological activities and industrial applications. Rhamnaceae is one of the families known to contain different kinds of anthraquinones. In this study, it was aimed to quantify rhein, emodin, chrysophanol and physcion in fruits of Rhamnus petiolaris Boiss. & Balansa belonging to Rhamnaceae by solid phase extraction and high performance liquid chromatography with ultraviolet detection. The anthraquinones were separated using a C18 analytical column. Gradient elution was performed using a mobile phase consisted of 0.1% o-phosphoric acid solution and methanol. Analytes were detected at 254 nm. Calibration curves were prepared in the range of 0.25-5.00 µg/mL for rhein, chrysophanol, physcion, 1.00-50.00 µg/mL for emodin. Limits of detection and quantification were between 0.07-0.11 and 0.20-0.34 µg/mL, respectively. Relative standard deviations were ≤ 5.78% in repeatability and intermediate precision studies. Accuracy was determined as relative mean error (8.17-12.06%). Extraction was achieved by maceration with acetone and ethanol, followed by hydrophilic-lipophilic balance solid phase extraction. Recoveries were between 96.2 and 109.6%. The developed and validated method was successfully performed to quantify rhein, emodin, chrysophanol and physcion in R. petiolaris fruit extracts. Only physcion was not detected above limit of detection.

Megx.net: integrated database resource for marine ecological genomics.

Megx.net is a database and portal that provides integrated access to georeferenced marker genes, environment data and marine genome and metagenome projects for microbial ecological genomics. All data are stored in the Microbial Ecological Genomics DataBase (MegDB), which is subdivided to hold both sequence and habitat data and global environmental data layers. The extended system provides access to several hundreds of genomes and metagenomes from prokaryotes and phages, as well as over a million small and large subunit ribosomal RNA sequences. With the refined Genes Mapserver, all data can be interactively visualized on a world map and statistics describing environmental parameters can be calculated. Sequence entries have been curated to comply with the proposed minimal standards for genomes and metagenomes (MIGS/MIMS) of the Genomic Standards Consortium. Access to data is facilitated by Web Services. The updated megx.net portal offers microbial ecologists greatly enhanced database content, and new features and tools for data analysis, all of which are freely accessible from our webpage http://www.megx.net.

MetaBar - a tool for consistent contextual data acquisition and standards compliant submission.

BACKGROUND: Environmental sequence datasets are increasing at an exponential rate; however, the vast majority of them lack appropriate descriptors like sampling location, time and depth/altitude: generally referred to as metadata or contextual data. The consistent capture and structured submission of these data is crucial for integrated data analysis and ecosystems modeling. The application MetaBar has been developed, to support consistent contextual data acquisition. RESULTS: MetaBar is a spreadsheet and web-based software tool designed to assist users in the consistent acquisition, electronic storage, and submission of contextual data associated to their samples. A preconfigured Microsoft Excel spreadsheet is used to initiate structured contextual data storage in the field or laboratory. Each sample is given a unique identifier and at any stage the sheets can be uploaded to the MetaBar database server. To label samples, identifiers can be printed as barcodes. An intuitive web interface provides quick access to the contextual data in the MetaBar database as well as user and project management capabilities. Export functions facilitate contextual and sequence data submission to the International Nucleotide Sequence Database Collaboration (INSDC), comprising of the DNA DataBase of Japan (DDBJ), the European Molecular Biology Laboratory database (EMBL) and GenBank. MetaBar requests and stores contextual data in compliance to the Genomic Standards Consortium specifications. The MetaBar open source code base for local installation is available under the GNU General Public License version 3 (GNU GPL3). CONCLUSION: The MetaBar software supports the typical workflow from data acquisition and field-sampling to contextual data enriched sequence submission to an INSDC database. The integration with the megx.net marine Ecological Genomics database and portal facilitates georeferenced data integration and metadata-based comparisons of sampling sites as well as interactive data visualization. The ample export functionalities and the INSDC submission support enable exchange of data across disciplines and safeguarding contextual data.

Role of Temperature and Growth Period in the Synthesis of Hydrothermally Grown TiO2 Nanorods.

Highly uniformed, surfactant free and vertically oriented titanium-di-oxide (TiO2) nanorods were grown on pre-treated fluorine doped tin oxide (FTO) using hydrothermal method through titanium tetra butoxide (Ti(OBu)4) as titanium source. Three different temperatures 130 °C, 150 °C and 180 °C were followed to grow the nanorods at a fixed reaction time of 4 h. The prepared TiO2 nanorods were annealed at the temperatures of 550 °C and 600 °C for 3 h. X-ray diffraction (XRD) analysis shows that obtained nanorods exhibit pure rutile phase. From scanning electron microscopy (SEM) analysis, it was found that increasing temperature led to decreasing the diameter of the nanorods. In addition to these, formation of hierarchical type TiO2 nanorods was also observed at 130 °C. UV-visible spectra analysis was carried out to find the influence of diameter of the nanorods on its optical properties. The plausible mechanism of the growth process is also discussed.