High-throughput isotopic analysis of RNA microarrays to quantify microbial resource use

Most microorganisms remain uncultivated, and typically their ecological roles must be inferred from diversity and genomic studies. To directly measure functional roles of uncultivated microbes, we developed Chip-stable isotope probing (SIP), a high-sensitivity, high-throughput SIP method performed on a phylogenetic microarray (chip). This approach consists of microbial community incubations with isotopically labeled substrates, hybridization of the extracted community rRNA to a microarray and measurement of isotope incorporation—and therefore substrate use—by secondary ion mass spectrometer imaging (NanoSIMS). Laboratory experiments demonstrated that Chip-SIP can detect isotopic enrichment of 0.5 atom % ¹³C and 0.1 atom % ¹⁵N, thus permitting experiments with short incubation times and low substrate concentrations. We applied Chip-SIP analysis to a natural estuarine community and quantified amino acid, nucleic acid or fatty acid incorporation by 81 distinct microbial taxa, thus demonstrating that resource partitioning occurs with relatively simple organic substrates. The Chip-SIP approach expands the repertoire of stable isotope-enabled methods available to microbial ecologists and provides a means to test genomics-generated hypotheses about biogeochemical function in any natural environment.     

Porphyromonas gingivalis Mediates Inflammasome Repression in Polymicrobial Cultures through a Novel Mechanism Involving Reduced Endocytosis

The interleukin (IL)-1β-processing inflammasome has recently been identified as a target for pathogenic evasion of the inflammatory response by a number of bacteria and viruses. We postulated that the periodontal pathogen, Porphyromonas gingivalis may suppress the inflammasome as a mechanism for its low immunogenicity and pathogenic synergy with other, more highly immunogenic periodontal bacteria. Our results show that P. gingivalis lacks signaling capability for the activation of the inflammasome in mouse macrophages. Furthermore, P. gingivalis can suppress inflammasome activation by another periodontal bacterium, Fusobacterium nucleatum. This repression affects IL-1β processing, as well as other inflammasome-mediated processes, including IL-18 processing and cell death, in both human and mouse macrophages. F. nucleatum activates IL-1β processing through the Nlrp3 inflammasome; however, P. gingivalis repression is not mediated through reduced levels of inflammasome components. P. gingivalis can repress Nlrp3 inflammasome activation by Escherichia coli, and by danger-associated molecular patterns and pattern-associated molecular patterns that mediate activation through endocytosis. However, P. gingivalis does not suppress Nlrp3 inflammasome activation by ATP or nigericin. This suggests that P. gingivalis may preferentially suppress endocytic pathways toward inflammasome activation. To directly test whether P. gingivalis infection affects endocytosis, we assessed the uptake of fluorescent particles in the presence or absence of P. gingivalis. Our results show that P. gingivalis limits both the number of cells taking up beads and the number of beads taken up for bead-positive cells. These results provide a novel mechanism of pathogen-mediated inflammasome inhibition through the suppression of endocytosis.     

Thermal stress responses in the bacterial biosphere of the Great Barrier Reef sponge,Rhopaloeides odorabile

Marine sponges are diverse, abundant and provide a crucial coupling point between benthic and pelagic habitats due to their high filtration rates. They also harbour extensive microbial communities, with many microbial phylotypes found exclusively in sponge hosts and not in the seawater or surrounding environment, i.e. so‐called sponge‐specific clusters (SCs) or sponge‐ and coral‐specific clusters (SCCs). We employed DNA (16S rRNA gene) and RNA (16S rRNA)‐based amplicon pyrosequencing to investigate the effects of sublethal thermal stress on the bacterial biosphere of the Great Barrier Reef sponge Rhopaloeides odorabile. A total of 8381 operational taxonomic units (OTUs) (97% sequence similarity) were identified, affiliated with 32 bacterial phyla from seawater samples, 23 bacterial phyla from sponge DNA extracts and 18 bacterial phyla from sponge RNA extracts. Sublethal thermal stress (31°C) had no effect on the present and/or active portions of the R. odorabile bacterial community but a shift in the bacterial assemblage was observed in necrotic sponges. Over two‐thirds of DNA and RNA sequences could be assigned to previously defined SCs/SCCs in healthy sponges whereas only 12% of reads from necrotic sponges could be assigned to SCs/SCCs. A rapid decline in host health over a 1°C temperature increment suggests that sponges such as R. odorabile may be highly vulnerable to the effects of global climate change.     

Skeletal muscle Nur77 expression enhances oxidative metabolism and substrate utilization

Mitochondrial dysfunction has been implicated in the pathogenesis of type 2 diabetes. Identifying novel regulators of mitochondrial bioenergetics will broaden our understanding of regulatory checkpoints that coordinate complex metabolic pathways. We previously showed that Nur77, an orphan nuclear receptor of the NR4A family, regulates the expression of genes linked to glucose utilization. Here we demonstrate that expression of Nur77 in skeletal muscle also enhances mitochondrial function. We generated MCK-Nur77 transgenic mice that express wild-type Nur77 specifically in skeletal muscle. Nur77-overexpressing muscle had increased abundance of oxidative muscle fibers and mitochondrial DNA content. Transgenic muscle also exhibited enhanced oxidative metabolism, suggestive of increased mitochondrial activity. Metabolomic analysis confirmed that Nur77 transgenic muscle favored fatty acid oxidation over glucose oxidation, mimicking the metabolic profile of fasting. Nur77 expression also improved the intrinsic respiratory capacity of isolated mitochondria, likely due to the increased abundance of complex I of the electron transport chain. These changes in mitochondrial metabolism translated to improved muscle contractile function ex vivo and improved cold tolerance in vivo. Our studies outline a novel role for Nur77 in the regulation of oxidative metabolism and mitochondrial activity in skeletal muscle.     

Are parents’ working patterns associated with their child’s sleep? An analysis of dualparent families in Australia

Insufficient sleep in children predicts emotional and behavioral problems, poorer school performance, and health problems. Child sleep durations have declined in recent decades, suggesting a need to identify and understand predictors of short sleep. The present study investigated whether aspects of parental employment (i.e. parental work hours, and non-standard work hours) were associated with sleep in children. Data collected from 2477 children aged 6-7 years as part of the Longitudinal Study of Australian Children were used in this paper. Child sleep duration, bedtimes, and wake times were determined from parent self-report using time-use diaries. Parents completed a survey assessing their work patterns as well as a range of other demographic and social factors. The results indicated that long mother work hours were associated with later bedtimes and increased odds of <9.5 h sleep in children. Long father work hours were associated with earlier waketimes, earlier bedtimes, and reduced odds of long sleep. Non-standard work hours were associated with longer sleep and earlier bedtimes. The present results indicate the need to develop strategies to limit any adverse effects of parental work on child sleep, perhaps by promoting earlier and regular bedtimes. These findings warrant further investigation given the importance of sleep in healthy child development.

     

Kinetics of Induction of the Lactose Operon on an Episome in Salmonella typhimurium

A kinetic study of induction of the enzymes of the lactose operon was carried out under conditions known to affect the kinetics of derepression of the enzymes of the histidine operon. The results show that the lactose system is similar to the histidine system in its responsiveness to conditions thought to affect the formylating capacity of the cell. This was demonstrated in the following ways: (i) trimethoprim, which is known to reduce the formylating capacity of the cell, gives rise to a relatively long interval between the times of induction of beta-galactosidase and transacetylase; (ii) under conditions in which the histidine operon is derepressed, chloramphenicol causes a prolongation of the interval between the times of induction of the two enzymes, and this prolongation is reversed by adenine, methionine, and serine, compounds known to enrich the one-carbon pool of the cell; and (iii) 4-amino-5-imidazolcarboxamide ribonucleoside, a compound which may act as a drain for formyl groups, reverses the effect of the latter compounds. The finding that the interval between the times of induction of the two enzymes is shortened under conditions expected to maintain a relatively high intracellular fo rmylating capacity suggests that under certain conditions translation of the polycistronic messenger ribonucleic acid of the lactose operon may be initiated at more than one site or may proceed more rapidly from the operator end.     

Blocking gap junctional intercellular communication in myoblasts inhibits myogenin and MRF4 expression

Cells rely heavily on cues from their extracellular environment and other cells to coordinate normal physiological processes, and the exchange of molecules via gap junctions has been suggested as an important avenue for cell-cell communication. Gap junctions are found in virtually all mammalian tissues with the notable exception of adult skeletal muscle. However, since functional gap junctions have been detected during the early stages of muscle development, gap junctional intercellular communication (GJIC) may play an important role in myogenesis. In this study, GJIC in normal L6 myoblasts was inhibited using the known blockers 1-octanal and β-glycyrrhetinic acid (β-GA). Under differentiation promoting conditions, L6 cells fused to form multinucleated myotubes, but when treated with either octanol or β-GA, no fusion was observed. The expression of two muscle regulatory factors (MRFs), myogenin and MRF4, was examined in both the blocked and control cells. As expected, the activation of both the myogenin and MRF4 genes coincided with the onset of differentiation in the control L6 cells. Neither of these genes were turned on in the blocked cells, even when grown under low serum conditions. This inhibition of differentiation by octanol and β-GA was reversible, since the activation of both MRF genes as well as myoblast fusion were observed when the blocking medium was replaced with normal differentiating medium. These results suggest that intercellular communication via gap junctions plays an important role in skeletal muscle development and perhaps in the cell signaling events that trigger the activation of muscle-specific MRF genes. Dev. Genet. 20:133–144. 1997. © 1997 Wiley-Liss, Inc.     

Bioethics and academic freedom

The author describes the events surrounding his attempts to lecture on the subject of euthanasia in West Germany in June 1989. Singer, who defends the view that active euthanasia for some newborns with handicaps may be ethically permissible, had been invited to speak to professional and academic groups. Strong public protests against Singer and his topic led to the cancellation of some of his engagements, disruptions during others, and harrassment of the German academics who had invited him to speak. These incidents and the subject of euthanasia became matters of intense national debate in West Germany, but there was little public or academic support for Singer's right to be heard. Singer argues that bioethics and bioethicists must have the freedom to challenge conventional moral beliefs, and that the events in West Germany illustrate the grave danger to that freedom from religious and political intolerance.     

Spermatozoa production in male <Emphasis Type="Italic">Varroa destructor</Emphasis> and its impact on reproduction in worker brood of <Emphasis Type="Italic">Apis mellifera</Emphasis>

Reproduction in Varroa destructor exclusively takes place within the sealed honey bee brood cell and is, therefore, limited by the duration of the postcapping period. Oogenesis, ontogenetic development and mating must be optimized to ensure the production of as many mated daughter mites as possible. One adult male mite has to mate with up to five sister mites and transfer 30–40 spermatozoa to each female. We analyzed the production and transfer of male spermatozoa during a reproductive cycle by counting all spermatozoa in the genital tracts of the male and daughter mites in 80 worker brood cells at defined times after cell capping. We could show that spermatozoa production in male mites is an ongoing process throughout their adult lifetime starting after the adult molt. The spermatozoa are transferred to the females in an early non-capacitated stage and require further maturation within the female’s genital tract. Our study points out that a Varroa male has at any time in the brood cell enough spermatozoa to inseminate all daughter mites but does not waste energy in producing a big surplus. In total one male produced, on average, 125 spermatozoa during a reproductive cycle in worker brood which is sufficient for successful matings with at least three daughter mites. Spermiogenesis in Varroa males represents therefore a further adaptation to the limited time available for reproduction.