Margaret K. Butler

Only three biological pathways are known to produce oxygen: photosynthesis, chlorate respiration and the detoxification of reactive oxygen species. Here we present evidence for a fourth pathway, possibly of considerable geochemical and evolutionary importance. The pathway was discovered after metagenomic sequencing of an enrichment culture that couples anaerobic oxidation of methane with the reduction of nitrite to dinitrogen. The complete genome of the dominant bacterium, named 'Candidatus Methylomirabilis oxyfera', was assembled. This apparently anaerobic, denitrifying bacterium encoded, transcribed and expressed the well-established aerobic pathway for methane oxidation, whereas it lacked known genes for dinitrogen production. Subsequent isotopic labelling indicated that 'M. oxyfera' bypassed the denitrification intermediate nitrous oxide by the conversion of two nitric oxide molecules to dinitrogen and oxygen, which was used to oxidize methane. These results extend our understanding of hydrocarbon degradation under anoxic conditions and explain the biochemical mechanism of a poorly understood freshwater methane sink. Because nitrogen oxides were already present on early Earth, our finding opens up the possibility that oxygen was available to microbial metabolism before the evolution of oxygenic photosynthesis.

Skin is a widely used route of delivery for local and systemic drugs and is potentially a route for their delivery as nanoparticles. The skin provides a natural physical barrier against particle penetration, but there are opportunities to deliver therapeutic nanoparticles, especially in diseased skin and to the openings of hair follicles. Whilst nanoparticle drug delivery has been touted as an enabling technology, its potential in treating local skin and systemic diseases has yet to be realised. Most drug delivery particle technologies are based on lipid carriers, i.e. solid lipid nanoparticles and nanoemulsions of around 300 nm in diameter, which are now considered microparticles. Metal nanoparticles are now recognized for seemingly small drug-like characteristics, i.e. antimicrobial activity and skin cancer prevention. We present our unpublished clinical data on nanoparticle penetration and previously published reports that support the hypothesis that nanoparticles > 10 nm in diameter are unlikely to penetrate through the stratum corneum into viable human skin but will accumulate in the hair follicle openings, especially after massage. However, significant uptake does occur after damage and in certain diseased skin. Current chemistry limits both atom by atom construction of complex particulates and delineating their molecular interactions within biological systems. In this review we discuss the skin as a nanoparticle barrier, recent work in the field of nanoparticle drug delivery to the skin, and future directions currently being explored.

The Ion Torrent Personal Genome Machine (PGM) is a new sequencing platform that substantially differs from other sequencing technologies by measuring pH rather than light to detect polymerisation events. Using re-sequencing datasets, we comprehensively characterise the biases and errors introduced by the PGM at both the base and flow level, across a combination of factors, including chip density, sequencing kit, template species and machine. We found two distinct insertion/deletion (indel) error types that accounted for the majority of errors introduced by the PGM. The main error source was inaccurate flow-calls, which introduced indels at a raw rate of 2.84% (1.38% after quality clipping) using the OneTouch 200 bp kit. Inaccurate flow-calls typically resulted in over-called short-homopolymers and under-called long-homopolymers. Flow-call accuracy decreased with consecutive flow cycles, but we also found significant periodic fluctuations in the flow error-rate, corresponding to specific positions within the flow-cycle pattern. Another less common PGM error, high frequency indel (HFI) errors, are indels that occur at very high frequency in the reads relative to a given base position in the reference genome, but in the majority of instances were not replicated consistently across separate runs. HFI errors occur approximately once every thousand bases in the reference, and correspond to 0.06% of bases in reads. Currently, the PGM does not achieve the accuracy of competing light-based technologies. However, flow-call inaccuracy is systematic and the statistical models of flow-values developed here will enable PGM-specific bioinformatics approaches to be developed, which will account for these errors. HFI errors may prove more challenging to address, especially for polymorphism and amplicon applications, but may be overcome by sequencing the same DNA template across multiple chips.

ABSTRACT Published pmoA primers do not match the pmoA sequence of “ Candidatus Methylomirabilis oxyfera,” a bacterium that performs nitrite-dependent anaerobic methane oxidation. Therefore, new pmoA primers for the detection of “ Ca . Methylomirabilis oxyfera”-like methanotrophs were developed and successfully tested on freshwater samples from different habitats. These primers expand existing molecular tools for the study of methanotrophs in the environment.

High-throughput sequencing libraries are typically limited by the requirement for nanograms to micrograms of input DNA. This bottleneck impedes the microscale analysis of ecosystems and the exploration of low biomass samples. Current methods for amplifying environmental DNA to bypass this bottleneck introduce considerable bias into metagenomic profiles. Here we describe and validate a simple modification of the Illumina Nextera XT DNA library preparation kit which allows creation of shotgun libraries from sub-nanogram amounts of input DNA. Community composition was reproducible down to 100 fg of input DNA based on analysis of a mock community comprising 54 phylogenetically diverse Bacteria and Archaea. The main technical issues with the low input libraries were a greater potential for contamination, limited DNA complexity which has a direct effect on assembly and binning, and an associated higher percentage of read duplicates. We recommend a lower limit of 1 pg (∼100-1,000 microbial cells) to ensure community composition fidelity, and the inclusion of negative controls to identify reagent-specific contaminants. Applying the approach to marine surface water, pronounced differences were observed between bacterial community profiles of microliter volume samples, which we attribute to biological variation. This result is consistent with expected microscale patchiness in marine communities. We thus envision that our benchmarked, slightly modified low input DNA protocol will be beneficial for microscale and low biomass metagenomics.

The Planctomycetes are a deep branching phylum of the domain Bacteria that incorporate a diverse group of organisms possessing a number of unusual and distinct characteristics. These features include budding reproduction, the planctomycetecharacteristic crateriform structures on their cell surface, a cell wall that lacks peptidoglycan, internal compartmentalisation and unique molecular features of their rRNA genes. This study chose to investigate a number of aspects of planctomycete cell biology and diversity to further our knowledge of this unique group. In a study of the diversity of ribonuclease P (RNase P) RNA, one molecule of relevance to cell biology and compartmentalisation in planctomycetes, RNase P RNA genes were sequenced for species from all genera of planctomycetes for which a pure culture exists. Secondary structures for RNase P RNA of these strains were deduced, taking to 26 the number of planctomycete RNase P RNA structures. Nucleotide positions were identified in which some planctomycetes possess a less common form, including one thought to be otherwise conserved within all Bacteria and Archaea. Phylogenetic analysis of RNase P RNA genes was relatively consistent with that of 16S rRNA genes with the exception that clustering of Gemmata and anammox sequences occurred, possibly due to either long-branch attraction or lateral gene transfer. Analysis of RNase P RNA secondary structures revealed unusual features of planctomycetes relative to all other bacteria, including an additional helix within the P13 helix of ‘Candidatus Brocadia anammoxidans’, ‘Candidatus Kuenenia stuttgartiensis’ and all Gemmata sequences. The longest P12 helix of any bacteria type A RNase P RNA was found in a Gemmatalike isolate. The short tandem repeats in P12 helices of two Gemmata-like isolates are possibly analogous to short tandem repetitive repeat sequences of some cyanobacteria RNase P RNA. In experiments using Gemmata obscuriglobus as a model for planctomycete cell biology and compartmentalisation functions, electron microscope-level in situ hybridisation (EMISH), and subsequent statistical analysis, was developed to localise 16S rRNA, 23S rRNA and RNase P RNA to particular regions within Gemmata obscuriglobus, the first instance of EMISH being applied in this way to bacteria. Statistical analysis localised 16S rRNA to both nuclear body and to riboplasm outside this region but it was absent from paryphoplasm. While co-localisation of both 16S rRNA and 23S rRNA molecules, which might indicate assembled ribosomes, was rarely observed, 23S rRNA, like 16S rRNA, was distributed in both riboplasm-containing areas of the cell. While statistical analysis revealed minor DNA within riboplasm outside the nuclear body, the majority was localised to that body. These results suggest at least some uncoupling of translation from transcription involving ribosomes in the riboplasm. RNase P RNA was localised both to the nuclear body and to the riboplasm outside this region, suggesting that pre-tRNA processing occurs both within nuclear body, where RNA transcripts are presumably generated, and outside nuclear body, separated from the origin of these transcripts. This is also consistent with the hypothesis that processed tRNA is required in the riboplasm outside the nuclear body, due to occurrence of some uncoupled translation. In research on planctomycetes not yet examined with respect to cell plan or structure, 16S rRNA gene sequencing of isolate ATCC 35122 confirmed its very close relationship to the type strain of Pirellula staleyi and its membership of the phylum Planctomycetes. Morphological characteristics, including polar crateriform structures and the occurrence of a unique internal, single membrane-bounded compartment enclosing nucleoid and ribosome-like particles, the pirellulosome, and a polar cap region, are also consistent with its membership of the planctomycetes and of genus Pirellula. Cells often displayed pointed, hump-like protrusions opposite each other on the cell, constituting prosthecae. Also re-examined using a number of methods were uncultured species Planctomyces bekefii and Pl. guttaeformis. Samples could be enriched for Pl. bekefii via either addition of ferric citrate or ampicillin. An application of a novel approach, laser microdissection and pressure catapulting, was also used physically to enrich P. bekefii rosettes. Fluorescent in situ hybridisation provided the first molecular evidence of Pl. bekefii and Pl. guttaeformis as Planctomycetes. Also confirming Planctomycetes membership of Pl. bekefii was the presence of a cytoplasm divided into two regions by an intracytoplasmic membrane, consistent with membership to the genus Planctomyces. Two new planctomycete-like organisms, MBLW1 and MBLW2, were isolated in this study and possessed a Gemmata-like cell plan. 16S rRNA gene sequencing confirmed these isolates belonged to the Gemmata clade within phylum Planctomycetes, though they may comprise a separate but closely related genus. Via EMISH, both ATCC 35122 and MBLW1 were hybridised with a planctomycete-specific probe, consistent with membership to the planctomycetes. Statistical analysis showed that 16S rRNA was present in both regions of the riboplasm of MBLW1, identical to the distribution observed G. obscuriglobus. This is another example of possible uncoupled translation within a member of the planctomycetes and within organisms in the Gemmata clade of planctomycetes.

Layered double hydroxide (LDH) nanoparticles have the potential to benefit a myriad of medical, consumer and industrial products if intricate control of the nanoscale architecture and understanding of the biological interactions and potential toxicity of the LDH nanomaterials are achieved. Here, we report the synthesis and fractionation of LDH nanomaterials of well defined spatial characteristics through the careful control of synthesis conditions and the use of ultracentrifugation. The appropriateness of a range of fluorescent dyes, for labelling LDH nanoparticles to enable biological tracking, has also been investigated. These dyes include fluorescein, fluorescein isothiocyanate (FITC), 8-aminonaphthelene-1,3,6-trisulfonic acid (ANTS) and 8-aminopyrene-1,3,6-trisulfonic acid (APTS). Thermal degradation of the popular FITC dye during nanoparticle synthesis was revealed and suitable alternative fluorescent molecules established. Furthermore, we report for the first time the application of size exclusion chromatography on LDH nanoparticles as a fast, reliable and efficient method to achieve purification without causing nanoparticle agglomeration.

The anaerobic nitrite-reducing methanotroph ‘ Candidatus Methylomirabilis oxyfera’ (‘ Ca. M. oxyfera’) produces oxygen from nitrite by a novel pathway. The major part of the O 2 is used for methane activation and oxidation, which proceeds by the route well known for aerobic methanotrophs. Residual oxygen may serve other purposes, such as respiration. We have found that the genome of ‘ Ca. M. oxyfera’ harbours four sets of genes encoding terminal respiratory oxidases: two cytochrome c oxidases, a third putative bo -type ubiquinol oxidase, and a cyanide-insensitive alternative oxidase. Illumina sequencing of reverse-transcribed total community RNA and quantitative real-time RT-PCR showed that all four sets of genes were transcribed, albeit at low levels. Oxygen-uptake and inhibition experiments, UV–visible absorption spectral characteristics and EPR spectroscopy of solubilized membranes showed that only one of the four oxidases is functionally produced by ‘ Ca. M. oxyfera’, notably the membrane-bound bo -type terminal oxidase. These findings open a new role for terminal respiratory oxidases in anaerobic systems, and are an additional indication of the flexibility of terminal oxidases, of which the distribution among anaerobic micro-organisms may be largely underestimated.

A gram-negative, budding, catalase negative, oxidase positive and non-motile bacterium (MBLW1T) with a complex endomembrane system has been isolated from a freshwater lake in southeast Queensland, Australia. Phylogeny based on 16S rRNA gene sequence analysis places the strain within the family Planctomycetaceae, related to Zavarzinella formosa (93.3 %), Telmatocola sphagniphila (93.3 %) and Gemmata obscuriglobus (91.9 %). Phenotypic and chemotaxonomic analysis demonstrates considerable differences to the type strains of the related genera. MBLW1T displays modest salt tolerance and grows optimally at pH values of 7.5-8.0 and at temperatures of 32-36 °C. Transmission electron microscopy analysis demonstrates the presence of a complex endomembrane system, however, without the typically condensed nucleoid structure found in related genera. The major fatty acids are 16 : 1 ω5c, 16 : 0 and 18 : 0. Based on discriminatory results from 16S rRNA gene sequence analysis, phenotypic, biochemical and chemotaxonomic analysis, MBLW1T should be considered as a new genus and species, for which the name Tuwongella immobilis gen. nov., sp. nov. is proposed. The type strain is MBLW1T (=CCUG 69661T=DSM 105045T).

Planctomycetes are distinguished from other Bacteria by compartmentalization of cells via internal membranes, interpretation of which has been subject to recent debate regarding potential relations to Gram-negative cell structure. In our interpretation of the available data, the planctomycete Gemmata obscuriglobus contains a nuclear body compartment, and thus possesses a type of cell organization with parallels to the eukaryote nucleus. Here we show that pore-like structures occur in internal membranes of G.obscuriglobus and that they have elements structurally similar to eukaryote nuclear pores, including a basket, ring-spoke structure, and eight-fold rotational symmetry. Bioinformatic analysis of proteomic data reveals that some of the G. obscuriglobus proteins associated with pore-containing membranes possess structural domains found in eukaryote nuclear pore complexes. Moreover, immunogold labelling demonstrates localization of one such protein, containing a β-propeller domain, specifically to the G. obscuriglobus pore-like structures. Finding bacterial pores within internal cell membranes and with structural similarities to eukaryote nuclear pore complexes raises the dual possibilities of either hitherto undetected homology or stunning evolutionary convergence.

Aims: To date, the description of a single, suitable method to observe in detail metal oxide nanoparticles in situ within sunscreens is currently lacking, despite growing concern as to how they interact with humans. This study explores the usefulness of transmission electron microscopy to characterize the nanoparticles in sunscreens. Materials & methods: High-pressure freezing then freeze substitution was used to prepare resin-embedded commercial sunscreen samples, and ultrathin sections of these were observed with transmission electron microscopy. Conventional room temperature processing for resin embedding was also trialed. Results: High-pressure frozen/freeze substituted samples provided clear visualization of the size and shape of the nanoparticles and agglomerates and allowed further characterization of the composition and crystal form of the metal oxides, while conventionally processed chemically fixed samples were subject to distribution/agglomeration artifacts. Conclusion: Transmission electron microscopy of high-pressure frozen/freeze substituted samples is an ideal method to completely observe metal oxide nanoparticles in situ in sunscreens.

The planctomycetes, order Planctomycetales, are a distinct phylum of domain Bacteria. Genes encoding the RNA portion of ribonuclease P (RNase P) of some planctomycete members were sequenced and compared with existing database planctomycete sequences. rnpB gene sequences encoding RNase P RNA were generated by a conserved primer PCR strategy for Planctomyces brasiliensis, Planctomyces limnophilus, Pirellula marina, Pirellula staleyi strain ATCC 35122, Isosphaera pallida, one other Isosphaera strain, Gemmata obscuriglobus and three other strains of the Gemmata group. These sequences were aligned against reference bacterial sequences and secondary structures of corresponding RNase P RNAs deduced by a comparative approach. P12 helices were found to be highly variable in length, as were helices P16.1 and P19, when present. RNase P RNA secondary structures of Gemmata isolates were found to have unusual features relative to other planctomycetes, including a long P9 helix and an insert in the P13 helix not found in any other member of domain Bacteria. These unique features are consistent with other unusual properties of this genus, distinguishing it from other bacteria. Phylogenetic analyses indicate that relationships between planctomycetes derived from RNase P RNA are consistent with 16S rRNA-based analyses.

deduced from isotropic conversion of enriched samples in a pressurized water reactor. A redetermination of the resonance integral for cobalt was conducted with a thin sample to avoid self-shielding problems. Group Constants. A special data tape of nuclear cross sections was prepared. The tape contains the best basic information currently available for a variety of strong parasitic absorbers, fuels, structural materials, etc. Definitive experiments and calculations are reported on the determination of the diffusion length of thermal neutrons in water. A very rapid and accurate scheme for digital computation of average thermal cross sections in core life studies was developed. Lattice Effects. The computer program SWAKRAUM IV is described: the mathematical and physical models employed and the several options available for calculation of thermal neutron distributions in both space and energy are included. Results are reported from PPA studies of spatial variations of thermal and epithermal neutron flux in the neighborhood of moderating and absorbing inhomogeneities. A theoretical investigation of several experiments is reported in which epithermal distributions play a decisive role. A diffusion theory routine was developed for determining gamma heating in reactors. Statistical methods were applied to the calculation of self-shielding of dispersions of absorbing particles. Experimental and calculated data are given relating tc PMA measurements with discrete, highly self-shielded absorbers and less complicated poison distributions. Reactor Kinetics. For the investigation of core instabilities, it is necessary to know the transfer function relating reactivity and neutron flux in the system. Perturbation theory results were developed for this function as part of the analysis required to described complicated, time-dependent reactor behavior induced by nonuniform variation of material properties. The technique of determining reactor subcriticality with pulsedneutron measurements was automated. A physicomathematical model was developed to study probabilities associated with occurrence of certain hazardous reactor conditions. Studies are reported on the determination of neutron generation to be expected from such phenomena as spontaneous fission of fuel, ( alpha ,n) reactions, cosmic rays, and flssion-product decay. Secular Transients. Techniques for obtaining accurate cross sections were improved and generalized for the production of nuclear data to be used with arbitrary energy-group widths in depletion studies. An N/sup 13/ positron activity in the coolant of a reactor was shown to be due to the O/sup 16/ (p, alpha )N/sup 13/ reaction. Reactor TRAM program, for three-dimensional Monte Carlo calculation of low ilexibility. One- and two-dimensional diffusion calculations of criticality, neutron fluxes, fuel and poison depletion, etc., are supplied by various components of the KARE system. Brief descriptions are given of a wide variety of calculations that are possible with KARE. A technique for generalized flux synthesis to permit increasingly accurate three-dimensional diffusion calculations is embodied in the CLAG program. Statistical problems that have arisen in connection with mathematical studies, sampling techniques,

The relationship of RNase P RNA from anammox bacteria 'Candidatus Brocadia anammoxidans' and 'Candidatus Kuenenia stuttgartiensis' with that from other Planctomycetes was investigated. Newly identified rnpB gene sequences were aligned against existing planctomycete RNase P RNA sequences and secondary structures deduced by a comparative approach. Deduced secondary structures were similar in both anammox bacteria and both possessed an insert within the P13 helix analogous to that present in all Gemmata isolates. Phylogenetic analysis also revealed a possible relationship between the RNase P RNA molecules of the two anammox organisms and the genus Gemmata.

Abstract Pi.rel'lu.la la L. fem. n. Pirellula , very small pear, referring to the shape of the bacterium. Planctomycetes / Planctomycetia / Pirellulales / Pirellulaceae / Pirellula The genus Pirellula belongs to the family Pirellulaceae of the order Pirellulales (phylum Planctomycetes /class Planctomycetia ) and comprises one named species, the type species Pirellula staleyi , isolated from a freshwater lake. P. staleyi is an obligately aerobic chemoorganotrophic heterotroph for which carbohydrates are carbon and energy sources. The type species possesses pear‐ or teardrop‐shaped cells reproducing via budding, motility via polar to subpolar monotrichous flagella, and white to light yellow colonies. The surfaces of whole cells observed via electron microscopy have polar electron‐dense pit‐like crateriform structures and may possess hump‐like protrusions. Sectioned cells prepared via cryosubstitution viewed by electron microscopy possess a major cell compartment, the pirellulosome. In this compartment, ribosomes and a condensed nucleoid appear to be enclosed by an intracytoplasmic membrane. The mol% G + C of the type strain of the type species Pirellula staleyi ATCC 27377 T is 57.5 via genome sequence. The genome size is 6.2 Mb. DNA G + C content (mol%) : 57.5 (genome sequence). Type species : Pirellula staleyi Schlesner and Hirsch 1987 VP homotypic synonym: (emend. Schlesner et al. 2004 (homotypic synonym and illegitimate name: Pirella staleyi Schlesner and Hirsch 1984)).

Today we can look back over the past thirty years and view the entire history of the electronic digital computer! In addressing the topic of prospective capabilities in hardware, this paper first attempts to extrapolate, from today's state-of-the-art and vantage point, general industry-wide trends and likely achievements. Then, an effort is made to cover in more detail specific areas of interest to the ERDA community. Subjects discussed include available large-scale computers---their architecture and viability. The microprocessor's impact on computer systems is considered, and potential applications of the microcomputer are identified. Then mass storage offerings and their role in predicted memory hierarchies is assessed; progress in the development of alternate storage technologies is reviewed. New products and anticipated innovations in peripheral and input-output equipment, probably the most lethargic segment of the dynamic hardware market, are described, and a survey of network and communications activity examines future directions this rapidly-expanding field might be expected to follow.

A freshwater isolate from Campus Lake, Baton Rouge, LA, USA, strain ATCC 35122 (= ICPB 4362 = Schmidt CLPM White = Tekniepe BT2 white), which had been proposed as a putative reference strain for 'Planctomyces staleyi' (later reclassified as Pirellula staleyi), has been re-examined to establish its relationship to the type strain of Pirellula staleyi, ATCC 27377T. 165 rRNA sequencing confirms its very close relationship to ATCC 27377T and its membership of the order Planctomycetales. Ultrastructural characteristics are also consistent with its membership of the planctomycetes and of the genus Pirellula. These characteristics include polar crateriform structures and the occurrence of the unique internal, single-membrane-bounded compartment enclosing the nucleoid and ribosome-like particles, the pirellulosome, and a polar cap region. Cells of strain ATCC 35122 often displayed pointed, hump-like protrusions opposite each other on the cell, constituting prosthecae, and these were also found to be present on cells of strain ATCC 27377T. The original identification of ATCC 35122 as a strain of Pirellula staleyi is confirmed on both molecular and phenotypic grounds.

"Information Retrieval Systems Characteristics, Testing, and Evaluation." Nuclear Science and Engineering, 40(2), p. 359

Gem.ma'ta. L. v. gemmare to put forth buds, to bud; N.L. fem. n. Gemmata (from L. fem. part. adj. gemmata put forth buds, budded) budded (bacteria), referring to the cell division mode of the bacterium. Planctomycetes / Planctomycetia / Planctomycetales / Planctomycetaceae / Gemmata Spherical to pear‐shaped cells , 1.4–3.0 × 1.4–3.0 µm. Gram‐stain‐negative. Cells reproduce by budding , with the single daughter cell a mirror image of the mother cell, and there may be a narrow bud attachment site. Cells can bud repeatedly. Cells possess a multitrichous bundle of flagella . Aerobic, having a strictly aerobic type of metabolism with oxygen as the terminal electron acceptor. Colonies have pink pigmentation . DNA G + C content ( mol %): 64.4 ± 1.0 ( T m ). Type species : Gemmata obscuriglobus Franzmann and Skerman 1985, 375 VP (Effective publication: Franzmann and Skerman 1984, 266.).

Today we can look back over the past thirty years and view the entire history of the electronic digital computer! In addressing the topic of prospective capabilities in hardware, this paper first attempts to extrapolate, from today's state-of-the-art and vantage point, general industry-wide trends and likely achievements. Then, an effort is made to cover in more detail specific areas of interest to the ERDA community. Subjects discussed include available large-scale computers---their architecture and viability. The microprocessor's impact on computer systems is considered, and potential applications of the microcomputer are identified. Then mass storage offerings and their role in predicted memory hierarchies is assessed; progress in the development of alternate storage technologies is reviewed. New products and anticipated innovations in peripheral and input-output equipment, probably the most lethargic segment of the dynamic hardware market, are described, and a survey of network and communications activity examines future directions this rapidly-expanding field might be expected to follow.Whenever possible in each of these areas, examples with descriptive characteristics, accompanied by cost and performance statistics, are presented in support of the initially-forecast broad technological trends. These examples, chosen for illustration, represent new hardware products, advanced technologies in the developmental stages, or planned enhancements of existing product lines.

describes the use of ANISN-L; this is a revised version of ANISN which handles both large and small problems efficiently on CDC-7600 computers. (RWR)

Annals of the New York Academy of SciencesVolume 157, Issue 1 p. 424-437 AUTOMATIC ANALYSIS OF 835 MARMOSET SPREADS* J. W. Butler, J. W. Butler Argonne National Laboratory Argonne, III. and Presbyterian-St. Lukes Hospital† Chicago, III.Search for more papers by this authorMargaret K. Butler, Margaret K. Butler Argonne National Laboratory Argonne, III. and Presbyterian-St. Lukes Hospital† Chicago, III.Search for more papers by this authorBarbara Marczynska†, Barbara Marczynska† Argonne National Laboratory Argonne, III. and Presbyterian-St. Lukes Hospital† Chicago, III.Search for more papers by this author J. W. Butler, J. W. Butler Argonne National Laboratory Argonne, III. and Presbyterian-St. Lukes Hospital† Chicago, III.Search for more papers by this authorMargaret K. Butler, Margaret K. Butler Argonne National Laboratory Argonne, III. and Presbyterian-St. Lukes Hospital† Chicago, III.Search for more papers by this authorBarbara Marczynska†, Barbara Marczynska† Argonne National Laboratory Argonne, III. and Presbyterian-St. Lukes Hospital† Chicago, III.Search for more papers by this author First published: March 1969 https://doi.org/10.1111/j.1749-6632.1969.tb12675.xCitations: 2 * Work performed in part under the auspices of the U. S. Atomic Energy Commission; supported in part by Public Health Service Research Contract PH 43-62-179 from the National Cancer Institute. AboutPDF ToolsRequest permissionExport citationAdd to favoritesTrack citation ShareShare Give accessShare full text accessShare full-text accessPlease review our Terms and Conditions of Use and check box below to share full-text version of article.I have read and accept the Wiley Online Library Terms and Conditions of UseShareable LinkUse the link below to share a full-text version of this article with your friends and colleagues. Learn more.Copy URL Share a linkShare onFacebookTwitterLinked InRedditWechat Citing Literature Volume157, Issue1Data Extraction and Processing of Optical Images in the Medical and Biological SciencesMarch 1969Pages 424-437 RelatedInformation

ABSTRACT Planctomycetes are distinguished from other Bacteria by compartmentalization of cells via internal membranes, interpretation of which has been subject to recent debate regarding potential relations to Gram-negative cell structure. In our interpretation of the available data, the planctomycete Gemmata obscuriglobus contains a nuclear body compartment, and thus possesses a type of cell organization with parallels to the eukaryote nucleus. Here we show that pore-like structures occur in internal membranes of G.obscuriglobus and that they have elements structurally similar to eukaryote nuclear pores, including a basket, ring-spoke structure, and eight-fold rotational symmetry. Bioinformatic analysis of proteomic data reveals that some of the G. obscuriglobus proteins associated with pore-containing membranes possess structural domains found in eukaryote nuclear pore complexes. Moreover, immuno-gold labelling demonstrates localization of one such protein, containing a β-propeller domain, specifically to the G. obscuriglobus pore-like structures. Finding bacterial pores within internal cell membranes and with structural similarities to eukaryote nuclear pore complexes raises the dual possibilities of either hitherto undetected homology or stunning evolutionary convergence.

Abstract Gem.ma'ta. L. past. part. used as L. fem. n. (from L. v. gemmare , to put forth buds), Gemmata , one provided with buds. Planctomycetota / Planctomycetia / Gemmatales / Gemmataceae / Gemmata Gem.ma'ta. L. fem. adj. used as L. fem. n. Gemmata, one provided with buds. The genus Gemmata belongs to the family Gemmataceae of the order Gemmatales (phylum Planctomycetota/ class Planctomycetia ) and comprises two named species, the type species Gemmata obscuriglobus , from a freshwater dam, and “ Gemmata massiliana ,” from a hospital water distribution system. Gemmata species are aerobic chemoorganotrophic heterotrophs for which carbohydrates are the carbon and energy sources, but the type species has the ability to take up proteins or polysaccharides from the external milieu. The type species and other members of the genus possess spherical cells, reproduce via budding, are motile via multitrichous flagella, and grow as pink colonies. The surfaces of whole cells, when observed by electron microscopy, have uniformly distributed round pit‐like crateriform structures, and at least in the type strain, sectioned cells viewed by electron microscopy display complex intracellular membranes. DNA G + C content (mol%) : 64–67 (genome sequence). Type species : Gemmata obscuriglobus Franzmann and Skerman 1984, VL18 emend. Scheuner et al. 2014.

High throughput sequencing libraries are typically limited by the requirement for nanograms to micrograms of input DNA.This bottleneck impedes the microscale analysis of ecosystems and the exploration of low biomass samples.Current methods for amplifying environmental DNA to bypass this bottleneck introduce considerable bias into metagenomic profiles.Here we describe and validate a simple modification of the Illumina Nextera XT DNA library preparation kit which allows creation of shotgun libraries from sub-nanogram amounts of input DNA.Community composition was reproducible down to 100fg of input DNA based on analysis of a mock community comprising 54 phylogenetically diverse Bacteria and Archaea.The main technical issues with the low input libraries were a greater potential for contamination, limited DNA complexity which has a direct effect on assembly and binning, and an associated higher percentage of read duplicates.We recommend a lower limit of 1pg (~100 to 1000 microbial cells) to ensure community composition fidelity, and the inclusion of negative controls to identify reagent-specific contaminants.Applying the approach to marine surface water, pronounced differences were observed between bacterial community profiles of microliter volume samples, which we attribute to biological variation.This result is consistent with expected microscale patchiness in marine communities.We thus envision that our benchmarked, slightly modified low input DNA protocol will be beneficial for microscale and low biomass metagenomics.

High throughput sequencing libraries are typically limited by the requirement for nanograms to micrograms of input DNA.This bottleneck impedes the microscale analysis of ecosystems and the exploration of low biomass samples.Current methods for amplifying environmental DNA to bypass this bottleneck introduce considerable bias into metagenomic profiles.Here we describe and validate a simple modification of the Illumina Nextera XT DNA library preparation kit which allows creation of shotgun libraries from sub-nanogram amounts of input DNA.Community composition was reproducible down to 100fg of input DNA based on analysis of a mock community comprising 54 phylogenetically diverse Bacteria and Archaea.The main technical issues with the low input libraries were a greater potential for contamination, limited DNA complexity which has a direct effect on assembly and binning, and an associated higher percentage of read duplicates.We recommend a lower limit of 1pg (~100 to 1000 microbial cells) to ensure community composition fidelity, and the inclusion of negative controls to identify reagent-specific contaminants.Applying the approach to marine surface water, pronounced differences were observed between bacterial community profiles of microliter volume samples, which we attribute to biological variation.This result is consistent with expected microscale patchiness in marine communities.We thus envision that our benchmarked, slightly modified low input DNA protocol will be beneficial for microscale and low biomass metagenomics.

Pi.rel'lu.la. L. n. pirum pear; L. fem. dim. ending ‐ ella ; L. fem. dim. ending ‐ ula ; N.L. fem. n. Pirellula very small pear, referring to the shape of the bacterium. Planctomycetes / Planctomycetia / Planctomycetales / Planctomycetaceae / Pirellula Pear or teardrop‐shaped cells with one pointed attachment pole, 0.5–3.0 × 1.0–5.0 µm. Gram‐stain‐negative. Cells do not possess a stalk , but may form a fibrillar holdfast. Frequently form rosettes by attachment with the pointed cell pole. The holdfast occurs on one pole of the cell (the narrow pole of ovoid cells) and facilitates attachment to other cells to form rosettes. Crateriform structures are distributed at one pole only . Reproduction is solely by bud formation . Buds are formed at or near the opposite, wider pole which thus constitutes the reproductive pole. Newly formed buds are motile by polar to subpolar monotrichous flagella . When thin sectioned cells prepared via cryosubstitution are examined via electron microscopy, they display a characteristic organization including a major cell compartment , the pirellulosome , in which ribosomes and a condensed nucleoid are enclosed by an intracytoplasmic membrane , and a ribosome‐free paryphoplasm region between this intracytoplasmic membrane and the closely apposed cytoplasmic membrane and cell wall . Chemoorganotrophic; obligately aerobic. The original description was emended following the description of Rhodopirellula and Blastopirellula to include more recent data (Schlesner et al., 2004). The major polyamine is sym homospermidine. The major respiratory lipoquinone present is MK‐6. The major phospholipid present is phosphatidylglycerol. A number of other lipids are present that have characteristic R f values, but whose structures are not currently known. The lipid pattern is characteristic . The major fatty acids present are C 14 : 0 , C 16 : 1 ω 7 , C 16 : 0 , C 18 : 1 ω 9 , C 18 : 1 ω 7 , C 18 : 0 , and C 20 : 1 ω 11 . DNA G + C content ( mol %): 56.4 ± 0.4 to 59.0 ( T m, Bd). Type species : Pirellula staleyi Schlesner and Hirsch 1987, 441 VP emend. Schlesner, Rensmann, Tindall, Gade, Rabus, Pfeiffer and Hirsch 2004, 1577.

High throughput sequencing libraries are typically limited by the requirement for nanograms to micrograms of input DNA.This bottleneck impedes the microscale analysis of ecosystems and the exploration of low biomass samples.Current methods for amplifying environmental DNA to bypass this bottleneck introduce considerable bias into metagenomic profiles.Here we describe and validate a simple modification of the Illumina Nextera XT DNA library preparation kit which allows creation of shotgun libraries from sub-nanogram amounts of input DNA.Community composition was reproducible down to 100fg of input DNA based on analysis of a mock community comprising 54 phylogenetically diverse Bacteria and Archaea.The main technical issues with the low input libraries were a greater potential for contamination, limited DNA complexity which has a direct effect on assembly and binning, and an associated higher percentage of read duplicates.We recommend a lower limit of 1pg (~100 to 1000 microbial cells) to ensure community composition fidelity, and the inclusion of negative controls to identify reagent-specific contaminants.Applying the approach to marine surface water, pronounced differences were observed between bacterial community profiles of microliter volume samples, which we attribute to biological variation.This result is consistent with expected microscale patchiness in marine communities.We thus envision that our benchmarked, slightly modified low input DNA protocol will be beneficial for microscale and low biomass metagenomics.

Scanning machine CHLOE, developed for photographic use, is combined with a digital computer to obtain quantitative and statistically significant data on chromosome shapes, distribution, density, and pairing. CHLOE permits data acquisition about a chromosome complement to be obtained two times faster than by manual pairing.

This chapter discusses the development of computer technology and describes various hardware and software developments. The concept of program sharing is almost as old as the use of the computer itself in some areas of nuclear science and technology, particularly, in reactor design and nuclear engineering. It came about in these areas largely as a result of two events: (1) the establishment of the AEC Computer Facility at New York University and (2) the compilation of an early bibliography of available computer programs for nuclear reactor problems. The chapter discusses this concept–program interchange. As both computing and nuclear energy shifted from research and development to industry status, the need for standardization was recognized. In 1966, when Tom Steel wrote his review of standards for computers and information processing, only 12 American National Standards had been published in that fast-growing field. The first such nuclear standard was the Glossary of Terms in Nuclear Science and Technology approved in 1957. Standards are generally developed by consensus within professional societies, technical or trade associations, or governmental agencies. The chapter discusses the standards sponsored by the American Nuclear Society and the Reactor Physics branch of the United States Atomic Energy Commission (USAEC) Reactor Research and Development Division, because it has been these efforts where nuclear practitioners have attempted to develop standards related to computing.

The software portability problem is examined from the viewpoint of experience gained in the operation of a software exchange and information center. First, the factors contributing to the program interchange to date are identified, then major problem areas remaining are noted. The import of the development of programming language and documentation standards is noted, and the program packaging procedures and dissemination practices employed by the Center to facilitate successful software transport are described. Organization, or installation, dependencies of the computing environment, often hidden from the program author, and data interchange complexities are seen as today's primary issues with dedicated processors and network communications offering an alternative solution.

The software portability problem is examined from the viewpoint of experience gained in the operation of a software exchange and information center. First, the factors contributing to the program interchange to date are identified, then major problem areas remaining are noted. The import of the development of programming language and documentation standards is noted, and the program packaging procedures and dissemination practices employed by the Center to facilitate successful software transport are described. Organization, or installation, dependencies of the computing environment, often hidden from the program author, and data interchange complexities are seen as today's primary issues with dedicated processors and network communications offering an alternative solution.