A common garden experiment with Porphyra umbilicalis (Rhodophyta) evaluates methods to study spatial differences in the macroalgal microbiome

While macroalgal microbiomes are the focus of many recent studies, there is little information about microbial spatial diversity across the thallus. Reliance on field material makes it difficult to discern whether recovered microbiomes belong to the host or its epiphytes, and technical comparisons of macroalgal samples for microbial studies are needed. Here, we use a common garden approach that avoids the problem of epiphytes, particularly at holdfasts, to examine the microbiome of Porphyra umbilicalis (strain Pum1). We used the V6 hypervariable region of the 16S rDNA with Illumina HiSeq sequencing and developed PNA clamps to block recovery of organelle V6 sequences. The common garden approach allowed us to determine differences in the microbiome at the holdfast versus blade margin. We found a notable increase in the relative abundance of Planctomycetes and Alphaproteobacteria at the holdfast, particularly of the possible symbiont Sulfitobacter sp. Nonadjacent 1.5 cm² samples of blade margin had microbiomes that were not statistically different. The most abundant phylum in the overall microbiome was Proteobacteria, followed by Bacteroidetes. Because phycologists often work in remote sites, we compared three stabilization and preparation techniques and found silica gel desiccation/bead‐beating and flash‐freezing/lyophilization/bead‐beating to be interchangeable. Core taxa (≥0.1% of sequences) across treatments were similar and accounted for ≥95% of all sequences. Finally, statistical conclusions for all comparisons were the same, regardless of which microbial community analysis tool was used: mothur or minimum entropy decomposition.     

Persistent chlamydiae: from cell culture to a paradigm for chlamydial pathogenesis.

Chlamydiae are medically important bacteria responsible for a wide range of human infections and diseases. Repeated episodes of infection promote chronic inflammation associated with detrimental immune system-mediated pathologic changes. However, the true nature of chlamydial pathogenesis may encompass repeated infection superimposed upon persistent infection, which would allow for heightened immune reactivity. During the course of chlamydial infection, numerous host elaborated factors with inhibitory or modifying effects may cause alterations in the chlamydia-host cell relationship such that the organism is maintained in a nonproductive stage of growth. Abnormal or persistent chlamydiae have been recognized under a variety of cell culture systems. The numerous factors associated with altered growth suggest an innate flexibility in the developmental cycle of chlamydiae. This review evaluates in vitro studies of chlamydial persistence and correlates these model systems to features of natural chlamydial disease.     

Real‐time monitoring of greenhouse gas emissions with tall chambers reveals diurnal N2O variation and increased emissions of CO2 and N2O from Miscanthus following compost addition

Miscanthus x giganteus's efficacy as an energy crop relies on maintaining low greenhouse gas (GHG) emissions. As demand for Miscanthus is expected to rise to meet bioenergy targets, fertilizers and composts may be employed to increase yields, but will also increase GHG emissions. Manipulation experiments are vital to investigate the consequences of any fertilizer additions, but there is currently no way to measure whole‐plant GHG fluxes from crops taller than 2.5 m, such as Miscanthus, at the experimental plot scale. We employed a unique combination of eddy covariance (EC), soil chambers and an entirely new automated chamber system, SkyBeam, to measure high frequency (ca. hourly) fluxes of carbon dioxide (CO₂), methane (CH₄) and nitrous oxide (N₂O) from a Miscanthus crop amended with green compost. Untreated controls were also monitored in a fully replicated experimental design. Net ecosystem exchange (NEE) of CO₂ was partitioned into soil respiration (R_s), gross primary productivity (GPP) and ecosystem respiration, and the crop was harvested to determine the effect of compost on crop productivity. Compost increased NEE emissions by 100% (p < .05), which was the result of a 20% increase of R_s (p < .06) and a 32% reduction in GPP (p < .05) and biomass of 37% (p < .06). Methane fluxes were small and unaffected by compost addition. N₂O emissions increased 34% under compost during an emission event; otherwise, fluxes were low and often negative, even under dry conditions. Diurnal variation in N₂O fluxes, with uptake during the day and emission at night was observed. These fluxes displayed a negative relationship with soil temperature and a hitherto undescribed diurnal temperature hysteresis. We conclude that compost addition negatively affected the productivity and environmental effects of Miscanthus cultivation during the first year following application.     

Multi-generational evaluation of genetic diversity and parentage in captive southern pygmy perch (<Emphasis Type="Italic">Nannoperca australis</Emphasis>)

Maintaining genetic diversity within captive breeding populations is a key challenge for conservation managers. We applied a multi-generational genetic approach to the captive breeding program of an endangered Australian freshwater fish, the southern pygmy perch (Nannoperca australis). During previous work, fish from the lower Murray-Darling Basin were rescued before drought exacerbated by irrigation resulted in local extinction. This endemic lineage of the species was captive-bred in genetically designed groups, and equal numbers of F1 individuals were reintroduced to the wild with the return of favourable habitat. Here, we implemented a contingency plan by continuing the genetic-based captive breeding in the event that a self-sustaining wild population was not established. F1 individuals were available as putative breeders from the subset of groups that produced an excess of fish in the original restoration program. We used microsatellite-based parentage analyses of these F1 fish to form breeding groups that minimized inbreeding. We assessed their subsequent parental contribution to F2 individuals and the maintenance of genetic diversity. We found skewed parental contribution to F2 individuals, yet minimal loss of genetic diversity from their parents. However, the diversity was substantially less than that of the original rescued population. We attribute this to the unavoidable use of F1 individuals from a limited number of the original breeding groups. Alternative genetic sources for supplementation or reintroduction should be assessed to determine their suitability. The genetic fate of the captive-bred population highlights the strong need to integrate DNA-based tools for monitoring and adaptive management of captive breeding programs.     

Integrated Delivery of Antiretroviral Treatment and Pre-exposure Prophylaxis to HIV-1–Serodiscordant Couples: A Prospective Implementation Study in Kenya and Uganda

BackgroundAntiretroviral-based interventions for HIV-1 prevention, including antiretroviral therapy (ART) to reduce the infectiousness of HIV-1 infected persons and pre-exposure prophylaxis (PrEP) to reduce the susceptibility of HIV-1 uninfected persons, showed high efficacy for HIV-1 protection in randomized clinical trials. We conducted a prospective implementation study to understand the feasibility and effectiveness of these interventions in delivery settings.ConclusionsIntegrated delivery of time-limited PrEP until sustained ART use in African HIV-1-serodiscordant couples was feasible, demonstrated high uptake and adherence, and resulted in near elimination of HIV-1 transmission, with an observed HIV incidence of <0.5% per year compared to an expected incidence of >5% per year.     

Genetic and Environmental Controls on the Establishment of the Invasive Grass, Phalaris arundinacea

Whether an exotic species becomes integrated into a community or aggressively takes it over depends upon many interacting factors. Using contextual analyses, we combined genetic data about an invasive plant with information about the neighboring species, the community, and the environment to determine what factors enable a genotype or species to invade. We transplanted 50 individuals of each of three clones of the invasive grass Phalaris arundinacea, reed canary grass, into 150 random locations within a Vermont pasture. For each individual, we recorded clonal identity, neighbor identity, community indices (species richness and species diversity), and an environmental variable (soil moisture). The response variables were survivorship, above-ground biomass, below-ground biomass and the ratio of above- to below-ground biomass. Clonal identity affected both survivorship and below-ground biomass. The fastest tillering clone had poor survivorship but survivors produced a large amount of below-ground biomass, making this clone more likely to successfully overwinter. Neighbor species affected above- and below-ground biomass. Reed canary grass produced more above- and below-ground biomass when Anthoxanthum odoratum, a common pasture grass species, was abundant. Community attributes also influenced growth. Although we expected diverse plots to repel the invasion, plants in the more diverse plots had higher amounts of below-ground biomass. Finally, environmental effects also influenced growth. Reed canary grass produced more above-ground biomass in wetter plots, confirming that it does well under wet conditions.     

Birth of rats following nuclear exchange at the 2-cell stage

We report full-term development of nuclear transfer embryos following nuclear exchange at the 2-cell stage. Nuclei from 2-cell rat embryos were transferred into enucleated 2-cell embryos and developed to term after transfer to recipients (NT2). Pronuclear exchange in zygotes was used for comparison (NT1). Zygotes and 2-cell embryos were harvested from 4-week-old female Sprague-Dawley rats. Nuclear transfer was performed by transferring the pronuclei or karyoplasts into the perivitelline space of recipient embryos followed by electrofusion to reconstruct embryos. Fused couplets were cultured for 4 or 24 h before being transferred into day 1 pseudopregnant recipients (Hooded Wistar) at the 1- or 2-cell stage. In vitro culture was also carried out to check the developmental competence of the embryos. In vitro development to the blastocyst stage was not significantly different between the two groups (NT1, 34.3%; NT2, 45.0%). Two of three recipients from NT1 and two of five recipients from NT2 became pregnant. Six pups (3 from NT1, 3 from NT2) were delivered from the four foster mothers. Three female pups survived; 2 from NT1 and 1 from NT2. At 2 months of age these pups appeared healthy, and were mated with Sprague-Dawley males. One rat derived from NT1 delivered 15 pups (5 males, 10 females) as did the rat from NT2 (7 males, 8 females). Our results show that by using karyoplasts from 2-cell stage embryos as nuclear donors and reconstructing them with enucleated 2-cell embryos, healthy rats can be produced.     

Cell-intrinsic differences between stem cells from different regions of the peripheral nervous system regulate the generation of neural diversity

Stem cells in different regions of the nervous system give rise to different types of mature cells. This diversity is assumed to arise in response to local environmental differences, but the contribution of cell-intrinsic differences between stem cells has been unclear. At embryonic day (E)14, neural crest stem cells (NCSCs) undergo primarily neurogenesis in the gut but gliogenesis in nerves. Yet gliogenic and neurogenic factors are expressed in both locations. NCSCs isolated by flow-cytometry from E14 sciatic nerve and gut exhibited heritable, cell-intrinsic differences in their responsiveness to lineage determination factors. Gut NCSCs were more responsive to neurogenic factors, while sciatic nerve NCSCs were more responsive to gliogenic factors. Upon transplantation of uncultured NCSCs into developing peripheral nerves in vivo, sciatic nerve NCSCs gave rise only to glia, while gut NCSCs gave rise primarily to neurons. Thus, cell fate in the nerve was stem cell determined.     

Lignin-carbohydrate complexes from Lolium perenne

Lignin-carbohydrate and lignin-hemicellulose complexes were extracted sequentially from four varieties of Lolium perenne which had previously been