Flp-recombinase mouse line for genetic manipulation of ipRGCs.

Light has myriad impacts on behavior, health, and physiology. These signals originate in the retina and are relayed to the brain by more than 40 types of retinal ganglion cells (RGCs). Despite a growing appreciation for the diversity of RGCs, how these diverse channels of light information are ultimately integrated by the ~50 retinorecipient brain targets to drive these light-evoked effects is a major open question. This gap in understanding primarily stems from a lack of genetic tools that specifically label, manipulate, or ablate specific RGC types. Here, we report the generation and characterization of a new mouse line (Opn4FlpO), in which FlpO is expressed from the Opn4 locus, to manipulate the melanopsin-expressing, intrinsically photosensitive retinal ganglion cells. We find that the Opn4FlpO line, when crossed to multiple reporters, drives expression that is confined to ipRGCs and primarily labels the M1-M3 subtypes. Labeled cells in this mouse line show the expected intrinsic, melanopsin-based light response and morphological features consistent with the M1-M3 subtypes. In alignment with the morphological and physiological findings, we see strong innervation of non-image forming brain targets by ipRGC axons, and weaker innervation of image forming targets in Opn4FlpO mice labeled using AAV-based and FlpO-reporter lines. Consistent with the FlpO insertion disrupting the endogenous Opn4 transcript, we find that Opn4FlpO/FlpO mice show deficits in the pupillary light reflex, demonstrating their utility for behavioral research in future experiments. Overall, the Opn4FlpO mouse line drives Flp-recombinase expression that is confined to ipRGCs and most effectively drives recombination in M1-M3 ipRGCs. This mouse line will be of broad use to those interested in manipulating ipRGCs through a Flp-based recombinase for intersectional studies or in combination with other, non-Opn4 Cre driver lines.

The Bacterial Connection between the Oral Cavity and the Gut Diseases.

More than 100 trillion symbiotic microorganisms constitutively colonize throughout the human body, including the oral cavity, the skin, and the gastrointestinal tract. The oral cavity harbors one of the most diverse and abundant microbial communities within the human body, second to the community that resides in the gastrointestinal tract, and is composed of >770 bacterial species. Advances in sequencing technologies help define the precise microbial landscape in our bodies. Environmental and functional differences render the composition of resident microbiota largely distinct between the mouth and the gut and lead to the development of unique microbial ecosystems in the 2 mucosal sites. However, it is apparent that there may be a microbial connection between these 2 mucosal sites in the context of disease pathogenesis. Accumulating evidence indicates that resident oral bacteria can translocate to the gastrointestinal tract through hematogenous and enteral routes. The dissemination of oral microbes to the gut may exacerbate various gastrointestinal diseases, including irritable bowel syndrome, inflammatory bowel disease, and colorectal cancer. However, the precise role that oral microbes play in the extraoral organs, including the gut, remains elusive. Here, we review the recent findings on the dissemination of oral bacteria to the gastrointestinal tract and their possible contribution to the pathogenesis of gastrointestinal diseases. Although little is known about the mechanisms of ectopic colonization of the gut by oral bacteria, we also discuss the potential factors that allow the oral bacteria to colonize the gut.

Acetogenesis from H2 plus CO2 by spirochetes from termite guts.

Pure cultures of termite gut spirochetes were obtained and were shown to catalyze the synthesis of acetate from H2 plus CO2. The 16S ribosomal DNA sequences of two strains were 98 percent similar and were affiliated with those of the genus Treponema. However, neither was closely related to any known treponeme. These findings imply an important role for spirochetes in termite nutrition, help to reconcile the dominance of acetogenesis over methanogenesis as an H2 sink in termite hindguts, suggest that the motility of termite gut protozoa by means of attached spirochetes may be based on interspecies H2 transfer, and underscore the importance of termites as a rich reservoir of novel microbial diversity.

An ab initio study of energetic stability and electronic confinement for different structural phases of ZnO nanowires.

We performed an ab initio total energy investigation of hexagonal (wurtzite and graphitic) and zinc blende ZnO nanowires (NWs) aligned along the [0001] and [111] directions, respectively, as a function of the NW diameter. We have considered unpassivated and (hydrogen) passivated NW surfaces. For the unpassivated system, we find that the wurtzite phase represents the energetically most favorable configuration. The width of the energy bandgap of wurtzite ZnO NWs increases by reducing the NW diameter, which is in accordance with the one-dimensional confinement effect. In contrast, this property fails in the zinc blende and graphitic NWs. In the former it is due to the high density of surface states within the fundamental bandgap, while in the latter system the energy bandgap becomes indirect and increases slowly by reducing the NW diameter. Our total energy results indicate that the hydrogen-passivated ZnO NWs are more stable than the unpassivated ones. For thin hydrogen-passivated NWs, we find that the graphitic phase becomes more stable than the wurtzite. For NW diameters around 2 nm, the graphitic and wurtzite phases present similar formation energies, while for larger diameters the wurtzite NWs become energetically more favorable. Finally, comparing the behavior and the positions of the valence and conduction band edges for the unpassivated ZnO NWs, we proposed the formation of type II band alignment for a hypothetical wurtzite/graphitic NW heterojunction.

rrndb: the Ribosomal RNA Operon Copy Number Database.

The Ribosomal RNA Operon Copy Number Database (rrndb) is an Internet-accessible database containing annotated information on rRNA operon copy number among prokaryotes. Gene redundancy is uncommon in prokaryotic genomes, yet the rRNA genes can vary from one to as many as 15 copies. Despite the widespread use of 16S rRNA gene sequences for identification of prokaryotes, information on the number and sequence of individual rRNA genes in a genome is not readily accessible. In an attempt to understand the evolutionary implications of rRNA operon redundancy, we have created a phylogenetically arranged report on rRNA gene copy number for a diverse collection of prokaryotic microorganisms. Each entry (organism) in the rrndb contains detailed information linked directly to external websites including the Ribosomal Database Project, GenBank, PubMed and several culture collections. Data contained in the rrndb will be valuable to researchers investigating microbial ecology and evolution using 16S rRNA gene sequences. The rrndb web site is directly accessible on the WWW at http://rrndb.cme. msu.edu.

The RDP-II (Ribosomal Database Project).

The Ribosomal Database Project (RDP-II), previously described by Maidak et al. [Nucleic Acids Res. (2000), 28, 173-174], continued during the past year to add new rRNA sequences to the aligned data and to improve the analysis commands. Release 8.0 (June 1, 2000) consisted of 16 277 aligned prokaryotic small subunit (SSU) rRNA sequences while the number of eukaryotic and mitochondrial SSU rRNA sequences in aligned form remained at 2055 and 1503, respectively. The number of prokaryotic SSU rRNA sequences more than doubled from the previous release 14 months earlier, and approximately 75% are longer than 899 bp. An RDP-II mirror site in Japan is now available (http://wdcm.nig.ac.jp/RDP/html/index.h tml). RDP-II provides aligned and annotated rRNA sequences, derived phylogenetic trees and taxonomic hierarchies, and analysis services through its WWW server (http://rdp.cme.msu.edu/). Analysis services include rRNA probe checking, approximate phylogenetic placement of user sequences, screening user sequences for possible chimeric rRNA sequences, automated alignment, production of similarity matrices and services to plan and analyze terminal restriction fragment polymorphism experiments. The RDP-II email address for questions and comments has been changed from curator@cme.msu.edu to rdpstaff@msu.edu.

The Ribosomal Database Project (RDP-II): previewing a new autoaligner that allows regular updates and the new prokaryotic taxonomy.

The Ribosomal Database Project-II (RDP-II) pro-vides data, tools and services related to ribosomal RNA sequences to the research community. Through its website (http://rdp.cme.msu.edu), RDP-II offers aligned and annotated rRNA sequence data, analysis services, and phylogenetic inferences (trees) derived from these data. RDP-II release 8.1 contains 16 277 prokaryotic, 5201 eukaryotic, and 1503 mitochondrial small subunit rRNA sequences in aligned and annotated format. The current public beta release of 9.0 debuts a new regularly updated alignment of over 50 000 annotated (eu)bacterial sequences. New analysis services include a sequence search and selection tool (Hierarchy Browser) and a phylogenetic tree building and visualization tool (Phylip Interface). A new interactive tutorial guides users through the basics of rRNA sequence analysis. Other services include probe checking, phylogenetic placement of user sequences, screening of users' sequences for chimeric rRNA sequences, automated alignment, production of similarity matrices, and services to plan and analyze terminal restriction fragment polymorphism (T-RFLP) experiments. The RDP-II email address for questions or comments is rdpstaff@msu.edu.

Variable responses of human microbiomes to dietary supplementation with resistant starch.

BACKGROUND: The fermentation of dietary fiber to various organic acids is a beneficial function provided by the microbiota in the human large intestine. In particular, butyric acid contributes to host health by facilitating maintenance of epithelial integrity, regulating inflammation, and influencing gene expression in colonocytes. We sought to increase the concentration of butyrate in 20 healthy young adults through dietary supplementation with resistant starch (unmodified potato starch-resistant starch (RS) type 2). METHODS: Fecal samples were collected from individuals to characterize butyrate concentration via liquid chromatography and composition of the microbiota via surveys of 16S rRNA-encoding gene sequences from the Illumina MiSeq platform. Random Forest and LEfSe analyses were used to associate responses in butyrate production to features of the microbiota. RESULTS: RS supplementation increased fecal butyrate concentrations in this cohort from 8 to 12 mmol/kg wet feces, but responses varied widely between individuals. Individuals could be categorized into three groups based upon butyrate concentrations before and during RS: enhanced, high, and low (n = 11, 3, and 6, respectively). Fecal butyrate increased by 67 % in the enhanced group (from 9 to 15 mmol/kg), while it remained ≥11 mmol/kg in the high group and ≤8 mmol/kg in the low group. Microbiota analyses revealed that the relative abundance of RS-degrading organisms-Bifidobacterium adolescentis or Ruminococcus bromii-increased from ~2 to 9 % in the enhanced and high groups, but remained at ~1.5 % in the low group. The lack of increase in RS-degrading bacteria in the low group may explain why there was no increase in fecal butyrate in response to RS. The microbiota of individuals in the high group were characterized by an elevated abundance of the butyrogenic microbe Eubacterium rectale (~6 % in high vs. 3 % in enhanced and low groups) throughout the study. CONCLUSIONS: We document the heterogeneous responses in butyrate concentrations upon RS supplementation and identify characteristic of the microbiota that appear to underlie this variation. This study complements and extends other studies that call for personalized approaches to manage beneficial functions provided by gut microbiomes.

A new class of large band gap quantum spin hall insulators: 2D fluorinated group-IV binary compounds.

We predict a new class of large band gap quantum spin Hall insulators, the fluorinated PbX (X = C, Si, Ge and Sn) compounds, that are mechanically stable two-dimensional materials. Based on first principles calculations we find that, while the PbX systems are not topological insulators, all fluorinated PbX (PbXF2) compounds are 2D topological insulators. The quantum spin Hall insulating phase was confirmed by the explicitly calculation of the Z2 invariant. In addition we performed a thorough investigation of the role played by the (i) fluorine saturation, (ii) crystal field, and (iii) spin-orbital coupling in PbXF2. By considering nanoribbon structures, we verify the appearance of a pair of topologically protected Dirac-like edge states connecting the conduction and valence bands. The insulating phase which is a result of the spin orbit interaction, reveals that this new class of two dimensional materials present exceptional nontrivial band gaps, reaching values up to 0.99 eV at the Γ point, and an indirect band gap of 0.77 eV. The topological phase is arisen without any external field, making this system promising for nanoscale applications, using topological properties.

Topological phase transitions of (BixSb1-x)2Se3 alloys by density functional theory.

We have performed an ab initio total energy investigation of the topological phase transition, and the electronic properties of topologically protected surface states of (BixSb1-x)2Se3 alloys. In order to provide an accurate alloy concentration for the phase transition, we have considered the special quasirandom structures to describe the alloy system. The trivial â†’ topological transition concentration was obtained by (i) the calculation of the band gap closing as a function of Bi concentration (x), and (ii) the calculation of the Z2 topological invariant number. We show that there is a topological phase transition, for x around 0.4, verified for both procedures (i) and (ii). We also show that in the concentration range 0.4 < x < 0.7, the alloy does not present any other band at the Fermi level besides the Dirac cone, where the Dirac point is far from the bulk states. This indicates that a possible suppression of the scattering process due to bulk states will occur.

The Structure of Microbial Communities in Soil and the Lasting Impact of Cultivation.

The structure of microbial communities was examined as a function of community composition and the relative abundance of specific microbial groups to examine the effects that plant community composition and land-use history have on microbial communities in the soil. The sites sampled were part of the Long Term Ecological Research (LTER) project in agricultural ecology at the W.K. Kellogg Biological Station of Michigan State University (Hickory Corners, MI) and included both active and abandoned agricultural fields as well as nearby fields that had never been cultivated. Microbial community structure was assessed by extracting total RNA from soil samples and using 16S rRNA-targeted oligonucleotide probes to quantify the abundance of rRNA from the alpha, beta, and gamma Proteobacteria, the Actinobacteria (Gram positive bacteria with a high mol % G+C genome), the Bacteria, and the Eukarya. In addition, soil microbial communities were characterized by examining fluorescently tagged terminal restriction fragment length polymorphisms (T-RFLP) in PCR amplified 16S rDNA. Microbial community structure was observed to be remarkably similar among plots that shared a long-term history of agricultural management despite differences in plant community composition and land management that have been maintained on the plots in recent years. In contrast, microbial community structure differed significantly between fields that had never been cultivated and those having a long-term history of cultivation.

Inwardly rectifying potassium channel Kir4.1 is responsible for the native inward potassium conductance of satellite glial cells in sensory ganglia.

Satellite glial cells (SGCs) surround primary afferent neurons in sensory ganglia, and increasing evidence has implicated the K(+) channels of SGCs in affecting or regulating sensory ganglion excitability. The inwardly rectifying K(+) (Kir) channel Kir4.1 is highly expressed in several types of glial cells in the central nervous system (CNS) where it has been implicated in extracellular K(+) concentration buffering. Upon neuronal activity, the extracellular K(+) concentration increases, and if not corrected, causes neuronal depolarization and uncontrolled changes in neuronal excitability. Recently, it has been demonstrated that knockdown of Kir4.1 expression in trigeminal ganglia leads to neuronal hyperexcitability in this ganglia and heightened nociception. Thus, we investigated the contribution of Kir4.1 to the membrane K(+) conductance of SGCs in neonatal and adult mouse trigeminal and dorsal root ganglia. Whole cell patch clamp recordings were performed in conjunction with immunocytochemistry and quantitative transcript analysis in various mouse lines. We found that in wild-type mice, the inward K(+) conductance of SGCs is blocked almost completely with extracellular barium, cesium and desipramine, consistent with a conductance mediated by Kir channels. We then utilized mouse lines in which genetic ablation led to partial or complete loss of Kir4.1 expression to assess the role of this channel subunit in SGCs. The inward K(+) currents of SGCs in Kir4.1+/- mice were decreased by about half while these currents were almost completely absent in Kir4.1-/- mice. These findings in combination with previous reports support the notion that Kir4.1 is the principal Kir channel type in SGCs. Therefore Kir4.1 emerges as a key regulator of SGC function and possibly neuronal excitability in sensory ganglia.

The effects of oxygen on the surface passivation of InP nanowires.

The effects of surface passivation on the electronic and structural properties of InP nanowires have been investigated by first-principles calculations. We compare the properties of nanowires whose surfaces have been passivated in several ways, always by H atoms and OH radicals. Taking as the initial reference nanowires that are fully passivated by H atoms, we find that the exchange of these atoms at the surface by OH radicals is always energetically favorable. A nanowire fully passivated by OH radicals is about 2.5 eV per passivated dangling bond more stable than a nanowire fully passivated by H atoms. However, the energetically most stable passivated surface is predicted to have all In atoms bonded to OH radicals and all P atoms bonded to H atoms. This mixed passivation is 2.66 eV per passivated dangling bond more stable than a nanowire fully passivated by H atoms. Our results show that, in comparison with the fully H-saturated nanowire, the fully OH-saturated nanowire has a smaller energy band gap and localized states near the energy band edges. Also, more interestingly, concerning optical applications, the most stable H+OH passivated nanowire has a well-defined energy band gap, only 10% smaller than the H-saturated nanowire energy gap, and few localized states always close to the valence band maximum.

Changes in Synechococcus population size and cellular ribosomal RNA content in response to predation and nutrient limitation.

A mathematical model of predator-prey interactions was used to predict the relationship between population size and cellular growth rate in a two-tiered trophic system consisting of Synechococcus PCC 6301 and Tetrahymena pyriformis. As predicted, axenic chemostat cultures of Synechococcus responded to increased nutrient availability by expanding the equilibrium population size without a concurrent change in growth rate. Likewise, the addition of the predator Tetrahymena pyriformis decreased the Synechococcus population size by 85% and increased the Synechococcus growth rate. Synechococcus populations in the surface waters of the Gulf of Mexico were sampled to ascertain whether the relationship between population size and cellular 16S rRNA concentration conformed to that predicted by the model. Direct counts of autofluorescent cells in size-fractionated seawater samples provided an estimate of Synechococcus population size. The growth rate of in situ populations was estimated by measuring the extent of hybridization of an oligonucleotide probes complementary to Synechococcus 16S rRNA, based on evidence that ribosomal RNA content increases concurrently with growth rate. The comparison of in situ population sizes and specific growth rates revealed that relatively large Synechococcus populations were growing slowly, indicative of nutrient limitation, and that quickly growing populations were relatively small, as predicted for predator-limited populations.

Growth rate-dependent accumulation of RNA from plasmid-borne rRNA operons in Escherichia coli.

Inadequate regulation of the expression of additional plasmid-borne rRNA operons in Escherichia coli was exaggerated at slow growth rates, resulting in increases of approximately 100% for RNA concentration and 33% for doubling time. These observations are consistent with the hypothesis that multiple rRNA operons constitute a metabolic burden at slow growth rates.

The first cellular bioenergetic process: primitive generation of a proton-motive force.

It is proposed that the energy-transducing system of the first cellular organism and its precursor was fueled by the oxidation of hydrogen sulfide and ferric sulfide to iron pyrites and two [H+] on the outside surface of a vesicle (the cell membrane), with the concomitant reduction of CO or CO2 on the interior. The resulting proton gradient across the cell membrane provides a proton-motive force, so that a variety of kinds of work can be done. It is envisioned as providing a selective advantage for cells capable of harvesting this potential. The proposed reactants for these reactions are consistent with the predicted composition of the Earth's early environment. Modern-day homologs of the ancestral components of the energy-transducing system are thought to be membrane-associated ferredoxins for the extracellular redox reaction, carbon monoxide dehydrogenase for the carbon fixation reaction, and ATPase for the harvesting of the proton gradient. With a source of consumable energy, the cell could drive chemical reactions and transport events in such a way as to be exploited by Darwinian evolution.

Environmental factors influencing the distribution of rRNA from Verrucomicrobia in soil.

The Verrucomicrobia constitute a newly discovered division of the Bacteria identified as a numerically abundant component of soil microbial communities in numerous sites around the world. The relative abundance of rRNA from Verrucomicrobia was investigated in the soil to examine the influence of specific environmental factors on the distribution of Verrucomicrobia and to better understand the distribution of this group in terrestrial ecosystems. The abundance of the verrucomicrobial rRNA was determined by using a novel oligonucleotide probe that is specific for verrucomicrobial 16S rRNA. The abundance of verrucomicrobial 16S rRNA in soil microbial communities was determined in relation to plant community composition and soil management history over a period of 2 years. Additional samples were analyzed to determine if verrucomicrobial rRNA relative abundance changes in relation to either soil depth or soil moisture content. The Verrucomicrobia composed 1.9+/-0.2% of the microbial community rRNA present in the 85 soil samples examined. The distribution of verrucomicrobial rRNA in the soil reveals that Verrucomicrobia are significantly affected by environmental characteristics that change in relation to time, soil history, and soil depth, and reveals that a statistically significant amount of the variation in verrucomicrobial rRNA abundance can be explained by changes in soil moisture content.