From plant neighbourhood to landscape scales: how grazing modifies native and exotic plant species richness in grassland

The interactive effect of grazing and soil resources on plant species richness and coexistence has been predicted to vary across spatial scales. When resources are not limiting, grazing should reduce competitive effects and increase colonisation and richness at fine scales. However, at broad scales richness is predicted to decline due to loss of grazing intolerant species. We examined these hypotheses in grasslands of southern Australia that varied in resources and ungulate grazing intensity since farming commenced 170 years ago. Fine-scale species richness was slightly greater in more intensively grazed upper slope sites with high nutrients but low water supply compared to those that were moderately grazed, largely due to a greater abundance of exotic species. At broader scales, exotic species richness declined with increasing grazing intensity whether nutrients or water supply were low or high. Native species richness declined at all scales in response to increasing grazing intensity and greater resource supply. Grazing also reduced fine-scale heterogeneity in native species richness and although exotics were also characterised by greater heterogeneity at fine scales, grazing effects varied across scales. In these grasslands patterns of plant species richness did not match predictions at all scales and this is likely to be due to differing responses of native and exotic species and their relative abundance in the regional species pool. Over the past 170 years intolerant native species have been eliminated from areas that are continually and heavily grazed, whereas transient, light grazing increases richness of both exotics and natives. The results support the observation that the processes and scales at which they operate differ between coevolved ungulate—grassland systems and those in transition due to recent invasion of herbivores and associated plant species.     

In Vitro Culture of Previously Uncultured Oral Bacterial Phylotypes

Around a third of oral bacteria cannot be grown using conventional bacteriological culture media. Community profiling targeting 16S rRNA and shotgun metagenomics methods have proved valuable in revealing the complexity of the oral bacterial community. Studies investigating the role of oral bacteria in health and disease require phenotypic characterizations that are possible only with live cultures. The aim of this study was to develop novel culture media and use an in vitro biofilm model to culture previously uncultured oral bacteria. Subgingival plaque samples collected from subjects with periodontitis were cultured on complex mucin-containing agar plates supplemented with proteose peptone (PPA), beef extract (BEA), or Gelysate (GA) as well as on fastidious anaerobe agar plus 5% horse blood (FAA). In vitro biofilms inoculated with the subgingival plaque samples and proteose peptone broth (PPB) as the growth medium were established using the Calgary biofilm device. Specific PCR primers were designed and validated for the previously uncultivated oral taxa Bacteroidetes bacteria HOT 365 and HOT 281, Lachnospiraceae bacteria HOT 100 and HOT 500, and Clostridiales bacterium HOT 093. All agar media were able to support the growth of 10 reference strains of oral bacteria. One previously uncultivated phylotype, Actinomyces sp. HOT 525, was cultivated on FAA. Of 93 previously uncultivated phylotypes found in the inocula, 26 were detected in in vitro-cultivated biofilms. Lachnospiraceae bacterium HOT 500 was successfully cultured from biofilm material harvested from PPA plates in coculture with Parvimonas micra or Veillonella dispar/parvula after colony hybridization-directed enrichment. The establishment of in vitro biofilms from oral inocula enables the cultivation of previously uncultured oral bacteria and provides source material for isolation in coculture.     

Flap Endonuclease 1 Limits Telomere Fragility on the Leading Strand

The existence of redundant replication and repair systems that ensure genome stability underscores the importance of faithful DNA replication. Nowhere is this complexity more evident than in challenging DNA templates, including highly repetitive or transcribed sequences. Here, we demonstrate that flap endonuclease 1 (FEN1), a canonical lagging strand DNA replication protein, is required for normal, complete leading strand replication at telomeres. We find that the loss of FEN1 nuclease activity, but not DNA repair activities, results in leading strand-specific telomere fragility. Furthermore, we show that FEN1 depletion-induced telomere fragility is increased by RNA polymerase II inhibition and is rescued by ectopic RNase H1 expression. These data suggest that FEN1 limits leading strand-specific telomere fragility by processing RNA:DNA hybrid/flap intermediates that arise from co-directional collisions occurring between the replisome and RNA polymerase. Our data reveal the first molecular mechanism for leading strand-specific telomere fragility and the first known role for FEN1 in leading strand DNA replication. Because FEN1 mutations have been identified in human cancers, our findings raise the possibility that unresolved RNA:DNA hybrid structures contribute to the genomic instability associated with cancer.     

DNA2 drives processing and restart of reversed replication forks in human cells

Accurate processing of stalled or damaged DNA replication forks is paramount to genomic integrity and recent work points to replication fork reversal and restart as a central mechanism to ensuring high-fidelity DNA replication. Here, we identify a novel DNA2- and WRN-dependent mechanism of reversed replication fork processing and restart after prolonged genotoxic stress. The human DNA2 nuclease and WRN ATPase activities functionally interact to degrade reversed replication forks with a 5′-to-3′ polarity and promote replication restart, thus preventing aberrant processing of unresolved replication intermediates. Unexpectedly, EXO1, MRE11, and CtIP are not involved in the same mechanism of reversed fork processing, whereas human RECQ1 limits DNA2 activity by preventing extensive nascent strand degradation. RAD51 depletion antagonizes this mechanism, presumably by preventing reversed fork formation. These studies define a new mechanism for maintaining genome integrity tightly controlled by specific nucleolytic activities and central homologous recombination factors.     

Rethinking the dispersal of Homo sapiens out of Africa

Current fossil, genetic, and archeological data indicate that Homo sapiens originated in Africa in the late Middle Pleistocene. By the end of the Late Pleistocene, our species was distributed across every continent except Antarctica, setting the foundations for the subsequent demographic and cultural changes of the Holocene. The intervening processes remain intensely debated and a key theme in hominin evolutionary studies. We review archeological, fossil, environmental, and genetic data to evaluate the current state of knowledge on the dispersal of Homo sapiens out of Africa. The emerging picture of the dispersal process suggests dynamic behavioral variability, complex interactions between populations, and an intricate genetic and cultural legacy. This evolutionary and historical complexity challenges simple narratives and suggests that hybrid models and the testing of explicit hypotheses are required to understand the expansion of Homo sapiens into Eurasia.     

Coxiella burnetii: turning hostility into a home

Coxiella burnetii, the causative agent of the human disease Q fever, is a unique intracellular bacterial pathogen. Coxiella replicates to high numbers within a pathogen‐derived lysosome‐like vacuole, thriving within a low pH, highly proteolytic and oxidative environment. In 2009, researchers developed means to axenically culture Coxiella paving the way for the development of tools to genetically manipulate the organism. These advances have revolutionized our capacity to examine the pathogenesis of Coxiella. In recent years, targeted and random mutant strains have been used to demonstrate that the Dot/Icm type IV secretion system is essential for intracellular replication of Coxiella. Current research is focused towards understanding the unique cohort of over 130 effector proteins that are translocated into the host cell. Mutagenesis screens have been employed to identify effectors that play important roles for the biogenesis of the Coxiella‐containing vacuole and intracellular replication of Coxiella. A surprisingly high number of effector mutants demonstrate significant intracellular growth defects, and future studies on the molecular function of these effectors will provide great insight into the pathogenesis of Coxiella. Already, this expanse of new data implicates many eukaryotic processes that are targeted by the arsenal of Coxiella effectors including autophagy, apoptosis and vesicular trafficking.     

Characterization of aggregates produced by the potential mycoherbistat Plectosporium alismatis in submerged culture: germination,UV-radiation tolerance and infectivity

Plectosporium alismatis, a potential mycoherbistat of Alismatacae spp., has been previously shown to produce aggregates which contain chlamydospores in liquid culture. Weevaluated the impact of medium composition on the formation and composition of aggregates. In shake flasks cultures using 5.74 gL^?1 sodium nitrate, 8.8 gL^?1 malt extract or glucose and 0.1% Tween 80, P. alismatis formed small, uniform (diameter of 75% aggregates <720 µm), dense, melanised aggregates containing 10⁴ conidia and 10³ chlamydospores, these numbers remained unchanged during growth. All 7-day-old aggregates exposed to desiccation or/ and UV-radiation germinated. In bioassays using leaf discs of Alisma plantago-aquatica, P. alismatis aggregates caused necrosis, regardless of whether aggregates had been exposed to desiccation and/or UV-radiation prior to application on leaf discs, whereas other propagules (10³ propagules disc^?1) exposed to drying and UV-radiation stress were unable to cause necrosis. This preliminary research shows the potential of aggregates to be used as part of a formulation of biocontrol agents, provided adequate conditions for optimal aggregate yields are found.     

HIF-VEGF pathways are critical for chronic otitis media in Junbo and Jeff mouse mutants

Otitis media with effusion (OME) is the commonest cause of hearing loss in children, yet the underlying genetic pathways and mechanisms involved are incompletely understood. Ventilation of the middle ear with tympanostomy tubes is the commonest surgical procedure in children and the best treatment for chronic OME, but the mechanism by which they work remains uncertain. As hypoxia is a common feature of inflamed microenvironments, moderation of hypoxia may be a significant contributory mechanism. We have investigated the occurrence of hypoxia and hypoxia-inducible factor (HIF) mediated responses in Junbo and Jeff mouse mutant models, which develop spontaneous chronic otitis media. We found that Jeff and Junbo mice labeled in vivo with pimonidazole showed cellular hypoxia in inflammatory cells in the bulla lumen, and in Junbo the middle ear mucosa was also hypoxic. The bulla fluid inflammatory cell numbers were greater and the upregulation of inflammatory gene networks were more pronounced in Junbo than Jeff. Hif-1α gene expression was elevated in bulla fluid inflammatory cells, and there was upregulation of its target genes including Vegfa in Junbo and Jeff. We therefore investigated the effects in Junbo of small-molecule inhibitors of VEGFR signaling (PTK787, SU-11248, and BAY 43-9006) and destabilizing HIF by inhibiting its chaperone HSP90 with 17-DMAG. We found that both classes of inhibitor significantly reduced hearing loss and the occurrence of bulla fluid and that VEGFR inhibitors moderated angiogenesis and lymphangiogenesis in the inflamed middle ear mucosa. The effectiveness of HSP90 and VEGFR signaling inhibitors in suppressing OM in the Junbo model implicates HIF-mediated VEGF as playing a pivotal role in OM pathogenesis. Our analysis of the Junbo and Jeff mutants highlights the role of hypoxia and HIF-mediated pathways, and we conclude that targeting molecules in HIF-VEGF signaling pathways has therapeutic potential in the treatment of chronic OM.     

Molecular phylogeny of treeshrews (Mammalia: Scandentia) and the timescale of diversification in Southeast Asia

Resolving the phylogeny of treeshrews (Order Scandentia) has historically proven difficult, in large part because of access to specimens and samples from critical taxa. We used "antique" DNA methods with non-destructive sampling of museum specimens to complete taxon sampling for the 20 currently recognized treeshrew species and to estimate their phylogeny and divergence times. Most divergence among extant species is estimated to have taken place within the past 20 million years, with deeper divergences between the two families (Ptilocercidae and Tupaiidae) and between Dendrogale and all other genera within Tupaiidae. All but one of the divergences between currently recognized species had occurred by 4Mya, suggesting that Miocene tectonics, volcanism, and geographic instability drove treeshrew diversification. These geologic processes may be associated with an increase in net diversification rate in the early Miocene. Most evolutionary relationships appear consistent with island-hopping or landbridge colonization between contiguous geographic areas, although there are exceptions in which extinction may play an important part. The single recent divergence is between Tupaia palawanensis and Tupaia moellendorffi, both endemic to the Philippines, and may be due to Pleistocene sea level fluctuations and post-landbridge isolation in allopatry. We provide a time-calibrated phylogenetic framework for answering evolutionary questions about treeshrews and about evolutionary patterns and processes in Euarchonta. We also propose subsuming the monotypic genus Urogale, a Philippine endemic, into Tupaia, thereby reducing the number of extant treeshrew genera from five to four.